/EXTERNAL BLUEPRINT/variants/K006418_14_lane_gembs
BACK
SAMPLE K006418_14_lane_gembs
Variant counts
| Type |
Total |
Pass |
% |
| SNPs |
1157149552 |
1039640661 |
89.84 % |
| Multiallelic |
0 |
0 |
0.00 % |
VCF Filtering Stats
| Type |
#Sites |
% |
#Non-Variant Sites |
% |
#Variant Sites |
% |
| All |
1157149552 |
100% |
1145047823 |
98.95 % |
12101729 |
1.05 % |
| |
|
|
|
|
|
|
| Passed |
1040592821 |
89.93 % |
1037156514 |
90.58 % |
3436307 |
0.33 % |
| Filtered |
116556731 |
10.07 % |
107891309 |
9.42 % |
8665422 |
0.83 % |
| |
|
|
|
|
|
|
| q20 |
84146403 |
72.19 % |
83391705 |
77.29 % |
754698 |
8.71 % |
| q20,mq40 |
12529735 |
10.75 % |
12424493 |
11.52 % |
105242 |
1.21 % |
| q20,qd2 |
11611457 |
9.96 % |
4309130 |
3.99 % |
7302327 |
84.27 % |
| mq40 |
3298659 |
2.83 % |
3108337 |
2.88 % |
190322 |
2.20 % |
| q20,qd2,mq40 |
3092737 |
2.65 % |
2924368 |
2.71 % |
168369 |
1.94 % |
| qd2 |
1828910 |
1.57 % |
1694908 |
1.57 % |
134002 |
1.55 % |
| qd2,mq40 |
47406 |
0.04 % |
38368 |
0.04 % |
9038 |
0.10 % |
| qd2,fs60,mq40 |
642 |
0.00 % |
0 |
0.00 % |
642 |
0.01 % |
| fs60,mq40 |
363 |
0.00 % |
0 |
0.00 % |
363 |
0.00 % |
| qd2,fs60 |
188 |
0.00 % |
0 |
0.00 % |
188 |
0.00 % |
| fs60 |
133 |
0.00 % |
0 |
0.00 % |
133 |
0.00 % |
| q20,qd2,fs60,mq40 |
72 |
0.00 % |
0 |
0.00 % |
72 |
0.00 % |
| q20,qd2,fs60 |
24 |
0.00 % |
0 |
0.00 % |
24 |
0.00 % |
| q20,fs60,mq40 |
2 |
0.00 % |
0 |
0.00 % |
2 |
0.00 % |
| q20,fs60 |
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 |
4510366 |
32.77 % |
| Transition |
G>A |
All |
943632 |
6.86 % |
| Transition |
T>C |
All |
4453005 |
32.36 % |
| Transition |
C>T |
All |
948362 |
6.89 % |
| Transversion |
A>C |
All |
227922 |
1.66 % |
| Transversion |
C>A |
All |
554063 |
4.03 % |
| Transversion |
T>G |
All |
228999 |
1.66 % |
| Transversion |
G>T |
All |
545359 |
3.96 % |
| Transversion |
A>T |
All |
468507 |
3.40 % |
| Transversion |
T>A |
All |
464299 |
3.37 % |
| Transversion |
C>G |
All |
208431 |
1.51 % |
| Transversion |
G>C |
All |
209176 |
1.52 % |
| |
|
|
|
|
| Transition |
A>G |
Passed |
634261 |
17.32 % |
| Transition |
G>A |
Passed |
590853 |
16.13 % |
| Transition |
T>C |
Passed |
635815 |
17.36 % |
| Transition |
C>T |
Passed |
592916 |
16.19 % |
| Transversion |
A>C |
Passed |
154769 |
4.23 % |
| Transversion |
C>A |
Passed |
159506 |
4.36 % |
| Transversion |
T>G |
Passed |
155138 |
4.24 % |
| Transversion |
G>T |
Passed |
160004 |
4.37 % |
| Transversion |
A>T |
Passed |
135958 |
3.71 % |
| Transversion |
T>A |
Passed |
136538 |
3.73 % |
| Transversion |
C>G |
Passed |
152971 |
4.18 % |
| Transversion |
G>C |
Passed |
153289 |
4.19 % |
| |
|
|
|
|
| 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 |
3.73 |
10855365 |
2906756 |
| Passed |
2.03 |
2453845 |
1208173 |
| dbSNPAll |
0 |
0 |
0 |
| dbSNPPassed |
0 |
0 |
0 |