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snp-sites VCF to SNP counts...
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| # mafft ncov.fna > msa.fna | |
| # snp-sites -c -v msa.fna > snp.vcf | |
| library(tidyverse) | |
| lines <- read_lines("snp.vcf") | |
| fields <- str_split(last(lines[startsWith(lines, "#")]), "\t")[[1]] | |
| read_tsv(lines, comment = "#", col_names = fields, col_types = cols(.default = "c")) %>% | |
| select(10:ncol(.)) %>% | |
| mutate_all(as.integer) %>% | |
| colSums() %>% | |
| sort(decreasing = T) %>% | |
| enframe(name = "key", value = "POS") %>% | |
| knitr::kable() | |
Author
dnanto
commented
Mar 9, 2020
•
| key | POS |
|---|---|
| BetaCoV/pangolin/Guangxi/P5E/2017|EPI_ISL_410541 | 3467 |
| BetaCoV/pangolin/Guangxi/P2V/2017|EPI_ISL_410542 | 3465 |
| BetaCoV/pangolin/Guangxi/P5L/2017|EPI_ISL_410540 | 3460 |
| BetaCoV/pangolin/Guangxi/P4L/2017|EPI_ISL_410538 | 3459 |
| BetaCoV/pangolin/Guangxi/P1E/2017|EPI_ISL_410539 | 3458 |
| BetaCoV/pangolin/China/MP789/2019|EPI_ISL_412860 | 2691 |
| BetaCoV/pangolin/Guandong/1/2019|EPI_ISL_410721 | 2651 |
| BetaCoV/Shenzhen/SZTH-001/2020|EPI_ISL_406592 | 22 |
| BetaCoV/Shenzhen/SZTH-004/2020|EPI_ISL_406595 | 9 |
| BetaCoV/South_Korea/SNU01/2020|EPI_ISL_411929 | 8 |
| BetaCoV/Sweden/01/2020|EPI_ISL_411951 | 8 |
| BetaCoV/USA/TX1/2020|EPI_ISL_411956 | 5 |
| BetaCoV/Jingzhou/HBCDC-HB-01/2020|EPI_ISL_412459 | 5 |
| BetaCoV/Korea/KCDC05/2020|EPI_ISL_412869 | 5 |
| BetaCoV/Shandong/IVDC-SD-001/2020|EPI_ISL_408482 | 4 |
| BetaCoV/France/RA739/2020|EPI_ISL_410486 | 4 |
| BetaCoV/Jiangsu/JS02/2020|EPI_ISL_411952 | 4 |
| BetaCoV/Korea/KCDC07/2020|EPI_ISL_412871 | 4 |
| BetaCoV/Wuhan/IPBCAMS-WH-01/2019|EPI_ISL_402123 | 3 |
| BetaCoV/Shenzhen/HKU-SZ-005/2020|EPI_ISL_405839 | 3 |
| BetaCoV/Taiwan/2/2020|EPI_ISL_406031 | 3 |
| BetaCoV/Australia/VIC01/2020|EPI_ISL_406844 | 3 |
| BetaCoV/Australia/QLD02/2020|EPI_ISL_407896 | 3 |
| BetaCoV/Japan/KY-V-029/2020|EPI_ISL_408669 | 3 |
| BetaCoV/Korea/KCDC24/2020|EPI_ISL_412873 | 3 |
| BetaCoV/Wuhan/IVDC-HB-04/2020|EPI_ISL_402120 | 2 |
| BetaCoV/Wuhan/IVDC-HB-05/2019|EPI_ISL_402121 | 2 |
