This work was supported by the National Science Foundation under Grant No. 0822258-DFBI
Name Last modified Size Description
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.