/EXTERNAL KNIH/variants/K006250_1_lane_gembs
BACK
SAMPLE K006250_1_lane_gembs
Variant counts
| Type |
Total |
Pass |
% |
| SNPs |
1141447388 |
442263220 |
38.75 % |
| Multiallelic |
0 |
0 |
0.00 % |
VCF Filtering Stats
| Type |
#Sites |
% |
#Non-Variant Sites |
% |
#Variant Sites |
% |
| All |
1141447388 |
100% |
1084815409 |
95.04 % |
56631979 |
4.96 % |
| |
|
|
|
|
|
|
| Passed |
453699201 |
39.75 % |
435169783 |
40.11 % |
18529418 |
4.08 % |
| Filtered |
687748187 |
60.25 % |
649645626 |
59.89 % |
38102561 |
8.40 % |
| |
|
|
|
|
|
|
| q20 |
601136604 |
87.41 % |
585919014 |
90.19 % |
15217590 |
39.94 % |
| q20,qd2 |
73400433 |
10.67 % |
51545031 |
7.93 % |
21855402 |
57.36 % |
| q20,mq40 |
5129419 |
0.75 % |
5005164 |
0.77 % |
124255 |
0.33 % |
| qd2 |
4910938 |
0.71 % |
4209067 |
0.65 % |
701871 |
1.84 % |
| q20,qd2,mq40 |
2729653 |
0.40 % |
2653273 |
0.41 % |
76380 |
0.20 % |
| mq40 |
419539 |
0.06 % |
298009 |
0.05 % |
121530 |
0.32 % |
| qd2,mq40 |
20661 |
0.00 % |
16068 |
0.00 % |
4593 |
0.01 % |
| fs60 |
347 |
0.00 % |
0 |
0.00 % |
347 |
0.00 % |
| q20,qd2,fs60 |
334 |
0.00 % |
0 |
0.00 % |
334 |
0.00 % |
| qd2,fs60 |
121 |
0.00 % |
0 |
0.00 % |
121 |
0.00 % |
| qd2,fs60,mq40 |
58 |
0.00 % |
0 |
0.00 % |
58 |
0.00 % |
| fs60,mq40 |
55 |
0.00 % |
0 |
0.00 % |
55 |
0.00 % |
| q20,qd2,fs60,mq40 |
23 |
0.00 % |
0 |
0.00 % |
23 |
0.00 % |
| q20,fs60 |
1 |
0.00 % |
0 |
0.00 % |
1 |
0.00 % |
| q20,fs60,mq40 |
1 |
0.00 % |
0 |
0.00 % |
1 |
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 |
17612246 |
29.69 % |
| Transition |
G>A |
All |
3761443 |
6.34 % |
| Transition |
T>C |
All |
17577761 |
29.63 % |
| Transition |
C>T |
All |
2582448 |
4.35 % |
| Transversion |
A>C |
All |
1566454 |
2.64 % |
| Transversion |
C>A |
All |
3491249 |
5.89 % |
| Transversion |
T>G |
All |
1797551 |
3.03 % |
| Transversion |
G>T |
All |
3252990 |
5.48 % |
| Transversion |
A>T |
All |
2437628 |
4.11 % |
| Transversion |
T>A |
All |
2739164 |
4.62 % |
| Transversion |
C>G |
All |
1271854 |
2.14 % |
| Transversion |
G>C |
All |
1229709 |
2.07 % |
| |
|
|
|
|
| Transition |
A>G |
Passed |
2004859 |
26.78 % |
| Transition |
G>A |
Passed |
762219 |
10.18 % |
| Transition |
T>C |
Passed |
2756777 |
36.82 % |
| Transition |
C>T |
Passed |
478973 |
6.40 % |
| Transversion |
A>C |
Passed |
186740 |
2.49 % |
| Transversion |
C>A |
Passed |
220217 |
2.94 % |
| Transversion |
T>G |
Passed |
214990 |
2.87 % |
| Transversion |
G>T |
Passed |
151546 |
2.02 % |
| Transversion |
A>T |
Passed |
108372 |
1.45 % |
| Transversion |
T>A |
Passed |
175260 |
2.34 % |
| Transversion |
C>G |
Passed |
210587 |
2.81 % |
| Transversion |
G>C |
Passed |
215713 |
2.88 % |
| |
|
|
|
|
| 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 |
2.34 |
41533898 |
17786599 |
| Passed |
4.05 |
6002828 |
1483425 |
| dbSNPAll |
0 |
0 |
0 |
| dbSNPPassed |
0 |
0 |
0 |