Research small-variant evidence report

STRESS_FFPE_LOW_DEPTH

MutationSieve 0.1.0.dev1 · somatic mode · sample state VARIANT_CANDIDATE_PRESENT_PARTIAL_NO_CALL

Not analytically or clinically validated. A REVIEW record is a sequencing hypothesis, not a diagnosis. A missing record is not a clinical negative. HIGH/PASS are disabled unless a separately validated, compatible analytical resource set is explicitly enabled.

Plain-language summary

The program examined high-quality DNA sequencing evidence inside the declared target regions. It found 8 candidate(s) worth human review and retained 89 additional candidate(s) with reasons they were rejected. It could assess approximately 100.0% of the target bases at the configured depth. These numbers describe this software run; they do not establish whether a person does or does not have a mutation.

8non-rejected hypotheses
89audited rejects
100.0%basewise primary-unit callable target
2,231alignment records used
0.056%high-quality reference mismatch fraction
compatible_empiricalerror model status

Candidate evidence

Alternate and reference depth use the same primary unit. Coordinate-family counts are shown only as an audit proxy and are not called molecules. QUAL is deliberately missing in VCF because the rank is not an independently calibrated probability.

TierAlleleSupportStrandsHaplotypeStatisticsRankFilters and review flags
REJECT
REJECTED_CANDIDATE
chrSynthetic:551 C>T
SNV · GENE_A
0/22
0.000% · paired_fragment
0/0
forward/reverse
0
local-haplotype favored
1
q 1
0.000
rank, not probability
below_assay_allele_fraction_floor; low_alt_base_quality; low_alt_mapping_quality; low_independent_alt_support; review: empirical_resolution_insufficient_for_reporting; review: exact_locus_unassessable_in_panel_of_normals; review: limited_fragment_start_diversity; review: no_validated_umi_family_consensus; review: one_alignment_strand_only
REJECT
REJECTED_CANDIDATE
chrSynthetic:893 T>G
SNV · GENE_A
1/21
4.762% · paired_fragment
0/1
forward/reverse
1
local-haplotype favored
1
q 1
0.004
rank, not probability
review: empirical_resolution_insufficient_for_reporting; review: exact_locus_unassessable_in_panel_of_normals; review: no_validated_umi_family_consensus; review: one_alignment_strand_only
REJECT
REJECTED_CANDIDATE
chrSynthetic:1041 G>A
SNV · GENE_A
1/21
4.762% · paired_fragment
1/0
forward/reverse
1
local-haplotype favored
1
q 1
0.004
rank, not probability
review: empirical_resolution_insufficient_for_reporting; review: exact_locus_unassessable_in_panel_of_normals; review: no_validated_umi_family_consensus; review: one_alignment_strand_only
REJECT
REJECTED_CANDIDATE
chrSynthetic:1083 T>A
SNV · GENE_A
1/27
3.704% · paired_fragment
1/0
forward/reverse
1
local-haplotype favored
1
q 1
0.004
rank, not probability
review: empirical_resolution_insufficient_for_reporting; review: exact_locus_unassessable_in_panel_of_normals; review: no_validated_umi_family_consensus; review: one_alignment_strand_only
REJECT
REJECTED_CANDIDATE
chrSynthetic:1095 T>A
SNV · GENE_A
0/26
0.000% · paired_fragment
0/0
forward/reverse
0
local-haplotype favored
1
q 1
0.000
rank, not probability
below_assay_allele_fraction_floor; low_alt_base_quality; low_alt_mapping_quality; low_independent_alt_support; review: empirical_resolution_insufficient_for_reporting; review: exact_locus_unassessable_in_panel_of_normals; review: limited_fragment_start_diversity; review: no_validated_umi_family_consensus; review: one_alignment_strand_only
REJECT
REJECTED_CANDIDATE
chrSynthetic:1170 C>T
SNV · GENE_A
1/29
3.448% · paired_fragment
1/0
forward/reverse
1
local-haplotype favored
1
q 1
0.004
rank, not probability
review: empirical_resolution_insufficient_for_reporting; review: exact_locus_unassessable_in_panel_of_normals; review: no_validated_umi_family_consensus; review: one_alignment_strand_only
REJECT
REJECTED_CANDIDATE
chrSynthetic:1185 A>C
SNV · GENE_A
1/30
3.333% · paired_fragment
0/1
forward/reverse
1
local-haplotype favored
1
q 1
0.004
rank, not probability
review: empirical_resolution_insufficient_for_reporting; review: exact_locus_unassessable_in_panel_of_normals; review: no_validated_umi_family_consensus; review: one_alignment_strand_only
REVIEW
REVIEW_CANDIDATE
chrSynthetic:1201 T>A
SNV · GENE_A
10/26
38.462% · paired_fragment
4/6
forward/reverse
10
local-haplotype favored
1
q 1
0.571
rank, not probability
review: empirical_resolution_insufficient_for_reporting; review: exact_locus_unassessable_in_panel_of_normals; review: no_validated_umi_family_consensus
REJECT
REJECTED_CANDIDATE
chrSynthetic:1360 C>T
SNV · GENE_A
1/12
8.333% · paired_fragment
1/0
forward/reverse
1
local-haplotype favored
1
q 1
0.004
rank, not probability
review: empirical_resolution_insufficient_for_reporting; review: exact_locus_unassessable_in_panel_of_normals; review: no_validated_umi_family_consensus; review: one_alignment_strand_only
REJECT
REJECTED_CANDIDATE
chrSynthetic:1520 C>T
SNV · GENE_A
1/15
6.667% · paired_fragment
1/0
forward/reverse
1
local-haplotype favored
1
q 1
0.004
rank, not probability
review: empirical_resolution_insufficient_for_reporting; review: exact_locus_unassessable_in_panel_of_normals; review: no_validated_umi_family_consensus; review: one_alignment_strand_only
REJECT
REJECTED_CANDIDATE
chrSynthetic:1568 C>T
SNV · GENE_A
1/15
6.667% · paired_fragment
1/0
forward/reverse
1
