mity report documentation

March 1, 2025 · View on GitHub

Description of column headings

Term	Definition and Information
SAMPLE	Sample name from the VCF (Variant Call Format) file.
HGVS	Variant annotation using HGVS (Human Genome Variation Society) syntax for SNPs, insertions, or deletions.
GENE/LOCUS	The gene the variant is located in, or the corresponding MITOMAP entry if not in a gene.
GENE/LOCUS DESCRIPTION	Description of the gene or locus where the variant is found.
TOTAL LOCUS DEPTH	The total sequencing depth (number of reads) at the locus of interest.
VARIANT HETEROPLASMY	The proportion of alternate allele reads to total reads: alt_depth / (ref_depth + alt_depth).
ALT DEPTH	The number of sequencing reads that contain the alternate (variant) allele.
REF DEPTH	The number of sequencing reads that contain the reference allele.
TOTAL SAMPLE DEPTH	The total number of sequencing reads for the sample at the given position: alt_depth + ref_depth.
VARIANT QUALITY	The Phred-scaled quality score of the variant call, representing confidence in the call.
TIER	Categorization based on heteroplasmy fraction: Tier 1 (VAF ≥ 1%), Tier 2 (VAF < 1% & alt_depth ≥ 10), Tier 3 (VAF < 1% & alt_depth < 10).
COHORT COUNT	The number of times the variant (defined by position and alternate allele) appears in all input VCFs.
COHORT FREQUENCY	The frequency of the variant in the cohort: COHORT COUNT / TOTAL SAMPLES.
MQM_INFO	Mean mapping quality of observed alternate alleles.
MQMR_INFO	Mean mapping quality for reference alleles.
QA_INFO	Sum of Phred-scaled quality scores for alternate allele reads.
QR_INFO	Sum of Phred-scaled quality scores for reference allele reads.
SAF_INFO	Number of alternate allele reads observed on the forward strand.
SAR_INFO	Number of alternate allele reads observed on the reverse strand.
SRF_INFO	Number of reference allele reads observed on the forward strand.
SRR_INFO	Number of reference allele reads observed on the reverse strand.
SBR_INFO	Signal Bias Ratio: For all alleles, if RO > 15 and (SBR > 0.9 or SBR < 0.1), it indicates strand bias.
SBA_INFO	Signal Bias for Alternate alleles: If AO > 15 and (SBA > 0.9 or SBA < 0.1), it indicates strand bias.
POS_FILTER	Indicates whether the variant falls within a known problematic region, such as MT:302-319 or MT:3105-3108.
SBR_FILTER	A filter flag for strand bias in reference alleles.
SBA_FILTER	A filter flag for strand bias in alternate alleles.
MQMR_FILTER	A filter flag applied when MQMR (reference mapping quality) is below 30.
AQR_FILTER	A filter flag applied when AQR (average quality of reference reads) is below 20.
ANTICODON	The anticodon sequence if the variant is located in a tRNA gene.
GENE	The gene name where the variant occurs.
GENE BIOTYPE	The biotype classification of the gene (e.g., protein-coding, tRNA, rRNA).
PHYLOTREE MUT	The mutation annotation from the PhyloTree database.
PHYLOTREE HAPLOTYPE	The associated haplogroup assignment based on PhyloTree.
MGRB FILTER	Indicates whether the variant passes filtering criteria in the MGRB dataset.
MGRB AN	Allele number in the MGRB dataset.
MGRB AC	Allele count in the MGRB dataset.
MGRB FREQUENCY	Frequency of the variant allele in the MGRB dataset.
MITOMAP DISEASE AC	Allele count of the variant in MITOMAP’s disease-associated dataset.
MITOMAP DISEASE AF	Allele frequency of the variant in MITOMAP’s disease-associated dataset.
MITOMAP DISEASE AACHANGE	The associated amino acid change if applicable.
MITOMAP DISEASE HOMOPLASMY	Whether the variant has been observed in a homoplasmic state in disease cases.
MITOMAP DISEASE HETEROPLASMY	Whether the variant has been observed in a heteroplasmic state in disease cases.
MITOMAP DISEASE PUBMED IDS	List of PubMed IDs of studies linking the variant to disease.
MITOMAP DISEASE DISEASE	Name of the disease(s) associated with the variant.
MITOMAP DISEASE DISEASE STATUS	Classification of the disease association (e.g., confirmed, probable, uncertain).
MITOMAP DISEASE HGFL	The Human Gene and Disease Feature List (HGFL) entry for mitochondrial diseases associated with specific variants.
MITOMAP CONFIRMED MUTATIONS LOCUS	The specific mitochondrial gene or locus where a confirmed pathogenic mutation occurs.
MITOMAP CONFIRMED MUTATIONS LOCUSTYPE	The classification of the locus (e.g., protein-coding gene, rRNA, tRNA, or control region).
MITOMAP CONFIRMED MUTATIONS ASSOCIATEDDISEASE	The disease or condition associated with the confirmed mitochondrial mutation.
MITOMAP CONFIRMED MUTATIONS ALLELE	The specific allele (variant) that has been confirmed as pathogenic in mitochondrial disease.
MITOMAP CONFIRMED MUTATIONS AMINOACIDCHANGE	The change in the amino acid sequence resulting from a confirmed pathogenic mutation, if applicable.
MITOMAP CONFIRMED MUTATIONS STATUSMITOMAPCLINGEN	The classification status of the mutation in MITOMAP and ClinGen, indicating whether it is pathogenic, likely pathogenic, or uncertain.
MITOMAP CONFIRMED MUTATIONS LASTUPDATE	The date when the mutation entry was last updated in MITOMAP.
MITOMAP MUTATIONS CODING CONTROL LOCUS	The mitochondrial gene or control region affected by a mutation.
MITOMAP MUTATIONS CODING CONTROL ALLELE	The specific allele involved in the mutation within the coding or control region.
