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RNA-Seq analysis

TAM_Ddeserti_VCD115 (De Groot et al, 2014, Genome Biol Evol 6:932 - Blanchard et al, 2017, MicrobiologyOpen 00:e477) : RNAseq Projects

Mapping Overview

Raw Read Count

Analysis

IGV

RD19-NI+TEX SSAHA2 version 2.5.1 dir mRNAseq solexa

Total read number	5284567	100 %	Reads quality
Nb of unmapped reads	982554	18.59 %
Nb of reads mapped at least once	4302013	81.41 %
Nb of reads mapped on rRNA	1133117	21.44 %
Nb of reliable reads	3035923	57.45 %
Nb of reads kept on chromosome Deide_ NC_012526	2608903	49.37 %
Nb of reads kept on plasmid Deide_2p NC_012529	199242	3.77 %
Nb of reads kept on plasmid Deide_1p NC_012527	130849	2.48 %
Nb of reads kept on plasmid Deide_3p NC_012528	96929	1.83 %
Total read count on genomic objects (except rRNA) for Organism	2163193	100 %
Total read count on genomic objects (except rRNA) into chromosome Deide_ NC_012526	1956750	90.46 %
Total read count on genomic objects (except rRNA) into plasmid Deide_1p NC_012527	70202	3.25 %
Total read count on genomic objects (except rRNA) into plasmid Deide_3p NC_012528	68974	3.19 %
Total read count on genomic objects (except rRNA) into plasmid Deide_2p NC_012529	67267	3.11 %
Download forward / reverse wig file	Download

RD19-NI SSAHA2 version 2.5.1 dir mRNAseq solexa

Total read number	4145852	100 %	Reads quality
Nb of unmapped reads	67640	1.63 %
Nb of reads mapped at least once	4078212	98.37 %
Nb of reads mapped on rRNA	990220	23.88 %
Nb of reliable reads	2891224	69.74 %
Nb of reads kept on chromosome Deide_ NC_012526	2469967	59.58 %
Nb of reads kept on plasmid Deide_2p NC_012529	181124	4.37 %
Nb of reads kept on plasmid Deide_1p NC_012527	135814	3.28 %
Nb of reads kept on plasmid Deide_3p NC_012528	104319	2.52 %
Total read count on genomic objects (except rRNA) for Organism	2416580	100 %
Total read count on genomic objects (except rRNA) into chromosome Deide_ NC_012526	2108590	87.26 %
Total read count on genomic objects (except rRNA) into plasmid Deide_2p NC_012529	127431	5.27 %
Total read count on genomic objects (except rRNA) into plasmid Deide_1p NC_012527	96317	3.99 %
Total read count on genomic objects (except rRNA) into plasmid Deide_3p NC_012528	84242	3.49 %
Download forward / reverse wig file	Download

RD19-IR+TEX SSAHA2 version 2.5.1 dir mRNAseq solexa

Total read number	6404558	100 %	Reads quality
Nb of unmapped reads	1246290	19.46 %
Nb of reads mapped at least once	5158268	80.54 %
Nb of reads mapped on rRNA	1509295	23.57 %
Nb of reliable reads	3526398	55.06 %
Nb of reads kept on chromosome Deide_ NC_012526	3088196	48.22 %
Nb of reads kept on plasmid Deide_2p NC_012529	196487	3.07 %
Nb of reads kept on plasmid Deide_1p NC_012527	146319	2.28 %
Nb of reads kept on plasmid Deide_3p NC_012528	95396	1.49 %
Total read count on genomic objects (except rRNA) for Organism	2078803	100 %
Total read count on genomic objects (except rRNA) into chromosome Deide_ NC_012526	1860487	89.5 %
Total read count on genomic objects (except rRNA) into plasmid Deide_1p NC_012527	76388	3.67 %
Total read count on genomic objects (except rRNA) into plasmid Deide_2p NC_012529	74023	3.56 %
Total read count on genomic objects (except rRNA) into plasmid Deide_3p NC_012528	67905	3.27 %
Download forward / reverse wig file	Download

RD19-IR SSAHA2 version 2.5.1 dir mRNAseq solexa

Total read number	4535823	100 %	Reads quality
Nb of unmapped reads	74191	1.64 %
Nb of reads mapped at least once	4461632	98.36 %
Nb of reads mapped on rRNA	1282308	28.27 %
Nb of reliable reads	3047736	67.19 %
Nb of reads kept on chromosome Deide_ NC_012526	2595690	57.23 %
Nb of reads kept on plasmid Deide_2p NC_012529	219877	4.85 %
Nb of reads kept on plasmid Deide_1p NC_012527	144149	3.18 %
Nb of reads kept on plasmid Deide_3p NC_012528	88020	1.94 %
Total read count on genomic objects (except rRNA) for Organism	2441824	100 %
Total read count on genomic objects (except rRNA) into chromosome Deide_ NC_012526	2102642	86.11 %
Total read count on genomic objects (except rRNA) into plasmid Deide_2p NC_012529	167008	6.84 %
Total read count on genomic objects (except rRNA) into plasmid Deide_1p NC_012527	100583	4.12 %
Total read count on genomic objects (except rRNA) into plasmid Deide_3p NC_012528	71591	2.93 %
Download forward / reverse wig file	Download

