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I have no experience in Bioinformatics and I need to understand what the annotations given here mean (I am including the first few lines, please see the link for more):

contig_id                         feature_id              type       location                                 start   stop    strand
gi|1045318032|gb|MAZB01000333.1|  fig|252393.25.peg.1     peg        gi|1045318032|gb|MAZB01000333.1|_511_2   511     2       -
gi|1045318033|gb|MAZB01000332.1|  fig|252393.25.repeat.1  repeat     gi|1045318033|gb|MAZB01000332.1|_1_128   1       128     +
gi|1045318033|gb|MAZB01000332.1|  fig|252393.25.repeat.2  repeat     gi|1045318033|gb|MAZB01000332.1|_318_532 318     532     +
gi|1045318033|gb|MAZB01000332.1|  fig|252393.25.peg.2     peg        gi|1045318033|gb|MAZB01000332.1|_530_321 530     321     -
gi|1045318034|gb|MAZB01000331.1|  fig|252393.25.repeat.3  repeat     gi|1045318034|gb|MAZB01000331.1|_1_534   1       534     +
gi|1045318034|gb|MAZB01000331.1|  fig|252393.25.peg.3     peg        gi|1045318034|gb|MAZB01000331.1|_3_410   3       410     +
gi|1045318035|gb|MAZB01000330.1|  fig|252393.25.repeat.4  repeat     gi|1045318035|gb|MAZB01000330.1|_1_128   1       128     +
gi|1045318035|gb|MAZB01000330.1|  fig|252393.25.peg.4     peg        gi|1045318035|gb|MAZB01000330.1|_3_539   3       539     +
gi|1045318035|gb|MAZB01000330.1|  fig|252393.25.repeat.5  repeat     gi|1045318035|gb|MAZB01000330.1|_413_539 413     539     +

Could someone help me to understand what these files and all annotations mean?

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You are looking at the supplementary data of a paper. That seems to have given you a list of features, and some information about those features. Specifically, you seem to have a list of two types of element:

  1. "peg". Based on the information there, I assume "peg" stands for "protein encoding gene". Note that all peg lines have a peptide sequence (not seen in your question but present in the original link) and their "function" column is always some sort of protein function (e.g. "hypothetical protein" or "Transposase").

  2. "repeat". These are presumably repetitive elements.

For each line, you are given an identifier for the sequence in which this element can be found. For example, your first line is on gi|1045318032|gb|MAZB01000333.1|. That is a GI (gi|1045318032) and a GenBank identifier (gb|MAZB01000333.1). If you go to the NCBI website, and search for 1045318032, you will find that it is the Candidatus Erwinia dacicola isolate Erw_SC contig_333, whole genome shotgun sequence.

So, your first line is telling you that the authors have identified a protein encoding gene on sequence gi|1045318032 and the gene starts at position 511 of that sequence and ends at position 2. This might sound odd, but that's because the gene is on the negative (-) strand and positions are calculated with respect to the positive strand. So, if you were to count on the negative, the gene would start at 2 and end at 511.

The same goes for all the other lines you have there. Just look up the GI number and you can know what sequences they are referring to.

Finally, the second column, the "feature_id" looks like something specific to this figshare service that is hosting the data. I dont' know what it is, but I would guess it's an identifier for this particular feature. I don't think it has any relevance outside http://figshare.com.

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  • $\begingroup$ Thank you very much terdon. This makes sense. Greatly appreciate your kind support. $\endgroup$ – Dendrobium Oct 31 '19 at 12:15
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gi looks like a Genbank Identifier. You can search for the 10 digit number following gi| at the Genbank website.

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