/EXTERNAL BLUEPRINT/variants/K006301_13_lane_gembs
BACK
SAMPLE K006301_13_lane_gembs
Variant counts
| Type |
Total |
Pass |
% |
| SNPs |
1114084490 |
666868444 |
59.86 % |
| Multiallelic |
0 |
0 |
0.00 % |
VCF Filtering Stats
| Type |
#Sites |
% |
#Non-Variant Sites |
% |
#Variant Sites |
% |
| All |
1114084490 |
100% |
1095568954 |
98.34 % |
18515536 |
1.66 % |
| |
|
|
|
|
|
|
| Passed |
668784826 |
60.03 % |
665493093 |
60.74 % |
3291733 |
0.49 % |
| Filtered |
445299664 |
39.97 % |
430075861 |
39.26 % |
15223803 |
2.28 % |
| |
|
|
|
|
|
|
| q20 |
372069944 |
83.55 % |
370322969 |
86.11 % |
1746975 |
11.48 % |
| q20,qd2 |
47739695 |
10.72 % |
34793751 |
8.09 % |
12945944 |
85.04 % |
| q20,mq40 |
13624076 |
3.06 % |
13531004 |
3.15 % |
93072 |
0.61 % |
| mq40 |
6802907 |
1.53 % |
6638553 |
1.54 % |
164354 |
1.08 % |
| q20,qd2,mq40 |
3024442 |
0.68 % |
2858909 |
0.66 % |
165533 |
1.09 % |
| qd2 |
1958352 |
0.44 % |
1866944 |
0.43 % |
91408 |
0.60 % |
| qd2,mq40 |
73671 |
0.02 % |
63731 |
0.01 % |
9940 |
0.07 % |
| q20,qd2,fs60 |
2001 |
0.00 % |
0 |
0.00 % |
2001 |
0.01 % |
| fs60 |
1448 |
0.00 % |
0 |
0.00 % |
1448 |
0.01 % |
| qd2,fs60,mq40 |
1237 |
0.00 % |
0 |
0.00 % |
1237 |
0.01 % |
| qd2,fs60 |
882 |
0.00 % |
0 |
0.00 % |
882 |
0.01 % |
| q20,qd2,fs60,mq40 |
506 |
0.00 % |
0 |
0.00 % |
506 |
0.00 % |
| fs60,mq40 |
499 |
0.00 % |
0 |
0.00 % |
499 |
0.00 % |
| q20,fs60,mq40 |
3 |
0.00 % |
0 |
0.00 % |
3 |
0.00 % |
| q20,fs60 |
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 |
3524159 |
16.27 % |
| Transition |
G>A |
All |
6102537 |
28.18 % |
| Transition |
T>C |
All |
3398112 |
15.69 % |
| Transition |
C>T |
All |
5964077 |
27.54 % |
| Transversion |
A>C |
All |
230716 |
1.07 % |
| Transversion |
C>A |
All |
526814 |
2.43 % |
| Transversion |
T>G |
All |
240049 |
1.11 % |
| Transversion |
G>T |
All |
512083 |
2.36 % |
| Transversion |
A>T |
All |
387622 |
1.79 % |
| Transversion |
T>A |
All |
382232 |
1.77 % |
| Transversion |
C>G |
All |
196583 |
0.91 % |
| Transversion |
G>C |
All |
189519 |
0.88 % |
| |
|
|
|
|
| Transition |
A>G |
Passed |
387312 |
18.87 % |
| Transition |
G>A |
Passed |
349606 |
17.03 % |
| Transition |
T>C |
Passed |
385615 |
18.79 % |
| Transition |
C>T |
Passed |
349457 |
17.03 % |
| Transversion |
A>C |
Passed |
77068 |
3.75 % |
| Transversion |
C>A |
Passed |
71058 |
3.46 % |
| Transversion |
T>G |
Passed |
76888 |
3.75 % |
| Transversion |
G>T |
Passed |
70459 |
3.43 % |
| Transversion |
A>T |
Passed |
49905 |
2.43 % |
| Transversion |
T>A |
Passed |
49933 |
2.43 % |
| Transversion |
C>G |
Passed |
92135 |
4.49 % |
| Transversion |
G>C |
Passed |
92988 |
4.53 % |
| |
|
|
|
|
| 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 |
7.12 |
18988885 |
2665618 |
| Passed |
2.54 |
1471990 |
580434 |
| dbSNPAll |
0 |
0 |
0 |
| dbSNPPassed |
0 |
0 |
0 |