/EXTERNAL BLUEPRINT/variants/K006262_19_lane_gembs
BACK
SAMPLE K006262_19_lane_gembs
Variant counts
| Type |
Total |
Pass |
% |
| SNPs |
1147428209 |
843905083 |
73.55 % |
| Multiallelic |
0 |
0 |
0.00 % |
VCF Filtering Stats
| Type |
#Sites |
% |
#Non-Variant Sites |
% |
#Variant Sites |
% |
| All |
1147428209 |
100% |
1130151158 |
98.49 % |
17277051 |
1.51 % |
| |
|
|
|
|
|
|
| Passed |
845012912 |
73.64 % |
842205882 |
74.52 % |
2807030 |
0.33 % |
| Filtered |
302415297 |
26.36 % |
287945276 |
25.48 % |
14470021 |
1.71 % |
| |
|
|
|
|
|
|
| q20 |
234527811 |
77.55 % |
233128626 |
80.96 % |
1399185 |
9.67 % |
| q20,qd2 |
31684930 |
10.48 % |
19411260 |
6.74 % |
12273670 |
84.82 % |
| q20,mq40 |
14483866 |
4.79 % |
14358401 |
4.99 % |
125465 |
0.87 % |
| mq40 |
11775490 |
3.89 % |
11549434 |
4.01 % |
226056 |
1.56 % |
| qd2 |
6704364 |
2.22 % |
6557818 |
2.28 % |
146546 |
1.01 % |
| q20,qd2,mq40 |
3045783 |
1.01 % |
2789216 |
0.97 % |
256567 |
1.77 % |
| qd2,mq40 |
169958 |
0.06 % |
150521 |
0.05 % |
19437 |
0.13 % |
| q20,qd2,fs60 |
11807 |
0.00 % |
0 |
0.00 % |
11807 |
0.08 % |
| fs60 |
3910 |
0.00 % |
0 |
0.00 % |
3910 |
0.03 % |
| qd2,fs60 |
2835 |
0.00 % |
0 |
0.00 % |
2835 |
0.02 % |
| qd2,fs60,mq40 |
2620 |
0.00 % |
0 |
0.00 % |
2620 |
0.02 % |
| fs60,mq40 |
1050 |
0.00 % |
0 |
0.00 % |
1050 |
0.01 % |
| q20,qd2,fs60,mq40 |
848 |
0.00 % |
0 |
0.00 % |
848 |
0.01 % |
| q20,fs60 |
16 |
0.00 % |
0 |
0.00 % |
16 |
0.00 % |
| q20,fs60,mq40 |
9 |
0.00 % |
0 |
0.00 % |
9 |
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 |
2693558 |
9.33 % |
| Transition |
G>A |
All |
10561553 |
36.57 % |
| Transition |
T>C |
All |
2587873 |
8.96 % |
| Transition |
C>T |
All |
10475818 |
36.27 % |
| Transversion |
A>C |
All |
203179 |
0.70 % |
| Transversion |
C>A |
All |
510327 |
1.77 % |
| Transversion |
T>G |
All |
211906 |
0.73 % |
| Transversion |
G>T |
All |
509900 |
1.77 % |
| Transversion |
A>T |
All |
377137 |
1.31 % |
| Transversion |
T>A |
All |
365670 |
1.27 % |
| Transversion |
C>G |
All |
197045 |
0.68 % |
| Transversion |
G>C |
All |
189213 |
0.66 % |
| |
|
|
|
|
| Transition |
A>G |
Passed |
469212 |
18.03 % |
| Transition |
G>A |
Passed |
445511 |
17.12 % |
| Transition |
T>C |
Passed |
472206 |
18.15 % |
| Transition |
C>T |
Passed |
445579 |
17.12 % |
| Transversion |
A>C |
Passed |
100614 |
3.87 % |
| Transversion |
C>A |
Passed |
97015 |
3.73 % |
| Transversion |
T>G |
Passed |
100416 |
3.86 % |
| Transversion |
G>T |
Passed |
96766 |
3.72 % |
| Transversion |
A>T |
Passed |
74003 |
2.84 % |
| Transversion |
T>A |
Passed |
73609 |
2.83 % |
| Transversion |
C>G |
Passed |
113750 |
4.37 % |
| Transversion |
G>C |
Passed |
113638 |
4.37 % |
| |
|
|
|
|
| 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 |
10.26 |
26318802 |
2564377 |
| Passed |
2.38 |
1832508 |
769811 |
| dbSNPAll |
0 |
0 |
0 |
| dbSNPPassed |
0 |
0 |
0 |