/CEMT/variants/B19819_2_lane_gembs
BACK
SAMPLE B19819_2_lane_gembs
Variant counts
| Type |
Total |
Pass |
% |
| SNPs |
1164353443 |
1074190000 |
92.26 % |
| Multiallelic |
0 |
0 |
0.00 % |
VCF Filtering Stats
| Type |
#Sites |
% |
#Non-Variant Sites |
% |
#Variant Sites |
% |
| All |
1164353443 |
100% |
1152988790 |
99.02 % |
11364653 |
0.98 % |
| |
|
|
|
|
|
|
| Passed |
1075174910 |
92.34 % |
1071509844 |
92.93 % |
3665066 |
0.34 % |
| Filtered |
89178533 |
7.66 % |
81478946 |
7.07 % |
7699587 |
0.72 % |
| |
|
|
|
|
|
|
| q20 |
61663997 |
69.15 % |
60667960 |
74.46 % |
996037 |
12.94 % |
| q20,mq40 |
9080659 |
10.18 % |
8951769 |
10.99 % |
128890 |
1.67 % |
| q20,qd2 |
8925450 |
10.01 % |
3218170 |
3.95 % |
5707280 |
74.12 % |
| mq40 |
4652890 |
5.22 % |
4350209 |
5.34 % |
302681 |
3.93 % |
| qd2 |
2561067 |
2.87 % |
2235382 |
2.74 % |
325685 |
4.23 % |
| q20,qd2,mq40 |
2163873 |
2.43 % |
1954057 |
2.40 % |
209816 |
2.73 % |
| qd2,mq40 |
121338 |
0.14 % |
101399 |
0.12 % |
19939 |
0.26 % |
| fs60 |
2386 |
0.00 % |
0 |
0.00 % |
2386 |
0.03 % |
| q20,qd2,fs60 |
2049 |
0.00 % |
0 |
0.00 % |
2049 |
0.03 % |
| qd2,fs60,mq40 |
1978 |
0.00 % |
0 |
0.00 % |
1978 |
0.03 % |
| qd2,fs60 |
1687 |
0.00 % |
0 |
0.00 % |
1687 |
0.02 % |
| fs60,mq40 |
796 |
0.00 % |
0 |
0.00 % |
796 |
0.01 % |
| q20,qd2,fs60,mq40 |
349 |
0.00 % |
0 |
0.00 % |
349 |
0.00 % |
| q20,fs60,mq40 |
12 |
0.00 % |
0 |
0.00 % |
12 |
0.00 % |
| q20,fs60 |
2 |
0.00 % |
0 |
0.00 % |
2 |
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 |
3624975 |
27.03 % |
| Transition |
G>A |
All |
1872071 |
13.96 % |
| Transition |
T>C |
All |
3604730 |
26.88 % |
| Transition |
C>T |
All |
1892103 |
14.11 % |
| Transversion |
A>C |
All |
281195 |
2.10 % |
| Transversion |
C>A |
All |
355857 |
2.65 % |
| Transversion |
T>G |
All |
288328 |
2.15 % |
| Transversion |
G>T |
All |
352995 |
2.63 % |
| Transversion |
A>T |
All |
322547 |
2.41 % |
| Transversion |
T>A |
All |
323987 |
2.42 % |
| Transversion |
C>G |
All |
247590 |
1.85 % |
| Transversion |
G>C |
All |
243238 |
1.81 % |
| |
|
|
|
|
| Transition |
A>G |
Passed |
702235 |
17.85 % |
| Transition |
G>A |
Passed |
622380 |
15.82 % |
| Transition |
T>C |
Passed |
705161 |
17.93 % |
| Transition |
C>T |
Passed |
624257 |
15.87 % |
| Transversion |
A>C |
Passed |
167512 |
4.26 % |
| Transversion |
C>A |
Passed |
171514 |
4.36 % |
| Transversion |
T>G |
Passed |
168367 |
4.28 % |
| Transversion |
G>T |
Passed |
164055 |
4.17 % |
| Transversion |
A>T |
Passed |
137004 |
3.48 % |
| Transversion |
T>A |
Passed |
138312 |
3.52 % |
| Transversion |
C>G |
Passed |
166453 |
4.23 % |
| Transversion |
G>C |
Passed |
166310 |
4.23 % |
| |
|
|
|
|
| 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 |
4.55 |
10993879 |
2415737 |
| Passed |
2.07 |
2654033 |
1279527 |
| dbSNPAll |
0 |
0 |
0 |
| dbSNPPassed |
0 |
0 |
0 |