/EXTERNAL McGill EMC/variants/K006164_1_lane_gembs
BACK
SAMPLE K006164_1_lane_gembs
Variant counts
| Type |
Total |
Pass |
% |
| SNPs |
1145351044 |
709118047 |
61.91 % |
| Multiallelic |
0 |
0 |
0.00 % |
VCF Filtering Stats
| Type |
#Sites |
% |
#Non-Variant Sites |
% |
#Variant Sites |
% |
| All |
1145351044 |
100% |
1133369482 |
98.95 % |
11981562 |
1.05 % |
| |
|
|
|
|
|
|
| Passed |
710859744 |
62.06 % |
707084828 |
62.39 % |
3774916 |
0.53 % |
| Filtered |
434491300 |
37.94 % |
426284654 |
37.61 % |
8206646 |
1.15 % |
| |
|
|
|
|
|
|
| q20 |
397938519 |
91.59 % |
396476225 |
93.01 % |
1462294 |
17.82 % |
| q20,qd2 |
16216191 |
3.73 % |
9888509 |
2.32 % |
6327682 |
77.10 % |
| q20,mq40 |
12146361 |
2.80 % |
12063288 |
2.83 % |
83073 |
1.01 % |
| qd2 |
3491445 |
0.80 % |
3425231 |
0.80 % |
66214 |
0.81 % |
| q20,qd2,mq40 |
2890851 |
0.67 % |
2771943 |
0.65 % |
118908 |
1.45 % |
| mq40 |
1759319 |
0.40 % |
1621359 |
0.38 % |
137960 |
1.68 % |
| qd2,mq40 |
46522 |
0.01 % |
38099 |
0.01 % |
8423 |
0.10 % |
| qd2,fs60,mq40 |
805 |
0.00 % |
0 |
0.00 % |
805 |
0.01 % |
| fs60 |
519 |
0.00 % |
0 |
0.00 % |
519 |
0.01 % |
| qd2,fs60 |
299 |
0.00 % |
0 |
0.00 % |
299 |
0.00 % |
| fs60,mq40 |
292 |
0.00 % |
0 |
0.00 % |
292 |
0.00 % |
| q20,qd2,fs60 |
98 |
0.00 % |
0 |
0.00 % |
98 |
0.00 % |
| q20,qd2,fs60,mq40 |
79 |
0.00 % |
0 |
0.00 % |
79 |
0.00 % |
| q20,fs60 |
0 |
0.00 % |
0 |
0.00 % |
0 |
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 |
3583086 |
26.24 % |
| Transition |
G>A |
All |
1051854 |
7.70 % |
| Transition |
T>C |
All |
3408364 |
24.96 % |
| Transition |
C>T |
All |
1065564 |
7.80 % |
| Transversion |
A>C |
All |
211081 |
1.55 % |
| Transversion |
C>A |
All |
1500293 |
10.99 % |
| Transversion |
T>G |
All |
220335 |
1.61 % |
| Transversion |
G>T |
All |
1495453 |
10.95 % |
| Transversion |
A>T |
All |
325080 |
2.38 % |
| Transversion |
T>A |
All |
328847 |
2.41 % |
| Transversion |
C>G |
All |
233888 |
1.71 % |
| Transversion |
G>C |
All |
228731 |
1.68 % |
| |
|
|
|
|
| Transition |
A>G |
Passed |
466246 |
16.44 % |
| Transition |
G>A |
Passed |
458097 |
16.15 % |
| Transition |
T>C |
Passed |
472924 |
16.67 % |
| Transition |
C>T |
Passed |
466037 |
16.43 % |
| Transversion |
A>C |
Passed |
119579 |
4.22 % |
| Transversion |
C>A |
Passed |
131704 |
4.64 % |
| Transversion |
T>G |
Passed |
120876 |
4.26 % |
| Transversion |
G>T |
Passed |
131039 |
4.62 % |
| Transversion |
A>T |
Passed |
113265 |
3.99 % |
| Transversion |
T>A |
Passed |
112516 |
3.97 % |
| Transversion |
C>G |
Passed |
121950 |
4.30 % |
| Transversion |
G>C |
Passed |
122570 |
4.32 % |
| |
|
|
|
|
| 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 |
2.00 |
9108868 |
4543708 |
| Passed |
1.91 |
1863304 |
973499 |
| dbSNPAll |
0 |
0 |
0 |
| dbSNPPassed |
0 |
0 |
0 |