/EXTERNAL BLUEPRINT/variants/K011802_K011819_K011820_K011821_K011822_K011823_K011824_K011825_K011826_K011853_K011854_11_lane_gembs
BACK
SAMPLE K011802_K011819_K011820_K011821_K011822_K011823_K011824_K011825_K011826_K011853_K011854_11_lane_gembs
Variant counts
| Type |
Total |
Pass |
% |
| SNPs |
955739066 |
14317082 |
1.50 % |
| Multiallelic |
0 |
0 |
0.00 % |
VCF Filtering Stats
| Type |
#Sites |
% |
#Non-Variant Sites |
% |
#Variant Sites |
% |
| All |
955739066 |
100% |
931641064 |
97.48 % |
24098002 |
2.52 % |
| |
|
|
|
|
|
|
| Passed |
26762563 |
2.80 % |
13337535 |
1.43 % |
13425028 |
50.16 % |
| Filtered |
928976503 |
97.20 % |
918303529 |
98.57 % |
10672974 |
39.88 % |
| |
|
|
|
|
|
|
| q20 |
730017175 |
78.58 % |
722807886 |
78.71 % |
7209289 |
67.55 % |
| q20,qd2 |
126395474 |
13.61 % |
124180870 |
13.52 % |
2214604 |
20.75 % |
| q20,mq40 |
52719313 |
5.67 % |
52298508 |
5.70 % |
420805 |
3.94 % |
| q20,qd2,mq40 |
18863763 |
2.03 % |
18751324 |
2.04 % |
112439 |
1.05 % |
| mq40 |
970856 |
0.10 % |
256105 |
0.03 % |
714751 |
6.70 % |
| qd2 |
7590 |
0.00 % |
7016 |
0.00 % |
574 |
0.01 % |
| qd2,mq40 |
2274 |
0.00 % |
1820 |
0.00 % |
454 |
0.00 % |
| fs60,mq40 |
24 |
0.00 % |
0 |
0.00 % |
24 |
0.00 % |
| qd2,fs60 |
18 |
0.00 % |
0 |
0.00 % |
18 |
0.00 % |
| fs60 |
10 |
0.00 % |
0 |
0.00 % |
10 |
0.00 % |
| qd2,fs60,mq40 |
3 |
0.00 % |
0 |
0.00 % |
3 |
0.00 % |
| q20,qd2,fs60,mq40 |
2 |
0.00 % |
0 |
0.00 % |
2 |
0.00 % |
| q20,qd2,fs60 |
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 |
6347500 |
22.35 % |
| Transition |
G>A |
All |
2400467 |
8.45 % |
| Transition |
T>C |
All |
8347675 |
29.39 % |
| Transition |
C>T |
All |
1067868 |
3.76 % |
| Transversion |
A>C |
All |
877743 |
3.09 % |
| Transversion |
C>A |
All |
1793679 |
6.32 % |
| Transversion |
T>G |
All |
1092582 |
3.85 % |
| Transversion |
G>T |
All |
1551994 |
5.46 % |
| Transversion |
A>T |
All |
1233371 |
4.34 % |
| Transversion |
T>A |
All |
1773069 |
6.24 % |
| Transversion |
C>G |
All |
869167 |
3.06 % |
| Transversion |
G>C |
All |
1046123 |
3.68 % |
| |
|
|
|
|
| Transition |
A>G |
Passed |
161642 |
16.60 % |
| Transition |
G>A |
Passed |
127677 |
13.11 % |
| Transition |
T>C |
Passed |
287191 |
29.48 % |
| Transition |
C>T |
Passed |
50974 |
5.23 % |
| Transversion |
A>C |
Passed |
37531 |
3.85 % |
| Transversion |
C>A |
Passed |
58799 |
6.04 % |
| Transversion |
T>G |
Passed |
43548 |
4.47 % |
| Transversion |
G>T |
Passed |
31519 |
3.24 % |
| Transversion |
A>T |
Passed |
22278 |
2.29 % |
| Transversion |
T>A |
Passed |
56726 |
5.82 % |
| Transversion |
C>G |
Passed |
40078 |
4.11 % |
| Transversion |
G>C |
Passed |
56062 |
5.76 % |
| |
|
|
|
|
| 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 |
1.77 |
18163510 |
10237728 |
| Passed |
1.81 |
627484 |
346541 |
| dbSNPAll |
0 |
0 |
0 |
| dbSNPPassed |
0 |
0 |
0 |