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 - [   ] Gsoja_BES.qual.bz2 2010-02-16 17:04 63M quality scores for Gsoja_BES.fasta [   ] Gsoja_BES.fasta.bz2 2010-02-16 17:02 50M Glycine soja BAC-end sequence [   ] Gsoja_BES.clipped.gff.bz2 2012-08-09 09:39 4.9M Gsoja_BES.clipped aligned to G. max [   ] Gsoja_BES.clipped.bz2 2010-02-16 17:05 41M quality-trimmed Gsoja_BES.fasta
Glycine soja BAC-end sequence from the SoyMap II project
=============================================================

CONTENTS
========

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

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

    SOD
    AGI constructed library
    GSS_Ba
    HindIII cut
    150kb average insert size
    12x genome coverage
    Complete set 240 plates
    Sequenced 240

    Sequencing stats:
    Phred20 Reads %ofReads
      0- 49  2486  1.3%     |X
     50- 99  1282  0.7%     |
    100-149   905  0.5%     |
    150-199   839  0.5%     |
    200-249   904  0.5%     |
    250-299   930  0.5%     |
    300-349  1066  0.6%     |
    350-399  1411  0.8%     |
    400-449  1786  1.0%     |
    450-499  2362  1.3%     |X
    500-549  3422  1.9%     |X
    550-599  4810  2.6%     |X
    600-649  6780  3.7%     |XX
    650-699 11547  6.3%     |XXX
    700-749 24218 13.1%     |XXXXXXX
    750-799 39229 21.3%     |XXXXXXXXXXX
    800-849 46936 25.5%     |XXXXXXXXXXXXX
    850-899 29748 16.1%     |XXXXXXXX
    900-949  3640  2.0%     |X
    950-999    19  0.0%     |

    Number of reads: 184,320
    Total bases: 178,074,447
    Total Phred 20 bases: 136,188,824
    Average length: 966.1
    Phred average: 738.9
    Phred average without failures: 747.9
    Percent failed: 1.2%

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

    Quality-trimmed BAC end reads from the file Gsoja_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 mate-pairing resulted, in
    which case all non-paired alignments for the BES were discarded. Mates
    were paired if and only if the resulting BAC insert spanned a region
    between 5,000bp and 300,000bp, and there was only one such pairing
    possible for each mate. 

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

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

    Total Reads

        180,099

    Aligned Reads

        179,987

    Reads having alignments with >= 90% coverage & identity

        171,264

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

        144,998

    Number of alignments for remaining reads

        176,545

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