/EXTERNAL BLUEPRINT/variants/K012002_K012003_K012004_K012005_K012006_K012007_K012008_K012009_K012010_K012011_K012012_11_lane_gembs
BACK
SAMPLE K012002_K012003_K012004_K012005_K012006_K012007_K012008_K012009_K012010_K012011_K012012_11_lane_gembs
Variant counts
| Type |
Total |
Pass |
% |
| SNPs |
924415505 |
9904902 |
1.07 % |
| Multiallelic |
0 |
0 |
0.00 % |
VCF Filtering Stats
| Type |
#Sites |
% |
#Non-Variant Sites |
% |
#Variant Sites |
% |
| All |
924415505 |
100% |
903455480 |
97.73 % |
20960025 |
2.27 % |
| |
|
|
|
|
|
|
| Passed |
18891042 |
2.04 % |
9225486 |
1.02 % |
9665556 |
51.16 % |
| Filtered |
905524463 |
97.96 % |
894229994 |
98.98 % |
11294469 |
59.79 % |
| |
|
|
|
|
|
|
| q20 |
687395955 |
75.91 % |
679496538 |
75.99 % |
7899417 |
69.94 % |
| q20,qd2 |
132613386 |
14.64 % |
130493840 |
14.59 % |
2119546 |
18.77 % |
| q20,mq40 |
60188387 |
6.65 % |
59635186 |
6.67 % |
553201 |
4.90 % |
| q20,qd2,mq40 |
24523884 |
2.71 % |
24391642 |
2.73 % |
132242 |
1.17 % |
| mq40 |
792638 |
0.09 % |
203711 |
0.02 % |
588927 |
5.21 % |
| qd2 |
7360 |
0.00 % |
6782 |
0.00 % |
578 |
0.01 % |
| qd2,mq40 |
2804 |
0.00 % |
2295 |
0.00 % |
509 |
0.00 % |
| fs60,mq40 |
20 |
0.00 % |
0 |
0.00 % |
20 |
0.00 % |
| qd2,fs60 |
10 |
0.00 % |
0 |
0.00 % |
10 |
0.00 % |
| fs60 |
9 |
0.00 % |
0 |
0.00 % |
9 |
0.00 % |
| qd2,fs60,mq40 |
6 |
0.00 % |
0 |
0.00 % |
6 |
0.00 % |
| q20,qd2,fs60,mq40 |
4 |
0.00 % |
0 |
0.00 % |
4 |
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 |
5720550 |
22.44 % |
| Transition |
G>A |
All |
2024285 |
7.94 % |
| Transition |
T>C |
All |
6976603 |
27.37 % |
| Transition |
C>T |
All |
913527 |
3.58 % |
| Transversion |
A>C |
All |
918043 |
3.60 % |
| Transversion |
C>A |
All |
1683943 |
6.61 % |
| Transversion |
T>G |
All |
1142010 |
4.48 % |
| Transversion |
G>T |
All |
1499144 |
5.88 % |
| Transversion |
A>T |
All |
1137196 |
4.46 % |
| Transversion |
T>A |
All |
1578049 |
6.19 % |
| Transversion |
C>G |
All |
891178 |
3.50 % |
| Transversion |
G>C |
All |
1008860 |
3.96 % |
| |
|
|
|
|
| Transition |
A>G |
Passed |
123888 |
18.30 % |
| Transition |
G>A |
Passed |
93304 |
13.79 % |
| Transition |
T>C |
Passed |
188538 |
27.86 % |
| Transition |
C>T |
Passed |
34030 |
5.03 % |
| Transversion |
A>C |
Passed |
25782 |
3.81 % |
| Transversion |
C>A |
Passed |
41099 |
6.07 % |
| Transversion |
T>G |
Passed |
29993 |
4.43 % |
| Transversion |
G>T |
Passed |
21419 |
3.16 % |
| Transversion |
A>T |
Passed |
12273 |
1.81 % |
| Transversion |
T>A |
Passed |
36897 |
5.45 % |
| Transversion |
C>G |
Passed |
28955 |
4.28 % |
| Transversion |
G>C |
Passed |
40660 |
6.01 % |
| |
|
|
|
|
| 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 |
1.59 |
15634965 |
9858423 |
| Passed |
1.85 |
439760 |
237078 |
| dbSNPAll |
0 |
0 |
0 |
| dbSNPPassed |
0 |
0 |
0 |