/EXTERNAL BLUEPRINT/variants/K006391_K006404_25_lane_gembs
BACK
SAMPLE K006391_K006404_25_lane_gembs
Variant counts
| Type |
Total |
Pass |
% |
| SNPs |
1152392716 |
1028091985 |
89.21 % |
| Multiallelic |
0 |
0 |
0.00 % |
VCF Filtering Stats
| Type |
#Sites |
% |
#Non-Variant Sites |
% |
#Variant Sites |
% |
| All |
1152392716 |
100% |
1141217735 |
99.03 % |
11174981 |
0.97 % |
| |
|
|
|
|
|
|
| Passed |
1029230777 |
89.31 % |
1025684818 |
89.88 % |
3545959 |
0.34 % |
| Filtered |
123161939 |
10.69 % |
115532917 |
10.12 % |
7629022 |
0.74 % |
| |
|
|
|
|
|
|
| q20 |
81806091 |
66.42 % |
80941966 |
70.06 % |
864125 |
11.33 % |
| q20,mq40 |
11404973 |
9.26 % |
11296564 |
9.78 % |
108409 |
1.42 % |
| qd2 |
10042040 |
8.15 % |
9880079 |
8.55 % |
161961 |
2.12 % |
| q20,qd2 |
9319977 |
7.57 % |
3278273 |
2.84 % |
6041704 |
79.19 % |
| mq40 |
7695447 |
6.25 % |
7473507 |
6.47 % |
221940 |
2.91 % |
| q20,qd2,mq40 |
2745981 |
2.23 % |
2549589 |
2.21 % |
196392 |
2.57 % |
| qd2,mq40 |
131385 |
0.11 % |
112939 |
0.10 % |
18446 |
0.24 % |
| fs60 |
4629 |
0.00 % |
0 |
0.00 % |
4629 |
0.06 % |
| qd2,fs60 |
3641 |
0.00 % |
0 |
0.00 % |
3641 |
0.05 % |
| q20,qd2,fs60 |
3552 |
0.00 % |
0 |
0.00 % |
3552 |
0.05 % |
| qd2,fs60,mq40 |
2818 |
0.00 % |
0 |
0.00 % |
2818 |
0.04 % |
| fs60,mq40 |
991 |
0.00 % |
0 |
0.00 % |
991 |
0.01 % |
| q20,qd2,fs60,mq40 |
404 |
0.00 % |
0 |
0.00 % |
404 |
0.01 % |
| q20,fs60,mq40 |
9 |
0.00 % |
0 |
0.00 % |
9 |
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 |
4152341 |
31.97 % |
| Transition |
G>A |
All |
1133793 |
8.73 % |
| Transition |
T>C |
All |
4109766 |
31.64 % |
| Transition |
C>T |
All |
1151583 |
8.87 % |
| Transversion |
A>C |
All |
216446 |
1.67 % |
| Transversion |
C>A |
All |
449039 |
3.46 % |
| Transversion |
T>G |
All |
220566 |
1.70 % |
| Transversion |
G>T |
All |
447178 |
3.44 % |
| Transversion |
A>T |
All |
356612 |
2.75 % |
| Transversion |
T>A |
All |
346078 |
2.66 % |
| Transversion |
C>G |
All |
204039 |
1.57 % |
| Transversion |
G>C |
All |
201701 |
1.55 % |
| |
|
|
|
|
| Transition |
A>G |
Passed |
609751 |
17.23 % |
| Transition |
G>A |
Passed |
583526 |
16.49 % |
| Transition |
T>C |
Passed |
609834 |
17.24 % |
| Transition |
C>T |
Passed |
587733 |
16.61 % |
| Transversion |
A>C |
Passed |
148836 |
4.21 % |
| Transversion |
C>A |
Passed |
149568 |
4.23 % |
| Transversion |
T>G |
Passed |
149117 |
4.21 % |
| Transversion |
G>T |
Passed |
149640 |
4.23 % |
| Transversion |
A>T |
Passed |
126818 |
3.58 % |
| Transversion |
T>A |
Passed |
126575 |
3.58 % |
| Transversion |
C>G |
Passed |
147957 |
4.18 % |
| Transversion |
G>C |
Passed |
148609 |
4.20 % |
| |
|
|
|
|
| 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 |
4.32 |
10547483 |
2441659 |
| Passed |
2.08 |
2390844 |
1147120 |
| dbSNPAll |
0 |
0 |
0 |
| dbSNPPassed |
0 |
0 |
0 |