/EXTERNAL BLUEPRINT/variants/K006311_21_lane_gembs
BACK
SAMPLE K006311_21_lane_gembs
Variant counts
| Type |
Total |
Pass |
% |
| SNPs |
1051430995 |
496966865 |
47.27 % |
| Multiallelic |
0 |
0 |
0.00 % |
VCF Filtering Stats
| Type |
#Sites |
% |
#Non-Variant Sites |
% |
#Variant Sites |
% |
| All |
1051430995 |
100% |
1034793344 |
98.42 % |
16637651 |
1.58 % |
| |
|
|
|
|
|
|
| Passed |
498533932 |
47.41 % |
495995654 |
47.93 % |
2538278 |
0.51 % |
| Filtered |
552897063 |
52.59 % |
538797690 |
52.07 % |
14099373 |
2.83 % |
| |
|
|
|
|
|
|
| q20 |
449815177 |
81.36 % |
447944212 |
83.14 % |
1870965 |
13.27 % |
| q20,qd2 |
65562982 |
11.86 % |
53828091 |
9.99 % |
11734891 |
83.23 % |
| q20,mq40 |
15008396 |
2.71 % |
14923032 |
2.77 % |
85364 |
0.61 % |
| qd2 |
11944449 |
2.16 % |
11853873 |
2.20 % |
90576 |
0.64 % |
| mq40 |
7063232 |
1.28 % |
6918027 |
1.28 % |
145205 |
1.03 % |
| q20,qd2,mq40 |
3388910 |
0.61 % |
3244342 |
0.60 % |
144568 |
1.03 % |
| qd2,mq40 |
99045 |
0.02 % |
86113 |
0.02 % |
12932 |
0.09 % |
| q20,qd2,fs60 |
4053 |
0.00 % |
0 |
0.00 % |
4053 |
0.03 % |
| qd2,fs60 |
4031 |
0.00 % |
0 |
0.00 % |
4031 |
0.03 % |
| qd2,fs60,mq40 |
2659 |
0.00 % |
0 |
0.00 % |
2659 |
0.02 % |
| fs60 |
2333 |
0.00 % |
0 |
0.00 % |
2333 |
0.02 % |
| q20,qd2,fs60,mq40 |
1023 |
0.00 % |
0 |
0.00 % |
1023 |
0.01 % |
| fs60,mq40 |
770 |
0.00 % |
0 |
0.00 % |
770 |
0.01 % |
| q20,fs60 |
3 |
0.00 % |
0 |
0.00 % |
3 |
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 |
2882461 |
9.96 % |
| Transition |
G>A |
All |
10575359 |
36.56 % |
| Transition |
T>C |
All |
2566477 |
8.87 % |
| Transition |
C>T |
All |
10449004 |
36.12 % |
| Transversion |
A>C |
All |
213413 |
0.74 % |
| Transversion |
C>A |
All |
464017 |
1.60 % |
| Transversion |
T>G |
All |
240891 |
0.83 % |
| Transversion |
G>T |
All |
444987 |
1.54 % |
| Transversion |
A>T |
All |
351411 |
1.21 % |
| Transversion |
T>A |
All |
368316 |
1.27 % |
| Transversion |
C>G |
All |
192685 |
0.67 % |
| Transversion |
G>C |
All |
177853 |
0.61 % |
| |
|
|
|
|
| Transition |
A>G |
Passed |
286932 |
19.74 % |
| Transition |
G>A |
Passed |
250233 |
17.21 % |
| Transition |
T>C |
Passed |
284777 |
19.59 % |
| Transition |
C>T |
Passed |
249425 |
17.16 % |
| Transversion |
A>C |
Passed |
50947 |
3.50 % |
| Transversion |
C>A |
Passed |
44978 |
3.09 % |
| Transversion |
T>G |
Passed |
50588 |
3.48 % |
| Transversion |
G>T |
Passed |
45291 |
3.12 % |
| Transversion |
A>T |
Passed |
28195 |
1.94 % |
| Transversion |
T>A |
Passed |
28136 |
1.94 % |
| Transversion |
C>G |
Passed |
66995 |
4.61 % |
| Transversion |
G>C |
Passed |
67180 |
4.62 % |
| |
|
|
|
|
| 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 |
10.79 |
26473301 |
2453573 |
| Passed |
2.80 |
1071367 |
382310 |
| dbSNPAll |
0 |
0 |
0 |
| dbSNPPassed |
0 |
0 |
0 |