Table · dataset · 2026
<p>Five second-site variants with asymmetric allele distributions between WT (Rd KW20) and MUT (<i>∆potE ∆speF</i>).</p>
Listed in HKU DataHub and figshare and Loughborough Research Repository — shown once because both records carry DOI 10.1371/journal.ppat.1014649.s004
<p>Each strain was single-colony passaged, and DNA was extracted for PacBio HiFi sequencing to ~300–400-fold genomic coverage.
Description
After minimap2 read alignment to the Rd KW20 reference sequence and FreeBayes variant calling in ‘pooled-continuous’ mode, 22,823 positions were identified with at least one read in one sample supporting an alternate (ALT) allele. Of these >99.9% showed agreement in reference (REF) allele frequencies between the WT and MUT, most agreeing with the REF allele at >75%.
A small set (n = 536 positions) supported an ALT allele in both WT and MUT, consistent with previously documented reference errors. An additional site was at ~50% allele frequency in both strains. The remaining 5 variants with asymmetric REF allele frequencies are shown in the table.
Read the rest (1 more)
POS is against an Rd KW20 reference permuted to the <i>dnaA</i> gene. GT refers to the FreeBayes-determined genotype, <i>i.e.,</i> 0 = REF, 1 = ALT1, <i>etc.</i> WT freq and MUT freq indicate the allele frequency of each allele.</p> <p>(XLSX)</p>
Links
Where it is published
- DOI doi.org/10.1371/journal.ppat.1014649.s004 ↗
DOI / persistent id · from datahub hku hk
Catalogue records · 1
- OAI-PMH record api.figshare.com/v2/oai?verb=GetRecord&metadataPrefix=oai_dc&identifier=oai%3Af… ↗
metadata API · from datahub hku hk
Topics
- From keywords
- Astronomy & Astrophysics · Cancer · Cancer · Cancer · Chemistry · Chemistry · Computer Science & AI · Computer Science & AI · Earth & Environmental Science · Earth & Environmental Science · Earth & Environmental Science · Ecology · Ecology · Ecology · Economics & Finance · Economics & Finance · Engineering · Engineering · Evolutionary biology · Evolutionary biology · Evolutionary biology · Genetics · Genetics · Genetics · Humanities · Humanities · Infectious diseases · Infectious diseases · Infectious diseases · Life Sciences · Life Sciences · Life Sciences · Materials Science · Mathematics & Statistics · Medicine & Health · Medicine & Health · Medicine & Health · Microbiology · Microbiology · Microbiology · Ocean & Atmospheric Science · Psychology & Behavioral Science · Social Science · Social Science · Virology · Virology · Virology
- Inferred from text
- Sequencing 75% · Tabular 65%
Provenance · 3 source records, 54 field assertions
| Source | Key | Last seen | Raw |
|---|---|---|---|
| HKU DataHub | oai:figshare.com:article/34000907 | 12 d ago | JSON v1 |
| figshare | oai:figshare.com:article/34000907 | 11 d ago | JSON v1 |
| Loughborough Research Repository | oai:figshare.com:article/34000907 | 11 d ago | JSON v1 |
| Field | Assertion | Extractor | Evidence |
|---|---|---|---|
| access_level | source · datahub hku hk | connector:datahub_hku_hk@1.0.0 | |
| concepts[disease].local:disease:cancer | mapping · datahub hku hk | vocabulary-mapper@1.0.0 | keywords['Cancer'] |
| concepts[disease].local:disease:cancer | mapping · repository lboro ac uk | vocabulary-mapper@1.0.0 | keywords['Cancer'] |
| concepts[disease].local:disease:cancer | mapping · figshare com | vocabulary-mapper@1.0.0 | keywords['Cancer'] |
| concepts[field].anzsrc:field:310706 | mapping · figshare com | vocabulary-mapper@1.0.0 | keywords['Virology'] |
| concepts[field].anzsrc:field:310706 | mapping · datahub hku hk | vocabulary-mapper@1.0.0 | keywords['Virology'] |
| concepts[field].anzsrc:field:310706 | mapping · repository lboro ac uk | vocabulary-mapper@1.0.0 | keywords['Virology'] |
| concepts[field].anzsrc:field:320211 | mapping · repository lboro ac uk | vocabulary-mapper@1.0.0 | keywords['Infectious Diseases'] |
| concepts[field].anzsrc:field:320211 | mapping · figshare com | vocabulary-mapper@1.0.0 | keywords['Infectious Diseases'] |
| concepts[field].anzsrc:field:320211 | mapping · datahub hku hk | vocabulary-mapper@1.0.0 | keywords['Infectious Diseases'] |
| concepts[field].anzsrc:group:3103 | mapping · figshare com | vocabulary-mapper@1.0.0 | keywords['Ecology'] |
| concepts[field].anzsrc:group:3103 | mapping · repository lboro ac uk | vocabulary-mapper@1.0.0 | keywords['Ecology'] |
| concepts[field].anzsrc:group:3103 | mapping · datahub hku hk | vocabulary-mapper@1.0.0 | keywords['Ecology'] |
| concepts[field].anzsrc:group:3104 | mapping · datahub hku hk | vocabulary-mapper@1.0.0 | keywords['Evolutionary Biology'] |
