/EXTERNAL BLUEPRINT/variants/K011724_1_lane_gembs
BACK
SAMPLE K011724_1_lane_gembs
Variant counts
| Type |
Total |
Pass |
% |
| SNPs |
687245948 |
441260 |
0.06 % |
| Multiallelic |
0 |
0 |
0.00 % |
VCF Filtering Stats
| Type |
#Sites |
% |
#Non-Variant Sites |
% |
#Variant Sites |
% |
| All |
687245948 |
100% |
678275529 |
98.69 % |
8970419 |
1.31 % |
| |
|
|
|
|
|
|
| Passed |
4486668 |
0.65 % |
347082 |
0.05 % |
4139586 |
92.26 % |
| Filtered |
682759280 |
99.35 % |
677928447 |
99.95 % |
4830833 |
107.67 % |
| |
|
|
|
|
|
|
| q20 |
446985025 |
65.47 % |
443070292 |
65.36 % |
3914733 |
81.04 % |
| q20,qd2 |
170867734 |
25.03 % |
170492587 |
25.15 % |
375147 |
7.77 % |
| q20,mq40 |
41181537 |
6.03 % |
40915423 |
6.04 % |
266114 |
5.51 % |
| q20,qd2,mq40 |
23451399 |
3.43 % |
23422232 |
3.45 % |
29167 |
0.60 % |
| mq40 |
268716 |
0.04 % |
23209 |
0.00 % |
245507 |
5.08 % |
| qd2 |
4307 |
0.00 % |
4266 |
0.00 % |
41 |
0.00 % |
| qd2,mq40 |
537 |
0.00 % |
438 |
0.00 % |
99 |
0.00 % |
| qd2,fs60 |
15 |
0.00 % |
0 |
0.00 % |
15 |
0.00 % |
| fs60 |
6 |
0.00 % |
0 |
0.00 % |
6 |
0.00 % |
| fs60,mq40 |
2 |
0.00 % |
0 |
0.00 % |
2 |
0.00 % |
| q20,qd2,fs60 |
1 |
0.00 % |
0 |
0.00 % |
1 |
0.00 % |
| qd2,fs60,mq40 |
1 |
0.00 % |
0 |
0.00 % |
1 |
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 % |
| q20,qd2,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 |
3295719 |
23.71 % |
| Transition |
G>A |
All |
988279 |
7.11 % |
| Transition |
T>C |
All |
4160252 |
29.93 % |
| Transition |
C>T |
All |
474253 |
3.41 % |
| Transversion |
A>C |
All |
675831 |
4.86 % |
| Transversion |
C>A |
All |
657333 |
4.73 % |
| Transversion |
T>G |
All |
811385 |
5.84 % |
| Transversion |
G>T |
All |
590852 |
4.25 % |
| Transversion |
A>T |
All |
491205 |
3.53 % |
| Transversion |
T>A |
All |
683015 |
4.91 % |
| Transversion |
C>G |
All |
508394 |
3.66 % |
| Transversion |
G>C |
All |
561506 |
4.04 % |
| |
|
|
|
|
| Transition |
A>G |
Passed |
13826 |
14.99 % |
| Transition |
G>A |
Passed |
13666 |
14.82 % |
| Transition |
T>C |
Passed |
25091 |
27.20 % |
| Transition |
C>T |
Passed |
6107 |
6.62 % |
| Transversion |
A>C |
Passed |
4229 |
4.58 % |
| Transversion |
C>A |
Passed |
4906 |
5.32 % |
| Transversion |
T>G |
Passed |
4234 |
4.59 % |
| Transversion |
G>T |
Passed |
3034 |
3.29 % |
| Transversion |
A>T |
Passed |
1988 |
2.16 % |
| Transversion |
T>A |
Passed |
4544 |
4.93 % |
| Transversion |
C>G |
Passed |
4320 |
4.68 % |
| Transversion |
G>C |
Passed |
6296 |
6.83 % |
| |
|
|
|
|
| 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 |
1.79 |
8918503 |
4979521 |
| Passed |
1.75 |
58690 |
33551 |
| dbSNPAll |
0 |
0 |
0 |
| dbSNPPassed |
0 |
0 |
0 |