/EXTERNAL DEEP/variants/K006071_K006072_K006073_K006074_4_lane_gembs
BACK
SAMPLE K006071_K006072_K006073_K006074_4_lane_gembs
Variant counts
| Type |
Total |
Pass |
% |
| SNPs |
1165709369 |
945568467 |
81.12 % |
| Multiallelic |
0 |
0 |
0.00 % |
VCF Filtering Stats
| Type |
#Sites |
% |
#Non-Variant Sites |
% |
#Variant Sites |
% |
| All |
1165709369 |
100% |
1143937257 |
98.13 % |
21772112 |
1.87 % |
| |
|
|
|
|
|
|
| Passed |
948251378 |
81.35 % |
942174202 |
82.36 % |
6077176 |
0.64 % |
| Filtered |
217457991 |
18.65 % |
201763055 |
17.64 % |
15694936 |
1.66 % |
| |
|
|
|
|
|
|
| q20 |
182346197 |
83.85 % |
179289980 |
88.86 % |
3056217 |
19.47 % |
| q20,qd2 |
19007265 |
8.74 % |
7190996 |
3.56 % |
11816269 |
75.29 % |
| q20,mq40 |
8540981 |
3.93 % |
8422007 |
4.17 % |
118974 |
0.76 % |
| qd2 |
3605979 |
1.66 % |
3245144 |
1.61 % |
360835 |
2.30 % |
| q20,qd2,mq40 |
2659359 |
1.22 % |
2535789 |
1.26 % |
123570 |
0.79 % |
| mq40 |
1257706 |
0.58 % |
1048880 |
0.52 % |
208826 |
1.33 % |
| qd2,mq40 |
38266 |
0.02 % |
30259 |
0.01 % |
8007 |
0.05 % |
| qd2,fs60,mq40 |
878 |
0.00 % |
0 |
0.00 % |
878 |
0.01 % |
| qd2,fs60 |
471 |
0.00 % |
0 |
0.00 % |
471 |
0.00 % |
| fs60 |
335 |
0.00 % |
0 |
0.00 % |
335 |
0.00 % |
| fs60,mq40 |
327 |
0.00 % |
0 |
0.00 % |
327 |
0.00 % |
| q20,qd2,fs60 |
134 |
0.00 % |
0 |
0.00 % |
134 |
0.00 % |
| q20,qd2,fs60,mq40 |
90 |
0.00 % |
0 |
0.00 % |
90 |
0.00 % |
| q20,fs60 |
3 |
0.00 % |
0 |
0.00 % |
3 |
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 |
7534171 |
31.94 % |
| Transition |
G>A |
All |
2081866 |
8.83 % |
| Transition |
T>C |
All |
8633793 |
36.60 % |
| Transition |
C>T |
All |
1459232 |
6.19 % |
| Transversion |
A>C |
All |
274537 |
1.16 % |
| Transversion |
C>A |
All |
788283 |
3.34 % |
| Transversion |
T>G |
All |
333153 |
1.41 % |
| Transversion |
G>T |
All |
732216 |
3.10 % |
| Transversion |
A>T |
All |
524407 |
2.22 % |
| Transversion |
T>A |
All |
584456 |
2.48 % |
| Transversion |
C>G |
All |
327463 |
1.39 % |
| Transversion |
G>C |
All |
314094 |
1.33 % |
| |
|
|
|
|
| Transition |
A>G |
Passed |
841325 |
18.66 % |
| Transition |
G>A |
Passed |
637731 |
14.15 % |
| Transition |
T>C |
Passed |
1167096 |
25.89 % |
| Transition |
C>T |
Passed |
595728 |
13.21 % |
| Transversion |
A>C |
Passed |
151874 |
3.37 % |
| Transversion |
C>A |
Passed |
178137 |
3.95 % |
| Transversion |
T>G |
Passed |
160629 |
3.56 % |
| Transversion |
G>T |
Passed |
165804 |
3.68 % |
| Transversion |
A>T |
Passed |
143878 |
3.19 % |
| Transversion |
T>A |
Passed |
156009 |
3.46 % |
| Transversion |
C>G |
Passed |
155745 |
3.45 % |
| Transversion |
G>C |
Passed |
154055 |
3.42 % |
| |
|
|
|
|
| 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 |
5.08 |
19709062 |
3878609 |
| Passed |
2.56 |
3241880 |
1266131 |
| dbSNPAll |
0 |
0 |
0 |
| dbSNPPassed |
0 |
0 |
0 |