/EXTERNAL BLUEPRINT/variants/K006425_11_lane_gembs
BACK
SAMPLE K006425_11_lane_gembs
Variant counts
| Type |
Total |
Pass |
% |
| SNPs |
1156791998 |
1046447980 |
90.46 % |
| Multiallelic |
0 |
0 |
0.00 % |
VCF Filtering Stats
| Type |
#Sites |
% |
#Non-Variant Sites |
% |
#Variant Sites |
% |
| All |
1156791998 |
100% |
1144949099 |
98.98 % |
11842899 |
1.02 % |
| |
|
|
|
|
|
|
| Passed |
1047329251 |
90.54 % |
1043898371 |
91.17 % |
3430880 |
0.33 % |
| Filtered |
109462747 |
9.46 % |
101050728 |
8.83 % |
8412019 |
0.80 % |
| |
|
|
|
|
|
|
| q20 |
76384235 |
69.78 % |
75680869 |
74.89 % |
703366 |
8.36 % |
| q20,mq40 |
12521968 |
11.44 % |
12416234 |
12.29 % |
105734 |
1.26 % |
| q20,qd2 |
11636875 |
10.63 % |
4548159 |
4.50 % |
7088716 |
84.27 % |
| mq40 |
3582989 |
3.27 % |
3389181 |
3.35 % |
193808 |
2.30 % |
| q20,qd2,mq40 |
3095747 |
2.83 % |
2927575 |
2.90 % |
168172 |
2.00 % |
| qd2 |
2195628 |
2.01 % |
2052887 |
2.03 % |
142741 |
1.70 % |
| qd2,mq40 |
43918 |
0.04 % |
35823 |
0.04 % |
8095 |
0.10 % |
| qd2,fs60,mq40 |
661 |
0.00 % |
0 |
0.00 % |
661 |
0.01 % |
| fs60,mq40 |
311 |
0.00 % |
0 |
0.00 % |
311 |
0.00 % |
| qd2,fs60 |
181 |
0.00 % |
0 |
0.00 % |
181 |
0.00 % |
| fs60 |
136 |
0.00 % |
0 |
0.00 % |
136 |
0.00 % |
| q20,qd2,fs60,mq40 |
65 |
0.00 % |
0 |
0.00 % |
65 |
0.00 % |
| q20,qd2,fs60 |
32 |
0.00 % |
0 |
0.00 % |
32 |
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 |
4334586 |
32.13 % |
| Transition |
G>A |
All |
1004530 |
7.45 % |
| Transition |
T>C |
All |
4295799 |
31.85 % |
| Transition |
C>T |
All |
1024289 |
7.59 % |
| Transversion |
A>C |
All |
219920 |
1.63 % |
| Transversion |
C>A |
All |
555231 |
4.12 % |
| Transversion |
T>G |
All |
221848 |
1.64 % |
| Transversion |
G>T |
All |
554499 |
4.11 % |
| Transversion |
A>T |
All |
440127 |
3.26 % |
| Transversion |
T>A |
All |
427342 |
3.17 % |
| Transversion |
C>G |
All |
205258 |
1.52 % |
| Transversion |
G>C |
All |
206016 |
1.53 % |
| |
|
|
|
|
| Transition |
A>G |
Passed |
636989 |
17.09 % |
| Transition |
G>A |
Passed |
613870 |
16.47 % |
| Transition |
T>C |
Passed |
637360 |
17.10 % |
| Transition |
C>T |
Passed |
618232 |
16.59 % |
| Transversion |
A>C |
Passed |
154420 |
4.14 % |
| Transversion |
C>A |
Passed |
163180 |
4.38 % |
| Transversion |
T>G |
Passed |
155313 |
4.17 % |
| Transversion |
G>T |
Passed |
163976 |
4.40 % |
| Transversion |
A>T |
Passed |
137905 |
3.70 % |
| Transversion |
T>A |
Passed |
137917 |
3.70 % |
| Transversion |
C>G |
Passed |
153971 |
4.13 % |
| Transversion |
G>C |
Passed |
154476 |
4.14 % |
| |
|
|
|
|
| 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 |
3.77 |
10659204 |
2830241 |
| Passed |
2.05 |
2506451 |
1221158 |
| dbSNPAll |
0 |
0 |
0 |
| dbSNPPassed |
0 |
0 |
0 |