/EXTERNAL KNIH/variants/K006239_1_lane_gembs
BACK
SAMPLE K006239_1_lane_gembs
Variant counts
| Type |
Total |
Pass |
% |
| SNPs |
1206345193 |
819318883 |
67.92 % |
| Multiallelic |
0 |
0 |
0.00 % |
VCF Filtering Stats
| Type |
#Sites |
% |
#Non-Variant Sites |
% |
#Variant Sites |
% |
| All |
1206345193 |
100% |
1144808048 |
94.90 % |
61537145 |
5.10 % |
| |
|
|
|
|
|
|
| Passed |
829505596 |
68.76 % |
808679006 |
70.64 % |
20826590 |
2.51 % |
| Filtered |
376839597 |
31.24 % |
336129042 |
29.36 % |
40710555 |
4.91 % |
| |
|
|
|
|
|
|
| q20 |
313065996 |
83.08 % |
300506751 |
89.40 % |
12559245 |
30.85 % |
| q20,qd2 |
42087604 |
11.17 % |
16688418 |
4.96 % |
25399186 |
62.39 % |
| qd2 |
13737207 |
3.65 % |
11503480 |
3.42 % |
2233727 |
5.49 % |
| q20,mq40 |
5045792 |
1.34 % |
4875296 |
1.45 % |
170496 |
0.42 % |
| q20,qd2,mq40 |
2114092 |
0.56 % |
1991025 |
0.59 % |
123067 |
0.30 % |
| mq40 |
748954 |
0.20 % |
541476 |
0.16 % |
207478 |
0.51 % |
| qd2,mq40 |
29690 |
0.01 % |
22596 |
0.01 % |
7094 |
0.02 % |
| fs60 |
5702 |
0.00 % |
0 |
0.00 % |
5702 |
0.01 % |
| q20,qd2,fs60 |
3139 |
0.00 % |
0 |
0.00 % |
3139 |
0.01 % |
| qd2,fs60 |
918 |
0.00 % |
0 |
0.00 % |
918 |
0.00 % |
| fs60,mq40 |
195 |
0.00 % |
0 |
0.00 % |
195 |
0.00 % |
| qd2,fs60,mq40 |
140 |
0.00 % |
0 |
0.00 % |
140 |
0.00 % |
| q20,fs60 |
118 |
0.00 % |
0 |
0.00 % |
118 |
0.00 % |
| q20,qd2,fs60,mq40 |
49 |
0.00 % |
0 |
0.00 % |
49 |
0.00 % |
| q20,fs60,mq40 |
1 |
0.00 % |
0 |
0.00 % |
1 |
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 |
20908625 |
32.75 % |
| Transition |
G>A |
All |
4572275 |
7.16 % |
| Transition |
T>C |
All |
24111423 |
37.76 % |
| Transition |
C>T |
All |
3262305 |
5.11 % |
| Transversion |
A>C |
All |
1246900 |
1.95 % |
| Transversion |
C>A |
All |
1834808 |
2.87 % |
| Transversion |
T>G |
All |
1349568 |
2.11 % |
| Transversion |
G>T |
All |
1745164 |
2.73 % |
| Transversion |
A>T |
All |
1512123 |
2.37 % |
| Transversion |
T>A |
All |
1668428 |
2.61 % |
| Transversion |
C>G |
All |
823588 |
1.29 % |
| Transversion |
G>C |
All |
814926 |
1.28 % |
| |
|
|
|
|
| Transition |
A>G |
Passed |
2863025 |
24.77 % |
| Transition |
G>A |
Passed |
992591 |
8.59 % |
| Transition |
T>C |
Passed |
5076203 |
43.93 % |
| Transition |
C>T |
Passed |
737025 |
6.38 % |
| Transversion |
A>C |
Passed |
235787 |
2.04 % |
| Transversion |
C>A |
Passed |
288459 |
2.50 % |
| Transversion |
T>G |
Passed |
253308 |
2.19 % |
| Transversion |
G>T |
Passed |
234298 |
2.03 % |
| Transversion |
A>T |
Passed |
181920 |
1.57 % |
| Transversion |
T>A |
Passed |
238134 |
2.06 % |
| Transversion |
C>G |
Passed |
228484 |
1.98 % |
| Transversion |
G>C |
Passed |
226963 |
1.96 % |
| |
|
|
|
|
| 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 |
4.81 |
52854628 |
10995505 |
| Passed |
5.12 |
9668844 |
1887353 |
| dbSNPAll |
0 |
0 |
0 |
| dbSNPPassed |
0 |
0 |
0 |