local-haplotype favored
1
q 1
0.004
rank, not probability
review: empirical_resolution_insufficient_for_reporting; review: exact_locus_unassessable_in_panel_of_normals; review: no_validated_umi_family_consensus; review: one_alignment_strand_only
REJECT
REJECTED_CANDIDATE
chrSynthetic:1598 C>T
SNV · GENE_A
0/19
0.000% · paired_fragment
0/0
forward/reverse
0
local-haplotype favored
1
q 1
0.000
rank, not probability
below_assay_allele_fraction_floor; low_alt_base_quality; low_alt_mapping_quality; low_independent_alt_support; review: empirical_resolution_insufficient_for_reporting; review: exact_locus_unassessable_in_panel_of_normals; review: limited_fragment_start_diversity; review: no_validated_umi_family_consensus; review: one_alignment_strand_only
REJECT
REJECTED_CANDIDATE
chrSynthetic:1673 C>T
SNV · GENE_A
1/26
3.846% · paired_fragment
0/1
forward/reverse
1
local-haplotype favored
1
q 1
0.002
rank, not probability
review: alt_evidence_concentrated_at_read_ends; review: empirical_resolution_insufficient_for_reporting; review: exact_locus_unassessable_in_panel_of_normals; review: no_validated_umi_family_consensus; review: one_alignment_strand_only
REJECT
REJECTED_CANDIDATE
chrSynthetic:1713 A>C
SNV · GENE_A
1/26
3.846% · paired_fragment
1/0
forward/reverse
1
local-haplotype favored
1
q 1
0.004
rank, not probability
review: empirical_resolution_insufficient_for_reporting; review: exact_locus_unassessable_in_panel_of_normals; review: no_validated_umi_family_consensus; review: one_alignment_strand_only
REJECT
REJECTED_CANDIDATE
chrSynthetic:1743 C>G
SNV · GENE_A
0/22
0.000% · paired_fragment
0/0
forward/reverse
0
local-haplotype favored
1
q 1
0.000
rank, not probability
below_assay_allele_fraction_floor; low_alt_base_quality; low_alt_mapping_quality; low_independent_alt_support; review: empirical_resolution_insufficient_for_reporting; review: exact_locus_unassessable_in_panel_of_normals; review: limited_fragment_start_diversity; review: no_validated_umi_family_consensus; review: one_alignment_strand_only
REJECT
REJECTED_CANDIDATE
chrSynthetic:1815 C>T
SNV · GENE_A
1/19
5.263% · paired_fragment
1/0
forward/reverse
1
local-haplotype favored
1
q 1
0.004
rank, not probability
review: empirical_resolution_insufficient_for_reporting; review: exact_locus_unassessable_in_panel_of_normals; review: no_validated_umi_family_consensus; review: one_alignment_strand_only
REJECT
REJECTED_CANDIDATE
chrSynthetic:1885 C>T
SNV · GENE_A
1/12
8.333% · paired_fragment
0/1
forward/reverse
1
local-haplotype favored
1
q 1
0.004
rank, not probability
review: empirical_resolution_insufficient_for_reporting; review: exact_locus_unassessable_in_panel_of_normals; review: no_validated_umi_family_consensus; review: one_alignment_strand_only
REJECT
REJECTED_CANDIDATE
chrSynthetic:1922 C>T
SNV · GENE_A
0/10
0.000% · paired_fragment
0/0
forward/reverse
0
local-haplotype favored
1
q 1
0.000
rank, not probability
below_assay_allele_fraction_floor; low_alt_base_quality; low_alt_mapping_quality; low_independent_alt_support; review: empirical_resolution_insufficient_for_reporting; review: exact_locus_unassessable_in_panel_of_normals; review: limited_fragment_start_diversity; review: no_validated_umi_family_consensus; review: one_alignment_strand_only
REJECT
REJECTED_CANDIDATE
chrSynthetic:2076 C>T
SNV · GENE_A
0/22
0.000% · paired_fragment
0/0
forward/reverse
0
local-haplotype favored
1
q 1
0.000
rank, not probability
below_assay_allele_fraction_floor; low_alt_base_quality; low_alt_mapping_quality; low_independent_alt_support; review: empirical_resolution_insufficient_for_reporting; review: exact_locus_unassessable_in_panel_of_normals; review: limited_fragment_start_diversity; review: no_validated_umi_family_consensus; review: one_alignment_strand_only
REVIEW
REVIEW_CANDIDATE
chrSynthetic:2201 C>A
SNV · GENE_A
5/29
17.241% · paired_fragment
0/5
forward/reverse
5
local-haplotype favored
1
q 1
0.083
rank, not probability
review: empirical_resolution_insufficient_for_reporting; review: exact_locus_unassessable_in_panel_of_normals; review: no_validated_umi_family_consensus; review: one_alignment_strand_only
REJECT
REJECTED_CANDIDATE
chrSynthetic:2241 C>G
SNV · GENE_A
1/26
3.846% · paired_fragment
1/0
forward/reverse
1
local-haplotype favored
1
q 1
0.004
rank, not probability
review: empirical_resolution_insufficient_for_reporting; review: exact_locus_unassessable_in_panel_of_normals; review: no_validated_umi_family_consensus; review: one_alignment_strand_only
REJECT
REJECTED_CANDIDATE
chrSynthetic:2259 C>T
SNV · GENE_A
1/25
4.000% · paired_fragment
1/0
forward/reverse
1
local-haplotype favored
1
q 1
0.004
rank, not probability
review: empirical_resolution_insufficient_for_reporting; review: exact_locus_unassessable_in_panel_of_normals; review: no_validated_umi_family_consensus; review: one_alignment_strand_only
REJECT
REJECTED_CANDIDATE
chrSynthetic:2283 T>A
SNV · GENE_A
1/28
3.571% · paired_fragment
1/0
forward/reverse
1
local-haplotype favored
1
q 1
0.002
rank, not probability
review: alt_evidence_concentrated_at_read_ends; review: empirical_resolution_insufficient_for_reporting; review: exact_locus_unassessable_in_panel_of_normals; review: no_validated_umi_family_consensus; review: one_alignment_strand_only
REJECT
REJECTED_CANDIDATE
chrSynthetic:2373 C>G
SNV · GENE_A
1/35
2.857% · paired_fragment
0/1
forward/reverse
1
