# Interpretation of mutation data files

**URL:** <https://forum.depmap.org/t/interpretation-of-mutation-data-files/1069>\
**Category:** Q&A\
**Tags:** data\
**Created:** [December 8, 2021, 2:15pm UTC](https://forum.depmap.org/t/interpretation-of-mutation-data-files/1069 "2021-12-08T14:15:28Z")\
**Posts on this page:** 3\
**Page:** 1

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**Author:** ![SyedHaider](https://avatars.discourse-cdn.com/v4/letter/s/da6949/32.png) [@SyedHaider](https://forum.depmap.org/u/SyedHaider)\
**Post date:** [December 8, 2021, 2:15pm UTC](https://forum.depmap.org/t/interpretation-of-mutation-data-files/1069/1 "2021-12-08T14:15:29Z")

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Hi,

We are using pre-processed mutation files:

CCLE\_mutations\_bool\_damaging.csv  
CCLE\_mutations\_bool\_nonconserving.csv

However, we are unable to find a perfect overlap between data in these files and all inclusive maf file:  
CCLE\_mutations.csv

For example, the full file (CCLE\_mutations.csv) contains the following record (x = CCLE\_mutations.csv):

```auto
x[which(x$DepMap_ID == "ACH-000842" & x$Hugo_Symbol == "ERBB2"),]

       Hugo_Symbol Entrez_Gene_Id NCBI_Build Chromosome Start_position
376648 ERBB2 2064 37 17 37884214
       End_position Strand Variant_Classification Variant_Type Reference_Allele
376648 37884214 + Nonsense_Mutation SNP G
       Tumor_Seq_Allele1 dbSNP_RS dbSNP_Val_Status Genome_Change
376648 T g.chr17:37884214G>T
       Annotation_Transcript DepMap_ID cDNA_Change Codon_Change
376648 ENST00000269571.5 ACH-000842 c.3685G>T c.(3685-3687)Gag>Tag
       Protein_Change isDeleterious isTCGAhotspot TCGAhsCnt isCOSMIChotspot
376648 p.E1229* True False 0 False
       COSMIChsCnt ExAC_AF Variant_annotation CGA_WES_AC HC_AC RD_AC
376648 0 NA damaging 9:29 167:554
       RNAseq_AC SangerWES_AC WGS_AC
376648 33:118

```

This appears as “damaging” but its not present in the boolean file: CCLE\_mutations\_bool\_damaging.csv

There appears to be many cases of this. It is likely we are misinterpreting the file names as in what they contain. Any help would be greatly appreciated.

Thank you,  
Syed

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<div class="post-metadata">

**Author:** ![jnoorbak](https://yyz1.discourse-cdn.com/flex035/user_avatar/forum.depmap.org/jnoorbak/32/12_2.png) [@jnoorbak](https://forum.depmap.org/u/jnoorbak)\
**Post date:** [December 8, 2021, 8:12pm UTC](https://forum.depmap.org/t/interpretation-of-mutation-data-files/1069/2 "2021-12-08T20:12:17Z")

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Hi. I suspect that many of these mutations are low allele frequency cases similar to the example that you have shared. In the boolean matrices we drop any mutation with allele frequency below 0.25.

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<div class="post-metadata">

**Author:** ![SyedHaider](https://avatars.discourse-cdn.com/v4/letter/s/da6949/32.png) [@SyedHaider](https://forum.depmap.org/u/SyedHaider)\
**Post date:** [December 9, 2021, 1:52pm UTC](https://forum.depmap.org/t/interpretation-of-mutation-data-files/1069/3 "2021-12-09T13:52:43Z")

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Thank you very much for your answer.