/EXTERNAL BLUEPRINT/variants/K006374_15_lane_gembs
BACK
SAMPLE K006374_15_lane_gembs
Variant counts
| Type |
Total |
Pass |
% |
| SNPs |
1156630600 |
1033255062 |
89.33 % |
| Multiallelic |
0 |
0 |
0.00 % |
VCF Filtering Stats
| Type |
#Sites |
% |
#Non-Variant Sites |
% |
#Variant Sites |
% |
| All |
1156630600 |
100% |
1145542550 |
99.04 % |
11088050 |
0.96 % |
| |
|
|
|
|
|
|
| Passed |
1034308497 |
89.42 % |
1031065042 |
90.01 % |
3243455 |
0.31 % |
| Filtered |
122322103 |
10.58 % |
114477508 |
9.99 % |
7844595 |
0.76 % |
| |
|
|
|
|
|
|
| q20 |
90359039 |
73.87 % |
89615171 |
78.28 % |
743868 |
9.48 % |
| q20,mq40 |
12740542 |
10.42 % |
12641601 |
11.04 % |
98941 |
1.26 % |
| q20,qd2 |
10416051 |
8.52 % |
3939661 |
3.44 % |
6476390 |
82.56 % |
| mq40 |
4246902 |
3.47 % |
4047476 |
3.54 % |
199426 |
2.54 % |
| q20,qd2,mq40 |
3011855 |
2.46 % |
2841392 |
2.48 % |
170463 |
2.17 % |
| qd2 |
1500018 |
1.23 % |
1354883 |
1.18 % |
145135 |
1.85 % |
| qd2,mq40 |
46233 |
0.04 % |
37324 |
0.03 % |
8909 |
0.11 % |
| qd2,fs60,mq40 |
683 |
0.00 % |
0 |
0.00 % |
683 |
0.01 % |
| fs60,mq40 |
286 |
0.00 % |
0 |
0.00 % |
286 |
0.00 % |
| qd2,fs60 |
217 |
0.00 % |
0 |
0.00 % |
217 |
0.00 % |
| fs60 |
163 |
0.00 % |
0 |
0.00 % |
163 |
0.00 % |
| q20,qd2,fs60,mq40 |
62 |
0.00 % |
0 |
0.00 % |
62 |
0.00 % |
| q20,qd2,fs60 |
52 |
0.00 % |
0 |
0.00 % |
52 |
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 % |
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 |
4159520 |
32.38 % |
| Transition |
G>A |
All |
889022 |
6.92 % |
| Transition |
T>C |
All |
4127044 |
32.13 % |
| Transition |
C>T |
All |
892287 |
6.95 % |
| Transversion |
A>C |
All |
225216 |
1.75 % |
| Transversion |
C>A |
All |
507783 |
3.95 % |
| Transversion |
T>G |
All |
227568 |
1.77 % |
| Transversion |
G>T |
All |
494652 |
3.85 % |
| Transversion |
A>T |
All |
458060 |
3.57 % |
| Transversion |
T>A |
All |
460634 |
3.59 % |
| Transversion |
C>G |
All |
201999 |
1.57 % |
| Transversion |
G>C |
All |
201406 |
1.57 % |
| |
|
|
|
|
| Transition |
A>G |
Passed |
592070 |
17.36 % |
| Transition |
G>A |
Passed |
546715 |
16.03 % |
| Transition |
T>C |
Passed |
593338 |
17.40 % |
| Transition |
C>T |
Passed |
549918 |
16.12 % |
| Transversion |
A>C |
Passed |
146026 |
4.28 % |
| Transversion |
C>A |
Passed |
147919 |
4.34 % |
| Transversion |
T>G |
Passed |
147253 |
4.32 % |
| Transversion |
G>T |
Passed |
147650 |
4.33 % |
| Transversion |
A>T |
Passed |
128074 |
3.75 % |
| Transversion |
T>A |
Passed |
127926 |
3.75 % |
| Transversion |
C>G |
Passed |
142088 |
4.17 % |
| Transversion |
G>C |
Passed |
141970 |
4.16 % |
| |
|
|
|
|
| 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 |
3.63 |
10067873 |
2777318 |
| Passed |
2.02 |
2282041 |
1128906 |
| dbSNPAll |
0 |
0 |
0 |
| dbSNPPassed |
0 |
0 |
0 |