/EXTERNAL McGill EMC/variants/K006188_1_lane_gembs
BACK
SAMPLE K006188_1_lane_gembs
Variant counts
| Type |
Total |
Pass |
% |
| SNPs |
1139776423 |
225919584 |
19.82 % |
| Multiallelic |
0 |
0 |
0.00 % |
VCF Filtering Stats
| Type |
#Sites |
% |
#Non-Variant Sites |
% |
#Variant Sites |
% |
| All |
1139776423 |
100% |
1124921082 |
98.70 % |
14855341 |
1.30 % |
| |
|
|
|
|
|
|
| Passed |
231653670 |
20.32 % |
224617884 |
19.97 % |
7035786 |
3.04 % |
| Filtered |
908122753 |
79.68 % |
900303198 |
80.03 % |
7819555 |
3.38 % |
| |
|
|
|
|
|
|
| q20 |
873584673 |
96.20 % |
870895626 |
96.73 % |
2689047 |
34.39 % |
| q20,qd2 |
16537528 |
1.82 % |
11643520 |
1.29 % |
4894008 |
62.59 % |
| q20,mq40 |
13477255 |
1.48 % |
13412221 |
1.49 % |
65034 |
0.83 % |
| q20,qd2,mq40 |
4190522 |
0.46 % |
4132142 |
0.46 % |
58380 |
0.75 % |
| mq40 |
302282 |
0.03 % |
192908 |
0.02 % |
109374 |
1.40 % |
| qd2 |
21300 |
0.00 % |
19642 |
0.00 % |
1658 |
0.02 % |
| qd2,mq40 |
9055 |
0.00 % |
7139 |
0.00 % |
1916 |
0.02 % |
| qd2,fs60,mq40 |
66 |
0.00 % |
0 |
0.00 % |
66 |
0.00 % |
| fs60,mq40 |
32 |
0.00 % |
0 |
0.00 % |
32 |
0.00 % |
| qd2,fs60 |
25 |
0.00 % |
0 |
0.00 % |
25 |
0.00 % |
| fs60 |
8 |
0.00 % |
0 |
0.00 % |
8 |
0.00 % |
| q20,qd2,fs60,mq40 |
6 |
0.00 % |
0 |
0.00 % |
6 |
0.00 % |
| q20,qd2,fs60 |
1 |
0.00 % |
0 |
0.00 % |
1 |
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 |
4876541 |
29.30 % |
| Transition |
G>A |
All |
940620 |
5.65 % |
| Transition |
T>C |
All |
4718554 |
28.35 % |
| Transition |
C>T |
All |
947030 |
5.69 % |
| Transversion |
A>C |
All |
299909 |
1.80 % |
| Transversion |
C>A |
All |
1187226 |
7.13 % |
| Transversion |
T>G |
All |
323799 |
1.95 % |
| Transversion |
G>T |
All |
1152731 |
6.93 % |
| Transversion |
A>T |
All |
797195 |
4.79 % |
| Transversion |
T>A |
All |
818124 |
4.91 % |
| Transversion |
C>G |
All |
299752 |
1.80 % |
| Transversion |
G>C |
All |
284399 |
1.71 % |
| |
|
|
|
|
| Transition |
A>G |
Passed |
226582 |
15.03 % |
| Transition |
G>A |
Passed |
213841 |
14.19 % |
| Transition |
T>C |
Passed |
227542 |
15.10 % |
| Transition |
C>T |
Passed |
217282 |
14.42 % |
| Transversion |
A>C |
Passed |
77998 |
5.18 % |
| Transversion |
C>A |
Passed |
81919 |
5.44 % |
| Transversion |
T>G |
Passed |
77833 |
5.16 % |
| Transversion |
G>T |
Passed |
82083 |
5.45 % |
| Transversion |
A>T |
Passed |
72063 |
4.78 % |
| Transversion |
T>A |
Passed |
71468 |
4.74 % |
| Transversion |
C>G |
Passed |
79170 |
5.25 % |
| Transversion |
G>C |
Passed |
79397 |
5.27 % |
| |
|
|
|
|
| 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 |
2.22 |
11482745 |
5163135 |
| Passed |
1.42 |
885247 |
621931 |
| dbSNPAll |
0 |
0 |
0 |
| dbSNPPassed |
0 |
0 |
0 |