/EXTERNAL McGill EMC/variants/K006135_1_lane_gembs
BACK
SAMPLE K006135_1_lane_gembs
Variant counts
| Type |
Total |
Pass |
% |
| SNPs |
1138061520 |
108933885 |
9.57 % |
| Multiallelic |
0 |
0 |
0.00 % |
VCF Filtering Stats
| Type |
#Sites |
% |
#Non-Variant Sites |
% |
#Variant Sites |
% |
| All |
1138061520 |
100% |
1124615487 |
98.82 % |
13446033 |
1.18 % |
| |
|
|
|
|
|
|
| Passed |
114653978 |
10.07 % |
107935982 |
9.60 % |
6717996 |
5.86 % |
| Filtered |
1023407542 |
89.93 % |
1016679505 |
90.40 % |
6728037 |
5.87 % |
| |
|
|
|
|
|
|
| q20 |
975349979 |
95.30 % |
972716041 |
95.68 % |
2633938 |
39.15 % |
| q20,qd2 |
26436008 |
2.58 % |
22580536 |
2.22 % |
3855472 |
57.30 % |
| q20,mq40 |
15994858 |
1.56 % |
15927013 |
1.57 % |
67845 |
1.01 % |
| q20,qd2,mq40 |
5340028 |
0.52 % |
5283951 |
0.52 % |
56077 |
0.83 % |
| mq40 |
258261 |
0.03 % |
147947 |
0.01 % |
110314 |
1.64 % |
| qd2 |
17257 |
0.00 % |
15242 |
0.00 % |
2015 |
0.03 % |
| qd2,mq40 |
10979 |
0.00 % |
8775 |
0.00 % |
2204 |
0.03 % |
| qd2,fs60,mq40 |
91 |
0.00 % |
0 |
0.00 % |
91 |
0.00 % |
| qd2,fs60 |
38 |
0.00 % |
0 |
0.00 % |
38 |
0.00 % |
| fs60,mq40 |
30 |
0.00 % |
0 |
0.00 % |
30 |
0.00 % |
| fs60 |
7 |
0.00 % |
0 |
0.00 % |
7 |
0.00 % |
| q20,qd2,fs60,mq40 |
4 |
0.00 % |
0 |
0.00 % |
4 |
0.00 % |
| q20,qd2,fs60 |
2 |
0.00 % |
0 |
0.00 % |
2 |
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 |
4215486 |
27.40 % |
| Transition |
G>A |
All |
885122 |
5.75 % |
| Transition |
T>C |
All |
3899530 |
25.35 % |
| Transition |
C>T |
All |
895458 |
5.82 % |
| Transversion |
A>C |
All |
310395 |
2.02 % |
| Transversion |
C>A |
All |
1264319 |
8.22 % |
| Transversion |
T>G |
All |
358325 |
2.33 % |
| Transversion |
G>T |
All |
1217995 |
7.92 % |
| Transversion |
A>T |
All |
856096 |
5.57 % |
| Transversion |
T>A |
All |
899108 |
5.84 % |
| Transversion |
C>G |
All |
304900 |
1.98 % |
| Transversion |
G>C |
All |
275945 |
1.79 % |
| |
|
|
|
|
| Transition |
A>G |
Passed |
155280 |
14.19 % |
| Transition |
G>A |
Passed |
148678 |
13.59 % |
| Transition |
T>C |
Passed |
156489 |
14.30 % |
| Transition |
C>T |
Passed |
151016 |
13.80 % |
| Transversion |
A>C |
Passed |
60488 |
5.53 % |
| Transversion |
C>A |
Passed |
63712 |
5.82 % |
| Transversion |
T>G |
Passed |
60168 |
5.50 % |
| Transversion |
G>T |
Passed |
64268 |
5.87 % |
| Transversion |
A>T |
Passed |
55276 |
5.05 % |
| Transversion |
T>A |
Passed |
55666 |
5.09 % |
| Transversion |
C>G |
Passed |
61231 |
5.60 % |
| Transversion |
G>C |
Passed |
62111 |
5.68 % |
| |
|
|
|
|
| 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 |
1.80 |
9895596 |
5487083 |
| Passed |
1.27 |
611463 |
482920 |
| dbSNPAll |
0 |
0 |
0 |
| dbSNPPassed |
0 |
0 |
0 |