Impact of the chemical modification of tRNAs anticodon loop on the variability and evolution of codon usage in proteobacteria (doi:10.34691/UCHILE/AYDRZL)

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Part 1: Document Description
Part 2: Study Description
Part 3: Data Files Description
Part 4: Variable Description
Part 5: Other Study-Related Materials
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Impact of the chemical modification of tRNAs anticodon loop on the variability and evolution of codon usage in proteobacteria

doi:10.34691/UCHILE/AYDRZL

Repositorio de datos de investigación de la Universidad de Chile

2024-03-06

3

Sebastian Delgado; Álvaro Armijo; Verónica Bravo; Omar Orellana; Juan Carlos Salazar; Assaf Katz, 2024, "Impact of the chemical modification of tRNAs anticodon loop on the variability and evolution of codon usage in proteobacteria", https://doi.org/10.34691/UCHILE/AYDRZL, Repositorio de datos de investigación de la Universidad de Chile, V3, UNF:6:H4RkW4KY33+u8SKNSXXA8A== [fileUNF]

Impact of the chemical modification of tRNAs anticodon loop on the variability and evolution of codon usage in proteobacteria

doi:10.34691/UCHILE/AYDRZL

Sebastian Delgado (Facultad de Ciencias, Universidad de Chile)

Álvaro Armijo (Facultad de Ciencias Químicas y Farmacéuticas Universidad de Chile, Santiago, Chile)

Verónica Bravo (Programa Centro de Investigacion Biomedica y Aplicada, (CIBAP), Escuela de Medicina, Facultad de Ciencias Medicas, Universidad de Santiago de Chile)

Omar Orellana (ICBM, Facultad de Medicina, Universidad de Chile)

Juan Carlos Salazar (ICBM, Facultad de Medicina, Universidad de Chile)

Assaf Katz (ICBM, Facultad de Medicina, Universidad de Chile)

Repositorio de datos de investigación de la Universidad de Chile

Katz, Assaf

Katz, Assaf

2024-03-04

https://doi.org/10.34691/UCHILE/AYDRZL

Medicine, Health and Life Sciences, Codon usage, Proteobacteria, tRNA, tRNA modifiaction enzyme, N6-threonylcarbamoyladenosine, glutamyl-queuosine, 2-lysidine, 2-thiouridine, Genome evolution

The data presented here corresponds to the supplementary data of the article entitled "Impact of the chemical modification of tRNAs anticodon loop on the variability and evolution of codon usage in proteobacteria" by Delgado et al. It contains supplementary figures, supplemntary tables and scripts including: - Relations between codon usage and GC% in proteobacteria - Phylogenetic trees coupled to bar graphs showing codon usage in proteobacteria - Relations between codon usage and the number of genes coding for tRNAs in proteobacteria - Relations between the presence of genes coding for tRNA modification enzymes and codon usage or GC% - Scripts required to perform the analyzes presented in the article and this supplementary data

Publication in review.

