/EXTERNAL BLUEPRINT/variants/K006428_17_lane_gembs
BACK
SAMPLE K006428_17_lane_gembs
Variant counts
| Type |
Total |
Pass |
% |
| SNPs |
1156843884 |
936804367 |
80.98 % |
| Multiallelic |
0 |
0 |
0.00 % |
VCF Filtering Stats
| Type |
#Sites |
% |
#Non-Variant Sites |
% |
#Variant Sites |
% |
| All |
1156843884 |
100% |
1143084577 |
98.81 % |
13759307 |
1.19 % |
| |
|
|
|
|
|
|
| Passed |
938888396 |
81.16 % |
934579106 |
81.76 % |
4309290 |
0.46 % |
| Filtered |
217955488 |
18.84 % |
208505471 |
18.24 % |
9450017 |
1.01 % |
| |
|
|
|
|
|
|
| q20 |
178053716 |
81.69 % |
176806558 |
84.80 % |
1247158 |
13.20 % |
| q20,qd2 |
14525618 |
6.66 % |
6901263 |
3.31 % |
7624355 |
80.68 % |
| q20,mq40 |
13347369 |
6.12 % |
13242172 |
6.35 % |
105197 |
1.11 % |
| mq40 |
4656859 |
2.14 % |
4476239 |
2.15 % |
180620 |
1.91 % |
| qd2 |
4285221 |
1.97 % |
4204785 |
2.02 % |
80436 |
0.85 % |
| q20,qd2,mq40 |
3030339 |
1.39 % |
2828145 |
1.36 % |
202194 |
2.14 % |
| qd2,mq40 |
54631 |
0.03 % |
46309 |
0.02 % |
8322 |
0.09 % |
| qd2,fs60,mq40 |
721 |
0.00 % |
0 |
0.00 % |
721 |
0.01 % |
| fs60,mq40 |
394 |
0.00 % |
0 |
0.00 % |
394 |
0.00 % |
| qd2,fs60 |
226 |
0.00 % |
0 |
0.00 % |
226 |
0.00 % |
| fs60 |
206 |
0.00 % |
0 |
0.00 % |
206 |
0.00 % |
| q20,qd2,fs60,mq40 |
113 |
0.00 % |
0 |
0.00 % |
113 |
0.00 % |
| q20,qd2,fs60 |
72 |
0.00 % |
0 |
0.00 % |
72 |
0.00 % |
| q20,fs60,mq40 |
3 |
0.00 % |
0 |
0.00 % |
3 |
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 |
4878093 |
31.58 % |
| Transition |
G>A |
All |
1067863 |
6.91 % |
| Transition |
T>C |
All |
4819476 |
31.20 % |
| Transition |
C>T |
All |
1078800 |
6.98 % |
| Transversion |
A>C |
All |
215113 |
1.39 % |
| Transversion |
C>A |
All |
951244 |
6.16 % |
| Transversion |
T>G |
All |
217081 |
1.41 % |
| Transversion |
G>T |
All |
953680 |
6.17 % |
| Transversion |
A>T |
All |
434208 |
2.81 % |
| Transversion |
T>A |
All |
423738 |
2.74 % |
| Transversion |
C>G |
All |
203899 |
1.32 % |
| Transversion |
G>C |
All |
202094 |
1.31 % |
| |
|
|
|
|
| Transition |
A>G |
Passed |
556927 |
17.18 % |
| Transition |
G>A |
Passed |
532926 |
16.44 % |
| Transition |
T>C |
Passed |
558048 |
17.21 % |
| Transition |
C>T |
Passed |
535380 |
16.51 % |
| Transversion |
A>C |
Passed |
136172 |
4.20 % |
| Transversion |
C>A |
Passed |
138338 |
4.27 % |
| Transversion |
T>G |
Passed |
136128 |
4.20 % |
| Transversion |
G>T |
Passed |
139102 |
4.29 % |
| Transversion |
A>T |
Passed |
112718 |
3.48 % |
| Transversion |
T>A |
Passed |
113074 |
3.49 % |
| Transversion |
C>G |
Passed |
141778 |
4.37 % |
| Transversion |
G>C |
Passed |
141741 |
4.37 % |
| |
|
|
|
|
| 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 |
3.29 |
11844232 |
3601057 |
| Passed |
2.06 |
2183281 |
1059051 |
| dbSNPAll |
0 |
0 |
0 |
| dbSNPPassed |
0 |
0 |
0 |