/EXTERNAL BLUEPRINT/variants/K006387_K006400_25_lane_gembs
BACK
SAMPLE K006387_K006400_25_lane_gembs
Variant counts
| Type |
Total |
Pass |
% |
| SNPs |
1151886960 |
1033329997 |
89.71 % |
| Multiallelic |
0 |
0 |
0.00 % |
VCF Filtering Stats
| Type |
#Sites |
% |
#Non-Variant Sites |
% |
#Variant Sites |
% |
| All |
1151886960 |
100% |
1140740352 |
99.03 % |
11146608 |
0.97 % |
| |
|
|
|
|
|
|
| Passed |
1034359886 |
89.80 % |
1030919289 |
90.37 % |
3440597 |
0.33 % |
| Filtered |
117527074 |
10.20 % |
109821063 |
9.63 % |
7706011 |
0.75 % |
| |
|
|
|
|
|
|
| q20 |
76675423 |
65.24 % |
75848046 |
69.07 % |
827377 |
10.74 % |
| q20,mq40 |
11225041 |
9.55 % |
11125726 |
10.13 % |
99315 |
1.29 % |
| qd2 |
10340081 |
8.80 % |
10184893 |
9.27 % |
155188 |
2.01 % |
| q20,qd2 |
9394121 |
7.99 % |
3182201 |
2.90 % |
6211920 |
80.61 % |
| mq40 |
7034321 |
5.99 % |
6827756 |
6.22 % |
206565 |
2.68 % |
| q20,qd2,mq40 |
2722605 |
2.32 % |
2549706 |
2.32 % |
172899 |
2.24 % |
| qd2,mq40 |
120804 |
0.10 % |
102735 |
0.09 % |
18069 |
0.23 % |
| fs60 |
4068 |
0.00 % |
0 |
0.00 % |
4068 |
0.05 % |
| qd2,fs60 |
3751 |
0.00 % |
0 |
0.00 % |
3751 |
0.05 % |
| qd2,fs60,mq40 |
2883 |
0.00 % |
0 |
0.00 % |
2883 |
0.04 % |
| q20,qd2,fs60 |
2605 |
0.00 % |
0 |
0.00 % |
2605 |
0.03 % |
| fs60,mq40 |
1013 |
0.00 % |
0 |
0.00 % |
1013 |
0.01 % |
| q20,qd2,fs60,mq40 |
356 |
0.00 % |
0 |
0.00 % |
356 |
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 |
4182837 |
32.38 % |
| Transition |
G>A |
All |
1107817 |
8.58 % |
| Transition |
T>C |
All |
4143773 |
32.08 % |
| Transition |
C>T |
All |
1125744 |
8.72 % |
| Transversion |
A>C |
All |
212085 |
1.64 % |
| Transversion |
C>A |
All |
421236 |
3.26 % |
| Transversion |
T>G |
All |
215241 |
1.67 % |
| Transversion |
G>T |
All |
417928 |
3.24 % |
| Transversion |
A>T |
All |
349814 |
2.71 % |
| Transversion |
T>A |
All |
340438 |
2.64 % |
| Transversion |
C>G |
All |
200364 |
1.55 % |
| Transversion |
G>C |
All |
198698 |
1.54 % |
| |
|
|
|
|
| Transition |
A>G |
Passed |
610453 |
17.21 % |
| Transition |
G>A |
Passed |
585740 |
16.52 % |
| Transition |
T>C |
Passed |
610483 |
17.21 % |
| Transition |
C>T |
Passed |
591881 |
16.69 % |
| Transversion |
A>C |
Passed |
148613 |
4.19 % |
| Transversion |
C>A |
Passed |
150195 |
4.23 % |
| Transversion |
T>G |
Passed |
148545 |
4.19 % |
| Transversion |
G>T |
Passed |
150535 |
4.24 % |
| Transversion |
A>T |
Passed |
127036 |
3.58 % |
| Transversion |
T>A |
Passed |
127448 |
3.59 % |
| Transversion |
C>G |
Passed |
147526 |
4.16 % |
| Transversion |
G>C |
Passed |
148129 |
4.18 % |
| |
|
|
|
|
| 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 |
4.48 |
10560171 |
2355804 |
| Passed |
2.09 |
2398557 |
1148027 |
| dbSNPAll |
0 |
0 |
0 |
| dbSNPPassed |
0 |
0 |
0 |