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 - [   ] Gdolichocarpa_BES.clipped.bz2 2010-02-16 17:10 61M quality-trimmed Gdolichocarpa_BES.fasta [   ] Gdolichocarpa_BES.clipped.gff.bz2 2012-08-08 16:45 1.9M Gdolichocarpa_BES.clipped aligned to G. max [   ] Gdolichocarpa_BES.fasta.bz2 2010-02-16 17:07 72M Glycine dolichocarpa BAC-end sequence [   ] Gdolichocarpa_BES.qual.bz2 2010-02-16 17:09 82M quality scores for Gdolichocarpa_BES.fasta
Glycine dolichocarpa BAC-end sequence from the SoyMap II project
=============================================================

CONTENTS
========

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

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

    SOE
    AGI constructed library
    GD_TBa
    HindIII cut
    151kb average insert size
    11x genome coverage
    Complete set 455 plates
    Sequenced 350

    Sequencing stats:
    Phred20 Reads %ofReads
      0- 49  3083  1.1%     |X
     50- 99  2501  0.9%     |
    100-149  1449  0.5%     |
    150-199  1100  0.4%     |
    200-249  1149  0.4%     |
    250-299  1179  0.4%     |
    300-349  1174  0.4%     |
    350-399  1423  0.5%     |
    400-449  1981  0.7%     |
    450-499  2954  1.1%     |X
    500-549  4587  1.7%     |X
    550-599  5876  2.2%     |X
    600-649  7914  2.9%     |X
    650-699 14965  5.6%     |XXX
    700-749 31225 11.6%     |XXXXXX
    750-799 59859 22.3%     |XXXXXXXXXXX
    800-849 82699 30.8%     |XXXXXXXXXXXXXXX
    850-899 40599 15.1%     |XXXXXXXX
    900-949  3073  1.1%     |X
    950-999    10  0.0%     |

    Number of reads: 268,800
    Total bases: 249,614,265
    Total Phred 20 bases: 200,666,708
    Average length: 928.6
    Phred average: 746.5
    Phred average without failures: 754.0
    Percent failed: 1.0%

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

    Quality-trimmed BAC end reads from the file Gdolichocarpa_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 Gdolichocarpa_BES.clipped.gff.

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

    Total Reads

        262,738

    Aligned Reads

        206,118

    Reads having alignments with >= 90% coverage & identity

        45,885

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

        44,905

    Number of alignments for remaining reads

        59,516

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