/EXTERNAL BLUEPRINT/variants/K006377_15_lane_gembs
BACK
SAMPLE K006377_15_lane_gembs
Variant counts
| Type |
Total |
Pass |
% |
| SNPs |
1150071882 |
1064620779 |
92.57 % |
| Multiallelic |
0 |
0 |
0.00 % |
VCF Filtering Stats
| Type |
#Sites |
% |
#Non-Variant Sites |
% |
#Variant Sites |
% |
| All |
1150071882 |
100% |
1140308489 |
99.15 % |
9763393 |
0.85 % |
| |
|
|
|
|
|
|
| Passed |
1065211713 |
92.62 % |
1062063236 |
93.14 % |
3148477 |
0.30 % |
| Filtered |
84860169 |
7.38 % |
78245253 |
6.86 % |
6614916 |
0.62 % |
| |
|
|
|
|
|
|
| q20 |
53101409 |
62.58 % |
52571005 |
67.19 % |
530404 |
8.02 % |
| q20,mq40 |
12605715 |
14.85 % |
12495384 |
15.97 % |
110331 |
1.67 % |
| q20,qd2 |
9217709 |
10.86 % |
3796959 |
4.85 % |
5420750 |
81.95 % |
| mq40 |
4539559 |
5.35 % |
4331162 |
5.54 % |
208397 |
3.15 % |
| q20,qd2,mq40 |
3035664 |
3.58 % |
2854469 |
3.65 % |
181195 |
2.74 % |
| qd2 |
2309965 |
2.72 % |
2156830 |
2.76 % |
153135 |
2.31 % |
| qd2,mq40 |
48760 |
0.06 % |
39444 |
0.05 % |
9316 |
0.14 % |
| qd2,fs60,mq40 |
625 |
0.00 % |
0 |
0.00 % |
625 |
0.01 % |
| fs60,mq40 |
368 |
0.00 % |
0 |
0.00 % |
368 |
0.01 % |
| qd2,fs60 |
152 |
0.00 % |
0 |
0.00 % |
152 |
0.00 % |
| fs60 |
124 |
0.00 % |
0 |
0.00 % |
124 |
0.00 % |
| q20,qd2,fs60,mq40 |
75 |
0.00 % |
0 |
0.00 % |
75 |
0.00 % |
| q20,qd2,fs60 |
41 |
0.00 % |
0 |
0.00 % |
41 |
0.00 % |
| q20,fs60,mq40 |
3 |
0.00 % |
0 |
0.00 % |
3 |
0.00 % |
| q20,fs60 |
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 |
3389370 |
29.74 % |
| Transition |
G>A |
All |
974797 |
8.55 % |
| Transition |
T>C |
All |
3356433 |
29.45 % |
| Transition |
C>T |
All |
993800 |
8.72 % |
| Transversion |
A>C |
All |
228182 |
2.00 % |
| Transversion |
C>A |
All |
490889 |
4.31 % |
| Transversion |
T>G |
All |
229775 |
2.02 % |
| Transversion |
G>T |
All |
488417 |
4.29 % |
| Transversion |
A>T |
All |
419074 |
3.68 % |
| Transversion |
T>A |
All |
410880 |
3.61 % |
| Transversion |
C>G |
All |
207352 |
1.82 % |
| Transversion |
G>C |
All |
208241 |
1.83 % |
| |
|
|
|
|
| Transition |
A>G |
Passed |
628966 |
16.80 % |
| Transition |
G>A |
Passed |
617624 |
16.49 % |
| Transition |
T>C |
Passed |
632407 |
16.89 % |
| Transition |
C>T |
Passed |
624405 |
16.67 % |
| Transversion |
A>C |
Passed |
158131 |
4.22 % |
| Transversion |
C>A |
Passed |
165814 |
4.43 % |
| Transversion |
T>G |
Passed |
158740 |
4.24 % |
| Transversion |
G>T |
Passed |
166219 |
4.44 % |
| Transversion |
A>T |
Passed |
141232 |
3.77 % |
| Transversion |
T>A |
Passed |
140310 |
3.75 % |
| Transversion |
C>G |
Passed |
155116 |
4.14 % |
| Transversion |
G>C |
Passed |
155862 |
4.16 % |
| |
|
|
|
|
| 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 |
3.25 |
8714400 |
2682810 |
| Passed |
2.02 |
2503402 |
1241424 |
| dbSNPAll |
0 |
0 |
0 |
| dbSNPPassed |
0 |
0 |
0 |