/EXTERNAL DEEP/variants/K006090_K006091_K006092_3_lane_gembs
BACK
SAMPLE K006090_K006091_K006092_3_lane_gembs
Variant counts
| Type |
Total |
Pass |
% |
| SNPs |
1178254673 |
756323434 |
64.19 % |
| Multiallelic |
0 |
0 |
0.00 % |
VCF Filtering Stats
| Type |
#Sites |
% |
#Non-Variant Sites |
% |
#Variant Sites |
% |
| All |
1178254673 |
100% |
1138988561 |
96.67 % |
39266112 |
3.33 % |
| |
|
|
|
|
|
|
| Passed |
763101061 |
64.77 % |
751589608 |
65.99 % |
11511453 |
1.51 % |
| Filtered |
415153612 |
35.23 % |
387398953 |
34.01 % |
27754659 |
3.64 % |
| |
|
|
|
|
|
|
| q20 |
365445976 |
88.03 % |
357927483 |
92.39 % |
7518493 |
27.09 % |
| q20,qd2 |
31170478 |
7.51 % |
11791349 |
3.04 % |
19379129 |
69.82 % |
| q20,mq40 |
9651600 |
2.32 % |
9480691 |
2.45 % |
170909 |
0.62 % |
| qd2 |
4836640 |
1.17 % |
4511407 |
1.16 % |
325233 |
1.17 % |
| q20,qd2,mq40 |
2976187 |
0.72 % |
2848001 |
0.74 % |
128186 |
0.46 % |
| mq40 |
1012298 |
0.24 % |
795357 |
0.21 % |
216941 |
0.78 % |
| qd2,mq40 |
53641 |
0.01 % |
44665 |
0.01 % |
8976 |
0.03 % |
| qd2,fs60 |
2379 |
0.00 % |
0 |
0.00 % |
2379 |
0.01 % |
| qd2,fs60,mq40 |
1584 |
0.00 % |
0 |
0.00 % |
1584 |
0.01 % |
| q20,qd2,fs60 |
1075 |
0.00 % |
0 |
0.00 % |
1075 |
0.00 % |
| fs60 |
975 |
0.00 % |
0 |
0.00 % |
975 |
0.00 % |
| fs60,mq40 |
427 |
0.00 % |
0 |
0.00 % |
427 |
0.00 % |
| q20,qd2,fs60,mq40 |
352 |
0.00 % |
0 |
0.00 % |
352 |
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 |
13854234 |
33.93 % |
| Transition |
G>A |
All |
3178065 |
7.78 % |
| Transition |
T>C |
All |
15371069 |
37.64 % |
| Transition |
C>T |
All |
2440869 |
5.98 % |
| Transversion |
A>C |
All |
502706 |
1.23 % |
| Transversion |
C>A |
All |
1156652 |
2.83 % |
| Transversion |
T>G |
All |
595829 |
1.46 % |
| Transversion |
G>T |
All |
1068860 |
2.62 % |
| Transversion |
A>T |
All |
793437 |
1.94 % |
| Transversion |
T>A |
All |
918508 |
2.25 % |
| Transversion |
C>G |
All |
489816 |
1.20 % |
| Transversion |
G>C |
All |
466754 |
1.14 % |
| |
|
|
|
|
| Transition |
A>G |
Passed |
1017811 |
19.80 % |
| Transition |
G>A |
Passed |
641726 |
12.48 % |
| Transition |
T>C |
Passed |
1454673 |
28.29 % |
| Transition |
C>T |
Passed |
583882 |
11.36 % |
| Transversion |
A>C |
Passed |
173452 |
3.37 % |
| Transversion |
C>A |
Passed |
206538 |
4.02 % |
| Transversion |
T>G |
Passed |
188773 |
3.67 % |
| Transversion |
G>T |
Passed |
188597 |
3.67 % |
| Transversion |
A>T |
Passed |
150885 |
2.93 % |
| Transversion |
T>A |
Passed |
175236 |
3.41 % |
| Transversion |
C>G |
Passed |
181417 |
3.53 % |
| Transversion |
G>C |
Passed |
178531 |
3.47 % |
| |
|
|
|
|
| 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 |
5.81 |
34844237 |
5992562 |
| Passed |
2.56 |
3698092 |
1443429 |
| dbSNPAll |
0 |
0 |
0 |
| dbSNPPassed |
0 |
0 |
0 |