/EXTERNAL KNIH/variants/K006225_1_lane_gembs
BACK
SAMPLE K006225_1_lane_gembs
Variant counts
| Type |
Total |
Pass |
% |
| SNPs |
1158545985 |
1050497237 |
90.67 % |
| Multiallelic |
0 |
0 |
0.00 % |
VCF Filtering Stats
| Type |
#Sites |
% |
#Non-Variant Sites |
% |
#Variant Sites |
% |
| All |
1158545985 |
100% |
1146549378 |
98.96 % |
11996607 |
1.04 % |
| |
|
|
|
|
|
|
| Passed |
1051429072 |
90.75 % |
1048019839 |
91.41 % |
3409233 |
0.32 % |
| Filtered |
107116913 |
9.25 % |
98529539 |
8.59 % |
8587374 |
0.82 % |
| |
|
|
|
|
|
|
| q20 |
71269182 |
66.53 % |
70593786 |
71.65 % |
675396 |
7.86 % |
| q20,mq40 |
14544586 |
13.58 % |
14410024 |
14.63 % |
134562 |
1.57 % |
| q20,qd2 |
9856924 |
9.20 % |
2965495 |
3.01 % |
6891429 |
80.25 % |
| mq40 |
6216350 |
5.80 % |
5927513 |
6.02 % |
288837 |
3.36 % |
| q20,qd2,mq40 |
3140009 |
2.93 % |
2903452 |
2.95 % |
236557 |
2.75 % |
| qd2 |
2013377 |
1.88 % |
1668562 |
1.69 % |
344815 |
4.02 % |
| qd2,mq40 |
73374 |
0.07 % |
60707 |
0.06 % |
12667 |
0.15 % |
| qd2,fs60,mq40 |
1390 |
0.00 % |
0 |
0.00 % |
1390 |
0.02 % |
| fs60 |
514 |
0.00 % |
0 |
0.00 % |
514 |
0.01 % |
| fs60,mq40 |
508 |
0.00 % |
0 |
0.00 % |
508 |
0.01 % |
| qd2,fs60 |
394 |
0.00 % |
0 |
0.00 % |
394 |
0.00 % |
| q20,qd2,fs60 |
173 |
0.00 % |
0 |
0.00 % |
173 |
0.00 % |
| q20,qd2,fs60,mq40 |
129 |
0.00 % |
0 |
0.00 % |
129 |
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 |
4852012 |
35.09 % |
| Transition |
G>A |
All |
872287 |
6.31 % |
| Transition |
T>C |
All |
4816802 |
34.84 % |
| Transition |
C>T |
All |
878000 |
6.35 % |
| Transversion |
A>C |
All |
222362 |
1.61 % |
| Transversion |
C>A |
All |
412238 |
2.98 % |
| Transversion |
T>G |
All |
223981 |
1.62 % |
| Transversion |
G>T |
All |
406921 |
2.94 % |
| Transversion |
A>T |
All |
365078 |
2.64 % |
| Transversion |
T>A |
All |
356010 |
2.57 % |
| Transversion |
C>G |
All |
210220 |
1.52 % |
| Transversion |
G>C |
All |
211380 |
1.53 % |
| |
|
|
|
|
| Transition |
A>G |
Passed |
707317 |
18.50 % |
| Transition |
G>A |
Passed |
597547 |
15.63 % |
| Transition |
T>C |
Passed |
708552 |
18.53 % |
| Transition |
C>T |
Passed |
603064 |
15.78 % |
| Transversion |
A>C |
Passed |
152863 |
4.00 % |
| Transversion |
C>A |
Passed |
158807 |
4.15 % |
| Transversion |
T>G |
Passed |
153080 |
4.00 % |
| Transversion |
G>T |
Passed |
158621 |
4.15 % |
| Transversion |
A>T |
Passed |
139552 |
3.65 % |
| Transversion |
T>A |
Passed |
139566 |
3.65 % |
| Transversion |
C>G |
Passed |
151898 |
3.97 % |
| Transversion |
G>C |
Passed |
152022 |
3.98 % |
| |
|
|
|
|
| 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 |
4.74 |
11419101 |
2408190 |
| Passed |
2.17 |
2616480 |
1206409 |
| dbSNPAll |
0 |
0 |
0 |
| dbSNPPassed |
0 |
0 |
0 |