/CEMT/variants/A56418_3_lane_gembs
BACK
SAMPLE A56418_3_lane_gembs
Variant counts
| Type |
Total |
Pass |
% |
| SNPs |
1166951851 |
725999426 |
62.21 % |
| Multiallelic |
0 |
0 |
0.00 % |
VCF Filtering Stats
| Type |
#Sites |
% |
#Non-Variant Sites |
% |
#Variant Sites |
% |
| All |
1166951851 |
100% |
1151115539 |
98.64 % |
15836312 |
1.36 % |
| |
|
|
|
|
|
|
| Passed |
729449577 |
62.51 % |
723753575 |
62.87 % |
5696002 |
0.78 % |
| Filtered |
437502274 |
37.49 % |
427361964 |
37.13 % |
10140310 |
1.39 % |
| |
|
|
|
|
|
|
| q20 |
401368803 |
91.74 % |
398812163 |
93.32 % |
2556640 |
25.21 % |
| q20,qd2 |
18957969 |
4.33 % |
12082491 |
2.83 % |
6875478 |
67.80 % |
| q20,mq40 |
10450529 |
2.39 % |
10333380 |
2.42 % |
117149 |
1.16 % |
| q20,qd2,mq40 |
2734433 |
0.63 % |
2597412 |
0.61 % |
137021 |
1.35 % |
| mq40 |
2152337 |
0.49 % |
1939511 |
0.45 % |
212826 |
2.10 % |
| qd2 |
1785946 |
0.41 % |
1555977 |
0.36 % |
229969 |
2.27 % |
| qd2,mq40 |
49226 |
0.01 % |
41030 |
0.01 % |
8196 |
0.08 % |
| qd2,fs60,mq40 |
1029 |
0.00 % |
0 |
0.00 % |
1029 |
0.01 % |
| qd2,fs60 |
705 |
0.00 % |
0 |
0.00 % |
705 |
0.01 % |
| fs60 |
545 |
0.00 % |
0 |
0.00 % |
545 |
0.01 % |
| q20,qd2,fs60 |
354 |
0.00 % |
0 |
0.00 % |
354 |
0.00 % |
| fs60,mq40 |
268 |
0.00 % |
0 |
0.00 % |
268 |
0.00 % |
| q20,qd2,fs60,mq40 |
129 |
0.00 % |
0 |
0.00 % |
129 |
0.00 % |
| q20,fs60 |
1 |
0.00 % |
0 |
0.00 % |
1 |
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 |
6242359 |
35.22 % |
| Transition |
G>A |
All |
879352 |
4.96 % |
| Transition |
T>C |
All |
6264643 |
35.34 % |
| Transition |
C>T |
All |
901379 |
5.09 % |
| Transversion |
A>C |
All |
493647 |
2.78 % |
| Transversion |
C>A |
All |
445919 |
2.52 % |
| Transversion |
T>G |
All |
493504 |
2.78 % |
| Transversion |
G>T |
All |
438812 |
2.48 % |
| Transversion |
A>T |
All |
396741 |
2.24 % |
| Transversion |
T>A |
All |
402819 |
2.27 % |
| Transversion |
C>G |
All |
382421 |
2.16 % |
| Transversion |
G>C |
All |
383826 |
2.17 % |
| |
|
|
|
|
| Transition |
A>G |
Passed |
610700 |
19.65 % |
| Transition |
G>A |
Passed |
451323 |
14.52 % |
| Transition |
T>C |
Passed |
591402 |
19.03 % |
| Transition |
C>T |
Passed |
452999 |
14.57 % |
| Transversion |
A>C |
Passed |
129573 |
4.17 % |
| Transversion |
C>A |
Passed |
132688 |
4.27 % |
| Transversion |
T>G |
Passed |
130405 |
4.20 % |
| Transversion |
G>T |
Passed |
128092 |
4.12 % |
| Transversion |
A>T |
Passed |
117964 |
3.80 % |
| Transversion |
T>A |
Passed |
119814 |
3.85 % |
| Transversion |
C>G |
Passed |
121396 |
3.91 % |
| Transversion |
G>C |
Passed |
121831 |
3.92 % |
| |
|
|
|
|
| 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 |
4.16 |
14287733 |
3437689 |
| Passed |
2.10 |
2106424 |
1001763 |
| dbSNPAll |
0 |
0 |
0 |
| dbSNPPassed |
0 |
0 |
0 |