/EXTERNAL McGill EMC/variants/K006183_1_lane_gembs
BACK
SAMPLE K006183_1_lane_gembs
Variant counts
| Type |
Total |
Pass |
% |
| SNPs |
1139202089 |
191951557 |
16.85 % |
| Multiallelic |
0 |
0 |
0.00 % |
VCF Filtering Stats
| Type |
#Sites |
% |
#Non-Variant Sites |
% |
#Variant Sites |
% |
| All |
1139202089 |
100% |
1124992133 |
98.75 % |
14209956 |
1.25 % |
| |
|
|
|
|
|
|
| Passed |
197077682 |
17.30 % |
190702616 |
16.95 % |
6375066 |
3.23 % |
| Filtered |
942124407 |
82.70 % |
934289517 |
83.05 % |
7834890 |
3.98 % |
| |
|
|
|
|
|
|
| q20 |
900938964 |
95.63 % |
898125460 |
96.13 % |
2813504 |
35.91 % |
| q20,mq40 |
18134836 |
1.92 % |
18046485 |
1.93 % |
88351 |
1.13 % |
| q20,qd2 |
17613919 |
1.87 % |
12888122 |
1.38 % |
4725797 |
60.32 % |
| q20,qd2,mq40 |
4995706 |
0.53 % |
4919128 |
0.53 % |
76578 |
0.98 % |
| mq40 |
399385 |
0.04 % |
275202 |
0.03 % |
124183 |
1.58 % |
| qd2 |
27280 |
0.00 % |
23975 |
0.00 % |
3305 |
0.04 % |
| qd2,mq40 |
14032 |
0.00 % |
11145 |
0.00 % |
2887 |
0.04 % |
| qd2,fs60,mq40 |
131 |
0.00 % |
0 |
0.00 % |
131 |
0.00 % |
| qd2,fs60 |
71 |
0.00 % |
0 |
0.00 % |
71 |
0.00 % |
| fs60,mq40 |
63 |
0.00 % |
0 |
0.00 % |
63 |
0.00 % |
| q20,qd2,fs60,mq40 |
10 |
0.00 % |
0 |
0.00 % |
10 |
0.00 % |
| fs60 |
6 |
0.00 % |
0 |
0.00 % |
6 |
0.00 % |
| q20,qd2,fs60 |
2 |
0.00 % |
0 |
0.00 % |
2 |
0.00 % |
| q20,fs60 |
1 |
0.00 % |
0 |
0.00 % |
1 |
0.00 % |
| q20,fs60,mq40 |
1 |
0.00 % |
0 |
0.00 % |
1 |
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 |
4648827 |
29.02 % |
| Transition |
G>A |
All |
927929 |
5.79 % |
| Transition |
T>C |
All |
4343143 |
27.11 % |
| Transition |
C>T |
All |
943128 |
5.89 % |
| Transversion |
A>C |
All |
265842 |
1.66 % |
| Transversion |
C>A |
All |
1154431 |
7.21 % |
| Transversion |
T>G |
All |
310474 |
1.94 % |
| Transversion |
G>T |
All |
1108373 |
6.92 % |
| Transversion |
A>T |
All |
867259 |
5.41 % |
| Transversion |
T>A |
All |
920804 |
5.75 % |
| Transversion |
C>G |
All |
276294 |
1.72 % |
| Transversion |
G>C |
All |
251045 |
1.57 % |
| |
|
|
|
|
| Transition |
A>G |
Passed |
210229 |
14.76 % |
| Transition |
G>A |
Passed |
200590 |
14.08 % |
| Transition |
T>C |
Passed |
212259 |
14.90 % |
| Transition |
C>T |
Passed |
204404 |
14.35 % |
| Transversion |
A>C |
Passed |
74031 |
5.20 % |
| Transversion |
C>A |
Passed |
79034 |
5.55 % |
| Transversion |
T>G |
Passed |
74753 |
5.25 % |
| Transversion |
G>T |
Passed |
79804 |
5.60 % |
| Transversion |
A>T |
Passed |
69726 |
4.90 % |
| Transversion |
T>A |
Passed |
69429 |
4.87 % |
| Transversion |
C>G |
Passed |
74890 |
5.26 % |
| Transversion |
G>C |
Passed |
75245 |
5.28 % |
| |
|
|
|
|
| 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 |
2.11 |
10863027 |
5154522 |
| Passed |
1.39 |
827482 |
596912 |
| dbSNPAll |
0 |
0 |
0 |
| dbSNPPassed |
0 |
0 |
0 |