Excluded repeat and phage regions in PNG MDUST348 2.1.7.2 completed reference sequence
Dyson, ZA
, Malau, E, Horwood, PF, Ford, R, Siba, V, Yoannes, M, Pomat, W, Passey, M, Judd, LM, Ingle, DJ, Williamson, DA, Dougan, G, Greenhill, AR and Holt, KE
(2022).
Excluded repeat and phage regions in PNG MDUST348 2.1.7.2 completed reference sequence.
[Dataset].
PLOS Neglected Tropical Diseases.
https://doi.org/10.1371/journal.pntd.0010306.s006
, Malau, E, Horwood, PF, Ford, R, Siba, V, Yoannes, M, Pomat, W, Passey, M, Judd, LM, Ingle, DJ, Williamson, DA, Dougan, G, Greenhill, AR and Holt, KE
(2022).
Excluded repeat and phage regions in PNG MDUST348 2.1.7.2 completed reference sequence.
[Dataset].
PLOS Neglected Tropical Diseases.
https://doi.org/10.1371/journal.pntd.0010306.s006
This table details regions filtered from PNG genotype 2.1.7 alignment, where repetitive regions were identified using the ncumer command in MUMmer (v3.23) and integrated prophage sequences detected using the PHAge Search Tool Enhanced Release. Further recombination were removed with Gubbins (v2.3.2).
Keywords
Salmonella typhi, Genomics, Antimicrobial resistance, Phylogenetics, Typhoid, Sequence alignment, Phylogenetic analysis, Fevers| Item Type | Dataset |
|---|---|
| Capture method | Unknown |
| Collection Period |
From To 1980 2010 |
| Date | 28 March 2022 |
| Geographical area covered (offline during plugin upgrade) |
North Latitude East Longitude South Latitude West Longitude -6.76889 144.331 -6.76889 144.331 |
| Language(s) of written materials | English |
| Creator(s) |
Dyson, ZA, Malau, E, Horwood, PF, Ford, R, Siba, V, Yoannes, M, Pomat, W, Passey, M, Judd, LM, Ingle, DJ, Williamson, DA, Dougan, G, Greenhill, AR and Holt, KE
|
| LSHTM Faculty/Department | Faculty of Infectious and Tropical Diseases > Department of Infection Biology |
| Participating Institutions | London School of Hygiene & Tropical Medicine, London, United Kingdom, Federation University, Churchill, Australia, James Cook University, Townsville, Australia, Papua New Guinea Institute of Medical Research, Goroka, Papua New Guinea, University of Sydney, Lismore, Australia, Monash University, Melbourne, Australia, The University of Melbourne at The Peter Doherty Institute for Infection and Immunity, Melbourne, Australia, University of Cambridge, Cambridge, United Kingdom |
| Funders |
Project Funder Grant Number Funder URI Emerging Leadership Fellowship GNT1195210 http://dx.doi.org/10.13039/501100000925 Emerging Leadership Fellowship GNT1174555 http://dx.doi.org/10.13039/501100000925 UNSPECIFIED UNSPECIFIED http://dx.doi.org/10.13039/100008717 |
| Date Deposited | 09 Dec 2022 10:17 |
| Last Modified | 09 Dec 2022 10:28 |
| Publisher | PLOS Neglected Tropical Diseases |
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