/EXTERNAL DEEP/variants/K009031_K009032_K009033_K009034_K009035_K009036_6_lane_gembs
BACK
SAMPLE K009031_K009032_K009033_K009034_K009035_K009036_6_lane_gembs
Variant counts
| Type |
Total |
Pass |
% |
| SNPs |
1169635967 |
814292869 |
69.62 % |
| Multiallelic |
0 |
0 |
0.00 % |
VCF Filtering Stats
| Type |
#Sites |
% |
#Non-Variant Sites |
% |
#Variant Sites |
% |
| All |
1169635967 |
100% |
1138691797 |
97.35 % |
30944170 |
2.65 % |
| |
|
|
|
|
|
|
| Passed |
819059776 |
70.03 % |
810786398 |
71.20 % |
8273378 |
1.01 % |
| Filtered |
350576191 |
29.97 % |
327905399 |
28.80 % |
22670792 |
2.77 % |
| |
|
|
|
|
|
|
| q20 |
303952733 |
86.70 % |
297424094 |
90.70 % |
6528639 |
28.80 % |
| q20,qd2 |
24443892 |
6.97 % |
9208974 |
2.81 % |
15234918 |
67.20 % |
| q20,mq40 |
9782007 |
2.79 % |
9618337 |
2.93 % |
163670 |
0.72 % |
| qd2 |
8013771 |
2.29 % |
7694174 |
2.35 % |
319597 |
1.41 % |
| q20,qd2,mq40 |
2817195 |
0.80 % |
2657673 |
0.81 % |
159522 |
0.70 % |
| mq40 |
1491542 |
0.43 % |
1248055 |
0.38 % |
243487 |
1.07 % |
| qd2,mq40 |
65207 |
0.02 % |
54092 |
0.02 % |
11115 |
0.05 % |
| qd2,fs60 |
3215 |
0.00 % |
0 |
0.00 % |
3215 |
0.01 % |
| qd2,fs60,mq40 |
2211 |
0.00 % |
0 |
0.00 % |
2211 |
0.01 % |
| q20,qd2,fs60 |
1874 |
0.00 % |
0 |
0.00 % |
1874 |
0.01 % |
| fs60 |
1576 |
0.00 % |
0 |
0.00 % |
1576 |
0.01 % |
| fs60,mq40 |
482 |
0.00 % |
0 |
0.00 % |
482 |
0.00 % |
| q20,qd2,fs60,mq40 |
481 |
0.00 % |
0 |
0.00 % |
481 |
0.00 % |
| q20,fs60,mq40 |
5 |
0.00 % |
0 |
0.00 % |
5 |
0.00 % |
| q20,fs60 |
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 |
11148915 |
32.73 % |
| Transition |
G>A |
All |
3488010 |
10.24 % |
| Transition |
T>C |
All |
12654910 |
37.15 % |
| Transition |
C>T |
All |
2876323 |
8.44 % |
| Transversion |
A>C |
All |
316310 |
0.93 % |
| Transversion |
C>A |
All |
736953 |
2.16 % |
| Transversion |
T>G |
All |
377766 |
1.11 % |
| Transversion |
G>T |
All |
699641 |
2.05 % |
| Transversion |
A>T |
All |
538945 |
1.58 % |
| Transversion |
T>A |
All |
586993 |
1.72 % |
| Transversion |
C>G |
All |
326658 |
0.96 % |
| Transversion |
G>C |
All |
310680 |
0.91 % |
| |
|
|
|
|
| Transition |
A>G |
Passed |
889084 |
20.19 % |
| Transition |
G>A |
Passed |
556112 |
12.63 % |
| Transition |
T>C |
Passed |
1335003 |
30.31 % |
| Transition |
C>T |
Passed |
512887 |
11.64 % |
| Transversion |
A>C |
Passed |
139686 |
3.17 % |
| Transversion |
C>A |
Passed |
151210 |
3.43 % |
| Transversion |
T>G |
Passed |
149934 |
3.40 % |
| Transversion |
G>T |
Passed |
142804 |
3.24 % |
| Transversion |
A>T |
Passed |
117147 |
2.66 % |
| Transversion |
T>A |
Passed |
129269 |
2.94 % |
| Transversion |
C>G |
Passed |
141219 |
3.21 % |
| Transversion |
G>C |
Passed |
140006 |
3.18 % |
| |
|
|
|
|
| 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 |
7.75 |
30168158 |
3893946 |
| Passed |
2.96 |
3293086 |
1111275 |
| dbSNPAll |
0 |
0 |
0 |
| dbSNPPassed |
0 |
0 |
0 |