/EXTERNAL BLUEPRINT/variants/K010534_K010535_2_lane_gembs
BACK
SAMPLE K010534_K010535_2_lane_gembs
Variant counts
| Type |
Total |
Pass |
% |
| SNPs |
1125744570 |
109443844 |
9.72 % |
| Multiallelic |
0 |
0 |
0.00 % |
VCF Filtering Stats
| Type |
#Sites |
% |
#Non-Variant Sites |
% |
#Variant Sites |
% |
| All |
1125744570 |
100% |
1113953862 |
98.95 % |
11790708 |
1.05 % |
| |
|
|
|
|
|
|
| Passed |
113794195 |
10.11 % |
108672248 |
9.76 % |
5121947 |
4.50 % |
| Filtered |
1011950375 |
89.89 % |
1005281614 |
90.24 % |
6668761 |
5.86 % |
| |
|
|
|
|
|
|
| q20 |
947470474 |
93.63 % |
944909974 |
93.99 % |
2560500 |
38.40 % |
| q20,qd2 |
42840511 |
4.23 % |
39005142 |
3.88 % |
3835369 |
57.51 % |
| q20,mq40 |
15916607 |
1.57 % |
15823284 |
1.57 % |
93323 |
1.40 % |
| q20,qd2,mq40 |
5380291 |
0.53 % |
5302811 |
0.53 % |
77480 |
1.16 % |
| mq40 |
303888 |
0.03 % |
207807 |
0.02 % |
96081 |
1.44 % |
| qd2 |
23678 |
0.00 % |
20615 |
0.00 % |
3063 |
0.05 % |
| qd2,mq40 |
14674 |
0.00 % |
11981 |
0.00 % |
2693 |
0.04 % |
| qd2,fs60,mq40 |
97 |
0.00 % |
0 |
0.00 % |
97 |
0.00 % |
| fs60,mq40 |
73 |
0.00 % |
0 |
0.00 % |
73 |
0.00 % |
| qd2,fs60 |
37 |
0.00 % |
0 |
0.00 % |
37 |
0.00 % |
| q20,qd2,fs60,mq40 |
23 |
0.00 % |
0 |
0.00 % |
23 |
0.00 % |
| fs60 |
19 |
0.00 % |
0 |
0.00 % |
19 |
0.00 % |
| q20,qd2,fs60 |
3 |
0.00 % |
0 |
0.00 % |
3 |
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 |
3254540 |
23.30 % |
| Transition |
G>A |
All |
895918 |
6.41 % |
| Transition |
T>C |
All |
3247344 |
23.25 % |
| Transition |
C>T |
All |
895611 |
6.41 % |
| Transversion |
A>C |
All |
279456 |
2.00 % |
| Transversion |
C>A |
All |
1367113 |
9.79 % |
| Transversion |
T>G |
All |
280251 |
2.01 % |
| Transversion |
G>T |
All |
1365057 |
9.77 % |
| Transversion |
A>T |
All |
954667 |
6.83 % |
| Transversion |
T>A |
All |
950191 |
6.80 % |
| Transversion |
C>G |
All |
242457 |
1.74 % |
| Transversion |
G>C |
All |
234828 |
1.68 % |
| |
|
|
|
|
| Transition |
A>G |
Passed |
127031 |
14.78 % |
| Transition |
G>A |
Passed |
127570 |
14.84 % |
| Transition |
T>C |
Passed |
128079 |
14.90 % |
| Transition |
C>T |
Passed |
127899 |
14.88 % |
| Transversion |
A>C |
Passed |
44018 |
5.12 % |
| Transversion |
C>A |
Passed |
45955 |
5.35 % |
| Transversion |
T>G |
Passed |
44135 |
5.13 % |
| Transversion |
G>T |
Passed |
45331 |
5.27 % |
| Transversion |
A>T |
Passed |
32840 |
3.82 % |
| Transversion |
T>A |
Passed |
32661 |
3.80 % |
| Transversion |
C>G |
Passed |
52141 |
6.07 % |
| Transversion |
G>C |
Passed |
51977 |
6.05 % |
| |
|
|
|
|
| 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 |
1.46 |
8293413 |
5674020 |
| Passed |
1.46 |
510579 |
349058 |
| dbSNPAll |
0 |
0 |
0 |
| dbSNPPassed |
0 |
0 |
0 |