inversions-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-inversions

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

This is the output of anvi-report-inversions.

Per sample inversion report table

anvi-report-inversions searches for inversions in every single sample at a time and thus genereates a TAB-delimited table for every sample: INVERSIONS-IN-SAMPLE_01.txt, INVERSIONS-IN-SAMPLE_02, …

Here is an example output:

entry_id sample_name contig_name first_seq midline second_seq first_start first_end first_oligo_primer first_oligo_reference second_start second_end second_oligo_primer second_oligo_reference num_mismatches num_gaps length distance
c_000000000001_10214_10541 S01 c_000000000001 TGTTTCAAAAAACGTTCGT ||||||||||x|||||||| ACGAACGTCTTTTGAAACA 10306 10325 TCGATCAATTGATGTTTCAAAA.ACGTTCGT CTTTTG 10493 10512 TCAGTAGTGAATGTGTTTCAAAA.ACGTTCGT TTAATA 1 0 19 168
c_000000000002_10148_11135 S01 c_000000000002 TGTTTCAAAAAACGTTCGT ||||||||||||||||||| ACGAACGTTTTTTGAAACA 10514 10533 AGATACGGTTTATGTTTCAAAAAACGTTCGT CTTTTG 10724 10743 AGAAAAGAAGGCGTGTTTCAAAAAACGTTCGT TCAATG 0 0 19 191

These tables contains the following columns:

  • Entry ID made with the contig’s name and the start and stop position of the stretch
  • The contig’s name
  • The first palindrome sequence
  • The aligment midline
  • The second palindrome sequence
  • The start and stop position of the first and second palindrome sequence
  • The number of mismatches
  • The number of gaps
  • The length of the palindrome sequence
  • The distance between the first and second palindrome seqeuences, i.e. the size of the inversion
  • The number of samples in which it was detected and confirmed
  • The in silico primers used to compute the inversion’s activity, for the first and second palindrome
  • The oligo corresponding to the reference sequence

Inversions consensus table

Anvi’o eventually create a consensus table with all the unique inversions found accross all your samples in a file called INVERSIONS-CONSENSUS.txt. This table has the same format as the individual sample outputs, with the ‘entry ID’ replaced by a unique inversion ID. It also has column reporting the samples where the inversion was detected.

The table should look like this:

inversion_id contig_name first_seq midline second_seq first_start first_end second_start second_end num_mismatches num_gaps length distance num_samples sample_names first_oligo_primer first_oligo_reference second_oligo_primer second_oligo_reference
INV_0001 c_000000000001 TGTTTCAAAAAACGTTCGT ||||||||||x|||||||| ACGAACGTCTTTTGAAACA 10306 10325 10493 10512 1 0 19 168 3 S01,S02,S03 TCGATCAATTGATGTTTCAAAA.ACGTTCGT CTTTTG TCAGTAGTGAATGTGTTTCAAAA.ACGTTCGT TTAATA
INV_0002 c_000000000002 TGTTTCAAAAAACGTTCGT ||||||||||||||||||| ACGAACGTTTTTTGAAACA 10514 10533 10724 10743 0 0 19 191 3 S01,S02,S03 AGATACGGTTTATGTTTCAAAAAACGTTCGT CTTTTG AGAAAAGAAGGCGTGTTTCAAAAAACGTTCGT TCAATG

All stretches considered

Another default output table is named ALL-STRETCHES-CONSIDERED.txt and it reports every stretch that passed the ‘Identifying regions of interest’ parameters. It reports the maximum coverage of FWD/FWD and REV/REV in that stretch, per sample. It also reports the number of palindromes found and if a true inversion was confirmed.

entry_id sequence_name sample_name contig_name start_stop max_coverage num_palindromes_found true_inversions_found
S01_c_000000000001_10214_10541 c_000000000001_10214_10541 S01 c_000000000001 10214-10541 16 4 False
S01_c_000000000002_10148_11135 c_000000000002_10148_11135 S01 c_000000000002 10148-11135 69 20 False
S02_c_000000000001_10283_10542 c_000000000001_10283_10542 S02 c_000000000001 10283-10542 11 3 False
S02_c_000000000002_10200_11052 c_000000000002_10200_11052 S02 c_000000000002 10200-11052 96 17 False
S03_c_000000000001_10033_10801 c_000000000001_10033_10801 S03 c_000000000001 10033-10801 30 12 False
S03_c_000000000002_10498_10764 c_000000000002_10498_10764 S03 c_000000000002 10498-10764 13 2 False

Surrounding genes and functions

If the user enable the reporting of the genomic context, two addition TAB-delimited tables are generated: INVERSIONS-CONSENSUS-SURROUNDING-GENES.txt and INVERSIONS-CONSENSUS-SURROUNDING-FUNCTIONS.txt.

