/EXTERNAL McGill EMC/variants/K006170_1_lane_gembs
BACK
SAMPLE K006170_1_lane_gembs
Variant counts
| Type |
Total |
Pass |
% |
| SNPs |
1138360258 |
481582121 |
42.30 % |
| Multiallelic |
0 |
0 |
0.00 % |
VCF Filtering Stats
| Type |
#Sites |
% |
#Non-Variant Sites |
% |
#Variant Sites |
% |
| All |
1138360258 |
100% |
1127635726 |
99.06 % |
10724532 |
0.94 % |
| |
|
|
|
|
|
|
| Passed |
483890440 |
42.51 % |
479950539 |
42.56 % |
3939901 |
0.81 % |
| Filtered |
654469818 |
57.49 % |
647685187 |
57.44 % |
6784631 |
1.40 % |
| |
|
|
|
|
|
|
| q20 |
619799720 |
94.70 % |
617994302 |
95.42 % |
1805418 |
26.61 % |
| q20,qd2 |
18306309 |
2.80 % |
13596588 |
2.10 % |
4709721 |
69.42 % |
| q20,mq40 |
11468284 |
1.75 % |
11399255 |
1.76 % |
69029 |
1.02 % |
| q20,qd2,mq40 |
3570114 |
0.55 % |
3502141 |
0.54 % |
67973 |
1.00 % |
| qd2 |
670661 |
0.10 % |
646610 |
0.10 % |
24051 |
0.35 % |
| mq40 |
628857 |
0.10 % |
526198 |
0.08 % |
102659 |
1.51 % |
| qd2,mq40 |
25199 |
0.00 % |
20093 |
0.00 % |
5106 |
0.08 % |
| qd2,fs60,mq40 |
371 |
0.00 % |
0 |
0.00 % |
371 |
0.01 % |
| fs60,mq40 |
145 |
0.00 % |
0 |
0.00 % |
145 |
0.00 % |
| qd2,fs60 |
89 |
0.00 % |
0 |
0.00 % |
89 |
0.00 % |
| q20,qd2,fs60,mq40 |
34 |
0.00 % |
0 |
0.00 % |
34 |
0.00 % |
| fs60 |
27 |
0.00 % |
0 |
0.00 % |
27 |
0.00 % |
| q20,qd2,fs60 |
8 |
0.00 % |
0 |
0.00 % |
8 |
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 |
3442171 |
27.62 % |
| Transition |
G>A |
All |
1112662 |
8.93 % |
| Transition |
T>C |
All |
3349019 |
26.88 % |
| Transition |
C>T |
All |
1123373 |
9.02 % |
| Transversion |
A>C |
All |
247768 |
1.99 % |
| Transversion |
C>A |
All |
758817 |
6.09 % |
| Transversion |
T>G |
All |
257375 |
2.07 % |
| Transversion |
G>T |
All |
738511 |
5.93 % |
| Transversion |
A>T |
All |
472395 |
3.79 % |
| Transversion |
T>A |
All |
477303 |
3.83 % |
| Transversion |
C>G |
All |
245024 |
1.97 % |
| Transversion |
G>C |
All |
236493 |
1.90 % |
| |
|
|
|
|
| Transition |
A>G |
Passed |
348793 |
15.97 % |
| Transition |
G>A |
Passed |
340204 |
15.58 % |
| Transition |
T>C |
Passed |
351223 |
16.08 % |
| Transition |
C>T |
Passed |
345812 |
15.83 % |
| Transversion |
A>C |
Passed |
99442 |
4.55 % |
| Transversion |
C>A |
Passed |
106132 |
4.86 % |
| Transversion |
T>G |
Passed |
99656 |
4.56 % |
| Transversion |
G>T |
Passed |
106955 |
4.90 % |
| Transversion |
A>T |
Passed |
96430 |
4.41 % |
| Transversion |
T>A |
Passed |
95948 |
4.39 % |
| Transversion |
C>G |
Passed |
96765 |
4.43 % |
| Transversion |
G>C |
Passed |
96930 |
4.44 % |
| |
|
|
|
|
| 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 |
2.63 |
9027225 |
3433686 |
| Passed |
1.74 |
1386032 |
798258 |
| dbSNPAll |
0 |
0 |
0 |
| dbSNPPassed |
0 |
0 |
0 |