Read pileup: depth is sampling

Sequencing

Mean coverage

Depth at the site is Poisson with this mean.

True genotype

0 is the reference allele C, 1 is the alternate T.

Base quality (Phred)

Q30 is a 0.1% chance the base is wrong; Q10 is 10%.

Read length

Mapping quality

Phred chance the read is placed in the wrong spot. At 0 a read carries no information.

Artefacts

Strand bias

Probability an alternate-allele read is on the forward strand. Real variants sit near 0.5.

Contamination

Fraction of reads that come from another person's genotype at this site.

Prior on a variant

P(0/1) before seeing reads; 1/1 gets half that.

Sites simulated

For the allele-balance panel: this many sites at the same settings.

Seed

Reads covering chr17:7,676,154

ACGT base at the site forward read reverse read contaminant

Depth-

Ref / alt reads-

Allele balance-

Called genotype-

GQ-