/EXTERNAL KNIH/variants/K006233_1_lane_gembs
BACK
SAMPLE K006233_1_lane_gembs
Variant counts
| Type |
Total |
Pass |
% |
| SNPs |
1199133806 |
800240359 |
66.73 % |
| Multiallelic |
0 |
0 |
0.00 % |
VCF Filtering Stats
| Type |
#Sites |
% |
#Non-Variant Sites |
% |
#Variant Sites |
% |
| All |
1199133806 |
100% |
1138280542 |
94.93 % |
60853264 |
5.07 % |
| |
|
|
|
|
|
|
| Passed |
810573752 |
67.60 % |
789025858 |
69.32 % |
21547894 |
2.66 % |
| Filtered |
388560054 |
32.40 % |
349254684 |
30.68 % |
39305370 |
4.85 % |
| |
|
|
|
|
|
|
| q20 |
326826104 |
84.11 % |
315081206 |
90.22 % |
11744898 |
29.88 % |
| q20,qd2 |
41524466 |
10.69 % |
16789448 |
4.81 % |
24735018 |
62.93 % |
| qd2 |
12428136 |
3.20 % |
10079192 |
2.89 % |
2348944 |
5.98 % |
| q20,mq40 |
4950646 |
1.27 % |
4793216 |
1.37 % |
157430 |
0.40 % |
| q20,qd2,mq40 |
2073695 |
0.53 % |
1961711 |
0.56 % |
111984 |
0.28 % |
| mq40 |
719100 |
0.19 % |
528778 |
0.15 % |
190322 |
0.48 % |
| qd2,mq40 |
27746 |
0.01 % |
21133 |
0.01 % |
6613 |
0.02 % |
| fs60 |
4994 |
0.00 % |
0 |
0.00 % |
4994 |
0.01 % |
| q20,qd2,fs60 |
3964 |
0.00 % |
0 |
0.00 % |
3964 |
0.01 % |
| qd2,fs60 |
799 |
0.00 % |
0 |
0.00 % |
799 |
0.00 % |
| fs60,mq40 |
136 |
0.00 % |
0 |
0.00 % |
136 |
0.00 % |
| q20,fs60 |
121 |
0.00 % |
0 |
0.00 % |
121 |
0.00 % |
| qd2,fs60,mq40 |
107 |
0.00 % |
0 |
0.00 % |
107 |
0.00 % |
| q20,qd2,fs60,mq40 |
40 |
0.00 % |
0 |
0.00 % |
40 |
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 |
20732974 |
32.83 % |
| Transition |
G>A |
All |
4674033 |
7.40 % |
| Transition |
T>C |
All |
23936874 |
37.91 % |
| Transition |
C>T |
All |
3320059 |
5.26 % |
| Transversion |
A>C |
All |
1086500 |
1.72 % |
| Transversion |
C>A |
All |
1759651 |
2.79 % |
| Transversion |
T>G |
All |
1210921 |
1.92 % |
| Transversion |
G>T |
All |
1654300 |
2.62 % |
| Transversion |
A>T |
All |
1517076 |
2.40 % |
| Transversion |
T>A |
All |
1689012 |
2.67 % |
| Transversion |
C>G |
All |
787799 |
1.25 % |
| Transversion |
G>C |
All |
775305 |
1.23 % |
| |
|
|
|
|
| Transition |
A>G |
Passed |
3049140 |
25.28 % |
| Transition |
G>A |
Passed |
1057167 |
8.77 % |
| Transition |
T>C |
Passed |
5196342 |
43.08 % |
| Transition |
C>T |
Passed |
774063 |
6.42 % |
| Transversion |
A>C |
Passed |
243537 |
2.02 % |
| Transversion |
C>A |
Passed |
306916 |
2.54 % |
| Transversion |
T>G |
Passed |
267335 |
2.22 % |
| Transversion |
G>T |
Passed |
248851 |
2.06 % |
| Transversion |
A>T |
Passed |
190636 |
1.58 % |
| Transversion |
T>A |
Passed |
251062 |
2.08 % |
| Transversion |
C>G |
Passed |
239214 |
1.98 % |
| Transversion |
G>C |
Passed |
236602 |
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 |
5.02 |
52663940 |
10480564 |
| Passed |
5.08 |
10076712 |
1984153 |
| dbSNPAll |
0 |
0 |
0 |
| dbSNPPassed |
0 |
0 |
0 |