/EXTERNAL DEEP/variants/K006087_K006088_K006089_3_lane_gembs
BACK
SAMPLE K006087_K006088_K006089_3_lane_gembs
Variant counts
| Type |
Total |
Pass |
% |
| SNPs |
1179323462 |
819048142 |
69.45 % |
| Multiallelic |
0 |
0 |
0.00 % |
VCF Filtering Stats
| Type |
#Sites |
% |
#Non-Variant Sites |
% |
#Variant Sites |
% |
| All |
1179323462 |
100% |
1140443333 |
96.70 % |
38880129 |
3.30 % |
| |
|
|
|
|
|
|
| Passed |
824953991 |
69.95 % |
813874832 |
71.36 % |
11079159 |
1.34 % |
| Filtered |
354369471 |
30.05 % |
326568501 |
28.64 % |
27800970 |
3.37 % |
| |
|
|
|
|
|
|
| q20 |
304010011 |
85.79 % |
297196487 |
91.01 % |
6813524 |
24.51 % |
| q20,qd2 |
31391578 |
8.86 % |
11372637 |
3.48 % |
20018941 |
72.01 % |
| q20,mq40 |
9710629 |
2.74 % |
9526460 |
2.92 % |
184169 |
0.66 % |
| qd2 |
5108621 |
1.44 % |
4713184 |
1.44 % |
395437 |
1.42 % |
| q20,qd2,mq40 |
2987423 |
0.84 % |
2846627 |
0.87 % |
140796 |
0.51 % |
| mq40 |
1100273 |
0.31 % |
867410 |
0.27 % |
232863 |
0.84 % |
| qd2,mq40 |
55222 |
0.02 % |
45696 |
0.01 % |
9526 |
0.03 % |
| qd2,fs60 |
1914 |
0.00 % |
0 |
0.00 % |
1914 |
0.01 % |
| qd2,fs60,mq40 |
1521 |
0.00 % |
0 |
0.00 % |
1521 |
0.01 % |
| fs60 |
831 |
0.00 % |
0 |
0.00 % |
831 |
0.00 % |
| q20,qd2,fs60 |
773 |
0.00 % |
0 |
0.00 % |
773 |
0.00 % |
| fs60,mq40 |
397 |
0.00 % |
0 |
0.00 % |
397 |
0.00 % |
| q20,qd2,fs60,mq40 |
276 |
0.00 % |
0 |
0.00 % |
276 |
0.00 % |
| q20,fs60 |
1 |
0.00 % |
0 |
0.00 % |
1 |
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 |
13927609 |
34.62 % |
| Transition |
G>A |
All |
3026712 |
7.52 % |
| Transition |
T>C |
All |
15326688 |
38.10 % |
| Transition |
C>T |
All |
2319918 |
5.77 % |
| Transversion |
A>C |
All |
504067 |
1.25 % |
| Transversion |
C>A |
All |
1036281 |
2.58 % |
| Transversion |
T>G |
All |
580259 |
1.44 % |
| Transversion |
G>T |
All |
977639 |
2.43 % |
| Transversion |
A>T |
All |
743698 |
1.85 % |
| Transversion |
T>A |
All |
839373 |
2.09 % |
| Transversion |
C>G |
All |
482662 |
1.20 % |
| Transversion |
G>C |
All |
464238 |
1.15 % |
| |
|
|
|
|
| Transition |
A>G |
Passed |
1111884 |
19.91 % |
| Transition |
G>A |
Passed |
701040 |
12.56 % |
| Transition |
T>C |
Passed |
1559478 |
27.93 % |
| Transition |
C>T |
Passed |
645118 |
11.55 % |
| Transversion |
A>C |
Passed |
191945 |
3.44 % |
| Transversion |
C>A |
Passed |
218290 |
3.91 % |
| Transversion |
T>G |
Passed |
205216 |
3.68 % |
| Transversion |
G>T |
Passed |
204336 |
3.66 % |
| Transversion |
A>T |
Passed |
165330 |
2.96 % |
| Transversion |
T>A |
Passed |
185416 |
3.32 % |
| Transversion |
C>G |
Passed |
199128 |
3.57 % |
| Transversion |
G>C |
Passed |
196235 |
3.51 % |
| |
|
|
|
|
| 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 |
6.15 |
34600927 |
5628217 |
| Passed |
2.57 |
4017520 |
1565896 |
| dbSNPAll |
0 |
0 |
0 |
| dbSNPPassed |
0 |
0 |
0 |