/EXTERNAL BLUEPRINT/variants/K010521_1_lane_gembs
BACK
SAMPLE K010521_1_lane_gembs
Variant counts
| Type |
Total |
Pass |
% |
| SNPs |
1101581191 |
617489749 |
56.05 % |
| Multiallelic |
0 |
0 |
0.00 % |
VCF Filtering Stats
| Type |
#Sites |
% |
#Non-Variant Sites |
% |
#Variant Sites |
% |
| All |
1101581191 |
100% |
1081539712 |
98.18 % |
20041479 |
1.82 % |
| |
|
|
|
|
|
|
| Passed |
619199655 |
56.21 % |
616203415 |
56.97 % |
2996240 |
0.48 % |
| Filtered |
482381536 |
43.79 % |
465336297 |
43.03 % |
17045239 |
2.75 % |
| |
|
|
|
|
|
|
| q20 |
395279704 |
81.94 % |
393440197 |
84.55 % |
1839507 |
10.79 % |
| q20,qd2 |
56630608 |
11.74 % |
42035938 |
9.03 % |
14594670 |
85.62 % |
| q20,mq40 |
14719403 |
3.05 % |
14611067 |
3.14 % |
108336 |
0.64 % |
| mq40 |
7610396 |
1.58 % |
7442503 |
1.60 % |
167893 |
0.98 % |
| qd2 |
4674498 |
0.97 % |
4567779 |
0.98 % |
106719 |
0.63 % |
| q20,qd2,mq40 |
3352126 |
0.69 % |
3149670 |
0.68 % |
202456 |
1.19 % |
| qd2,mq40 |
102298 |
0.02 % |
89143 |
0.02 % |
13155 |
0.08 % |
| q20,qd2,fs60 |
4187 |
0.00 % |
0 |
0.00 % |
4187 |
0.02 % |
| fs60 |
2702 |
0.00 % |
0 |
0.00 % |
2702 |
0.02 % |
| qd2,fs60 |
2223 |
0.00 % |
0 |
0.00 % |
2223 |
0.01 % |
| qd2,fs60,mq40 |
1944 |
0.00 % |
0 |
0.00 % |
1944 |
0.01 % |
| q20,qd2,fs60,mq40 |
791 |
0.00 % |
0 |
0.00 % |
791 |
0.00 % |
| fs60,mq40 |
651 |
0.00 % |
0 |
0.00 % |
651 |
0.00 % |
| q20,fs60 |
4 |
0.00 % |
0 |
0.00 % |
4 |
0.00 % |
| q20,fs60,mq40 |
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 |
3318068 |
10.96 % |
| Transition |
G>A |
All |
10663449 |
35.21 % |
| Transition |
T>C |
All |
3053130 |
10.08 % |
| Transition |
C>T |
All |
10467330 |
34.57 % |
| Transversion |
A>C |
All |
212721 |
0.70 % |
| Transversion |
C>A |
All |
550683 |
1.82 % |
| Transversion |
T>G |
All |
233193 |
0.77 % |
| Transversion |
G>T |
All |
538726 |
1.78 % |
| Transversion |
A>T |
All |
432752 |
1.43 % |
| Transversion |
T>A |
All |
433050 |
1.43 % |
| Transversion |
C>G |
All |
194971 |
0.64 % |
| Transversion |
G>C |
All |
184303 |
0.61 % |
| |
|
|
|
|
| Transition |
A>G |
Passed |
361758 |
19.11 % |
| Transition |
G>A |
Passed |
325245 |
17.19 % |
| Transition |
T>C |
Passed |
361056 |
19.08 % |
| Transition |
C>T |
Passed |
325545 |
17.20 % |
| Transversion |
A>C |
Passed |
69176 |
3.66 % |
| Transversion |
C>A |
Passed |
62985 |
3.33 % |
| Transversion |
T>G |
Passed |
69042 |
3.65 % |
| Transversion |
G>T |
Passed |
63059 |
3.33 % |
| Transversion |
A>T |
Passed |
42687 |
2.26 % |
| Transversion |
T>A |
Passed |
42291 |
2.23 % |
| Transversion |
C>G |
Passed |
84481 |
4.46 % |
| Transversion |
G>C |
Passed |
85280 |
4.51 % |
| |
|
|
|
|
| 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 |
9.89 |
27501977 |
2780399 |
| Passed |
2.65 |
1373604 |
519001 |
| dbSNPAll |
0 |
0 |
0 |
| dbSNPPassed |
0 |
0 |
0 |