The first table report the gene calls surrounging every inversion when possible:

inversion_id entry_type gene_callers_id start stop direction partial call_type source version contig
INV_0001 FIRST_PALINDROME   10306 10325           c_000000000001
INV_0001 SECOND_PALINDROME   10493 10512           c_000000000001
INV_0001 GENE 6 6818 7595 r 0 1 prodigal v2.6.3 c_000000000001
INV_0001 GENE 7 7632 8976 r 0 1 prodigal v2.6.3 c_000000000001
INV_0001 GENE 8 9145 9616 r 0 1 prodigal v2.6.3 c_000000000001
INV_0001 GENE 9 9651 10170 r 0 1 prodigal v2.6.3 c_000000000001
INV_0001 GENE 10 11311 14161 r 0 1 prodigal v2.6.3 c_000000000001
INV_0001 GENE 11 14165 14495 r 0 1 prodigal v2.6.3 c_000000000001
INV_0001 GENE 12 14524 16072 r 0 1 prodigal v2.6.3 c_000000000001

The second table report the function associated to every gene call reported in the first file:

inversion_id gene_callers_id source accession function
INV_0001 6 COG20_FUNCTION COG1208 NDP-sugar pyrophosphorylase, includes eIF-2Bgamma, eIF-2Bepsilon, and LPS biosynthesis protein s (GCD1) (PDB:6JQ8)
INV_0001 6 COG20_CATEGORY J Translation, ribosomal structure and biogenesis
INV_0001 6 KOfam K00978 glucose-1-phosphate cytidylyltransferase [EC:2.7.7.33]
INV_0001 7 COG20_FUNCTION COG0399 dTDP-4-amino-4,6-dideoxygalactose transaminase (WecE) (PDB:4PIW) (PUBMED:15271350)
INV_0001 7 COG20_CATEGORY M Cell wall/membrane/envelope biogenesis
INV_0001 7 KOfam K12452 CDP-4-dehydro-6-deoxyglucose reductase, E1 [EC:1.17.1.1]
INV_0001 9 COG20_FUNCTION COG0250 Transcription termination/antitermination protein NusG (NusG) (PDB:3EWG) (PUBMED:19500594)
INV_0001 9 COG20_CATEGORY K Transcription
INV_0001 10 COG20_FUNCTION COG2605 Predicted kinase related to galactokinase and mevalonate kinase (PDB:4USK)
INV_0001 10 COG20_CATEGORY R General function prediction only
INV_0001 10 KOfam K05305 fucokinase [EC:2.7.1.52]
INV_0001 11 COG20_FUNCTION COG3254 L-rhamnose mutarotase (RhaM) (PDB:1X8D)
INV_0001 11 COG20_CATEGORY M Cell wall/membrane/envelope biogenesis
INV_0001 11 KOfam K03534 L-rhamnose mutarotase [EC:5.1.3.32]
INV_0001 12 COG20_FUNCTION COG0305 Replicative DNA helicase (DnaB) (PDB:1B79)
INV_0001 12 COG20_CATEGORY L Replication, recombination and repair
INV_0001 12 KOfam K02314 replicative DNA helicase [EC:3.6.4.12]

Inversion’s activity

Finally, if the user provide R1 and R2 fastq files and enable the reporting of inversion’s activity, anvi-report-inversions will generate a long-format file named INVERSION-ACTIVITY.txt. This file reports, for every inversion and sample, the relative proportion and read abundance of unique oligos, which either correspond to the reference contig (no inversion), or to an inversion sequence. The inversion’s activity is computed and reported for both side of each inversion.

sample inversion_id oligo_primer oligo reference frequency_count relative_abundance
S01 INV_0001 first_oligo_primer TTAATA False 6 0.097
S01 INV_0001 first_oligo_primer CTTTTG True 55 0.887
S01 INV_0001 first_oligo_primer CTTTTT False 1 0.016
S01 INV_0001 second_oligo_primer CTTTTG False 11 0.169
S01 INV_0001 second_oligo_primer TTAATA True 54 0.831
S01 INV_0002 first_oligo_primer TCAATG False 37 0.587
S01 INV_0002 first_oligo_primer CTTTTG True 25 0.397
S01 INV_0002 first_oligo_primer TCAATT False 1 0.016
S01 INV_0002 second_oligo_primer CTTTTG False 53 0.609
S01 INV_0002 second_oligo_primer TCAATG True 33 0.379
S01 INV_0002 second_oligo_primer TCAATC False 1 0.011

Edit this file to update this information.

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