/EXTERNAL Roadmap/variants/K012809_1_lane_gembs
BACK
SAMPLE K012809_1_lane_gembs
Variant counts
| Type |
Total |
Pass |
% |
| SNPs |
1162382003 |
791909425 |
68.13 % |
| Multiallelic |
0 |
0 |
0.00 % |
VCF Filtering Stats
| Type |
#Sites |
% |
#Non-Variant Sites |
% |
#Variant Sites |
% |
| All |
1162382003 |
100% |
1140744187 |
98.14 % |
21637816 |
1.86 % |
| |
|
|
|
|
|
|
| Passed |
795075844 |
68.40 % |
789426592 |
69.20 % |
5649252 |
0.71 % |
| Filtered |
367306159 |
31.60 % |
351317595 |
30.80 % |
15988564 |
2.01 % |
| |
|
|
|
|
|
|
| q20 |
319552000 |
87.00 % |
316642534 |
90.13 % |
2909466 |
18.20 % |
| q20,qd2 |
20617561 |
5.61 % |
8343537 |
2.37 % |
12274024 |
76.77 % |
| q20,mq40 |
16860203 |
4.59 % |
16713566 |
4.76 % |
146637 |
0.92 % |
| q20,qd2,mq40 |
3642410 |
0.99 % |
3445507 |
0.98 % |
196903 |
1.23 % |
| qd2 |
3442363 |
0.94 % |
3240602 |
0.92 % |
201761 |
1.26 % |
| mq40 |
3147580 |
0.86 % |
2896682 |
0.82 % |
250898 |
1.57 % |
| qd2,mq40 |
43023 |
0.01 % |
35167 |
0.01 % |
7856 |
0.05 % |
| qd2,fs60,mq40 |
531 |
0.00 % |
0 |
0.00 % |
531 |
0.00 % |
| fs60,mq40 |
222 |
0.00 % |
0 |
0.00 % |
222 |
0.00 % |
| qd2,fs60 |
151 |
0.00 % |
0 |
0.00 % |
151 |
0.00 % |
| fs60 |
59 |
0.00 % |
0 |
0.00 % |
59 |
0.00 % |
| q20,qd2,fs60,mq40 |
46 |
0.00 % |
0 |
0.00 % |
46 |
0.00 % |
| q20,qd2,fs60 |
9 |
0.00 % |
0 |
0.00 % |
9 |
0.00 % |
| q20,fs60 |
1 |
0.00 % |
0 |
0.00 % |
1 |
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 |
8911235 |
38.37 % |
| Transition |
G>A |
All |
1620126 |
6.98 % |
| Transition |
T>C |
All |
6537700 |
28.15 % |
| Transition |
C>T |
All |
1759046 |
7.57 % |
| Transversion |
A>C |
All |
279026 |
1.20 % |
| Transversion |
C>A |
All |
902550 |
3.89 % |
| Transversion |
T>G |
All |
377307 |
1.62 % |
| Transversion |
G>T |
All |
818293 |
3.52 % |
| Transversion |
A>T |
All |
639240 |
2.75 % |
| Transversion |
T>A |
All |
706338 |
3.04 % |
| Transversion |
C>G |
All |
383953 |
1.65 % |
| Transversion |
G>C |
All |
291894 |
1.26 % |
| |
|
|
|
|
| Transition |
A>G |
Passed |
663734 |
20.51 % |
| Transition |
G>A |
Passed |
485392 |
15.00 % |
| Transition |
T>C |
Passed |
549867 |
16.99 % |
| Transition |
C>T |
Passed |
495148 |
15.30 % |
| Transversion |
A>C |
Passed |
128266 |
3.96 % |
| Transversion |
C>A |
Passed |
137228 |
4.24 % |
| Transversion |
T>G |
Passed |
131245 |
4.06 % |
| Transversion |
G>T |
Passed |
137223 |
4.24 % |
| Transversion |
A>T |
Passed |
123814 |
3.83 % |
| Transversion |
T>A |
Passed |
123822 |
3.83 % |
| Transversion |
C>G |
Passed |
130926 |
4.05 % |
| Transversion |
G>C |
Passed |
129075 |
3.99 % |
| |
|
|
|
|
| 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 |
4.28 |
18828107 |
4398601 |
| Passed |
2.11 |
2194141 |
1041599 |
| dbSNPAll |
0 |
0 |
0 |
| dbSNPPassed |
0 |
0 |
0 |