/EXTERNAL BLUEPRINT/variants/K006291_10_lane_gembs
BACK
SAMPLE K006291_10_lane_gembs
Variant counts
| Type |
Total |
Pass |
% |
| SNPs |
1107817246 |
623163925 |
56.25 % |
| Multiallelic |
0 |
0 |
0.00 % |
VCF Filtering Stats
| Type |
#Sites |
% |
#Non-Variant Sites |
% |
#Variant Sites |
% |
| All |
1107817246 |
100% |
1091642494 |
98.54 % |
16174752 |
1.46 % |
| |
|
|
|
|
|
|
| Passed |
624847340 |
56.40 % |
621912183 |
56.97 % |
2935157 |
0.47 % |
| Filtered |
482969906 |
43.60 % |
469730311 |
43.03 % |
13239595 |
2.12 % |
| |
|
|
|
|
|
|
| q20 |
407618523 |
84.40 % |
406089592 |
86.45 % |
1528931 |
11.55 % |
| q20,qd2 |
49242808 |
10.20 % |
38028233 |
8.10 % |
11214575 |
84.70 % |
| q20,mq40 |
14707222 |
3.05 % |
14616036 |
3.11 % |
91186 |
0.69 % |
| mq40 |
5955447 |
1.23 % |
5802610 |
1.24 % |
152837 |
1.15 % |
| q20,qd2,mq40 |
3366941 |
0.70 % |
3210414 |
0.68 % |
156527 |
1.18 % |
| qd2 |
1991932 |
0.41 % |
1914196 |
0.41 % |
77736 |
0.59 % |
| qd2,mq40 |
80292 |
0.02 % |
69230 |
0.01 % |
11062 |
0.08 % |
| q20,qd2,fs60 |
1694 |
0.00 % |
0 |
0.00 % |
1694 |
0.01 % |
| qd2,fs60,mq40 |
1474 |
0.00 % |
0 |
0.00 % |
1474 |
0.01 % |
| qd2,fs60 |
1201 |
0.00 % |
0 |
0.00 % |
1201 |
0.01 % |
| fs60 |
1188 |
0.00 % |
0 |
0.00 % |
1188 |
0.01 % |
| q20,qd2,fs60,mq40 |
595 |
0.00 % |
0 |
0.00 % |
595 |
0.00 % |
| fs60,mq40 |
586 |
0.00 % |
0 |
0.00 % |
586 |
0.00 % |
| q20,fs60,mq40 |
2 |
0.00 % |
0 |
0.00 % |
2 |
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 |
3039920 |
15.32 % |
| Transition |
G>A |
All |
5682318 |
28.63 % |
| Transition |
T>C |
All |
2925371 |
14.74 % |
| Transition |
C>T |
All |
5528745 |
27.85 % |
| Transversion |
A>C |
All |
203385 |
1.02 % |
| Transversion |
C>A |
All |
561907 |
2.83 % |
| Transversion |
T>G |
All |
212564 |
1.07 % |
| Transversion |
G>T |
All |
553836 |
2.79 % |
| Transversion |
A>T |
All |
389710 |
1.96 % |
| Transversion |
T>A |
All |
382594 |
1.93 % |
| Transversion |
C>G |
All |
187439 |
0.94 % |
| Transversion |
G>C |
All |
180867 |
0.91 % |
| |
|
|
|
|
| Transition |
A>G |
Passed |
355234 |
18.77 % |
| Transition |
G>A |
Passed |
325532 |
17.20 % |
| Transition |
T>C |
Passed |
354472 |
18.73 % |
| Transition |
C>T |
Passed |
326293 |
17.24 % |
| Transversion |
A>C |
Passed |
70093 |
3.70 % |
| Transversion |
C>A |
Passed |
64851 |
3.43 % |
| Transversion |
T>G |
Passed |
69842 |
3.69 % |
| Transversion |
G>T |
Passed |
64955 |
3.43 % |
| Transversion |
A>T |
Passed |
44495 |
2.35 % |
| Transversion |
T>A |
Passed |
44535 |
2.35 % |
| Transversion |
C>G |
Passed |
85977 |
4.54 % |
| Transversion |
G>C |
Passed |
86643 |
4.58 % |
| |
|
|
|
|
| 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 |
6.43 |
17176354 |
2672302 |
| Passed |
2.56 |
1361531 |
531391 |
| dbSNPAll |
0 |
0 |
0 |
| dbSNPPassed |
0 |
0 |
0 |