/cemt/variants/K005736_K005719_2_lane_gembs
BACK
SAMPLE K005736_K005719_2_lane_gembs
Variant counts
| Type |
Total |
Pass |
% |
| SNPs |
1163194456 |
1102870204 |
94.81 % |
| Multiallelic |
0 |
0 |
0.00 % |
VCF Filtering Stats
| Type |
#Sites |
% |
#Non-Variant Sites |
% |
#Variant Sites |
% |
| All |
1163194456 |
100% |
1154311517 |
99.24 % |
8882939 |
0.76 % |
| |
|
|
|
|
|
|
| Passed |
1103177677 |
94.84 % |
1099832703 |
95.28 % |
3344974 |
0.30 % |
| Filtered |
60016779 |
5.16 % |
54478814 |
4.72 % |
5537965 |
0.50 % |
| |
|
|
|
|
|
|
| q20 |
22211959 |
37.01 % |
21630897 |
39.71 % |
581062 |
10.49 % |
| q20,mq40 |
11123529 |
18.53 % |
10782175 |
19.79 % |
341354 |
6.16 % |
| qd2 |
9579977 |
15.96 % |
9056676 |
16.62 % |
523301 |
9.45 % |
| mq40 |
8719880 |
14.53 % |
8250052 |
15.14 % |
469828 |
8.48 % |
| q20,qd2 |
5457171 |
9.09 % |
2282481 |
4.19 % |
3174690 |
57.33 % |
| q20,qd2,mq40 |
2730309 |
4.55 % |
2319185 |
4.26 % |
411124 |
7.42 % |
| qd2,mq40 |
188710 |
0.31 % |
157348 |
0.29 % |
31362 |
0.57 % |
| qd2,fs60,mq40 |
1807 |
0.00 % |
0 |
0.00 % |
1807 |
0.03 % |
| fs60 |
1147 |
0.00 % |
0 |
0.00 % |
1147 |
0.02 % |
| fs60,mq40 |
1041 |
0.00 % |
0 |
0.00 % |
1041 |
0.02 % |
| qd2,fs60 |
847 |
0.00 % |
0 |
0.00 % |
847 |
0.02 % |
| q20,qd2,fs60,mq40 |
181 |
0.00 % |
0 |
0.00 % |
181 |
0.00 % |
| q20,qd2,fs60 |
178 |
0.00 % |
0 |
0.00 % |
178 |
0.00 % |
| q20,fs60 |
33 |
0.00 % |
0 |
0.00 % |
33 |
0.00 % |
| q20,fs60,mq40 |
10 |
0.00 % |
0 |
0.00 % |
10 |
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 |
2687988 |
25.30 % |
| Transition |
G>A |
All |
1016886 |
9.57 % |
| Transition |
T>C |
All |
2634177 |
24.79 % |
| Transition |
C>T |
All |
1028982 |
9.68 % |
| Transversion |
A>C |
All |
336521 |
3.17 % |
| Transversion |
C>A |
All |
493202 |
4.64 % |
| Transversion |
T>G |
All |
344028 |
3.24 % |
| Transversion |
G>T |
All |
478622 |
4.50 % |
| Transversion |
A>T |
All |
492773 |
4.64 % |
| Transversion |
T>A |
All |
504849 |
4.75 % |
| Transversion |
C>G |
All |
307373 |
2.89 % |
| Transversion |
G>C |
All |
299784 |
2.82 % |
| |
|
|
|
|
| Transition |
A>G |
Passed |
767113 |
17.74 % |
| Transition |
G>A |
Passed |
667307 |
15.43 % |
| Transition |
T>C |
Passed |
757587 |
17.52 % |
| Transition |
C>T |
Passed |
669463 |
15.48 % |
| Transversion |
A>C |
Passed |
184384 |
4.26 % |
| Transversion |
C>A |
Passed |
195949 |
4.53 % |
| Transversion |
T>G |
Passed |
184698 |
4.27 % |
| Transversion |
G>T |
Passed |
191951 |
4.44 % |
| Transversion |
A>T |
Passed |
175702 |
4.06 % |
| Transversion |
T>A |
Passed |
175613 |
4.06 % |
| Transversion |
C>G |
Passed |
177240 |
4.10 % |
| Transversion |
G>C |
Passed |
177383 |
4.10 % |
| |
|
|
|
|
| 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 |
2.26 |
7368033 |
3257152 |
| Passed |
1.96 |
2861470 |
1462920 |
| dbSNPAll |
0 |
0 |
0 |
| dbSNPPassed |
0 |
0 |
0 |