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Updated.

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gkarthik committed Jul 11, 2019
1 parent 2028aaf commit 51685060002e44d69e3550f14319a2150c36c579
@@ -1,9 +1,9 @@
Location,Typing Institution,Outcome,Status ,ID,A,A.1,B,B.1,C,C.1,DPA1,DPA1.1,DPB1,DPB1.1,DQA1,DQA1.1,DQB1,DQB1.1,DRB1,DRB1.1,DRB3,DRB3.1,DRB4,DRB4.1,DRB5,DRB5.1
Sierra Leone,TSRI,Contact,EBOV Contact,3ae16dd5c555cf2a70e3edaf365bc3b7,A*340201,A*660101,B*150301,B*450101,C*060201,C*160101,DPA1*0202@14,DPA1*0301,DPB1*850101,DPB1*1050101,DQA1*010201,DQA1*050501,DQB1*030101,DQB1*050101,DRB1*120101,DRB1*130201,DRB3*020201,DRB3*030101,-,-,-,-
Sierra Leone,TSRI,Contact,EBOV Contact,4ee2b6b2b25968aaa1b4db552fef88c5,A*030101,A*330101,B*350101,B*510101,C*040101,C*160101,DPA1*020101,DPA1*020101,DPB1*130101,DPB1*130101,DQA1*030301,DQA1*050501,DQB1*030101,DQB1*030201,DRB1*130301,DRB1*040101,DRB3*010102,-,DRB4*010101,-,-,-
Sierra Leone,TSRI,Contact,EBOV Contact,c3659dbac0732f90452ffd4134cf248f,A*240201,A*330101,B*140201,B*180101,C*040101,C*080201,DPA1*020101,DPA1*020108,DPB1*010101,DPB1*140101,DQA1*030301,DQA1*050101,DQB1*020101,DQB1*050201,DRB1*160201,DRB1*030101,DRB3*020201,-,-,-,DRB5*02@7,-
Sierra Leone,TSRI,Contact,EBOV Contact,18eb8ed917f6c63e91a5af626110316c,A*330301,A*340201,B*410301,B*580101,C*030202,C*170301,DPA1*010301,DPA1*020101,DPB1*020102,DPB1*170101,DQA1*010202,DQA1*050501,DQB1*030201,DQB1*031901,DRB1*130101,DRB1*1304,DRB3*010102,DRB3*020201,-,-,-,-
Sierra Leone,TSRI,Contact,EBOV Contact,d90d32ba31cb07228c4a20304731abd2,A*290201,A*340201,B*2703,B*780101,C*020202,C*160101,DPA1*020107,DPA1*020202,DPB1*010101,DPB1*130101,DQA1*010501,DQA1*030301,DQB1*020201,DQB1*050101,DRB1*100101,DRB1*090102,-,-,DRB4*010101,DRB4*01@13,-,-
Sierra Leone,TSRI,Contact,Control,3ae16dd5c555cf2a70e3edaf365bc3b7,A*340201,A*660101,B*150301,B*450101,C*060201,C*160101,DPA1*0202@14,DPA1*0301,DPB1*850101,DPB1*1050101,DQA1*010201,DQA1*050501,DQB1*030101,DQB1*050101,DRB1*120101,DRB1*130201,DRB3*020201,DRB3*030101,-,-,-,-
Sierra Leone,TSRI,Contact,Control,4ee2b6b2b25968aaa1b4db552fef88c5,A*030101,A*330101,B*350101,B*510101,C*040101,C*160101,DPA1*020101,DPA1*020101,DPB1*130101,DPB1*130101,DQA1*030301,DQA1*050501,DQB1*030101,DQB1*030201,DRB1*130301,DRB1*040101,DRB3*010102,-,DRB4*010101,-,-,-
