/EXTERNAL BLUEPRINT/variants/K006384_K006397_20_lane_gembs
BACK
SAMPLE K006384_K006397_20_lane_gembs
Variant counts
| Type |
Total |
Pass |
% |
| SNPs |
1153638609 |
1004890256 |
87.11 % |
| Multiallelic |
0 |
0 |
0.00 % |
VCF Filtering Stats
| Type |
#Sites |
% |
#Non-Variant Sites |
% |
#Variant Sites |
% |
| All |
1153638609 |
100% |
1141403166 |
98.94 % |
12235443 |
1.06 % |
| |
|
|
|
|
|
|
| Passed |
1006107890 |
87.21 % |
1002517732 |
87.83 % |
3590158 |
0.36 % |
| Filtered |
147530719 |
12.79 % |
138885434 |
12.17 % |
8645285 |
0.86 % |
| |
|
|
|
|
|
|
| q20 |
96181518 |
65.19 % |
95173073 |
68.53 % |
1008445 |
11.66 % |
| qd2 |
18635548 |
12.63 % |
18476231 |
13.30 % |
159317 |
1.84 % |
| q20,mq40 |
11951453 |
8.10 % |
11849872 |
8.53 % |
101581 |
1.17 % |
| q20,qd2 |
10594393 |
7.18 % |
3628349 |
2.61 % |
6966044 |
80.58 % |
| mq40 |
7178810 |
4.87 % |
6973632 |
5.02 % |
205178 |
2.37 % |
| q20,qd2,mq40 |
2855014 |
1.94 % |
2684084 |
1.93 % |
170930 |
1.98 % |
| qd2,mq40 |
117008 |
0.08 % |
100193 |
0.07 % |
16815 |
0.19 % |
| qd2,fs60 |
5832 |
0.00 % |
0 |
0.00 % |
5832 |
0.07 % |
| fs60 |
4087 |
0.00 % |
0 |
0.00 % |
4087 |
0.05 % |
| qd2,fs60,mq40 |
2861 |
0.00 % |
0 |
0.00 % |
2861 |
0.03 % |
| q20,qd2,fs60 |
2733 |
0.00 % |
0 |
0.00 % |
2733 |
0.03 % |
| fs60,mq40 |
933 |
0.00 % |
0 |
0.00 % |
933 |
0.01 % |
| q20,qd2,fs60,mq40 |
525 |
0.00 % |
0 |
0.00 % |
525 |
0.01 % |
| q20,fs60 |
2 |
0.00 % |
0 |
0.00 % |
2 |
0.00 % |
| q20,fs60,mq40 |
2 |
0.00 % |
0 |
0.00 % |
2 |
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 |
4720490 |
33.62 % |
| Transition |
G>A |
All |
1120235 |
7.98 % |
| Transition |
T>C |
All |
4662430 |
33.21 % |
| Transition |
C>T |
All |
1126425 |
8.02 % |
| Transversion |
A>C |
All |
217417 |
1.55 % |
| Transversion |
C>A |
All |
421494 |
3.00 % |
| Transversion |
T>G |
All |
219549 |
1.56 % |
| Transversion |
G>T |
All |
413251 |
2.94 % |
| Transversion |
A>T |
All |
367034 |
2.61 % |
| Transversion |
T>A |
All |
364875 |
2.60 % |
| Transversion |
C>G |
All |
203491 |
1.45 % |
| Transversion |
G>C |
All |
202159 |
1.44 % |
| |
|
|
|
|
| Transition |
A>G |
Passed |
602988 |
17.46 % |
| Transition |
G>A |
Passed |
557682 |
16.15 % |
| Transition |
T>C |
Passed |
603283 |
17.47 % |
| Transition |
C>T |
Passed |
560175 |
16.22 % |
| Transversion |
A>C |
Passed |
147300 |
4.27 % |
| Transversion |
C>A |
Passed |
145341 |
4.21 % |
| Transversion |
T>G |
Passed |
147386 |
4.27 % |
| Transversion |
G>T |
Passed |
145677 |
4.22 % |
| Transversion |
A>T |
Passed |
125687 |
3.64 % |
| Transversion |
T>A |
Passed |
125038 |
3.62 % |
| Transversion |
C>G |
Passed |
146106 |
4.23 % |
| Transversion |
G>C |
Passed |
146608 |
4.25 % |
| |
|
|
|
|
| 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 |
4.83 |
11629580 |
2409270 |
| Passed |
2.06 |
2324128 |
1129143 |
| dbSNPAll |
0 |
0 |
0 |
| dbSNPPassed |
0 |
0 |
0 |