Changes

From Genome Analysis Wiki
Jump to navigationJump to search
662 bytes added ,  17:15, 4 October 2012
Line 259: Line 259:     
</pre>
 
</pre>
 +
 +
Each column represents
 +
* CHROM : Chromosome Name
 +
* BEGIN, END : Base position of the variant on each side
 +
* MARKER_ID : [CHROM]:[POS]_[REF]/[ALT]_[ANNOTATION] formatted marker ID. [ANNOTATION] information will be available only with --anno option
 +
* NS : Number of samples with non-missing genotypes
 +
* AC : Non-reference allele count
 +
* CALLRATE : Genotype call rate
 +
* MAF : Minor allele frequency
 +
* PVALUE : P-value
 +
 +
The rest of columns varies by statistical tests. For example, in b.score test, SCORE represents score test statistics, N.CASE and N.CTRL represents the case/control counts, and AF.CASE and AF.CTRL represents the case/control allele frequencies.

Navigation menu