/EXTERNAL BLUEPRINT/variants/K010430_K010431_K010432_K010433_K010434_K010435_K010436_K010437_K010438_K010439_K010440_11_lane_gembs
BACK
SAMPLE K010430_K010431_K010432_K010433_K010434_K010435_K010436_K010437_K010438_K010439_K010440_11_lane_gembs
Variant counts
| Type |
Total |
Pass |
% |
| SNPs |
977381590 |
19875567 |
2.03 % |
| Multiallelic |
0 |
0 |
0.00 % |
VCF Filtering Stats
| Type |
#Sites |
% |
#Non-Variant Sites |
% |
#Variant Sites |
% |
| All |
977381590 |
100% |
950134175 |
97.21 % |
27247415 |
2.79 % |
| |
|
|
|
|
|
|
| Passed |
30795969 |
3.15 % |
18873234 |
1.99 % |
11922735 |
38.72 % |
| Filtered |
946585621 |
96.85 % |
931260941 |
98.01 % |
15324680 |
49.76 % |
| |
|
|
|
|
|
|
| q20 |
727169662 |
76.82 % |
717072371 |
77.00 % |
10097291 |
65.89 % |
| q20,qd2 |
110682517 |
11.69 % |
107497655 |
11.54 % |
3184862 |
20.78 % |
| q20,mq40 |
79867439 |
8.44 % |
78993438 |
8.48 % |
874001 |
5.70 % |
| q20,qd2,mq40 |
27448837 |
2.90 % |
27227984 |
2.92 % |
220853 |
1.44 % |
| mq40 |
1403686 |
0.15 % |
457902 |
0.05 % |
945784 |
6.17 % |
| qd2 |
10014 |
0.00 % |
8830 |
0.00 % |
1184 |
0.01 % |
| qd2,mq40 |
3406 |
0.00 % |
2761 |
0.00 % |
645 |
0.00 % |
| fs60,mq40 |
24 |
0.00 % |
0 |
0.00 % |
24 |
0.00 % |
| qd2,fs60 |
14 |
0.00 % |
0 |
0.00 % |
14 |
0.00 % |
| fs60 |
13 |
0.00 % |
0 |
0.00 % |
13 |
0.00 % |
| qd2,fs60,mq40 |
4 |
0.00 % |
0 |
0.00 % |
4 |
0.00 % |
| q20,qd2,fs60,mq40 |
3 |
0.00 % |
0 |
0.00 % |
3 |
0.00 % |
| q20,qd2,fs60 |
2 |
0.00 % |
0 |
0.00 % |
2 |
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 |
7233523 |
22.90 % |
| Transition |
G>A |
All |
2457840 |
7.78 % |
| Transition |
T>C |
All |
8778704 |
27.79 % |
| Transition |
C>T |
All |
1092406 |
3.46 % |
| Transversion |
A>C |
All |
1141222 |
3.61 % |
| Transversion |
C>A |
All |
2008344 |
6.36 % |
| Transversion |
T>G |
All |
1369873 |
4.34 % |
| Transversion |
G>T |
All |
1817042 |
5.75 % |
| Transversion |
A>T |
All |
1441610 |
4.56 % |
| Transversion |
T>A |
All |
1966162 |
6.22 % |
| Transversion |
C>G |
All |
1052843 |
3.33 % |
| Transversion |
G>C |
All |
1227960 |
3.89 % |
| |
|
|
|
|
| Transition |
A>G |
Passed |
188361 |
18.81 % |
| Transition |
G>A |
Passed |
134122 |
13.39 % |
| Transition |
T>C |
Passed |
297552 |
29.71 % |
| Transition |
C>T |
Passed |
48135 |
4.81 % |
| Transversion |
A>C |
Passed |
38476 |
3.84 % |
| Transversion |
C>A |
Passed |
56692 |
5.66 % |
| Transversion |
T>G |
Passed |
42045 |
4.20 % |
| Transversion |
G>T |
Passed |
28733 |
2.87 % |
| Transversion |
A>T |
Passed |
18006 |
1.80 % |
| Transversion |
T>A |
Passed |
52946 |
5.29 % |
| Transversion |
C>G |
Passed |
39205 |
3.91 % |
| Transversion |
G>C |
Passed |
57167 |
5.71 % |
| |
|
|
|
|
| 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 |
1.63 |
19562473 |
12025056 |
| Passed |
2.00 |
668170 |
333270 |
| dbSNPAll |
0 |
0 |
0 |
| dbSNPPassed |
0 |
0 |
0 |