/EXTERNAL KNIH/variants/K006235_1_lane_gembs
BACK
SAMPLE K006235_1_lane_gembs
Variant counts
| Type |
Total |
Pass |
% |
| SNPs |
1201429825 |
827781275 |
68.90 % |
| Multiallelic |
0 |
0 |
0.00 % |
VCF Filtering Stats
| Type |
#Sites |
% |
#Non-Variant Sites |
% |
#Variant Sites |
% |
| All |
1201429825 |
100% |
1140486457 |
94.93 % |
60943368 |
5.07 % |
| |
|
|
|
|
|
|
| Passed |
837486822 |
69.71 % |
816873009 |
71.62 % |
20613813 |
2.46 % |
| Filtered |
363943003 |
30.29 % |
323613448 |
28.38 % |
40329555 |
4.82 % |
| |
|
|
|
|
|
|
| q20 |
301084470 |
82.73 % |
289086363 |
89.33 % |
11998107 |
29.75 % |
| q20,qd2 |
41605568 |
11.43 % |
16026201 |
4.95 % |
25579367 |
63.43 % |
| qd2 |
13211041 |
3.63 % |
10985536 |
3.39 % |
2225505 |
5.52 % |
| q20,mq40 |
5108719 |
1.40 % |
4931850 |
1.52 % |
176869 |
0.44 % |
| q20,qd2,mq40 |
2152580 |
0.59 % |
2027470 |
0.63 % |
125110 |
0.31 % |
| mq40 |
741001 |
0.20 % |
532872 |
0.16 % |
208129 |
0.52 % |
| qd2,mq40 |
30435 |
0.01 % |
23156 |
0.01 % |
7279 |
0.02 % |
| fs60 |
4983 |
0.00 % |
0 |
0.00 % |
4983 |
0.01 % |
| q20,qd2,fs60 |
2810 |
0.00 % |
0 |
0.00 % |
2810 |
0.01 % |
| qd2,fs60 |
859 |
0.00 % |
0 |
0.00 % |
859 |
0.00 % |
| fs60,mq40 |
225 |
0.00 % |
0 |
0.00 % |
225 |
0.00 % |
| qd2,fs60,mq40 |
146 |
0.00 % |
0 |
0.00 % |
146 |
0.00 % |
| q20,fs60 |
123 |
0.00 % |
0 |
0.00 % |
123 |
0.00 % |
| q20,qd2,fs60,mq40 |
43 |
0.00 % |
0 |
0.00 % |
43 |
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 |
20419093 |
32.29 % |
| Transition |
G>A |
All |
4727433 |
7.48 % |
| Transition |
T>C |
All |
23800188 |
37.64 % |
| Transition |
C>T |
All |
3338478 |
5.28 % |
| Transversion |
A>C |
All |
1295618 |
2.05 % |
| Transversion |
C>A |
All |
1761398 |
2.79 % |
| Transversion |
T>G |
All |
1414713 |
2.24 % |
| Transversion |
G>T |
All |
1660548 |
2.63 % |
| Transversion |
A>T |
All |
1468138 |
2.32 % |
| Transversion |
T>A |
All |
1633827 |
2.58 % |
| Transversion |
C>G |
All |
863325 |
1.37 % |
| Transversion |
G>C |
All |
846346 |
1.34 % |
| |
|
|
|
|
| Transition |
A>G |
Passed |
2900396 |
24.53 % |
| Transition |
G>A |
Passed |
1040257 |
8.80 % |
| Transition |
T>C |
Passed |
5157632 |
43.62 % |
| Transition |
C>T |
Passed |
759954 |
6.43 % |
| Transversion |
A>C |
Passed |
246732 |
2.09 % |
| Transversion |
C>A |
Passed |
299445 |
2.53 % |
| Transversion |
T>G |
Passed |
267143 |
2.26 % |
| Transversion |
G>T |
Passed |
240854 |
2.04 % |
| Transversion |
A>T |
Passed |
188819 |
1.60 % |
| Transversion |
T>A |
Passed |
247194 |
2.09 % |
| Transversion |
C>G |
Passed |
238459 |
2.02 % |
| Transversion |
G>C |
Passed |
236669 |
2.00 % |
| |
|
|
|
|
| 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 |
4.78 |
52285192 |
10943913 |
| Passed |
5.02 |
9858239 |
1965315 |
| dbSNPAll |
0 |
0 |
0 |
| dbSNPPassed |
0 |
0 |
0 |