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 - [   ] Gstenophita_BES.clipped.gff.bz2 2012-08-08 16:51 687K Gstenophita_BES.clipped aligned to G. max [   ] Gstenophita_BES.clipped.bz2 2010-04-18 11:14 21M quality-trimmed Gstenophita_BES.fasta [   ] Gstenophita_BES.fasta.bz2 2010-04-18 11:15 27M Glycine stenophita BAC-end sequence [   ] Gstenophita_BES.qual.bz2 2010-04-18 11:15 35M quality scores for Gstenophita_BES.fasta
Glycine stenophita BAC-end sequence from the SoyMap II project
=============================================================

CONTENTS
========

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

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

    SOK
    AGI constructed library
    GS_ABa
    HindIII cut
    149kb average insert size
    12x genome coverage
    Complete set 175 plates
    Sequencing 120

    Sequencing stats:
    Phred20 Reads %ofReads
      0- 49  3849  4.2%     |XX
     50- 99  1026  1.1%     |X
    100-149   682  0.7%     |
    150-199   565  0.6%     |
    200-249   531  0.6%     |
    250-299   474  0.5%     |
    300-349   524  0.6%     |
    350-399   606  0.7%     |
    400-449   689  0.7%     |
    450-499   893  1.0%     |
    500-549  1223  1.3%     |X
    550-599  1851  2.0%     |X
    600-649  3049  3.3%     |XX
    650-699  5827  6.3%     |XXX
    700-749 11198 12.2%     |XXXXXX
    750-799 19290 20.9%     |XXXXXXXXXX
    800-849 23664 25.7%     |XXXXXXXXXXXXX
    850-899 14484 15.7%     |XXXXXXXX
    900-949  1731  1.9%     |X
    950-999     4  0.0%     |

    Number of reads: 92,160
    Total bases: 94,599,393
    Total Phred 20 bases: 66,041,381
    Average length: 1026.5
    Phred average: 716.6
    Phred average without failures: 745.2
    Percent failed: 3.9%

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

    Quality-trimmed BAC end reads from the file Gstenophita_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 Gstenophita_BES.clipped.gff.

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

    Total Reads

        86,958

    Aligned Reads

        71,263

    Reads having alignments with >= 90% coverage & identity

        16,078

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

        15,749

    Number of alignments for remaining reads

        20,838

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