Oligotyping Results for "mock-env-aligned"
A user-friendly interface to make sense of oligotyping results.

» A summary of what happened.

Oligotyping analysis was performed on 2,500 reads from 10 samples for "mock-env-aligned" with oligotyping pipeline version 0.96 (available from http://oligotyping.org) using 2 components automatically selected form the highest entropy values following the initial entropy analysis. To reduce the noise, each oligotype required to (1) appear in at least 1 sample, (2) occur in more than 1.0% of the reads for at least one sample, (3) represent a minimum of 0 reads in all samples combined, and (4) have a most abundant unique sequence with a minimum abundance of 0. Oligotypes that did not meet these criteria were removed from the analysis. The final number of quality controlled oligotypes revealed by the analysis was , and they represented 2478 reads, which was equivalent to 99.12% of all reads analyzed.

General Information

» Meta

Run date 26 Jul 13 13:45:28
Library version 0.96

» Given Parameters

Number of entropy components to be selected automatically2
Min number of samples oligotype expected to appear 1
Min % abundance of oligotype in at least one sample 1.0%
Min total abundance of oligotype in all samples 0
Min substantive abundance of an oligotype (-M) 0
Quality scores were provided False
Oligotype sets were requested to be generated False

» Components used for Oligotyping

Base locations of interest in the alignment 16, 62

» Quality filtering results

Number of sequences analyzed 2,500
Number of unique oligotypes (raw) 8
Oligotypes after "min number of samples" elimination 8
Oligotypes after "min % abundance in a sample" elimination 2
Number of sequences analyzed 2,500
Number of samples found 10
Number of sequences represented after quality filtering 2,478
Percentage of reads represented in results99.12%

» Files to analyze results further via third partry applications

Representative sequences per oligotypeoligo-representatives.fa.txt
Sample/oligotype abundance data matrix (percents)matrix_percents.txt
Sample/oligotype abundance data matrix (counts)matrix_counts.txt
Read distribution among samples tableread_distribution.txt
GEXF file for network analysisnetwork.gexf
Environment fileenvironment.txt
FASTA file for abundant oligotypesoligos.fa.txt
NEXUS file for abundant oligotypesoligos.nex.txt

» Entropy values that components were picked from


» Figure shows the oligotype distribution profiles among samples. TAB separated files matrix_percents.txt and matrix_counts.txt hold the information that were used to generate this figure.

Read Distribution per Sample

» Total number of reads for each sample that were analyzed.


» Abundant oligotypes along with their frequencies within the project are shown below. Every oligotype is followed by a representative sequence, which is the most frequent read in all reads that were collected by the given oligotype. Mouseover on an oligotype will popup a figure that shows the abundance distribution of unique sequences within the oligotype, along with the new entropy (in an ideal world there should be only one unique read with 0 entropy, but due to the random sequencing errors it is almost never the case). indicates that the most frequent sequence which was represented by the given oligotype hit something during the BLAST search with 100% identity in NCBI's nr database. In contrary, sign means that there was no perfect hit during the BLAST search.

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» Overview of samples.

Basic Analyses

» Deafult

» cluster_analysis






» nmds_analysis






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