The info column of raw-snps-filtered.ann.vcf file showing more than one gene for a single position of RNA editing sites.

Question

[Genetics]

Hi All, I am first time trying to identify the RNA editing sites from (A TO I )changes.I have used GATK pipeline and at the very end when I have generated raw_snps filtered annotation file by snpEff tool,the info column looks like this .I am not sure why in this info column showing two/three genes. I am not able to understand where I did the mistake.

AC=1;AF=0.500;AN=2;BaseQRankSum=-1.834;DP=16;ExcessHet=0.0000;FS=0.000;MLEAC=1;MLEAF=0.500;MQ=60.00;MQRankSum=0.000;QD=3.19;ReadPosRankSum=-2.499;SOR=0.105;ANN=A|splice_donor_variant&intron_variant|HIGH|EXON_supercont1.1_10978_11929|gene:MVLG_00003|transcript|transcript:MVLG_00003T0|protein_coding|3/7|c.137+1G>T||||||WARNING_TRANSCRIPT_NO_STOP_CODON,A|upstream_gene_variant|MODIFIER|EXON_supercont1.1_13591_13831|gene:MVLG_00004|transcript|transcript:MVLG_00004T0|protein_coding||c.-681C>A|||||565|WARNING_TRANSCRIPT_NO_STOP_CODON,A|upstream_gene_variant|MODIFIER|EXON_supercont1.1_15696_15743|gene:MVLG_00005|transcript|transcript:MVLG_00005T0|protein_coding||c.-2704C>A|||||2670|WARNING_TRANSCRIPT_NO_STOP_CODON,A|downstream_gene_variant|MODIFIER|EXON_supercont1.1_8132_8438|gene:MVLG_00002|transcript|transcript:MVLG_00002T0|protein_coding||c.*2144C>A|||||1953|WARNING_TRANSCRIPT_NO_STOP_CODON;LOF=(EXON_supercont1.1_10978_11929|gene:MVLG_00003|1|1.00

Answer 1

[Pierre Lindenbaum]

A  splice_donor_variant&intron_variant  HIGH      EXON_supercont1.1_10978_11929  gene:MVLG_00003  transcript  transcript:MVLG_00003T0  protein_coding  3/7         c.137+1G>T  WARNING_TRANSCRIPT_NO_STOP_CODON
A  upstream_gene_variant                MODIFIER  EXON_supercont1.1_13591_13831  gene:MVLG_00004  transcript  transcript:MVLG_00004T0  protein_coding  c.-681C>A   565         WARNING_TRANSCRIPT_NO_STOP_CODON
A  upstream_gene_variant                MODIFIER  EXON_supercont1.1_15696_15743  gene:MVLG_00005  transcript  transcript:MVLG_00005T0  protein_coding  c.-2704C>A  2670        WARNING_TRANSCRIPT_NO_STOP_CODON
A  downstream_gene_variant              MODIFIER  EXON_supercont1.1_8132_8438    gene:MVLG_00002  transcript  transcript:MVLG_00002T0  protein_coding  c.*2144C>A  1953        WARNING_TRANSCRIPT_NO_STOP_CODON

looking in google cache ( http://webcache.googleusercontent.com/search?q=cache:TailYV6oll4J:ftp://ftp.broadinstitute.org/pub/annotation/fungi/microbotryum/genomes/microbotryum_violaceum_p1a1_lamole_1_genome_summary_per_gene.txt ) . The 4 genes overlap.

MVLG_00002          2942    8132    11073   +   hypothetical protein    1                               PF02838.8,PF00728.15        
MVLG_00003          2468    10978   13445   -   T-complex protein 1 subunit theta   1                               PF00118.17,TIGR02346        
MVLG_00004          2028    13591   15618   +   hypothetical protein    1                               PF00153.20      
MVLG_00005          2412    15696   18107   +   hypothetical protein    1                               PF00160.14      

[Genetics]

Thank you so much for your reply. In this case how could I able to identify where the actual editing occured because for the above example the vcf file is showing that at this "13026 " position C(REF) to A(ALT) changes occured but when I checked the MVLG_00003 exon I didnt find "C" at that position.In that case how do I know in which gene among the four(MVLG_00002,MVLG_00003,MVLG_00004,MVLG_00005) actually the editing happened?

[Pierre Lindenbaum]

which genome is it ? which build ?

[Genetics]

This is genome of Microbotryum violaceum(fungi) https://fungi.ensembl.org/Microbotryum_violaceum/Info/Index

[Pierre Lindenbaum]

and I got a C at this genomic position.

$ samtools  faidx Microbotryum_violaceum.GCA_000166175.1.dna.toplevel.fa "supercont1.1:13026-13026" 
>supercont1.1:13026-13026
C

[Genetics]

Thank you.I was trying to see manually.

[Genetics]

When there is more than one annotation at a perticular RNA editing sites,how do you know in which gene the editing happened? I have used "ud 0 " at the time of database creation using snpEff,but still getting samething.