/EXTERNAL KNIH/variants/K006244_1_lane_gembs
BACK
SAMPLE K006244_1_lane_gembs
Variant counts
| Type |
Total |
Pass |
% |
| SNPs |
1196077189 |
690257428 |
57.71 % |
| Multiallelic |
0 |
0 |
0.00 % |
VCF Filtering Stats
| Type |
#Sites |
% |
#Non-Variant Sites |
% |
#Variant Sites |
% |
| All |
1196077189 |
100% |
1133709685 |
94.79 % |
62367504 |
5.21 % |
| |
|
|
|
|
|
|
| Passed |
701838337 |
58.68 % |
680477869 |
60.02 % |
21360468 |
3.04 % |
| Filtered |
494238852 |
41.32 % |
453231816 |
39.98 % |
41007036 |
5.84 % |
| |
|
|
|
|
|
|
| q20 |
426393750 |
86.27 % |
411422926 |
90.78 % |
14970824 |
36.51 % |
| q20,qd2 |
50690054 |
10.26 % |
26480967 |
5.84 % |
24209087 |
59.04 % |
| qd2 |
9500096 |
1.92 % |
8052979 |
1.78 % |
1447117 |
3.53 % |
| q20,mq40 |
4929572 |
1.00 % |
4788482 |
1.06 % |
141090 |
0.34 % |
| q20,qd2,mq40 |
2175415 |
0.44 % |
2091599 |
0.46 % |
83816 |
0.20 % |
| mq40 |
526956 |
0.11 % |
379087 |
0.08 % |
147869 |
0.36 % |
| qd2,mq40 |
20205 |
0.00 % |
15776 |
0.00 % |
4429 |
0.01 % |
| fs60 |
1419 |
0.00 % |
0 |
0.00 % |
1419 |
0.00 % |
| q20,qd2,fs60 |
895 |
0.00 % |
0 |
0.00 % |
895 |
0.00 % |
| qd2,fs60 |
302 |
0.00 % |
0 |
0.00 % |
302 |
0.00 % |
| qd2,fs60,mq40 |
81 |
0.00 % |
0 |
0.00 % |
81 |
0.00 % |
| fs60,mq40 |
78 |
0.00 % |
0 |
0.00 % |
78 |
0.00 % |
| q20,qd2,fs60,mq40 |
21 |
0.00 % |
0 |
0.00 % |
21 |
0.00 % |
| q20,fs60 |
8 |
0.00 % |
0 |
0.00 % |
8 |
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 |
20834210 |
32.45 % |
| Transition |
G>A |
All |
4637875 |
7.22 % |
| Transition |
T>C |
All |
23336793 |
36.35 % |
| Transition |
C>T |
All |
3298983 |
5.14 % |
| Transversion |
A>C |
All |
1428242 |
2.22 % |
| Transversion |
C>A |
All |
1978640 |
3.08 % |
| Transversion |
T>G |
All |
1563134 |
2.43 % |
| Transversion |
G>T |
All |
1871960 |
2.92 % |
| Transversion |
A>T |
All |
1488016 |
2.32 % |
| Transversion |
T>A |
All |
1678565 |
2.61 % |
| Transversion |
C>G |
All |
1041547 |
1.62 % |
| Transversion |
G>C |
All |
1049061 |
1.63 % |
| |
|
|
|
|
| Transition |
A>G |
Passed |
2418165 |
23.78 % |
| Transition |
G>A |
Passed |
985857 |
9.70 % |
| Transition |
T>C |
Passed |
4129716 |
40.61 % |
| Transition |
C>T |
Passed |
755218 |
7.43 % |
| Transversion |
A>C |
Passed |
238001 |
2.34 % |
| Transversion |
C>A |
Passed |
273979 |
2.69 % |
| Transversion |
T>G |
Passed |
252400 |
2.48 % |
| Transversion |
G>T |
Passed |
227019 |
2.23 % |
| Transversion |
A>T |
Passed |
170904 |
1.68 % |
| Transversion |
T>A |
Passed |
220444 |
2.17 % |
| Transversion |
C>G |
Passed |
246146 |
2.42 % |
| Transversion |
G>C |
Passed |
250204 |
2.46 % |
| |
|
|
|
|
| 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 |
4.31 |
52107861 |
12099165 |
| Passed |
4.41 |
8288956 |
1879097 |
| dbSNPAll |
0 |
0 |
0 |
| dbSNPPassed |
0 |
0 |
0 |