/EXTERNAL Roadmap/variants/K006552_K006553_K006554_K006555_K006556_K006557_K006558_7_lane_gembs
BACK
SAMPLE K006552_K006553_K006554_K006555_K006556_K006557_K006558_7_lane_gembs
Variant counts
| Type |
Total |
Pass |
% |
| SNPs |
1180039986 |
923063028 |
78.22 % |
| Multiallelic |
0 |
0 |
0.00 % |
VCF Filtering Stats
| Type |
#Sites |
% |
#Non-Variant Sites |
% |
#Variant Sites |
% |
| All |
1180039986 |
100% |
1136557706 |
96.32 % |
43482280 |
3.68 % |
| |
|
|
|
|
|
|
| Passed |
925675587 |
78.44 % |
917477669 |
80.72 % |
8197918 |
0.89 % |
| Filtered |
254364399 |
21.56 % |
219080037 |
19.28 % |
35284362 |
3.81 % |
| |
|
|
|
|
|
|
| q20 |
161052009 |
63.32 % |
147733556 |
67.43 % |
13318453 |
37.75 % |
| q20,qd2 |
27034952 |
10.63 % |
8590568 |
3.92 % |
18444384 |
52.27 % |
| q20,mq40 |
26999956 |
10.61 % |
25884920 |
11.82 % |
1115036 |
3.16 % |
| mq40 |
23218477 |
9.13 % |
22448674 |
10.25 % |
769803 |
2.18 % |
| qd2 |
11014648 |
4.33 % |
10438201 |
4.76 % |
576447 |
1.63 % |
| q20,qd2,mq40 |
4766058 |
1.87 % |
3743405 |
1.71 % |
1022653 |
2.90 % |
| qd2,mq40 |
273302 |
0.11 % |
240713 |
0.11 % |
32589 |
0.09 % |
| fs60 |
1987 |
0.00 % |
0 |
0.00 % |
1987 |
0.01 % |
| fs60,mq40 |
1208 |
0.00 % |
0 |
0.00 % |
1208 |
0.00 % |
| qd2,fs60 |
574 |
0.00 % |
0 |
0.00 % |
574 |
0.00 % |
| q20,qd2,fs60 |
459 |
0.00 % |
0 |
0.00 % |
459 |
0.00 % |
| qd2,fs60,mq40 |
445 |
0.00 % |
0 |
0.00 % |
445 |
0.00 % |
| q20,qd2,fs60,mq40 |
226 |
0.00 % |
0 |
0.00 % |
226 |
0.00 % |
| q20,fs60 |
71 |
0.00 % |
0 |
0.00 % |
71 |
0.00 % |
| q20,fs60,mq40 |
27 |
0.00 % |
0 |
0.00 % |
27 |
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 |
16431920 |
36.21 % |
| Transition |
G>A |
All |
2871984 |
6.33 % |
| Transition |
T>C |
All |
18911179 |
41.67 % |
| Transition |
C>T |
All |
2439885 |
5.38 % |
| Transversion |
A>C |
All |
667868 |
1.47 % |
| Transversion |
C>A |
All |
551218 |
1.21 % |
| Transversion |
T>G |
All |
778159 |
1.71 % |
| Transversion |
G>T |
All |
546937 |
1.21 % |
| Transversion |
A>T |
All |
645456 |
1.42 % |
| Transversion |
T>A |
All |
618783 |
1.36 % |
| Transversion |
C>G |
All |
497081 |
1.10 % |
| Transversion |
G>C |
All |
419841 |
0.93 % |
| |
|
|
|
|
| Transition |
A>G |
Passed |
1731129 |
27.36 % |
| Transition |
G>A |
Passed |
573397 |
9.06 % |
| Transition |
T>C |
Passed |
2182698 |
34.50 % |
| Transition |
C>T |
Passed |
582295 |
9.20 % |
| Transversion |
A>C |
Passed |
187617 |
2.97 % |
| Transversion |
C>A |
Passed |
139584 |
2.21 % |
| Transversion |
T>G |
Passed |
200431 |
3.17 % |
| Transversion |
G>T |
Passed |
141932 |
2.24 % |
| Transversion |
A>T |
Passed |
120720 |
1.91 % |
| Transversion |
T>A |
Passed |
120166 |
1.90 % |
| Transversion |
C>G |
Passed |
177088 |
2.80 % |
| Transversion |
G>C |
Passed |
170491 |
2.69 % |
| |
|
|
|
|
| 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 |
8.60 |
40654968 |
4725343 |
| Passed |
4.03 |
5069519 |
1258029 |
| dbSNPAll |
0 |
0 |
0 |
| dbSNPPassed |
0 |
0 |
0 |