/EXTERNAL BLUEPRINT/variants/K006378_15_lane_gembs
BACK
SAMPLE K006378_15_lane_gembs
Variant counts
| Type |
Total |
Pass |
% |
| SNPs |
1149608135 |
1074416959 |
93.46 % |
| Multiallelic |
0 |
0 |
0.00 % |
VCF Filtering Stats
| Type |
#Sites |
% |
#Non-Variant Sites |
% |
#Variant Sites |
% |
| All |
1149608135 |
100% |
1140719691 |
99.23 % |
8888444 |
0.77 % |
| |
|
|
|
|
|
|
| Passed |
1074882562 |
93.50 % |
1071849284 |
93.96 % |
3033278 |
0.28 % |
| Filtered |
74725573 |
6.50 % |
68870407 |
6.04 % |
5855166 |
0.54 % |
| |
|
|
|
|
|
|
| q20 |
43609713 |
58.36 % |
43172344 |
62.69 % |
437369 |
7.47 % |
| q20,mq40 |
12534423 |
16.77 % |
12425090 |
18.04 % |
109333 |
1.87 % |
| q20,qd2 |
8213946 |
10.99 % |
3476057 |
5.05 % |
4737889 |
80.92 % |
| mq40 |
5052168 |
6.76 % |
4837535 |
7.02 % |
214633 |
3.67 % |
| q20,qd2,mq40 |
2940836 |
3.94 % |
2756356 |
4.00 % |
184480 |
3.15 % |
| qd2 |
2322314 |
3.11 % |
2162292 |
3.14 % |
160022 |
2.73 % |
| qd2,mq40 |
50713 |
0.07 % |
40733 |
0.06 % |
9980 |
0.17 % |
| qd2,fs60,mq40 |
637 |
0.00 % |
0 |
0.00 % |
637 |
0.01 % |
| fs60,mq40 |
387 |
0.00 % |
0 |
0.00 % |
387 |
0.01 % |
| qd2,fs60 |
155 |
0.00 % |
0 |
0.00 % |
155 |
0.00 % |
| fs60 |
146 |
0.00 % |
0 |
0.00 % |
146 |
0.00 % |
| q20,qd2,fs60,mq40 |
85 |
0.00 % |
0 |
0.00 % |
85 |
0.00 % |
| q20,qd2,fs60 |
47 |
0.00 % |
0 |
0.00 % |
47 |
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 |
3015361 |
28.65 % |
| Transition |
G>A |
All |
952025 |
9.04 % |
| Transition |
T>C |
All |
2980184 |
28.31 % |
| Transition |
C>T |
All |
967908 |
9.20 % |
| Transversion |
A>C |
All |
225959 |
2.15 % |
| Transversion |
C>A |
All |
471140 |
4.48 % |
| Transversion |
T>G |
All |
228269 |
2.17 % |
| Transversion |
G>T |
All |
467269 |
4.44 % |
| Transversion |
A>T |
All |
404327 |
3.84 % |
| Transversion |
T>A |
All |
398214 |
3.78 % |
| Transversion |
C>G |
All |
207062 |
1.97 % |
| Transversion |
G>C |
All |
208124 |
1.98 % |
| |
|
|
|
|
| Transition |
A>G |
Passed |
634289 |
16.80 % |
| Transition |
G>A |
Passed |
624751 |
16.55 % |
| Transition |
T>C |
Passed |
636551 |
16.86 % |
| Transition |
C>T |
Passed |
630727 |
16.70 % |
| Transversion |
A>C |
Passed |
158379 |
4.19 % |
| Transversion |
C>A |
Passed |
166730 |
4.42 % |
| Transversion |
T>G |
Passed |
159532 |
4.22 % |
| Transversion |
G>T |
Passed |
167549 |
4.44 % |
| Transversion |
A>T |
Passed |
141909 |
3.76 % |
| Transversion |
T>A |
Passed |
142361 |
3.77 % |
| Transversion |
C>G |
Passed |
156117 |
4.13 % |
| Transversion |
G>C |
Passed |
157154 |
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 |
3.03 |
7915478 |
2610364 |
| Passed |
2.02 |
2526318 |
1249731 |
| dbSNPAll |
0 |
0 |
0 |
| dbSNPPassed |
0 |
0 |
0 |