| BetaCoV/Wuhan/WIV02/2019|EPI_ISL_402127 | 2 |
| BetaCoV/Wuhan/WIV05/2019|EPI_ISL_402128 | 2 |
| BetaCoV/USA/CA2/2020|EPI_ISL_406036 | 2 |
| BetaCoV/Guangzhou/20SF206/2020|EPI_ISL_406533 | 2 |
| BetaCoV/France/IDF0372/2020|EPI_ISL_406596 | 2 |
| BetaCoV/France/IDF0373/2020|EPI_ISL_406597 | 2 |
| BetaCoV/England/02/2020|EPI_ISL_407073 | 2 |
| BetaCoV/Japan/AI/I-004/2020|EPI_ISL_407084 | 2 |
| BetaCoV/Korea/KCDC03/2020|EPI_ISL_407193 | 2 |
| BetaCoV/USA/CA3/2020|EPI_ISL_408008 | 2 |
| BetaCoV/USA/CA4/2020|EPI_ISL_408009 | 2 |
| BetaCoV/Chongqing/YC01/2020|EPI_ISL_408478 | 2 |
| BetaCoV/Wuhan/IVDC-HB-envF13-21/2020|EPI_ISL_408515 | 2 |
| BetaCoV/Japan/TY-WK-012/2020|EPI_ISL_408665 | 2 |
| BetaCoV/USA/MA1/2020|EPI_ISL_409067 | 2 |
| BetaCov/Taiwan/NTU02/2020|EPI_ISL_410218 | 2 |
| BetaCoV/Singapore/5/2020|EPI_ISL_410536 | 2 |
| BetaCoV/Singapore/7/2020|EPI_ISL_410713 | 2 |
| BetaCoV/Singapore/8/2020|EPI_ISL_410714 | 2 |
| BetaCoV/Singapore/9/2020|EPI_ISL_410715 | 2 |
| BetaCoV/Singapore/10/2020|EPI_ISL_410716 | 2 |
| BetaCoV/Australia/QLD03/2020|EPI_ISL_410717 | 2 |
| BetaCoV/Singapore/11/2020|EPI_ISL_410719 | 2 |
| BetaCoV/France/IDF0372-isl/2020|EPI_ISL_410720 | 2 |
| BetaCoV/France/IDF0386-islP1/2020|EPI_ISL_411219 | 2 |
| BetaCoV/France/IDF0386-islP3/2020|EPI_ISL_411220 | 2 |
| BetaCoV/Jiangsu/JS01/2020|EPI_ISL_411950 | 2 |
| BetaCoV/Hong_Kong/VM20001061/2020|EPI_ISL_412028 | 2 |
| BetaCoV/Hong_Kong/VM20001988/2020|EPI_ISL_412029 | 2 |
| BetaCoV/England/09c/2020|EPI_ISL_412116 | 2 |
| BetaCoV/Korea/KCDC06/2020|EPI_ISL_412870 | 2 |
| BetaCoV/Wuhan/WIV07/2019|EPI_ISL_402130 | 1 |
| BetaCoV/Guangdong/20SF012/2020|EPI_ISL_403932 | 1 |
| BetaCoV/Guangdong/20SF013/2020|EPI_ISL_403933 | 1 |
| BetaCoV/Guangdong/20SF014/2020|EPI_ISL_403934 | 1 |
| BetaCoV/Guangdong/20SF025/2020|EPI_ISL_403935 | 1 |
| BetaCoV/Zhejiang/WZ-01/2020|EPI_ISL_404227 | 1 |
| BetaCoV/USA/WA1/2020|EPI_ISL_404895 | 1 |
| BetaCoV/Shenzhen/HKU-SZ-002/2020|EPI_ISL_406030 | 1 |
| BetaCoV/USA/CA1/2020|EPI_ISL_406034 | 1 |
| BetaCoV/USA/AZ1/2020|EPI_ISL_406223 | 1 |
| BetaCoV/Foshan/20SF207/2020|EPI_ISL_406534 | 1 |
