/EXTERNAL McGill EMC/variants/K006220_1_lane_gembs
BACK
SAMPLE K006220_1_lane_gembs
Variant counts
| Type |
Total |
Pass |
% |
| SNPs |
1156126836 |
972308690 |
84.10 % |
| Multiallelic |
0 |
0 |
0.00 % |
VCF Filtering Stats
| Type |
#Sites |
% |
#Non-Variant Sites |
% |
#Variant Sites |
% |
| All |
1156126836 |
100% |
1136723317 |
98.32 % |
19403519 |
1.68 % |
| |
|
|
|
|
|
|
| Passed |
973764903 |
84.23 % |
967976289 |
85.15 % |
5788614 |
0.59 % |
| Filtered |
182361933 |
15.77 % |
168747028 |
14.85 % |
13614905 |
1.40 % |
| |
|
|
|
|
|
|
| q20 |
140633711 |
77.12 % |
139052733 |
82.40 % |
1580978 |
11.61 % |
| q20,qd2 |
17827093 |
9.78 % |
6647391 |
3.94 % |
11179702 |
82.11 % |
| q20,mq40 |
14333579 |
7.86 % |
14213586 |
8.42 % |
119993 |
0.88 % |
| mq40 |
3806199 |
2.09 % |
3563811 |
2.11 % |
242388 |
1.78 % |
| q20,qd2,mq40 |
2908299 |
1.59 % |
2697149 |
1.60 % |
211150 |
1.55 % |
| qd2 |
2820458 |
1.55 % |
2546755 |
1.51 % |
273703 |
2.01 % |
| qd2,mq40 |
31778 |
0.02 % |
25603 |
0.02 % |
6175 |
0.05 % |
| qd2,fs60,mq40 |
357 |
0.00 % |
0 |
0.00 % |
357 |
0.00 % |
| qd2,fs60 |
178 |
0.00 % |
0 |
0.00 % |
178 |
0.00 % |
| fs60,mq40 |
162 |
0.00 % |
0 |
0.00 % |
162 |
0.00 % |
| fs60 |
66 |
0.00 % |
0 |
0.00 % |
66 |
0.00 % |
| q20,qd2,fs60,mq40 |
36 |
0.00 % |
0 |
0.00 % |
36 |
0.00 % |
| q20,qd2,fs60 |
15 |
0.00 % |
0 |
0.00 % |
15 |
0.00 % |
| q20,fs60,mq40 |
2 |
0.00 % |
0 |
0.00 % |
2 |
0.00 % |
| q20,fs60 |
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 |
6967219 |
34.46 % |
| Transition |
G>A |
All |
1385733 |
6.85 % |
| Transition |
T>C |
All |
6808876 |
33.68 % |
| Transition |
C>T |
All |
1384119 |
6.85 % |
| Transversion |
A>C |
All |
269333 |
1.33 % |
| Transversion |
C>A |
All |
844010 |
4.17 % |
| Transversion |
T>G |
All |
273403 |
1.35 % |
| Transversion |
G>T |
All |
836394 |
4.14 % |
| Transversion |
A>T |
All |
445408 |
2.20 % |
| Transversion |
T>A |
All |
433413 |
2.14 % |
| Transversion |
C>G |
All |
285781 |
1.41 % |
| Transversion |
G>C |
All |
283324 |
1.40 % |
| |
|
|
|
|
| Transition |
A>G |
Passed |
826525 |
17.31 % |
| Transition |
G>A |
Passed |
748130 |
15.67 % |
| Transition |
T>C |
Passed |
825015 |
17.28 % |
| Transition |
C>T |
Passed |
754435 |
15.80 % |
| Transversion |
A>C |
Passed |
199264 |
4.17 % |
| Transversion |
C>A |
Passed |
216024 |
4.52 % |
| Transversion |
T>G |
Passed |
199851 |
4.19 % |
| Transversion |
G>T |
Passed |
216262 |
4.53 % |
| Transversion |
A>T |
Passed |
187160 |
3.92 % |
| Transversion |
T>A |
Passed |
187011 |
3.92 % |
| Transversion |
C>G |
Passed |
206970 |
4.34 % |
| Transversion |
G>C |
Passed |
207372 |
4.34 % |
| |
|
|
|
|
| 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 |
4.51 |
16545947 |
3671066 |
| Passed |
1.95 |
3154105 |
1619914 |
| dbSNPAll |
0 |
0 |
0 |
| dbSNPPassed |
0 |
0 |
0 |