/EXTERNAL McGill EMC/variants/K006153_1_lane_gembs
BACK
SAMPLE K006153_1_lane_gembs
Variant counts
| Type |
Total |
Pass |
% |
| SNPs |
1130854006 |
262248680 |
23.19 % |
| Multiallelic |
0 |
0 |
0.00 % |
VCF Filtering Stats
| Type |
#Sites |
% |
#Non-Variant Sites |
% |
#Variant Sites |
% |
| All |
1130854006 |
100% |
1120894569 |
99.12 % |
9959437 |
0.88 % |
| |
|
|
|
|
|
|
| Passed |
264683223 |
23.41 % |
261033504 |
23.29 % |
3649719 |
1.38 % |
| Filtered |
866170783 |
76.59 % |
859861065 |
76.71 % |
6309718 |
2.38 % |
| |
|
|
|
|
|
|
| q20 |
823555659 |
95.08 % |
821237079 |
95.51 % |
2318580 |
36.75 % |
| q20,qd2 |
23920331 |
2.76 % |
20175080 |
2.35 % |
3745251 |
59.36 % |
| q20,mq40 |
14177130 |
1.64 % |
14098058 |
1.64 % |
79072 |
1.25 % |
| q20,qd2,mq40 |
3881473 |
0.45 % |
3824300 |
0.44 % |
57173 |
0.91 % |
| mq40 |
436124 |
0.05 % |
339675 |
0.04 % |
96449 |
1.53 % |
| qd2 |
178740 |
0.02 % |
170099 |
0.02 % |
8641 |
0.14 % |
| qd2,mq40 |
20785 |
0.00 % |
16774 |
0.00 % |
4011 |
0.06 % |
| qd2,fs60,mq40 |
272 |
0.00 % |
0 |
0.00 % |
272 |
0.00 % |
| fs60,mq40 |
135 |
0.00 % |
0 |
0.00 % |
135 |
0.00 % |
| qd2,fs60 |
96 |
0.00 % |
0 |
0.00 % |
96 |
0.00 % |
| q20,qd2,fs60,mq40 |
21 |
0.00 % |
0 |
0.00 % |
21 |
0.00 % |
| fs60 |
13 |
0.00 % |
0 |
0.00 % |
13 |
0.00 % |
| q20,qd2,fs60 |
4 |
0.00 % |
0 |
0.00 % |
4 |
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 |
2502298 |
21.28 % |
| Transition |
G>A |
All |
1291978 |
10.99 % |
| Transition |
T>C |
All |
2418606 |
20.57 % |
| Transition |
C>T |
All |
1296162 |
11.02 % |
| Transversion |
A>C |
All |
367305 |
3.12 % |
| Transversion |
C>A |
All |
861037 |
7.32 % |
| Transversion |
T>G |
All |
377931 |
3.21 % |
| Transversion |
G>T |
All |
836213 |
7.11 % |
| Transversion |
A>T |
All |
601160 |
5.11 % |
| Transversion |
T>A |
All |
606568 |
5.16 % |
| Transversion |
C>G |
All |
302759 |
2.57 % |
| Transversion |
G>C |
All |
296489 |
2.52 % |
| |
|
|
|
|
| Transition |
A>G |
Passed |
229620 |
15.32 % |
| Transition |
G>A |
Passed |
224665 |
14.99 % |
| Transition |
T>C |
Passed |
232489 |
15.52 % |
| Transition |
C>T |
Passed |
227697 |
15.20 % |
| Transversion |
A>C |
Passed |
73282 |
4.89 % |
| Transversion |
C>A |
Passed |
77113 |
5.15 % |
| Transversion |
T>G |
Passed |
73485 |
4.90 % |
| Transversion |
G>T |
Passed |
77353 |
5.16 % |
| Transversion |
A>T |
Passed |
68992 |
4.60 % |
| Transversion |
T>A |
Passed |
68933 |
4.60 % |
| Transversion |
C>G |
Passed |
72267 |
4.82 % |
| Transversion |
G>C |
Passed |
72447 |
4.84 % |
| |
|
|
|
|
| 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 |
1.77 |
7509044 |
4249462 |
| Passed |
1.57 |
914471 |
583872 |
| dbSNPAll |
0 |
0 |
0 |
| dbSNPPassed |
0 |
0 |
0 |