/EXTERNAL BLUEPRINT/variants/K011716_1_lane_gembs
BACK
SAMPLE K011716_1_lane_gembs
Variant counts
| Type |
Total |
Pass |
% |
| SNPs |
1066649274 |
522305466 |
48.97 % |
| Multiallelic |
0 |
0 |
0.00 % |
VCF Filtering Stats
| Type |
#Sites |
% |
#Non-Variant Sites |
% |
#Variant Sites |
% |
| All |
1066649274 |
100% |
1049166260 |
98.36 % |
17483014 |
1.64 % |
| |
|
|
|
|
|
|
| Passed |
523998838 |
49.13 % |
521261442 |
49.68 % |
2737396 |
0.52 % |
| Filtered |
542650436 |
50.87 % |
527904818 |
50.32 % |
14745618 |
2.81 % |
| |
|
|
|
|
|
|
| q20 |
447543098 |
82.47 % |
445818414 |
84.45 % |
1724684 |
11.70 % |
| q20,qd2 |
65131871 |
12.00 % |
52652916 |
9.97 % |
12478955 |
84.63 % |
| q20,mq40 |
16024845 |
2.95 % |
15922554 |
3.02 % |
102291 |
0.69 % |
| mq40 |
6763448 |
1.25 % |
6607307 |
1.25 % |
156141 |
1.06 % |
| q20,qd2,mq40 |
3623536 |
0.67 % |
3442191 |
0.65 % |
181345 |
1.23 % |
| qd2 |
3467387 |
0.64 % |
3386910 |
0.64 % |
80477 |
0.55 % |
| qd2,mq40 |
86576 |
0.02 % |
74526 |
0.01 % |
12050 |
0.08 % |
| q20,qd2,fs60 |
2898 |
0.00 % |
0 |
0.00 % |
2898 |
0.02 % |
| qd2,fs60 |
2019 |
0.00 % |
0 |
0.00 % |
2019 |
0.01 % |
| fs60 |
1809 |
0.00 % |
0 |
0.00 % |
1809 |
0.01 % |
| qd2,fs60,mq40 |
1614 |
0.00 % |
0 |
0.00 % |
1614 |
0.01 % |
| q20,qd2,fs60,mq40 |
774 |
0.00 % |
0 |
0.00 % |
774 |
0.01 % |
| fs60,mq40 |
558 |
0.00 % |
0 |
0.00 % |
558 |
0.00 % |
| q20,fs60 |
2 |
0.00 % |
0 |
0.00 % |
2 |
0.00 % |
| q20,fs60,mq40 |
1 |
0.00 % |
0 |
0.00 % |
1 |
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 |
3046299 |
12.02 % |
| Transition |
G>A |
All |
8527831 |
33.66 % |
| Transition |
T>C |
All |
2722488 |
10.75 % |
| Transition |
C>T |
All |
8289930 |
32.72 % |
| Transversion |
A>C |
All |
205695 |
0.81 % |
| Transversion |
C>A |
All |
544502 |
2.15 % |
| Transversion |
T>G |
All |
231765 |
0.91 % |
| Transversion |
G>T |
All |
527934 |
2.08 % |
| Transversion |
A>T |
All |
423471 |
1.67 % |
| Transversion |
T>A |
All |
439831 |
1.74 % |
| Transversion |
C>G |
All |
194270 |
0.77 % |
| Transversion |
G>C |
All |
181318 |
0.72 % |
| |
|
|
|
|
| Transition |
A>G |
Passed |
306493 |
19.67 % |
| Transition |
G>A |
Passed |
266736 |
17.12 % |
| Transition |
T>C |
Passed |
305656 |
19.62 % |
| Transition |
C>T |
Passed |
265964 |
17.07 % |
| Transversion |
A>C |
Passed |
55443 |
3.56 % |
| Transversion |
C>A |
Passed |
48776 |
3.13 % |
| Transversion |
T>G |
Passed |
55116 |
3.54 % |
| Transversion |
G>T |
Passed |
48613 |
3.12 % |
| Transversion |
A>T |
Passed |
31326 |
2.01 % |
| Transversion |
T>A |
Passed |
31075 |
1.99 % |
| Transversion |
C>G |
Passed |
71270 |
4.57 % |
| Transversion |
G>C |
Passed |
71477 |
4.59 % |
| |
|
|
|
|
| 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 |
8.22 |
22586548 |
2748786 |
| Passed |
2.77 |
1144849 |
413096 |
| dbSNPAll |
0 |
0 |
0 |
| dbSNPPassed |
0 |
0 |
0 |