/EXTERNAL McGill EMC/variants/K006181_1_lane_gembs
BACK
SAMPLE K006181_1_lane_gembs
Variant counts
| Type |
Total |
Pass |
% |
| SNPs |
1153131831 |
955894307 |
82.90 % |
| Multiallelic |
0 |
0 |
0.00 % |
VCF Filtering Stats
| Type |
#Sites |
% |
#Non-Variant Sites |
% |
#Variant Sites |
% |
| All |
1153131831 |
100% |
1137477366 |
98.64 % |
15654465 |
1.36 % |
| |
|
|
|
|
|
|
| Passed |
957344097 |
83.02 % |
953487610 |
83.82 % |
3856487 |
0.40 % |
| Filtered |
195787734 |
16.98 % |
183989756 |
16.18 % |
11797978 |
1.23 % |
| |
|
|
|
|
|
|
| q20 |
154855347 |
79.09 % |
153220069 |
83.28 % |
1635278 |
13.86 % |
| q20,qd2 |
17649205 |
9.01 % |
8062515 |
4.38 % |
9586690 |
81.26 % |
| q20,mq40 |
13228990 |
6.76 % |
13116767 |
7.13 % |
112223 |
0.95 % |
| qd2 |
3891084 |
1.99 % |
3802143 |
2.07 % |
88941 |
0.75 % |
| q20,qd2,mq40 |
3208441 |
1.64 % |
3026638 |
1.65 % |
181803 |
1.54 % |
| mq40 |
2913028 |
1.49 % |
2728730 |
1.48 % |
184298 |
1.56 % |
| qd2,mq40 |
40669 |
0.02 % |
32894 |
0.02 % |
7775 |
0.07 % |
| qd2,fs60,mq40 |
477 |
0.00 % |
0 |
0.00 % |
477 |
0.00 % |
| fs60,mq40 |
207 |
0.00 % |
0 |
0.00 % |
207 |
0.00 % |
| qd2,fs60 |
167 |
0.00 % |
0 |
0.00 % |
167 |
0.00 % |
| fs60 |
71 |
0.00 % |
0 |
0.00 % |
71 |
0.00 % |
| q20,qd2,fs60,mq40 |
29 |
0.00 % |
0 |
0.00 % |
29 |
0.00 % |
| q20,qd2,fs60 |
18 |
0.00 % |
0 |
0.00 % |
18 |
0.00 % |
| q20,fs60,mq40 |
1 |
0.00 % |
0 |
0.00 % |
1 |
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 |
5932671 |
34.29 % |
| Transition |
G>A |
All |
1205595 |
6.97 % |
| Transition |
T>C |
All |
5528891 |
31.95 % |
| Transition |
C>T |
All |
1226159 |
7.09 % |
| Transversion |
A>C |
All |
201789 |
1.17 % |
| Transversion |
C>A |
All |
918896 |
5.31 % |
| Transversion |
T>G |
All |
213827 |
1.24 % |
| Transversion |
G>T |
All |
903928 |
5.22 % |
| Transversion |
A>T |
All |
370430 |
2.14 % |
| Transversion |
T>A |
All |
371513 |
2.15 % |
| Transversion |
C>G |
All |
218568 |
1.26 % |
| Transversion |
G>C |
All |
209920 |
1.21 % |
| |
|
|
|
|
| Transition |
A>G |
Passed |
611894 |
17.64 % |
| Transition |
G>A |
Passed |
561929 |
16.20 % |
| Transition |
T>C |
Passed |
600108 |
17.30 % |
| Transition |
C>T |
Passed |
568331 |
16.38 % |
| Transversion |
A>C |
Passed |
140438 |
4.05 % |
| Transversion |
C>A |
Passed |
150943 |
4.35 % |
| Transversion |
T>G |
Passed |
140912 |
4.06 % |
| Transversion |
G>T |
Passed |
150439 |
4.34 % |
| Transversion |
A>T |
Passed |
127780 |
3.68 % |
| Transversion |
T>A |
Passed |
126806 |
3.65 % |
| Transversion |
C>G |
Passed |
145009 |
4.18 % |
| Transversion |
G>C |
Passed |
145048 |
4.18 % |
| |
|
|
|
|
| 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 |
4.08 |
13893316 |
3408871 |
| Passed |
2.08 |
2342262 |
1127375 |
| dbSNPAll |
0 |
0 |
0 |
| dbSNPPassed |
0 |
0 |
0 |