/EXTERNAL CREST/variants/K006436_1_lane_gembs
BACK
SAMPLE K006436_1_lane_gembs
Variant counts
| Type |
Total |
Pass |
% |
| SNPs |
1225011053 |
634970790 |
51.83 % |
| Multiallelic |
0 |
0 |
0.00 % |
VCF Filtering Stats
| Type |
#Sites |
% |
#Non-Variant Sites |
% |
#Variant Sites |
% |
| All |
1225011053 |
100% |
1108395173 |
90.48 % |
116615880 |
9.52 % |
| |
|
|
|
|
|
|
| Passed |
653425805 |
53.34 % |
627554008 |
56.62 % |
25871797 |
3.96 % |
| Filtered |
571585248 |
46.66 % |
480841165 |
43.38 % |
90744083 |
13.89 % |
| |
|
|
|
|
|
|
| q20 |
405079461 |
70.87 % |
380745136 |
79.18 % |
24334325 |
26.82 % |
| q20,qd2 |
88213963 |
15.43 % |
28418632 |
5.91 % |
59795331 |
65.89 % |
| q20,mq40 |
44711108 |
7.82 % |
42918207 |
8.93 % |
1792901 |
1.98 % |
| mq40 |
20358798 |
3.56 % |
18432381 |
3.83 % |
1926417 |
2.12 % |
| q20,qd2,mq40 |
7486713 |
1.31 % |
5195681 |
1.08 % |
2291032 |
2.52 % |
| qd2 |
5652971 |
0.99 % |
5064861 |
1.05 % |
588110 |
0.65 % |
| qd2,mq40 |
81588 |
0.01 % |
66267 |
0.01 % |
15321 |
0.02 % |
| fs60 |
311 |
0.00 % |
0 |
0.00 % |
311 |
0.00 % |
| fs60,mq40 |
271 |
0.00 % |
0 |
0.00 % |
271 |
0.00 % |
| q20,qd2,fs60 |
30 |
0.00 % |
0 |
0.00 % |
30 |
0.00 % |
| q20,fs60 |
13 |
0.00 % |
0 |
0.00 % |
13 |
0.00 % |
| qd2,fs60 |
10 |
0.00 % |
0 |
0.00 % |
10 |
0.00 % |
| qd2,fs60,mq40 |
5 |
0.00 % |
0 |
0.00 % |
5 |
0.00 % |
| q20,qd2,fs60,mq40 |
5 |
0.00 % |
0 |
0.00 % |
5 |
0.00 % |
| q20,fs60,mq40 |
1 |
0.00 % |
0 |
0.00 % |
1 |
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 |
27492057 |
23.16 % |
| Transition |
G>A |
All |
10155697 |
8.55 % |
| Transition |
T>C |
All |
32988467 |
27.78 % |
| Transition |
C>T |
All |
6920715 |
5.83 % |
| Transversion |
A>C |
All |
3027786 |
2.55 % |
| Transversion |
C>A |
All |
5541215 |
4.67 % |
| Transversion |
T>G |
All |
4767777 |
4.02 % |
| Transversion |
G>T |
All |
5163374 |
4.35 % |
| Transversion |
A>T |
All |
8591884 |
7.24 % |
| Transversion |
T>A |
All |
9083865 |
7.65 % |
| Transversion |
C>G |
All |
2943713 |
2.48 % |
| Transversion |
G>C |
All |
2053333 |
1.73 % |
| |
|
|
|
|
| Transition |
A>G |
Passed |
1637832 |
20.63 % |
| Transition |
G>A |
Passed |
705337 |
8.88 % |
| Transition |
T>C |
Passed |
2532911 |
31.90 % |
| Transition |
C>T |
Passed |
437431 |
5.51 % |
| Transversion |
A>C |
Passed |
287371 |
3.62 % |
| Transversion |
C>A |
Passed |
354165 |
4.46 % |
| Transversion |
T>G |
Passed |
474404 |
5.98 % |
| Transversion |
G>T |
Passed |
190451 |
2.40 % |
| Transversion |
A>T |
Passed |
229083 |
2.89 % |
| Transversion |
T>A |
Passed |
503475 |
6.34 % |
| Transversion |
C>G |
Passed |
342020 |
4.31 % |
| Transversion |
G>C |
Passed |
244503 |
3.08 % |
| |
|
|
|
|
| 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 |
1.88 |
77556936 |
41172947 |
| Passed |
2.02 |
5313511 |
2625472 |
| dbSNPAll |
0 |
0 |
0 |
| dbSNPPassed |
0 |
0 |
0 |