contig-circularity-report-txt

TXT

A TXT-type anvi’o artifact. This artifact is typically generated, used, and/or exported by anvi’o (and not provided by the user)..

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Provided by

anvi-report-circularity

Required or used by

There are no anvi’o tools that use or require this artifact directly, which means it is most likely an end-product for the user.

Description

A report produced by anvi-report-circularity will have 12 TAB-delimited columns. Here is a snippet from an example output file:

contig contig_length status circularity_support edge_coherence num_fr_pairs expected_rf_pairs observed_rf_pairs supporting_rf_pairs num_edge_reads num_edge_reads_incoherent flags
c_001045 6184 linear 0.0000 0.6613 3264 204.74 5 0 685 232  
c_001380 4450 linear 0.0000 0.6452 1497 133.76 1 0 451 160  
c_001206 4129 circular 0.7459 0.9247 2662 258.14 122 91 930 70  
c_001137 5761 linear 0.0000 0.8947 97 6.56 0 0 19 2 low_fr_coverage (n=97);low_edge_coverage (n=19)
c_001925 2771 circular 0.9275 0.8053 1322 200.55 69 64 673 131  
c_001947 2784 indeterminate 1.0000 1.0000 47 7.09 3 3 20 0 low_fr_coverage (n=47);ambiguous_evidence
c_002285 42768 linear 0.0000 0.9936 26431 227.51 107 0 2195 14  
c_002729 2044 circular 0.7380 0.9527 2782 604.78 271 200 1967 93  
c_003377 1704 linear 0.0000 0.6584 2087 568.90 1 0 2181 745  
c_005100 16122 linear 0.0000 0.9892 9051 209.66 5 0 277 3  
c_002482 2237 linear 0.0000 0.6667 23 4.48 0 0 9 3 low_fr_coverage (n=23);low_expected_rf_pairs (expected=4.5);low_edge_coverage (n=9)
c_009498 7406 linear 0.0000 0.9603 6083 315.34 61 0 378 15  
c_009666 7209 linear 0.0000 0.9735 7456 397.64 41 0 339 9  
c_009940 6893 linear 0.0000 0.8895 3494 195.36 16 0 371 41  
c_007466 10285 circular 0.8000 0.9302 551 20.27 10 8 86 6  

where,

  • contig: name of the reference sequence in the bam-file.
  • contig_length: the actual length of the reference sequence.
  • status: the classification result, and whether the contig determined to be ‘circular’, ‘linear’, or none (‘indeterminate’).
  • circularity_support: a score that ranges from 0 to 1 and indicates the strenght of evidence that support circularity.
  • edge_coherence: a score that ranges from 0 to 1 and indicates the fraction of edge-mapping reads whose mates also map to this contig.
  • num_fr_pairs: number of FR (forward-reverse) pairs (these are the normal pairs that map like normal people do).
  • expected_rf_pairs: the expected number of RF pairs if the contig were circular, calculated from num_fr_pairs and the geometry of insert size vs contig length.
  • observed_rf_pairs: the total number of RF-oriented read pairs that are actually found on this contig.
  • supporting_rf_pairs: the umber of RF pairs whose circular insert size fell within the expected insert size distribution (i.e., weird pairs that do look like plausible junction-spanning pairs).
  • num_edge_reads: the number of reads mapping within ‘average insert size’ length of contig edges.
  • num_edge_reads_incoherent: the number of edge reads whose mate maps to a different contig.
  • flags: warning flags for edge cases.

Edit this file to update this information.

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