/EXTERNAL KNIH/variants/K006231_1_lane_gembs
BACK
SAMPLE K006231_1_lane_gembs
Variant counts
| Type |
Total |
Pass |
% |
| SNPs |
1153757659 |
1068838089 |
92.64 % |
| Multiallelic |
0 |
0 |
0.00 % |
VCF Filtering Stats
| Type |
#Sites |
% |
#Non-Variant Sites |
% |
#Variant Sites |
% |
| All |
1153757659 |
100% |
1141339601 |
98.92 % |
12418058 |
1.08 % |
| |
|
|
|
|
|
|
| Passed |
1069642940 |
92.71 % |
1066238859 |
93.42 % |
3404081 |
0.32 % |
| Filtered |
84114719 |
7.29 % |
75100742 |
6.58 % |
9013977 |
0.84 % |
| |
|
|
|
|
|
|
| q20 |
47011909 |
55.89 % |
46367279 |
61.74 % |
644630 |
7.15 % |
| q20,mq40 |
14236848 |
16.93 % |
14088251 |
18.76 % |
148597 |
1.65 % |
| q20,qd2 |
9646495 |
11.47 % |
2516403 |
3.35 % |
7130092 |
79.10 % |
| mq40 |
7533265 |
8.96 % |
7214418 |
9.61 % |
318847 |
3.54 % |
| q20,qd2,mq40 |
3055974 |
3.63 % |
2798396 |
3.73 % |
257578 |
2.86 % |
| qd2 |
2559246 |
3.04 % |
2060214 |
2.74 % |
499032 |
5.54 % |
| qd2,mq40 |
68374 |
0.08 % |
55781 |
0.07 % |
12593 |
0.14 % |
| qd2,fs60,mq40 |
1127 |
0.00 % |
0 |
0.00 % |
1127 |
0.01 % |
| fs60,mq40 |
528 |
0.00 % |
0 |
0.00 % |
528 |
0.01 % |
| fs60 |
392 |
0.00 % |
0 |
0.00 % |
392 |
0.00 % |
| qd2,fs60 |
285 |
0.00 % |
0 |
0.00 % |
285 |
0.00 % |
| q20,qd2,fs60 |
149 |
0.00 % |
0 |
0.00 % |
149 |
0.00 % |
| q20,qd2,fs60,mq40 |
122 |
0.00 % |
0 |
0.00 % |
122 |
0.00 % |
| q20,fs60,mq40 |
5 |
0.00 % |
0 |
0.00 % |
5 |
0.00 % |
| q20,fs60 |
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 |
5137524 |
36.13 % |
| Transition |
G>A |
All |
864859 |
6.08 % |
| Transition |
T>C |
All |
5107191 |
35.91 % |
| Transition |
C>T |
All |
870840 |
6.12 % |
| Transversion |
A>C |
All |
228595 |
1.61 % |
| Transversion |
C>A |
All |
365738 |
2.57 % |
| Transversion |
T>G |
All |
230634 |
1.62 % |
| Transversion |
G>T |
All |
360935 |
2.54 % |
| Transversion |
A>T |
All |
318522 |
2.24 % |
| Transversion |
T>A |
All |
311876 |
2.19 % |
| Transversion |
C>G |
All |
212715 |
1.50 % |
| Transversion |
G>C |
All |
211895 |
1.49 % |
| |
|
|
|
|
| Transition |
A>G |
Passed |
756474 |
19.24 % |
| Transition |
G>A |
Passed |
601352 |
15.30 % |
| Transition |
T>C |
Passed |
759972 |
19.33 % |
| Transition |
C>T |
Passed |
605692 |
15.41 % |
| Transversion |
A>C |
Passed |
154286 |
3.92 % |
| Transversion |
C>A |
Passed |
158111 |
4.02 % |
| Transversion |
T>G |
Passed |
154845 |
3.94 % |
| Transversion |
G>T |
Passed |
157224 |
4.00 % |
| Transversion |
A>T |
Passed |
137570 |
3.50 % |
| Transversion |
T>A |
Passed |
137322 |
3.49 % |
| Transversion |
C>G |
Passed |
154186 |
3.92 % |
| Transversion |
G>C |
Passed |
153850 |
3.91 % |
| |
|
|
|
|
| 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 |
5.35 |
11980414 |
2240910 |
| Passed |
2.26 |
2723490 |
1207394 |
| dbSNPAll |
0 |
0 |
0 |
| dbSNPPassed |
0 |
0 |
0 |