/CEMT/variants/A91240_2_lane_gembs
BACK
SAMPLE A91240_2_lane_gembs
Variant counts
| Type |
Total |
Pass |
% |
| SNPs |
1171100714 |
1108391543 |
94.65 % |
| Multiallelic |
0 |
0 |
0.00 % |
VCF Filtering Stats
| Type |
#Sites |
% |
#Non-Variant Sites |
% |
#Variant Sites |
% |
| All |
1171100714 |
100% |
1161026775 |
99.14 % |
10073939 |
0.86 % |
| |
|
|
|
|
|
|
| Passed |
1109088076 |
94.70 % |
1105423582 |
95.21 % |
3664494 |
0.33 % |
| Filtered |
62012638 |
5.30 % |
55603193 |
4.79 % |
6409445 |
0.58 % |
| |
|
|
|
|
|
|
| q20 |
35672887 |
57.53 % |
35244265 |
63.39 % |
428622 |
6.69 % |
| q20,mq40 |
9792342 |
15.79 % |
9657304 |
17.37 % |
135038 |
2.11 % |
| q20,qd2 |
6915550 |
11.15 % |
2012199 |
3.62 % |
4903351 |
76.50 % |
| mq40 |
4260163 |
6.87 % |
3937260 |
7.08 % |
322903 |
5.04 % |
| qd2 |
2914065 |
4.70 % |
2529125 |
4.55 % |
384940 |
6.01 % |
| q20,qd2,mq40 |
2356285 |
3.80 % |
2144520 |
3.86 % |
211765 |
3.30 % |
| qd2,mq40 |
95841 |
0.15 % |
78520 |
0.14 % |
17321 |
0.27 % |
| qd2,fs60,mq40 |
1871 |
0.00 % |
0 |
0.00 % |
1871 |
0.03 % |
| fs60 |
1302 |
0.00 % |
0 |
0.00 % |
1302 |
0.02 % |
| qd2,fs60 |
1222 |
0.00 % |
0 |
0.00 % |
1222 |
0.02 % |
| fs60,mq40 |
591 |
0.00 % |
0 |
0.00 % |
591 |
0.01 % |
| q20,qd2,fs60 |
364 |
0.00 % |
0 |
0.00 % |
364 |
0.01 % |
| q20,qd2,fs60,mq40 |
148 |
0.00 % |
0 |
0.00 % |
148 |
0.00 % |
| q20,fs60 |
4 |
0.00 % |
0 |
0.00 % |
4 |
0.00 % |
| q20,fs60,mq40 |
3 |
0.00 % |
0 |
0.00 % |
3 |
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 |
3682624 |
31.22 % |
| Transition |
G>A |
All |
894208 |
7.58 % |
| Transition |
T>C |
All |
3672402 |
31.13 % |
| Transition |
C>T |
All |
898348 |
7.62 % |
| Transversion |
A>C |
All |
307963 |
2.61 % |
| Transversion |
C>A |
All |
375860 |
3.19 % |
| Transversion |
T>G |
All |
314368 |
2.67 % |
| Transversion |
G>T |
All |
370385 |
3.14 % |
| Transversion |
A>T |
All |
366584 |
3.11 % |
| Transversion |
T>A |
All |
372683 |
3.16 % |
| Transversion |
C>G |
All |
271322 |
2.30 % |
| Transversion |
G>C |
All |
268507 |
2.28 % |
| |
|
|
|
|
| Transition |
A>G |
Passed |
766897 |
17.85 % |
| Transition |
G>A |
Passed |
656128 |
15.28 % |
| Transition |
T>C |
Passed |
771998 |
17.97 % |
| Transition |
C>T |
Passed |
658611 |
15.33 % |
| Transversion |
A>C |
Passed |
189400 |
4.41 % |
| Transversion |
C>A |
Passed |
192382 |
4.48 % |
| Transversion |
T>G |
Passed |
189788 |
4.42 % |
| Transversion |
G>T |
Passed |
183624 |
4.27 % |
| Transversion |
A>T |
Passed |
164609 |
3.83 % |
| Transversion |
T>A |
Passed |
166549 |
3.88 % |
| Transversion |
C>G |
Passed |
177997 |
4.14 % |
| Transversion |
G>C |
Passed |
177396 |
4.13 % |
| |
|
|
|
|
| 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 |
3.45 |
9147582 |
2647672 |
| Passed |
1.98 |
2853634 |
1441745 |
| dbSNPAll |
0 |
0 |
0 |
| dbSNPPassed |
0 |
0 |
0 |