/EXTERNAL KNIH/variants/K006249_1_lane_gembs
BACK
SAMPLE K006249_1_lane_gembs
Variant counts
| Type |
Total |
Pass |
% |
| SNPs |
1190732563 |
419759405 |
35.25 % |
| Multiallelic |
0 |
0 |
0.00 % |
VCF Filtering Stats
| Type |
#Sites |
% |
#Non-Variant Sites |
% |
#Variant Sites |
% |
| All |
1190732563 |
100% |
1106067538 |
92.89 % |
84665025 |
7.11 % |
| |
|
|
|
|
|
|
| Passed |
442275507 |
37.14 % |
410754493 |
37.14 % |
31521014 |
7.13 % |
| Filtered |
748457056 |
62.86 % |
695313045 |
62.86 % |
53144011 |
12.02 % |
| |
|
|
|
|
|
|
| q20 |
664586525 |
88.79 % |
642803489 |
92.45 % |
21783036 |
40.99 % |
| q20,qd2 |
71532516 |
9.56 % |
41256626 |
5.93 % |
30275890 |
56.97 % |
| q20,mq40 |
5942017 |
0.79 % |
5769046 |
0.83 % |
172971 |
0.33 % |
| q20,qd2,mq40 |
2991861 |
0.40 % |
2892251 |
0.42 % |
99610 |
0.19 % |
| qd2 |
2911035 |
0.39 % |
2278960 |
0.33 % |
632075 |
1.19 % |
| mq40 |
477355 |
0.06 % |
300786 |
0.04 % |
176569 |
0.33 % |
| qd2,mq40 |
15248 |
0.00 % |
11887 |
0.00 % |
3361 |
0.01 % |
| fs60 |
211 |
0.00 % |
0 |
0.00 % |
211 |
0.00 % |
| q20,qd2,fs60 |
102 |
0.00 % |
0 |
0.00 % |
102 |
0.00 % |
| qd2,fs60 |
85 |
0.00 % |
0 |
0.00 % |
85 |
0.00 % |
| qd2,fs60,mq40 |
40 |
0.00 % |
0 |
0.00 % |
40 |
0.00 % |
| fs60,mq40 |
38 |
0.00 % |
0 |
0.00 % |
38 |
0.00 % |
| q20,qd2,fs60,mq40 |
23 |
0.00 % |
0 |
0.00 % |
23 |
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 |
29278164 |
33.28 % |
| Transition |
G>A |
All |
4587246 |
5.21 % |
| Transition |
T>C |
All |
30404571 |
34.56 % |
| Transition |
C>T |
All |
3126545 |
3.55 % |
| Transversion |
A>C |
All |
2430101 |
2.76 % |
| Transversion |
C>A |
All |
3502277 |
3.98 % |
| Transversion |
T>G |
All |
2700750 |
3.07 % |
| Transversion |
G>T |
All |
3316797 |
3.77 % |
| Transversion |
A>T |
All |
2328611 |
2.65 % |
| Transversion |
T>A |
All |
2675865 |
3.04 % |
| Transversion |
C>G |
All |
1821541 |
2.07 % |
| Transversion |
G>C |
All |
1795092 |
2.04 % |
| |
|
|
|
|
| Transition |
A>G |
Passed |
2913216 |
31.11 % |
| Transition |
G>A |
Passed |
734522 |
7.84 % |
| Transition |
T>C |
Passed |
3521263 |
37.60 % |
| Transition |
C>T |
Passed |
433349 |
4.63 % |
| Transversion |
A>C |
Passed |
217581 |
2.32 % |
| Transversion |
C>A |
Passed |
317438 |
3.39 % |
| Transversion |
T>G |
Passed |
249145 |
2.66 % |
| Transversion |
G>T |
Passed |
211545 |
2.26 % |
| Transversion |
A>T |
Passed |
118540 |
1.27 % |
| Transversion |
T>A |
Passed |
205587 |
2.20 % |
| Transversion |
C>G |
Passed |
215046 |
2.30 % |
| Transversion |
G>C |
Passed |
228108 |
2.44 % |
| |
|
|
|
|
| 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 |
3.28 |
67396526 |
20571034 |
| Passed |
4.31 |
7602350 |
1762990 |
| dbSNPAll |
0 |
0 |
0 |
| dbSNPPassed |
0 |
0 |
0 |