====== PolyPhen-2 annotation summary report explained ======

Following is a description of **PolyPhen-2** annotation summary report. Reports in this format are produced by both PolyPhen-2 **Batch query** web service, as well as by **standalone** PolyPhen-2 software. It is a plain text tab-separated file with each line annotating single protein variant (amino acid residue substitution).

Fourteen columns highlighted below (1-2, 6-11, 41, 45-48, 91) are the ones included in the **Short** version of the report available via **Batch query** web page. These are sufficient if you are interested in PolyPhen-2 prediction outcome and prediction confidence scores. The rest of the columns in **Full** report version are mostly useful only if you want to investigate all features supporting the prediction in detail.

^  Column\\ No.  ^  Column\\ Name  ^ Description  ^
| **Original query** (as copied from user input):   |||
^   1 |  query_no    | input query ordinal  |
^   2 |  o_acc       | original protein identifier |
|   3 |  o_pos       | original substitution position in the protein sequence |
|   4 |  o_aa1       | original wild type (reference) amino acid residue |
|   5 |  o_aa2       | original mutant (substitution) amino acid residue |
| **Annotated query**:   |||
^   6 |  rsid        | dbSNP reference SNP identifier (rsID) if available |
^   7 |  acc         | UniProtKB accession if known protein, otherwise same as o_acc |
^   8 |  length      | Length of the protein sequence |
^   9 |  pos         | substitution position in UniProtKB protein sequence, otherwise same as o_pos |
^  10 |  aa1         | wild type amino acid residue in relation to UniProtKB sequence  |
^  11 |  aa2         | mutant amino acid residue in relation to UniProtKB sequence |
| **Nucleotide sequence context annotations**:  |||
|  12 |  chr_pos     | SNP chromosome:position (chromosome coordinates are 1-based)  |
|  13 |  str         | transcript strand ("+" or "-") |
|  14 |  gene        | gene symbol |
|  15 |  transcript  | UCSC transcript name (unique identifier) |
|  16 |  canon       | UCSC knowCanonical representative transcript flag: 1\ -\ canonical, 0\ -\ alternative |
|  17 |  cid      | UCSC knownCanonical cluster identifier (number) |
|  18 |  txcov    | transcript coverage, the number of transcipts in UCSC cluster overlapping the mutation position / total number of transcripts in the cluster |
|  19 |  ntlen    | full transcript length (number of nucleotides) |
|  20 |  ntpos    | mutation position in the full transcript nucleotide sequence (in the direction of transcription) |
|  21 |  nt1      | reference nucleotide (transcript strand) |
|  22 |  nt2      | variant nucleotide (transcript strand) |
|  23 |   PtGgPaNl  | orthologous alleles in chimp\ (Pt), gorilla\ (Gg), Orangutan\ (Pa) and gibbon\ (Nl) if different from human reference allele, ?\ -\ otherwise; .\ -\ data not available |
|  24 |  dref     | putative derived allele found in human reference, score: 0\ -\ no evidence, 1\ -\ variant allele matches orthologous ancestral allele, 2\ -\ dbSNP minor allele matches reference allele, 3\ -\ both dbSNP and orthologous evidence present, ?\ -\ not enough evidence to score |
|  25 |  gerprs   | Genomic Evolutionary Rate Profiling (GERP++) position-specific conservation score, RS; 0\ -\ when alignment coverage is insufficient  |
|  26 |  phylop   | conservation scoring by phyloP (phylogenetic p-values) from the [[http://compgen.bscb.cornell.edu/phast/|PHAST package]] for multiple alignments of 99 vertebrate genomes to the human genome |
|  27 |  trv      | transversion mutation flag: 0\ -\ transition, 1\ -\ transversion |
|  28 |  CpG      | CpG context: 0\ -\ non-CpG context retained, 1\ -\ mutation removes CpG site, 2\ -\ mutation creates new CpG site, 3\ -\ CpG context retained: C(C/G)G substitution |
|  29 |  JXmin    | distance from mutation position to the nearest exon / intron junction ("-" for upstream, "+" for downstream) |
|  30 |  JXc      | mutation in a codon that is split across two exons: ?\ -\ no, 1\ -\ yes  |
|  31 |  exon     | mutation in exon # / of total exons (exons are enumerated in the direction of transcription)  |
|  32 |  cexon    | same as above but only coding (CDS) exons are being enumerated  |
|  33 |  cdnpos   | number of the mutated codon within transcript's CDS (1-base)  |
|  34 |  frame    | mutation position offset within the codon (0..2)  |
|  35 |  dgn      | degeneracy index for mutated codon position, by Nei & Kumar (2000) "Molecular Evolution and Phylogenetics", page 64: 0\ -\ non-degenerate, 2\ -\ simple 2-fold degenerate, 3\ -\ complex 2-fold degenerate, 4\ -\ 4-fold degenerate  |
|  36 |  cdn1     | reference codon  |
|  37 |  cdn2     | mutated codon  |
| **dbNSP annotations**:  |||
|  38 |  dbrsid    | dbSNP SNP rsID  |
|  39 |  dbminor   | dbSNP minor allele nucleotide (transcript strand)  |
|  40 |  dbmaf     | dbSNP minor allele frequency  |
| **PolyPhen-2 prediction outcome**:  |||
^  41 |  prediction  | qualitative ternary classification appraised at 5%/10% (HumDiv) or 10%/15% (HumVar) False Discovery Rate (FDR) thresholds: "benign", "possibly damaging", "probably damaging"  |
| **PolyPhen-1 prediction description** (obsolete, please ignore):  |||
|  42 |  based_on    | prediction basis  |
