/EXTERNAL Roadmap/variants/K006516_K006517_K006518_K006519_K006520_5_lane_gembs
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SAMPLE K006516_K006517_K006518_K006519_K006520_5_lane_gembs
Variant counts
| Type |
Total |
Pass |
% |
| SNPs |
1157550191 |
1080333818 |
93.33 % |
| Multiallelic |
0 |
0 |
0.00 % |
VCF Filtering Stats
| Type |
#Sites |
% |
#Non-Variant Sites |
% |
#Variant Sites |
% |
| All |
1157550191 |
100% |
1149188605 |
99.28 % |
8361586 |
0.72 % |
| |
|
|
|
|
|
|
| Passed |
1080429228 |
93.34 % |
1075899490 |
93.62 % |
4529738 |
0.42 % |
| Filtered |
77120963 |
6.66 % |
73289115 |
6.38 % |
3831848 |
0.35 % |
| |
|
|
|
|
|
|
| mq40 |
46337533 |
60.08 % |
45731792 |
62.40 % |
605741 |
15.81 % |
| q20,mq40 |
15801088 |
20.49 % |
15579151 |
21.26 % |
221937 |
5.79 % |
| q20 |
7817550 |
10.14 % |
7654737 |
10.44 % |
162813 |
4.25 % |
| q20,qd2,mq40 |
2265962 |
2.94 % |
1643502 |
2.24 % |
622460 |
16.24 % |
| qd2 |
2239258 |
2.90 % |
1676398 |
2.29 % |
562860 |
14.69 % |
| q20,qd2 |
2021445 |
2.62 % |
663390 |
0.91 % |
1358055 |
35.44 % |
| qd2,mq40 |
426344 |
0.55 % |
340145 |
0.46 % |
86199 |
2.25 % |
| q20,qd2,fs60 |
90331 |
0.12 % |
0 |
0.00 % |
90331 |
2.36 % |
| fs60 |
81680 |
0.11 % |
0 |
0.00 % |
81680 |
2.13 % |
| q20,fs60 |
15747 |
0.02 % |
0 |
0.00 % |
15747 |
0.41 % |
| fs60,mq40 |
14894 |
0.02 % |
0 |
0.00 % |
14894 |
0.39 % |
| qd2,fs60 |
6406 |
0.01 % |
0 |
0.00 % |
6406 |
0.17 % |
| q20,qd2,fs60,mq40 |
1295 |
0.00 % |
0 |
0.00 % |
1295 |
0.03 % |
| qd2,fs60,mq40 |
1239 |
0.00 % |
0 |
0.00 % |
1239 |
0.03 % |
| q20,fs60,mq40 |
191 |
0.00 % |
0 |
0.00 % |
191 |
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 |
1947246 |
21.15 % |
| Transition |
G>A |
All |
1208076 |
13.12 % |
| Transition |
T>C |
All |
1959094 |
21.28 % |
| Transition |
C>T |
All |
1222606 |
13.28 % |
| Transversion |
A>C |
All |
283450 |
3.08 % |
| Transversion |
C>A |
All |
447017 |
4.86 % |
| Transversion |
T>G |
All |
283525 |
3.08 % |
| Transversion |
G>T |
All |
452350 |
4.91 % |
| Transversion |
A>T |
All |
420772 |
4.57 % |
| Transversion |
T>A |
All |
411101 |
4.47 % |
| Transversion |
C>G |
All |
283904 |
3.08 % |
| Transversion |
G>C |
All |
287923 |
3.13 % |
| |
|
|
|
|
| Transition |
A>G |
Passed |
871453 |
17.14 % |
| Transition |
G>A |
Passed |
804821 |
15.83 % |
| Transition |
T>C |
Passed |
886802 |
17.44 % |
| Transition |
C>T |
Passed |
819080 |
16.11 % |
| Transversion |
A>C |
Passed |
214711 |
4.22 % |
| Transversion |
C>A |
Passed |
221193 |
4.35 % |
| Transversion |
T>G |
Passed |
212966 |
4.19 % |
| Transversion |
G>T |
Passed |
221644 |
4.36 % |
| Transversion |
A>T |
Passed |
197853 |
3.89 % |
| Transversion |
T>A |
Passed |
196274 |
3.86 % |
| Transversion |
C>G |
Passed |
217142 |
4.27 % |
| Transversion |
G>C |
Passed |
219525 |
4.32 % |
| |
|
|
|
|
| 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 |
2.21 |
6337022 |
2870042 |
| Passed |
1.99 |
3382156 |
1701308 |
| dbSNPAll |
0 |
0 |
0 |
| dbSNPPassed |
0 |
0 |
0 |