| concepts[field].anzsrc:group:3104 | mapping · figshare com | vocabulary-mapper@1.0.0 | keywords['Evolutionary Biology'] |
| concepts[field].anzsrc:group:3104 | mapping · repository lboro ac uk | vocabulary-mapper@1.0.0 | keywords['Evolutionary Biology'] |
| concepts[field].anzsrc:group:3105 | mapping · figshare com | vocabulary-mapper@1.0.0 | keywords['Genetics'] |
| concepts[field].anzsrc:group:3105 | mapping · repository lboro ac uk | vocabulary-mapper@1.0.0 | keywords['Genetics'] |
| concepts[field].anzsrc:group:3105 | mapping · datahub hku hk | vocabulary-mapper@1.0.0 | keywords['Genetics'] |
| concepts[field].anzsrc:group:3107 | mapping · repository lboro ac uk | vocabulary-mapper@1.0.0 | keywords['Microbiology'] |
| concepts[field].anzsrc:group:3107 | mapping · datahub hku hk | vocabulary-mapper@1.0.0 | keywords['Microbiology'] |
| concepts[field].anzsrc:group:3107 | mapping · figshare com | vocabulary-mapper@1.0.0 | keywords['Microbiology'] |
| concepts[field].local:field:astronomy | mapping · figshare com | connector:figshare_com@1.0.0 | |
| concepts[field].local:field:chemistry | mapping · figshare com | connector:figshare_com@1.0.0 | |
| concepts[field].local:field:chemistry | mapping · repository lboro ac uk | connector:repository_lboro_ac_uk@1.0.0 | |
| concepts[field].local:field:computer-science-ai | mapping · figshare com | connector:figshare_com@1.0.0 | |
| concepts[field].local:field:computer-science-ai | mapping · repository lboro ac uk | connector:repository_lboro_ac_uk@1.0.0 | |
| concepts[field].local:field:earth-environmental | mapping · datahub hku hk | connector:datahub_hku_hk@1.0.0 | |
| concepts[field].local:field:earth-environmental | mapping · figshare com | connector:figshare_com@1.0.0 | |
| concepts[field].local:field:earth-environmental | mapping · repository lboro ac uk | connector:repository_lboro_ac_uk@1.0.0 | |
| concepts[field].local:field:economics-finance | mapping · repository lboro ac uk | connector:repository_lboro_ac_uk@1.0.0 | |
| concepts[field].local:field:economics-finance | mapping · figshare com | connector:figshare_com@1.0.0 | |
| concepts[field].local:field:engineering | mapping · repository lboro ac uk | connector:repository_lboro_ac_uk@1.0.0 | |
| concepts[field].local:field:engineering | mapping · figshare com | connector:figshare_com@1.0.0 | |
| concepts[field].local:field:humanities | mapping · figshare com | connector:figshare_com@1.0.0 | |
| concepts[field].local:field:humanities | mapping · repository lboro ac uk | connector:repository_lboro_ac_uk@1.0.0 | |
| concepts[field].local:field:life-sciences | mapping · repository lboro ac uk | connector:repository_lboro_ac_uk@1.0.0 | |
| concepts[field].local:field:life-sciences | mapping · figshare com | connector:figshare_com@1.0.0 | |
| concepts[field].local:field:life-sciences | mapping · datahub hku hk | connector:datahub_hku_hk@1.0.0 | |
| concepts[field].local:field:materials-science | mapping · repository lboro ac uk | connector:repository_lboro_ac_uk@1.0.0 | |
| concepts[field].local:field:mathematics-statistics | mapping · repository lboro ac uk | connector:repository_lboro_ac_uk@1.0.0 | |
| concepts[field].local:field:medicine-health | mapping · figshare com | connector:figshare_com@1.0.0 | |
| concepts[field].local:field:medicine-health | mapping · repository lboro ac uk | connector:repository_lboro_ac_uk@1.0.0 | |
| concepts[field].local:field:medicine-health | mapping · datahub hku hk | connector:datahub_hku_hk@1.0.0 | |
| concepts[field].local:field:ocean-atmospheric | mapping · figshare com | connector:figshare_com@1.0.0 | |
| concepts[field].local:field:psychology-behavioral | mapping · repository lboro ac uk | connector:repository_lboro_ac_uk@1.0.0 | |
| concepts[field].local:field:social-science | mapping · repository lboro ac uk | connector:repository_lboro_ac_uk@1.0.0 | |
| concepts[field].local:field:social-science | mapping · figshare com | connector:figshare_com@1.0.0 | |
| concepts[modality].local:modality:sequencing | enrichment · datahub hku hk | keyword-concept-rules@1.0.0 | title+description (75%) |
| concepts[modality].local:modality:tabular | enrichment · datahub hku hk | keyword-concept-rules@1.0.0 | title+description (65%) |
| description | source · datahub hku hk | connector:datahub_hku_hk@1.0.0 | /metadata/dc/description |
| license | source · datahub hku hk | connector:datahub_hku_hk@1.0.0 | /metadata/dc/rights |
| publication_date | source · datahub hku hk | connector:datahub_hku_hk@1.0.0 | |
| title | source · datahub hku hk | connector:datahub_hku_hk@1.0.0 | /metadata/dc/title |