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 - [   ] Gcyrtoloba_BES.clipped.gff.bz2 2012-08-08 16:43 876K Gcyrtoloba_BES.clipped aligned to G. max [   ] Gcyrtoloba_BES.fasta.bz2 2010-07-22 09:01 39M Glycine cyrtoloba BAC-end sequence [   ] Gcyrtoloba_BES.qual.bz2 2010-07-22 09:04 45M quality scores for Gcyrtoloba_BES.fasta [   ] Gcyrtoloba_BES.clipped.bz2 2010-07-22 09:04 34M quality-trimmed Gcyrtoloba_BES.fasta
Glycine cyrtoloba BAC-end sequence from the SoyMap II project
=============================================================

CONTENTS
========

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

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

    SOH
    AGI constructed library
    GC_Bb
    HindIII cut
    147kb average insert size
    12x genome coverage
    Complete set 288 plates
    Sequenced 200

    Sequencing stats:
    Phred20 Reads %ofReads
      0- 49  1804  1.2%     |X
     50- 99  1185  0.8%     |
    100-149   802  0.5%     |
    150-199   702  0.5%     |
    200-249   716  0.5%     |
    250-299   827  0.5%     |
    300-349   859  0.6%     |
    350-399   993  0.6%     |
    400-449  1294  0.8%     |
    450-499  1683  1.1%     |X
    500-549  2383  1.6%     |X
    550-599  3679  2.4%     |X
    600-649  6168  4.0%     |XX
    650-699 11801  7.7%     |XXXX
    700-749 23001 15.0%     |XXXXXXX
    750-799 38305 24.9%     |XXXXXXXXXXXX
    800-849 44642 29.1%     |XXXXXXXXXXXXXXX
    850-899 12427  8.1%     |XXXX
    900-949   329  0.2%     |

    Number of reads: 153,600
    Total bases: 138,204,169
    Total Phred 20 bases: 112,184,554
    Average length: 899.8
    Phred average: 730.4
    Phred average without failures: 738.0
    Percent failed: 1.1%

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

    Quality-trimmed BAC end reads from the file Gcyrtoloba_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 Gcyrtoloba_BES.clipped.gff.

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

    Total Reads

        150,528

    Aligned Reads

        113,422

    Reads having alignments with >= 90% coverage & identity

        20,869

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

        20,470

    Number of alignments for remaining reads

        27,472

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