/EXTERNAL CREST/variants/K006469_1_lane_gembs
BACK
SAMPLE K006469_1_lane_gembs
Variant counts
| Type |
Total |
Pass |
% |
| SNPs |
1011677084 |
20811834 |
2.06 % |
| Multiallelic |
0 |
0 |
0.00 % |
VCF Filtering Stats
| Type |
#Sites |
% |
#Non-Variant Sites |
% |
#Variant Sites |
% |
| All |
1011677084 |
100% |
968192605 |
95.70 % |
43484479 |
4.30 % |
| |
|
|
|
|
|
|
| Passed |
39031334 |
3.86 % |
20138295 |
2.08 % |
18893039 |
48.40 % |
| Filtered |
972645750 |
96.14 % |
948054310 |
97.92 % |
24591440 |
63.00 % |
| |
|
|
|
|
|
|
| q20 |
751784445 |
77.29 % |
738530563 |
77.90 % |
13253882 |
53.90 % |
| q20,qd2 |
134037581 |
13.78 % |
125039943 |
13.19 % |
8997638 |
36.59 % |
| q20,mq40 |
60528891 |
6.22 % |
59716755 |
6.30 % |
812136 |
3.30 % |
| q20,qd2,mq40 |
24746216 |
2.54 % |
24375945 |
2.57 % |
370271 |
1.51 % |
| mq40 |
1534754 |
0.16 % |
380387 |
0.04 % |
1154367 |
4.69 % |
| qd2 |
9454 |
0.00 % |
7443 |
0.00 % |
2011 |
0.01 % |
| qd2,mq40 |
4388 |
0.00 % |
3274 |
0.00 % |
1114 |
0.00 % |
| fs60,mq40 |
10 |
0.00 % |
0 |
0.00 % |
10 |
0.00 % |
| fs60 |
7 |
0.00 % |
0 |
0.00 % |
7 |
0.00 % |
| q20,qd2,fs60 |
2 |
0.00 % |
0 |
0.00 % |
2 |
0.00 % |
| q20,qd2,fs60,mq40 |
2 |
0.00 % |
0 |
0.00 % |
2 |
0.00 % |
| q20,fs60 |
0 |
0.00 % |
0 |
0.00 % |
0 |
0.00 % |
| qd2,fs60 |
0 |
0.00 % |
0 |
0.00 % |
0 |
0.00 % |
| q20,fs60,mq40 |
0 |
0.00 % |
0 |
0.00 % |
0 |
0.00 % |
| qd2,fs60,mq40 |
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 |
8483407 |
16.91 % |
| Transition |
G>A |
All |
2846755 |
5.68 % |
| Transition |
T>C |
All |
7515964 |
14.98 % |
| Transition |
C>T |
All |
2150275 |
4.29 % |
| Transversion |
A>C |
All |
1925542 |
3.84 % |
| Transversion |
C>A |
All |
4618417 |
9.21 % |
| Transversion |
T>G |
All |
3469255 |
6.92 % |
| Transversion |
G>T |
All |
4144377 |
8.26 % |
| Transversion |
A>T |
All |
5058096 |
10.08 % |
| Transversion |
T>A |
All |
5762807 |
11.49 % |
| Transversion |
C>G |
All |
2618307 |
5.22 % |
| Transversion |
G>C |
All |
1567060 |
3.12 % |
| |
|
|
|
|
| Transition |
A>G |
Passed |
130807 |
19.31 % |
| Transition |
G>A |
Passed |
59849 |
8.84 % |
| Transition |
T>C |
Passed |
107360 |
15.85 % |
| Transition |
C>T |
Passed |
48915 |
7.22 % |
| Transversion |
A>C |
Passed |
46401 |
6.85 % |
| Transversion |
C>A |
Passed |
39530 |
5.84 % |
| Transversion |
T>G |
Passed |
66202 |
9.77 % |
| Transversion |
G>T |
Passed |
28871 |
4.26 % |
| Transversion |
A>T |
Passed |
21213 |
3.13 % |
| Transversion |
T>A |
Passed |
33947 |
5.01 % |
| Transversion |
C>G |
Passed |
54557 |
8.05 % |
| Transversion |
G>C |
Passed |
39720 |
5.86 % |
| |
|
|
|
|
| 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 |
0.72 |
20996401 |
29163861 |
| Passed |
1.05 |
346931 |
330441 |
| dbSNPAll |
0 |
0 |
0 |
| dbSNPPassed |
0 |
0 |
0 |