/EXTERNAL BLUEPRINT/variants/K006276_K006280_11_lane_gembs
BACK
SAMPLE K006276_K006280_11_lane_gembs
Variant counts
| Type |
Total |
Pass |
% |
| SNPs |
1132189433 |
731651162 |
64.62 % |
| Multiallelic |
0 |
0 |
0.00 % |
VCF Filtering Stats
| Type |
#Sites |
% |
#Non-Variant Sites |
% |
#Variant Sites |
% |
| All |
1132189433 |
100% |
1114740487 |
98.46 % |
17448946 |
1.54 % |
| |
|
|
|
|
|
|
| Passed |
733395914 |
64.78 % |
730111381 |
65.50 % |
3284533 |
0.45 % |
| Filtered |
398793519 |
35.22 % |
384629106 |
34.50 % |
14164413 |
1.93 % |
| |
|
|
|
|
|
|
| q20 |
318245105 |
79.80 % |
316640913 |
82.32 % |
1604192 |
11.33 % |
| q20,qd2 |
37022400 |
9.28 % |
25125867 |
6.53 % |
11896533 |
83.99 % |
| qd2 |
18479158 |
4.63 % |
18333260 |
4.77 % |
145898 |
1.03 % |
| q20,mq40 |
13540967 |
3.40 % |
13439714 |
3.49 % |
101253 |
0.71 % |
| mq40 |
8322534 |
2.09 % |
8134196 |
2.11 % |
188338 |
1.33 % |
| q20,qd2,mq40 |
3039481 |
0.76 % |
2844225 |
0.74 % |
195256 |
1.38 % |
| qd2,mq40 |
127713 |
0.03 % |
110931 |
0.03 % |
16782 |
0.12 % |
| q20,qd2,fs60 |
5407 |
0.00 % |
0 |
0.00 % |
5407 |
0.04 % |
| qd2,fs60 |
3502 |
0.00 % |
0 |
0.00 % |
3502 |
0.02 % |
| qd2,fs60,mq40 |
2705 |
0.00 % |
0 |
0.00 % |
2705 |
0.02 % |
| fs60 |
2634 |
0.00 % |
0 |
0.00 % |
2634 |
0.02 % |
| q20,qd2,fs60,mq40 |
999 |
0.00 % |
0 |
0.00 % |
999 |
0.01 % |
| fs60,mq40 |
906 |
0.00 % |
0 |
0.00 % |
906 |
0.01 % |
| q20,fs60 |
5 |
0.00 % |
0 |
0.00 % |
5 |
0.00 % |
| q20,fs60,mq40 |
3 |
0.00 % |
0 |
0.00 % |
3 |
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 |
3375824 |
10.79 % |
| Transition |
G>A |
All |
11107122 |
35.50 % |
| Transition |
T>C |
All |
3278229 |
10.48 % |
| Transition |
C>T |
All |
11040427 |
35.29 % |
| Transversion |
A>C |
All |
196845 |
0.63 % |
| Transversion |
C>A |
All |
487974 |
1.56 % |
| Transversion |
T>G |
All |
205635 |
0.66 % |
| Transversion |
G>T |
All |
479213 |
1.53 % |
| Transversion |
A>T |
All |
374211 |
1.20 % |
| Transversion |
T>A |
All |
364181 |
1.16 % |
| Transversion |
C>G |
All |
192695 |
0.62 % |
| Transversion |
G>C |
All |
184484 |
0.59 % |
| |
|
|
|
|
| Transition |
A>G |
Passed |
422573 |
18.53 % |
| Transition |
G>A |
Passed |
386384 |
16.94 % |
| Transition |
T>C |
Passed |
422338 |
18.52 % |
| Transition |
C>T |
Passed |
385564 |
16.91 % |
| Transversion |
A>C |
Passed |
87621 |
3.84 % |
| Transversion |
C>A |
Passed |
82577 |
3.62 % |
| Transversion |
T>G |
Passed |
86880 |
3.81 % |
| Transversion |
G>T |
Passed |
81908 |
3.59 % |
| Transversion |
A>T |
Passed |
60371 |
2.65 % |
| Transversion |
T>A |
Passed |
60310 |
2.64 % |
| Transversion |
C>G |
Passed |
101409 |
4.45 % |
| Transversion |
G>C |
Passed |
102420 |
4.49 % |
| |
|
|
|
|
| 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 |
11.59 |
28801602 |
2485238 |
| Passed |
2.44 |
1616859 |
663496 |
| dbSNPAll |
0 |
0 |
0 |
| dbSNPPassed |
0 |
0 |
0 |