/EXTERNAL DEEP/variants/K008971_K008972_K008973_3_lane_gembs
BACK
SAMPLE K008971_K008972_K008973_3_lane_gembs
Variant counts
| Type |
Total |
Pass |
% |
| SNPs |
1174352329 |
741120132 |
63.11 % |
| Multiallelic |
0 |
0 |
0.00 % |
VCF Filtering Stats
| Type |
#Sites |
% |
#Non-Variant Sites |
% |
#Variant Sites |
% |
| All |
1174352329 |
100% |
1140678077 |
97.13 % |
33674252 |
2.87 % |
| |
|
|
|
|
|
|
| Passed |
746271961 |
63.55 % |
737002394 |
64.61 % |
9269567 |
1.24 % |
| Filtered |
428080368 |
36.45 % |
403675683 |
35.39 % |
24404685 |
3.27 % |
| |
|
|
|
|
|
|
| q20 |
382608410 |
89.38 % |
375332526 |
92.98 % |
7275884 |
29.81 % |
| q20,qd2 |
27198081 |
6.35 % |
11020243 |
2.73 % |
16177838 |
66.29 % |
| q20,mq40 |
10100652 |
2.36 % |
9884157 |
2.45 % |
216495 |
0.89 % |
| qd2 |
3849739 |
0.90 % |
3518988 |
0.87 % |
330751 |
1.36 % |
| q20,qd2,mq40 |
3218623 |
0.75 % |
3056445 |
0.76 % |
162178 |
0.66 % |
| mq40 |
1061496 |
0.25 % |
829250 |
0.21 % |
232246 |
0.95 % |
| qd2,mq40 |
41574 |
0.01 % |
34074 |
0.01 % |
7500 |
0.03 % |
| qd2,fs60,mq40 |
731 |
0.00 % |
0 |
0.00 % |
731 |
0.00 % |
| qd2,fs60 |
329 |
0.00 % |
0 |
0.00 % |
329 |
0.00 % |
| fs60,mq40 |
280 |
0.00 % |
0 |
0.00 % |
280 |
0.00 % |
| fs60 |
217 |
0.00 % |
0 |
0.00 % |
217 |
0.00 % |
| q20,qd2,fs60,mq40 |
126 |
0.00 % |
0 |
0.00 % |
126 |
0.00 % |
| q20,qd2,fs60 |
108 |
0.00 % |
0 |
0.00 % |
108 |
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 |
11463245 |
32.15 % |
| Transition |
G>A |
All |
2579114 |
7.23 % |
| Transition |
T>C |
All |
12928161 |
36.26 % |
| Transition |
C>T |
All |
1837610 |
5.15 % |
| Transversion |
A>C |
All |
647484 |
1.82 % |
| Transversion |
C>A |
All |
1348003 |
3.78 % |
| Transversion |
T>G |
All |
753454 |
2.11 % |
| Transversion |
G>T |
All |
1243145 |
3.49 % |
| Transversion |
A>T |
All |
779083 |
2.19 % |
| Transversion |
T>A |
All |
905147 |
2.54 % |
| Transversion |
C>G |
All |
600050 |
1.68 % |
| Transversion |
G>C |
All |
570283 |
1.60 % |
| |
|
|
|
|
| Transition |
A>G |
Passed |
1000890 |
20.22 % |
| Transition |
G>A |
Passed |
589834 |
11.92 % |
| Transition |
T>C |
Passed |
1501682 |
30.34 % |
| Transition |
C>T |
Passed |
499905 |
10.10 % |
| Transversion |
A>C |
Passed |
168171 |
3.40 % |
| Transversion |
C>A |
Passed |
210629 |
4.26 % |
| Transversion |
T>G |
Passed |
192027 |
3.88 % |
| Transversion |
G>T |
Passed |
181625 |
3.67 % |
| Transversion |
A>T |
Passed |
129942 |
2.63 % |
| Transversion |
T>A |
Passed |
161400 |
3.26 % |
| Transversion |
C>G |
Passed |
158899 |
3.21 % |
| Transversion |
G>C |
Passed |
154329 |
3.12 % |
| |
|
|
|
|
| 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 |
4.21 |
28808130 |
6846649 |
| Passed |
2.65 |
3592311 |
1357022 |
| dbSNPAll |
0 |
0 |
0 |
| dbSNPPassed |
0 |
0 |
0 |