local-haplotype favored
1
q 1
0.004
rank, not probability
review: empirical_resolution_insufficient_for_reporting; review: exact_locus_unassessable_in_panel_of_normals; review: no_validated_umi_family_consensus; review: one_alignment_strand_only
REJECT
REJECTED_CANDIDATE
chrSynthetic:2677 C>T
SNV · GENE_A
0/41
0.000% · paired_fragment
0/0
forward/reverse
0
local-haplotype favored
1
q 1
0.000
rank, not probability
below_assay_allele_fraction_floor; low_alt_base_quality; low_alt_mapping_quality; low_independent_alt_support; review: empirical_resolution_insufficient_for_reporting; review: exact_locus_unassessable_in_panel_of_normals; review: limited_fragment_start_diversity; review: no_validated_umi_family_consensus; review: one_alignment_strand_only
REJECT
REJECTED_CANDIDATE
chrSynthetic:2690 C>T
SNV · GENE_A
1/39
2.564% · paired_fragment
0/1
forward/reverse
1
local-haplotype favored
1
q 1
0.004
rank, not probability
review: empirical_resolution_insufficient_for_reporting; review: exact_locus_unassessable_in_panel_of_normals; review: no_validated_umi_family_consensus; review: one_alignment_strand_only
REJECT
REJECTED_CANDIDATE
chrSynthetic:2713 A>T
SNV · GENE_A
1/35
2.857% · paired_fragment
0/1
forward/reverse
1
local-haplotype favored
1
q 1
0.004
rank, not probability
review: empirical_resolution_insufficient_for_reporting; review: exact_locus_unassessable_in_panel_of_normals; review: no_validated_umi_family_consensus; review: one_alignment_strand_only
REJECT
REJECTED_CANDIDATE
chrSynthetic:2796 C>T
SNV · GENE_A
1/30
3.333% · paired_fragment
1/0
forward/reverse
1
local-haplotype favored
1
q 1
0.004
rank, not probability
review: empirical_resolution_insufficient_for_reporting; review: exact_locus_unassessable_in_panel_of_normals; review: no_validated_umi_family_consensus; review: one_alignment_strand_only
REJECT
REJECTED_CANDIDATE
chrSynthetic:2910 C>T
SNV · GENE_A
0/28
0.000% · paired_fragment
0/0
forward/reverse
0
local-haplotype favored
1
q 1
0.000
rank, not probability
below_assay_allele_fraction_floor; low_alt_base_quality; low_alt_mapping_quality; low_independent_alt_support; review: empirical_resolution_insufficient_for_reporting; review: exact_locus_unassessable_in_panel_of_normals; review: limited_fragment_start_diversity; review: no_validated_umi_family_consensus; review: one_alignment_strand_only
REJECT
REJECTED_CANDIDATE
chrSynthetic:3001 A>C
SNV · GENE_A
7/26
26.923% · paired_fragment
5/2
forward/reverse
5
local-haplotype favored
1
q 1
0.500
rank, not probability
redundant_component_of_mnv_candidate; review: empirical_resolution_insufficient_for_reporting; review: exact_locus_unassessable_in_panel_of_normals; review: no_validated_umi_family_consensus
REVIEW
REVIEW_CANDIDATE
chrSynthetic:3001 AG>CA
MNV · GENE_A
7/25
28.000% · paired_fragment
5/2
forward/reverse
7
local-haplotype favored
1
q 1
0.499
rank, not probability
review: empirical_resolution_insufficient_for_reporting; review: exact_locus_unassessable_in_panel_of_normals; review: no_validated_umi_family_consensus
REJECT
REJECTED_CANDIDATE
chrSynthetic:3002 G>A
SNV · GENE_A
7/25
28.000% · paired_fragment
5/2
forward/reverse
7
local-haplotype favored
1
q 1
0.499
rank, not probability
redundant_component_of_mnv_candidate; review: empirical_resolution_insufficient_for_reporting; review: exact_locus_unassessable_in_panel_of_normals; review: no_validated_umi_family_consensus
REJECT
REJECTED_CANDIDATE
chrSynthetic:3089 C>T
SNV · GENE_A
1/32
3.125% · paired_fragment
1/0
forward/reverse
1
local-haplotype favored
1
q 1
0.004
rank, not probability
review: empirical_resolution_insufficient_for_reporting; review: exact_locus_unassessable_in_panel_of_normals; review: no_validated_umi_family_consensus; review: one_alignment_strand_only
REJECT
REJECTED_CANDIDATE
chrSynthetic:3147 C>T
SNV · GENE_A
1/28
3.571% · paired_fragment
1/0
forward/reverse
1
local-haplotype favored
1
q 1
0.004
rank, not probability
review: empirical_resolution_insufficient_for_reporting; review: exact_locus_unassessable_in_panel_of_normals; review: no_validated_umi_family_consensus; review: one_alignment_strand_only
REJECT
REJECTED_CANDIDATE
chrSynthetic:3174 C>T
SNV · GENE_A
0/26
0.000% · paired_fragment
0/0
forward/reverse
0
local-haplotype favored
1
q 1
0.000
rank, not probability
below_assay_allele_fraction_floor; low_alt_base_quality; low_alt_mapping_quality; low_independent_alt_support; review: empirical_resolution_insufficient_for_reporting; review: exact_locus_unassessable_in_panel_of_normals; review: limited_fragment_start_diversity; review: no_validated_umi_family_consensus; review: one_alignment_strand_only
REJECT
REJECTED_CANDIDATE
chrSynthetic:3269 G>A
SNV · GENE_A
1/31
3.226% · paired_fragment
0/1
forward/reverse
1
local-haplotype favored
1
q 1
0.004
rank, not probability
review: empirical_resolution_insufficient_for_reporting; review: exact_locus_unassessable_in_panel_of_normals; review: no_validated_umi_family_consensus; review: one_alignment_strand_only
REJECT
REJECTED_CANDIDATE
chrSynthetic:3289 T>G
SNV · GENE_A
1/31
3.226% · paired_fragment
1/0
forward/reverse
1
local-haplotype favored
1
q 1
0.004
rank, not probability
review: empirical_resolution_insufficient_for_reporting; review: exact_locus_unassessable_in_panel_of_normals; review: no_validated_umi_family_consensus; review: one_alignment_strand_only
REVIEW
REVIEW_CANDIDATE
