/EXTERNAL Roadmap/variants/K012818_1_lane_gembs
BACK
SAMPLE K012818_1_lane_gembs
Variant counts
| Type |
Total |
Pass |
% |
| SNPs |
1133596023 |
30465043 |
2.69 % |
| Multiallelic |
0 |
0 |
0.00 % |
VCF Filtering Stats
| Type |
#Sites |
% |
#Non-Variant Sites |
% |
#Variant Sites |
% |
| All |
1133596023 |
100% |
1104461920 |
97.43 % |
29134103 |
2.57 % |
| |
|
|
|
|
|
|
| Passed |
41321687 |
3.65 % |
29770414 |
2.70 % |
11551273 |
27.95 % |
| Filtered |
1092274336 |
96.35 % |
1074691506 |
97.30 % |
17582830 |
42.55 % |
| |
|
|
|
|
|
|
| q20 |
1009481930 |
92.42 % |
1000890044 |
93.13 % |
8591886 |
48.87 % |
| q20,qd2 |
53096165 |
4.86 % |
44534532 |
4.14 % |
8561633 |
48.69 % |
| q20,mq40 |
21058130 |
1.93 % |
20909003 |
1.95 % |
149127 |
0.85 % |
| q20,qd2,mq40 |
8321579 |
0.76 % |
8229419 |
0.77 % |
92160 |
0.52 % |
| mq40 |
289474 |
0.03 % |
105331 |
0.01 % |
184143 |
1.05 % |
| qd2 |
16375 |
0.00 % |
14860 |
0.00 % |
1515 |
0.01 % |
| qd2,mq40 |
10498 |
0.00 % |
8317 |
0.00 % |
2181 |
0.01 % |
| qd2,fs60,mq40 |
77 |
0.00 % |
0 |
0.00 % |
77 |
0.00 % |
| fs60,mq40 |
51 |
0.00 % |
0 |
0.00 % |
51 |
0.00 % |
| qd2,fs60 |
36 |
0.00 % |
0 |
0.00 % |
36 |
0.00 % |
| fs60 |
10 |
0.00 % |
0 |
0.00 % |
10 |
0.00 % |
| q20,qd2,fs60,mq40 |
9 |
0.00 % |
0 |
0.00 % |
9 |
0.00 % |
| q20,qd2,fs60 |
1 |
0.00 % |
0 |
0.00 % |
1 |
0.00 % |
| q20,fs60,mq40 |
1 |
0.00 % |
0 |
0.00 % |
1 |
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 |
8632568 |
27.21 % |
| Transition |
G>A |
All |
1527731 |
4.81 % |
| Transition |
T>C |
All |
4898842 |
15.44 % |
| Transition |
C>T |
All |
1600798 |
5.05 % |
| Transversion |
A>C |
All |
834314 |
2.63 % |
| Transversion |
C>A |
All |
2637717 |
8.31 % |
| Transversion |
T>G |
All |
1415949 |
4.46 % |
| Transversion |
G>T |
All |
2391747 |
7.54 % |
| Transversion |
A>T |
All |
2850471 |
8.98 % |
| Transversion |
T>A |
All |
3314646 |
10.45 % |
| Transversion |
C>G |
All |
983441 |
3.10 % |
| Transversion |
G>C |
All |
640588 |
2.02 % |
| |
|
|
|
|
| Transition |
A>G |
Passed |
118285 |
16.50 % |
| Transition |
G>A |
Passed |
78965 |
11.01 % |
| Transition |
T>C |
Passed |
91341 |
12.74 % |
| Transition |
C>T |
Passed |
84159 |
11.74 % |
| Transversion |
A>C |
Passed |
42301 |
5.90 % |
| Transversion |
C>A |
Passed |
43688 |
6.09 % |
| Transversion |
T>G |
Passed |
46540 |
6.49 % |
| Transversion |
G>T |
Passed |
43569 |
6.08 % |
| Transversion |
A>T |
Passed |
40449 |
5.64 % |
| Transversion |
T>A |
Passed |
41271 |
5.76 % |
| Transversion |
C>G |
Passed |
44343 |
6.18 % |
| Transversion |
G>C |
Passed |
42059 |
5.87 % |
| |
|
|
|
|
| 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 |
1.11 |
16659939 |
15068873 |
| Passed |
1.08 |
372750 |
344220 |
| dbSNPAll |
0 |
0 |
0 |
| dbSNPPassed |
0 |
0 |
0 |