• Number of cases: 1484

• No. of variables per record: 67

• Type of File: text/tab-separated-values

UNF:6:HmAzkR8a99szs+OCJnRS9g==

• Number of cases: 3592

• No. of variables per record: 18

• Type of File: text/tab-separated-values

UNF:6:pKcK/V3hph5rx13Vse2D4w==

• Number of cases: 1484

• No. of variables per record: 10

• Type of File: text/tab-separated-values

UNF:6:Wxc4E386AXyXDr7n6nwPhw==

• genoma - genoma
• Ala-AGC - Ala-AGC
• Ala-GGC - Ala-GGC
• Ala-TGC - Ala-TGC
• Ala-CGC - Ala-CGC
• Arg-ACG - Arg-ACG
• Arg-GCG - Arg-GCG
• Arg-TCG - Arg-TCG
• Arg-CCG - Arg-CCG
• Arg-TCT - Arg-TCT
• Arg-CCT - Arg-CCT
• Asn-ATT - Asn-ATT
• Asn-GTT - Asn-GTT
• Asp-ATC - Asp-ATC
• Asp-GTC - Asp-GTC
• Cys-ACA - Cys-ACA
• Cys-GCA - Cys-GCA
• Gln-TTG - Gln-TTG
• Gln-CTG - Gln-CTG
• Glu-TTC - Glu-TTC
• Glu-CTC - Glu-CTC
• Gly-ACC - Gly-ACC
• Gly-GCC - Gly-GCC
• Gly-TCC - Gly-TCC
• Gly-CCC - Gly-CCC
• His-ATG - His-ATG
• His-GTG - His-GTG
• Ile-AAT - Ile-AAT
• Ile-GAT - Ile-GAT
• Ile-TAT - Ile-TAT
• Leu-TAA - Leu-TAA
• Leu-CAA - Leu-CAA
• Leu-AAG - Leu-AAG
• Leu-GAG - Leu-GAG
• Leu-TAG - Leu-TAG
• Leu-CAG - Leu-CAG
• Lys-TTT - Lys-TTT
• Lys-CTT - Lys-CTT
• fMet-CAT - fMet-CAT
• Met-CAT - Met-CAT
• Phe-AAA - Phe-AAA
• Phe-GAA - Phe-GAA
• Pro-AGG - Pro-AGG
• Pro-GGG - Pro-GGG
• Pro-TGG - Pro-TGG
• Pro-CGG - Pro-CGG
• Pyl-CTA - Pyl-CTA
• Sec-TCA - Sec-TCA
• Ser-AGA - Ser-AGA
• Ser-GGA - Ser-GGA
• Ser-TGA - Ser-TGA
• Ser-CGA - Ser-CGA
• Ser-ACT - Ser-ACT
• Ser-GCT - Ser-GCT
• Thr-AGT - Thr-AGT
• Thr-GGT - Thr-GGT
• Thr-TGT - Thr-TGT
• Thr-CGT - Thr-CGT
• Trp-CCA - Trp-CCA
• Tyr-ATA - Tyr-ATA
• Tyr-GTA - Tyr-GTA
• Val-AAC - Val-AAC
• Val-GAC - Val-GAC
• Val-TAC - Val-TAC
• Val-CAC - Val-CAC
• TOTAL - TOTAL
• notes - notes
• Gene - Gene
• Non-unique Gene name - Non-unique Gene name
• Annotation - Annotation
• Number_pos_present_in - Number_pos_present_in
• Number_neg_present_in - Number_neg_present_in
• Number_pos_not_present_in - Number_pos_not_present_in
• Number_neg_not_present_in - Number_neg_not_present_in
• Sensitivity - Sensitivity
• Specificity - Specificity
• Odds_ratio - Odds_ratio
• Naive_p - Naive_p
• Bonferroni_p - Bonferroni_p
• Benjamini_H_p - Benjamini_H_p
• Max_Pairwise_comparisons - Max_Pairwise_comparisons
• Max_supporting_pairs - Max_supporting_pairs
• Max_opposing_pairs - Max_opposing_pairs
• Best_pairwise_comp_p - Best_pairwise_comp_p
• Worst_pairwise_comp_p - Worst_pairwise_comp_p
• #Genome - #Genome
• A_count - A_count
• C_count - C_count
• G_count - G_count
• T_count - T_count
• A_frac - A_frac
• C_frac - C_frac
• G_frac - G_frac
• T_frac - T_frac
• GC_frac - GC_frac

f1499 Location:

Variable Format: character

Notes: UNF:6:cf4HZDs3noEdCv2eakbREg==

f1499 Location:

Summary Statistics: Mean 0.0013477088948786937; Max. 1.0; Min. 0.0; StDev 0.03669877549545732; Valid 1484.0

Variable Format: numeric

Notes: UNF:6:TghnnFGHeB6RfpHzCEAMIw==

f1499 Location:

Summary Statistics: StDev 0.8091798642551815; Min. 0.0; Valid 1484.0; Mean 1.4029649595687321; Max. 6.0;

Variable Format: numeric

Notes: UNF:6:h6HREi9Hnuz1cIxGiohUcg==

f1499 Location:

Summary Statistics: Min. 0.0; Mean 3.0249326145552518; StDev 1.5838185233191304; Max. 11.0; Valid 1484.0

Variable Format: numeric

Notes: UNF:6:BHYnUL1ieRsJMOkPUvOryg==

f1499 Location:

Summary Statistics: StDev 0.5184875135601186; Min. 0.0; Valid 1484.0; Max. 3.0; Mean 0.3719676549865226;

Variable Format: numeric

Notes: UNF:6:vKwWY7hSH/nOJRCHHyK4DA==

f1499 Location:

Summary Statistics: Mean 1.974393530997305; Max. 12.0; StDev 1.4700945502360632; Valid 1484.0; Min. 0.0;

Variable Format: numeric

Notes: UNF:6:7RQmh/lLFaar0XnMwfNvJA==

f1499 Location:

Summary Statistics: Valid 1484.0; StDev 0.21207339981716675; Min. 0.0; Max. 1.0; Mean 0.04716981132075463

Variable Format: numeric

Notes: UNF:6:3llkLwA6be3VdraY27EfOQ==

f1499 Location:

