/EXTERNAL DEEP/variants/K006100_K006101_K006102_K006103_4_lane_gembs
BACK
SAMPLE K006100_K006101_K006102_K006103_4_lane_gembs
Variant counts
| Type |
Total |
Pass |
% |
| SNPs |
1178682915 |
759744126 |
64.46 % |
| Multiallelic |
0 |
0 |
0.00 % |
VCF Filtering Stats
| Type |
#Sites |
% |
#Non-Variant Sites |
% |
#Variant Sites |
% |
| All |
1178682915 |
100% |
1134328780 |
96.24 % |
44354135 |
3.76 % |
| |
|
|
|
|
|
|
| Passed |
766773157 |
65.05 % |
753064587 |
66.39 % |
13708570 |
1.79 % |
| Filtered |
411909758 |
34.95 % |
381264193 |
33.61 % |
30645565 |
4.00 % |
| |
|
|
|
|
|
|
| q20 |
356447895 |
86.54 % |
347259613 |
91.08 % |
9188282 |
29.98 % |
| q20,qd2 |
33416319 |
8.11 % |
13339343 |
3.50 % |
20076976 |
65.51 % |
| q20,mq40 |
10217505 |
2.48 % |
9982968 |
2.62 % |
234537 |
0.77 % |
| qd2 |
7210259 |
1.75 % |
6568946 |
1.72 % |
641313 |
2.09 % |
| q20,qd2,mq40 |
3093618 |
0.75 % |
2884720 |
0.76 % |
208898 |
0.68 % |
| mq40 |
1472248 |
0.36 % |
1187583 |
0.31 % |
284665 |
0.93 % |
| qd2,mq40 |
50060 |
0.01 % |
41020 |
0.01 % |
9040 |
0.03 % |
| qd2,fs60,mq40 |
678 |
0.00 % |
0 |
0.00 % |
678 |
0.00 % |
| qd2,fs60 |
370 |
0.00 % |
0 |
0.00 % |
370 |
0.00 % |
| fs60,mq40 |
256 |
0.00 % |
0 |
0.00 % |
256 |
0.00 % |
| fs60 |
244 |
0.00 % |
0 |
0.00 % |
244 |
0.00 % |
| q20,qd2,fs60 |
189 |
0.00 % |
0 |
0.00 % |
189 |
0.00 % |
| q20,qd2,fs60,mq40 |
117 |
0.00 % |
0 |
0.00 % |
117 |
0.00 % |
| q20,fs60 |
0 |
0.00 % |
0 |
0.00 % |
0 |
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 |
14743098 |
32.26 % |
| Transition |
G>A |
All |
3238996 |
7.09 % |
| Transition |
T>C |
All |
17652957 |
38.63 % |
| Transition |
C>T |
All |
2336306 |
5.11 % |
| Transversion |
A>C |
All |
625942 |
1.37 % |
| Transversion |
C>A |
All |
1621650 |
3.55 % |
| Transversion |
T>G |
All |
791601 |
1.73 % |
| Transversion |
G>T |
All |
1503199 |
3.29 % |
| Transversion |
A>T |
All |
1002647 |
2.19 % |
| Transversion |
T>A |
All |
1125578 |
2.46 % |
| Transversion |
C>G |
All |
538744 |
1.18 % |
| Transversion |
G>C |
All |
515159 |
1.13 % |
| |
|
|
|
|
| Transition |
A>G |
Passed |
1466898 |
20.91 % |
| Transition |
G>A |
Passed |
756509 |
10.78 % |
| Transition |
T>C |
Passed |
2593882 |
36.97 % |
| Transition |
C>T |
Passed |
622585 |
8.87 % |
| Transversion |
A>C |
Passed |
180763 |
2.58 % |
| Transversion |
C>A |
Passed |
247062 |
3.52 % |
| Transversion |
T>G |
Passed |
205866 |
2.93 % |
| Transversion |
G>T |
Passed |
212402 |
3.03 % |
| Transversion |
A>T |
Passed |
151772 |
2.16 % |
| Transversion |
T>A |
Passed |
189509 |
2.70 % |
| Transversion |
C>G |
Passed |
197904 |
2.82 % |
| Transversion |
G>C |
Passed |
191354 |
2.73 % |
| |
|
|
|
|
| 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 |
4.92 |
37971357 |
7724520 |
| Passed |
3.45 |
5439874 |
1576632 |
| dbSNPAll |
0 |
0 |
0 |
| dbSNPPassed |
0 |
0 |
0 |