| BetaCoV/Foshan/20SF210/2020|EPI_ISL_406535 | 1 |
| BetaCoV/Foshan/20SF211/2020|EPI_ISL_406536 | 1 |
| BetaCoV/Shenzhen/SZTH-002/2020|EPI_ISL_406593 | 1 |
| BetaCoV/Shenzhen/SZTH-003/2020|EPI_ISL_406594 | 1 |
| BetaCov/Wuhan/WH01/2019|EPI_ISL_406798 | 1 |
| BetaCoV/Germany/BavPat1/2020|EPI_ISL_406862 | 1 |
| BetaCoV/Singapore/1/2020|EPI_ISL_406973 | 1 |
| BetaCoV/England/01/2020|EPI_ISL_407071 | 1 |
| BetaCoV/USA/WA1-A12/2020|EPI_ISL_407214 | 1 |
| BetaCoV/USA/WA1-F6/2020|EPI_ISL_407215 | 1 |
| BetaCoV/Australia/QLD01/2020|EPI_ISL_407894 | 1 |
| BetaCoV/Singapore/2/2020|EPI_ISL_407987 | 1 |
| BetaCoV/USA/CA5/2020|EPI_ISL_408010 | 1 |
| BetaCoV/France/IDF0515/2020|EPI_ISL_408430 | 1 |
| BetaCoV/Sichuan/IVDC-SC-001/2020|EPI_ISL_408484 | 1 |
| BetaCoV/Japan/TY-WK-501/2020|EPI_ISL_408666 | 1 |
| BetaCoV/Japan/TY-WK-521/2020|EPI_ISL_408667 | 1 |
| BetaCoV/USA/WI1/2020|EPI_ISL_408670 | 1 |
| BetaCoV/Sydney/2/2020|EPI_ISL_408976 | 1 |
| BetaCoV/Sydney/3/2020|EPI_ISL_408977 | 1 |
| BetaCoV/Singapore/4/2020|EPI_ISL_410535 | 1 |
| BetaCoV/Singapore/6/2020|EPI_ISL_410537 | 1 |
| BetaCoV/Italy/INMI1-isl/2020|EPI_ISL_410545 | 1 |
| BetaCoV/Italy/INMI1-cs/2020|EPI_ISL_410546 | 1 |
| BetaCoV/Australia/QLD04/2020|EPI_ISL_410718 | 1 |
| BetaCoV/France/IDF0515-isl/2020|EPI_ISL_410984 | 1 |
| BetaCoV/Fujian/8/2020|EPI_ISL_411060 | 1 |
| BetaCoV/Fujian/13/2020|EPI_ISL_411066 | 1 |
| BetaCoV/France/IDF0571/2020|EPI_ISL_411218 | 1 |
| BetaCoV/Cambodia/0012/2020|EPI_ISL_411902 | 1 |
| BetaCoV/USA/CA7/2020|EPI_ISL_411954 | 1 |
| BetaCoV/USA/CA8/2020|EPI_ISL_411955 | 1 |
| BetaCoV/USA/CA9/2020|EPI_ISL_412862 | 1 |
| _BetaCoV/Wuhan/HBCDC-HB-02/2019|EPI_ISL_412898 | 1 |
| BetaCoV/Wuhan/IVDC-HB-01/2019|EPI_ISL_402119 | 0 |
| BetaCoV/Wuhan/WIV04/2019|EPI_ISL_402124 | 0 |
| BetaCoV/Wuhan-Hu-1/2019|EPI_ISL_402125 | 0 |
| BetaCoV/Wuhan/WIV06/2019|EPI_ISL_402129 | 0 |
| BetaCoV/Wuhan/HBCDC-HB-01/2019|EPI_ISL_402132 | 0 |
| BetaCoV/Wuhan/IPBCAMS-WH-05/2020|EPI_ISL_403928 | 0 |
| BetaCoV/Wuhan/IPBCAMS-WH-04/2019|EPI_ISL_403929 | 0 |
| BetaCoV/Wuhan/IPBCAMS-WH-03/2019|EPI_ISL_403930 | 0 |
