/EXTERNAL McGill EMC/variants/K006177_1_lane_gembs
BACK
SAMPLE K006177_1_lane_gembs
Variant counts
| Type |
Total |
Pass |
% |
| SNPs |
1141865002 |
147353877 |
12.90 % |
| Multiallelic |
0 |
0 |
0.00 % |
VCF Filtering Stats
| Type |
#Sites |
% |
#Non-Variant Sites |
% |
#Variant Sites |
% |
| All |
1141865002 |
100% |
1127917809 |
98.78 % |
13947193 |
1.22 % |
| |
|
|
|
|
|
|
| Passed |
153131100 |
13.41 % |
146237854 |
12.97 % |
6893246 |
4.50 % |
| Filtered |
988733902 |
86.59 % |
981679955 |
87.03 % |
7053947 |
4.61 % |
| |
|
|
|
|
|
|
| q20 |
942804898 |
95.35 % |
940046064 |
95.76 % |
2758834 |
39.11 % |
| q20,qd2 |
22539633 |
2.28 % |
18515440 |
1.89 % |
4024193 |
57.05 % |
| q20,mq40 |
17795124 |
1.80 % |
17719695 |
1.81 % |
75429 |
1.07 % |
| q20,qd2,mq40 |
5220056 |
0.53 % |
5154656 |
0.53 % |
65400 |
0.93 % |
| mq40 |
342804 |
0.03 % |
217705 |
0.02 % |
125099 |
1.77 % |
| qd2 |
19488 |
0.00 % |
17153 |
0.00 % |
2335 |
0.03 % |
| qd2,mq40 |
11747 |
0.00 % |
9242 |
0.00 % |
2505 |
0.04 % |
| qd2,fs60,mq40 |
87 |
0.00 % |
0 |
0.00 % |
87 |
0.00 % |
| fs60,mq40 |
30 |
0.00 % |
0 |
0.00 % |
30 |
0.00 % |
| qd2,fs60 |
20 |
0.00 % |
0 |
0.00 % |
20 |
0.00 % |
| fs60 |
9 |
0.00 % |
0 |
0.00 % |
9 |
0.00 % |
| q20,qd2,fs60,mq40 |
4 |
0.00 % |
0 |
0.00 % |
4 |
0.00 % |
| q20,qd2,fs60 |
2 |
0.00 % |
0 |
0.00 % |
2 |
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 |
4965293 |
31.36 % |
| Transition |
G>A |
All |
850535 |
5.37 % |
| Transition |
T>C |
All |
4349238 |
27.47 % |
| Transition |
C>T |
All |
876857 |
5.54 % |
| Transversion |
A>C |
All |
238320 |
1.51 % |
| Transversion |
C>A |
All |
1007669 |
6.36 % |
| Transversion |
T>G |
All |
332202 |
2.10 % |
| Transversion |
G>T |
All |
933223 |
5.89 % |
| Transversion |
A>T |
All |
824977 |
5.21 % |
| Transversion |
T>A |
All |
926096 |
5.85 % |
| Transversion |
C>G |
All |
291690 |
1.84 % |
| Transversion |
G>C |
All |
238442 |
1.51 % |
| |
|
|
|
|
| Transition |
A>G |
Passed |
183978 |
14.69 % |
| Transition |
G>A |
Passed |
172341 |
13.76 % |
| Transition |
T>C |
Passed |
186257 |
14.87 % |
| Transition |
C>T |
Passed |
177259 |
14.16 % |
| Transversion |
A>C |
Passed |
66030 |
5.27 % |
| Transversion |
C>A |
Passed |
70050 |
5.59 % |
| Transversion |
T>G |
Passed |
66853 |
5.34 % |
| Transversion |
G>T |
Passed |
70442 |
5.63 % |
| Transversion |
A>T |
Passed |
62044 |
4.95 % |
| Transversion |
T>A |
Passed |
61901 |
4.94 % |
| Transversion |
C>G |
Passed |
67337 |
5.38 % |
| Transversion |
G>C |
Passed |
67776 |
5.41 % |
| |
|
|
|
|
| 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 |
2.30 |
11041923 |
4792619 |
| Passed |
1.35 |
719835 |
532433 |
| dbSNPAll |
0 |
0 |
0 |
| dbSNPPassed |
0 |
0 |
0 |