/EXTERNAL Roadmap/variants/K006542_K006543_K006544_K006545_4_lane_gembs
BACK
SAMPLE K006542_K006543_K006544_K006545_4_lane_gembs
Variant counts
| Type |
Total |
Pass |
% |
| SNPs |
1163771435 |
841684492 |
72.32 % |
| Multiallelic |
0 |
0 |
0.00 % |
VCF Filtering Stats
| Type |
#Sites |
% |
#Non-Variant Sites |
% |
#Variant Sites |
% |
| All |
1163771435 |
100% |
1144032994 |
98.30 % |
19738441 |
1.70 % |
| |
|
|
|
|
|
|
| Passed |
845130988 |
72.62 % |
839415063 |
73.37 % |
5715925 |
0.68 % |
| Filtered |
318640447 |
27.38 % |
304617931 |
26.63 % |
14022516 |
1.66 % |
| |
|
|
|
|
|
|
| q20 |
225396529 |
70.74 % |
220947007 |
72.53 % |
4449522 |
31.73 % |
| mq40 |
42800154 |
13.43 % |
42054696 |
13.81 % |
745458 |
5.32 % |
| q20,mq40 |
30253808 |
9.49 % |
29765160 |
9.77 % |
488648 |
3.48 % |
| q20,qd2 |
12771942 |
4.01 % |
5517364 |
1.81 % |
7254578 |
51.74 % |
| q20,qd2,mq40 |
3969347 |
1.25 % |
3170663 |
1.04 % |
798684 |
5.70 % |
| qd2 |
3145117 |
0.99 % |
2923521 |
0.96 % |
221596 |
1.58 % |
| qd2,mq40 |
287547 |
0.09 % |
239520 |
0.08 % |
48027 |
0.34 % |
| fs60 |
9181 |
0.00 % |
0 |
0.00 % |
9181 |
0.07 % |
| fs60,mq40 |
4489 |
0.00 % |
0 |
0.00 % |
4489 |
0.03 % |
| q20,qd2,fs60 |
826 |
0.00 % |
0 |
0.00 % |
826 |
0.01 % |
| qd2,fs60 |
728 |
0.00 % |
0 |
0.00 % |
728 |
0.01 % |
| q20,qd2,fs60,mq40 |
273 |
0.00 % |
0 |
0.00 % |
273 |
0.00 % |
| q20,fs60 |
233 |
0.00 % |
0 |
0.00 % |
233 |
0.00 % |
| qd2,fs60,mq40 |
208 |
0.00 % |
0 |
0.00 % |
208 |
0.00 % |
| q20,fs60,mq40 |
65 |
0.00 % |
0 |
0.00 % |
65 |
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 |
7209002 |
33.19 % |
| Transition |
G>A |
All |
1264544 |
5.82 % |
| Transition |
T>C |
All |
7987659 |
36.78 % |
| Transition |
C>T |
All |
1164597 |
5.36 % |
| Transversion |
A>C |
All |
451256 |
2.08 % |
| Transversion |
C>A |
All |
506461 |
2.33 % |
| Transversion |
T>G |
All |
544109 |
2.51 % |
| Transversion |
G>T |
All |
528347 |
2.43 % |
| Transversion |
A>T |
All |
723614 |
3.33 % |
| Transversion |
T>A |
All |
696726 |
3.21 % |
| Transversion |
C>G |
All |
345178 |
1.59 % |
| Transversion |
G>C |
All |
298820 |
1.38 % |
| |
|
|
|
|
| Transition |
A>G |
Passed |
661734 |
21.15 % |
| Transition |
G>A |
Passed |
436342 |
13.94 % |
| Transition |
T>C |
Passed |
689345 |
22.03 % |
| Transition |
C>T |
Passed |
441492 |
14.11 % |
| Transversion |
A>C |
Passed |
125574 |
4.01 % |
| Transversion |
C>A |
Passed |
105958 |
3.39 % |
| Transversion |
T>G |
Passed |
127472 |
4.07 % |
| Transversion |
G>T |
Passed |
106920 |
3.42 % |
| Transversion |
A>T |
Passed |
87445 |
2.79 % |
| Transversion |
T>A |
Passed |
87591 |
2.80 % |
| Transversion |
C>G |
Passed |
130161 |
4.16 % |
| Transversion |
G>C |
Passed |
129342 |
4.13 % |
| |
|
|
|
|
| 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 |
4.30 |
17625802 |
4094511 |
| Passed |
2.48 |
2228913 |
900463 |
| dbSNPAll |
0 |
0 |
0 |
| dbSNPPassed |
0 |
0 |
0 |