/EXTERNAL KNIH/variants/K006226_1_lane_gembs
BACK
SAMPLE K006226_1_lane_gembs
Variant counts
| Type |
Total |
Pass |
% |
| SNPs |
1160291619 |
1058548999 |
91.23 % |
| Multiallelic |
0 |
0 |
0.00 % |
VCF Filtering Stats
| Type |
#Sites |
% |
#Non-Variant Sites |
% |
#Variant Sites |
% |
| All |
1160291619 |
100% |
1147127507 |
98.87 % |
13164112 |
1.13 % |
| |
|
|
|
|
|
|
| Passed |
1059626298 |
91.32 % |
1055996039 |
92.06 % |
3630259 |
0.34 % |
| Filtered |
100665321 |
8.68 % |
91131468 |
7.94 % |
9533853 |
0.90 % |
| |
|
|
|
|
|
|
| q20 |
63537866 |
63.12 % |
62779436 |
68.89 % |
758430 |
7.96 % |
| q20,mq40 |
14123738 |
14.03 % |
13986071 |
15.35 % |
137667 |
1.44 % |
| q20,qd2 |
10371462 |
10.30 % |
2746175 |
3.01 % |
7625287 |
79.98 % |
| mq40 |
7165216 |
7.12 % |
6861274 |
7.53 % |
303942 |
3.19 % |
| q20,qd2,mq40 |
3048631 |
3.03 % |
2792729 |
3.06 % |
255902 |
2.68 % |
| qd2 |
2331742 |
2.32 % |
1896819 |
2.08 % |
434923 |
4.56 % |
| qd2,mq40 |
83141 |
0.08 % |
68964 |
0.08 % |
14177 |
0.15 % |
| qd2,fs60,mq40 |
1424 |
0.00 % |
0 |
0.00 % |
1424 |
0.01 % |
| fs60 |
633 |
0.00 % |
0 |
0.00 % |
633 |
0.01 % |
| fs60,mq40 |
566 |
0.00 % |
0 |
0.00 % |
566 |
0.01 % |
| qd2,fs60 |
461 |
0.00 % |
0 |
0.00 % |
461 |
0.00 % |
| q20,qd2,fs60 |
286 |
0.00 % |
0 |
0.00 % |
286 |
0.00 % |
| q20,qd2,fs60,mq40 |
151 |
0.00 % |
0 |
0.00 % |
151 |
0.00 % |
| q20,fs60,mq40 |
4 |
0.00 % |
0 |
0.00 % |
4 |
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 |
5488994 |
36.62 % |
| Transition |
G>A |
All |
882652 |
5.89 % |
| Transition |
T>C |
All |
5417463 |
36.15 % |
| Transition |
C>T |
All |
888604 |
5.93 % |
| Transversion |
A>C |
All |
218713 |
1.46 % |
| Transversion |
C>A |
All |
389823 |
2.60 % |
| Transversion |
T>G |
All |
220734 |
1.47 % |
| Transversion |
G>T |
All |
386530 |
2.58 % |
| Transversion |
A>T |
All |
344197 |
2.30 % |
| Transversion |
T>A |
All |
333983 |
2.23 % |
| Transversion |
C>G |
All |
208023 |
1.39 % |
| Transversion |
G>C |
All |
207882 |
1.39 % |
| |
|
|
|
|
| Transition |
A>G |
Passed |
759844 |
19.53 % |
| Transition |
G>A |
Passed |
598521 |
15.38 % |
| Transition |
T>C |
Passed |
735563 |
18.90 % |
| Transition |
C>T |
Passed |
602835 |
15.49 % |
| Transversion |
A>C |
Passed |
152640 |
3.92 % |
| Transversion |
C>A |
Passed |
155502 |
4.00 % |
| Transversion |
T>G |
Passed |
152827 |
3.93 % |
| Transversion |
G>T |
Passed |
155906 |
4.01 % |
| Transversion |
A>T |
Passed |
136789 |
3.52 % |
| Transversion |
T>A |
Passed |
136130 |
3.50 % |
| Transversion |
C>G |
Passed |
152486 |
3.92 % |
| Transversion |
G>C |
Passed |
152435 |
3.92 % |
| |
|
|
|
|
| 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 |
5.49 |
12677713 |
2309885 |
| Passed |
2.26 |
2696763 |
1194715 |
| dbSNPAll |
0 |
0 |
0 |
| dbSNPPassed |
0 |
0 |
0 |