/EXTERNAL DEEP/variants/K006084_K006085_K006086_K006126_4_lane_gembs
BACK
SAMPLE K006084_K006085_K006086_K006126_4_lane_gembs
Variant counts
| Type |
Total |
Pass |
% |
| SNPs |
1164373604 |
1021459767 |
87.73 % |
| Multiallelic |
0 |
0 |
0.00 % |
VCF Filtering Stats
| Type |
#Sites |
% |
#Non-Variant Sites |
% |
#Variant Sites |
% |
| All |
1164373604 |
100% |
1139675303 |
97.88 % |
24698301 |
2.12 % |
| |
|
|
|
|
|
|
| Passed |
1023322594 |
87.89 % |
1016478795 |
89.19 % |
6843799 |
0.67 % |
| Filtered |
141051010 |
12.11 % |
123196508 |
10.81 % |
17854502 |
1.74 % |
| |
|
|
|
|
|
|
| q20 |
102682010 |
72.80 % |
100884051 |
81.89 % |
1797959 |
10.07 % |
| q20,qd2 |
20904424 |
14.82 % |
6342752 |
5.15 % |
14561672 |
81.56 % |
| q20,mq40 |
9249937 |
6.56 % |
9101021 |
7.39 % |
148916 |
0.83 % |
| qd2 |
3722905 |
2.64 % |
2819686 |
2.29 % |
903219 |
5.06 % |
| q20,qd2,mq40 |
3071165 |
2.18 % |
2899496 |
2.35 % |
171669 |
0.96 % |
| mq40 |
1378427 |
0.98 % |
1117963 |
0.91 % |
260464 |
1.46 % |
| qd2,mq40 |
40369 |
0.03 % |
31539 |
0.03 % |
8830 |
0.05 % |
| qd2,fs60,mq40 |
718 |
0.00 % |
0 |
0.00 % |
718 |
0.00 % |
| fs60,mq40 |
321 |
0.00 % |
0 |
0.00 % |
321 |
0.00 % |
| qd2,fs60 |
287 |
0.00 % |
0 |
0.00 % |
287 |
0.00 % |
| fs60 |
235 |
0.00 % |
0 |
0.00 % |
235 |
0.00 % |
| q20,qd2,fs60 |
150 |
0.00 % |
0 |
0.00 % |
150 |
0.00 % |
| q20,qd2,fs60,mq40 |
61 |
0.00 % |
0 |
0.00 % |
61 |
0.00 % |
| q20,fs60,mq40 |
1 |
0.00 % |
0 |
0.00 % |
1 |
0.00 % |
| q20,fs60 |
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 |
9382498 |
36.38 % |
| Transition |
G>A |
All |
1533532 |
5.95 % |
| Transition |
T>C |
All |
9371437 |
36.34 % |
| Transition |
C>T |
All |
1537175 |
5.96 % |
| Transversion |
A>C |
All |
309676 |
1.20 % |
| Transversion |
C>A |
All |
819299 |
3.18 % |
| Transversion |
T>G |
All |
309489 |
1.20 % |
| Transversion |
G>T |
All |
833654 |
3.23 % |
| Transversion |
A>T |
All |
546231 |
2.12 % |
| Transversion |
T>A |
All |
536699 |
2.08 % |
| Transversion |
C>G |
All |
303976 |
1.18 % |
| Transversion |
G>C |
All |
306894 |
1.19 % |
| |
|
|
|
|
| Transition |
A>G |
Passed |
1095591 |
19.92 % |
| Transition |
G>A |
Passed |
805860 |
14.66 % |
| Transition |
T>C |
Passed |
1099167 |
19.99 % |
| Transition |
C>T |
Passed |
811097 |
14.75 % |
| Transversion |
A>C |
Passed |
208088 |
3.78 % |
| Transversion |
C>A |
Passed |
233638 |
4.25 % |
| Transversion |
T>G |
Passed |
207313 |
3.77 % |
| Transversion |
G>T |
Passed |
233659 |
4.25 % |
| Transversion |
A>T |
Passed |
190224 |
3.46 % |
| Transversion |
T>A |
Passed |
189785 |
3.45 % |
| Transversion |
C>G |
Passed |
211601 |
3.85 % |
| Transversion |
G>C |
Passed |
212738 |
3.87 % |
| |
|
|
|
|
| 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 |
5.50 |
21824642 |
3965918 |
| Passed |
2.26 |
3811715 |
1687046 |
| dbSNPAll |
0 |
0 |
0 |
| dbSNPPassed |
0 |
0 |
0 |