chrSynthetic:3301 CGA>AT
COMPLEX · GENE_A
6/32
18.750% · paired_fragment
5/1
forward/reverse
6
local-haplotype favored
1
q 1
0.475
rank, not probability
review: empirical_resolution_insufficient_for_reporting; review: exact_locus_unassessable_in_panel_of_normals; review: no_validated_umi_family_consensus
REJECT
REJECTED_CANDIDATE
chrSynthetic:3406 A>C
SNV · GENE_A
1/33
3.030% · paired_fragment
1/0
forward/reverse
1
local-haplotype favored
1
q 1
0.004
rank, not probability
review: empirical_resolution_insufficient_for_reporting; review: exact_locus_unassessable_in_panel_of_normals; review: no_validated_umi_family_consensus; review: one_alignment_strand_only
REJECT
REJECTED_CANDIDATE
chrSynthetic:3420 C>T
SNV · GENE_A
1/30
3.333% · paired_fragment
0/1
forward/reverse
1
local-haplotype favored
1
q 1
0.004
rank, not probability
review: empirical_resolution_insufficient_for_reporting; review: exact_locus_unassessable_in_panel_of_normals; review: no_validated_umi_family_consensus; review: one_alignment_strand_only
REJECT
REJECTED_CANDIDATE
chrSynthetic:3466 C>T
SNV · GENE_A
0/31
0.000% · paired_fragment
0/0
forward/reverse
0
local-haplotype favored
1
q 1
0.000
rank, not probability
below_assay_allele_fraction_floor; low_alt_base_quality; low_alt_mapping_quality; low_independent_alt_support; review: empirical_resolution_insufficient_for_reporting; review: exact_locus_unassessable_in_panel_of_normals; review: limited_fragment_start_diversity; review: no_validated_umi_family_consensus; review: one_alignment_strand_only
REJECT
REJECTED_CANDIDATE
chrSynthetic:4131 C>T
SNV · GENE_H
0/23
0.000% · paired_fragment
0/0
forward/reverse
0
local-haplotype favored
1
q 1
0.000
rank, not probability
below_assay_allele_fraction_floor; low_alt_base_quality; low_alt_mapping_quality; low_independent_alt_support; review: empirical_resolution_insufficient_for_reporting; review: exact_locus_unassessable_in_panel_of_normals; review: limited_fragment_start_diversity; review: no_validated_umi_family_consensus; review: one_alignment_strand_only
REJECT
REJECTED_CANDIDATE
chrSynthetic:4205 G>C
SNV · GENE_H
1/22
4.545% · paired_fragment
0/1
forward/reverse
1
local-haplotype favored
1
q 1
0.004
rank, not probability
review: empirical_resolution_insufficient_for_reporting; review: exact_locus_unassessable_in_panel_of_normals; review: no_validated_umi_family_consensus; review: one_alignment_strand_only
REJECT
REJECTED_CANDIDATE
chrSynthetic:4366 A>G
SNV · GENE_H
1/31
3.226% · paired_fragment
0/1
forward/reverse
1
local-haplotype favored
1
q 1
0.004
rank, not probability
review: empirical_resolution_insufficient_for_reporting; review: exact_locus_unassessable_in_panel_of_normals; review: no_validated_umi_family_consensus; review: one_alignment_strand_only
REJECT
REJECTED_CANDIDATE
chrSynthetic:4377 C>A
SNV · GENE_H
1/32
3.125% · paired_fragment
0/1
forward/reverse
1
local-haplotype favored
1
q 1
0.004
rank, not probability
review: empirical_resolution_insufficient_for_reporting; review: exact_locus_unassessable_in_panel_of_normals; review: no_validated_umi_family_consensus; review: one_alignment_strand_only
REVIEW
REVIEW_CANDIDATE
chrSynthetic:4480 C>CAA
INS · GENE_H
4/20
20.000% · paired_fragment
1/3
forward/reverse
4
local-haplotype favored
1
q 1
0.129
rank, not probability
review: conflicting_or_multiallelic_fragment_evidence; review: empirical_resolution_insufficient_for_reporting; review: exact_locus_unassessable_in_panel_of_normals; review: no_validated_umi_family_consensus; review: repeat_or_homopolymer_indel_context
REJECT
REJECTED_CANDIDATE
chrSynthetic:4591 C>T
SNV · GENE_H
1/27
3.704% · paired_fragment
0/1
forward/reverse
1
local-haplotype favored
1
q 1
0.002
rank, not probability
review: alt_evidence_concentrated_at_read_ends; review: empirical_resolution_insufficient_for_reporting; review: exact_locus_unassessable_in_panel_of_normals; review: no_validated_umi_family_consensus; review: one_alignment_strand_only
REJECT
REJECTED_CANDIDATE
chrSynthetic:4667 C>T
SNV · GENE_H
1/29
3.448% · paired_fragment
1/0
forward/reverse
1
local-haplotype favored
1
q 1
0.002
rank, not probability
review: alt_evidence_concentrated_at_read_ends; review: empirical_resolution_insufficient_for_reporting; review: exact_locus_unassessable_in_panel_of_normals; review: no_validated_umi_family_consensus; review: one_alignment_strand_only
REJECT
REJECTED_CANDIDATE
chrSynthetic:4778 T>C
SNV · GENE_H
1/31
3.226% · paired_fragment
1/0
forward/reverse
1
local-haplotype favored
1
q 1
0.004
rank, not probability
review: empirical_resolution_insufficient_for_reporting; review: exact_locus_unassessable_in_panel_of_normals; review: no_validated_umi_family_consensus; review: one_alignment_strand_only
REJECT
REJECTED_CANDIDATE
chrSynthetic:4943 C>A
SNV · GENE_H
1/29
3.448% · paired_fragment
0/1
forward/reverse
1
local-haplotype favored
1
q 1
0.004
rank, not probability
review: empirical_resolution_insufficient_for_reporting; review: exact_locus_unassessable_in_panel_of_normals; review: no_validated_umi_family_consensus; review: one_alignment_strand_only
REJECT
REJECTED_CANDIDATE
chrSynthetic:4951 C>T
SNV · GENE_H
1/31
3.226% · paired_fragment
0/1
forward/reverse
1
local-haplotype favored
1
q 1
0.004
rank, not probability
review: empirical_resolution_insufficient_for_reporting; review: exact_locus_unassessable_in_panel_of_normals; review: no_validated_umi_family_consensus; review: one_alignment_strand_only
