/EXTERNAL BLUEPRINT/variants/K006371_8_lane_gembs
BACK
SAMPLE K006371_8_lane_gembs
Variant counts
| Type |
Total |
Pass |
% |
| SNPs |
1150364542 |
1059704028 |
92.12 % |
| Multiallelic |
0 |
0 |
0.00 % |
VCF Filtering Stats
| Type |
#Sites |
% |
#Non-Variant Sites |
% |
#Variant Sites |
% |
| All |
1150364542 |
100% |
1139782603 |
99.08 % |
10581939 |
0.92 % |
| |
|
|
|
|
|
|
| Passed |
1060339545 |
92.17 % |
1057153881 |
92.75 % |
3185664 |
0.30 % |
| Filtered |
90024997 |
7.83 % |
82628722 |
7.25 % |
7396275 |
0.70 % |
| |
|
|
|
|
|
|
| q20 |
59077411 |
65.62 % |
58520017 |
70.82 % |
557394 |
7.54 % |
| q20,mq40 |
12171343 |
13.52 % |
12072245 |
14.61 % |
99098 |
1.34 % |
| q20,qd2 |
10157515 |
11.28 % |
3912090 |
4.73 % |
6245425 |
84.44 % |
| mq40 |
3675149 |
4.08 % |
3484707 |
4.22 % |
190442 |
2.57 % |
| q20,qd2,mq40 |
3014799 |
3.35 % |
2858471 |
3.46 % |
156328 |
2.11 % |
| qd2 |
1882981 |
2.09 % |
1745083 |
2.11 % |
137898 |
1.86 % |
| qd2,mq40 |
44559 |
0.05 % |
36109 |
0.04 % |
8450 |
0.11 % |
| qd2,fs60,mq40 |
616 |
0.00 % |
0 |
0.00 % |
616 |
0.01 % |
| fs60,mq40 |
282 |
0.00 % |
0 |
0.00 % |
282 |
0.00 % |
| qd2,fs60 |
151 |
0.00 % |
0 |
0.00 % |
151 |
0.00 % |
| fs60 |
102 |
0.00 % |
0 |
0.00 % |
102 |
0.00 % |
| q20,qd2,fs60,mq40 |
64 |
0.00 % |
0 |
0.00 % |
64 |
0.00 % |
| q20,qd2,fs60 |
23 |
0.00 % |
0 |
0.00 % |
23 |
0.00 % |
| q20,fs60,mq40 |
2 |
0.00 % |
0 |
0.00 % |
2 |
0.00 % |
| q20,fs60 |
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 |
3845824 |
31.52 % |
| Transition |
G>A |
All |
962674 |
7.89 % |
| Transition |
T>C |
All |
3779168 |
30.97 % |
| Transition |
C>T |
All |
977492 |
8.01 % |
| Transversion |
A>C |
All |
218528 |
1.79 % |
| Transversion |
C>A |
All |
490734 |
4.02 % |
| Transversion |
T>G |
All |
219624 |
1.80 % |
| Transversion |
G>T |
All |
484847 |
3.97 % |
| Transversion |
A>T |
All |
411160 |
3.37 % |
| Transversion |
T>A |
All |
403908 |
3.31 % |
| Transversion |
C>G |
All |
204456 |
1.68 % |
| Transversion |
G>C |
All |
204264 |
1.67 % |
| |
|
|
|
|
| Transition |
A>G |
Passed |
635417 |
16.97 % |
| Transition |
G>A |
Passed |
619670 |
16.55 % |
| Transition |
T>C |
Passed |
638318 |
17.05 % |
| Transition |
C>T |
Passed |
623909 |
16.67 % |
| Transversion |
A>C |
Passed |
155706 |
4.16 % |
| Transversion |
C>A |
Passed |
162660 |
4.34 % |
| Transversion |
T>G |
Passed |
156015 |
4.17 % |
| Transversion |
G>T |
Passed |
163463 |
4.37 % |
| Transversion |
A>T |
Passed |
139442 |
3.72 % |
| Transversion |
T>A |
Passed |
139222 |
3.72 % |
| Transversion |
C>G |
Passed |
154810 |
4.14 % |
| Transversion |
G>C |
Passed |
155087 |
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 |
3.63 |
9565158 |
2637521 |
| Passed |
2.05 |
2517314 |
1226405 |
| dbSNPAll |
0 |
0 |
0 |
| dbSNPPassed |
0 |
0 |
0 |