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RNA-Seq analysis

RNAseq_B4KT2B_Aminobacter_MD1 : RNAseq Projects

Mapping Overview

Raw Read Count

Analysis

IGV

DIM1 bwa Version: 0.7.4-r385 dir mRNAseq solexa

Total read number	12038669	100 %	Reads quality
Nb of unmapped reads	367497	3.05 %
Nb of reads mapped at least once	11671172	96.95 %
Nb of reads mapped on rRNA	107283	0.89 %
Nb of reliable reads	11039502	91.70 %
Nb of reads kept on chromosome AMD1_ AMD1_v1	10448764	86.79 %
Nb of reads kept on plasmid AMD1_pa AMD1_v1_p	533580	4.43 %
Nb of reads kept on plasmid AMD1_pc 23004	38476	0.32 %
Nb of reads kept on plasmid AMD1_pb 23005	18682	0.16 %
Total read count on genomic objects (except rRNA) for Organism	7320280	100 %
Total read count on genomic objects (except rRNA) into chromosome AMD1_ AMD1_v1	6723349	91.85 %
Total read count on genomic objects (except rRNA) into plasmid AMD1_pa AMD1_v1_p	549176	7.5 %
Total read count on genomic objects (except rRNA) into plasmid AMD1_pc 23004	29556	0.4 %
Total read count on genomic objects (except rRNA) into plasmid AMD1_pb 23005	18199	0.25 %
Download forward / reverse wig file	Download

DIM2 bwa Version: 0.7.4-r385 dir mRNAseq solexa

Total read number	13393161	100 %	Reads quality
Nb of unmapped reads	241564	1.80 %
Nb of reads mapped at least once	13151597	98.20 %
Nb of reads mapped on rRNA	2869658	21.43 %
Nb of reliable reads	9677668	72.26 %
Nb of reads kept on chromosome AMD1_ AMD1_v1	9174656	68.5 %
Nb of reads kept on plasmid AMD1_pa AMD1_v1_p	445766	3.33 %
Nb of reads kept on plasmid AMD1_pc 23004	37513	0.28 %
Nb of reads kept on plasmid AMD1_pb 23005	19733	0.15 %
Total read count on genomic objects (except rRNA) for Organism	6720048	100 %
Total read count on genomic objects (except rRNA) into chromosome AMD1_ AMD1_v1	6217007	92.51 %
Total read count on genomic objects (except rRNA) into plasmid AMD1_pa AMD1_v1_p	455683	6.78 %
Total read count on genomic objects (except rRNA) into plasmid AMD1_pc 23004	28474	0.42 %
Total read count on genomic objects (except rRNA) into plasmid AMD1_pb 23005	18884	0.28 %
Download forward / reverse wig file	Download

DIM3 bwa Version: 0.7.4-r385 dir mRNAseq solexa

Total read number	14388917	100 %	Reads quality
Nb of unmapped reads	389846	2.71 %
Nb of reads mapped at least once	13999071	97.29 %
Nb of reads mapped on rRNA	11834	0.08 %
Nb of reliable reads	13358677	92.84 %
Nb of reads kept on chromosome AMD1_ AMD1_v1	12610097	87.64 %
Nb of reads kept on plasmid AMD1_pa AMD1_v1_p	676510	4.7 %
Nb of reads kept on plasmid AMD1_pc 23004	49984	0.35 %
Nb of reads kept on plasmid AMD1_pb 23005	22086	0.15 %
Total read count on genomic objects (except rRNA) for Organism	9712646	100 %
Total read count on genomic objects (except rRNA) into chromosome AMD1_ AMD1_v1	8956257	92.21 %
Total read count on genomic objects (except rRNA) into plasmid AMD1_pa AMD1_v1_p	696106	7.17 %
Total read count on genomic objects (except rRNA) into plasmid AMD1_pc 23004	38442	0.4 %
Total read count on genomic objects (except rRNA) into plasmid AMD1_pb 23005	21841	0.22 %
Download forward / reverse wig file	Download

