/EXTERNAL BLUEPRINT/variants/K006365_20_lane_gembs
BACK
SAMPLE K006365_20_lane_gembs
Variant counts
| Type |
Total |
Pass |
% |
| SNPs |
1148001991 |
853518434 |
74.35 % |
| Multiallelic |
0 |
0 |
0.00 % |
VCF Filtering Stats
| Type |
#Sites |
% |
#Non-Variant Sites |
% |
#Variant Sites |
% |
| All |
1148001991 |
100% |
1135297839 |
98.89 % |
12704152 |
1.11 % |
| |
|
|
|
|
|
|
| Passed |
855459053 |
74.52 % |
851490796 |
75.00 % |
3968257 |
0.46 % |
| Filtered |
292542938 |
25.48 % |
283807043 |
25.00 % |
8735895 |
1.02 % |
| |
|
|
|
|
|
|
| q20 |
250576111 |
85.65 % |
248673741 |
87.62 % |
1902370 |
21.78 % |
| q20,qd2 |
16283504 |
5.57 % |
10193007 |
3.59 % |
6090497 |
69.72 % |
| q20,mq40 |
13189915 |
4.51 % |
13025578 |
4.59 % |
164337 |
1.88 % |
| mq40 |
5468288 |
1.87 % |
5274242 |
1.86 % |
194046 |
2.22 % |
| qd2 |
3829497 |
1.31 % |
3713870 |
1.31 % |
115627 |
1.32 % |
| q20,qd2,mq40 |
3114692 |
1.06 % |
2860313 |
1.01 % |
254379 |
2.91 % |
| qd2,mq40 |
77578 |
0.03 % |
66292 |
0.02 % |
11286 |
0.13 % |
| qd2,fs60,mq40 |
1021 |
0.00 % |
0 |
0.00 % |
1021 |
0.01 % |
| q20,qd2,fs60 |
643 |
0.00 % |
0 |
0.00 % |
643 |
0.01 % |
| fs60,mq40 |
530 |
0.00 % |
0 |
0.00 % |
530 |
0.01 % |
| fs60 |
480 |
0.00 % |
0 |
0.00 % |
480 |
0.01 % |
| qd2,fs60 |
387 |
0.00 % |
0 |
0.00 % |
387 |
0.00 % |
| q20,qd2,fs60,mq40 |
288 |
0.00 % |
0 |
0.00 % |
288 |
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 |
4058680 |
27.82 % |
| Transition |
G>A |
All |
1305658 |
8.95 % |
| Transition |
T>C |
All |
4023611 |
27.58 % |
| Transition |
C>T |
All |
1321238 |
9.05 % |
| Transversion |
A>C |
All |
292262 |
2.00 % |
| Transversion |
C>A |
All |
725197 |
4.97 % |
| Transversion |
T>G |
All |
293758 |
2.01 % |
| Transversion |
G>T |
All |
744345 |
5.10 % |
| Transversion |
A>T |
All |
699095 |
4.79 % |
| Transversion |
T>A |
All |
666602 |
4.57 % |
| Transversion |
C>G |
All |
231941 |
1.59 % |
| Transversion |
G>C |
All |
228980 |
1.57 % |
| |
|
|
|
|
| Transition |
A>G |
Passed |
510699 |
17.50 % |
| Transition |
G>A |
Passed |
487394 |
16.70 % |
| Transition |
T>C |
Passed |
511447 |
17.53 % |
| Transition |
C>T |
Passed |
490968 |
16.83 % |
| Transversion |
A>C |
Passed |
120095 |
4.12 % |
| Transversion |
C>A |
Passed |
118792 |
4.07 % |
| Transversion |
T>G |
Passed |
119175 |
4.08 % |
| Transversion |
G>T |
Passed |
119586 |
4.10 % |
| Transversion |
A>T |
Passed |
91948 |
3.15 % |
| Transversion |
T>A |
Passed |
91574 |
3.14 % |
| Transversion |
C>G |
Passed |
127599 |
4.37 % |
| Transversion |
G>C |
Passed |
128393 |
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 |
2.76 |
10709187 |
3882180 |
| Passed |
2.18 |
2000508 |
917162 |
| dbSNPAll |
0 |
0 |
0 |
| dbSNPPassed |
0 |
0 |
0 |