/EXTERNAL BLUEPRINT/variants/K006420_14_lane_gembs
BACK
SAMPLE K006420_14_lane_gembs
Variant counts
| Type |
Total |
Pass |
% |
| SNPs |
1155456940 |
1029572111 |
89.11 % |
| Multiallelic |
0 |
0 |
0.00 % |
VCF Filtering Stats
| Type |
#Sites |
% |
#Non-Variant Sites |
% |
#Variant Sites |
% |
| All |
1155456940 |
100% |
1143429909 |
98.96 % |
12027031 |
1.04 % |
| |
|
|
|
|
|
|
| Passed |
1030618750 |
89.20 % |
1027190909 |
89.83 % |
3427841 |
0.33 % |
| Filtered |
124838190 |
10.80 % |
116239000 |
10.17 % |
8599190 |
0.83 % |
| |
|
|
|
|
|
|
| q20 |
90940626 |
72.85 % |
90157371 |
77.56 % |
783255 |
9.11 % |
| q20,mq40 |
12667617 |
10.15 % |
12560697 |
10.81 % |
106920 |
1.24 % |
| q20,qd2 |
12583715 |
10.08 % |
5387927 |
4.64 % |
7195788 |
83.68 % |
| mq40 |
3635441 |
2.91 % |
3440207 |
2.96 % |
195234 |
2.27 % |
| q20,qd2,mq40 |
3129233 |
2.51 % |
2955470 |
2.54 % |
173763 |
2.02 % |
| qd2 |
1836670 |
1.47 % |
1701744 |
1.46 % |
134926 |
1.57 % |
| qd2,mq40 |
43596 |
0.03 % |
35584 |
0.03 % |
8012 |
0.09 % |
| qd2,fs60,mq40 |
619 |
0.00 % |
0 |
0.00 % |
619 |
0.01 % |
| fs60,mq40 |
322 |
0.00 % |
0 |
0.00 % |
322 |
0.00 % |
| qd2,fs60 |
148 |
0.00 % |
0 |
0.00 % |
148 |
0.00 % |
| fs60 |
105 |
0.00 % |
0 |
0.00 % |
105 |
0.00 % |
| q20,qd2,fs60,mq40 |
73 |
0.00 % |
0 |
0.00 % |
73 |
0.00 % |
| q20,qd2,fs60 |
25 |
0.00 % |
0 |
0.00 % |
25 |
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 |
4468953 |
32.56 % |
| Transition |
G>A |
All |
935383 |
6.82 % |
| Transition |
T>C |
All |
4440113 |
32.35 % |
| Transition |
C>T |
All |
937493 |
6.83 % |
| Transversion |
A>C |
All |
224875 |
1.64 % |
| Transversion |
C>A |
All |
575972 |
4.20 % |
| Transversion |
T>G |
All |
226402 |
1.65 % |
| Transversion |
G>T |
All |
567802 |
4.14 % |
| Transversion |
A>T |
All |
466748 |
3.40 % |
| Transversion |
T>A |
All |
466554 |
3.40 % |
| Transversion |
C>G |
All |
207415 |
1.51 % |
| Transversion |
G>C |
All |
206839 |
1.51 % |
| |
|
|
|
|
| Transition |
A>G |
Passed |
615533 |
17.32 % |
| Transition |
G>A |
Passed |
572116 |
16.10 % |
| Transition |
T>C |
Passed |
617716 |
17.38 % |
| Transition |
C>T |
Passed |
575250 |
16.18 % |
| Transversion |
A>C |
Passed |
150485 |
4.23 % |
| Transversion |
C>A |
Passed |
154902 |
4.36 % |
| Transversion |
T>G |
Passed |
151063 |
4.25 % |
| Transversion |
G>T |
Passed |
155119 |
4.36 % |
| Transversion |
A>T |
Passed |
132082 |
3.72 % |
| Transversion |
T>A |
Passed |
132074 |
3.72 % |
| Transversion |
C>G |
Passed |
149053 |
4.19 % |
| Transversion |
G>C |
Passed |
149195 |
4.20 % |
| |
|
|
|
|
| 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 |
3.66 |
10781942 |
2942607 |
| Passed |
2.03 |
2380615 |
1173973 |
| dbSNPAll |
0 |
0 |
0 |
| dbSNPPassed |
0 |
0 |
0 |