/EXTERNAL BLUEPRINT/variants/K011856_K011920_28libs_28_lane_gembs
BACK
SAMPLE K011856_K011920_28libs_28_lane_gembs
Variant counts
| Type |
Total |
Pass |
% |
| SNPs |
1067927598 |
96067396 |
9.00 % |
| Multiallelic |
0 |
0 |
0.00 % |
VCF Filtering Stats
| Type |
#Sites |
% |
#Non-Variant Sites |
% |
#Variant Sites |
% |
| All |
1067927598 |
100% |
1028429339 |
96.30 % |
39498259 |
3.70 % |
| |
|
|
|
|
|
|
| Passed |
113611633 |
10.64 % |
93709894 |
9.11 % |
19901739 |
17.52 % |
| Filtered |
954315965 |
89.36 % |
934719445 |
90.89 % |
19596520 |
17.25 % |
| |
|
|
|
|
|
|
| q20 |
849738592 |
89.04 % |
838735476 |
89.73 % |
11003116 |
56.15 % |
| q20,mq40 |
60075271 |
6.30 % |
59517140 |
6.37 % |
558131 |
2.85 % |
| q20,qd2 |
34048024 |
3.57 % |
27120735 |
2.90 % |
6927289 |
35.35 % |
| q20,qd2,mq40 |
8498985 |
0.89 % |
8304619 |
0.89 % |
194366 |
0.99 % |
| mq40 |
1899194 |
0.20 % |
998056 |
0.11 % |
901138 |
4.60 % |
| qd2 |
50654 |
0.01 % |
39536 |
0.00 % |
11118 |
0.06 % |
| qd2,mq40 |
5138 |
0.00 % |
3883 |
0.00 % |
1255 |
0.01 % |
| fs60,mq40 |
46 |
0.00 % |
0 |
0.00 % |
46 |
0.00 % |
| qd2,fs60 |
26 |
0.00 % |
0 |
0.00 % |
26 |
0.00 % |
| fs60 |
18 |
0.00 % |
0 |
0.00 % |
18 |
0.00 % |
| qd2,fs60,mq40 |
13 |
0.00 % |
0 |
0.00 % |
13 |
0.00 % |
| q20,qd2,fs60 |
2 |
0.00 % |
0 |
0.00 % |
2 |
0.00 % |
| q20,qd2,fs60,mq40 |
2 |
0.00 % |
0 |
0.00 % |
2 |
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 % |
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 |
9322440 |
21.86 % |
| Transition |
G>A |
All |
3266842 |
7.66 % |
| Transition |
T>C |
All |
12166436 |
28.53 % |
| Transition |
C>T |
All |
1549370 |
3.63 % |
| Transversion |
A>C |
All |
1569817 |
3.68 % |
| Transversion |
C>A |
All |
2836371 |
6.65 % |
| Transversion |
T>G |
All |
1639215 |
3.84 % |
| Transversion |
G>T |
All |
2582651 |
6.06 % |
| Transversion |
A>T |
All |
1843467 |
4.32 % |
| Transversion |
T>A |
All |
2600448 |
6.10 % |
| Transversion |
C>G |
All |
1507801 |
3.54 % |
| Transversion |
G>C |
All |
1764275 |
4.14 % |
| |
|
|
|
|
| Transition |
A>G |
Passed |
420122 |
17.70 % |
| Transition |
G>A |
Passed |
262280 |
11.05 % |
| Transition |
T>C |
Passed |
769434 |
32.42 % |
| Transition |
C>T |
Passed |
135806 |
5.72 % |
| Transversion |
A>C |
Passed |
105533 |
4.45 % |
| Transversion |
C>A |
Passed |
98243 |
4.14 % |
| Transversion |
T>G |
Passed |
95043 |
4.00 % |
| Transversion |
G>T |
Passed |
71575 |
3.02 % |
| Transversion |
A>T |
Passed |
61628 |
2.60 % |
| Transversion |
T>A |
Passed |
125494 |
5.29 % |
| Transversion |
C>G |
Passed |
99443 |
4.19 % |
| Transversion |
G>C |
Passed |
128589 |
5.42 % |
| |
|
|
|
|
| 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 |
1.61 |
26305088 |
16344045 |
| Passed |
2.02 |
1587642 |
785548 |
| dbSNPAll |
0 |
0 |
0 |
| dbSNPPassed |
0 |
0 |
0 |