/EXTERNAL BLUEPRINT/variants/K006302_18_lane_gembs
BACK
SAMPLE K006302_18_lane_gembs
Variant counts
| Type |
Total |
Pass |
% |
| SNPs |
1128709774 |
613570892 |
54.36 % |
| Multiallelic |
0 |
0 |
0.00 % |
VCF Filtering Stats
| Type |
#Sites |
% |
#Non-Variant Sites |
% |
#Variant Sites |
% |
| All |
1128709774 |
100% |
1115748057 |
98.85 % |
12961717 |
1.15 % |
| |
|
|
|
|
|
|
| Passed |
616532546 |
54.62 % |
612110516 |
54.86 % |
4422030 |
0.72 % |
| Filtered |
512177228 |
45.38 % |
503637541 |
45.14 % |
8539687 |
1.39 % |
| |
|
|
|
|
|
|
| q20 |
464004930 |
90.59 % |
462180644 |
91.77 % |
1824286 |
21.36 % |
| q20,qd2 |
30802883 |
6.01 % |
24503384 |
4.87 % |
6299499 |
73.77 % |
| q20,mq40 |
10868523 |
2.12 % |
10794498 |
2.14 % |
74025 |
0.87 % |
| q20,qd2,mq40 |
3289393 |
0.64 % |
3189451 |
0.63 % |
99942 |
1.17 % |
| mq40 |
1745124 |
0.34 % |
1617634 |
0.32 % |
127490 |
1.49 % |
| qd2 |
1405599 |
0.27 % |
1304570 |
0.26 % |
101029 |
1.18 % |
| qd2,mq40 |
56788 |
0.01 % |
47360 |
0.01 % |
9428 |
0.11 % |
| qd2,fs60,mq40 |
1091 |
0.00 % |
0 |
0.00 % |
1091 |
0.01 % |
| q20,qd2,fs60 |
858 |
0.00 % |
0 |
0.00 % |
858 |
0.01 % |
| fs60 |
674 |
0.00 % |
0 |
0.00 % |
674 |
0.01 % |
| qd2,fs60 |
521 |
0.00 % |
0 |
0.00 % |
521 |
0.01 % |
| q20,qd2,fs60,mq40 |
447 |
0.00 % |
0 |
0.00 % |
447 |
0.01 % |
| fs60,mq40 |
394 |
0.00 % |
0 |
0.00 % |
394 |
0.00 % |
| q20,fs60 |
2 |
0.00 % |
0 |
0.00 % |
2 |
0.00 % |
| q20,fs60,mq40 |
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 |
4486628 |
29.87 % |
| Transition |
G>A |
All |
1521368 |
10.13 % |
| Transition |
T>C |
All |
4437741 |
29.55 % |
| Transition |
C>T |
All |
1522729 |
10.14 % |
| Transversion |
A>C |
All |
253623 |
1.69 % |
| Transversion |
C>A |
All |
573726 |
3.82 % |
| Transversion |
T>G |
All |
260867 |
1.74 % |
| Transversion |
G>T |
All |
566406 |
3.77 % |
| Transversion |
A>T |
All |
492618 |
3.28 % |
| Transversion |
T>A |
All |
481073 |
3.20 % |
| Transversion |
C>G |
All |
214714 |
1.43 % |
| Transversion |
G>C |
All |
207960 |
1.38 % |
| |
|
|
|
|
| Transition |
A>G |
Passed |
413417 |
19.61 % |
| Transition |
G>A |
Passed |
338470 |
16.05 % |
| Transition |
T>C |
Passed |
403554 |
19.14 % |
| Transition |
C>T |
Passed |
338850 |
16.07 % |
| Transversion |
A>C |
Passed |
81249 |
3.85 % |
| Transversion |
C>A |
Passed |
76465 |
3.63 % |
| Transversion |
T>G |
Passed |
80929 |
3.84 % |
| Transversion |
G>T |
Passed |
76123 |
3.61 % |
| Transversion |
A>T |
Passed |
54390 |
2.58 % |
| Transversion |
T>A |
Passed |
54881 |
2.60 % |
| Transversion |
C>G |
Passed |
94906 |
4.50 % |
| Transversion |
G>C |
Passed |
95331 |
4.52 % |
| |
|
|
|
|
| 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 |
3.92 |
11968466 |
3050987 |
| Passed |
2.43 |
1494291 |
614274 |
| dbSNPAll |
0 |
0 |
0 |
| dbSNPPassed |
0 |
0 |
0 |