/EXTERNAL KNIH/variants/K006253_1_lane_gembs
BACK
SAMPLE K006253_1_lane_gembs
Variant counts
| Type |
Total |
Pass |
% |
| SNPs |
1127075783 |
376128941 |
33.37 % |
| Multiallelic |
0 |
0 |
0.00 % |
VCF Filtering Stats
| Type |
#Sites |
% |
#Non-Variant Sites |
% |
#Variant Sites |
% |
| All |
1127075783 |
100% |
1071969407 |
95.11 % |
55106376 |
4.89 % |
| |
|
|
|
|
|
|
| Passed |
387635420 |
34.39 % |
370241446 |
34.54 % |
17393974 |
4.49 % |
| Filtered |
739440363 |
65.61 % |
701727961 |
65.46 % |
37712402 |
9.73 % |
| |
|
|
|
|
|
|
| q20 |
648445941 |
87.69 % |
632497276 |
90.13 % |
15948665 |
42.29 % |
| q20,qd2 |
78518191 |
10.62 % |
57498953 |
8.19 % |
21019238 |
55.74 % |
| q20,mq40 |
5718701 |
0.77 % |
5596043 |
0.80 % |
122658 |
0.33 % |
| qd2 |
3242299 |
0.44 % |
2808024 |
0.40 % |
434275 |
1.15 % |
| q20,qd2,mq40 |
3165045 |
0.43 % |
3096081 |
0.44 % |
68964 |
0.18 % |
| mq40 |
336858 |
0.05 % |
221547 |
0.03 % |
115311 |
0.31 % |
| qd2,mq40 |
12905 |
0.00 % |
10037 |
0.00 % |
2868 |
0.01 % |
| fs60 |
145 |
0.00 % |
0 |
0.00 % |
145 |
0.00 % |
| q20,qd2,fs60 |
133 |
0.00 % |
0 |
0.00 % |
133 |
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 |
20 |
0.00 % |
0 |
0.00 % |
20 |
0.00 % |
| q20,qd2,fs60,mq40 |
18 |
0.00 % |
0 |
0.00 % |
18 |
0.00 % |
| q20,fs60 |
2 |
0.00 % |
0 |
0.00 % |
2 |
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 |
16397017 |
28.31 % |
| Transition |
G>A |
All |
3690525 |
6.37 % |
| Transition |
T>C |
All |
16346631 |
28.22 % |
| Transition |
C>T |
All |
2554209 |
4.41 % |
| Transversion |
A>C |
All |
1743058 |
3.01 % |
| Transversion |
C>A |
All |
3612136 |
6.24 % |
| Transversion |
T>G |
All |
1942453 |
3.35 % |
| Transversion |
G>T |
All |
3403781 |
5.88 % |
| Transversion |
A>T |
All |
2592285 |
4.48 % |
| Transversion |
T>A |
All |
2888420 |
4.99 % |
| Transversion |
C>G |
All |
1379001 |
2.38 % |
| Transversion |
G>C |
All |
1369490 |
2.36 % |
| |
|
|
|
|
| Transition |
A>G |
Passed |
1655012 |
26.61 % |
| Transition |
G>A |
Passed |
644552 |
10.36 % |
| Transition |
T>C |
Passed |
2193730 |
35.27 % |
| Transition |
C>T |
Passed |
409600 |
6.59 % |
| Transversion |
A>C |
Passed |
168680 |
2.71 % |
| Transversion |
C>A |
Passed |
189527 |
3.05 % |
| Transversion |
T>G |
Passed |
189582 |
3.05 % |
| Transversion |
G>T |
Passed |
138798 |
2.23 % |
| Transversion |
A>T |
Passed |
94498 |
1.52 % |
| Transversion |
T>A |
Passed |
147915 |
2.38 % |
| Transversion |
C>G |
Passed |
187064 |
3.01 % |
| Transversion |
G>C |
Passed |
200350 |
3.22 % |
| |
|
|
|
|
| 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 |
2.06 |
38988382 |
18930624 |
| Passed |
3.72 |
4902894 |
1316414 |
| dbSNPAll |
0 |
0 |
0 |
| dbSNPPassed |
0 |
0 |
0 |