Feature | Description | Value range: 5th–95th percentile (median) |
---|---|---|
DP | NGS read depth at the variant position. | 78–433 (222) |
AD | Number of reads that support the variant call. | 25–393 (110) |
AF | Fraction of reads that support the variant call, i.e. AD / DP. | 0.13–0.56 (0.49) |
GC @ 5, 20, 50 | Fraction of GC content in the 5, 20, and 50 bases around the variant position. | 0.18–0.73 (0.45) 0.29–0.69 (0.44) 0.30–0.68 (0.42) |
MQ | Root Mean Square of the mapping quality of the call. | 59.3–60 (60) |
GQ | Genotype Quality of the call. | 50–99 (99) |
WHR | Weighted Homopolymer Rate in a window of 20 bases around the variant position: the sum of squares of the homopolymer lengths, divided by the number of homopolymers. | 1.6–4.3 (2.4) |
HPL-D | Distance to the longest homopolymer within 20 bases from the call position. | 0–15 (5) |
HPL-L | Length of the longest homopolymer within 20 bases from the call position. | 2–6 (4) |
QUAL | Quality score assigned by the GATK HaplotypeCaller to the call. | 142–5448 (2564) |
QD | QUAL, normalized by DP. | 1.6–16.9 (11.3) |
FS | Phred-scaled p-value using Fisher’s exact test, to detect strand bias. | 0–9.2 (1.7) |