/EXTERNAL McGill EMC/variants/K006141_1_lane_gembs
BACK
SAMPLE K006141_1_lane_gembs
Variant counts
| Type |
Total |
Pass |
% |
| SNPs |
1146417677 |
719038767 |
62.72 % |
| Multiallelic |
0 |
0 |
0.00 % |
VCF Filtering Stats
| Type |
#Sites |
% |
#Non-Variant Sites |
% |
#Variant Sites |
% |
| All |
1146417677 |
100% |
1135673308 |
99.06 % |
10744369 |
0.94 % |
| |
|
|
|
|
|
|
| Passed |
720753293 |
62.87 % |
716901160 |
63.13 % |
3852133 |
0.53 % |
| Filtered |
425664384 |
37.13 % |
418772148 |
36.87 % |
6892236 |
0.96 % |
| |
|
|
|
|
|
|
| q20 |
394121356 |
92.59 % |
392723298 |
93.78 % |
1398058 |
20.28 % |
| q20,mq40 |
12621245 |
2.97 % |
12525239 |
2.99 % |
96006 |
1.39 % |
| q20,qd2 |
12407821 |
2.91 % |
7332860 |
1.75 % |
5074961 |
73.63 % |
| q20,qd2,mq40 |
3706687 |
0.87 % |
3610047 |
0.86 % |
96640 |
1.40 % |
| qd2 |
1464667 |
0.34 % |
1385995 |
0.33 % |
78672 |
1.14 % |
| mq40 |
1303309 |
0.31 % |
1163829 |
0.28 % |
139480 |
2.02 % |
| qd2,mq40 |
38152 |
0.01 % |
30880 |
0.01 % |
7272 |
0.11 % |
| qd2,fs60,mq40 |
545 |
0.00 % |
0 |
0.00 % |
545 |
0.01 % |
| fs60,mq40 |
225 |
0.00 % |
0 |
0.00 % |
225 |
0.00 % |
| fs60 |
155 |
0.00 % |
0 |
0.00 % |
155 |
0.00 % |
| qd2,fs60 |
150 |
0.00 % |
0 |
0.00 % |
150 |
0.00 % |
| q20,qd2,fs60,mq40 |
50 |
0.00 % |
0 |
0.00 % |
50 |
0.00 % |
| q20,qd2,fs60 |
22 |
0.00 % |
0 |
0.00 % |
22 |
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 |
3622317 |
29.09 % |
| Transition |
G>A |
All |
1210953 |
9.73 % |
| Transition |
T>C |
All |
3489509 |
28.03 % |
| Transition |
C>T |
All |
1218649 |
9.79 % |
| Transversion |
A>C |
All |
233073 |
1.87 % |
| Transversion |
C>A |
All |
613676 |
4.93 % |
| Transversion |
T>G |
All |
240554 |
1.93 % |
| Transversion |
G>T |
All |
599293 |
4.81 % |
| Transversion |
A>T |
All |
383275 |
3.08 % |
| Transversion |
T>A |
All |
379683 |
3.05 % |
| Transversion |
C>G |
All |
232718 |
1.87 % |
| Transversion |
G>C |
All |
227030 |
1.82 % |
| |
|
|
|
|
| Transition |
A>G |
Passed |
519500 |
17.48 % |
| Transition |
G>A |
Passed |
457248 |
15.39 % |
| Transition |
T>C |
Passed |
542719 |
18.26 % |
| Transition |
C>T |
Passed |
464286 |
15.62 % |
| Transversion |
A>C |
Passed |
123228 |
4.15 % |
| Transversion |
C>A |
Passed |
132762 |
4.47 % |
| Transversion |
T>G |
Passed |
122670 |
4.13 % |
| Transversion |
G>T |
Passed |
132570 |
4.46 % |
| Transversion |
A>T |
Passed |
116059 |
3.91 % |
| Transversion |
T>A |
Passed |
115433 |
3.88 % |
| Transversion |
C>G |
Passed |
122181 |
4.11 % |
| Transversion |
G>C |
Passed |
123127 |
4.14 % |
| |
|
|
|
|
| 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 |
3.28 |
9541428 |
2909302 |
| Passed |
2.01 |
1983753 |
988030 |
| dbSNPAll |
0 |
0 |
0 |
| dbSNPPassed |
0 |
0 |
0 |