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 - [   ] Gfalcata_BES.clipped.gff.bz2 2012-08-08 16:46 728K Gfalcata_BES.clipped aligned to G. max [   ] Gfalcata_BES.clipped.bz2 2010-10-28 15:32 31M quality-trimmed Gfalcata_BES.fasta [   ] Gfalcata_BES.fasta.bz2 2010-10-29 09:04 38M Glycine falcata BAC-end sequence [   ] Gfalcata_BES.qual.bz2 2010-10-29 09:03 50M quality scores for Gfalcata_BES.fasta
Glycine falcata BAC-end sequence from the SoyMap II project
=============================================================

CONTENTS
========

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

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

    SOI
    AGI constructed library
    GF_Ba
    HindIII cut
    146kb average insert size
    12x genome coverage
    Complete set 283 plates
    Sequenced 190

    Sequencing stats:
    Phred20 Reads %ofReads
      0- 49  2078  1.4%     |X
     50- 99  1069  0.7%     |
    100-149   602  0.4%     |
    150-199   602  0.4%     |
    200-249   612  0.4%     |
    250-299   781  0.5%     |
    300-349   906  0.6%     |
    350-399  1018  0.7%     |
    400-449  1230  0.8%     |
    450-499  1645  1.1%     |X
    500-549  2306  1.6%     |X
    550-599  3634  2.5%     |X
    600-649  6445  4.4%     |XX
    650-699 12120  8.3%     |XXXX
    700-749 22358 15.3%     |XXXXXXXX
    750-799 35690 24.5%     |XXXXXXXXXXXX
    800-849 38175 26.2%     |XXXXXXXXXXXXX
    850-899 13861  9.5%     |XXXXX
    900-949   786  0.5%     |
    950-999     2  0.0%     |

    Number of reads: 145,920
    Total bases: 138,901,523
    Total Phred 20 bases: 106,277,030
    Average length: 951.9
    Phred average: 728.3
    Phred average without failures: 737.6
    Percent failed: 1.3%

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

    Quality-trimmed BAC end reads from the file Gfalcata_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 Gfalcata_BES.clipped.gff.

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

    Total Reads

        142,489

    Aligned Reads

        119,176

    Reads having alignments with >= 90% coverage & identity

        16,909

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

        16,521

    Number of alignments for remaining reads

        22,013

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