/EXTERNAL BLUEPRINT/variants/K012035_K012056_K012057_K012058_K012059_K012060_K012061_K012062_K012063_K012110_K012111_11_lane_gembs
BACK
SAMPLE K012035_K012056_K012057_K012058_K012059_K012060_K012061_K012062_K012063_K012110_K012111_11_lane_gembs
Variant counts
| Type |
Total |
Pass |
% |
| SNPs |
879739341 |
4709093 |
0.54 % |
| Multiallelic |
0 |
0 |
0.00 % |
VCF Filtering Stats
| Type |
#Sites |
% |
#Non-Variant Sites |
% |
#Variant Sites |
% |
| All |
879739341 |
100% |
862561950 |
98.05 % |
17177391 |
1.95 % |
| |
|
|
|
|
|
|
| Passed |
12820602 |
1.46 % |
4161901 |
0.48 % |
8658701 |
67.54 % |
| Filtered |
866918739 |
98.54 % |
858400049 |
99.52 % |
8518690 |
66.45 % |
| |
|
|
|
|
|
|
| q20 |
643542750 |
74.23 % |
637572154 |
74.27 % |
5970596 |
70.09 % |
| q20,qd2 |
141371504 |
16.31 % |
139920014 |
16.30 % |
1451490 |
17.04 % |
| q20,mq40 |
56897311 |
6.56 % |
56443939 |
6.58 % |
453372 |
5.32 % |
| q20,qd2,mq40 |
24451972 |
2.82 % |
24339328 |
2.84 % |
112644 |
1.32 % |
| mq40 |
648216 |
0.07 % |
118223 |
0.01 % |
529993 |
6.22 % |
| qd2 |
5430 |
0.00 % |
5196 |
0.00 % |
234 |
0.00 % |
| qd2,mq40 |
1522 |
0.00 % |
1195 |
0.00 % |
327 |
0.00 % |
| qd2,fs60 |
12 |
0.00 % |
0 |
0.00 % |
12 |
0.00 % |
| fs60,mq40 |
12 |
0.00 % |
0 |
0.00 % |
12 |
0.00 % |
| fs60 |
6 |
0.00 % |
0 |
0.00 % |
6 |
0.00 % |
| qd2,fs60,mq40 |
4 |
0.00 % |
0 |
0.00 % |
4 |
0.00 % |
| q20,fs60 |
0 |
0.00 % |
0 |
0.00 % |
0 |
0.00 % |
| q20,qd2,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 |
4920214 |
22.40 % |
| Transition |
G>A |
All |
1726670 |
7.86 % |
| Transition |
T>C |
All |
6020281 |
27.40 % |
| Transition |
C>T |
All |
826501 |
3.76 % |
| Transversion |
A>C |
All |
738168 |
3.36 % |
| Transversion |
C>A |
All |
1492303 |
6.79 % |
| Transversion |
T>G |
All |
894485 |
4.07 % |
| Transversion |
G>T |
All |
1329755 |
6.05 % |
| Transversion |
A>T |
All |
1046875 |
4.77 % |
| Transversion |
T>A |
All |
1426556 |
6.49 % |
| Transversion |
C>G |
All |
720636 |
3.28 % |
| Transversion |
G>C |
All |
827479 |
3.77 % |
| |
|
|
|
|
| Transition |
A>G |
Passed |
99586 |
18.35 % |
| Transition |
G>A |
Passed |
70659 |
13.02 % |
| Transition |
T>C |
Passed |
145389 |
26.78 % |
| Transition |
C>T |
Passed |
25899 |
4.77 % |
| Transversion |
A>C |
Passed |
20830 |
3.84 % |
| Transversion |
C>A |
Passed |
35370 |
6.52 % |
| Transversion |
T>G |
Passed |
23967 |
4.42 % |
| Transversion |
G>T |
Passed |
20251 |
3.73 % |
| Transversion |
A>T |
Passed |
11788 |
2.17 % |
| Transversion |
T>A |
Passed |
32886 |
6.06 % |
| Transversion |
C>G |
Passed |
23507 |
4.33 % |
| Transversion |
G>C |
Passed |
32675 |
6.02 % |
| |
|
|
|
|
| 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 |
13493666 |
8476257 |
| Passed |
1.70 |
341533 |
201274 |
| dbSNPAll |
0 |
0 |
0 |
| dbSNPPassed |
0 |
0 |
0 |