MITOMAP MUTATIONS CODING CONTROL DISEASE	The disease or disorder linked to the mutation occurring in the coding or control region.
MITOMAP MUTATIONS CODING CONTROL NUCLEOTIDECHANGE	The specific nucleotide-level alteration in the coding or control region of the mitochondrial genome.
MITOMAP MUTATIONS CODING CONTROL AMINOACIDCHANGE	The resulting change in the amino acid sequence due to a coding-region mutation, if applicable.
MITOMAP MUTATIONS CODING CONTROL PLASMY	The type of heteroplasmy (heteroplasmic or homoplasmic) observed for the mutation.
MITOMAP MUTATIONS CODING CONTROL STATUS	The classification status of the mutation (e.g., pathogenic, likely pathogenic, uncertain, or benign).
MITOMAP MUTATIONS CODING CONTROL GB FREQ	The frequency of the mutation in GenBank mitochondrial sequences.
MITOMAP MUTATIONS CODING CONTROL GB SEQS	The number of GenBank mitochondrial genome sequences in which the mutation has been observed.
MITOMAP MUTATIONS CODING CONTROL REFERENCES	Research articles or curated references that discuss the mutation's significance.
MITOMAP MUTATIONS RNA LOCUS	The specific mitochondrial RNA gene (tRNA or rRNA) affected by a mutation.
MITOMAP MUTATIONS RNA DISEASE	The disease or disorder associated with the mitochondrial RNA mutation.
MITOMAP MUTATIONS RNA ALLELE	The specific allele variant of the mitochondrial RNA gene that has been mutated.
MITOMAP MUTATIONS RNA RNA	The affected RNA sequence or structural change resulting from the mutation.
MITOMAP MUTATIONS RNA HOMOPLASMY	Indicates whether the mutation is present in all copies of mitochondrial DNA in a cell (homoplasmic state).
MITOMAP MUTATIONS RNA HETEROPLASMY	Indicates whether the mutation is present in only a subset of mitochondrial DNA copies in a cell (heteroplasmic state).
MITOMAP MUTATIONS RNA STATUS	The classification status of the RNA mutation (e.g., pathogenic, likely pathogenic, uncertain).
MITOMAP MUTATIONS RNA MITOTIP	MitoTIP score, a computational prediction tool used to assess the pathogenicity of mitochondrial tRNA mutations.
MITOMAP MUTATIONS RNA GB FREQ	The frequency of the RNA mutation in GenBank mitochondrial sequences.
MITOMAP MUTATIONS RNA GB SEQS	The number of GenBank mitochondrial genome sequences in which the RNA mutation has been observed.
MITOMAP MUTATIONS RNA REFERENCES	Published studies or curated references discussing the mitochondrial RNA mutation and its biological significance.
MITOMAP POLYMORPHISMS AC	Allele count in MITOMAP’s polymorphism dataset.
MITOMAP POLYMORPHISMS AF	Allele frequency in MITOMAP’s polymorphism dataset.
MITOMAP POLYMORPHISMS HGFL	Haplogroup Frequency List, indicating common haplogroups for the variant.
MITOMAP VARIANTS CODING LOCUS	The specific gene or locus in the mitochondrial genome where a coding-region variant occurs.
MITOMAP VARIANTS CODING NUCLEOTIDECHANGE	The specific nucleotide alteration (substitution, deletion, or insertion) observed in the coding region of the mitochondrial genome.
MITOMAP VARIANTS CODING CODONNUMBER	The codon number in the gene where the variant occurs, indicating its position in the coding sequence.
MITOMAP VARIANTS CODING CODONPOSITION	The specific position within the codon affected by the nucleotide change (first, second, or third base of the codon).
MITOMAP VARIANTS CODING AMINOACIDCHANGE	The resulting amino acid substitution due to the nucleotide change, if it leads to a missense or nonsense mutation.
MITOMAP VARIANTS CODING GB FREQ	The frequency of the variant observed in GenBank mitochondrial genome sequences, indicating how common it is in public databases.
MITOMAP VARIANTS CODING GB SEQS	The number of GenBank mitochondrial genome sequences in which the variant has been observed.
MITOMAP VARIANTS CODING CURATEDREFERENCES	Published research articles or curated references that discuss the variant in the coding region, supporting its biological significance.
MITOMAP VARIANTS CONTROL LOCUS	The specific locus in the mitochondrial control region where a variant occurs.
MITOMAP VARIANTS CONTROL NUCLEOTIDECHANGE	The nucleotide change observed in the control region of the mitochondrial genome.
MITOMAP VARIANTS CONTROL GB FREQ	The frequency of the control-region variant in GenBank mitochondrial genome sequences.
MITOMAP VARIANTS CONTROL GB SEQS	The number of GenBank sequences containing this variant in the control region.
MITOMAP VARIANTS CONTROL CURATED REFERENCES	Research articles or curated sources discussing the significance of the control-region variant.
MITOTIP SCORE	A computational pathogenicity score for tRNA variants.
MITOTIP PERCENTILE	Percentile ranking of the MITOTIP score.
MITOTIP QUARTILE	Quartile-based ranking of MITOTIP score (Q1-Q4).
MITOTIP SCORE INTERPRETATION	Interpretation of the pathogenicity score based on its percentile.
MITOMAP STATUS	The strength of evidence supporting the MITOMAP annotation.
COUNT	Count of MITOTIP-associated observations.
PERCENTAGE	Percentage of MITOTIP observations.
GT_FORMAT	Genotype format field in the VCF.
QR_FORMAT	Sum of Phred-scaled base quality scores for reference allele reads (per sample).
AQR_FORMAT	Average base quality of the reference reads: AQR = QR / RO.
QA_FORMAT	Sum of Phred-scaled base quality scores for alternate allele reads (per sample).
AQA_FORMAT	Average base quality of the alternate reads: AQA = QA / AO.

