/EXTERNAL BLUEPRINT/variants/K011940_K011941_K011942_K011943_K011946_5_lane_gembs
BACK
SAMPLE K011940_K011941_K011942_K011943_K011946_5_lane_gembs
Variant counts
| Type |
Total |
Pass |
% |
| SNPs |
597438606 |
127842 |
0.02 % |
| Multiallelic |
0 |
0 |
0.00 % |
VCF Filtering Stats
| Type |
#Sites |
% |
#Non-Variant Sites |
% |
#Variant Sites |
% |
| All |
597438606 |
100% |
592714730 |
99.21 % |
4723876 |
0.79 % |
| |
|
|
|
|
|
|
| Passed |
2345227 |
0.39 % |
83717 |
0.01 % |
2261510 |
96.43 % |
| Filtered |
595093379 |
99.61 % |
592631013 |
99.99 % |
2462366 |
104.99 % |
| |
|
|
|
|
|
|
| q20 |
422058535 |
70.92 % |
420126900 |
70.89 % |
1931635 |
78.45 % |
| q20,qd2 |
108203223 |
18.18 % |
107985893 |
18.22 % |
217330 |
8.83 % |
| q20,mq40 |
46421262 |
7.80 % |
46270266 |
7.81 % |
150996 |
6.13 % |
| q20,qd2,mq40 |
18249778 |
3.07 % |
18229182 |
3.08 % |
20596 |
0.84 % |
| mq40 |
156672 |
0.03 % |
15030 |
0.00 % |
141642 |
5.75 % |
| qd2 |
3339 |
0.00 % |
3278 |
0.00 % |
61 |
0.00 % |
| qd2,mq40 |
557 |
0.00 % |
464 |
0.00 % |
93 |
0.00 % |
| fs60,mq40 |
5 |
0.00 % |
0 |
0.00 % |
5 |
0.00 % |
| qd2,fs60 |
4 |
0.00 % |
0 |
0.00 % |
4 |
0.00 % |
| fs60 |
2 |
0.00 % |
0 |
0.00 % |
2 |
0.00 % |
| q20,qd2,fs60 |
1 |
0.00 % |
0 |
0.00 % |
1 |
0.00 % |
| qd2,fs60,mq40 |
1 |
0.00 % |
0 |
0.00 % |
1 |
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 % |
| q20,qd2,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 |
2055312 |
22.12 % |
| Transition |
G>A |
All |
705778 |
7.60 % |
| Transition |
T>C |
All |
2577400 |
27.74 % |
| Transition |
C>T |
All |
360032 |
3.88 % |
| Transversion |
A>C |
All |
370179 |
3.98 % |
| Transversion |
C>A |
All |
565368 |
6.09 % |
| Transversion |
T>G |
All |
414554 |
4.46 % |
| Transversion |
G>T |
All |
509654 |
5.49 % |
| Transversion |
A>T |
All |
454464 |
4.89 % |
| Transversion |
T>A |
All |
618544 |
6.66 % |
| Transversion |
C>G |
All |
302477 |
3.26 % |
| Transversion |
G>C |
All |
356984 |
3.84 % |
| |
|
|
|
|
| Transition |
A>G |
Passed |
6646 |
15.20 % |
| Transition |
G>A |
Passed |
6002 |
13.73 % |
| Transition |
T>C |
Passed |
9989 |
22.85 % |
| Transition |
C>T |
Passed |
2343 |
5.36 % |
| Transversion |
A>C |
Passed |
2068 |
4.73 % |
| Transversion |
C>A |
Passed |
3091 |
7.07 % |
| Transversion |
T>G |
Passed |
2305 |
5.27 % |
| Transversion |
G>T |
Passed |
1834 |
4.20 % |
| Transversion |
A>T |
Passed |
1021 |
2.34 % |
| Transversion |
T>A |
Passed |
2692 |
6.16 % |
| Transversion |
C>G |
Passed |
2368 |
5.42 % |
| Transversion |
G>C |
Passed |
3355 |
7.67 % |
| |
|
|
|
|
| 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 |
1.59 |
5698522 |
3592224 |
| Passed |
1.33 |
24980 |
18734 |
| dbSNPAll |
0 |
0 |
0 |
| dbSNPPassed |
0 |
0 |
0 |