/EXTERNAL BLUEPRINT/variants/K006288_14_lane_gembs
BACK
SAMPLE K006288_14_lane_gembs
Variant counts
| Type |
Total |
Pass |
% |
| SNPs |
1104530198 |
617817035 |
55.93 % |
| Multiallelic |
0 |
0 |
0.00 % |
VCF Filtering Stats
| Type |
#Sites |
% |
#Non-Variant Sites |
% |
#Variant Sites |
% |
| All |
1104530198 |
100% |
1085813218 |
98.31 % |
18716980 |
1.69 % |
| |
|
|
|
|
|
|
| Passed |
619667579 |
56.10 % |
616569901 |
56.78 % |
3097678 |
0.50 % |
| Filtered |
484862619 |
43.90 % |
469243317 |
43.22 % |
15619302 |
2.52 % |
| |
|
|
|
|
|
|
| q20 |
404228862 |
83.37 % |
402626152 |
85.80 % |
1602710 |
10.26 % |
| q20,qd2 |
54659774 |
11.27 % |
41166926 |
8.77 % |
13492848 |
86.39 % |
| q20,mq40 |
14306767 |
2.95 % |
14216266 |
3.03 % |
90501 |
0.58 % |
| mq40 |
6176029 |
1.27 % |
6015624 |
1.28 % |
160405 |
1.03 % |
| q20,qd2,mq40 |
3270983 |
0.67 % |
3107224 |
0.66 % |
163759 |
1.05 % |
| qd2 |
2134591 |
0.44 % |
2044233 |
0.44 % |
90358 |
0.58 % |
| qd2,mq40 |
77726 |
0.02 % |
66892 |
0.01 % |
10834 |
0.07 % |
| q20,qd2,fs60 |
2700 |
0.00 % |
0 |
0.00 % |
2700 |
0.02 % |
| fs60 |
1662 |
0.00 % |
0 |
0.00 % |
1662 |
0.01 % |
| qd2,fs60 |
1218 |
0.00 % |
0 |
0.00 % |
1218 |
0.01 % |
| qd2,fs60,mq40 |
1201 |
0.00 % |
0 |
0.00 % |
1201 |
0.01 % |
| q20,qd2,fs60,mq40 |
561 |
0.00 % |
0 |
0.00 % |
561 |
0.00 % |
| fs60,mq40 |
541 |
0.00 % |
0 |
0.00 % |
541 |
0.00 % |
| q20,fs60,mq40 |
3 |
0.00 % |
0 |
0.00 % |
3 |
0.00 % |
| q20,fs60 |
1 |
0.00 % |
0 |
0.00 % |
1 |
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 |
3274054 |
13.25 % |
| Transition |
G>A |
All |
7964471 |
32.24 % |
| Transition |
T>C |
All |
3187349 |
12.90 % |
| Transition |
C>T |
All |
7790819 |
31.54 % |
| Transversion |
A>C |
All |
188482 |
0.76 % |
| Transversion |
C>A |
All |
506187 |
2.05 % |
| Transversion |
T>G |
All |
197842 |
0.80 % |
| Transversion |
G>T |
All |
498968 |
2.02 % |
| Transversion |
A>T |
All |
372278 |
1.51 % |
| Transversion |
T>A |
All |
363238 |
1.47 % |
| Transversion |
C>G |
All |
184208 |
0.75 % |
| Transversion |
G>C |
All |
175590 |
0.71 % |
| |
|
|
|
|
| Transition |
A>G |
Passed |
349953 |
18.83 % |
| Transition |
G>A |
Passed |
322406 |
17.34 % |
| Transition |
T>C |
Passed |
350020 |
18.83 % |
| Transition |
C>T |
Passed |
323175 |
17.39 % |
| Transversion |
A>C |
Passed |
67261 |
3.62 % |
| Transversion |
C>A |
Passed |
62632 |
3.37 % |
| Transversion |
T>G |
Passed |
67453 |
3.63 % |
| Transversion |
G>T |
Passed |
62442 |
3.36 % |
| Transversion |
A>T |
Passed |
42871 |
2.31 % |
| Transversion |
T>A |
Passed |
42778 |
2.30 % |
| Transversion |
C>G |
Passed |
83555 |
4.50 % |
| Transversion |
G>C |
Passed |
84280 |
4.53 % |
| |
|
|
|
|
| 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 |
8.93 |
22216693 |
2486793 |
| Passed |
2.62 |
1345554 |
513272 |
| dbSNPAll |
0 |
0 |
0 |
| dbSNPPassed |
0 |
0 |
0 |