/EXTERNAL DEEP/variants/K008990_K008991_K008992_K008993_K008994_K008995_K008996_K008997_K008998_K008999_K009000_K009001_K009002_K009003_K009004_K009005_16_lane_gembs
BACK
SAMPLE K008990_K008991_K008992_K008993_K008994_K008995_K008996_K008997_K008998_K008999_K009000_K009001_K009002_K009003_K009004_K009005_16_lane_gembs
Variant counts
| Type |
Total |
Pass |
% |
| SNPs |
1179026414 |
917694492 |
77.83 % |
| Multiallelic |
0 |
0 |
0.00 % |
VCF Filtering Stats
| Type |
#Sites |
% |
#Non-Variant Sites |
% |
#Variant Sites |
% |
| All |
1179026414 |
100% |
1144719401 |
97.09 % |
34307013 |
2.91 % |
| |
|
|
|
|
|
|
| Passed |
921672864 |
78.17 % |
913273575 |
79.78 % |
8399289 |
0.91 % |
| Filtered |
257353550 |
21.83 % |
231445826 |
20.22 % |
25907724 |
2.81 % |
| |
|
|
|
|
|
|
| q20 |
199027687 |
77.34 % |
193705688 |
83.69 % |
5321999 |
20.54 % |
| q20,qd2 |
31691599 |
12.31 % |
12878474 |
5.56 % |
18813125 |
72.62 % |
| q20,mq40 |
11133711 |
4.33 % |
10775673 |
4.66 % |
358038 |
1.38 % |
| qd2 |
9953751 |
3.87 % |
9305756 |
4.02 % |
647995 |
2.50 % |
| q20,qd2,mq40 |
3634538 |
1.41 % |
3247834 |
1.40 % |
386704 |
1.49 % |
| mq40 |
1846492 |
0.72 % |
1479511 |
0.64 % |
366981 |
1.42 % |
| qd2,mq40 |
63013 |
0.02 % |
52890 |
0.02 % |
10123 |
0.04 % |
| qd2,fs60,mq40 |
930 |
0.00 % |
0 |
0.00 % |
930 |
0.00 % |
| qd2,fs60 |
556 |
0.00 % |
0 |
0.00 % |
556 |
0.00 % |
| fs60 |
429 |
0.00 % |
0 |
0.00 % |
429 |
0.00 % |
| q20,qd2,fs60 |
350 |
0.00 % |
0 |
0.00 % |
350 |
0.00 % |
| fs60,mq40 |
339 |
0.00 % |
0 |
0.00 % |
339 |
0.00 % |
| q20,qd2,fs60,mq40 |
152 |
0.00 % |
0 |
0.00 % |
152 |
0.00 % |
| q20,fs60 |
3 |
0.00 % |
0 |
0.00 % |
3 |
0.00 % |
| q20,fs60,mq40 |
0 |
0.00 % |
0 |
0.00 % |
0 |
0.00 % |
Coverage and Quality
| Coverage Variants |
Quality Variants |
 |
 |
Filtering Criteria Distribution
| Phred scale strand bias estimated using Fisher's Exact Test. |
 |
| Allele-specific call confidence normalized by depth of sample reads supporting the allele. Variants. |
Allele-specific call confidence normalized by depth of sample reads supporting the allele. Non-Variants. |
 |
 |
| Root Mean Square of the mapping quality of reads. Variants. |
Root Mean Square of the mapping quality of reads. Non-Variants. |
 |
 |
Mutations
| Type |
Mutation |
Status |
# |
% |
| Transition |
A>G |
All |
11419490 |
31.41 % |
| Transition |
G>A |
All |
2720291 |
7.48 % |
| Transition |
T>C |
All |
13311559 |
36.61 % |
| Transition |
C>T |
All |
2246904 |
6.18 % |
| Transversion |
A>C |
All |
449977 |
1.24 % |
| Transversion |
C>A |
All |
1671541 |
4.60 % |
| Transversion |
T>G |
All |
487839 |
1.34 % |
| Transversion |
G>T |
All |
1640346 |
4.51 % |
| Transversion |
A>T |
All |
770805 |
2.12 % |
| Transversion |
T>A |
All |
818933 |
2.25 % |
| Transversion |
C>G |
All |
414650 |
1.14 % |
| Transversion |
G>C |
All |
407584 |
1.12 % |
| |
|
|
|
|
| Transition |
A>G |
Passed |
1015426 |
18.75 % |
| Transition |
G>A |
Passed |
660023 |
12.19 % |
| Transition |
T>C |
Passed |
1704056 |
31.46 % |
| Transition |
C>T |
Passed |
603589 |
11.14 % |
| Transversion |
A>C |
Passed |
160476 |
2.96 % |
| Transversion |
C>A |
Passed |
250582 |
4.63 % |
| Transversion |
T>G |
Passed |
168205 |
3.11 % |
| Transversion |
G>T |
Passed |
236617 |
4.37 % |
| Transversion |
A>T |
Passed |
136586 |
2.52 % |
| Transversion |
T>A |
Passed |
151749 |
2.80 % |
| Transversion |
C>G |
Passed |
165143 |
3.05 % |
| Transversion |
G>C |
Passed |
164006 |
3.03 % |
| |
|
|
|
|
| Transition |
A>G |
dbSNPAll |
0 |
0.00 % |
| Transition |
G>A |
dbSNPAll |
0 |
0.00 % |
| Transition |
T>C |
dbSNPAll |
0 |
0.00 % |
| Transition |
C>T |
dbSNPAll |
0 |
0.00 % |
| Transversion |
A>C |
dbSNPAll |
0 |
0.00 % |
| Transversion |
C>A |
dbSNPAll |
0 |
0.00 % |
| Transversion |
T>G |
dbSNPAll |
0 |
0.00 % |
| Transversion |
G>T |
dbSNPAll |
0 |
0.00 % |
| Transversion |
A>T |
dbSNPAll |
0 |
0.00 % |
| Transversion |
T>A |
dbSNPAll |
0 |
0.00 % |
| Transversion |
C>G |
dbSNPAll |
0 |
0.00 % |
| Transversion |
G>C |
dbSNPAll |
0 |
0.00 % |
| |
|
|
|
|
| Transition |
A>G |
dbSNPPassed |
0 |
0.00 % |
| Transition |
G>A |
dbSNPPassed |
0 |
0.00 % |
| Transition |
T>C |
dbSNPPassed |
0 |
0.00 % |
| Transition |
C>T |
dbSNPPassed |
0 |
0.00 % |
| Transversion |
A>C |
dbSNPPassed |
0 |
0.00 % |
| Transversion |
C>A |
dbSNPPassed |
0 |
0.00 % |
| Transversion |
T>G |
dbSNPPassed |
0 |
0.00 % |
| Transversion |
G>T |
dbSNPPassed |
0 |
0.00 % |
| Transversion |
A>T |
dbSNPPassed |
0 |
0.00 % |
| Transversion |
T>A |
dbSNPPassed |
0 |
0.00 % |
| Transversion |
C>G |
dbSNPPassed |
0 |
0.00 % |
| Transversion |
G>C |
dbSNPPassed |
0 |
0.00 % |
| |
|
|
|
|
Ti/Tv Ratio
| Status |
Ratio |
Transitions |
Transversions |
| All |
4.46 |
29698244 |
6661675 |
| Passed |
2.78 |
3983094 |
1433364 |
| dbSNPAll |
0 |
0 |
0 |
| dbSNPPassed |
0 |
0 |
0 |