Summary Statistics: Valid 1484.0; Max. 2.0; Min. 0.0; Mean 0.12129380053908274; StDev 0.33271509796622645;

Variable Format: numeric

Notes: UNF:6:A0sozqC/m9UgQAKW9ZodUw==

f1499 Location:

Summary Statistics: Mean 0.976415094339623; Min. 0.0; StDev 0.34073274766055134; Max. 4.0; Valid 1484.0;

Variable Format: numeric

Notes: UNF:6:+QLQCS+rI06VXFeEdrj+0A==

f1499 Location:

Summary Statistics: StDev 0.2442966958843487; Min. 0.0; Valid 1484.0; Max. 3.0; Mean 1.0485175202156334

Variable Format: numeric

Notes: UNF:6:qCsszblmwnKQw7T+Jjn2oQ==

f1499 Location:

Summary Statistics: Valid 1484.0; Max. 3.0; Mean 0.9184636118598382; Min. 0.0; StDev 0.3571201371198533;

Variable Format: numeric

Notes: UNF:6:EHxWlIzg820SYAXQU4PoHg==

f1499 Location:

Summary Statistics: Valid 1484.0; Max. 1.0; Mean 0.0013477088948787132; Min. 0.0; StDev 0.03669877549545738

Variable Format: numeric

Notes: UNF:6:Mnlwjj7BUrkyqA9/s2uUug==

f1499 Location:

Summary Statistics: Min. 0.0; Mean 2.0276280323450173; StDev 1.3487756368622899; Valid 1484.0; Max. 9.0

Variable Format: numeric

Notes: UNF:6:bHA9Poz6qKwIEWO9nOc4ww==

f1499 Location:

Summary Statistics: StDev 0.04493147033293988; Max. 1.0; Valid 1484.0; Mean 0.00202156334231807; Min. 0.0;

Variable Format: numeric

Notes: UNF:6:kjOuLBNDT8brEkZyk8iurQ==

f1499 Location:

Summary Statistics: Min. 0.0; Max. 13.0; StDev 1.422912018635624; Valid 1484.0; Mean 2.38274932614555

Variable Format: numeric

Notes: UNF:6:kHIpvuPF2gB0tKnyRUs1uQ==

f1499 Location:

Summary Statistics: Mean 0.001347708894878702; Min. 0.0; Max. 1.0; Valid 1484.0; StDev 0.036698775495457525

Variable Format: numeric

Notes: UNF:6:3R79IDV9K44UgDk8ajsDUA==

f1499 Location:

Summary Statistics: Max. 7.0; StDev 0.5590615966637261; Mean 1.182614555256065; Valid 1484.0; Min. 0.0

Variable Format: numeric

Notes: UNF:6:uJA8NCVwAV0F941he44xPA==

f1499 Location:

Summary Statistics: Mean 1.5606469002695416; Min. 0.0; Valid 1484.0; StDev 1.0320363241475157; Max. 10.0

Variable Format: numeric

Notes: UNF:6:jArcdMfm3viRs73aQvd9gg==

f1499 Location:

Summary Statistics: Mean 0.5026954177897578; Max. 3.0; StDev 0.666605018781457; Valid 1484.0; Min. 0.0;

Variable Format: numeric

Notes: UNF:6:au+YugqGYY5fDNmSK4LO1Q==

f1499 Location:

Summary Statistics: StDev 1.7098870102370503; Max. 13.0; Mean 2.5276280323450178; Valid 1484.0; Min. 0.0;

Variable Format: numeric

Notes: UNF:6:VE8w7kCdMBIwLu3xGHUMoQ==

f1499 Location:

Summary Statistics: Max. 4.0; Min. 0.0; Valid 1484.0; Mean 0.2654986522911052; StDev 0.5031214306406147

Variable Format: numeric

Notes: UNF:6:pz9BWvHMj1pyyEW+IC2iMw==

f1499 Location:

Summary Statistics: Mean 0.004043126684636135; StDev 0.09707711250346646; Max. 3.0; Min. 0.0; Valid 1484.0;

Variable Format: numeric

Notes: UNF:6:JQlENnBS+myLEz3cvcLJ5g==

f1499 Location:

Summary Statistics: Valid 1484.0; Mean 2.5633423180592936; StDev 1.872007987607366; Max. 16.0; Min. 0.0;

Variable Format: numeric

Notes: UNF:6:twStkyw8dW64p8Xh7yWWlw==

f1499 Location:

Summary Statistics: Min. 0.0; Valid 1484.0; Mean 1.0828840970350404; Max. 4.0; StDev 0.3568095457879511

Variable Format: numeric

Notes: UNF:6:74vWotHCJEliEdT7RP+xWg==

f1499 Location:

