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 - [   ] Gsyndetika_BES.fasta.bz2 2010-04-26 14:38 41M Glycine syndetika BAC-end sequence [   ] Gsyndetika_BES.clipped.bz2 2010-04-26 14:38 34M quality-trimmed Gsyndetika_BES.fasta [   ] Gsyndetika_BES.qual.bz2 2010-04-26 14:43 49M quality scores for Gsyndetika_BES.fasta [   ] Gsyndetika_BES.clipped.gff.bz2 2012-08-09 09:30 1.4M Gsyndetika_BES.clipped aligned to G. max
Glycine syndetika BAC-end sequence from the SoyMap II project
=============================================================

CONTENTS
========

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

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

    SOG
    AGI constructed library
    GS_Ba
    HindIII cut
    168kb average insert size
    14x genome coverage
    Complete set 292 plates
    Sequenced 200

    Sequencing stats:
    Phred20 Reads %ofReads
      0- 49  2627  1.7%     |X
     50- 99  1356  0.9%     |
    100-149   811  0.5%     |
    150-199   670  0.4%     |
    200-249   667  0.4%     |
    250-299   643  0.4%     |
    300-349   756  0.5%     |
    350-399   864  0.6%     |
    400-449  1135  0.7%     |
    450-499  1687  1.1%     |X
    500-549  2800  1.8%     |X
    550-599  4069  2.6%     |X
    600-649  5973  3.9%     |XX
    650-699 10319  6.7%     |XXX
    700-749 20334 13.2%     |XXXXXXX
    750-799 36055 23.5%     |XXXXXXXXXXXX
    800-849 45305 29.5%     |XXXXXXXXXXXXXXX
    850-899 17019 11.1%     |XXXXXX
    900-949   510  0.3%     |

    Number of reads: 153,600
    Total bases: 142,723,366
    Total Phred 20 bases: 112,381,753
    Average length: 929.2
    Phred average: 731.7
    Phred average without failures: 743.0
    Percent failed: 1.6%

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

    Quality-trimmed BAC end reads from the file Gsyndetika_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 Gsyndetika_BES.clipped.gff.

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

    Total Reads

        148,982

    Aligned Reads

        121,361

    Reads having alignments with >= 90% coverage & identity

         32,936

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

         32,328

    Number of alignments for remaining reads

         43,403

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