/EXTERNAL KNIH/variants/K006257_1_lane_gembs
BACK
SAMPLE K006257_1_lane_gembs
Variant counts
| Type |
Total |
Pass |
% |
| SNPs |
1122689933 |
377461928 |
33.62 % |
| Multiallelic |
0 |
0 |
0.00 % |
VCF Filtering Stats
| Type |
#Sites |
% |
#Non-Variant Sites |
% |
#Variant Sites |
% |
| All |
1122689933 |
100% |
1067445299 |
95.08 % |
55244634 |
4.92 % |
| |
|
|
|
|
|
|
| Passed |
388942582 |
34.64 % |
371651268 |
34.82 % |
17291314 |
4.45 % |
| Filtered |
733747351 |
65.36 % |
695794031 |
65.18 % |
37953320 |
9.76 % |
| |
|
|
|
|
|
|
| q20 |
640683058 |
87.32 % |
624505769 |
89.75 % |
16177289 |
42.62 % |
| q20,qd2 |
80511366 |
10.97 % |
59486395 |
8.55 % |
21024971 |
55.40 % |
| q20,mq40 |
5480076 |
0.75 % |
5364779 |
0.77 % |
115297 |
0.30 % |
| qd2 |
3679313 |
0.50 % |
3219211 |
0.46 % |
460102 |
1.21 % |
| q20,qd2,mq40 |
3062554 |
0.42 % |
2998481 |
0.43 % |
64073 |
0.17 % |
| mq40 |
318109 |
0.04 % |
209701 |
0.03 % |
108408 |
0.29 % |
| qd2,mq40 |
12367 |
0.00 % |
9695 |
0.00 % |
2672 |
0.01 % |
| fs60 |
176 |
0.00 % |
0 |
0.00 % |
176 |
0.00 % |
| q20,qd2,fs60 |
170 |
0.00 % |
0 |
0.00 % |
170 |
0.00 % |
| qd2,fs60 |
82 |
0.00 % |
0 |
0.00 % |
82 |
0.00 % |
| fs60,mq40 |
42 |
0.00 % |
0 |
0.00 % |
42 |
0.00 % |
| qd2,fs60,mq40 |
19 |
0.00 % |
0 |
0.00 % |
19 |
0.00 % |
| q20,qd2,fs60,mq40 |
18 |
0.00 % |
0 |
0.00 % |
18 |
0.00 % |
| q20,fs60,mq40 |
1 |
0.00 % |
0 |
0.00 % |
1 |
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 |
16434619 |
28.31 % |
| Transition |
G>A |
All |
3675475 |
6.33 % |
| Transition |
T>C |
All |
16605932 |
28.61 % |
| Transition |
C>T |
All |
2506009 |
4.32 % |
| Transversion |
A>C |
All |
1763595 |
3.04 % |
| Transversion |
C>A |
All |
3630638 |
6.25 % |
| Transversion |
T>G |
All |
1967997 |
3.39 % |
| Transversion |
G>T |
All |
3399762 |
5.86 % |
| Transversion |
A>T |
All |
2493941 |
4.30 % |
| Transversion |
T>A |
All |
2795977 |
4.82 % |
| Transversion |
C>G |
All |
1400077 |
2.41 % |
| Transversion |
G>C |
All |
1378204 |
2.37 % |
| |
|
|
|
|
| Transition |
A>G |
Passed |
1600937 |
26.07 % |
| Transition |
G>A |
Passed |
649176 |
10.57 % |
| Transition |
T>C |
Passed |
2224112 |
36.22 % |
| Transition |
C>T |
Passed |
396575 |
6.46 % |
| Transversion |
A>C |
Passed |
163162 |
2.66 % |
| Transversion |
C>A |
Passed |
184649 |
3.01 % |
| Transversion |
T>G |
Passed |
184333 |
3.00 % |
| Transversion |
G>T |
Passed |
127341 |
2.07 % |
| Transversion |
A>T |
Passed |
86951 |
1.42 % |
| Transversion |
T>A |
Passed |
143200 |
2.33 % |
| Transversion |
C>G |
Passed |
184728 |
3.01 % |
| Transversion |
G>C |
Passed |
195856 |
3.19 % |
| |
|
|
|
|
| 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 |
2.08 |
39222035 |
18830191 |
| Passed |
3.83 |
4870800 |
1270220 |
| dbSNPAll |
0 |
0 |
0 |
| dbSNPPassed |
0 |
0 |
0 |