Summary Statistics: Valid 1484.0; Mean 0.6880053908355797; Max. 2.0; StDev 0.490328922008315; Min. 0.0

Variable Format: numeric

Notes: UNF:6:65S2TzwSF6NOX2gXMStnww==

f1499 Location:

Summary Statistics: Max. 2.0; Valid 1484.0; Min. 0.0; Mean 0.002695417789757416; StDev 0.06354984519707722

Variable Format: numeric

Notes: UNF:6:TpKh7od1igTGoXKlWd138g==

f1499 Location:

Summary Statistics: StDev 0.4038620845050608; Valid 1484.0; Min. 0.0; Mean 1.1684636118598384; Max. 4.0;

Variable Format: numeric

Notes: UNF:6:UNWSmccDh1s2n7hqFrzMng==

f1499 Location:

Summary Statistics: Mean 0.001347708894878704; Min. 0.0; Valid 1484.0; Max. 1.0; StDev 0.03669877549545769;

Variable Format: numeric

Notes: UNF:6:qauzTMSaodO93Ic9MUXjIg==

f1499 Location:

Summary Statistics: Valid 1484.0; Min. 0.0; StDev 1.5764950076637194; Mean 2.971024258760106; Max. 11.0;

Variable Format: numeric

Notes: UNF:6:ITCAdZCqhw3z2begZoEnUA==

f1499 Location:

Summary Statistics: Max. 2.0; Mean 0.014824797843665785; Min. 0.0; Valid 1484.0; StDev 0.1263467022744023;

Variable Format: numeric

Notes: UNF:6:Tb5++Q2c5bwibPjUHgo4/A==

f1499 Location:

Summary Statistics: StDev 0.6207976830083524; Mean 1.1084905660377358; Max. 5.0; Min. 0.0; Valid 1484.0

Variable Format: numeric

Notes: UNF:6:lDFJeyO9RCJT0A6B0FwAgQ==

f1499 Location:

Summary Statistics: Max. 3.0; Mean 1.0188679245283023; Valid 1484.0; StDev 0.2589877308205603; Min. 0.0

Variable Format: numeric

Notes: UNF:6:M6efWvMRHdQsDM9V+yGj/w==

f1499 Location:

Summary Statistics: StDev 0.09321600506200026; Mean 0.008760107816711589; Max. 1.0; Valid 1484.0; Min. 0.0

Variable Format: numeric

Notes: UNF:6:QrSNWzDz+LhoGB30N5kJYQ==

f1499 Location:

Summary Statistics: Min. 0.0; StDev 0.2991304991662062; Max. 4.0; Mean 1.074797843665768; Valid 1484.0

Variable Format: numeric

Notes: UNF:6:U9ZuXPvmdLttPjnHqokwRw==

f1499 Location:

Summary Statistics: Mean 1.3066037735849059; Max. 17.0; Min. 0.0; Valid 1484.0; StDev 1.246842345610334;

Variable Format: numeric

Notes: UNF:6:4Awk6g1Ss4evvTCL7eMN6A==

f1499 Location:

Summary Statistics: Mean 1.5505390835579507; Min. 0.0; StDev 1.3023164093890403; Valid 1484.0; Max. 6.0

Variable Format: numeric

Notes: UNF:6:K3q7ASM/WMOrF9YUDGzRPQ==

f1499 Location:

Summary Statistics: Valid 1484.0; Mean 2.1132075471698117; StDev 1.8171619725757875; Min. 0.0; Max. 17.0;

Variable Format: numeric

Notes: UNF:6:s0Y5l0FLTyt325fucdgZbw==

f1499 Location:

Summary Statistics: Max. 4.0; Mean 0.6293800539083555; StDev 0.6939479390975544; Valid 1484.0; Min. 0.0;

Variable Format: numeric

Notes: UNF:6:vIBPfPqlae4xR4wfJID3OQ==

f1499 Location:

Summary Statistics: Valid 1484.0; StDev 1.5866821362837535; Min. 1.0; Max. 11.0; Mean 2.43935309973046

Variable Format: numeric

Notes: UNF:6:hb1NKs/jBl/fqYtmn5SpYw==

f1499 Location:

Summary Statistics: StDev 0.6295976292511581; Valid 1484.0; Min. 0.0; Max. 5.0; Mean 1.355121293800539

Variable Format: numeric

Notes: UNF:6:m5WHGaMPynKsBO11OmAtgA==

f1499 Location:

Summary Statistics: StDev 0.14078464972305638; Min. 0.0; Valid 1484.0; Mean 0.020215633423180588; Max. 1.0;

