Output summary files - SnpEff & SnpSift Documentation
Author: Pablo Cingolani
Description: SnpEff and SnpSift documentation

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# Output summary Files

SnpEff creates an additional output file showing overall statistics. This "stats" file is an HTML file which can be opened using a web browser. You can find an example of a 'stats' file here.

### HTML summary (snpEff_summary.html)

The program performs some statistics and saves them to the file 'snpEff_summary.html' on the directory where snpEff is being executed. You can see the file, by opening it in your browser.

Info

You can change the default location by using the `-stats` command line option. This also changes the location of the TXT summary file.

Info

Summary can be create in CSV format using command line option `-csvStats`. This allows easy downstream processing.

E.g.: In the stats file, you can see coverage histogram plots like this one:

"Effects by type" vs "Effects by region"

SnpEff annotates variants. Variants produce effect of difference "types" (e.g. NON_SYNONYMOUS_CODING, STOP_GAINED). These variants affect regions of the genome (e.g. EXON, INTRON). The two tables count how many effects for each type and for each region exists.

E.g.: In an EXON region, you can have all the following effect types: NON_SYNONYMOUS_CODING, SYNONYMOUS_CODING, FRAME_SHIFT, STOP_GAINED, etc.

The complicated part is that some effect types affect a region that has the same name (yes, I know, this is confusing).

E.g.: In a UTR_5_PRIME region you can have UTR_5_PRIME and START_GAINED effect type.

This means that the number of both tables are not exactly the same, because the labels don't mean the same. See the next figure as an example:

So the number of effects that affect a UTR_5_PRIME region is 206. Of those, 57 are effects type START_GAINED and 149 are effects type UTR_5_PRIME.

How exactly are effect type and effect region related? See the following table:

Effect Type | Region
--- | ---
NONE CHROMOSOME CUSTOM CDS | NONE
INTERGENIC INTERGENIC_CONSERVED | INTERGENIC
UPSTREAM | UPSTREAM
UTR_5_PRIME UTR_5_DELETED START_GAINED | UTR_5_PRIME
SPLICE_SITE_ACCEPTOR | SPLICE_SITE_ACCEPTOR
SPLICE_SITE_DONOR | SPLICE_SITE_DONOR
SPLICE_SITE_REGION | SPLICE_SITE_REGION
INTRAGENIC START_LOST SYNONYMOUS_START NON_SYNONYMOUS_START GENE TRANSCRIPT | EXON or NONE
EXON EXON_DELETED NON_SYNONYMOUS_CODING SYNONYMOUS_CODING FRAME_SHIFT CODON_CHANGE CODON_INSERTION CODON_CHANGE_PLUS_CODON_INSERTION CODON_DELETION CODON_CHANGE_PLUS_CODON_DELETION STOP_GAINED SYNONYMOUS_STOP STOP_LOST RARE_AMINO_ACID | EXON
INTRON INTRON_CONSERVED | INTRON
UTR_3_PRIME UTR_3_DELETED | UTR_3_PRIME
DOWNSTREAM | DOWNSTREAM
REGULATION | REGULATION

### Gene counts summary (snpEff_genes.txt)

SnpEff also generates a TXT (tab separated) file having counts of number of variants affecting each transcript and gene. By default, the file name is `snpEff_genes.txt`, but it can be changed using the `-stats` command line option.

Here is an example of this file:

