/EXTERNAL BLUEPRINT/variants/K006304_K006315_17_lane_gembs
BACK
SAMPLE K006304_K006315_17_lane_gembs
Variant counts
| Type |
Total |
Pass |
% |
| SNPs |
1112391920 |
590085784 |
53.05 % |
| Multiallelic |
0 |
0 |
0.00 % |
VCF Filtering Stats
| Type |
#Sites |
% |
#Non-Variant Sites |
% |
#Variant Sites |
% |
| All |
1112391920 |
100% |
1096007445 |
98.53 % |
16384475 |
1.47 % |
| |
|
|
|
|
|
|
| Passed |
592101854 |
53.23 % |
588704962 |
53.71 % |
3396892 |
0.57 % |
| Filtered |
520290066 |
46.77 % |
507302483 |
46.29 % |
12987583 |
2.19 % |
| |
|
|
|
|
|
|
| q20 |
450599759 |
86.61 % |
448554750 |
88.42 % |
2045009 |
15.75 % |
| q20,qd2 |
47448721 |
9.12 % |
36985359 |
7.29 % |
10463362 |
80.56 % |
| q20,mq40 |
12470557 |
2.40 % |
12381145 |
2.44 % |
89412 |
0.69 % |
| q20,qd2,mq40 |
3638093 |
0.70 % |
3511386 |
0.69 % |
126707 |
0.98 % |
| qd2 |
3394007 |
0.65 % |
3278238 |
0.65 % |
115769 |
0.89 % |
| mq40 |
2662373 |
0.51 % |
2533531 |
0.50 % |
128842 |
0.99 % |
| qd2,mq40 |
68331 |
0.01 % |
58074 |
0.01 % |
10257 |
0.08 % |
| q20,qd2,fs60 |
2300 |
0.00 % |
0 |
0.00 % |
2300 |
0.02 % |
| qd2,fs60 |
1801 |
0.00 % |
0 |
0.00 % |
1801 |
0.01 % |
| qd2,fs60,mq40 |
1610 |
0.00 % |
0 |
0.00 % |
1610 |
0.01 % |
| fs60 |
1383 |
0.00 % |
0 |
0.00 % |
1383 |
0.01 % |
| q20,qd2,fs60,mq40 |
644 |
0.00 % |
0 |
0.00 % |
644 |
0.00 % |
| fs60,mq40 |
478 |
0.00 % |
0 |
0.00 % |
478 |
0.00 % |
| q20,fs60 |
7 |
0.00 % |
0 |
0.00 % |
7 |
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 |
3506683 |
15.93 % |
| Transition |
G>A |
All |
6001953 |
27.27 % |
| Transition |
T>C |
All |
3276207 |
14.89 % |
| Transition |
C>T |
All |
5988530 |
27.21 % |
| Transversion |
A>C |
All |
229614 |
1.04 % |
| Transversion |
C>A |
All |
666667 |
3.03 % |
| Transversion |
T>G |
All |
257763 |
1.17 % |
| Transversion |
G>T |
All |
649941 |
2.95 % |
| Transversion |
A>T |
All |
508345 |
2.31 % |
| Transversion |
T>A |
All |
509719 |
2.32 % |
| Transversion |
C>G |
All |
213709 |
0.97 % |
| Transversion |
G>C |
All |
200948 |
0.91 % |
| |
|
|
|
|
| Transition |
A>G |
Passed |
388952 |
19.73 % |
| Transition |
G>A |
Passed |
326858 |
16.58 % |
| Transition |
T>C |
Passed |
386000 |
19.58 % |
| Transition |
C>T |
Passed |
325728 |
16.52 % |
| Transversion |
A>C |
Passed |
71411 |
3.62 % |
| Transversion |
C>A |
Passed |
67521 |
3.43 % |
| Transversion |
T>G |
Passed |
71120 |
3.61 % |
| Transversion |
G>T |
Passed |
66797 |
3.39 % |
| Transversion |
A>T |
Passed |
47046 |
2.39 % |
| Transversion |
T>A |
Passed |
46957 |
2.38 % |
| Transversion |
C>G |
Passed |
86191 |
4.37 % |
| Transversion |
G>C |
Passed |
86832 |
4.40 % |
| |
|
|
|
|
| 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 |
5.80 |
18773373 |
3236706 |
| Passed |
2.62 |
1427538 |
543875 |
| dbSNPAll |
0 |
0 |
0 |
| dbSNPPassed |
0 |
0 |
0 |