/EXTERNAL McGill EMC/variants/K006206_1_lane_gembs
BACK
SAMPLE K006206_1_lane_gembs
Variant counts
| Type |
Total |
Pass |
% |
| SNPs |
1140867410 |
203584591 |
17.84 % |
| Multiallelic |
0 |
0 |
0.00 % |
VCF Filtering Stats
| Type |
#Sites |
% |
#Non-Variant Sites |
% |
#Variant Sites |
% |
| All |
1140867410 |
100% |
1125567925 |
98.66 % |
15299485 |
1.34 % |
| |
|
|
|
|
|
|
| Passed |
209786401 |
18.39 % |
202292138 |
17.97 % |
7494263 |
3.57 % |
| Filtered |
931081009 |
81.61 % |
923275787 |
82.03 % |
7805222 |
3.72 % |
| |
|
|
|
|
|
|
| q20 |
898154541 |
96.46 % |
895286889 |
96.97 % |
2867652 |
36.74 % |
| q20,qd2 |
15256792 |
1.64 % |
10559686 |
1.14 % |
4697106 |
60.18 % |
| q20,mq40 |
13225101 |
1.42 % |
13160446 |
1.43 % |
64655 |
0.83 % |
| q20,qd2,mq40 |
4071313 |
0.44 % |
4012578 |
0.43 % |
58735 |
0.75 % |
| mq40 |
336109 |
0.04 % |
225081 |
0.02 % |
111028 |
1.42 % |
| qd2 |
24344 |
0.00 % |
21324 |
0.00 % |
3020 |
0.04 % |
| qd2,mq40 |
12595 |
0.00 % |
9783 |
0.00 % |
2812 |
0.04 % |
| qd2,fs60,mq40 |
108 |
0.00 % |
0 |
0.00 % |
108 |
0.00 % |
| fs60,mq40 |
61 |
0.00 % |
0 |
0.00 % |
61 |
0.00 % |
| qd2,fs60 |
32 |
0.00 % |
0 |
0.00 % |
32 |
0.00 % |
| q20,qd2,fs60,mq40 |
8 |
0.00 % |
0 |
0.00 % |
8 |
0.00 % |
| fs60 |
5 |
0.00 % |
0 |
0.00 % |
5 |
0.00 % |
| q20,fs60 |
0 |
0.00 % |
0 |
0.00 % |
0 |
0.00 % |
| q20,qd2,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 |
4758746 |
27.81 % |
| Transition |
G>A |
All |
1074984 |
6.28 % |
| Transition |
T>C |
All |
4717182 |
27.57 % |
| Transition |
C>T |
All |
1080956 |
6.32 % |
| Transversion |
A>C |
All |
298580 |
1.75 % |
| Transversion |
C>A |
All |
1085857 |
6.35 % |
| Transversion |
T>G |
All |
304142 |
1.78 % |
| Transversion |
G>T |
All |
1066155 |
6.23 % |
| Transversion |
A>T |
All |
1051062 |
6.14 % |
| Transversion |
T>A |
All |
1052338 |
6.15 % |
| Transversion |
C>G |
All |
311416 |
1.82 % |
| Transversion |
G>C |
All |
307942 |
1.80 % |
| |
|
|
|
|
| Transition |
A>G |
Passed |
220143 |
14.94 % |
| Transition |
G>A |
Passed |
209346 |
14.21 % |
| Transition |
T>C |
Passed |
221378 |
15.03 % |
| Transition |
C>T |
Passed |
210058 |
14.26 % |
| Transversion |
A>C |
Passed |
76265 |
5.18 % |
| Transversion |
C>A |
Passed |
80747 |
5.48 % |
| Transversion |
T>G |
Passed |
76333 |
5.18 % |
| Transversion |
G>T |
Passed |
80560 |
5.47 % |
| Transversion |
A>T |
Passed |
70248 |
4.77 % |
| Transversion |
T>A |
Passed |
69634 |
4.73 % |
| Transversion |
C>G |
Passed |
79056 |
5.37 % |
| Transversion |
G>C |
Passed |
79497 |
5.40 % |
| |
|
|
|
|
| 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 |
2.12 |
11631868 |
5477492 |
| Passed |
1.41 |
860925 |
612340 |
| dbSNPAll |
0 |
0 |
0 |
| dbSNPPassed |
0 |
0 |
0 |