REJECT
REJECTED_CANDIDATE
chrSynthetic:4993 C>T
SNV · GENE_H
1/28
3.571% · paired_fragment
0/1
forward/reverse
1
local-haplotype favored
1
q 1
0.004
rank, not probability
review: empirical_resolution_insufficient_for_reporting; review: exact_locus_unassessable_in_panel_of_normals; review: no_validated_umi_family_consensus; review: one_alignment_strand_only
REJECT
REJECTED_CANDIDATE
chrSynthetic:5191 C>T
SNV · GENE_H
1/21
4.762% · paired_fragment
0/1
forward/reverse
1
local-haplotype favored
1
q 1
0.002
rank, not probability
review: alt_evidence_concentrated_at_read_ends; review: empirical_resolution_insufficient_for_reporting; review: exact_locus_unassessable_in_panel_of_normals; review: no_validated_umi_family_consensus; review: one_alignment_strand_only
REVIEW
REVIEW_CANDIDATE
chrSynthetic:5299 CAGA>C
DEL · GENE_H
5/20
25.000% · paired_fragment
2/3
forward/reverse
5
local-haplotype favored
1
q 1
0.430
rank, not probability
review: empirical_resolution_insufficient_for_reporting; review: exact_locus_unassessable_in_panel_of_normals; review: no_validated_umi_family_consensus
REJECT
REJECTED_CANDIDATE
chrSynthetic:5334 G>A
SNV · GENE_H
1/26
3.846% · paired_fragment
0/1
forward/reverse
1
local-haplotype favored
1
q 1
0.004
rank, not probability
review: empirical_resolution_insufficient_for_reporting; review: exact_locus_unassessable_in_panel_of_normals; review: no_validated_umi_family_consensus; review: one_alignment_strand_only
REJECT
REJECTED_CANDIDATE
chrSynthetic:5529 G>A
SNV · GENE_H
1/27
3.704% · paired_fragment
1/0
forward/reverse
1
local-haplotype favored
1
q 1
0.004
rank, not probability
review: empirical_resolution_insufficient_for_reporting; review: exact_locus_unassessable_in_panel_of_normals; review: no_validated_umi_family_consensus; review: one_alignment_strand_only
REJECT
REJECTED_CANDIDATE
chrSynthetic:5749 C>G
SNV · GENE_H
0/24
0.000% · paired_fragment
0/0
forward/reverse
0
local-haplotype favored
1
q 1
0.000
rank, not probability
below_assay_allele_fraction_floor; low_alt_base_quality; low_alt_mapping_quality; low_independent_alt_support; review: empirical_resolution_insufficient_for_reporting; review: exact_locus_unassessable_in_panel_of_normals; review: limited_fragment_start_diversity; review: no_validated_umi_family_consensus; review: one_alignment_strand_only
REJECT
REJECTED_CANDIDATE
chrSynthetic:5784 C>T
SNV · GENE_H
1/31
3.226% · paired_fragment
0/1
forward/reverse
1
local-haplotype favored
1
q 1
0.004
rank, not probability
review: empirical_resolution_insufficient_for_reporting; review: exact_locus_unassessable_in_panel_of_normals; review: no_validated_umi_family_consensus; review: one_alignment_strand_only
REJECT
REJECTED_CANDIDATE
chrSynthetic:5968 G>A
SNV · GENE_H
1/24
4.167% · paired_fragment
1/0
forward/reverse
1
local-haplotype favored
1
q 1
0.004
rank, not probability
review: empirical_resolution_insufficient_for_reporting; review: exact_locus_unassessable_in_panel_of_normals; review: no_validated_umi_family_consensus; review: one_alignment_strand_only
REJECT
REJECTED_CANDIDATE
chrSynthetic:7108 A>T
SNV · GENE_T
1/22
4.545% · paired_fragment
1/0
forward/reverse
1
local-haplotype favored
1
q 1
0.004
rank, not probability
review: empirical_resolution_insufficient_for_reporting; review: exact_locus_unassessable_in_panel_of_normals; review: no_validated_umi_family_consensus; review: one_alignment_strand_only
REJECT
REJECTED_CANDIDATE
chrSynthetic:7156 T>C
SNV · GENE_T
0/25
0.000% · paired_fragment
0/0
forward/reverse
0
local-haplotype favored
1
q 1
0.000
rank, not probability
below_assay_allele_fraction_floor; low_alt_base_quality; low_alt_mapping_quality; low_independent_alt_support; review: empirical_resolution_insufficient_for_reporting; review: exact_locus_unassessable_in_panel_of_normals; review: limited_fragment_start_diversity; review: no_validated_umi_family_consensus; review: one_alignment_strand_only
REJECT
REJECTED_CANDIDATE
chrSynthetic:7159 G>T
SNV · GENE_T
0/25
0.000% · paired_fragment
0/0
forward/reverse
0
local-haplotype favored
1
q 1
0.000
rank, not probability
below_assay_allele_fraction_floor; low_alt_base_quality; low_alt_mapping_quality; low_independent_alt_support; review: empirical_resolution_insufficient_for_reporting; review: exact_locus_unassessable_in_panel_of_normals; review: limited_fragment_start_diversity; review: no_validated_umi_family_consensus; review: one_alignment_strand_only
REJECT
REJECTED_CANDIDATE
chrSynthetic:7224 A>G
SNV · GENE_T
1/24
4.167% · paired_fragment
0/1
forward/reverse
1
local-haplotype favored
1
q 1
0.004
rank, not probability
review: empirical_resolution_insufficient_for_reporting; review: exact_locus_unassessable_in_panel_of_normals; review: no_validated_umi_family_consensus; review: one_alignment_strand_only
REJECT
REJECTED_CANDIDATE
chrSynthetic:7337 A>G
SNV · GENE_T
1/24
4.167% · paired_fragment
1/0
forward/reverse
1
local-haplotype favored
1
q 1
0.004
rank, not probability
review: empirical_resolution_insufficient_for_reporting; review: exact_locus_unassessable_in_panel_of_normals; review: no_validated_umi_family_consensus; review: one_alignment_strand_only
REJECT
REJECTED_CANDIDATE
chrSynthetic:7381 G>A
SNV · GENE_T
1/22
4.545% · paired_fragment
0/1
forward/reverse
1
local-haplotype favored
1
q 1
0.004
rank, not probability
