/EXTERNAL BLUEPRINT/variants/K006372_8_lane_gembs
BACK
SAMPLE K006372_8_lane_gembs
Variant counts
| Type |
Total |
Pass |
% |
| SNPs |
1156726168 |
1050477796 |
90.81 % |
| Multiallelic |
0 |
0 |
0.00 % |
VCF Filtering Stats
| Type |
#Sites |
% |
#Non-Variant Sites |
% |
#Variant Sites |
% |
| All |
1156726168 |
100% |
1145153637 |
99.00 % |
11572531 |
1.00 % |
| |
|
|
|
|
|
|
| Passed |
1051332482 |
90.89 % |
1047948636 |
91.51 % |
3383846 |
0.32 % |
| Filtered |
105393686 |
9.11 % |
97205001 |
8.49 % |
8188685 |
0.78 % |
| |
|
|
|
|
|
|
| q20 |
73647134 |
69.88 % |
72986927 |
75.09 % |
660207 |
8.06 % |
| q20,mq40 |
12273721 |
11.65 % |
12177304 |
12.53 % |
96417 |
1.18 % |
| q20,qd2 |
10986659 |
10.42 % |
4060751 |
4.18 % |
6925908 |
84.58 % |
| mq40 |
3629212 |
3.44 % |
3438644 |
3.54 % |
190568 |
2.33 % |
| q20,qd2,mq40 |
3008055 |
2.85 % |
2852712 |
2.93 % |
155343 |
1.90 % |
| qd2 |
1800853 |
1.71 % |
1650740 |
1.70 % |
150113 |
1.83 % |
| qd2,mq40 |
46597 |
0.04 % |
37923 |
0.04 % |
8674 |
0.11 % |
| qd2,fs60,mq40 |
710 |
0.00 % |
0 |
0.00 % |
710 |
0.01 % |
| fs60,mq40 |
383 |
0.00 % |
0 |
0.00 % |
383 |
0.00 % |
| qd2,fs60 |
160 |
0.00 % |
0 |
0.00 % |
160 |
0.00 % |
| fs60 |
115 |
0.00 % |
0 |
0.00 % |
115 |
0.00 % |
| q20,qd2,fs60,mq40 |
61 |
0.00 % |
0 |
0.00 % |
61 |
0.00 % |
| q20,qd2,fs60 |
26 |
0.00 % |
0 |
0.00 % |
26 |
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 |
4316089 |
32.64 % |
| Transition |
G>A |
All |
974067 |
7.37 % |
| Transition |
T>C |
All |
4245070 |
32.11 % |
| Transition |
C>T |
All |
987476 |
7.47 % |
| Transversion |
A>C |
All |
219115 |
1.66 % |
| Transversion |
C>A |
All |
508951 |
3.85 % |
| Transversion |
T>G |
All |
220466 |
1.67 % |
| Transversion |
G>T |
All |
503758 |
3.81 % |
| Transversion |
A>T |
All |
422436 |
3.19 % |
| Transversion |
T>A |
All |
415200 |
3.14 % |
| Transversion |
C>G |
All |
204523 |
1.55 % |
| Transversion |
G>C |
All |
204765 |
1.55 % |
| |
|
|
|
|
| Transition |
A>G |
Passed |
640801 |
17.17 % |
| Transition |
G>A |
Passed |
612749 |
16.42 % |
| Transition |
T>C |
Passed |
641682 |
17.20 % |
| Transition |
C>T |
Passed |
618581 |
16.58 % |
| Transversion |
A>C |
Passed |
154426 |
4.14 % |
| Transversion |
C>A |
Passed |
161382 |
4.33 % |
| Transversion |
T>G |
Passed |
154953 |
4.15 % |
| Transversion |
G>T |
Passed |
162331 |
4.35 % |
| Transversion |
A>T |
Passed |
138434 |
3.71 % |
| Transversion |
T>A |
Passed |
138067 |
3.70 % |
| Transversion |
C>G |
Passed |
153661 |
4.12 % |
| Transversion |
G>C |
Passed |
154094 |
4.13 % |
| |
|
|
|
|
| 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 |
3.90 |
10522702 |
2699214 |
| Passed |
2.06 |
2513813 |
1217348 |
| dbSNPAll |
0 |
0 |
0 |
| dbSNPPassed |
0 |
0 |
0 |