/EXTERNAL CREST/variants/K006431_1_lane_gembs
BACK
SAMPLE K006431_1_lane_gembs
Variant counts
| Type |
Total |
Pass |
% |
| SNPs |
1213757463 |
713804568 |
58.81 % |
| Multiallelic |
0 |
0 |
0.00 % |
VCF Filtering Stats
| Type |
#Sites |
% |
#Non-Variant Sites |
% |
#Variant Sites |
% |
| All |
1213757463 |
100% |
1120961296 |
92.35 % |
92796167 |
7.65 % |
| |
|
|
|
|
|
|
| Passed |
727092573 |
59.90 % |
707304117 |
63.10 % |
19788456 |
2.72 % |
| Filtered |
486664890 |
40.10 % |
413657179 |
36.90 % |
73007711 |
10.04 % |
| |
|
|
|
|
|
|
| q20 |
331778346 |
68.17 % |
313775571 |
75.85 % |
18002775 |
24.66 % |
| q20,qd2 |
74733712 |
15.36 % |
25959840 |
6.28 % |
48773872 |
66.81 % |
| q20,mq40 |
39375332 |
8.09 % |
37848754 |
9.15 % |
1526578 |
2.09 % |
| mq40 |
25061879 |
5.15 % |
23353463 |
5.65 % |
1708416 |
2.34 % |
| qd2 |
8721548 |
1.79 % |
8008038 |
1.94 % |
713510 |
0.98 % |
| q20,qd2,mq40 |
6827195 |
1.40 % |
4575383 |
1.11 % |
2251812 |
3.08 % |
| qd2,mq40 |
165838 |
0.03 % |
136130 |
0.03 % |
29708 |
0.04 % |
| fs60 |
564 |
0.00 % |
0 |
0.00 % |
564 |
0.00 % |
| fs60,mq40 |
340 |
0.00 % |
0 |
0.00 % |
340 |
0.00 % |
| q20,qd2,fs60 |
78 |
0.00 % |
0 |
0.00 % |
78 |
0.00 % |
| q20,fs60 |
31 |
0.00 % |
0 |
0.00 % |
31 |
0.00 % |
| qd2,fs60 |
13 |
0.00 % |
0 |
0.00 % |
13 |
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 |
4 |
0.00 % |
0 |
0.00 % |
4 |
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 |
22480865 |
23.72 % |
| Transition |
G>A |
All |
8437319 |
8.90 % |
| Transition |
T>C |
All |
25288929 |
26.68 % |
| Transition |
C>T |
All |
6427181 |
6.78 % |
| Transversion |
A>C |
All |
2209717 |
2.33 % |
| Transversion |
C>A |
All |
4280122 |
4.52 % |
| Transversion |
T>G |
All |
3955373 |
4.17 % |
| Transversion |
G>T |
All |
4033251 |
4.26 % |
| Transversion |
A>T |
All |
6719261 |
7.09 % |
| Transversion |
T>A |
All |
7013271 |
7.40 % |
| Transversion |
C>G |
All |
2428278 |
2.56 % |
| Transversion |
G>C |
All |
1514617 |
1.60 % |
| |
|
|
|
|
| Transition |
A>G |
Passed |
1538102 |
21.52 % |
| Transition |
G>A |
Passed |
712084 |
9.96 % |
| Transition |
T>C |
Passed |
2049815 |
28.68 % |
| Transition |
C>T |
Passed |
484080 |
6.77 % |
| Transversion |
A>C |
Passed |
241163 |
3.37 % |
| Transversion |
C>A |
Passed |
305659 |
4.28 % |
| Transversion |
T>G |
Passed |
469322 |
6.57 % |
| Transversion |
G>T |
Passed |
174490 |
2.44 % |
| Transversion |
A>T |
Passed |
202744 |
2.84 % |
| Transversion |
T>A |
Passed |
422553 |
5.91 % |
| Transversion |
C>G |
Passed |
340508 |
4.76 % |
| Transversion |
G>C |
Passed |
206292 |
2.89 % |
| |
|
|
|
|
| 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 |
1.95 |
62634294 |
32153890 |
| Passed |
2.02 |
4784081 |
2362731 |
| dbSNPAll |
0 |
0 |
0 |
| dbSNPPassed |
0 |
0 |
0 |