/EXTERNAL BLUEPRINT/variants/K010506_1_lane_gembs
BACK
SAMPLE K010506_1_lane_gembs
Variant counts
| Type |
Total |
Pass |
% |
| SNPs |
1158886688 |
766228206 |
66.12 % |
| Multiallelic |
0 |
0 |
0.00 % |
VCF Filtering Stats
| Type |
#Sites |
% |
#Non-Variant Sites |
% |
#Variant Sites |
% |
| All |
1158886688 |
100% |
1138262874 |
98.22 % |
20623814 |
1.78 % |
| |
|
|
|
|
|
|
| Passed |
769866016 |
66.43 % |
763994697 |
67.12 % |
5871319 |
0.76 % |
| Filtered |
389020672 |
33.57 % |
374268177 |
32.88 % |
14752495 |
1.92 % |
| |
|
|
|
|
|
|
| q20 |
345523462 |
88.82 % |
343203325 |
91.70 % |
2320137 |
15.73 % |
| q20,qd2 |
21798079 |
5.60 % |
9857337 |
2.63 % |
11940742 |
80.94 % |
| q20,mq40 |
15376660 |
3.95 % |
15255515 |
4.08 % |
121145 |
0.82 % |
| q20,qd2,mq40 |
3494645 |
0.90 % |
3333318 |
0.89 % |
161327 |
1.09 % |
| mq40 |
1885274 |
0.48 % |
1706157 |
0.46 % |
179117 |
1.21 % |
| qd2 |
913146 |
0.23 % |
889357 |
0.24 % |
23789 |
0.16 % |
| qd2,mq40 |
28766 |
0.01 % |
23168 |
0.01 % |
5598 |
0.04 % |
| qd2,fs60,mq40 |
310 |
0.00 % |
0 |
0.00 % |
310 |
0.00 % |
| fs60,mq40 |
157 |
0.00 % |
0 |
0.00 % |
157 |
0.00 % |
| qd2,fs60 |
89 |
0.00 % |
0 |
0.00 % |
89 |
0.00 % |
| fs60 |
42 |
0.00 % |
0 |
0.00 % |
42 |
0.00 % |
| q20,qd2,fs60,mq40 |
36 |
0.00 % |
0 |
0.00 % |
36 |
0.00 % |
| q20,qd2,fs60 |
4 |
0.00 % |
0 |
0.00 % |
4 |
0.00 % |
| q20,fs60,mq40 |
2 |
0.00 % |
0 |
0.00 % |
2 |
0.00 % |
| q20,fs60 |
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 |
7353465 |
32.98 % |
| Transition |
G>A |
All |
1332923 |
5.98 % |
| Transition |
T>C |
All |
7322733 |
32.84 % |
| Transition |
C>T |
All |
1337351 |
6.00 % |
| Transversion |
A>C |
All |
244068 |
1.09 % |
| Transversion |
C>A |
All |
1355728 |
6.08 % |
| Transversion |
T>G |
All |
246910 |
1.11 % |
| Transversion |
G>T |
All |
1358986 |
6.09 % |
| Transversion |
A>T |
All |
648292 |
2.91 % |
| Transversion |
T>A |
All |
629673 |
2.82 % |
| Transversion |
C>G |
All |
235138 |
1.05 % |
| Transversion |
G>C |
All |
231833 |
1.04 % |
| |
|
|
|
|
| Transition |
A>G |
Passed |
514000 |
16.84 % |
| Transition |
G>A |
Passed |
483906 |
15.86 % |
| Transition |
T>C |
Passed |
516879 |
16.94 % |
| Transition |
C>T |
Passed |
488739 |
16.02 % |
| Transversion |
A>C |
Passed |
131848 |
4.32 % |
| Transversion |
C>A |
Passed |
140274 |
4.60 % |
| Transversion |
T>G |
Passed |
132014 |
4.33 % |
| Transversion |
G>T |
Passed |
140868 |
4.62 % |
| Transversion |
A>T |
Passed |
117556 |
3.85 % |
| Transversion |
T>A |
Passed |
117479 |
3.85 % |
| Transversion |
C>G |
Passed |
133825 |
4.39 % |
| Transversion |
G>C |
Passed |
134122 |
4.40 % |
| |
|
|
|
|
| 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 |
3.50 |
17346472 |
4950628 |
| Passed |
1.91 |
2003524 |
1047986 |
| dbSNPAll |
0 |
0 |
0 |
| dbSNPPassed |
0 |
0 |
0 |