review: empirical_resolution_insufficient_for_reporting; review: exact_locus_unassessable_in_panel_of_normals; review: no_validated_umi_family_consensus; review: one_alignment_strand_only
REJECT
REJECTED_CANDIDATE
chrSynthetic:7388 C>T
SNV · GENE_T
1/21
4.762% · paired_fragment
0/1
forward/reverse
1
local-haplotype favored
1
q 1
0.004
rank, not probability
review: empirical_resolution_insufficient_for_reporting; review: exact_locus_unassessable_in_panel_of_normals; review: no_validated_umi_family_consensus; review: one_alignment_strand_only
REJECT
REJECTED_CANDIDATE
chrSynthetic:7446 G>T
SNV · GENE_T
1/23
4.348% · paired_fragment
0/1
forward/reverse
1
local-haplotype favored
1
q 1
0.002
rank, not probability
review: alt_evidence_concentrated_at_read_ends; review: empirical_resolution_insufficient_for_reporting; review: exact_locus_unassessable_in_panel_of_normals; review: no_validated_umi_family_consensus; review: one_alignment_strand_only
REVIEW
REVIEW_CANDIDATE
chrSynthetic:7601 G>GTGA
INS · GENE_T
3/16
18.750% · paired_fragment
1/2
forward/reverse
3
local-haplotype favored
1
q 1
0.140
rank, not probability
review: conflicting_or_multiallelic_fragment_evidence; review: empirical_resolution_insufficient_for_reporting; review: exact_locus_unassessable_in_panel_of_normals; review: no_validated_umi_family_consensus
REJECT
REJECTED_CANDIDATE
chrSynthetic:7692 C>T
SNV · GENE_T
0/18
0.000% · paired_fragment
0/0
forward/reverse
0
local-haplotype favored
1
q 1
0.000
rank, not probability
below_assay_allele_fraction_floor; low_alt_base_quality; low_alt_mapping_quality; low_independent_alt_support; review: empirical_resolution_insufficient_for_reporting; review: exact_locus_unassessable_in_panel_of_normals; review: limited_fragment_start_diversity; review: no_validated_umi_family_consensus; review: one_alignment_strand_only
REJECT
REJECTED_CANDIDATE
chrSynthetic:7708 C>G
SNV · GENE_T
1/21
4.762% · paired_fragment
1/0
forward/reverse
1
local-haplotype favored
1
q 1
0.004
rank, not probability
review: empirical_resolution_insufficient_for_reporting; review: exact_locus_unassessable_in_panel_of_normals; review: no_validated_umi_family_consensus; review: one_alignment_strand_only
REJECT
REJECTED_CANDIDATE
chrSynthetic:7720 G>T
SNV · GENE_T
0/23
0.000% · paired_fragment
0/0
forward/reverse
0
local-haplotype favored
1
q 1
0.000
rank, not probability
below_assay_allele_fraction_floor; low_alt_base_quality; low_alt_mapping_quality; low_independent_alt_support; review: empirical_resolution_insufficient_for_reporting; review: exact_locus_unassessable_in_panel_of_normals; review: limited_fragment_start_diversity; review: no_validated_umi_family_consensus; review: one_alignment_strand_only
REJECT
REJECTED_CANDIDATE
chrSynthetic:7779 T>A
SNV · GENE_T
1/24
4.167% · paired_fragment
0/1
forward/reverse
1
local-haplotype favored
1
q 1
0.004
rank, not probability
review: empirical_resolution_insufficient_for_reporting; review: exact_locus_unassessable_in_panel_of_normals; review: no_validated_umi_family_consensus; review: one_alignment_strand_only
REJECT
REJECTED_CANDIDATE
chrSynthetic:7861 C>T
SNV · GENE_T
1/24
4.167% · paired_fragment
1/0
forward/reverse
1
local-haplotype favored
1
q 1
0.004
rank, not probability
review: empirical_resolution_insufficient_for_reporting; review: exact_locus_unassessable_in_panel_of_normals; review: no_validated_umi_family_consensus; review: one_alignment_strand_only
REJECT
REJECTED_CANDIDATE
chrSynthetic:7908 G>C
SNV · GENE_T
1/23
4.348% · paired_fragment
0/1
forward/reverse
1
local-haplotype favored
1
q 1
0.004
rank, not probability
review: empirical_resolution_insufficient_for_reporting; review: exact_locus_unassessable_in_panel_of_normals; review: no_validated_umi_family_consensus; review: one_alignment_strand_only
REJECT
REJECTED_CANDIDATE
chrSynthetic:8020 C>T
SNV · GENE_T
1/22
4.545% · paired_fragment
0/1
forward/reverse
1
local-haplotype favored
1
q 1
0.004
rank, not probability
review: empirical_resolution_insufficient_for_reporting; review: exact_locus_unassessable_in_panel_of_normals; review: no_validated_umi_family_consensus; review: one_alignment_strand_only
REJECT
REJECTED_CANDIDATE
chrSynthetic:8065 A>T
SNV · GENE_T
0/23
0.000% · paired_fragment
0/0
forward/reverse
0
local-haplotype favored
1
q 1
0.000
rank, not probability
below_assay_allele_fraction_floor; low_alt_base_quality; low_alt_mapping_quality; low_independent_alt_support; review: empirical_resolution_insufficient_for_reporting; review: exact_locus_unassessable_in_panel_of_normals; review: limited_fragment_start_diversity; review: no_validated_umi_family_consensus; review: one_alignment_strand_only
REJECT
REJECTED_CANDIDATE
chrSynthetic:8112 C>T
SNV · GENE_T
1/23
4.348% · paired_fragment
0/1
forward/reverse
1
local-haplotype favored
1
q 1
0.004
rank, not probability
review: empirical_resolution_insufficient_for_reporting; review: exact_locus_unassessable_in_panel_of_normals; review: no_validated_umi_family_consensus; review: one_alignment_strand_only
REJECT
REJECTED_CANDIDATE
chrSynthetic:8144 T>G
SNV · GENE_T
0/24
0.000% · paired_fragment
0/0
forward/reverse
0
local-haplotype favored
1
q 1
0.000
rank, not probability
below_assay_allele_fraction_floor; low_alt_base_quality; low_alt_mapping_quality; low_independent_alt_support; review: empirical_resolution_insufficient_for_reporting; review: exact_locus_unassessable_in_panel_of_normals; review: limited_fragment_start_diversity; review: no_validated_umi_family_consensus; review: one_alignment_strand_only
