/EXTERNAL BLUEPRINT/variants/K006322_8_lane_gembs
BACK
SAMPLE K006322_8_lane_gembs
Variant counts
| Type |
Total |
Pass |
% |
| SNPs |
1106970001 |
244949568 |
22.13 % |
| Multiallelic |
0 |
0 |
0.00 % |
VCF Filtering Stats
| Type |
#Sites |
% |
#Non-Variant Sites |
% |
#Variant Sites |
% |
| All |
1106970001 |
100% |
1080339002 |
97.59 % |
26630999 |
2.41 % |
| |
|
|
|
|
|
|
| Passed |
252570038 |
22.82 % |
243855952 |
22.57 % |
8714086 |
3.45 % |
| Filtered |
854399963 |
77.18 % |
836483050 |
77.43 % |
17916913 |
7.09 % |
| |
|
|
|
|
|
|
| q20 |
771673662 |
90.32 % |
764860948 |
91.44 % |
6812714 |
38.02 % |
| q20,qd2 |
64094352 |
7.50 % |
53285639 |
6.37 % |
10808713 |
60.33 % |
| q20,mq40 |
12572220 |
1.47 % |
12477543 |
1.49 % |
94677 |
0.53 % |
| q20,qd2,mq40 |
5496532 |
0.64 % |
5427926 |
0.65 % |
68606 |
0.38 % |
| mq40 |
384136 |
0.04 % |
272075 |
0.03 % |
112061 |
0.63 % |
| qd2 |
161570 |
0.02 % |
144710 |
0.02 % |
16860 |
0.09 % |
| qd2,mq40 |
17076 |
0.00 % |
14209 |
0.00 % |
2867 |
0.02 % |
| qd2,fs60,mq40 |
212 |
0.00 % |
0 |
0.00 % |
212 |
0.00 % |
| fs60,mq40 |
78 |
0.00 % |
0 |
0.00 % |
78 |
0.00 % |
| qd2,fs60 |
57 |
0.00 % |
0 |
0.00 % |
57 |
0.00 % |
| q20,qd2,fs60,mq40 |
48 |
0.00 % |
0 |
0.00 % |
48 |
0.00 % |
| q20,qd2,fs60 |
13 |
0.00 % |
0 |
0.00 % |
13 |
0.00 % |
| fs60 |
7 |
0.00 % |
0 |
0.00 % |
7 |
0.00 % |
| q20,fs60 |
0 |
0.00 % |
0 |
0.00 % |
0 |
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 |
8802753 |
30.71 % |
| Transition |
G>A |
All |
1258325 |
4.39 % |
| Transition |
T>C |
All |
8837268 |
30.83 % |
| Transition |
C>T |
All |
1259167 |
4.39 % |
| Transversion |
A>C |
All |
434273 |
1.52 % |
| Transversion |
C>A |
All |
1508430 |
5.26 % |
| Transversion |
T>G |
All |
433823 |
1.51 % |
| Transversion |
G>T |
All |
1498655 |
5.23 % |
| Transversion |
A>T |
All |
1985494 |
6.93 % |
| Transversion |
T>A |
All |
1996291 |
6.96 % |
| Transversion |
C>G |
All |
323587 |
1.13 % |
| Transversion |
G>C |
All |
324876 |
1.13 % |
| |
|
|
|
|
| Transition |
A>G |
Passed |
261343 |
19.24 % |
| Transition |
G>A |
Passed |
196990 |
14.51 % |
| Transition |
T>C |
Passed |
260098 |
19.15 % |
| Transition |
C>T |
Passed |
198674 |
14.63 % |
| Transversion |
A>C |
Passed |
54455 |
4.01 % |
| Transversion |
C>A |
Passed |
59218 |
4.36 % |
| Transversion |
T>G |
Passed |
54690 |
4.03 % |
| Transversion |
G>T |
Passed |
58709 |
4.32 % |
| Transversion |
A>T |
Passed |
55438 |
4.08 % |
| Transversion |
T>A |
Passed |
56166 |
4.14 % |
| Transversion |
C>G |
Passed |
51258 |
3.77 % |
| Transversion |
G>C |
Passed |
51004 |
3.76 % |
| |
|
|
|
|
| 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 |
2.37 |
20157513 |
8505429 |
| Passed |
2.08 |
917105 |
440938 |
| dbSNPAll |
0 |
0 |
0 |
| dbSNPPassed |
0 |
0 |
0 |