/EXTERNAL BLUEPRINT/variants/K006289_14_lane_gembs
BACK
SAMPLE K006289_14_lane_gembs
Variant counts
| Type |
Total |
Pass |
% |
| SNPs |
1117023170 |
640284858 |
57.32 % |
| Multiallelic |
0 |
0 |
0.00 % |
VCF Filtering Stats
| Type |
#Sites |
% |
#Non-Variant Sites |
% |
#Variant Sites |
% |
| All |
1117023170 |
100% |
1102109153 |
98.66 % |
14914017 |
1.34 % |
| |
|
|
|
|
|
|
| Passed |
642077759 |
57.48 % |
638956253 |
57.98 % |
3121506 |
0.49 % |
| Filtered |
474945411 |
42.52 % |
463152900 |
42.02 % |
11792511 |
1.84 % |
| |
|
|
|
|
|
|
| q20 |
407141440 |
85.72 % |
405619881 |
87.58 % |
1521559 |
12.90 % |
| q20,qd2 |
43561625 |
9.17 % |
33765240 |
7.29 % |
9796385 |
83.07 % |
| q20,mq40 |
13904293 |
2.93 % |
13819460 |
2.98 % |
84833 |
0.72 % |
| mq40 |
5163874 |
1.09 % |
5015549 |
1.08 % |
148325 |
1.26 % |
| q20,qd2,mq40 |
3220935 |
0.68 % |
3075536 |
0.66 % |
145399 |
1.23 % |
| qd2 |
1873834 |
0.39 % |
1793750 |
0.39 % |
80084 |
0.68 % |
| qd2,mq40 |
73816 |
0.02 % |
63484 |
0.01 % |
10332 |
0.09 % |
| q20,qd2,fs60 |
1360 |
0.00 % |
0 |
0.00 % |
1360 |
0.01 % |
| qd2,fs60,mq40 |
1313 |
0.00 % |
0 |
0.00 % |
1313 |
0.01 % |
| fs60 |
1043 |
0.00 % |
0 |
0.00 % |
1043 |
0.01 % |
| qd2,fs60 |
868 |
0.00 % |
0 |
0.00 % |
868 |
0.01 % |
| fs60,mq40 |
537 |
0.00 % |
0 |
0.00 % |
537 |
0.00 % |
| q20,qd2,fs60,mq40 |
472 |
0.00 % |
0 |
0.00 % |
472 |
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 |
3176596 |
18.18 % |
| Transition |
G>A |
All |
4355725 |
24.92 % |
| Transition |
T>C |
All |
3072274 |
17.58 % |
| Transition |
C>T |
All |
4207254 |
24.07 % |
| Transversion |
A>C |
All |
196801 |
1.13 % |
| Transversion |
C>A |
All |
558744 |
3.20 % |
| Transversion |
T>G |
All |
205521 |
1.18 % |
| Transversion |
G>T |
All |
549007 |
3.14 % |
| Transversion |
A>T |
All |
398377 |
2.28 % |
| Transversion |
T>A |
All |
388702 |
2.22 % |
| Transversion |
C>G |
All |
187610 |
1.07 % |
| Transversion |
G>C |
All |
180320 |
1.03 % |
| |
|
|
|
|
| Transition |
A>G |
Passed |
367730 |
18.57 % |
| Transition |
G>A |
Passed |
340424 |
17.19 % |
| Transition |
T>C |
Passed |
367079 |
18.54 % |
| Transition |
C>T |
Passed |
340927 |
17.21 % |
| Transversion |
A>C |
Passed |
74104 |
3.74 % |
| Transversion |
C>A |
Passed |
69340 |
3.50 % |
| Transversion |
T>G |
Passed |
73845 |
3.73 % |
| Transversion |
G>T |
Passed |
69455 |
3.51 % |
| Transversion |
A>T |
Passed |
48771 |
2.46 % |
| Transversion |
T>A |
Passed |
48446 |
2.45 % |
| Transversion |
C>G |
Passed |
89997 |
4.54 % |
| Transversion |
G>C |
Passed |
90341 |
4.56 % |
| |
|
|
|
|
| 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 |
5.56 |
14811849 |
2665082 |
| Passed |
2.51 |
1416160 |
564299 |
| dbSNPAll |
0 |
0 |
0 |
| dbSNPPassed |
0 |
0 |
0 |