Variable Format: numeric

Notes: UNF:6:+9vRLjR0kEAYbnY59t3WSA==

f1499 Location:

Summary Statistics: Max. 11.0; Valid 1484.0; Mean 1.3874663072776288; StDev 0.7509072387882307; Min. 0.0

Variable Format: numeric

Notes: UNF:6:504t1prKqX3UDRclIIr9lA==

f1499 Location:

Summary Statistics: Valid 1484.0; Min. 0.0; Mean 0.0020215633423180546; StDev 0.04493147033293983; Max. 1.0

Variable Format: numeric

Notes: UNF:6:bFS6W88Jc9FvMJUl6YVSaA==

f1499 Location:

Summary Statistics: StDev 0.41028484917435054; Valid 1484.0; Mean 0.9164420485175199; Max. 3.0; Min. 0.0;

Variable Format: numeric

Notes: UNF:6:u6BRlu9EFni3FiLkGwAfEQ==

f1499 Location:

Summary Statistics: Valid 1484.0; Min. 0.0; Max. 8.0; Mean 1.3477088948787055; StDev 0.6694278563948927;

Variable Format: numeric

Notes: UNF:6:x/BlEJrPFSMiLRH3qSm02w==

f1499 Location:

Summary Statistics: Min. 0.0; Valid 1484.0; StDev 0.5683507346163168; Max. 3.0; Mean 0.6556603773584906

Variable Format: numeric

Notes: UNF:6:RBJwIJyXbO6Yqwx+jNACJA==

f1499 Location:

Summary Statistics: Mean 0.0; Valid 1484.0; Min. 0.0; StDev 0.0; Max. 0.0

Variable Format: numeric

Notes: UNF:6:3pYGJT7LvyFQyrohLzqxqQ==

f1499 Location:

Summary Statistics: Valid 1484.0; Max. 2.0; Mean 0.33018867924528295; StDev 0.4900958024678874; Min. 0.0

Variable Format: numeric

Notes: UNF:6:qfWhOwUibq3i9trz0+2UYg==

f1499 Location:

Summary Statistics: Min. 0.0; StDev 0.07324882226465011; Valid 1484.0; Mean 0.005390835579514824; Max. 1.0

Variable Format: numeric

Notes: UNF:6:PJIurGxUo3OKIM344DaNYQ==

f1499 Location:

Summary Statistics: StDev 0.409288560564037; Valid 1484.0; Min. 0.0; Mean 1.1435309973045835; Max. 3.0

Variable Format: numeric

Notes: UNF:6:V7Xc5bNErvDvJ4sHzpgCkw==

f1499 Location:

Summary Statistics: Min. 0.0; Valid 1484.0; StDev 0.8544611166924452; Mean 1.3234501347708894; Max. 11.0;

Variable Format: numeric

Notes: UNF:6:g5jpuvdMiZiUCzvO/AWPIQ==

f1499 Location:

Summary Statistics: Mean 0.7318059299191376; Max. 5.0; Valid 1484.0; Min. 0.0; StDev 0.6118953233918538;

Variable Format: numeric

Notes: UNF:6:3HQSi0qgfKhdpqI7+3pOSQ==

f1499 Location:

Summary Statistics: StDev 0.036698775495457296; Mean 0.0013477088948786998; Min. 0.0; Max. 1.0; Valid 1484.0;

Variable Format: numeric

Notes: UNF:6:DdyOBM3gj1LtiITNatrEMA==

f1499 Location:

Summary Statistics: Max. 4.0; Mean 1.0781671159029649; Min. 0.0; Valid 1484.0; StDev 0.29939545128082

Variable Format: numeric

Notes: UNF:6:HRjDws/cCgP4GDgLz4xmZw==

f1499 Location:

Summary Statistics: Min. 0.0; Mean 0.0033692722371967683; StDev 0.05796709857384237; Max. 1.0; Valid 1484.0

Variable Format: numeric

Notes: UNF:6:G6TfwUmw/JSvUPKUQ6uXCw==

f1499 Location:

Summary Statistics: Mean 1.1880053908355797; StDev 0.4142981423399974; Valid 1484.0; Min. 0.0; Max. 3.0;

Variable Format: numeric

Notes: UNF:6:VwLovHX4hAiAZxrePs/RSg==

f1499 Location:

Summary Statistics: Valid 1484.0; StDev 0.7833173371712763; Mean 1.2971698113207542; Min. 0.0; Max. 8.0

Variable Format: numeric

Notes: UNF:6:g6/pakRbWR8XlADtzepfxg==

f1499 Location:

Summary Statistics: Valid 1484.0; Max. 2.0; StDev 0.4856845652873285; Min. 0.0; Mean 0.7190026954177902

