/EXTERNAL BLUEPRINT/variants/K006295_K006299_22_lane_gembs
BACK
SAMPLE K006295_K006299_22_lane_gembs
Variant counts
| Type |
Total |
Pass |
% |
| SNPs |
1075730172 |
543918797 |
50.56 % |
| Multiallelic |
0 |
0 |
0.00 % |
VCF Filtering Stats
| Type |
#Sites |
% |
#Non-Variant Sites |
% |
#Variant Sites |
% |
| All |
1075730172 |
100% |
1055151741 |
98.09 % |
20578431 |
1.91 % |
| |
|
|
|
|
|
|
| Passed |
545434470 |
50.70 % |
542878692 |
51.45 % |
2555778 |
0.47 % |
| Filtered |
530295702 |
49.30 % |
512273049 |
48.55 % |
18022653 |
3.30 % |
| |
|
|
|
|
|
|
| q20 |
404165278 |
76.22 % |
401723877 |
78.42 % |
2441401 |
13.55 % |
| q20,qd2 |
65830172 |
12.41 % |
50913376 |
9.94 % |
14916796 |
82.77 % |
| qd2 |
34244128 |
6.46 % |
34105615 |
6.66 % |
138513 |
0.77 % |
| q20,mq40 |
14364236 |
2.71 % |
14250985 |
2.78 % |
113251 |
0.63 % |
| mq40 |
7975002 |
1.50 % |
7803998 |
1.52 % |
171004 |
0.95 % |
| q20,qd2,mq40 |
3557053 |
0.67 % |
3353735 |
0.65 % |
203318 |
1.13 % |
| qd2,mq40 |
137542 |
0.03 % |
121463 |
0.02 % |
16079 |
0.09 % |
| q20,qd2,fs60 |
7969 |
0.00 % |
0 |
0.00 % |
7969 |
0.04 % |
| qd2,fs60 |
5346 |
0.00 % |
0 |
0.00 % |
5346 |
0.03 % |
| fs60 |
3745 |
0.00 % |
0 |
0.00 % |
3745 |
0.02 % |
| qd2,fs60,mq40 |
3160 |
0.00 % |
0 |
0.00 % |
3160 |
0.02 % |
| q20,qd2,fs60,mq40 |
1087 |
0.00 % |
0 |
0.00 % |
1087 |
0.01 % |
| fs60,mq40 |
972 |
0.00 % |
0 |
0.00 % |
972 |
0.01 % |
| q20,fs60 |
8 |
0.00 % |
0 |
0.00 % |
8 |
0.00 % |
| q20,fs60,mq40 |
4 |
0.00 % |
0 |
0.00 % |
4 |
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 |
2990263 |
6.80 % |
| Transition |
G>A |
All |
17793862 |
40.48 % |
| Transition |
T>C |
All |
2692839 |
6.13 % |
| Transition |
C>T |
All |
17650487 |
40.16 % |
| Transversion |
A>C |
All |
222696 |
0.51 % |
| Transversion |
C>A |
All |
535948 |
1.22 % |
| Transversion |
T>G |
All |
255803 |
0.58 % |
| Transversion |
G>T |
All |
522948 |
1.19 % |
| Transversion |
A>T |
All |
440981 |
1.00 % |
| Transversion |
T>A |
All |
441868 |
1.01 % |
| Transversion |
C>G |
All |
212518 |
0.48 % |
| Transversion |
G>C |
All |
192855 |
0.44 % |
| |
|
|
|
|
| Transition |
A>G |
Passed |
302638 |
19.22 % |
| Transition |
G>A |
Passed |
274870 |
17.46 % |
| Transition |
T>C |
Passed |
300742 |
19.10 % |
| Transition |
C>T |
Passed |
273278 |
17.36 % |
| Transversion |
A>C |
Passed |
56236 |
3.57 % |
| Transversion |
C>A |
Passed |
50418 |
3.20 % |
| Transversion |
T>G |
Passed |
56083 |
3.56 % |
| Transversion |
G>T |
Passed |
50338 |
3.20 % |
| Transversion |
A>T |
Passed |
33325 |
2.12 % |
| Transversion |
T>A |
Passed |
32927 |
2.09 % |
| Transversion |
C>G |
Passed |
71602 |
4.55 % |
| Transversion |
G>C |
Passed |
71779 |
4.56 % |
| |
|
|
|
|
| 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 |
14.56 |
41127451 |
2825617 |
| Passed |
2.72 |
1151528 |
422708 |
| dbSNPAll |
0 |
0 |
0 |
| dbSNPPassed |
0 |
0 |
0 |