/EXTERNAL BLUEPRINT/variants/K006386_K006399_19_lane_gembs
BACK
SAMPLE K006386_K006399_19_lane_gembs
Variant counts
| Type |
Total |
Pass |
% |
| SNPs |
1158584947 |
996789884 |
86.04 % |
| Multiallelic |
0 |
0 |
0.00 % |
VCF Filtering Stats
| Type |
#Sites |
% |
#Non-Variant Sites |
% |
#Variant Sites |
% |
| All |
1158584947 |
100% |
1146189447 |
98.93 % |
12395500 |
1.07 % |
| |
|
|
|
|
|
|
| Passed |
998238449 |
86.16 % |
994447421 |
86.76 % |
3791028 |
0.38 % |
| Filtered |
160346498 |
13.84 % |
151742026 |
13.24 % |
8604472 |
0.86 % |
| |
|
|
|
|
|
|
| q20 |
112097353 |
69.91 % |
111038728 |
73.18 % |
1058625 |
12.30 % |
| qd2 |
16255210 |
10.14 % |
16093432 |
10.61 % |
161778 |
1.88 % |
| q20,mq40 |
11554153 |
7.21 % |
11459111 |
7.55 % |
95042 |
1.10 % |
| q20,qd2 |
10415067 |
6.50 % |
3524961 |
2.32 % |
6890106 |
80.08 % |
| mq40 |
7176608 |
4.48 % |
6979362 |
4.60 % |
197246 |
2.29 % |
| q20,qd2,mq40 |
2715051 |
1.69 % |
2546030 |
1.68 % |
169021 |
1.96 % |
| qd2,mq40 |
116310 |
0.07 % |
100402 |
0.07 % |
15908 |
0.18 % |
| qd2,fs60 |
5471 |
0.00 % |
0 |
0.00 % |
5471 |
0.06 % |
| fs60 |
4058 |
0.00 % |
0 |
0.00 % |
4058 |
0.05 % |
| qd2,fs60,mq40 |
3010 |
0.00 % |
0 |
0.00 % |
3010 |
0.03 % |
| q20,qd2,fs60 |
2820 |
0.00 % |
0 |
0.00 % |
2820 |
0.03 % |
| fs60,mq40 |
937 |
0.00 % |
0 |
0.00 % |
937 |
0.01 % |
| q20,qd2,fs60,mq40 |
447 |
0.00 % |
0 |
0.00 % |
447 |
0.01 % |
| 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 |
4782964 |
33.65 % |
| Transition |
G>A |
All |
1108752 |
7.80 % |
| Transition |
T>C |
All |
4730983 |
33.29 % |
| Transition |
C>T |
All |
1112118 |
7.83 % |
| Transversion |
A>C |
All |
214259 |
1.51 % |
| Transversion |
C>A |
All |
448978 |
3.16 % |
| Transversion |
T>G |
All |
219005 |
1.54 % |
| Transversion |
G>T |
All |
440288 |
3.10 % |
| Transversion |
A>T |
All |
376422 |
2.65 % |
| Transversion |
T>A |
All |
375262 |
2.64 % |
| Transversion |
C>G |
All |
201989 |
1.42 % |
| Transversion |
G>C |
All |
200932 |
1.41 % |
| |
|
|
|
|
| Transition |
A>G |
Passed |
600835 |
17.49 % |
| Transition |
G>A |
Passed |
556036 |
16.19 % |
| Transition |
T>C |
Passed |
601167 |
17.50 % |
| Transition |
C>T |
Passed |
558347 |
16.25 % |
| Transversion |
A>C |
Passed |
145570 |
4.24 % |
| Transversion |
C>A |
Passed |
144040 |
4.19 % |
| Transversion |
T>G |
Passed |
146689 |
4.27 % |
| Transversion |
G>T |
Passed |
144369 |
4.20 % |
| Transversion |
A>T |
Passed |
123777 |
3.60 % |
| Transversion |
T>A |
Passed |
123341 |
3.59 % |
| Transversion |
C>G |
Passed |
145225 |
4.23 % |
| Transversion |
G>C |
Passed |
145540 |
4.24 % |
| |
|
|
|
|
| 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 |
4.74 |
11734817 |
2477135 |
| Passed |
2.07 |
2316385 |
1118551 |
| dbSNPAll |
0 |
0 |
0 |
| dbSNPPassed |
0 |
0 |
0 |