REJECT
REJECTED_CANDIDATE
chrSynthetic:8196 C>T
SNV · GENE_T
0/26
0.000% · paired_fragment
0/0
forward/reverse
0
local-haplotype favored
1
q 1
0.000
rank, not probability
below_assay_allele_fraction_floor; low_alt_base_quality; low_alt_mapping_quality; low_independent_alt_support; review: empirical_resolution_insufficient_for_reporting; review: exact_locus_unassessable_in_panel_of_normals; review: limited_fragment_start_diversity; review: no_validated_umi_family_consensus; review: one_alignment_strand_only
REJECT
REJECTED_CANDIDATE
chrSynthetic:8324 G>C
SNV · GENE_T
1/19
5.263% · paired_fragment
0/1
forward/reverse
1
local-haplotype favored
1
q 1
0.002
rank, not probability
review: alt_evidence_concentrated_at_read_ends; review: empirical_resolution_insufficient_for_reporting; review: exact_locus_unassessable_in_panel_of_normals; review: no_validated_umi_family_consensus; review: one_alignment_strand_only
REJECT
REJECTED_CANDIDATE
chrSynthetic:8480 C>T
SNV · GENE_T
1/26
3.846% · paired_fragment
0/1
forward/reverse
1
local-haplotype favored
1
q 1
0.004
rank, not probability
review: empirical_resolution_insufficient_for_reporting; review: exact_locus_unassessable_in_panel_of_normals; review: no_validated_umi_family_consensus; review: one_alignment_strand_only
REJECT
REJECTED_CANDIDATE
chrSynthetic:8547 C>T
SNV · GENE_T
0/19
0.000% · paired_fragment
0/0
forward/reverse
0
local-haplotype favored
1
q 1
0.000
rank, not probability
below_assay_allele_fraction_floor; low_alt_base_quality; low_alt_mapping_quality; low_independent_alt_support; review: empirical_resolution_insufficient_for_reporting; review: exact_locus_unassessable_in_panel_of_normals; review: limited_fragment_start_diversity; review: no_validated_umi_family_consensus; review: one_alignment_strand_only
REVIEW
REVIEW_CANDIDATE
chrSynthetic:8601 ATTC>A
DEL · GENE_T
3/23
13.043% · paired_fragment
1/2
forward/reverse
3
local-haplotype favored
1
q 1
0.243
rank, not probability
review: empirical_resolution_insufficient_for_reporting; review: exact_locus_unassessable_in_panel_of_normals; review: no_validated_umi_family_consensus
REJECT
REJECTED_CANDIDATE
chrSynthetic:8762 G>T
SNV · GENE_T
1/20
5.000% · paired_fragment
0/1
forward/reverse
1
local-haplotype favored
1
q 1
0.004
rank, not probability
review: empirical_resolution_insufficient_for_reporting; review: exact_locus_unassessable_in_panel_of_normals; review: no_validated_umi_family_consensus; review: one_alignment_strand_only
REJECT
REJECTED_CANDIDATE
chrSynthetic:8801 C>T
SNV · GENE_T
1/19
5.263% · paired_fragment
0/1
forward/reverse
1
local-haplotype favored
1
q 1
0.004
rank, not probability
review: empirical_resolution_insufficient_for_reporting; review: exact_locus_unassessable_in_panel_of_normals; review: no_validated_umi_family_consensus; review: one_alignment_strand_only
REJECT
REJECTED_CANDIDATE
chrSynthetic:8982 T>G
SNV · GENE_T
1/23
4.348% · paired_fragment
0/1
forward/reverse
1
local-haplotype favored
1
q 1
0.004
rank, not probability
review: empirical_resolution_insufficient_for_reporting; review: exact_locus_unassessable_in_panel_of_normals; review: no_validated_umi_family_consensus; review: one_alignment_strand_only
REJECT
REJECTED_CANDIDATE
chrSynthetic:8995 A>G
SNV · GENE_T
1/23
4.348% · paired_fragment
0/1
forward/reverse
1
local-haplotype favored
1
q 1
0.002
rank, not probability
review: alt_evidence_concentrated_at_read_ends; review: empirical_resolution_insufficient_for_reporting; review: exact_locus_unassessable_in_panel_of_normals; review: no_validated_umi_family_consensus; review: one_alignment_strand_only
REJECT
REJECTED_CANDIDATE
chrSynthetic:9060 G>A
SNV · GENE_T
1/20
5.000% · paired_fragment
0/1
forward/reverse
1
local-haplotype favored
1
q 1
0.004
rank, not probability
review: empirical_resolution_insufficient_for_reporting; review: exact_locus_unassessable_in_panel_of_normals; review: no_validated_umi_family_consensus; review: one_alignment_strand_only
REJECT
REJECTED_CANDIDATE
chrSynthetic:9227 C>T
SNV · GENE_T
1/15
6.667% · paired_fragment
0/1
forward/reverse
1
local-haplotype favored
1
q 1
0.004
rank, not probability
review: empirical_resolution_insufficient_for_reporting; review: exact_locus_unassessable_in_panel_of_normals; review: no_validated_umi_family_consensus; review: one_alignment_strand_only
REJECT
REJECTED_CANDIDATE
chrSynthetic:9255 C>T
SNV · GENE_T
0/17
0.000% · paired_fragment
0/0
forward/reverse
0
local-haplotype favored
1
q 1
0.000
rank, not probability
below_assay_allele_fraction_floor; low_alt_base_quality; low_alt_mapping_quality; low_independent_alt_support; review: empirical_resolution_insufficient_for_reporting; review: exact_locus_unassessable_in_panel_of_normals; review: limited_fragment_start_diversity; review: no_validated_umi_family_consensus; review: one_alignment_strand_only
REJECT
REJECTED_CANDIDATE
chrSynthetic:9485 C>T
SNV · GENE_T
1/24
4.167% · paired_fragment
1/0
forward/reverse
1
local-haplotype favored
1
q 1
0.002
rank, not probability
review: alt_evidence_concentrated_at_read_ends; review: empirical_resolution_insufficient_for_reporting; review: exact_locus_unassessable_in_panel_of_normals; review: no_validated_umi_family_consensus; review: one_alignment_strand_only