RD42-NI SSAHA2 version 2.5.1 dir mRNAseq solexa

Total read number	43980748	100 %	Reads quality
Nb of unmapped reads	960107	2.18 %
Nb of reads mapped at least once	43020641	97.82 %
Nb of reads mapped on rRNA	6011070	13.67 %
Nb of reliable reads	35360333	80.40 %
Nb of reads kept on chromosome Deide_ NC_012526	29607711	67.32 %
Nb of reads kept on plasmid Deide_2p NC_012529	2539461	5.77 %
Nb of reads kept on plasmid Deide_1p NC_012527	1848882	4.2 %
Nb of reads kept on plasmid Deide_3p NC_012528	1364279	3.1 %
Total read count on genomic objects (except rRNA) for Organism	31364336	100 %
Total read count on genomic objects (except rRNA) into chromosome Deide_ NC_012526	26808328	85.47 %
Total read count on genomic objects (except rRNA) into plasmid Deide_2p NC_012529	2032651	6.48 %
Total read count on genomic objects (except rRNA) into plasmid Deide_1p NC_012527	1414696	4.51 %
Total read count on genomic objects (except rRNA) into plasmid Deide_3p NC_012528	1108661	3.53 %
Download forward / reverse wig file	Download

RD42-IR SSAHA2 version 2.5.1 dir mRNAseq solexa

Total read number	38850426	100 %	Reads quality
Nb of unmapped reads	1593197	4.10 %
Nb of reads mapped at least once	37257229	95.90 %
Nb of reads mapped on rRNA	11575479	29.79 %
Nb of reliable reads	20432060	52.59 %
Nb of reads kept on chromosome Deide_ NC_012526	17869411	46 %
Nb of reads kept on plasmid Deide_2p NC_012529	1090088	2.81 %
Nb of reads kept on plasmid Deide_1p NC_012527	928983	2.39 %
Nb of reads kept on plasmid Deide_3p NC_012528	543578	1.4 %
Total read count on genomic objects (except rRNA) for Organism	18025609	100 %
Total read count on genomic objects (except rRNA) into chromosome Deide_ NC_012526	16018225	88.86 %
Total read count on genomic objects (except rRNA) into plasmid Deide_2p NC_012529	911248	5.06 %
Total read count on genomic objects (except rRNA) into plasmid Deide_1p NC_012527	644297	3.57 %
Total read count on genomic objects (except rRNA) into plasmid Deide_3p NC_012528	451839	2.51 %
Download forward / reverse wig file	Download

RD62-NI SSAHA2 version 2.5.1 dir mRNAseq solexa

Total read number	46512614	100 %	Reads quality
Nb of unmapped reads	1139768	2.45 %
Nb of reads mapped at least once	45372846	97.55 %
Nb of reads mapped on rRNA	9828798	21.13 %
Nb of reliable reads	29788867	64.04 %
Nb of reads kept on chromosome Deide_ NC_012526	26292504	56.53 %
Nb of reads kept on plasmid Deide_2p NC_012529	1371565	2.95 %
Nb of reads kept on plasmid Deide_1p NC_012527	1260718	2.71 %
Nb of reads kept on plasmid Deide_3p NC_012528	864080	1.86 %
Total read count on genomic objects (except rRNA) for Organism	25738206	100 %
Total read count on genomic objects (except rRNA) into chromosome Deide_ NC_012526	23165989	90.01 %
Total read count on genomic objects (except rRNA) into plasmid Deide_2p NC_012529	1043386	4.05 %
Total read count on genomic objects (except rRNA) into plasmid Deide_1p NC_012527	833461	3.24 %
Total read count on genomic objects (except rRNA) into plasmid Deide_3p NC_012528	695370	2.7 %
Download forward / reverse wig file	Download

RD62-IR SSAHA2 version 2.5.1 dir mRNAseq solexa

Total read number	41492855	100 %	Reads quality
Nb of unmapped reads	1042587	2.51 %
Nb of reads mapped at least once	40450268	97.49 %
Nb of reads mapped on rRNA	11285355	27.20 %
Nb of reliable reads	26603880	64.12 %
Nb of reads kept on chromosome Deide_ NC_012526	23697831	57.11 %
Nb of reads kept on plasmid Deide_2p NC_012529	1245093	3 %
Nb of reads kept on plasmid Deide_1p NC_012527	1064057	2.56 %
Nb of reads kept on plasmid Deide_3p NC_012528	596899	1.44 %
Total read count on genomic objects (except rRNA) for Organism	21539440	100 %
Total read count on genomic objects (except rRNA) into chromosome Deide_ NC_012526	19439929	90.25 %
Total read count on genomic objects (except rRNA) into plasmid Deide_2p NC_012529	966327	4.49 %
Total read count on genomic objects (except rRNA) into plasmid Deide_1p NC_012527	648353	3.01 %
Total read count on genomic objects (except rRNA) into plasmid Deide_3p NC_012528	484831	2.25 %
Download forward / reverse wig file	Download