/EXTERNAL BLUEPRINT/variants/K006381_K006410_26_lane_gembs
BACK
SAMPLE K006381_K006410_26_lane_gembs
Variant counts
| Type |
Total |
Pass |
% |
| SNPs |
1153612872 |
1007893587 |
87.37 % |
| Multiallelic |
0 |
0 |
0.00 % |
VCF Filtering Stats
| Type |
#Sites |
% |
#Non-Variant Sites |
% |
#Variant Sites |
% |
| All |
1153612872 |
100% |
1141134708 |
98.92 % |
12478164 |
1.08 % |
| |
|
|
|
|
|
|
| Passed |
1009128436 |
87.48 % |
1005478308 |
88.11 % |
3650128 |
0.36 % |
| Filtered |
144484436 |
12.52 % |
135656400 |
11.89 % |
8828036 |
0.87 % |
| |
|
|
|
|
|
|
| q20 |
94486787 |
65.40 % |
93475094 |
68.91 % |
1011693 |
11.46 % |
| qd2 |
16485927 |
11.41 % |
16329557 |
12.04 % |
156370 |
1.77 % |
| q20,mq40 |
11669152 |
8.08 % |
11565941 |
8.53 % |
103211 |
1.17 % |
| q20,qd2 |
11127709 |
7.70 % |
3993298 |
2.94 % |
7134411 |
80.82 % |
| mq40 |
7798465 |
5.40 % |
7590588 |
5.60 % |
207877 |
2.35 % |
| q20,qd2,mq40 |
2784617 |
1.93 % |
2601457 |
1.92 % |
183160 |
2.07 % |
| qd2,mq40 |
116960 |
0.08 % |
100465 |
0.07 % |
16495 |
0.19 % |
| qd2,fs60 |
5438 |
0.00 % |
0 |
0.00 % |
5438 |
0.06 % |
| fs60 |
3382 |
0.00 % |
0 |
0.00 % |
3382 |
0.04 % |
| qd2,fs60,mq40 |
2607 |
0.00 % |
0 |
0.00 % |
2607 |
0.03 % |
| q20,qd2,fs60 |
2187 |
0.00 % |
0 |
0.00 % |
2187 |
0.02 % |
| fs60,mq40 |
820 |
0.00 % |
0 |
0.00 % |
820 |
0.01 % |
| q20,qd2,fs60,mq40 |
380 |
0.00 % |
0 |
0.00 % |
380 |
0.00 % |
| q20,fs60,mq40 |
3 |
0.00 % |
0 |
0.00 % |
3 |
0.00 % |
| q20,fs60 |
2 |
0.00 % |
0 |
0.00 % |
2 |
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 |
4756655 |
33.38 % |
| Transition |
G>A |
All |
1174139 |
8.24 % |
| Transition |
T>C |
All |
4663912 |
32.73 % |
| Transition |
C>T |
All |
1195615 |
8.39 % |
| Transversion |
A>C |
All |
213099 |
1.50 % |
| Transversion |
C>A |
All |
454903 |
3.19 % |
| Transversion |
T>G |
All |
215716 |
1.51 % |
| Transversion |
G>T |
All |
449012 |
3.15 % |
| Transversion |
A>T |
All |
364000 |
2.55 % |
| Transversion |
T>A |
All |
358205 |
2.51 % |
| Transversion |
C>G |
All |
203203 |
1.43 % |
| Transversion |
G>C |
All |
201605 |
1.41 % |
| |
|
|
|
|
| Transition |
A>G |
Passed |
602528 |
17.25 % |
| Transition |
G>A |
Passed |
572693 |
16.40 % |
| Transition |
T>C |
Passed |
601733 |
17.23 % |
| Transition |
C>T |
Passed |
575546 |
16.48 % |
| Transversion |
A>C |
Passed |
147094 |
4.21 % |
| Transversion |
C>A |
Passed |
148416 |
4.25 % |
| Transversion |
T>G |
Passed |
147027 |
4.21 % |
| Transversion |
G>T |
Passed |
149210 |
4.27 % |
| Transversion |
A>T |
Passed |
126856 |
3.63 % |
| Transversion |
T>A |
Passed |
127359 |
3.65 % |
| Transversion |
C>G |
Passed |
146598 |
4.20 % |
| Transversion |
G>C |
Passed |
147253 |
4.22 % |
| |
|
|
|
|
| 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 |
4.79 |
11790321 |
2459743 |
| Passed |
2.06 |
2352500 |
1139813 |
| dbSNPAll |
0 |
0 |
0 |
| dbSNPPassed |
0 |
0 |
0 |