/EXTERNAL BLUEPRINT/variants/K006346_9_lane_gembs
BACK
SAMPLE K006346_9_lane_gembs
Variant counts
| Type |
Total |
Pass |
% |
| SNPs |
1144094944 |
747017706 |
65.29 % |
| Multiallelic |
0 |
0 |
0.00 % |
VCF Filtering Stats
| Type |
#Sites |
% |
#Non-Variant Sites |
% |
#Variant Sites |
% |
| All |
1144094944 |
100% |
1132394661 |
98.98 % |
11700283 |
1.02 % |
| |
|
|
|
|
|
|
| Passed |
749392913 |
65.50 % |
745328696 |
65.82 % |
4064217 |
0.54 % |
| Filtered |
394702031 |
34.50 % |
387065965 |
34.18 % |
7636066 |
1.02 % |
| |
|
|
|
|
|
|
| q20 |
349485000 |
88.54 % |
348028046 |
89.91 % |
1456954 |
19.08 % |
| q20,qd2 |
21498926 |
5.45 % |
15888009 |
4.10 % |
5610917 |
73.48 % |
| q20,mq40 |
13430821 |
3.40 % |
13328707 |
3.44 % |
102114 |
1.34 % |
| mq40 |
4901527 |
1.24 % |
4732798 |
1.22 % |
168729 |
2.21 % |
| q20,qd2,mq40 |
3050904 |
0.77 % |
2860617 |
0.74 % |
190287 |
2.49 % |
| qd2 |
2277092 |
0.58 % |
2180975 |
0.56 % |
96117 |
1.26 % |
| qd2,mq40 |
55156 |
0.01 % |
46813 |
0.01 % |
8343 |
0.11 % |
| q20,qd2,fs60 |
814 |
0.00 % |
0 |
0.00 % |
814 |
0.01 % |
| qd2,fs60,mq40 |
542 |
0.00 % |
0 |
0.00 % |
542 |
0.01 % |
| fs60 |
434 |
0.00 % |
0 |
0.00 % |
434 |
0.01 % |
| fs60,mq40 |
289 |
0.00 % |
0 |
0.00 % |
289 |
0.00 % |
| qd2,fs60 |
267 |
0.00 % |
0 |
0.00 % |
267 |
0.00 % |
| q20,qd2,fs60,mq40 |
258 |
0.00 % |
0 |
0.00 % |
258 |
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 |
4194092 |
31.00 % |
| Transition |
G>A |
All |
1067244 |
7.89 % |
| Transition |
T>C |
All |
4113645 |
30.40 % |
| Transition |
C>T |
All |
1053510 |
7.79 % |
| Transversion |
A>C |
All |
220042 |
1.63 % |
| Transversion |
C>A |
All |
648809 |
4.80 % |
| Transversion |
T>G |
All |
227519 |
1.68 % |
| Transversion |
G>T |
All |
647464 |
4.79 % |
| Transversion |
A>T |
All |
490357 |
3.62 % |
| Transversion |
T>A |
All |
479515 |
3.54 % |
| Transversion |
C>G |
All |
196753 |
1.45 % |
| Transversion |
G>C |
All |
191706 |
1.42 % |
| |
|
|
|
|
| Transition |
A>G |
Passed |
448769 |
18.24 % |
| Transition |
G>A |
Passed |
407085 |
16.55 % |
| Transition |
T>C |
Passed |
446932 |
18.17 % |
| Transition |
C>T |
Passed |
408070 |
16.59 % |
| Transversion |
A>C |
Passed |
99205 |
4.03 % |
| Transversion |
C>A |
Passed |
94606 |
3.85 % |
| Transversion |
T>G |
Passed |
99121 |
4.03 % |
| Transversion |
G>T |
Passed |
94743 |
3.85 % |
| Transversion |
A>T |
Passed |
69790 |
2.84 % |
| Transversion |
T>A |
Passed |
69766 |
2.84 % |
| Transversion |
C>G |
Passed |
110701 |
4.50 % |
| Transversion |
G>C |
Passed |
111337 |
4.53 % |
| |
|
|
|
|
| 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 |
3.36 |
10428491 |
3102165 |
| Passed |
2.28 |
1710856 |
749269 |
| dbSNPAll |
0 |
0 |
0 |
| dbSNPPassed |
0 |
0 |
0 |