Sierra Leone,TSRI,Contact,Control,c3659dbac0732f90452ffd4134cf248f,A*240201,A*330101,B*140201,B*180101,C*040101,C*080201,DPA1*020101,DPA1*020108,DPB1*010101,DPB1*140101,DQA1*030301,DQA1*050101,DQB1*020101,DQB1*050201,DRB1*160201,DRB1*030101,DRB3*020201,-,-,-,DRB5*02@7,-
Sierra Leone,TSRI,Contact,Control,18eb8ed917f6c63e91a5af626110316c,A*330301,A*340201,B*410301,B*580101,C*030202,C*170301,DPA1*010301,DPA1*020101,DPB1*020102,DPB1*170101,DQA1*010202,DQA1*050501,DQB1*030201,DQB1*031901,DRB1*130101,DRB1*1304,DRB3*010102,DRB3*020201,-,-,-,-
Sierra Leone,TSRI,Contact,Control,d90d32ba31cb07228c4a20304731abd2,A*290201,A*340201,B*2703,B*780101,C*020202,C*160101,DPA1*020107,DPA1*020202,DPB1*010101,DPB1*130101,DQA1*010501,DQA1*030301,DQB1*020201,DQB1*050101,DRB1*100101,DRB1*090102,-,-,DRB4*010101,DRB4*01@13,-,-
Sierra Leone,Broad,Control,Control,41a2d1d7001079c404ad3c1b4f1650ba,A*680201,A*300101,B*151001,B*420201,C*030402,C*170101,DPA1*020108,DPA1*020108,DPB1*010101,DPB1*010101,DQA1*050101,DQA1*050501,DQB1*020101,DQB1*030104,DRB1*030101,DRB1*080401,DRB3*020201,DRB3*020201,-,-,-,-
Sierra Leone,Broad,Control,Control,af7d76c519b48d3338d6637e1e184f61,A*030101,A*020101,B*070201,B*490101,C*070102,C*070201,DPA1*020101,DPA1*0301,DPB1*1701,DPB1*10501,DQA1*020101,DQA1*030301,DQB1*020201,DQB1*020201,DRB1*070101,DRB1*090102,-,-,DRB4*010101,DRB4*01@41,-,-
Sierra Leone,Broad,Control,Control,fd66fcd9c8323f0aeaa678135ee5fdff,A*680101,A*300201,B*070201,B*500101,C*060201,C*150502,DPA1*010301,DPA1*020101,DPB1*130101,DPB1*040201,DQA1*010201,DQA1*050501,DQB1*031901,DQB1*050101,DRB1*110201,DRB1*130201,DRB3*020201,DRB3*030101,-,-,-,-
@@ -1,12 +1,12 @@
Gene,Obs_Alleles_EBOV,Total_Alleles_EBOV,Individuals_EBOV,Obs_Alleles_LASV,Total_Alleles_LASV,Individuals_LASV,Obs_Alleles_CTRL,Total_Alleles_CTRL,Individuals_CTRL
HLA-A,20.0,98.0,49.0,27.0,326.0,163.0,27.0,278.0,139.0
HLA-B,27.0,98.0,49.0,40.0,326.0,163.0,40.0,276.0,138.0
HLA-C,19.0,98.0,49.0,31.0,326.0,163.0,25.0,278.0,139.0
HLA-DPA1,11.0,92.0,46.0,20.0,308.0,154.0,17.0,276.0,138.0
HLA-DPB1,16.0,98.0,49.0,35.0,326.0,163.0,33.0,277.0,139.0
HLA-DQA1,11.0,98.0,49.0,13.0,326.0,163.0,16.0,278.0,139.0
HLA-DQB1,17.0,98.0,49.0,20.0,323.0,162.0,18.0,277.0,139.0
