/EXTERNAL KNIH/variants/K006258_1_lane_gembs
BACK
SAMPLE K006258_1_lane_gembs
Variant counts
| Type |
Total |
Pass |
% |
| SNPs |
1194299566 |
420883147 |
35.24 % |
| Multiallelic |
0 |
0 |
0.00 % |
VCF Filtering Stats
| Type |
#Sites |
% |
#Non-Variant Sites |
% |
#Variant Sites |
% |
| All |
1194299566 |
100% |
1107715389 |
92.75 % |
86584177 |
7.25 % |
| |
|
|
|
|
|
|
| Passed |
443199868 |
37.11 % |
412303697 |
37.22 % |
30896171 |
6.97 % |
| Filtered |
751099698 |
62.89 % |
695411692 |
62.78 % |
55688006 |
12.56 % |
| |
|
|
|
|
|
|
| q20 |
662621147 |
88.22 % |
639046656 |
91.89 % |
23574491 |
42.33 % |
| q20,qd2 |
75704393 |
10.08 % |
44673598 |
6.42 % |
31030795 |
55.72 % |
| q20,mq40 |
5943838 |
0.79 % |
5768744 |
0.83 % |
175094 |
0.31 % |
| qd2 |
3342010 |
0.44 % |
2695935 |
0.39 % |
646075 |
1.16 % |
| q20,qd2,mq40 |
3041062 |
0.40 % |
2949171 |
0.42 % |
91891 |
0.17 % |
| mq40 |
432422 |
0.06 % |
266389 |
0.04 % |
166033 |
0.30 % |
| qd2,mq40 |
14415 |
0.00 % |
11199 |
0.00 % |
3216 |
0.01 % |
| fs60 |
150 |
0.00 % |
0 |
0.00 % |
150 |
0.00 % |
| q20,qd2,fs60 |
99 |
0.00 % |
0 |
0.00 % |
99 |
0.00 % |
| qd2,fs60 |
63 |
0.00 % |
0 |
0.00 % |
63 |
0.00 % |
| fs60,mq40 |
42 |
0.00 % |
0 |
0.00 % |
42 |
0.00 % |
| qd2,fs60,mq40 |
39 |
0.00 % |
0 |
0.00 % |
39 |
0.00 % |
| q20,qd2,fs60,mq40 |
18 |
0.00 % |
0 |
0.00 % |
18 |
0.00 % |
| q20,fs60 |
0 |
0.00 % |
0 |
0.00 % |
0 |
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 |
30383122 |
33.77 % |
| Transition |
G>A |
All |
4508307 |
5.01 % |
| Transition |
T>C |
All |
30683050 |
34.10 % |
| Transition |
C>T |
All |
3044227 |
3.38 % |
| Transversion |
A>C |
All |
2927566 |
3.25 % |
| Transversion |
C>A |
All |
3287048 |
3.65 % |
| Transversion |
T>G |
All |
3213044 |
3.57 % |
| Transversion |
G>T |
All |
3058581 |
3.40 % |
| Transversion |
A>T |
All |
2205183 |
2.45 % |
| Transversion |
T>A |
All |
2572761 |
2.86 % |
| Transversion |
C>G |
All |
2064546 |
2.29 % |
| Transversion |
G>C |
All |
2023686 |
2.25 % |
| |
|
|
|
|
| Transition |
A>G |
Passed |
2720797 |
30.38 % |
| Transition |
G>A |
Passed |
687369 |
7.68 % |
| Transition |
T>C |
Passed |
3338923 |
37.28 % |
| Transition |
C>T |
Passed |
431562 |
4.82 % |
| Transversion |
A>C |
Passed |
264818 |
2.96 % |
| Transversion |
C>A |
Passed |
264394 |
2.95 % |
| Transversion |
T>G |
Passed |
297522 |
3.32 % |
| Transversion |
G>T |
Passed |
195494 |
2.18 % |
| Transversion |
A>T |
Passed |
112083 |
1.25 % |
| Transversion |
T>A |
Passed |
182840 |
2.04 % |
| Transversion |
C>G |
Passed |
226335 |
2.53 % |
| Transversion |
G>C |
Passed |
233514 |
2.61 % |
| |
|
|
|
|
| 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 |
3.21 |
68618706 |
21352415 |
| Passed |
4.04 |
7178651 |
1777000 |
| dbSNPAll |
0 |
0 |
0 |
| dbSNPPassed |
0 |
0 |
0 |