/EXTERNAL BLUEPRINT/variants/K010525_1_lane_gembs
BACK
SAMPLE K010525_1_lane_gembs
Variant counts
| Type |
Total |
Pass |
% |
| SNPs |
1103659509 |
225689571 |
20.45 % |
| Multiallelic |
0 |
0 |
0.00 % |
VCF Filtering Stats
| Type |
#Sites |
% |
#Non-Variant Sites |
% |
#Variant Sites |
% |
| All |
1103659509 |
100% |
1077829388 |
97.66 % |
25830121 |
2.34 % |
| |
|
|
|
|
|
|
| Passed |
233551212 |
21.16 % |
224631682 |
20.84 % |
8919530 |
3.82 % |
| Filtered |
870108297 |
78.84 % |
853197706 |
79.16 % |
16910591 |
7.24 % |
| |
|
|
|
|
|
|
| q20 |
789138087 |
90.69 % |
782624198 |
91.73 % |
6513889 |
38.52 % |
| q20,qd2 |
62718571 |
7.21 % |
52595742 |
6.16 % |
10122829 |
59.86 % |
| q20,mq40 |
12371996 |
1.42 % |
12283592 |
1.44 % |
88404 |
0.52 % |
| q20,qd2,mq40 |
5423100 |
0.62 % |
5360249 |
0.63 % |
62851 |
0.37 % |
| mq40 |
338880 |
0.04 % |
230464 |
0.03 % |
108416 |
0.64 % |
| qd2 |
102703 |
0.01 % |
91451 |
0.01 % |
11252 |
0.07 % |
| qd2,mq40 |
14556 |
0.00 % |
12010 |
0.00 % |
2546 |
0.02 % |
| qd2,fs60,mq40 |
209 |
0.00 % |
0 |
0.00 % |
209 |
0.00 % |
| fs60,mq40 |
73 |
0.00 % |
0 |
0.00 % |
73 |
0.00 % |
| qd2,fs60 |
71 |
0.00 % |
0 |
0.00 % |
71 |
0.00 % |
| q20,qd2,fs60,mq40 |
36 |
0.00 % |
0 |
0.00 % |
36 |
0.00 % |
| fs60 |
12 |
0.00 % |
0 |
0.00 % |
12 |
0.00 % |
| q20,qd2,fs60 |
3 |
0.00 % |
0 |
0.00 % |
3 |
0.00 % |
| q20,fs60 |
0 |
0.00 % |
0 |
0.00 % |
0 |
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 |
8644324 |
31.01 % |
| Transition |
G>A |
All |
1229470 |
4.41 % |
| Transition |
T>C |
All |
8682037 |
31.15 % |
| Transition |
C>T |
All |
1231125 |
4.42 % |
| Transversion |
A>C |
All |
425027 |
1.52 % |
| Transversion |
C>A |
All |
1441731 |
5.17 % |
| Transversion |
T>G |
All |
423318 |
1.52 % |
| Transversion |
G>T |
All |
1430175 |
5.13 % |
| Transversion |
A>T |
All |
1859487 |
6.67 % |
| Transversion |
T>A |
All |
1870286 |
6.71 % |
| Transversion |
C>G |
All |
317045 |
1.14 % |
| Transversion |
G>C |
All |
320158 |
1.15 % |
| |
|
|
|
|
| Transition |
A>G |
Passed |
248943 |
19.15 % |
| Transition |
G>A |
Passed |
188374 |
14.49 % |
| Transition |
T>C |
Passed |
247751 |
19.05 % |
| Transition |
C>T |
Passed |
188716 |
14.51 % |
| Transversion |
A>C |
Passed |
53166 |
4.09 % |
| Transversion |
C>A |
Passed |
57502 |
4.42 % |
| Transversion |
T>G |
Passed |
53054 |
4.08 % |
| Transversion |
G>T |
Passed |
56086 |
4.31 % |
| Transversion |
A>T |
Passed |
53704 |
4.13 % |
| Transversion |
T>A |
Passed |
54326 |
4.18 % |
| Transversion |
C>G |
Passed |
49337 |
3.79 % |
| Transversion |
G>C |
Passed |
49269 |
3.79 % |
| |
|
|
|
|
| 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 |
2.45 |
19786956 |
8087227 |
| Passed |
2.05 |
873784 |
426444 |
| dbSNPAll |
0 |
0 |
0 |
| dbSNPPassed |
0 |
0 |
0 |