/EXTERNAL DEEP/variants/K009037_K009038_K009039_K009040_K009041_K009042_5_lane_gembs
BACK
SAMPLE K009037_K009038_K009039_K009040_K009041_K009042_5_lane_gembs
Variant counts
| Type |
Total |
Pass |
% |
| SNPs |
1142572645 |
164573126 |
14.40 % |
| Multiallelic |
0 |
0 |
0.00 % |
VCF Filtering Stats
| Type |
#Sites |
% |
#Non-Variant Sites |
% |
#Variant Sites |
% |
| All |
1142572645 |
100% |
1112217052 |
97.34 % |
30355593 |
2.66 % |
| |
|
|
|
|
|
|
| Passed |
176233733 |
15.42 % |
162337719 |
14.60 % |
13896014 |
7.88 % |
| Filtered |
966338912 |
84.58 % |
949879333 |
85.40 % |
16459579 |
9.34 % |
| |
|
|
|
|
|
|
| q20 |
872715376 |
90.31 % |
866524379 |
91.22 % |
6190997 |
37.61 % |
| q20,mq40 |
54881554 |
5.68 % |
54387499 |
5.73 % |
494055 |
3.00 % |
| q20,qd2 |
26032346 |
2.69 % |
17681032 |
1.86 % |
8351314 |
50.74 % |
| q20,qd2,mq40 |
10232234 |
1.06 % |
9853225 |
1.04 % |
379009 |
2.30 % |
| mq40 |
2417664 |
0.25 % |
1382665 |
0.15 % |
1034999 |
6.29 % |
| qd2 |
46670 |
0.00 % |
41053 |
0.00 % |
5617 |
0.03 % |
| qd2,mq40 |
12916 |
0.00 % |
9480 |
0.00 % |
3436 |
0.02 % |
| fs60,mq40 |
69 |
0.00 % |
0 |
0.00 % |
69 |
0.00 % |
| qd2,fs60,mq40 |
28 |
0.00 % |
0 |
0.00 % |
28 |
0.00 % |
| fs60 |
27 |
0.00 % |
0 |
0.00 % |
27 |
0.00 % |
| qd2,fs60 |
23 |
0.00 % |
0 |
0.00 % |
23 |
0.00 % |
| q20,qd2,fs60,mq40 |
4 |
0.00 % |
0 |
0.00 % |
4 |
0.00 % |
| q20,qd2,fs60 |
1 |
0.00 % |
0 |
0.00 % |
1 |
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 |
8660188 |
26.90 % |
| Transition |
G>A |
All |
1820721 |
5.66 % |
| Transition |
T>C |
All |
8595629 |
26.70 % |
| Transition |
C>T |
All |
1758902 |
5.46 % |
| Transversion |
A>C |
All |
688547 |
2.14 % |
| Transversion |
C>A |
All |
2465712 |
7.66 % |
| Transversion |
T>G |
All |
730838 |
2.27 % |
| Transversion |
G>T |
All |
2413369 |
7.50 % |
| Transversion |
A>T |
All |
1925737 |
5.98 % |
| Transversion |
T>A |
All |
1974189 |
6.13 % |
| Transversion |
C>G |
All |
599779 |
1.86 % |
| Transversion |
G>C |
All |
562616 |
1.75 % |
| |
|
|
|
|
| Transition |
A>G |
Passed |
506176 |
22.12 % |
| Transition |
G>A |
Passed |
222576 |
9.73 % |
| Transition |
T>C |
Passed |
516198 |
22.56 % |
| Transition |
C>T |
Passed |
226765 |
9.91 % |
| Transversion |
A>C |
Passed |
96379 |
4.21 % |
| Transversion |
C>A |
Passed |
120302 |
5.26 % |
| Transversion |
T>G |
Passed |
98530 |
4.31 % |
| Transversion |
G>T |
Passed |
118839 |
5.19 % |
| Transversion |
A>T |
Passed |
88283 |
3.86 % |
| Transversion |
T>A |
Passed |
90986 |
3.98 % |
| Transversion |
C>G |
Passed |
102042 |
4.46 % |
| Transversion |
G>C |
Passed |
101001 |
4.41 % |
| |
|
|
|
|
| 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 |
1.83 |
20835440 |
11360787 |
| Passed |
1.80 |
1471715 |
816362 |
| dbSNPAll |
0 |
0 |
0 |
| dbSNPPassed |
0 |
0 |
0 |