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Read Assembly and Annotation Pipeline Tool
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Question about ANI tax report #18

Open jhgffhgjf opened 9 months ago

jhgffhgjf commented 9 months ago

This might be a little stupid question. But i have a question about the ANI report, and i cant seem to find a description anywhere. In the output (see the next example) there are three numeric values in every row. The first value is the ANI, but it is unclear to me wat the numbers between the brackets indicate. Example: ANI report for assembly: skesa_out.fa Submitted organism: Paenibacillus xylanexedens (taxid = 528191, rank = species, lineage = Bacteria; Bacillota; Bacilli; Bacillales; Paenibacillaceae; Paenibacillus) Predicted organism: Paenibacillus xylanexedens (taxid = 528191, rank = species, lineage = Bacteria; Bacillota; Bacilli; Bacillales; Paenibacillaceae; Paenibacillus) Submitted organism has type: Yes Status: CONFIRMED Confidence: HIGH 98.007 (90.3 93.7) 8202498 assembly 2794858 Paenibacillus amylolyticus (GCA_004001025.1, ASM400102v1) 96.104 (80.9 85.4) 26148418 assembly 3983832 Paenibacillus xylanexedens (GCA_017874615.1, ASM1787461v1) 83.763 (48.2 48.5) 2788808 assembly 23349 Paenibacillus pabuli NBRC 13638 (GCA_001514495.1, ASM151449v1) 83.703 (46.2 48.1) 2311378 assembly 23858 Paenibacillus xylanivorans (GCA_001280595.1, ASM128059v1)

thibaudnis commented 9 months ago

Hi - Thank you for your question.

Please see: https://github.com/ncbi/pgap/wiki/Taxonomy-Check#description-of-the-reports (There is a link to this page in https://github.com/ncbi/rapt/wiki/Standalone_RAPT_doc#rapt-output). The numbers in parenthesis are query coverage and subject coverage.

The number after "assembly" (2794858 in the first row) is the count of bases in your assembly that map best to the assembly Paenibacillus amylolyticus (GCA_004001025.1, ASM400102v1), among all the other assemblies reported.