REJECT
REJECTED_CANDIDATE
chrSynthetic:9498 A>C
SNV · GENE_T
1/21
4.762% · paired_fragment
0/1
forward/reverse
1
local-haplotype favored
1
q 1
0.004
rank, not probability
review: empirical_resolution_insufficient_for_reporting; review: exact_locus_unassessable_in_panel_of_normals; review: no_validated_umi_family_consensus; review: one_alignment_strand_only
REJECT
REJECTED_CANDIDATE
chrSynthetic:9529 C>T
SNV · GENE_T
1/22
4.545% · paired_fragment
1/0
forward/reverse
1
local-haplotype favored
1
q 1
0.004
rank, not probability
review: empirical_resolution_insufficient_for_reporting; review: exact_locus_unassessable_in_panel_of_normals; review: no_validated_umi_family_consensus; review: one_alignment_strand_only
REJECT
REJECTED_CANDIDATE
chrSynthetic:9563 C>T
SNV · GENE_T
1/27
3.704% · paired_fragment
1/0
forward/reverse
1
local-haplotype favored
1
q 1
0.004
rank, not probability
review: empirical_resolution_insufficient_for_reporting; review: exact_locus_unassessable_in_panel_of_normals; review: no_validated_umi_family_consensus; review: one_alignment_strand_only
REJECT
REJECTED_CANDIDATE
chrSynthetic:9845 C>T
SNV · GENE_T
0/25
0.000% · paired_fragment
0/0
forward/reverse
0
local-haplotype favored
1
q 1
0.000
rank, not probability
below_assay_allele_fraction_floor; low_alt_base_quality; low_alt_mapping_quality; low_independent_alt_support; review: empirical_resolution_insufficient_for_reporting; review: exact_locus_unassessable_in_panel_of_normals; review: limited_fragment_start_diversity; review: no_validated_umi_family_consensus; review: one_alignment_strand_only
REJECT
REJECTED_CANDIDATE
chrSynthetic:9847 C>T
SNV · GENE_T
1/24
4.167% · paired_fragment
1/0
forward/reverse
1
local-haplotype favored
1
q 1
0.004
rank, not probability
review: empirical_resolution_insufficient_for_reporting; review: exact_locus_unassessable_in_panel_of_normals; review: no_validated_umi_family_consensus; review: one_alignment_strand_only
REJECT
REJECTED_CANDIDATE
chrSynthetic:9904 C>G
SNV · GENE_T
1/22
4.545% · paired_fragment
0/1
forward/reverse
1
local-haplotype favored
1
q 1
0.004
rank, not probability
review: empirical_resolution_insufficient_for_reporting; review: exact_locus_unassessable_in_panel_of_normals; review: no_validated_umi_family_consensus; review: one_alignment_strand_only

What the pipeline did

  1. Validated the BGZF/BAM container, BAM records, reference identity, contig lengths, and analysis configuration.
  2. Generated permissive SNV and small-indel candidates from quality-qualified aligned bases and CIGAR events.
  3. Re-read every candidate locus, reconciled overlapping mates, separated fragments, coordinate-family audit groups, and explicit UMI families, and rescored supporting reads against local reference and alternate haplotypes.
  4. Compared evidence with a compatible panel of normals when one was supplied, adjusted over the declared full callable search rather than emitted candidates alone, and applied explicit hard and soft rules.
  5. Wrote normalized VCF, reviewer and complete-audit TSVs, JSON, QC, callability, HTML, and a hash-validated manifest.

Important limitations

How to use the files

variants.vcf
Normalized non-rejected hypotheses for standard genomics tools; genotype and QUAL remain missing.
variants.tsv
Human-sortable review list.
all-candidates.tsv and mutationsieve.json
Complete audit trail, including rejected candidates and exact reasons.
callability.bed and qc.json
Basewise depth plus maximum same-unit REF span at each start; MNV/indel negatives require enough span, and incomplete territory cannot support a negative interpretation.
manifest.json
Completion marker and SHA-256 identity of the other output files.
Resolved configuration
{
  "assay": "somatic",
  "assay_compatibility_token": "",
  "cram_reference_fasta": "",
  "drop_duplicates": true,
  "enable_reportable_tiers": false,
  "fdr": 0.01,
  "full_search_alleles_per_base": 2612,
  "llm_band": [
    0.25,
    0.9
  ],
  "llm_enabled": false,
  "llm_max_candidates": 25,
  "llm_max_logit_shift": 1.5,
  "llm_model": "claude-opus-5",
  "max_candidates": 25000,
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  "max_indel_length": 50,
  "max_mnv_length": 10,
  "max_normal_af": 0.02,
  "max_pending_mates": 50000,
  "max_query_bases_per_record": 1000,
  "max_records": 1000000,
  "max_recount_observations": 1000000,
  "max_reference_mismatch_fraction": 0.08,
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  "min_af_somatic": 0.01,
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  "min_alt_mean_mapq": 30.0,
  "min_alt_start_positions": 1,
  "min_alt_support": 1,
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  "min_depth": 3,
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  "min_family_members": 2,
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  "min_normal_depth": 1,
  "min_raw_alt_reads": 1,
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  "outdir": "${MUTATIONSIEVE_PROJECT_ROOT}\\benchmark\\sample-results\\STRESS_FFPE_LOW_DEPTH",
  "pon_max_sample_fraction": 0.5,
  "pon_min_alt_support": 2,
  "pon_min_samples": 2,
  "pon_path": "${MUTATIONSIEVE_PROJECT_ROOT}\\benchmark\\panel-of-normals.json",
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}
Provenance and compatibility identity
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