MTF1 bwa Version: 0.7.4-r385 dir mRNAseq solexa

Total read number	12954853	100 %	Reads quality
Nb of unmapped reads	327507	2.53 %
Nb of reads mapped at least once	12627346	97.47 %
Nb of reads mapped on rRNA	12476	0.10 %
Nb of reliable reads	12045758	92.98 %
Nb of reads kept on chromosome AMD1_ AMD1_v1	11423588	88.18 %
Nb of reads kept on plasmid AMD1_pa AMD1_v1_p	552223	4.26 %
Nb of reads kept on plasmid AMD1_pc 23004	49748	0.38 %
Nb of reads kept on plasmid AMD1_pb 23005	20199	0.16 %
Total read count on genomic objects (except rRNA) for Organism	8172864	100 %
Total read count on genomic objects (except rRNA) into chromosome AMD1_ AMD1_v1	7545620	92.33 %
Total read count on genomic objects (except rRNA) into plasmid AMD1_pa AMD1_v1_p	569319	6.97 %
Total read count on genomic objects (except rRNA) into plasmid AMD1_pc 23004	37986	0.46 %
Total read count on genomic objects (except rRNA) into plasmid AMD1_pb 23005	19939	0.24 %
Download forward / reverse wig file	Download

MTF2 bwa Version: 0.7.4-r385 dir mRNAseq solexa

Total read number	12529594	100 %	Reads quality
Nb of unmapped reads	330788	2.64 %
Nb of reads mapped at least once	12198806	97.36 %
Nb of reads mapped on rRNA	17471	0.14 %
Nb of reliable reads	11669622	93.14 %
Nb of reads kept on chromosome AMD1_ AMD1_v1	11011250	87.88 %
Nb of reads kept on plasmid AMD1_pa AMD1_v1_p	588127	4.69 %
Nb of reads kept on plasmid AMD1_pc 23004	51204	0.41 %
Nb of reads kept on plasmid AMD1_pb 23005	19041	0.15 %
Total read count on genomic objects (except rRNA) for Organism	8086361	100 %
Total read count on genomic objects (except rRNA) into chromosome AMD1_ AMD1_v1	7423578	91.8 %
Total read count on genomic objects (except rRNA) into plasmid AMD1_pa AMD1_v1_p	604479	7.48 %
Total read count on genomic objects (except rRNA) into plasmid AMD1_pc 23004	39541	0.49 %
Total read count on genomic objects (except rRNA) into plasmid AMD1_pb 23005	18763	0.23 %
Download forward / reverse wig file	Download

MTF3 bwa Version: 0.7.4-r385 dir mRNAseq solexa

Total read number	13312948	100 %	Reads quality
Nb of unmapped reads	290315	2.18 %
Nb of reads mapped at least once	13022633	97.82 %
Nb of reads mapped on rRNA	14124	0.11 %
Nb of reliable reads	12457687	93.58 %
Nb of reads kept on chromosome AMD1_ AMD1_v1	11688205	87.8 %
Nb of reads kept on plasmid AMD1_pa AMD1_v1_p	698290	5.25 %
Nb of reads kept on plasmid AMD1_pc 23004	51868	0.39 %
Nb of reads kept on plasmid AMD1_pb 23005	19324	0.15 %
Total read count on genomic objects (except rRNA) for Organism	8912629	100 %
Total read count on genomic objects (except rRNA) into chromosome AMD1_ AMD1_v1	8131685	91.24 %
Total read count on genomic objects (except rRNA) into plasmid AMD1_pa AMD1_v1_p	721225	8.09 %
Total read count on genomic objects (except rRNA) into plasmid AMD1_pc 23004	40464	0.45 %
Total read count on genomic objects (except rRNA) into plasmid AMD1_pb 23005	19255	0.22 %
Download forward / reverse wig file	Download

