/EXTERNAL CREST/variants/K006451_1_lane_gembs
BACK
SAMPLE K006451_1_lane_gembs
Variant counts
| Type |
Total |
Pass |
% |
| SNPs |
1183375848 |
572081342 |
48.34 % |
| Multiallelic |
0 |
0 |
0.00 % |
VCF Filtering Stats
| Type |
#Sites |
% |
#Non-Variant Sites |
% |
#Variant Sites |
% |
| All |
1183375848 |
100% |
1109584609 |
93.76 % |
73791239 |
6.24 % |
| |
|
|
|
|
|
|
| Passed |
590138314 |
49.87 % |
568105858 |
51.20 % |
22032456 |
3.73 % |
| Filtered |
593237534 |
50.13 % |
541478751 |
48.80 % |
51758783 |
8.77 % |
| |
|
|
|
|
|
|
| q20 |
495541165 |
83.53 % |
478053084 |
88.29 % |
17488081 |
33.79 % |
| q20,qd2 |
64378869 |
10.85 % |
32223356 |
5.95 % |
32155513 |
62.13 % |
| q20,mq40 |
15624216 |
2.63 % |
15155583 |
2.80 % |
468633 |
0.91 % |
| qd2 |
9073467 |
1.53 % |
8537506 |
1.58 % |
535961 |
1.04 % |
| q20,qd2,mq40 |
5869425 |
0.99 % |
5397905 |
1.00 % |
471520 |
0.91 % |
| mq40 |
2689354 |
0.45 % |
2066768 |
0.38 % |
622586 |
1.20 % |
| qd2,mq40 |
56987 |
0.01 % |
44549 |
0.01 % |
12438 |
0.02 % |
| q20,qd2,fs60 |
2766 |
0.00 % |
0 |
0.00 % |
2766 |
0.01 % |
| fs60 |
552 |
0.00 % |
0 |
0.00 % |
552 |
0.00 % |
| qd2,fs60 |
240 |
0.00 % |
0 |
0.00 % |
240 |
0.00 % |
| qd2,fs60,mq40 |
208 |
0.00 % |
0 |
0.00 % |
208 |
0.00 % |
| fs60,mq40 |
181 |
0.00 % |
0 |
0.00 % |
181 |
0.00 % |
| q20,qd2,fs60,mq40 |
92 |
0.00 % |
0 |
0.00 % |
92 |
0.00 % |
| q20,fs60 |
12 |
0.00 % |
0 |
0.00 % |
12 |
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 |
18760504 |
24.32 % |
| Transition |
G>A |
All |
5251160 |
6.81 % |
| Transition |
T>C |
All |
18340839 |
23.77 % |
| Transition |
C>T |
All |
4380899 |
5.68 % |
| Transversion |
A>C |
All |
2319456 |
3.01 % |
| Transversion |
C>A |
All |
4048618 |
5.25 % |
| Transversion |
T>G |
All |
3289956 |
4.26 % |
| Transversion |
G>T |
All |
3842880 |
4.98 % |
| Transversion |
A>T |
All |
6464445 |
8.38 % |
| Transversion |
T>A |
All |
6910195 |
8.96 % |
| Transversion |
C>G |
All |
1979113 |
2.57 % |
| Transversion |
G>C |
All |
1562747 |
2.03 % |
| |
|
|
|
|
| Transition |
A>G |
Passed |
973476 |
21.75 % |
| Transition |
G>A |
Passed |
473255 |
10.57 % |
| Transition |
T>C |
Passed |
1124709 |
25.13 % |
| Transition |
C>T |
Passed |
426292 |
9.52 % |
| Transversion |
A>C |
Passed |
192715 |
4.31 % |
| Transversion |
C>A |
Passed |
174516 |
3.90 % |
| Transversion |
T>G |
Passed |
258613 |
5.78 % |
| Transversion |
G>T |
Passed |
138284 |
3.09 % |
| Transversion |
A>T |
Passed |
137943 |
3.08 % |
| Transversion |
T>A |
Passed |
203185 |
4.54 % |
| Transversion |
C>G |
Passed |
206362 |
4.61 % |
| Transversion |
G>C |
Passed |
166821 |
3.73 % |
| |
|
|
|
|
| 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 |
1.54 |
46733402 |
30417410 |
| Passed |
2.03 |
2997732 |
1478439 |
| dbSNPAll |
0 |
0 |
0 |
| dbSNPPassed |
0 |
0 |
0 |