|  43 |  effect      | predicted substitution effect on the protein structure or function  |
| **PolyPhen-2 classifier outcome and scores**:  |||
|  44 |  pph2_class  | probabilistic binary classifier outcome: "damaging" or "neutral"  |
^  45 |  pph2_prob   | classifier probability of the variation being damaging  |
^  46 |  pph2_FPR    | classifier model False Positive Rate (1 - specificity) at the above probability  |
^  47 |  pph2_TPR    | classifier model True Positive Rate (sensitivity) at the above probability  |
^  48 |  pph2_FDR    | classifier model False Discovery Rate at the above probability  |
| **UniProtKB/Swiss-Prot/Pfam protein annotations**:   |||
|  49 |  PfamHit     | Pfam identifier of the protein family or domain to which substitution maps  |
|  50 |  site        | substitution SITE annotation  |
|  51 |  region      | substitution REGION annotation  |
|  52 |  PHAT        | PHAT matrix element for substitutions in the TRANSMEM region  |
| **Multiple sequence alignment scores**:   |||
|  53 |  dScore      | difference of PSIC scores for two amino acid residue variants (Score1-Score2)  |
|  54 |  Score1      | PSIC score for wild type amino acid residue (aa1)  |
|  55 |  Score2      | PSIC score for mutant amino acid residue (aa2)  |
|  56 |  MSAv        | version of the multiple sequence alignment used in conservation scores calculations: 1 - pairwise BLAST HSP (obsolete), 2 - MAFFT-Leon-Cluspack (default), 3 - MultiZ CDS  |
|  57 |  Nobs        | number of residues observed at the substitution position in multiple alignment (without gaps)  |
|  58 |  Nseqs       | number of sequences observed at the substitution position in multiple alignment (including gaps)  |
|  59 |  Nsubs       | number of residues different from reference residue (aa1) observed at the substitution position in multiple alignment  |
|  60 |  Nvars       | number of residues same as substitution residue (aa2) observed at the substitution position in multiple alignment (without gaps)  |
|  61 |  Nres        | number of unique residues observed at the substitution position in multiple alignment (without gaps)  |
| **Substitution scores**:  |||
|  62 |  IdPmax      | maximum congruency of the substitution amino acid residue across all sequences with a substitution at the substitution position in multiple alignment  |
|  63 |  IdPSNP      | maximum congruency of the substitution amino acid residue to the sequences in multiple alignment with the substitution residue at the substitution position in multiple alignment  |
|  64 |  IdQmax      | query sequence identity with the closest homologue deviating from the wild type amino acid residue (aa1)  |
| **Phylogenetic tree based scores**:  |||
|  65 |  DistPmin    | minimum normalized distance along the phylogenetic tree across all substitution types encountered at the substitution position  |
|  66 |  DistPSNP    | minimum normalized distance along the phylogenetic tree for substitution residues (aa2) encountered at the substitution position  |
|  67 |  DistQmin    | minimum distance (sum of branch lengths) along the phylogenetic tree across all substitution types encountered at the substitution position  |
|  68 |  BaRE        | Bayesian Rate Estimator for scoring evolutionary conservation, D.M. Jordan (2015)  |
| **Gene-based scores**:  |||
|  69 |  RVISraw     | Residual Variation Intolerance Score (raw), Petrovski //et al.// (2013)  |
|  70 |  RVISranked  | Residual Variation Intolerance Score (normalized by rank), Petrovski //et al.// (2013)  |
| **RCSB PDB annotations**:  |||
|  71 |  Nstruct     | initial number of BLAST hits to similar proteins with 3D structures in PDB  |
|  72 |  Nfilt       | number of 3D BLAST hits after identity threshold filtering  |
|  73 |  PDB_id      | PDB protein structure identifier  |
|  74 |  PDB_ch      | PDB polypeptide chain identifier  |
|  75 |  PDB_len     | PDB sequence alignment length  |
|  76 |  PDB_pos     | position of substitution in the PDB protein sequence  |
|  77 |  PDB_idn     | sequence identity between query sequence and the aligned PDB sequence  |
| **Amino acid residues structural features**:  |||
|  78 |  dVol        | change in residue side chain volume |
|  79 |  dProp       | change in solvent accessible surface propensity resulting from the substitution |
| **Protein 3D structure features**:  |||
|  80 |  SecStr      | DSSP secondary structure assignment |
|  81 |  MapReg      | region of the phi-psi map (Ramachandran map) derived from the residue dihedral angles |
|  82 |  NormASA     | normalized accessible surface |
|  83 |  B-fact      | normalized B-factor (temperature factor) for the residue |
|  84 |  H-bonds     | number of hydrogen sidechain-sidechain and sidechain-mainchain bonds formed by the residue |
|  85 |  AveNHet     | number of residue contacts with heteroatoms, average per homologous PDB chain |
|  86 |  MinDHet     | closest residue contact with a heteroatom, Å |
|  87 |  AveNInt     | number of residue contacts with other chains, average per homologous PDB chain |
|  88 |  MinDInt     | closest residue contact with other chain, Å |
|  89 |  AveNSit     | number of residue contacts with critical sites, average per homologous PDB chain |
|  90 |  MinDSit     | closest residue contact with a critical site, Å |
| **Comments**:   |||
^  91 |  Comments    | optional user comments, copied from input |