/EXTERNAL KNIH/variants/K006222_1_lane_gembs
BACK
SAMPLE K006222_1_lane_gembs
Variant counts
| Type |
Total |
Pass |
% |
| SNPs |
1157004254 |
1024052748 |
88.51 % |
| Multiallelic |
0 |
0 |
0.00 % |
VCF Filtering Stats
| Type |
#Sites |
% |
#Non-Variant Sites |
% |
#Variant Sites |
% |
| All |
1157004254 |
100% |
1141063056 |
98.62 % |
15941198 |
1.38 % |
| |
|
|
|
|
|
|
| Passed |
1026151144 |
88.69 % |
1021590196 |
89.53 % |
4560948 |
0.44 % |
| Filtered |
130853110 |
11.31 % |
119472860 |
10.47 % |
11380250 |
1.11 % |
| |
|
|
|
|
|
|
| q20 |
91616432 |
70.01 % |
90290745 |
75.57 % |
1325687 |
11.65 % |
| q20,mq40 |
13608311 |
10.40 % |
13474788 |
11.28 % |
133523 |
1.17 % |
| q20,qd2 |
11799052 |
9.02 % |
2852646 |
2.39 % |
8946406 |
78.61 % |
| mq40 |
8662961 |
6.62 % |
8351701 |
6.99 % |
311260 |
2.74 % |
| q20,qd2,mq40 |
2862483 |
2.19 % |
2604850 |
2.18 % |
257633 |
2.26 % |
| qd2 |
2207892 |
1.69 % |
1824359 |
1.53 % |
383533 |
3.37 % |
| qd2,mq40 |
89695 |
0.07 % |
73771 |
0.06 % |
15924 |
0.14 % |
| qd2,fs60,mq40 |
1641 |
0.00 % |
0 |
0.00 % |
1641 |
0.01 % |
| fs60 |
1367 |
0.00 % |
0 |
0.00 % |
1367 |
0.01 % |
| q20,qd2,fs60 |
1313 |
0.00 % |
0 |
0.00 % |
1313 |
0.01 % |
| qd2,fs60 |
1052 |
0.00 % |
0 |
0.00 % |
1052 |
0.01 % |
| fs60,mq40 |
651 |
0.00 % |
0 |
0.00 % |
651 |
0.01 % |
| q20,qd2,fs60,mq40 |
256 |
0.00 % |
0 |
0.00 % |
256 |
0.00 % |
| q20,fs60,mq40 |
4 |
0.00 % |
0 |
0.00 % |
4 |
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 |
6750341 |
37.82 % |
| Transition |
G>A |
All |
1116521 |
6.26 % |
| Transition |
T>C |
All |
6711952 |
37.60 % |
| Transition |
C>T |
All |
1109837 |
6.22 % |
| Transversion |
A>C |
All |
218218 |
1.22 % |
| Transversion |
C>A |
All |
358852 |
2.01 % |
| Transversion |
T>G |
All |
220781 |
1.24 % |
| Transversion |
G>T |
All |
354030 |
1.98 % |
| Transversion |
A>T |
All |
307021 |
1.72 % |
| Transversion |
T>A |
All |
297045 |
1.66 % |
| Transversion |
C>G |
All |
203381 |
1.14 % |
| Transversion |
G>C |
All |
201922 |
1.13 % |
| |
|
|
|
|
| Transition |
A>G |
Passed |
728918 |
19.58 % |
| Transition |
G>A |
Passed |
568150 |
15.26 % |
| Transition |
T>C |
Passed |
736474 |
19.78 % |
| Transition |
C>T |
Passed |
572040 |
15.36 % |
| Transversion |
A>C |
Passed |
144576 |
3.88 % |
| Transversion |
C>A |
Passed |
143813 |
3.86 % |
| Transversion |
T>G |
Passed |
145018 |
3.89 % |
| Transversion |
G>T |
Passed |
143576 |
3.86 % |
| Transversion |
A>T |
Passed |
123927 |
3.33 % |
| Transversion |
T>A |
Passed |
123785 |
3.32 % |
| Transversion |
C>G |
Passed |
146456 |
3.93 % |
| Transversion |
G>C |
Passed |
146656 |
3.94 % |
| |
|
|
|
|
| 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 |
7.26 |
15688651 |
2161250 |
| Passed |
2.33 |
2605582 |
1117807 |
| dbSNPAll |
0 |
0 |
0 |
| dbSNPPassed |
0 |
0 |
0 |