Variable Format: numeric

Notes: UNF:6:V9CkowexurPkZH+sKa2p8Q==

f1499 Location:

Summary Statistics: Min. 0.0; Mean 1.1233153638814013; StDev 0.3748978628357388; Max. 4.0; Valid 1484.0

Variable Format: numeric

Notes: UNF:6:G6HO1vwDCD/clCnOzMclXw==

f1499 Location:

Summary Statistics: StDev 0.07324882226464983; Mean 0.005390835579514833; Min. 0.0; Valid 1484.0; Max. 1.0

Variable Format: numeric

Notes: UNF:6:XYJijcCWI9C7c5I/p2lYiQ==

f1499 Location:

Summary Statistics: Valid 1484.0; Min. 0.0; Max. 9.0; Mean 1.506064690026954; StDev 1.1440265033868804

Variable Format: numeric

Notes: UNF:6:/GagIOX6G5m/Mp202C+iMQ==

f1499 Location:

Summary Statistics: Max. 1.0; Valid 1484.0; StDev 0.036698775495458136; Min. 0.0; Mean 0.0013477088948787024

Variable Format: numeric

Notes: UNF:6:HyZClWcmCmfZSRBNbEEb2w==

f1499 Location:

Summary Statistics: Min. 0.0; Valid 1484.0; Mean 1.3888140161725093; Max. 6.0; StDev 0.7375189004828524

Variable Format: numeric

Notes: UNF:6:23jDGebienfY9I6PxtYQrg==

f1499 Location:

Summary Statistics: Max. 23.0; StDev 1.68765857116227; Min. 0.0; Valid 1484.0; Mean 2.0094339622641493

Variable Format: numeric

Notes: UNF:6:ARyj8BcGvbQES5VkrZ84nQ==

f1499 Location:

Summary Statistics: Valid 1484.0; Min. 0.0; StDev 0.6224117060536812; Mean 0.4818059299191378; Max. 5.0;

Variable Format: numeric

Notes: UNF:6:JaEcf0cHVBB9AVM5ZArStg==

f1499 Location:

Summary Statistics: Max. 201.0; StDev 20.99345331111098; Valid 1484.0; Min. 14.0; Mean 60.561994609164394

Variable Format: numeric

Notes: UNF:6:0nrmVDZaOgWWq24REBID3Q==

f1499 Location:

Variable Format: character

Notes: UNF:6:WwL6t52HJ3WhtTC8EWcBaQ==

f1525 Location:

Variable Format: character

Notes: UNF:6:fPkV5Ko7/iNV+nuh1NWkuA==

f1525 Location:

Variable Format: character

Notes: UNF:6:Sdz7G+9iUe7cgZNCOX/5hw==

f1525 Location:

Variable Format: character

Notes: UNF:6:hR+cGVOn4Nho4NuDIdBKIw==

f1525 Location:

Summary Statistics: Valid 3592.0; Min. 0.0; StDev 4.821732849703456; Max. 25.0; Mean 9.579064587973225;

Variable Format: numeric

Notes: UNF:6:fMXqfzIvBOVWwUp37arSfg==

f1525 Location:

Summary Statistics: Min. 0.0; Valid 3592.0; Max. 25.0; StDev 2.9359229622312633; Mean 1.1937639198218204

Variable Format: numeric

Notes: UNF:6:fxbFQI2XxlJmrkrP6sxooQ==

f1525 Location:

Summary Statistics: StDev 4.821732849703456; Mean 15.420935412026775; Max. 25.0; Valid 3592.0; Min. 0.0

Variable Format: numeric

Notes: UNF:6:BAth38jc78Z6Gz6iDJQFbQ==

f1525 Location:

Summary Statistics: Min. 0.0; Mean 23.80623608017818; StDev 2.935922962231264; Valid 3592.0; Max. 25.0

Variable Format: numeric

Notes: UNF:6:5kD4WcNxa35FUPlR0Vu4Og==

f1525 Location:

Summary Statistics: Min. 0.0; Valid 3592.0; StDev 19.286931398813824; Max. 100.0; Mean 38.3162583518929

Variable Format: numeric

Notes: UNF:6:JTF9iifh/5W6o5HErq1+aQ==

f1525 Location:

Summary Statistics: StDev 11.743691848925057; Valid 3592.0; Max. 100.0; Min. 0.0; Mean 95.22494432071272

Variable Format: numeric

Notes: UNF:6:2LaEjuUxvVgOR2aSiC5W8A==

f1525 Location:

Summary Statistics: Valid 3592.0; Min. 0.0; StDev NaN; Mean NaN; Max. Infinity;

