SOLiD Software Development Community > Projects > SOLiD™ System E. Coli DH10B Mate-Pair

SOLiD™ System E.Coli DH10B Mate-Pair Data Set

Description

This data is sample re-sequencing data from DNA originating from E.Coli DH10B and is prepared using the SOLiD™ Mate-Paired Library Sequencing Kit from Applied Biosytems. These data are direct results from 1/16 of the panels of a run and statistical analysis outputs used to evaluate a mate-pair run. The mate pair run allows for the discovery of structural variations that would not be detected with non-mate pair runs. The mate pair run was able to discover a duplicated region in this E.Coli strain that could not have been detected from non-paired runs. This feature is made possible via mate distance information that is not contained in non-paired runs. This information is used in the mate pair data analysis to determine the exact position of tags that hit more than one place on the genome.

The "Consensus Sequence" and "SNP files" are also very useful for re-sequencing projects. Both of these files are generated based on the counts of reads that agree with the reference versus the reads that agree with the consensus. They also take into account other information generated by the system. There are not any SNPs present in our E. coli sequence. However, in this data we observe two reported SNPs in the SNPs file. These are most likely the result of errors due to a low coverage region (11x) and a mapping error. From this information one can determine an estimate of the accuracy of the whole pipeline, which in this case, it extremely high. Further information on the complete genome sequence of DH10B can be obtained from Durfee et. al. (J. Bacteriol 2008 190:2597-2606)

Licensing

This data is being licensed to you under the Applied Biosystems SOLiD™ System Data Use Agreement (Unsupported). Please read the license in its entirety and ensure that you understand the licensing conditions for use. Your use of this data indicates your acceptance of this licensing agreement. Click on this link to read the licensing agreement.

Support

This data is being released as "unsupported data" by Applied Bioysystems

Download

The diagram below describes the pipeline workflow and the various data fles that are downloadable for this data set. Click on a link in the table below the diagram to download a file.

Name on Figure	File name	Description
.csfasta	SHIRAZ_20080320_MP_2_Sample1_F3.csfasta.zip	Color space fasta file which contains the color calls generated for each tag, containing the color space calls with the last base of the template strand adaptor prepended
.csfasta	SHIRAZ_20080320_MP_2_Sample1_R3.csfasta.zip	Color space fasta file which contains the color calls generated for each tag, containing the color space calls with the last base of the template strand adaptor prepended
.qv	SHIRAZ_20080320_MP_2_Sample1_F3_QV.qual.zip	These are FASTA-like files that list the quality values in sequence order (not cycle order) for the color space calls (i.e. the QV maps to the csfasta file result and is calculated at the same time as the color call is made
.qv	SHIRAZ_20080320_MP_2_Sample1_R3_QV.qual.zip	These are FASTA-like files that list the quality values in sequence order (not cycle order) for the color space calls (i.e. the QV maps to the csfasta file result and is calculated at the same time as the color call is made
.bc.txt	SHIRAZ_20080320_MP_2_V1_F3.25.3.bc.txt.zip	This file reports the paired tags (as a single line) and the category that pairing falls into
.bc.txt	SHIRAZ_20080320_MP_2_V1_R3.25.3.bc.txt.zip	This file reports the paired tags (as a single line) and the category that pairing falls into
Coverage Files	fwd_rev_coverage.txt.zip	Contains information regarding the coverage of forward and reverse strand of each position. In this file there will be two columns. The first column contains the amount of time that particular forward strand base (in color space) is covered. The second column contains that the exact same information but for the reverse strand.
Stats.txt	SHIRAZ_20080320_MP_2_V1_F3.25.3.stats.txt.zip	The stats file contains a summary of the data for that run
Stats.txt	SHIRAZ_20080320_MP_2_V1_R3.25.3.stats.txt.zip	The stats file contains a summary of the data for that run
.ma	SHIRAZ_20080320_MP_2_Sample1_F3.csfasta.ma.25.3.zip	Color space fasta file containing matches to the reference sequence
.ma	SHIRAZ_20080320_MP_2_Sample1_R3.csfasta.ma.25.3.zip	Color space fasta file containing matches to the reference sequence
.mates	F3_R3.mates.zip	A comprehensive description of this file output is located here
gff	mates_v2_base.gff.gz	A comprehensive description of this file output is located here
SNPs	snps_sorted.txt.zip	File containing SNP calls for the run
Consensus fasta	bp_consensus_confirmed_sequence_with_Ns.fasta.zip	Contains information derived from the variation pipeline and is in base space. It reports the SNPs detected in the run.
Reference Genome (FASTA)	DH10B_WithDup_FinalEdit_validated.fasta.zip	Refererence Genome

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Description
Applied Biosystems SOLiD™ System E.Coli DH10B Mate-Pair Data
Developer Info
SOLiD™ System Developer
Trove Categorization
Development Status: 5 - Production/Stable Intended Audience: Developers, End Users/Desktop License: Applied Biosystems SOLiD™ System Data Use Agreement (Unsupported) Operating System: Not Applicable Programming Language: Not Applicable Spoken Language: Not Applicable Topic: Bio-Informatics

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SOLiD™ System E. Coli DH10B Mate-Pair