/EXTERNAL BLUEPRINT/variants/K006393_K006406_19_lane_gembs
BACK
SAMPLE K006393_K006406_19_lane_gembs
Variant counts
| Type |
Total |
Pass |
% |
| SNPs |
1153026442 |
1029840499 |
89.32 % |
| Multiallelic |
0 |
0 |
0.00 % |
VCF Filtering Stats
| Type |
#Sites |
% |
#Non-Variant Sites |
% |
#Variant Sites |
% |
| All |
1153026442 |
100% |
1141783235 |
99.02 % |
11243207 |
0.98 % |
| |
|
|
|
|
|
|
| Passed |
1031025435 |
89.42 % |
1027409044 |
89.98 % |
3616391 |
0.35 % |
| Filtered |
122001007 |
10.58 % |
114374191 |
10.02 % |
7626816 |
0.74 % |
| |
|
|
|
|
|
|
| q20 |
85326261 |
69.94 % |
84417509 |
73.81 % |
908752 |
11.92 % |
| q20,mq40 |
11434521 |
9.37 % |
11332812 |
9.91 % |
101709 |
1.33 % |
| q20,qd2 |
9295641 |
7.62 % |
3265116 |
2.85 % |
6030525 |
79.07 % |
| mq40 |
6972632 |
5.72 % |
6760833 |
5.91 % |
211799 |
2.78 % |
| qd2 |
6059127 |
4.97 % |
5900929 |
5.16 % |
158198 |
2.07 % |
| q20,qd2,mq40 |
2784315 |
2.28 % |
2599470 |
2.27 % |
184845 |
2.42 % |
| qd2,mq40 |
115171 |
0.09 % |
97522 |
0.09 % |
17649 |
0.23 % |
| fs60 |
3770 |
0.00 % |
0 |
0.00 % |
3770 |
0.05 % |
| qd2,fs60 |
3086 |
0.00 % |
0 |
0.00 % |
3086 |
0.04 % |
| q20,qd2,fs60 |
2704 |
0.00 % |
0 |
0.00 % |
2704 |
0.04 % |
| qd2,fs60,mq40 |
2488 |
0.00 % |
0 |
0.00 % |
2488 |
0.03 % |
| fs60,mq40 |
923 |
0.00 % |
0 |
0.00 % |
923 |
0.01 % |
| q20,qd2,fs60,mq40 |
361 |
0.00 % |
0 |
0.00 % |
361 |
0.00 % |
| q20,fs60,mq40 |
6 |
0.00 % |
0 |
0.00 % |
6 |
0.00 % |
| q20,fs60 |
1 |
0.00 % |
0 |
0.00 % |
1 |
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 |
4237197 |
32.54 % |
| Transition |
G>A |
All |
1072071 |
8.23 % |
| Transition |
T>C |
All |
4198134 |
32.24 % |
| Transition |
C>T |
All |
1076249 |
8.27 % |
| Transversion |
A>C |
All |
220461 |
1.69 % |
| Transversion |
C>A |
All |
438832 |
3.37 % |
| Transversion |
T>G |
All |
223233 |
1.71 % |
| Transversion |
G>T |
All |
431313 |
3.31 % |
| Transversion |
A>T |
All |
359189 |
2.76 % |
| Transversion |
T>A |
All |
355120 |
2.73 % |
| Transversion |
C>G |
All |
205780 |
1.58 % |
| Transversion |
G>C |
All |
203783 |
1.56 % |
| |
|
|
|
|
| Transition |
A>G |
Passed |
617709 |
17.41 % |
| Transition |
G>A |
Passed |
578400 |
16.30 % |
| Transition |
T>C |
Passed |
619069 |
17.45 % |
| Transition |
C>T |
Passed |
580900 |
16.37 % |
| Transversion |
A>C |
Passed |
151325 |
4.27 % |
| Transversion |
C>A |
Passed |
148010 |
4.17 % |
| Transversion |
T>G |
Passed |
151744 |
4.28 % |
| Transversion |
G>T |
Passed |
148427 |
4.18 % |
| Transversion |
A>T |
Passed |
126514 |
3.57 % |
| Transversion |
T>A |
Passed |
126071 |
3.55 % |
| Transversion |
C>G |
Passed |
149722 |
4.22 % |
| Transversion |
G>C |
Passed |
150045 |
4.23 % |
| |
|
|
|
|
| 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 |
4.34 |
10583651 |
2437711 |
| Passed |
2.08 |
2396078 |
1151858 |
| dbSNPAll |
0 |
0 |
0 |
| dbSNPPassed |
0 |
0 |
0 |