/EXTERNAL McGill EMC/variants/K006213_1_lane_gembs
BACK
SAMPLE K006213_1_lane_gembs
Variant counts
| Type |
Total |
Pass |
% |
| SNPs |
1187899899 |
743025925 |
62.55 % |
| Multiallelic |
0 |
0 |
0.00 % |
VCF Filtering Stats
| Type |
#Sites |
% |
#Non-Variant Sites |
% |
#Variant Sites |
% |
| All |
1187899899 |
100% |
1147285320 |
96.58 % |
40614579 |
3.42 % |
| |
|
|
|
|
|
|
| Passed |
750745772 |
63.20 % |
736985152 |
64.24 % |
13760620 |
1.83 % |
| Filtered |
437154127 |
36.80 % |
410300168 |
35.76 % |
26853959 |
3.58 % |
| |
|
|
|
|
|
|
| q20 |
381083703 |
87.17 % |
373591947 |
91.05 % |
7491756 |
27.90 % |
| q20,qd2 |
30801432 |
7.05 % |
13236227 |
3.23 % |
17565205 |
65.41 % |
| q20,mq40 |
12290533 |
2.81 % |
12104716 |
2.95 % |
185817 |
0.69 % |
| qd2 |
6620961 |
1.51 % |
5521411 |
1.35 % |
1099550 |
4.09 % |
| mq40 |
3554849 |
0.81 % |
3290620 |
0.80 % |
264229 |
0.98 % |
| q20,qd2,mq40 |
2735442 |
0.63 % |
2500844 |
0.61 % |
234598 |
0.87 % |
| qd2,mq40 |
65432 |
0.01 % |
54403 |
0.01 % |
11029 |
0.04 % |
| qd2,fs60 |
569 |
0.00 % |
0 |
0.00 % |
569 |
0.00 % |
| qd2,fs60,mq40 |
436 |
0.00 % |
0 |
0.00 % |
436 |
0.00 % |
| q20,qd2,fs60 |
291 |
0.00 % |
0 |
0.00 % |
291 |
0.00 % |
| fs60 |
264 |
0.00 % |
0 |
0.00 % |
264 |
0.00 % |
| fs60,mq40 |
130 |
0.00 % |
0 |
0.00 % |
130 |
0.00 % |
| q20,qd2,fs60,mq40 |
82 |
0.00 % |
0 |
0.00 % |
82 |
0.00 % |
| q20,fs60,mq40 |
2 |
0.00 % |
0 |
0.00 % |
2 |
0.00 % |
| q20,fs60 |
1 |
0.00 % |
0 |
0.00 % |
1 |
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 |
16831808 |
39.48 % |
| Transition |
G>A |
All |
1747808 |
4.10 % |
| Transition |
T>C |
All |
13394657 |
31.42 % |
| Transition |
C>T |
All |
1925749 |
4.52 % |
| Transversion |
A>C |
All |
556241 |
1.30 % |
| Transversion |
C>A |
All |
2158120 |
5.06 % |
| Transversion |
T>G |
All |
796980 |
1.87 % |
| Transversion |
G>T |
All |
2022721 |
4.74 % |
| Transversion |
A>T |
All |
995805 |
2.34 % |
| Transversion |
T>A |
All |
1166367 |
2.74 % |
| Transversion |
C>G |
All |
576467 |
1.35 % |
| Transversion |
G>C |
All |
458747 |
1.08 % |
| |
|
|
|
|
| Transition |
A>G |
Passed |
2495825 |
36.65 % |
| Transition |
G>A |
Passed |
455808 |
6.69 % |
| Transition |
T>C |
Passed |
2356954 |
34.61 % |
| Transition |
C>T |
Passed |
463286 |
6.80 % |
| Transversion |
A>C |
Passed |
130390 |
1.91 % |
| Transversion |
C>A |
Passed |
124792 |
1.83 % |
| Transversion |
T>G |
Passed |
140591 |
2.06 % |
| Transversion |
G>T |
Passed |
126200 |
1.85 % |
| Transversion |
A>T |
Passed |
104980 |
1.54 % |
| Transversion |
T>A |
Passed |
103613 |
1.52 % |
| Transversion |
C>G |
Passed |
157243 |
2.31 % |
| Transversion |
G>C |
Passed |
149996 |
2.20 % |
| |
|
|
|
|
| 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 |
3.88 |
33900022 |
8731448 |
| Passed |
5.56 |
5771873 |
1037805 |
| dbSNPAll |
0 |
0 |
0 |
| dbSNPPassed |
0 |
0 |
0 |