    $ head snpEff_genes.txt
    # The following table is formatted as tab separated values.
    #GeneName   GeneId  TranscriptId    BioType variants_impact_HIGH    variants_impact_LOW variants_impact_MODERATE    variants_impact_MODIFIER    variants_effect_3_prime_UTR_variant variants_effect_5_prime_UTR_premature_start_codon_gain_variant  variants_effect_5_prime_UTR_variant variants_effect_downstream_gene_variant variants_effect_intron_variant  variants_effect_missense_variant    variants_effect_non_coding_exon_variant variants_effect_splice_acceptor_variant variants_effect_splice_donor_variant    variants_effect_splice_region_variant   variants_effect_start_lost  variants_effect_stop_gained variants_effect_stop_lost   variants_effect_synonymous_variant  variants_effect_upstream_gene_variant   bases_affected_DOWNSTREAM   total_score_DOWNSTREAM  length_DOWNSTREAM   bases_affected_EXON total_score_EXON    length_EXON bases_affected_INTRON   total_score_INTRON  length_INTRON   bases_affected_SPLICE_SITE_ACCEPTOR total_score_SPLICE_SITE_ACCEPTOR    length_SPLICE_SITE_ACCEPTOR bases_affected_SPLICE_SITE_DONOR    total_score_SPLICE_SITE_DONOR   length_SPLICE_SITE_DONOR    bases_affected_SPLICE_SITE_REGION   total_score_SPLICE_SITE_REGION  length_SPLICE_SITE_REGION   bases_affected_TRANSCRIPT   total_score_TRANSCRIPT  length_TRANSCRIPT   bases_affected_UPSTREAM total_score_UPSTREAM    length_UPSTREAM bases_affected_UTR_3_PRIME  total_score_UTR_3_PRIME length_UTR_3_PRIME  bases_affected_UTR_5_PRIME  total_score_UTR_5_PRIME length_UTR_5_PRIME
    AC000029.1  ENSG00000221069 ENST00000408142 miRNA   0   0   0   2   0   0   0   2   0   0   0   0   0   0   0   0   5000    0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0
    AC000068.5  ENSG00000185065 ENST00000431090 antisense   0   0   0   1   0   0   0   0   0   0   0   0   0   0   0   5000    0   0   0   0   0   0
    AC000081.2  ENSG00000230194 ENST00000433141 processed_pseudogene    0   0   0   8   0   0   0   3   0   0   0   0   0   0   5000    0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   5   0   5000    0   0
    AC000089.3  ENSG00000235776 ENST00000424559 processed_pseudogene    0   0   0   1   0   0   0   0   0   0   0   0   0   0   5000    0   0   0   0   0   0
    AC002472.1  ENSG00000269103 ENST00000547793 protein_coding  0   0   0   6   0   0   0   5   0   0   0   0   0   0   0   5000    0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   1   0   5000    0   0
    AC002472.11 ENSG00000226872 ENST00000450652 antisense   0   0   0   13  0   0   0   5   2   0   0   0   0   0   0   5000    0   0   0   2   0   11199   0   0   0   0   0   0   0   0   0   0   0   0   6   0   5000    0   0
    AC002472.13 ENSG00000187905 ENST00000342608 protein_coding  0   1   6   1   0   0   0   0   1   6   0   0   0   1   0   116 1   0   934 0   0   0   0   0   0   1   0   3   0   0   0   0   0   0   0   0   0   0   0
    AC002472.13 ENSG00000187905 ENST00000442047 protein_coding  0   1   6   1   0   0   0   0   1   6   0   0   0   1   0   116 1   0   934 0   0   0   0   0   0   1   0   3   0   0   0   0   0   0   0   0   0   0   0

The columns in this table are:

Column name | Meaning
--- | ---
GeneName | Gene name (usually HUGO)
GeneId | Gene's ID
TranscriptId | Transcript's ID
BioType | Transcript's bio-type (if available)
| The following column is repeated for each impact {HIGH, MODERATE, LOW, MODIFIER}
variants_impact_* | Count number of variants for each impact category
| The following column is repeated for each annotated effect (e.g. missense_variant, synonymous_variant, stop_lost, etc.)
variants_effect_* | Count number of variants for each effect type
| The following columns are repeated for several genomic regions (DOWNSTREAM, EXON, INTRON, UPSTREAM, etc.)
bases_affected_* | Number of bases that variants overlap genomic region
total_score_* | Sum of scores overlapping this genomic region. Note: Scores are only available when input files are type 'BED' (e.g. when annotating ChipSeq experiments)
length_* | Genomic region length