/EXTERNAL BLUEPRINT/variants/K006330_15_lane_gembs
BACK
SAMPLE K006330_15_lane_gembs
Variant counts
| Type |
Total |
Pass |
% |
| SNPs |
1076375218 |
552818344 |
51.36 % |
| Multiallelic |
0 |
0 |
0.00 % |
VCF Filtering Stats
| Type |
#Sites |
% |
#Non-Variant Sites |
% |
#Variant Sites |
% |
| All |
1076375218 |
100% |
1057738038 |
98.27 % |
18637180 |
1.73 % |
| |
|
|
|
|
|
|
| Passed |
554456783 |
51.51 % |
551692251 |
52.16 % |
2764532 |
0.50 % |
| Filtered |
521918435 |
48.49 % |
506045787 |
47.84 % |
15872648 |
2.86 % |
| |
|
|
|
|
|
|
| q20 |
429124717 |
82.22 % |
427311022 |
84.44 % |
1813695 |
11.43 % |
| q20,qd2 |
63281286 |
12.12 % |
49790193 |
9.84 % |
13491093 |
85.00 % |
| q20,mq40 |
15724835 |
3.01 % |
15616587 |
3.09 % |
108248 |
0.68 % |
| mq40 |
6973105 |
1.34 % |
6817594 |
1.35 % |
155511 |
0.98 % |
| q20,qd2,mq40 |
3589027 |
0.69 % |
3392849 |
0.67 % |
196178 |
1.24 % |
| qd2 |
3129599 |
0.60 % |
3042103 |
0.60 % |
87496 |
0.55 % |
| qd2,mq40 |
86062 |
0.02 % |
75439 |
0.01 % |
10623 |
0.07 % |
| q20,qd2,fs60 |
3342 |
0.00 % |
0 |
0.00 % |
3342 |
0.02 % |
| fs60 |
1938 |
0.00 % |
0 |
0.00 % |
1938 |
0.01 % |
| qd2,fs60 |
1855 |
0.00 % |
0 |
0.00 % |
1855 |
0.01 % |
| qd2,fs60,mq40 |
1491 |
0.00 % |
0 |
0.00 % |
1491 |
0.01 % |
| q20,qd2,fs60,mq40 |
693 |
0.00 % |
0 |
0.00 % |
693 |
0.00 % |
| fs60,mq40 |
483 |
0.00 % |
0 |
0.00 % |
483 |
0.00 % |
| q20,fs60 |
2 |
0.00 % |
0 |
0.00 % |
2 |
0.00 % |
| q20,fs60,mq40 |
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 |
3069028 |
11.56 % |
| Transition |
G>A |
All |
9002913 |
33.90 % |
| Transition |
T>C |
All |
2837670 |
10.68 % |
| Transition |
C>T |
All |
8823277 |
33.22 % |
| Transversion |
A>C |
All |
216441 |
0.81 % |
| Transversion |
C>A |
All |
572445 |
2.16 % |
| Transversion |
T>G |
All |
236146 |
0.89 % |
| Transversion |
G>T |
All |
560012 |
2.11 % |
| Transversion |
A>T |
All |
426730 |
1.61 % |
| Transversion |
T>A |
All |
431101 |
1.62 % |
| Transversion |
C>G |
All |
196989 |
0.74 % |
| Transversion |
G>C |
All |
185369 |
0.70 % |
| |
|
|
|
|
| Transition |
A>G |
Passed |
321699 |
19.43 % |
| Transition |
G>A |
Passed |
286136 |
17.29 % |
| Transition |
T>C |
Passed |
320390 |
19.35 % |
| Transition |
C>T |
Passed |
285175 |
17.23 % |
| Transversion |
A>C |
Passed |
59246 |
3.58 % |
| Transversion |
C>A |
Passed |
52646 |
3.18 % |
| Transversion |
T>G |
Passed |
58511 |
3.53 % |
| Transversion |
G>T |
Passed |
53364 |
3.22 % |
| Transversion |
A>T |
Passed |
34414 |
2.08 % |
| Transversion |
T>A |
Passed |
34183 |
2.06 % |
| Transversion |
C>G |
Passed |
74504 |
4.50 % |
| Transversion |
G>C |
Passed |
75129 |
4.54 % |
| |
|
|
|
|
| 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 |
8.40 |
23732888 |
2825233 |
| Passed |
2.75 |
1213400 |
441997 |
| dbSNPAll |
0 |
0 |
0 |
| dbSNPPassed |
0 |
0 |
0 |