/EXTERNAL McGill EMC/variants/K006134_1_lane_gembs
BACK
SAMPLE K006134_1_lane_gembs
Variant counts
| Type |
Total |
Pass |
% |
| SNPs |
1146118487 |
729677134 |
63.67 % |
| Multiallelic |
0 |
0 |
0.00 % |
VCF Filtering Stats
| Type |
#Sites |
% |
#Non-Variant Sites |
% |
#Variant Sites |
% |
| All |
1146118487 |
100% |
1124042786 |
98.07 % |
22075701 |
1.93 % |
| |
|
|
|
|
|
|
| Passed |
731019447 |
63.78 % |
727376671 |
64.71 % |
3642776 |
0.50 % |
| Filtered |
415099040 |
36.22 % |
396666115 |
35.29 % |
18432925 |
2.52 % |
| |
|
|
|
|
|
|
| q20 |
343738979 |
82.81 % |
341990728 |
86.22 % |
1748251 |
9.48 % |
| q20,qd2 |
42964618 |
10.35 % |
26948509 |
6.79 % |
16016109 |
86.89 % |
| q20,mq40 |
13898357 |
3.35 % |
13750164 |
3.47 % |
148193 |
0.80 % |
| qd2 |
9047452 |
2.18 % |
8986358 |
2.27 % |
61094 |
0.33 % |
| q20,qd2,mq40 |
3639931 |
0.88 % |
3348104 |
0.84 % |
291827 |
1.58 % |
| mq40 |
1765895 |
0.43 % |
1606367 |
0.40 % |
159528 |
0.87 % |
| qd2,mq40 |
42966 |
0.01 % |
35885 |
0.01 % |
7081 |
0.04 % |
| qd2,fs60,mq40 |
397 |
0.00 % |
0 |
0.00 % |
397 |
0.00 % |
| fs60,mq40 |
198 |
0.00 % |
0 |
0.00 % |
198 |
0.00 % |
| qd2,fs60 |
126 |
0.00 % |
0 |
0.00 % |
126 |
0.00 % |
| fs60 |
81 |
0.00 % |
0 |
0.00 % |
81 |
0.00 % |
| q20,qd2,fs60,mq40 |
33 |
0.00 % |
0 |
0.00 % |
33 |
0.00 % |
| q20,qd2,fs60 |
7 |
0.00 % |
0 |
0.00 % |
7 |
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 |
3180833 |
13.40 % |
| Transition |
G>A |
All |
1168719 |
4.92 % |
| Transition |
T>C |
All |
3093166 |
13.03 % |
| Transition |
C>T |
All |
1182264 |
4.98 % |
| Transversion |
A>C |
All |
223019 |
0.94 % |
| Transversion |
C>A |
All |
6636643 |
27.95 % |
| Transversion |
T>G |
All |
229015 |
0.96 % |
| Transversion |
G>T |
All |
6697399 |
28.21 % |
| Transversion |
A>T |
All |
375997 |
1.58 % |
| Transversion |
T>A |
All |
372727 |
1.57 % |
| Transversion |
C>G |
All |
292462 |
1.23 % |
| Transversion |
G>C |
All |
288991 |
1.22 % |
| |
|
|
|
|
| Transition |
A>G |
Passed |
480059 |
15.32 % |
| Transition |
G>A |
Passed |
477806 |
15.25 % |
| Transition |
T>C |
Passed |
483152 |
15.42 % |
| Transition |
C>T |
Passed |
484048 |
15.45 % |
| Transversion |
A>C |
Passed |
124196 |
3.96 % |
| Transversion |
C>A |
Passed |
226107 |
7.22 % |
| Transversion |
T>G |
Passed |
124604 |
3.98 % |
| Transversion |
G>T |
Passed |
226313 |
7.22 % |
| Transversion |
A>T |
Passed |
117609 |
3.75 % |
| Transversion |
T>A |
Passed |
117848 |
3.76 % |
| Transversion |
C>G |
Passed |
135995 |
4.34 % |
| Transversion |
G>C |
Passed |
135896 |
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 |
0.57 |
8624982 |
15116253 |
| Passed |
1.59 |
1925065 |
1208568 |
| dbSNPAll |
0 |
0 |
0 |
| dbSNPPassed |
0 |
0 |
0 |