/EXTERNAL BLUEPRINT/variants/K012034_K012109_29libs_29_lane_gembs
BACK
SAMPLE K012034_K012109_29libs_29_lane_gembs
Variant counts
| Type |
Total |
Pass |
% |
| SNPs |
1061827672 |
71769573 |
6.76 % |
| Multiallelic |
0 |
0 |
0.00 % |
VCF Filtering Stats
| Type |
#Sites |
% |
#Non-Variant Sites |
% |
#Variant Sites |
% |
| All |
1061827672 |
100% |
1024274052 |
96.46 % |
37553620 |
3.54 % |
| |
|
|
|
|
|
|
| Passed |
88825563 |
8.37 % |
69675243 |
6.80 % |
19150320 |
21.56 % |
| Filtered |
973002109 |
91.63 % |
954598809 |
93.20 % |
18403300 |
20.72 % |
| |
|
|
|
|
|
|
| q20 |
855204431 |
87.89 % |
844419382 |
88.46 % |
10785049 |
58.60 % |
| q20,mq40 |
57758983 |
5.94 % |
57212488 |
5.99 % |
546495 |
2.97 % |
| q20,qd2 |
47193487 |
4.85 % |
41193443 |
4.32 % |
6000044 |
32.60 % |
| q20,qd2,mq40 |
11164816 |
1.15 % |
10979960 |
1.15 % |
184856 |
1.00 % |
| mq40 |
1647089 |
0.17 % |
767753 |
0.08 % |
879336 |
4.78 % |
| qd2 |
28949 |
0.00 % |
22581 |
0.00 % |
6368 |
0.03 % |
| qd2,mq40 |
4256 |
0.00 % |
3202 |
0.00 % |
1054 |
0.01 % |
| fs60,mq40 |
31 |
0.00 % |
0 |
0.00 % |
31 |
0.00 % |
| qd2,fs60 |
24 |
0.00 % |
0 |
0.00 % |
24 |
0.00 % |
| fs60 |
22 |
0.00 % |
0 |
0.00 % |
22 |
0.00 % |
| qd2,fs60,mq40 |
17 |
0.00 % |
0 |
0.00 % |
17 |
0.00 % |
| q20,qd2,fs60 |
3 |
0.00 % |
0 |
0.00 % |
3 |
0.00 % |
| q20,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 % |
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 |
9288251 |
22.81 % |
| Transition |
G>A |
All |
3307511 |
8.12 % |
| Transition |
T>C |
All |
11935163 |
29.31 % |
| Transition |
C>T |
All |
1535169 |
3.77 % |
| Transversion |
A>C |
All |
1397148 |
3.43 % |
| Transversion |
C>A |
All |
2449158 |
6.02 % |
| Transversion |
T>G |
All |
1509914 |
3.71 % |
| Transversion |
G>T |
All |
2208272 |
5.42 % |
| Transversion |
A>T |
All |
1774161 |
4.36 % |
| Transversion |
T>A |
All |
2471942 |
6.07 % |
| Transversion |
C>G |
All |
1293662 |
3.18 % |
| Transversion |
G>C |
All |
1544370 |
3.79 % |
| |
|
|
|
|
| Transition |
A>G |
Passed |
374149 |
17.76 % |
| Transition |
G>A |
Passed |
245101 |
11.64 % |
| Transition |
T>C |
Passed |
683724 |
32.46 % |
| Transition |
C>T |
Passed |
125987 |
5.98 % |
| Transversion |
A>C |
Passed |
87969 |
4.18 % |
| Transversion |
C>A |
Passed |
88687 |
4.21 % |
| Transversion |
T>G |
Passed |
84461 |
4.01 % |
| Transversion |
G>T |
Passed |
63197 |
3.00 % |
| Transversion |
A>T |
Passed |
50596 |
2.40 % |
| Transversion |
T>A |
Passed |
107310 |
5.10 % |
| Transversion |
C>G |
Passed |
83458 |
3.96 % |
| Transversion |
G>C |
Passed |
111522 |
5.30 % |
| |
|
|
|
|
| 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 |
1.78 |
26066094 |
14648627 |
| Passed |
2.11 |
1428961 |
677200 |
| dbSNPAll |
0 |
0 |
0 |
| dbSNPPassed |
0 |
0 |
0 |