/EXTERNAL BLUEPRINT/variants/K006278_K006282_11_lane_gembs
BACK
SAMPLE K006278_K006282_11_lane_gembs
Variant counts
| Type |
Total |
Pass |
% |
| SNPs |
1126499632 |
713981906 |
63.38 % |
| Multiallelic |
0 |
0 |
0.00 % |
VCF Filtering Stats
| Type |
#Sites |
% |
#Non-Variant Sites |
% |
#Variant Sites |
% |
| All |
1126499632 |
100% |
1106213129 |
98.20 % |
20286503 |
1.80 % |
| |
|
|
|
|
|
|
| Passed |
715558751 |
63.52 % |
712625533 |
64.42 % |
2933218 |
0.41 % |
| Filtered |
410940881 |
36.48 % |
393587596 |
35.58 % |
17353285 |
2.43 % |
| |
|
|
|
|
|
|
| q20 |
319273993 |
77.69 % |
317557029 |
80.68 % |
1716964 |
9.89 % |
| q20,qd2 |
47514490 |
11.56 % |
32511193 |
8.26 % |
15003297 |
86.46 % |
| qd2 |
19925354 |
4.85 % |
19774451 |
5.02 % |
150903 |
0.87 % |
| q20,mq40 |
13159674 |
3.20 % |
13067343 |
3.32 % |
92331 |
0.53 % |
| mq40 |
7887393 |
1.92 % |
7717451 |
1.96 % |
169942 |
0.98 % |
| q20,qd2,mq40 |
3044699 |
0.74 % |
2857002 |
0.73 % |
187697 |
1.08 % |
| qd2,mq40 |
117600 |
0.03 % |
103127 |
0.03 % |
14473 |
0.08 % |
| q20,qd2,fs60 |
7335 |
0.00 % |
0 |
0.00 % |
7335 |
0.04 % |
| fs60 |
3164 |
0.00 % |
0 |
0.00 % |
3164 |
0.02 % |
| qd2,fs60 |
3152 |
0.00 % |
0 |
0.00 % |
3152 |
0.02 % |
| qd2,fs60,mq40 |
2240 |
0.00 % |
0 |
0.00 % |
2240 |
0.01 % |
| q20,qd2,fs60,mq40 |
928 |
0.00 % |
0 |
0.00 % |
928 |
0.01 % |
| fs60,mq40 |
846 |
0.00 % |
0 |
0.00 % |
846 |
0.00 % |
| q20,fs60 |
9 |
0.00 % |
0 |
0.00 % |
9 |
0.00 % |
| q20,fs60,mq40 |
4 |
0.00 % |
0 |
0.00 % |
4 |
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 |
3176628 |
8.34 % |
| Transition |
G>A |
All |
14728472 |
38.65 % |
| Transition |
T>C |
All |
3093258 |
8.12 % |
| Transition |
C>T |
All |
14770446 |
38.76 % |
| Transversion |
A>C |
All |
189167 |
0.50 % |
| Transversion |
C>A |
All |
452696 |
1.19 % |
| Transversion |
T>G |
All |
197214 |
0.52 % |
| Transversion |
G>T |
All |
446017 |
1.17 % |
| Transversion |
A>T |
All |
351088 |
0.92 % |
| Transversion |
T>A |
All |
339902 |
0.89 % |
| Transversion |
C>G |
All |
185010 |
0.49 % |
| Transversion |
G>C |
All |
174796 |
0.46 % |
| |
|
|
|
|
| Transition |
A>G |
Passed |
394435 |
18.74 % |
| Transition |
G>A |
Passed |
359443 |
17.08 % |
| Transition |
T>C |
Passed |
392067 |
18.63 % |
| Transition |
C>T |
Passed |
358803 |
17.05 % |
| Transversion |
A>C |
Passed |
79743 |
3.79 % |
| Transversion |
C>A |
Passed |
73483 |
3.49 % |
| Transversion |
T>G |
Passed |
79549 |
3.78 % |
| Transversion |
G>T |
Passed |
73455 |
3.49 % |
| Transversion |
A>T |
Passed |
53385 |
2.54 % |
| Transversion |
T>A |
Passed |
53364 |
2.54 % |
| Transversion |
C>G |
Passed |
93030 |
4.42 % |
| Transversion |
G>C |
Passed |
93704 |
4.45 % |
| |
|
|
|
|
| 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 |
15.31 |
35768804 |
2335890 |
| Passed |
2.51 |
1504748 |
599713 |
| dbSNPAll |
0 |
0 |
0 |
| dbSNPPassed |
0 |
0 |
0 |