/EXTERNAL BLUEPRINT/variants/K011857_K011872_K011873_K011874_K011875_K011876_K011877_K011878_K011879_K011921_K011922_11_lane_gembs
BACK
SAMPLE K011857_K011872_K011873_K011874_K011875_K011876_K011877_K011878_K011879_K011921_K011922_11_lane_gembs
Variant counts
| Type |
Total |
Pass |
% |
| SNPs |
988038196 |
20767675 |
2.10 % |
| Multiallelic |
0 |
0 |
0.00 % |
VCF Filtering Stats
| Type |
#Sites |
% |
#Non-Variant Sites |
% |
#Variant Sites |
% |
| All |
988038196 |
100% |
960780407 |
97.24 % |
27257789 |
2.76 % |
| |
|
|
|
|
|
|
| Passed |
33881304 |
3.43 % |
19877344 |
2.07 % |
14003960 |
41.33 % |
| Filtered |
954156892 |
96.57 % |
940903063 |
97.93 % |
13253829 |
39.12 % |
| |
|
|
|
|
|
|
| q20 |
783541194 |
82.12 % |
774802543 |
82.35 % |
8738651 |
65.93 % |
| q20,qd2 |
90664987 |
9.50 % |
87521582 |
9.30 % |
3143405 |
23.72 % |
| q20,mq40 |
60192330 |
6.31 % |
59686165 |
6.34 % |
506165 |
3.82 % |
| q20,qd2,mq40 |
18752858 |
1.97 % |
18612602 |
1.98 % |
140256 |
1.06 % |
| mq40 |
994453 |
0.10 % |
270444 |
0.03 % |
724009 |
5.46 % |
| qd2 |
8834 |
0.00 % |
8000 |
0.00 % |
834 |
0.01 % |
| qd2,mq40 |
2181 |
0.00 % |
1727 |
0.00 % |
454 |
0.00 % |
| qd2,fs60 |
18 |
0.00 % |
0 |
0.00 % |
18 |
0.00 % |
| fs60,mq40 |
18 |
0.00 % |
0 |
0.00 % |
18 |
0.00 % |
| fs60 |
11 |
0.00 % |
0 |
0.00 % |
11 |
0.00 % |
| qd2,fs60,mq40 |
6 |
0.00 % |
0 |
0.00 % |
6 |
0.00 % |
| q20,qd2,fs60 |
1 |
0.00 % |
0 |
0.00 % |
1 |
0.00 % |
| q20,qd2,fs60,mq40 |
1 |
0.00 % |
0 |
0.00 % |
1 |
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 |
6969492 |
22.35 % |
| Transition |
G>A |
All |
2539606 |
8.14 % |
| Transition |
T>C |
All |
8706503 |
27.92 % |
| Transition |
C>T |
All |
1179569 |
3.78 % |
| Transversion |
A>C |
All |
1063627 |
3.41 % |
| Transversion |
C>A |
All |
2068812 |
6.63 % |
| Transversion |
T>G |
All |
1229871 |
3.94 % |
| Transversion |
G>T |
All |
1847036 |
5.92 % |
| Transversion |
A>T |
All |
1411345 |
4.53 % |
| Transversion |
T>A |
All |
1971075 |
6.32 % |
| Transversion |
C>G |
All |
1007195 |
3.23 % |
| Transversion |
G>C |
All |
1194593 |
3.83 % |
| |
|
|
|
|
| Transition |
A>G |
Passed |
151984 |
17.07 % |
| Transition |
G>A |
Passed |
116784 |
13.12 % |
| Transition |
T>C |
Passed |
262354 |
29.47 % |
| Transition |
C>T |
Passed |
57379 |
6.45 % |
| Transversion |
A>C |
Passed |
35931 |
4.04 % |
| Transversion |
C>A |
Passed |
45200 |
5.08 % |
| Transversion |
T>G |
Passed |
36927 |
4.15 % |
| Transversion |
G>T |
Passed |
29086 |
3.27 % |
| Transversion |
A>T |
Passed |
19874 |
2.23 % |
| Transversion |
T>A |
Passed |
46064 |
5.17 % |
| Transversion |
C>G |
Passed |
37727 |
4.24 % |
| Transversion |
G>C |
Passed |
50832 |
5.71 % |
| |
|
|
|
|
| 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 |
1.64 |
19395170 |
11793554 |
| Passed |
1.95 |
588501 |
301641 |
| dbSNPAll |
0 |
0 |
0 |
| dbSNPPassed |
0 |
0 |
0 |