/EXTERNAL BLUEPRINT/variants/K010529_1_lane_gembs
BACK
SAMPLE K010529_1_lane_gembs
Variant counts
| Type |
Total |
Pass |
% |
| SNPs |
1146215986 |
220156639 |
19.21 % |
| Multiallelic |
0 |
0 |
0.00 % |
VCF Filtering Stats
| Type |
#Sites |
% |
#Non-Variant Sites |
% |
#Variant Sites |
% |
| All |
1146215986 |
100% |
1125387624 |
98.18 % |
20828362 |
1.82 % |
| |
|
|
|
|
|
|
| Passed |
226392275 |
19.75 % |
218830382 |
19.44 % |
7561893 |
3.34 % |
| Filtered |
919823711 |
80.25 % |
906557242 |
80.56 % |
13266469 |
5.86 % |
| |
|
|
|
|
|
|
| q20 |
874241380 |
95.04 % |
870633416 |
96.04 % |
3607964 |
27.20 % |
| q20,qd2 |
24498649 |
2.66 % |
15208646 |
1.68 % |
9290003 |
70.03 % |
| q20,mq40 |
15962072 |
1.74 % |
15843701 |
1.75 % |
118371 |
0.89 % |
| q20,qd2,mq40 |
4647627 |
0.51 % |
4533024 |
0.50 % |
114603 |
0.86 % |
| mq40 |
420736 |
0.05 % |
292307 |
0.03 % |
128429 |
0.97 % |
| qd2 |
37434 |
0.00 % |
33703 |
0.00 % |
3731 |
0.03 % |
| qd2,mq40 |
15568 |
0.00 % |
12445 |
0.00 % |
3123 |
0.02 % |
| qd2,fs60,mq40 |
96 |
0.00 % |
0 |
0.00 % |
96 |
0.00 % |
| fs60,mq40 |
83 |
0.00 % |
0 |
0.00 % |
83 |
0.00 % |
| qd2,fs60 |
36 |
0.00 % |
0 |
0.00 % |
36 |
0.00 % |
| fs60 |
14 |
0.00 % |
0 |
0.00 % |
14 |
0.00 % |
| q20,qd2,fs60,mq40 |
13 |
0.00 % |
0 |
0.00 % |
13 |
0.00 % |
| q20,qd2,fs60 |
3 |
0.00 % |
0 |
0.00 % |
3 |
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 |
5072662 |
22.33 % |
| Transition |
G>A |
All |
1216898 |
5.36 % |
| Transition |
T>C |
All |
5024805 |
22.12 % |
| Transition |
C>T |
All |
1221182 |
5.38 % |
| Transversion |
A>C |
All |
317741 |
1.40 % |
| Transversion |
C>A |
All |
3295768 |
14.51 % |
| Transversion |
T>G |
All |
328317 |
1.45 % |
| Transversion |
G>T |
All |
3272434 |
14.40 % |
| Transversion |
A>T |
All |
1195277 |
5.26 % |
| Transversion |
T>A |
All |
1169716 |
5.15 % |
| Transversion |
C>G |
All |
308913 |
1.36 % |
| Transversion |
G>C |
All |
294589 |
1.30 % |
| |
|
|
|
|
| Transition |
A>G |
Passed |
231201 |
15.04 % |
| Transition |
G>A |
Passed |
219315 |
14.27 % |
| Transition |
T>C |
Passed |
231434 |
15.06 % |
| Transition |
C>T |
Passed |
222075 |
14.45 % |
| Transversion |
A>C |
Passed |
79028 |
5.14 % |
| Transversion |
C>A |
Passed |
86052 |
5.60 % |
| Transversion |
T>G |
Passed |
79534 |
5.17 % |
| Transversion |
G>T |
Passed |
86158 |
5.61 % |
| Transversion |
A>T |
Passed |
71496 |
4.65 % |
| Transversion |
T>A |
Passed |
71658 |
4.66 % |
| Transversion |
C>G |
Passed |
79435 |
5.17 % |
| Transversion |
G>C |
Passed |
79568 |
5.18 % |
| |
|
|
|
|
| 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 |
1.23 |
12535547 |
10182755 |
| Passed |
1.43 |
904025 |
632929 |
| dbSNPAll |
0 |
0 |
0 |
| dbSNPPassed |
0 |
0 |
0 |