/EXTERNAL BLUEPRINT/variants/K010532_1_lane_gembs
BACK
SAMPLE K010532_1_lane_gembs
Variant counts
| Type |
Total |
Pass |
% |
| SNPs |
1091131547 |
6582072 |
0.60 % |
| Multiallelic |
0 |
0 |
0.00 % |
VCF Filtering Stats
| Type |
#Sites |
% |
#Non-Variant Sites |
% |
#Variant Sites |
% |
| All |
1091131547 |
100% |
1080684456 |
99.04 % |
10447091 |
0.96 % |
| |
|
|
|
|
|
|
| Passed |
10407178 |
0.95 % |
6265621 |
0.58 % |
4141557 |
39.80 % |
| Filtered |
1080724369 |
99.05 % |
1074418835 |
99.42 % |
6305534 |
60.59 % |
| |
|
|
|
|
|
|
| q20 |
954513289 |
88.32 % |
951527802 |
88.56 % |
2985487 |
47.35 % |
| q20,qd2 |
98308060 |
9.10 % |
95235040 |
8.86 % |
3073020 |
48.74 % |
| q20,mq40 |
18239745 |
1.69 % |
18135587 |
1.69 % |
104158 |
1.65 % |
| q20,qd2,mq40 |
9501829 |
0.88 % |
9434710 |
0.88 % |
67119 |
1.06 % |
| mq40 |
147234 |
0.01 % |
73714 |
0.01 % |
73520 |
1.17 % |
| qd2,mq40 |
7082 |
0.00 % |
5762 |
0.00 % |
1320 |
0.02 % |
| qd2 |
7052 |
0.00 % |
6220 |
0.00 % |
832 |
0.01 % |
| fs60,mq40 |
29 |
0.00 % |
0 |
0.00 % |
29 |
0.00 % |
| qd2,fs60,mq40 |
20 |
0.00 % |
0 |
0.00 % |
20 |
0.00 % |
| qd2,fs60 |
12 |
0.00 % |
0 |
0.00 % |
12 |
0.00 % |
| fs60 |
9 |
0.00 % |
0 |
0.00 % |
9 |
0.00 % |
| q20,qd2,fs60,mq40 |
8 |
0.00 % |
0 |
0.00 % |
8 |
0.00 % |
| q20,fs60 |
0 |
0.00 % |
0 |
0.00 % |
0 |
0.00 % |
| q20,qd2,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 |
2562331 |
19.52 % |
| Transition |
G>A |
All |
712633 |
5.43 % |
| Transition |
T>C |
All |
2555062 |
19.46 % |
| Transition |
C>T |
All |
712948 |
5.43 % |
| Transversion |
A>C |
All |
318885 |
2.43 % |
| Transversion |
C>A |
All |
1614240 |
12.30 % |
| Transversion |
T>G |
All |
323019 |
2.46 % |
| Transversion |
G>T |
All |
1594711 |
12.15 % |
| Transversion |
A>T |
All |
1122949 |
8.55 % |
| Transversion |
T>A |
All |
1115504 |
8.50 % |
| Transversion |
C>G |
All |
250239 |
1.91 % |
| Transversion |
G>C |
All |
243960 |
1.86 % |
| |
|
|
|
|
| Transition |
A>G |
Passed |
36934 |
11.51 % |
| Transition |
G>A |
Passed |
38652 |
12.04 % |
| Transition |
T>C |
Passed |
37580 |
11.71 % |
| Transition |
C>T |
Passed |
39272 |
12.24 % |
| Transversion |
A>C |
Passed |
21176 |
6.60 % |
| Transversion |
C>A |
Passed |
22428 |
6.99 % |
| Transversion |
T>G |
Passed |
21334 |
6.65 % |
| Transversion |
G>T |
Passed |
22330 |
6.96 % |
| Transversion |
A>T |
Passed |
18213 |
5.68 % |
| Transversion |
T>A |
Passed |
18215 |
5.68 % |
| Transversion |
C>G |
Passed |
22447 |
6.99 % |
| Transversion |
G>C |
Passed |
22335 |
6.96 % |
| |
|
|
|
|
| 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 |
0.99 |
6542974 |
6583507 |
| Passed |
0.90 |
152438 |
168478 |
| dbSNPAll |
0 |
0 |
0 |
| dbSNPPassed |
0 |
0 |
0 |