/EXTERNAL CREST/variants/K006439_1_lane_gembs
BACK
SAMPLE K006439_1_lane_gembs
Variant counts
| Type |
Total |
Pass |
% |
| SNPs |
1191128031 |
577519647 |
48.49 % |
| Multiallelic |
0 |
0 |
0.00 % |
VCF Filtering Stats
| Type |
#Sites |
% |
#Non-Variant Sites |
% |
#Variant Sites |
% |
| All |
1191128031 |
100% |
1113813404 |
93.51 % |
77314627 |
6.49 % |
| |
|
|
|
|
|
|
| Passed |
595590533 |
50.00 % |
572690118 |
51.42 % |
22900415 |
3.84 % |
| Filtered |
595537498 |
50.00 % |
541123286 |
48.58 % |
54414212 |
9.14 % |
| |
|
|
|
|
|
|
| q20 |
493585048 |
82.88 % |
475348212 |
87.84 % |
18236836 |
33.51 % |
| q20,qd2 |
65781259 |
11.05 % |
31923925 |
5.90 % |
33857334 |
62.22 % |
| q20,mq40 |
16298513 |
2.74 % |
15813027 |
2.92 % |
485486 |
0.89 % |
| qd2 |
10902835 |
1.83 % |
10231209 |
1.89 % |
671626 |
1.23 % |
| q20,qd2,mq40 |
6037005 |
1.01 % |
5552772 |
1.03 % |
484233 |
0.89 % |
| mq40 |
2872514 |
0.48 % |
2208377 |
0.41 % |
664137 |
1.22 % |
| qd2,mq40 |
57433 |
0.01 % |
45764 |
0.01 % |
11669 |
0.02 % |
| q20,qd2,fs60 |
1604 |
0.00 % |
0 |
0.00 % |
1604 |
0.00 % |
| fs60 |
655 |
0.00 % |
0 |
0.00 % |
655 |
0.00 % |
| qd2,fs60 |
191 |
0.00 % |
0 |
0.00 % |
191 |
0.00 % |
| qd2,fs60,mq40 |
173 |
0.00 % |
0 |
0.00 % |
173 |
0.00 % |
| fs60,mq40 |
166 |
0.00 % |
0 |
0.00 % |
166 |
0.00 % |
| q20,qd2,fs60,mq40 |
95 |
0.00 % |
0 |
0.00 % |
95 |
0.00 % |
| q20,fs60 |
6 |
0.00 % |
0 |
0.00 % |
6 |
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 |
16887753 |
20.96 % |
| Transition |
G>A |
All |
6326941 |
7.85 % |
| Transition |
T>C |
All |
19655981 |
24.39 % |
| Transition |
C>T |
All |
4959260 |
6.15 % |
| Transversion |
A>C |
All |
2731284 |
3.39 % |
| Transversion |
C>A |
All |
4403101 |
5.46 % |
| Transversion |
T>G |
All |
3395080 |
4.21 % |
| Transversion |
G>T |
All |
4198470 |
5.21 % |
| Transversion |
A>T |
All |
6765386 |
8.40 % |
| Transversion |
T>A |
All |
7403085 |
9.19 % |
| Transversion |
C>G |
All |
2041862 |
2.53 % |
| Transversion |
G>C |
All |
1805681 |
2.24 % |
| |
|
|
|
|
| Transition |
A>G |
Passed |
907638 |
17.20 % |
| Transition |
G>A |
Passed |
579117 |
10.98 % |
| Transition |
T>C |
Passed |
1394723 |
26.43 % |
| Transition |
C>T |
Passed |
490287 |
9.29 % |
| Transversion |
A>C |
Passed |
270072 |
5.12 % |
| Transversion |
C>A |
Passed |
234979 |
4.45 % |
| Transversion |
T>G |
Passed |
286160 |
5.42 % |
| Transversion |
G>T |
Passed |
194884 |
3.69 % |
| Transversion |
A>T |
Passed |
191536 |
3.63 % |
| Transversion |
T>A |
Passed |
279663 |
5.30 % |
| Transversion |
C>G |
Passed |
228953 |
4.34 % |
| Transversion |
G>C |
Passed |
218229 |
4.14 % |
| |
|
|
|
|
| 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 |
1.46 |
47829935 |
32743949 |
| Passed |
1.77 |
3371765 |
1904476 |
| dbSNPAll |
0 |
0 |
0 |
| dbSNPPassed |
0 |
0 |
0 |