Microbial 'omics


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seeds-specific-txt [artifact]

Table of Contents

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

There are no anvi’o tools that generate this artifact, which means it is most likely provided to the anvi’o ecosystem by the user.

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 tabular file contains data on the specific coverages of tRNA-seq seeds.

Specific coverage represents reads that are assigned uniquely to a tRNA seed. See the trnaseq-profile-db artifact for a fuller explanation of specific versus nonspecific coverage. The rows and columns of this table are identical to seeds-non-specific-txt except the type of coverage data reported in each.

This file is produced by anvi-tabulate-trnaseq. The artifact for that program describes this and related tables in detail.

This tab-delimited file can be easily manipulated by the user. It is required input for anvi-plot-trnaseq.

Example

The seeds shown in this table are also shown in the seeds-non-specific-txt example. Modifications from these seeds are shown in the modifications-txt example.

gene_callers_id contig_name anticodon aa domain phylum class order family genus species taxon_percent_id sample_name mean_coverage relative_mean_coverage relative_discriminator_coverage 0 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 17a 18 19 20 20a 20b 21 22 23 24 25 26 27 28 29 30 31 32 33 34 35 36 37 38 39 40 41 42 43 44.01 44.02 44.03 44.04 44.05 44.06 44.07 44.08 44.09 44.1 44.11 44.12 44.13 44.14 44.15 44.16 44.17 44.18 44.19 44.2 44.21 44.22 44.23 49 50 51 52 53 54 55 56 57 58 59 60 61 62 63 64 65 66 67 68 69 70 71 72 73
0 c_000000684460_DB_R05_06 TAC Val Bacteria Firmicutes Clostridia Lachnospirales Lachnospiraceae     100 DB_01 71456.2 0.25805309 0.2578848   71392 71398 71398 71400 71413 71414 71414 71414 71419 71425 71426 71426 71426 71437 71445 71451 71451   71451 71455 71457     71460 71467 71467 71471 71468 71470 71470 71470 71475 71489 71540 71534 71529 71606 71579 71582 71583 71586 71586 71583 71583 71583 71585 71584 71584 71584 71587 71587                                     71586 71586 71572 71572 71570 71504 71505 71504 71503 71503 71503 71503 71503 71503 71503 71503 71502 71500 71500 71500 71497 71496 71488 71466 68324
0 c_000000684460_DB_R05_06 TAC Val Bacteria Firmicutes Clostridia Lachnospirales Lachnospiraceae     100 DB_03 87746.6 0.22523292 0.22512637   87568 87582 87588 87594 87598 87599 87596 87597 87598 87606 87608 87611 87611 87611 87612 87615 87615   87614 87614 87616     87617 87619 87619 87620 87620 87620 87621 87619 87620 87630 87689 87683 87694 87732 87898 87912 87921 87925 87926 87926 87926 87931 87924 87925 87929 87981 87986 87986                                     87985 87985 87981 87980 87978 87952 87952 87951 87952 87954 87952 87950 87946 87946 87946 87943 87941 87939 87939 87939 87936 87935 87929 87909 84530
0 c_000000684460_DB_R05_06 TAC Val Bacteria Firmicutes Clostridia Lachnospirales Lachnospiraceae     100 DB_05 29533 0.22692849 0.22190602   29490 29494 29499 29509 29516 29516 29518 29521 29525 29528 29536 29536 29536 29538 29539 29547 29550   29550 29549 29553     29552 29552 29553 29552 29553 29553 29549 29550 29552 29553 29564 29561 29559 29638 29605 29602 29604 29607 29607 29607 29608 29607 29607 29607 29607 29607 29609 29609                                     29609 29609 29606 29606 29605 29601 29601 29601 29601 29601 29599 29599 29599 29599 29596 29596 29597 29595 29595 29594 29593 29504 29486 29451 26980
0 c_000000684460_DB_R05_06 TAC Val Bacteria Firmicutes Clostridia Lachnospirales Lachnospiraceae     100 DB_07 47065 0.181019 0.18087983   47078 47087 47105 47113 47114 47114 47114 47116 47124 47127 47129 47129 47131 47133 47139 47139 47139   47135 47138 47141     47145 47142 47147 47145 47145 47142 47143 47135 47134 47133 47154 47125 47093 47111 47051 47058 47067 47071 47073 47072 47069 47069 47069 47072 47072 47073 47073 47074                                     47074 47074 47073 47069 47069 47042 47043 47042 47038 47042 47042 47042 47042 47041 47041 47040 47040 47040 47040 47040 47033 47032 47031 47018 45352
1 c_000000805276_DB_R05_05 ACG Arg Bacteria Firmicutes           98.649 DB_01 142.4 0.00051437 0.00052465   141 142 142 142 142 142 142 142 142 142 142 142 142 142 142 142 142   142 142 142 142   142 142 142 142 142 142 142 142 142 142 142 142 141 141 143 143 143 143 143 143 143 143 143 143 143 143 143 143                                     143 143 143 143 143 143 143 143 143 143 143 143 143 143 143 143 143 143 143 143 143 143 143 143 139
1 c_000000805276_DB_R05_05 ACG Arg Bacteria Firmicutes           98.649 DB_03 1006.4 0.00258316 0.00249815   1010 1010 1010 1010 1011 1011 1011 1011 1011 1010 1010 1010 1010 1010 1010 1010 1011   1011 1011 1014 1014   1014 1014 1014 1014 1014 1014 1014 1014 1014 1014 1014 1014 1013 1012 1012 1003 1003 1003 1003 1003 1003 1003 1003 1003 1003 1003 1003 1003                                     1003 1003 1003 1003 1003 1003 1003 1003 1003 1003 1003 1003 1003 1003 1003 1003 1003 1003 1003 1003 1003 1003 998 998 938
1 c_000000805276_DB_R05_05 ACG Arg Bacteria Firmicutes           98.649 DB_05 297.5 0.00228586 0.00285402   225 227 227 227 227 227 225 228 228 230 230 230 230 230 230 230 230   230 230 230 230   232 232 232 232 232 232 232 232 232 232 232 232 232 232 232 233 238 360 367 367 367 370 370 370 370 370 370 370                                     370 370 370 370 370 370 370 370 370 370 370 370 370 370 370 370 370 370 370 370 370 370 362 362 347
1 c_000000805276_DB_R05_05 ACG Arg Bacteria Firmicutes           98.649 DB_07 120 0.00046169 0.00046664   116 116 116 116 116 116 116 116 116 119 119 119 118 118 118 118 118   119 122 126 126   126 126 126 126 126 126 126 126 126 126 126 124 124 122 123 120 120 120 120 119 119 119 119 119 119 119 119 119                                     119 119 119 119 119 119 119 119 119 119 119 119 119 119 119 119 119 119 119 119 119 119 117 117 117

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