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Is the paired value the P value?

I have a VCF file, and am looking at it in Excel. I see under the Info tab "paired values" they are between 0 and 1. Is this my P value?

Thank you!!

snp assembly genome
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written by tmrhyd • tmrhyd

There should be a header line explaining it or check the documentation of the variant caller. With the given information, we cannot help. Which caller, show the header and an example.

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written by ATpoint ATpoint

the program I used is Freebayes, and the header is INFO, and the information inside of it is below.

AB=0;ABP=0;AC=2;AF=1;AN=2;AO=1062;CIGAR=1X;DP=1063;DPB=1063;DPRA=0;
EPP=4.85053;EPPR=0;GTI=0;LEN=1;MEANALT=2;MQM=59.9962;MQMR=0;NS=1;
NUMALT=1;ODDS=1476.85;PAIRED=0.991525;PAIREDR=0;PAO=0;PQA=0;PQR=0;
PRO=0;QA=41510;QR=0;RO=0;RPL=517;RPP=4.61335;RPPR=0;RPR=545;RUN=1;
SAF=539;SAP=3.53374;SAR=523;SRF=0;SRP=0;SRR=0;TYPE=snp;technology.
LLUMINA=1

The documentation says this about the paired values.

INFO=<ID=PAIRED,Number=A,Type=Float,Description="Proportion of observed alternate alleles which are supported by properly paired read fragments">                                   
INFO=<ID=PAIREDR,Number=1,Type=Float,Description="Proportion of observed reference alleles which are supported by properly paired read fragments">

But I am still confused. Are these P values? can I get P values from them?

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updated by GenoMax GenoMax • written by tmrhyd • tmrhyd

It is the number of properly-paired reads that support the call being reference or alternate. This is not a statistical probability value. Is this an assignment question?

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written by ATpoint ATpoint

It is not an assignment question. I am pretty confused through. I need the P values, and have bam files and VCF files, and am getting no phenotype data errors in PLINK. Is there some way to calculate my P values ?

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written by tmrhyd • tmrhyd

Check the manual, searching for probability.

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written by ATpoint ATpoint

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