| BetaCoV/Wuhan/IPBCAMS-WH-02/2019|EPI_ISL_403931 | 0 |
| BetaCoV/Guangdong/20SF028/2020|EPI_ISL_403936 | 0 |
| BetaCoV/Guangdong/20SF040/2020|EPI_ISL_403937 | 0 |
| BetaCoV/Nonthaburi/61/2020|EPI_ISL_403962 | 0 |
| BetaCoV/Nonthaburi/74/2020|EPI_ISL_403963 | 0 |
| BetaCoV/Zhejiang/WZ-02/2020|EPI_ISL_404228 | 0 |
| BetaCoV/USA/IL1/2020|EPI_ISL_404253 | 0 |
| BetaCoV/Guangdong/20SF174/2020|EPI_ISL_406531 | 0 |
| BetaCoV/Guangdong/20SF201/2020|EPI_ISL_406538 | 0 |
| BetaCoV/China/WHU01/2020|EPI_ISL_406716 | 0 |
| BetaCoV/China/WHU02/2020|EPI_ISL_406717 | 0 |
| BetaCov/Wuhan/WH03/2020|EPI_ISL_406800 | 0 |
| BetaCov/Wuhan/WH04/2020|EPI_ISL_406801 | 0 |
| BetaCoV/Hangzhou/HZ-1/2020|EPI_ISL_406970 | 0 |
| BetaCoV/Finland/1/2020|EPI_ISL_407079 | 0 |
| BetaCoV/Hangzhou/HZCDC0001/2020|EPI_ISL_407313 | 0 |
| BetaCoV/Australia/NSW01/2020|EPI_ISL_407893 | 0 |
| BetaCoV/Belgium/GHB-03021/2020|EPI_ISL_407976 | 0 |
| BetaCoV/Singapore/3/2020|EPI_ISL_407988 | 0 |
| BetaCov/France/IDF0626/2020|EPI_ISL_408431 | 0 |
| BetaCoV/Chongqing/ZX01/2020|EPI_ISL_408479 | 0 |
| BetaCoV/Yunnan/IVDC-YN-003/2020|EPI_ISL_408480 | 0 |
| BetaCoV/Chongqing/IVDC-CQ-001/2020|EPI_ISL_408481 | 0 |
| BetaCoV/Jiangxi/IVDC-JX-002/2020|EPI_ISL_408486 | 0 |
| BetaCoV/Jiangsu/IVDC-JS-001/2020|EPI_ISL_408488 | 0 |
| BetaCoV/Taiwan/NTU01/2020|EPI_ISL_408489 | 0 |
| BetaCoV/Wuhan/IVDC-HB-envF13-20/2020|EPI_ISL_408514 | 0 |
| BetaCoV/USA/CA6/2020|EPI_ISL_410044 | 0 |
| BetaCoV/USA/IL2/2020|EPI_ISL_410045 | 0 |
| BetaCoV/Nepal/61/2020|EPI_ISL_410301 | 0 |
| BetaCoV/Japan/NA-20-05-1/2020|EPI_ISL_410531 | 0 |
| BetaCoV/Japan/OS-20-07-1/2020|EPI_ISL_410532 | 0 |
| BetaCoV/Taiwan/CGMH-CGU-01/2020|EPI_ISL_411915 | 0 |
| BetaCoV/Taiwan/3/2020|EPI_ISL_411926 | 0 |
| BetaCoV/Taiwan/4/2020|EPI_ISL_411927 | 0 |
| BetaCoV/Jiangsu/JS03/2020|EPI_ISL_411953 | 0 |
| BetaCoV/China/WH-09/2020|EPI_ISL_411957 | 0 |
| BetaCoV/Hefei/2/2020|EPI_ISL_412026 | 0 |
| BetaCoV/Hong_Kong/VB20026565/2020|EPI_ISL_412030 | 0 |
| BetaCoV/Korea/KCDC12/2020|EPI_ISL_412872 | 0 |
| _BetaCoV/Wuhan/HBCDC-HB-03/2019|EPI_ISL_412899 | 0 |
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