/EXTERNAL McGill EMC/variants/K006167_1_lane_gembs
BACK
SAMPLE K006167_1_lane_gembs
Variant counts
| Type |
Total |
Pass |
% |
| SNPs |
1144843496 |
621839828 |
54.32 % |
| Multiallelic |
0 |
0 |
0.00 % |
VCF Filtering Stats
| Type |
#Sites |
% |
#Non-Variant Sites |
% |
#Variant Sites |
% |
| All |
1144843496 |
100% |
1132920650 |
98.96 % |
11922846 |
1.04 % |
| |
|
|
|
|
|
|
| Passed |
623955934 |
54.50 % |
619970955 |
54.72 % |
3984979 |
0.64 % |
| Filtered |
520887562 |
45.50 % |
512949695 |
45.28 % |
7937867 |
1.27 % |
| |
|
|
|
|
|
|
| q20 |
485872634 |
93.28 % |
484190526 |
94.39 % |
1682108 |
21.19 % |
| q20,qd2 |
15528856 |
2.98 % |
9672373 |
1.89 % |
5856483 |
73.78 % |
| q20,mq40 |
12301044 |
2.36 % |
12209768 |
2.38 % |
91276 |
1.15 % |
| q20,qd2,mq40 |
2905937 |
0.56 % |
2799253 |
0.55 % |
106684 |
1.34 % |
| qd2 |
2626645 |
0.50 % |
2574023 |
0.50 % |
52622 |
0.66 % |
| mq40 |
1606313 |
0.31 % |
1467911 |
0.29 % |
138402 |
1.74 % |
| qd2,mq40 |
44034 |
0.01 % |
35841 |
0.01 % |
8193 |
0.10 % |
| qd2,fs60,mq40 |
763 |
0.00 % |
0 |
0.00 % |
763 |
0.01 % |
| fs60 |
432 |
0.00 % |
0 |
0.00 % |
432 |
0.01 % |
| qd2,fs60 |
375 |
0.00 % |
0 |
0.00 % |
375 |
0.00 % |
| fs60,mq40 |
278 |
0.00 % |
0 |
0.00 % |
278 |
0.00 % |
| q20,qd2,fs60 |
166 |
0.00 % |
0 |
0.00 % |
166 |
0.00 % |
| q20,qd2,fs60,mq40 |
85 |
0.00 % |
0 |
0.00 % |
85 |
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 |
3682597 |
26.97 % |
| Transition |
G>A |
All |
1037294 |
7.60 % |
| Transition |
T>C |
All |
3443598 |
25.22 % |
| Transition |
C>T |
All |
1055843 |
7.73 % |
| Transversion |
A>C |
All |
286089 |
2.10 % |
| Transversion |
C>A |
All |
1287483 |
9.43 % |
| Transversion |
T>G |
All |
297645 |
2.18 % |
| Transversion |
G>T |
All |
1276892 |
9.35 % |
| Transversion |
A>T |
All |
360446 |
2.64 % |
| Transversion |
T>A |
All |
365055 |
2.67 % |
| Transversion |
C>G |
All |
285876 |
2.09 % |
| Transversion |
G>C |
All |
276944 |
2.03 % |
| |
|
|
|
|
| Transition |
A>G |
Passed |
423870 |
16.50 % |
| Transition |
G>A |
Passed |
404991 |
15.76 % |
| Transition |
T>C |
Passed |
427126 |
16.63 % |
| Transition |
C>T |
Passed |
411168 |
16.00 % |
| Transversion |
A>C |
Passed |
111906 |
4.36 % |
| Transversion |
C>A |
Passed |
122395 |
4.76 % |
| Transversion |
T>G |
Passed |
112208 |
4.37 % |
| Transversion |
G>T |
Passed |
120713 |
4.70 % |
| Transversion |
A>T |
Passed |
103524 |
4.03 % |
| Transversion |
T>A |
Passed |
103345 |
4.02 % |
| Transversion |
C>G |
Passed |
114019 |
4.44 % |
| Transversion |
G>C |
Passed |
113845 |
4.43 % |
| |
|
|
|
|
| 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 |
2.08 |
9219332 |
4436430 |
| Passed |
1.85 |
1667155 |
901955 |
| dbSNPAll |
0 |
0 |
0 |
| dbSNPPassed |
0 |
0 |
0 |