/EXTERNAL DEEP/variants/K009006_K009007_K009008_K009009_K009010_K009011_K009012_K009013_K009014_K009015_K009016_K009017_K009018_K009019_K009020_K009021_16_lane_gembs
BACK
SAMPLE K009006_K009007_K009008_K009009_K009010_K009011_K009012_K009013_K009014_K009015_K009016_K009017_K009018_K009019_K009020_K009021_16_lane_gembs
Variant counts
| Type |
Total |
Pass |
% |
| SNPs |
1178233751 |
945623499 |
80.26 % |
| Multiallelic |
0 |
0 |
0.00 % |
VCF Filtering Stats
| Type |
#Sites |
% |
#Non-Variant Sites |
% |
#Variant Sites |
% |
| All |
1178233751 |
100% |
1144859282 |
97.17 % |
33374469 |
2.83 % |
| |
|
|
|
|
|
|
| Passed |
949253630 |
80.57 % |
941207416 |
82.21 % |
8046214 |
0.85 % |
| Filtered |
228980121 |
19.43 % |
203651866 |
17.79 % |
25328255 |
2.67 % |
| |
|
|
|
|
|
|
| q20 |
172901331 |
75.51 % |
168071751 |
82.53 % |
4829580 |
19.07 % |
| q20,qd2 |
30407488 |
13.28 % |
11693923 |
5.74 % |
18713565 |
73.88 % |
| q20,mq40 |
10856893 |
4.74 % |
10517175 |
5.16 % |
339718 |
1.34 % |
| qd2 |
9357003 |
4.09 % |
8655769 |
4.25 % |
701234 |
2.77 % |
| q20,qd2,mq40 |
3471623 |
1.52 % |
3109303 |
1.53 % |
362320 |
1.43 % |
| mq40 |
1918048 |
0.84 % |
1549970 |
0.76 % |
368078 |
1.45 % |
| qd2,mq40 |
65119 |
0.03 % |
53975 |
0.03 % |
11144 |
0.04 % |
| qd2,fs60,mq40 |
903 |
0.00 % |
0 |
0.00 % |
903 |
0.00 % |
| qd2,fs60 |
437 |
0.00 % |
0 |
0.00 % |
437 |
0.00 % |
| fs60 |
387 |
0.00 % |
0 |
0.00 % |
387 |
0.00 % |
| fs60,mq40 |
379 |
0.00 % |
0 |
0.00 % |
379 |
0.00 % |
| q20,qd2,fs60 |
362 |
0.00 % |
0 |
0.00 % |
362 |
0.00 % |
| q20,qd2,fs60,mq40 |
146 |
0.00 % |
0 |
0.00 % |
146 |
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 |
11374107 |
32.13 % |
| Transition |
G>A |
All |
2579119 |
7.29 % |
| Transition |
T>C |
All |
13085137 |
36.97 % |
| Transition |
C>T |
All |
2189891 |
6.19 % |
| Transversion |
A>C |
All |
412910 |
1.17 % |
| Transversion |
C>A |
All |
1540637 |
4.35 % |
| Transversion |
T>G |
All |
442169 |
1.25 % |
| Transversion |
G>T |
All |
1512226 |
4.27 % |
| Transversion |
A>T |
All |
728357 |
2.06 % |
| Transversion |
T>A |
All |
761970 |
2.15 % |
| Transversion |
C>G |
All |
386150 |
1.09 % |
| Transversion |
G>C |
All |
382291 |
1.08 % |
| |
|
|
|
|
| Transition |
A>G |
Passed |
1041971 |
19.11 % |
| Transition |
G>A |
Passed |
662984 |
12.16 % |
| Transition |
T>C |
Passed |
1677818 |
30.77 % |
| Transition |
C>T |
Passed |
617503 |
11.32 % |
| Transversion |
A>C |
Passed |
162827 |
2.99 % |
| Transversion |
C>A |
Passed |
256228 |
4.70 % |
| Transversion |
T>G |
Passed |
168705 |
3.09 % |
| Transversion |
G>T |
Passed |
242574 |
4.45 % |
| Transversion |
A>T |
Passed |
139780 |
2.56 % |
| Transversion |
T>A |
Passed |
151035 |
2.77 % |
| Transversion |
C>G |
Passed |
166203 |
3.05 % |
| Transversion |
G>C |
Passed |
164981 |
3.03 % |
| |
|
|
|
|
| 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 |
4.74 |
29228254 |
6166710 |
| Passed |
2.75 |
4000276 |
1452333 |
| dbSNPAll |
0 |
0 |
0 |
| dbSNPPassed |
0 |
0 |
0 |