/EXTERNAL BLUEPRINT/variants/K006349_12_lane_gembs
BACK
SAMPLE K006349_12_lane_gembs
Variant counts
| Type |
Total |
Pass |
% |
| SNPs |
1103965576 |
615494003 |
55.75 % |
| Multiallelic |
0 |
0 |
0.00 % |
VCF Filtering Stats
| Type |
#Sites |
% |
#Non-Variant Sites |
% |
#Variant Sites |
% |
| All |
1103965576 |
100% |
1087548810 |
98.51 % |
16416766 |
1.49 % |
| |
|
|
|
|
|
|
| Passed |
617410203 |
55.93 % |
614196023 |
56.48 % |
3214180 |
0.52 % |
| Filtered |
486555373 |
44.07 % |
473352787 |
43.52 % |
13202586 |
2.14 % |
| |
|
|
|
|
|
|
| q20 |
411107223 |
84.49 % |
409545551 |
86.52 % |
1561672 |
11.83 % |
| q20,qd2 |
48932571 |
10.06 % |
37873810 |
8.00 % |
11058761 |
83.76 % |
| q20,mq40 |
14858647 |
3.05 % |
14749967 |
3.12 % |
108680 |
0.82 % |
| mq40 |
6158224 |
1.27 % |
5988023 |
1.27 % |
170201 |
1.29 % |
| q20,qd2,mq40 |
3350997 |
0.69 % |
3146836 |
0.66 % |
204161 |
1.55 % |
| qd2 |
2068695 |
0.43 % |
1985904 |
0.42 % |
82791 |
0.63 % |
| qd2,mq40 |
72877 |
0.01 % |
62696 |
0.01 % |
10181 |
0.08 % |
| q20,qd2,fs60 |
2090 |
0.00 % |
0 |
0.00 % |
2090 |
0.02 % |
| fs60 |
1340 |
0.00 % |
0 |
0.00 % |
1340 |
0.01 % |
| qd2,fs60,mq40 |
959 |
0.00 % |
0 |
0.00 % |
959 |
0.01 % |
| qd2,fs60 |
776 |
0.00 % |
0 |
0.00 % |
776 |
0.01 % |
| q20,qd2,fs60,mq40 |
492 |
0.00 % |
0 |
0.00 % |
492 |
0.00 % |
| fs60,mq40 |
478 |
0.00 % |
0 |
0.00 % |
478 |
0.00 % |
| q20,fs60 |
2 |
0.00 % |
0 |
0.00 % |
2 |
0.00 % |
| q20,fs60,mq40 |
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 |
3373925 |
17.48 % |
| Transition |
G>A |
All |
4926028 |
25.53 % |
| Transition |
T>C |
All |
3230332 |
16.74 % |
| Transition |
C>T |
All |
4809925 |
24.92 % |
| Transversion |
A>C |
All |
210985 |
1.09 % |
| Transversion |
C>A |
All |
634673 |
3.29 % |
| Transversion |
T>G |
All |
222782 |
1.15 % |
| Transversion |
G>T |
All |
629342 |
3.26 % |
| Transversion |
A>T |
All |
447242 |
2.32 % |
| Transversion |
T>A |
All |
442692 |
2.29 % |
| Transversion |
C>G |
All |
188077 |
0.97 % |
| Transversion |
G>C |
All |
182167 |
0.94 % |
| |
|
|
|
|
| Transition |
A>G |
Passed |
363645 |
18.94 % |
| Transition |
G>A |
Passed |
328591 |
17.12 % |
| Transition |
T>C |
Passed |
361266 |
18.82 % |
| Transition |
C>T |
Passed |
328251 |
17.10 % |
| Transversion |
A>C |
Passed |
71950 |
3.75 % |
| Transversion |
C>A |
Passed |
65690 |
3.42 % |
| Transversion |
T>G |
Passed |
71610 |
3.73 % |
| Transversion |
G>T |
Passed |
65777 |
3.43 % |
| Transversion |
A>T |
Passed |
44447 |
2.32 % |
| Transversion |
T>A |
Passed |
44362 |
2.31 % |
| Transversion |
C>G |
Passed |
86895 |
4.53 % |
| Transversion |
G>C |
Passed |
87272 |
4.55 % |
| |
|
|
|
|
| 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 |
5.52 |
16340210 |
2957960 |
| Passed |
2.57 |
1381753 |
538003 |
| dbSNPAll |
0 |
0 |
0 |
| dbSNPPassed |
0 |
0 |
0 |