Data from the SoyMap II project: "Leveraging untapped genetic diversity in soybean", with these project sites: BAC-end and region data in browser context; Hudson-Alpha Intitute sequencing; Project outreach.

This work was supported by the National Science Foundation under Grant No. 0822258-DFBI

Icon  Name                              Last modified      Size  Description
[PARENTDIR] Parent Directory - [   ] GtomentellaD3_BES.clipped.bz2 2011-04-18 11:29 31M quality-trimmed GtomentellaD3_BES.fasta [   ] GtomentellaD3_BES.clipped.gff.bz2 2012-08-09 09:18 1.0M GtomentellaD3_BES.clipped aligned to G. max [   ] GtomentellaD3_BES.fasta.bz2 2011-04-18 11:30 36M Glycine tomentellaD3 BAC-end sequence [   ] GtomentellaD3_BES.qual.bz2 2011-04-18 11:31 41M quality scores for GtomentellaD3_BES.fasta
Glycine tomentella BAC-end sequence from the SoyMap II project
=============================================================

CONTENTS
========

    GtomentellaD3_BES.clipped.bz2     - quality-trimmed GtomentellaD3_BES.fasta
    GtomentellaD3_BES.clipped.gff.bz2 - GtomentellaD3_BES.clipped aligned to G. max
    GtomentellaD3_BES.fasta.bz2       - Glycine tomentella BAC-end sequence
    GtomentellaD3_BES.qual.bz2        - quality scores for GtomentellaD3_BES.fasta
    README.txt                        - This README file

BAC LIBRARY INFORMATION
=======================

    SOF
    AGI constructed library
    GT_DBa
    HindIII cut
    147kb average insert size
    12x genome coverage
    Complete set 262 plates
    Sequenced 180

    Sequencing stats:
    Phred20 Reads %ofReads
      0- 49   976  0.7%     |
     50- 99  1179  0.9%     |
    100-149   683  0.5%     |
    150-199   522  0.4%     |
    200-249   537  0.4%     |
    250-299   542  0.4%     |
    300-349   574  0.4%     |
    350-399   731  0.5%     |
    400-449   872  0.6%     |
    450-499  1140  0.8%     |
    500-549  1842  1.3%     |X
    550-599  2770  2.0%     |X
    600-649  4397  3.2%     |XX
    650-699  8671  6.3%     |XXX
    700-749 20029 14.5%     |XXXXXXX
    750-799 41114 29.7%     |XXXXXXXXXXXXXXX
    800-849 40337 29.2%     |XXXXXXXXXXXXXXX
    850-899 11008  8.0%     |XXXX
    900-949   316  0.2%     |

    Number of reads: 138,240
    Total bases: 123,817,120
    Total Phred 20 bases: 102,597,872
    Average length: 895.7
    Phred average: 742.2
    Phred average without failures: 746.4
    Percent failed: 0.6%

ALIGNMENT PROTOCOL
==================

    Quality-trimmed BAC end reads from the file GtomentellaD3_BES.clipped were
    aligned with LASTZ 1.02.00 using "--chain --gapped --ambiguous=n" and
    filtered by requiring a minimum of 90% coverage and 90% identity; if more
    than two alignments for a read satisfied this criteria, all alignments for
    the read were discarded unless at least one alignment was within
    1,000,000bp of a mate's alignment.

    The resulting alignments are available in GtomentellaD3_BES.clipped.gff.

ALIGNMENT STATISTICS
====================

    Total Reads

        135,828

    Aligned Reads

        105,575

    Reads having alignments with >= 90% coverage & identity

         23,982

    Reads remaining after filtering those with more than 2 alignments and no
    alignments within a 1,000,000bp window of a mate's alignment

         23,450

    Number of alignments for remaining reads

         31,164

ACKNOWLEDGEMENTS
================
This work was supported by the National Science Foundation under Grant No.
0822258-DFBI.