HLA-DRB1,22.0,98.0,49.0,27.0,326.0,163.0,28.0,277.0,139.0
HLA-DRB3,4.0,81.0,44.0,7.0,211.0,130.0,9.0,188.0,115.0
HLA-DRB4,3.0,12.0,8.0,3.0,71.0,54.0,4.0,72.0,54.0
HLA-DRB5,2.0,3.0,3.0,5.0,32.0,28.0,3.0,13.0,12.0
HLA-A,20.0,98.0,49.0,27.0,326.0,163.0,27.0,288.0,144.0
HLA-B,27.0,98.0,49.0,40.0,326.0,163.0,40.0,286.0,143.0
HLA-C,19.0,98.0,49.0,31.0,326.0,163.0,25.0,288.0,144.0
HLA-DPA1,11.0,92.0,46.0,20.0,308.0,154.0,17.0,286.0,143.0
HLA-DPB1,16.0,98.0,49.0,35.0,326.0,163.0,33.0,287.0,144.0
HLA-DQA1,11.0,98.0,49.0,13.0,326.0,163.0,16.0,288.0,144.0
HLA-DQB1,17.0,98.0,49.0,20.0,323.0,162.0,18.0,287.0,144.0
HLA-DRB1,22.0,98.0,49.0,27.0,326.0,163.0,28.0,287.0,144.0
HLA-DRB3,4.0,81.0,44.0,7.0,211.0,130.0,9.0,194.0,119.0
HLA-DRB4,3.0,12.0,8.0,3.0,71.0,54.0,4.0,75.0,56.0
HLA-DRB5,2.0,3.0,3.0,5.0,32.0,28.0,3.0,14.0,13.0
@@ -14,6 +14,7 @@ A comprehensive list of the 259 observed HLA alleles sequenced in the Lassa, Ebo
| MHC-I | | | MHC-II | | |
| :-- | :-- | :-- | :-- | :-- | :-- |
| Gene | Allele | Allelic Frequency | Gene | Allele | Allelic Frequency |
| --- | --- | --- | --- | --- | --- |
| HLA-A | A*020101 | 0.14 | HLA-DPA1 | DPA1*020101 | 0.23 |
| HLA-A | A*230101 | 0.13 | HLA-DPA1 | DPA1*020202 | 0.2 |
| HLA-A | A*300101 | 0.09 | HLA-DPA1 | DPA1*020108 | 0.19 |
@@ -23,10 +24,10 @@ A comprehensive list of the 259 observed HLA alleles sequenced in the Lassa, Ebo
| HLA-B | B*350101 | 0.13 | HLA-DPB1 | DPB1*130101 | 0.05 |
| HLA-B | B*530101 | 0.12 | HLA-DQA1 | DQA1*010201 | 0.21 |
| HLA-B | B*420101 | 0.07 | HLA-DQA1 | DQA1*050501 | 0.18 |
| HLA-B | B*450101 | 0.06 | HLA-DQA1 | DQA1*040101 | 0.16 |
| HLA-B | B*440301 | 0.06 | HLA-DQA1 | DQA1*030301 | 0.14 |
| HLA-B | B*580101 | 0.06 | HLA-DQA1 | DQA1*020101 | 0.07 |
| HLA-B | B*070201 | 0.06 | HLA-DQA1 | DQA1*010102 | 0.05 |
| HLA-B | B*440301 | 0.06 | HLA-DQA1 | DQA1*040101 | 0.16 |
| HLA-B | B*450101 | 0.06 | HLA-DQA1 | DQA1*030301 | 0.14 |
| HLA-B | B*070201 | 0.06 | HLA-DQA1 | DQA1*020101 | 0.07 |
| HLA-B | B*580101 | 0.06 | HLA-DQA1 | DQA1*010102 | 0.05 |
| HLA-B | B*150301 | 0.05 | HLA-DQB1 | DQB1*040201 | 0.15 |
| HLA-C | C*040101 | 0.22 | HLA-DQB1 | DQB1*050101 | 0.15 |
| HLA-C | C*160101 | 0.18 | HLA-DQB1 | DQB1*031901 | 0.14 |

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