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Table 6 Descriptions of ribotyper errors within ribosensor and mapping to the GenBank errors they trigger

From: Ribovore: ribosomal RNA sequence analysis for GenBank submissions and database curation

Ribotyper error

Associated GenBank error

Cause/explanation

R_NoHits

SEQ_HOM_NotSSUOrLSUrRNA

No hits reported

R_MultipleFamilies

SEQ_HOM_SSUAndLSUrRNA

SSU and LSU hits

R_LowScore

SEQ_HOM_LowSimilarity

Bits/position score is < 0.5

R_BothStrands

SEQ_HOM_MisAsBothStrands

Hits on both strands

R_InconsistentHits

SEQ_HOM_MisAsHitOrder

Hits are in different order in sequence and model

R_DuplicateRegion

SEQ_HOM_MisAsDupRegion

Hits overlap by 10 or more model positions

R_UnacceptableModel

SEQ_HOM_TaxNotExpectedSSUrRNA

Best hit is to model other than expected set 16S expected set: SSU.Archaea, SSU.Bacteria, SSU.Cyanobacteria, SSU.Chloroplast 18S expected set: SSU.Eukarya

R_LowCoverage

SEQ_HOM_LowCoverage

Coverage of all hits is < 0.80 (if ≤ 350 nt) or 0.86 (if > 350 nt)

R_QuestionableModel+

SEQ_HOM_TaxQuestionableSSUrRNA

Best hit is to a ’questionable’ model (if mode is 16S: SSU.Chloroplast)

R_MultipleHits+

SEQ_HOM_MultipleHits

More than 1 hit reported

  1. ‘+’: these errors errors do not trigger a GenBank error if sequence is ’RFSP’ (fails ribotyper and passes rRNA_sensor)