/EXTERNAL BLUEPRINT/variants/K006345_12_lane_gembs
BACK
SAMPLE K006345_12_lane_gembs
Variant counts
| Type |
Total |
Pass |
% |
| SNPs |
1127005784 |
687342319 |
60.99 % |
| Multiallelic |
0 |
0 |
0.00 % |
VCF Filtering Stats
| Type |
#Sites |
% |
#Non-Variant Sites |
% |
#Variant Sites |
% |
| All |
1127005784 |
100% |
1111396991 |
98.62 % |
15608793 |
1.38 % |
| |
|
|
|
|
|
|
| Passed |
689162207 |
61.15 % |
685878338 |
61.71 % |
3283869 |
0.48 % |
| Filtered |
437843577 |
38.85 % |
425518653 |
38.29 % |
12324924 |
1.79 % |
| |
|
|
|
|
|
|
| q20 |
371683260 |
84.89 % |
370134521 |
86.98 % |
1548739 |
12.57 % |
| q20,qd2 |
39763092 |
9.08 % |
29590872 |
6.95 % |
10172220 |
82.53 % |
| q20,mq40 |
14376334 |
3.28 % |
14264096 |
3.35 % |
112238 |
0.91 % |
| mq40 |
6441830 |
1.47 % |
6272291 |
1.47 % |
169539 |
1.38 % |
| q20,qd2,mq40 |
3204992 |
0.73 % |
2996024 |
0.70 % |
208968 |
1.70 % |
| qd2 |
2285694 |
0.52 % |
2189379 |
0.51 % |
96315 |
0.78 % |
| qd2,mq40 |
82075 |
0.02 % |
71470 |
0.02 % |
10605 |
0.09 % |
| q20,qd2,fs60 |
2032 |
0.00 % |
0 |
0.00 % |
2032 |
0.02 % |
| fs60 |
1337 |
0.00 % |
0 |
0.00 % |
1337 |
0.01 % |
| qd2,fs60,mq40 |
1173 |
0.00 % |
0 |
0.00 % |
1173 |
0.01 % |
| qd2,fs60 |
833 |
0.00 % |
0 |
0.00 % |
833 |
0.01 % |
| q20,qd2,fs60,mq40 |
469 |
0.00 % |
0 |
0.00 % |
469 |
0.00 % |
| fs60,mq40 |
456 |
0.00 % |
0 |
0.00 % |
456 |
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 |
3368800 |
18.75 % |
| Transition |
G>A |
All |
4255082 |
23.69 % |
| Transition |
T>C |
All |
3207968 |
17.86 % |
| Transition |
C>T |
All |
4126234 |
22.97 % |
| Transversion |
A>C |
All |
218920 |
1.22 % |
| Transversion |
C>A |
All |
638159 |
3.55 % |
| Transversion |
T>G |
All |
232356 |
1.29 % |
| Transversion |
G>T |
All |
641190 |
3.57 % |
| Transversion |
A>T |
All |
452796 |
2.52 % |
| Transversion |
T>A |
All |
440226 |
2.45 % |
| Transversion |
C>G |
All |
195265 |
1.09 % |
| Transversion |
G>C |
All |
186762 |
1.04 % |
| |
|
|
|
|
| Transition |
A>G |
Passed |
397361 |
18.30 % |
| Transition |
G>A |
Passed |
372528 |
17.16 % |
| Transition |
T>C |
Passed |
396527 |
18.26 % |
| Transition |
C>T |
Passed |
374320 |
17.24 % |
| Transversion |
A>C |
Passed |
83657 |
3.85 % |
| Transversion |
C>A |
Passed |
79063 |
3.64 % |
| Transversion |
T>G |
Passed |
83324 |
3.84 % |
| Transversion |
G>T |
Passed |
79494 |
3.66 % |
| Transversion |
A>T |
Passed |
55081 |
2.54 % |
| Transversion |
T>A |
Passed |
55213 |
2.54 % |
| Transversion |
C>G |
Passed |
97173 |
4.47 % |
| Transversion |
G>C |
Passed |
97761 |
4.50 % |
| |
|
|
|
|
| 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 |
4.98 |
14958084 |
3005674 |
| Passed |
2.44 |
1540736 |
630766 |
| dbSNPAll |
0 |
0 |
0 |
| dbSNPPassed |
0 |
0 |
0 |