Sucrose1 bwa Version: 0.7.4-r385 dir mRNAseq solexa

Total read number	12759999	100 %	Reads quality
Nb of unmapped reads	295335	2.31 %
Nb of reads mapped at least once	12464664	97.69 %
Nb of reads mapped on rRNA	17491	0.14 %
Nb of reliable reads	11939300	93.57 %
Nb of reads kept on chromosome AMD1_ AMD1_v1	11694369	91.65 %
Nb of reads kept on plasmid AMD1_pa AMD1_v1_p	165597	1.3 %
Nb of reads kept on plasmid AMD1_pc 23004	57418	0.45 %
Nb of reads kept on plasmid AMD1_pb 23005	21916	0.17 %
Total read count on genomic objects (except rRNA) for Organism	8268263	100 %
Total read count on genomic objects (except rRNA) into chromosome AMD1_ AMD1_v1	8036805	97.2 %
Total read count on genomic objects (except rRNA) into plasmid AMD1_pa AMD1_v1_p	165921	2.01 %
Total read count on genomic objects (except rRNA) into plasmid AMD1_pc 23004	43929	0.53 %
Total read count on genomic objects (except rRNA) into plasmid AMD1_pb 23005	21608	0.26 %
Download forward / reverse wig file	Download

Sucrose2 bwa Version: 0.7.4-r385 dir mRNAseq solexa

Total read number	11621876	100 %	Reads quality
Nb of unmapped reads	274936	2.37 %
Nb of reads mapped at least once	11346940	97.63 %
Nb of reads mapped on rRNA	7996	0.07 %
Nb of reliable reads	10885112	93.66 %
Nb of reads kept on chromosome AMD1_ AMD1_v1	10672607	91.83 %
Nb of reads kept on plasmid AMD1_pa AMD1_v1_p	148887	1.28 %
Nb of reads kept on plasmid AMD1_pc 23004	45926	0.4 %
Nb of reads kept on plasmid AMD1_pb 23005	17692	0.15 %
Total read count on genomic objects (except rRNA) for Organism	7110910	100 %
Total read count on genomic objects (except rRNA) into chromosome AMD1_ AMD1_v1	6909611	97.17 %
Total read count on genomic objects (except rRNA) into plasmid AMD1_pa AMD1_v1_p	148635	2.09 %
Total read count on genomic objects (except rRNA) into plasmid AMD1_pc 23004	35349	0.5 %
Total read count on genomic objects (except rRNA) into plasmid AMD1_pb 23005	17315	0.24 %
Download forward / reverse wig file	Download

Sucrose3 bwa Version: 0.7.4-r385 dir mRNAseq solexa

Total read number	14169755	100 %	Reads quality
Nb of unmapped reads	318122	2.25 %
Nb of reads mapped at least once	13851633	97.75 %
Nb of reads mapped on rRNA	7754	0.05 %
Nb of reliable reads	13358060	94.27 %
Nb of reads kept on chromosome AMD1_ AMD1_v1	13092858	92.4 %
Nb of reads kept on plasmid AMD1_pa AMD1_v1_p	184396	1.3 %
Nb of reads kept on plasmid AMD1_pc 23004	59442	0.42 %
Nb of reads kept on plasmid AMD1_pb 23005	21364	0.15 %
Total read count on genomic objects (except rRNA) for Organism	8674449	100 %
Total read count on genomic objects (except rRNA) into chromosome AMD1_ AMD1_v1	8423867	97.11 %
Total read count on genomic objects (except rRNA) into plasmid AMD1_pa AMD1_v1_p	184124	2.12 %
Total read count on genomic objects (except rRNA) into plasmid AMD1_pc 23004	45618	0.53 %
Total read count on genomic objects (except rRNA) into plasmid AMD1_pb 23005	20840	0.24 %
Download forward / reverse wig file	Download