/EXTERNAL BLUEPRINT/variants/K011974_K011975_K011998_K011999_4_lane_gembs
BACK
SAMPLE K011974_K011975_K011998_K011999_4_lane_gembs
Variant counts
| Type |
Total |
Pass |
% |
| SNPs |
478074245 |
41390 |
0.01 % |
| Multiallelic |
0 |
0 |
0.00 % |
VCF Filtering Stats
| Type |
#Sites |
% |
#Non-Variant Sites |
% |
#Variant Sites |
% |
| All |
478074245 |
100% |
475160509 |
99.39 % |
2913736 |
0.61 % |
| |
|
|
|
|
|
|
| Passed |
1563466 |
0.33 % |
20644 |
0.00 % |
1542822 |
98.68 % |
| Filtered |
476510779 |
99.67 % |
475139865 |
100.00 % |
1370914 |
87.68 % |
| |
|
|
|
|
|
|
| q20 |
295256323 |
61.96 % |
294195414 |
61.92 % |
1060909 |
77.39 % |
| q20,qd2 |
136575169 |
28.66 % |
136444399 |
28.72 % |
130770 |
9.54 % |
| q20,mq40 |
27648401 |
5.80 % |
27574622 |
5.80 % |
73779 |
5.38 % |
| q20,qd2,mq40 |
16928058 |
3.55 % |
16916551 |
3.56 % |
11507 |
0.84 % |
| mq40 |
100122 |
0.02 % |
6276 |
0.00 % |
93846 |
6.85 % |
| qd2 |
2474 |
0.00 % |
2433 |
0.00 % |
41 |
0.00 % |
| qd2,mq40 |
223 |
0.00 % |
170 |
0.00 % |
53 |
0.00 % |
| fs60 |
5 |
0.00 % |
0 |
0.00 % |
5 |
0.00 % |
| qd2,fs60 |
2 |
0.00 % |
0 |
0.00 % |
2 |
0.00 % |
| fs60,mq40 |
2 |
0.00 % |
0 |
0.00 % |
2 |
0.00 % |
| q20,fs60 |
0 |
0.00 % |
0 |
0.00 % |
0 |
0.00 % |
| q20,qd2,fs60 |
0 |
0.00 % |
0 |
0.00 % |
0 |
0.00 % |
| q20,fs60,mq40 |
0 |
0.00 % |
0 |
0.00 % |
0 |
0.00 % |
| qd2,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 |
1526488 |
21.97 % |
| Transition |
G>A |
All |
560663 |
8.07 % |
| Transition |
T>C |
All |
1997210 |
28.74 % |
| Transition |
C>T |
All |
278549 |
4.01 % |
| Transversion |
A>C |
All |
230063 |
3.31 % |
| Transversion |
C>A |
All |
425465 |
6.12 % |
| Transversion |
T>G |
All |
287523 |
4.14 % |
| Transversion |
G>T |
All |
390462 |
5.62 % |
| Transversion |
A>T |
All |
329199 |
4.74 % |
| Transversion |
T>A |
All |
450576 |
6.48 % |
| Transversion |
C>G |
All |
217430 |
3.13 % |
| Transversion |
G>C |
All |
255509 |
3.68 % |
| |
|
|
|
|
| Transition |
A>G |
Passed |
3078 |
15.06 % |
| Transition |
G>A |
Passed |
2775 |
13.58 % |
| Transition |
T>C |
Passed |
4698 |
22.99 % |
| Transition |
C>T |
Passed |
1191 |
5.83 % |
| Transversion |
A>C |
Passed |
898 |
4.40 % |
| Transversion |
C>A |
Passed |
1434 |
7.02 % |
| Transversion |
T>G |
Passed |
1020 |
4.99 % |
| Transversion |
G>T |
Passed |
885 |
4.33 % |
| Transversion |
A>T |
Passed |
539 |
2.64 % |
| Transversion |
T>A |
Passed |
1313 |
6.43 % |
| Transversion |
C>G |
Passed |
1103 |
5.40 % |
| Transversion |
G>C |
Passed |
1498 |
7.33 % |
| |
|
|
|
|
| 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 |
1.69 |
4362910 |
2586227 |
| Passed |
1.35 |
11742 |
8690 |
| dbSNPAll |
0 |
0 |
0 |
| dbSNPPassed |
0 |
0 |
0 |