Mitomap source links and conversions

Mitomap Annotation File	Source	Python script to generate vcf
mitomap_disease.vcf.gz	https://www.mitomap.org/foswiki/bin/view/MITOMAP/Resources
mitomap_polymorphisms.vcf.gz	https://www.mitomap.org/foswiki/bin/view/MITOMAP/Resources
mitotip_scores.vcf.gz	https://www.mitomap.org/foswiki/bin/view/MITOMAP/MitoTipInfo	convert_mitomap_scores_to_vcf.py
mitomap_mutations_rna.vcf.gz	https://www.mitomap.org/foswiki/bin/view/MITOMAP/MutationsRNA	convert_mitomap_mutations_rna_to_vcf.py
mitomap_mutations_coding_control.vcf.gz	https://www.mitomap.org/foswiki/bin/view/MITOMAP/MutationsCodingControl	convert_mitomap_mutations_coding_control_to_vcf.py
mitomap_variants_control.vcf.gz	https://www.mitomap.org/foswiki/bin/view/MITOMAP/VariantsControl	convert_mitomap_variants_control_to_vcf.py
mitomap_variants_coding.vcf.gz	https://www.mitomap.org/foswiki/bin/view/MITOMAP/VariantsCoding	convert_mitomap_variants_coding_to_vcf.py
mitomap_confirmed_mutations.vcf.gz	https://www.mitomap.org/foswiki/bin/view/MITOMAP/ConfirmedMutations	convert_mitomap_confirmed_mutations_to_vcf.py

Most of the mitomap sources come in other forms, e.g. csv or tsv, but we need vcfs to properly annotate with vcfanno so in tools/ we have a series of conversion scripts unique to each mitomap source.

Notes

mitomap_variants_control.vcf.gz from the original VariantsControl MITOMAP Foswiki.csv has 4 lines which were somewhat difficult to convert to the vcf version. Namely these lines:

"568","MT-HV3","C-C(2-8)","0.000%(0.000%)","0","2"
"573","MT-HV3","C-C(2-8)","0.000%(0.000%)","0","40"
"16184","MT-HV1","C-C(2-5)","0.000%(0.000%)","0","12"
"16193","MT-HV1","C-C(2-3)","0.000%(0.000%)","0","18"