Variable Format: numeric

Notes: UNF:6:t28nvCl5nWRM0KZWOjJPTw==

f1525 Location:

Summary Statistics: Valid 3592.0; StDev 0.010702064116963216; Max. 0.04879715369571884; Mean 0.00942949441131568; Min. 1.5821457204897244E-14

Variable Format: numeric

Notes: UNF:6:HTWjQYuQ86D4rH0sI038Eg==

f1525 Location:

Summary Statistics: Valid 3592.0; Mean 0.9434328503759392; Max. 1.0; StDev 0.2154367991328631; Min. 1.2207361735582567E-9;

Variable Format: numeric

Notes: UNF:6:ozzV+VhFNJMgnt7aTG2qKg==

f1525 Location:

Summary Statistics: Min. 2.4414723471165137E-10; Mean 0.24232646044839984; Valid 3592.0; Max. 0.7841086094917842; StDev 0.2102666719820398

Variable Format: numeric

Notes: UNF:6:GuG5eH7TQaEl6Nuwv7LhXQ==

f1525 Location:

Summary Statistics: Mean 1.0; Min. 1.0; Valid 3592.0; Max. 1.0; StDev 0.0

Variable Format: numeric

Notes: UNF:6:YxlafifurvWxc3inu7zlhQ==

f1525 Location:

Summary Statistics: Min. 0.0; Max. 1.0; Mean 0.9716035634743877; Valid 3592.0; StDev 0.16612574164429877

Variable Format: numeric

Notes: UNF:6:SGKcsEs9eg1kdDRhBUKIIg==

f1525 Location:

Summary Statistics: Valid 3592.0; Max. 1.0; Mean 0.24805122494432166; Min. 0.0; StDev 0.4319418435586271;

Variable Format: numeric

Notes: UNF:6:Jz2h7mZ5OcXTkm1m76jXOA==

f1525 Location:

Summary Statistics: StDev 0.0; Max. 1.0; Mean 1.0; Valid 3592.0; Min. 1.0

Variable Format: numeric

Notes: UNF:6:YxlafifurvWxc3inu7zlhQ==

f1525 Location:

Summary Statistics: Max. 1.0; Min. 1.0; Mean 1.0; Valid 3592.0; StDev 0.0;

Variable Format: numeric

Notes: UNF:6:YxlafifurvWxc3inu7zlhQ==

f1497 Location:

Variable Format: character

Notes: UNF:6:cf4HZDs3noEdCv2eakbREg==

f1497 Location:

Summary Statistics: StDev 332712.8411104588; Min. 28012.0; Mean 935460.6307277626; Valid 1484.0; Max. 2195410.0

Variable Format: numeric

Notes: UNF:6:GH+dvwd8HG3dCzJru1SgHg==

f1497 Location:

Summary Statistics: Mean 1263088.1280323465; Valid 1484.0; Max. 4649278.0; Min. 9300.0; StDev 670144.9066948249;

Variable Format: numeric

Notes: UNF:6:UeBePcvFMY7srHlW1hsO8w==

f1497 Location:

Summary Statistics: Valid 1484.0; Mean 1262507.011455525; Max. 4653678.0; StDev 669629.0227756081; Min. 9316.0

Variable Format: numeric

Notes: UNF:6:GXacekFLRWt5N3mO9lOh8Q==

f1497 Location:

Summary Statistics: StDev 332867.91772405175; Mean 935185.473045822; Max. 2209004.0; Min. 29182.0; Valid 1484.0;

Variable Format: numeric

Notes: UNF:6:Arh960wfonQz0ryP60/lYw==

f1497 Location:

Summary Statistics: Mean 0.22843201803463759; StDev 0.05807251304908572; Valid 1484.0; Max. 0.410457819710616; Min. 0.12523569473245;

Variable Format: numeric

Notes: UNF:6:rsFUJ77mPJ8LNunEKgvm1g==

f1497 Location:

Summary Statistics: Max. 0.374530981311956; Valid 1484.0; Mean 0.2716607858901129; StDev 0.05814845898867729; Min. 0.0830127375458578;

Variable Format: numeric

Notes: UNF:6:ycTgsKM3CtYO1vtYPoquxg==

f1497 Location:

Summary Statistics: StDev 0.057867109965473396; Min. 0.08315555515884; Max. 0.373875856640704; Valid 1484.0; Mean 0.2715997901953958

Variable Format: numeric

Notes: UNF:6:tN+Q1+JWzOOBj3xcD11ydQ==

f1497 Location:

Summary Statistics: Mean 0.22830740587985368; Min. 0.12635746731489; Valid 1484.0; StDev 0.057905062360065346; Max. 0.423373887584686;

