/EXTERNAL Roadmap/variants/K006481_K006482_K006483_K006484_K006485_5_lane_gembs
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SAMPLE K006481_K006482_K006483_K006484_K006485_5_lane_gembs
Variant counts
| Type |
Total |
Pass |
% |
| SNPs |
1156025901 |
1080714088 |
93.49 % |
| Multiallelic |
0 |
0 |
0.00 % |
VCF Filtering Stats
| Type |
#Sites |
% |
#Non-Variant Sites |
% |
#Variant Sites |
% |
| All |
1156025901 |
100% |
1149926095 |
99.47 % |
6099806 |
0.53 % |
| |
|
|
|
|
|
|
| Passed |
1080805169 |
93.49 % |
1078007563 |
93.75 % |
2797606 |
0.26 % |
| Filtered |
75220732 |
6.51 % |
71918532 |
6.25 % |
3302200 |
0.31 % |
| |
|
|
|
|
|
|
| mq40 |
47468031 |
63.10 % |
46924323 |
65.25 % |
543708 |
16.47 % |
| q20,mq40 |
14523566 |
19.31 % |
14303657 |
19.89 % |
219909 |
6.66 % |
| q20 |
6817183 |
9.06 % |
6658577 |
9.26 % |
158606 |
4.80 % |
| q20,qd2,mq40 |
2262034 |
3.01 % |
1670167 |
2.32 % |
591867 |
17.92 % |
| q20,qd2 |
1806184 |
2.40 % |
597677 |
0.83 % |
1208507 |
36.60 % |
| qd2 |
1726674 |
2.30 % |
1430266 |
1.99 % |
296408 |
8.98 % |
| qd2,mq40 |
418876 |
0.56 % |
333865 |
0.46 % |
85011 |
2.57 % |
| fs60 |
84353 |
0.11 % |
0 |
0.00 % |
84353 |
2.55 % |
| q20,qd2,fs60 |
61235 |
0.08 % |
0 |
0.00 % |
61235 |
1.85 % |
| fs60,mq40 |
24576 |
0.03 % |
0 |
0.00 % |
24576 |
0.74 % |
| q20,fs60 |
11292 |
0.02 % |
0 |
0.00 % |
11292 |
0.34 % |
| qd2,fs60 |
10891 |
0.01 % |
0 |
0.00 % |
10891 |
0.33 % |
| qd2,fs60,mq40 |
3556 |
0.00 % |
0 |
0.00 % |
3556 |
0.11 % |
| q20,qd2,fs60,mq40 |
2043 |
0.00 % |
0 |
0.00 % |
2043 |
0.06 % |
| q20,fs60,mq40 |
238 |
0.00 % |
0 |
0.00 % |
238 |
0.01 % |
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 |
1727870 |
22.64 % |
| Transition |
G>A |
All |
969538 |
12.70 % |
| Transition |
T>C |
All |
1734033 |
22.72 % |
| Transition |
C>T |
All |
968054 |
12.68 % |
| Transversion |
A>C |
All |
226772 |
2.97 % |
| Transversion |
C>A |
All |
348185 |
4.56 % |
| Transversion |
T>G |
All |
228934 |
3.00 % |
| Transversion |
G>T |
All |
352713 |
4.62 % |
| Transversion |
A>T |
All |
324986 |
4.26 % |
| Transversion |
T>A |
All |
315072 |
4.13 % |
| Transversion |
C>G |
All |
217613 |
2.85 % |
| Transversion |
G>C |
All |
219303 |
2.87 % |
| |
|
|
|
|
| Transition |
A>G |
Passed |
721070 |
18.20 % |
| Transition |
G>A |
Passed |
623591 |
15.74 % |
| Transition |
T>C |
Passed |
737895 |
18.62 % |
| Transition |
C>T |
Passed |
632333 |
15.96 % |
| Transversion |
A>C |
Passed |
162432 |
4.10 % |
| Transversion |
C>A |
Passed |
157889 |
3.98 % |
| Transversion |
T>G |
Passed |
161670 |
4.08 % |
| Transversion |
G>T |
Passed |
158296 |
3.99 % |
| Transversion |
A>T |
Passed |
144204 |
3.64 % |
| Transversion |
T>A |
Passed |
143408 |
3.62 % |
| Transversion |
C>G |
Passed |
159151 |
4.02 % |
| Transversion |
G>C |
Passed |
160587 |
4.05 % |
| |
|
|
|
|
| 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 |
2.42 |
5399495 |
2233578 |
| Passed |
2.18 |
2714889 |
1247637 |
| dbSNPAll |
0 |
0 |
0 |
| dbSNPPassed |
0 |
0 |
0 |