Variable Format: numeric

Notes: UNF:6:8N98Vdj37F02yvlg+tyXng==

f1497 Location:

Summary Statistics: Mean 0.5432605760855087; Min. 0.166168292704698; Valid 1484.0; StDev 0.11595564971903011; Max. 0.74840683795266

Variable Format: numeric

Notes: UNF:6:WSdb9kA8NPaS8k+d8bL9CQ==

Label:

AGCT_count_V2.pl

application/octet-stream

Label:

Codon_counter-V1.pl

application/octet-stream

Label:

Codon_statistics-V2.pl

application/octet-stream

Label:

Compiled_supplementary_figures.pdf

Text:

A file that compiles all supplementary figures of the paper in a single file

application/pdf

Label:

Compiled_supplementary_tables.ods

Text:

Single file including the data of all supplementary tables of the paper

application/vnd.oasis.opendocument.spreadsheet

Label:

Fig_S1.pdf

application/pdf

Label:

Fig_S10.pdf

application/pdf

Label:

Fig_S11.pdf

application/pdf

Label:

Fig_S12.pdf

application/pdf

Label:

Fig_S13.pdf

application/pdf

Label:

Fig_S14.pdf

application/pdf

Label:

Fig_S15.pdf

application/pdf

Label:

Fig_S16.pdf

application/pdf

Label:

Fig_S17.pdf

application/pdf

Label:

Fig_S18A.pdf

application/pdf

Label:

Fig_S18B.pdf

application/pdf

Label:

Fig_S19.pdf

application/pdf

Label:

Fig_S2.pdf

application/pdf

Label:

Fig_S20.pdf

application/pdf

Label:

Fig_S21.pdf

application/pdf

Label:

Fig_S22.pdf

application/pdf

Label:

Fig_S23.pdf

application/pdf

Label:

Fig_S24A.pdf

application/pdf

Label:

Fig_S24B.pdf

application/pdf

Label:

Fig_S25.pdf

application/pdf

Label:

Fig_S3.pdf

application/pdf

Label:

Fig_S4.pdf

application/pdf

Label:

Fig_S5.pdf

application/pdf

Label:

Fig_S6.pdf

application/pdf

Label:

Fig_S7.pdf

application/pdf

Label:

Fig_S8.pdf

application/pdf

Label:

Fig_S9.pdf

application/pdf

Label:

Histogram-all-columns-compare-all_vs_high-bars.pl

application/octet-stream

Label:

Legends for supplementary figures and tables.pdf

Text:

Contains a list of figures and tables included in the dataset with their corresponding description. Please refer to "README.pdf" for a list and description of the scripts included in this dataset.

application/pdf

Label:

MANIFEST.TXT

text/plain

Label:

README.pdf

Text:

Contains a list and description of the scripts included in this dataset. Please refer to "Legends for supplementary figures and tables.pdf" for a list of figures and tables included in the dataset with their corresponding description.

application/pdf

Label:

RPSB-criteria-example.txt

text/plain

Label:

Table_S1.ods

application/vnd.oasis.opendocument.spreadsheet

Label:

Table_S3.ods

application/vnd.oasis.opendocument.spreadsheet

Label:

Table_S4.pdf

application/pdf

Label:

Table_S5.ods

application/vnd.oasis.opendocument.spreadsheet

Label:

Table_S6.ods

application/vnd.oasis.opendocument.spreadsheet

Label:

Table_S7-Codon_usage_considering_all_genes.txt

text/plain

Label:

Table_S8-Codon_usage_considering_high_expression_genes.txt

text/plain

Label:

batch-separate_file_by_gene_presence_and_plot_histograms-Wilcoxon.pl

application/octet-stream

Label:

batch-separate_file_by_gene_presence_and_plot_histograms.pl

application/octet-stream

Label:

codon_usage_by_gene_presence-ALL-V3.1.pl

application/octet-stream

Label:

codon_usage_by_gene_presence-ALL-Wilcoxon-V3.1.pl

application/octet-stream

Label:

codons.txt

text/plain

Label:

count_trnascan.pl

application/octet-stream

Label:

plot-codonusage-vs-GC-V3-High_expression-vs-all-genes.pl

application/octet-stream

Label:

plot-codonusage-vs-tRNAgenes-V3.pl

application/octet-stream

Label:

rpsblast-summary-V4.pl

application/octet-stream

Label:

separate_file_by_gene_presence-v2.pl

application/octet-stream

Label:

statistics-all-columns-V2.pl

application/octet-stream

Label:

trnascan_all_v2.pl

application/octet-stream