This work was supported by the National Science Foundation under Grant No. 0822258-DFBI
Name Last modified Size Description
Parent Directory - GtomentellaD3_BES.clipped.gff.bz2 2012-08-09 09:18 1.0M GtomentellaD3_BES.clipped aligned to G. max GtomentellaD3_BES.clipped.bz2 2011-04-18 11:29 31M quality-trimmed GtomentellaD3_BES.fasta GtomentellaD3_BES.fasta.bz2 2011-04-18 11:30 36M Glycine tomentellaD3 BAC-end sequence GtomentellaD3_BES.qual.bz2 2011-04-18 11:31 41M quality scores for GtomentellaD3_BES.fasta
Glycine tomentella BAC-end sequence from the SoyMap II project ============================================================= CONTENTS ======== GtomentellaD3_BES.clipped.bz2 - quality-trimmed GtomentellaD3_BES.fasta GtomentellaD3_BES.clipped.gff.bz2 - GtomentellaD3_BES.clipped aligned to G. max GtomentellaD3_BES.fasta.bz2 - Glycine tomentella BAC-end sequence GtomentellaD3_BES.qual.bz2 - quality scores for GtomentellaD3_BES.fasta README.txt - This README file BAC LIBRARY INFORMATION ======================= SOF AGI constructed library GT_DBa HindIII cut 147kb average insert size 12x genome coverage Complete set 262 plates Sequenced 180 Sequencing stats: Phred20 Reads %ofReads 0- 49 976 0.7% | 50- 99 1179 0.9% | 100-149 683 0.5% | 150-199 522 0.4% | 200-249 537 0.4% | 250-299 542 0.4% | 300-349 574 0.4% | 350-399 731 0.5% | 400-449 872 0.6% | 450-499 1140 0.8% | 500-549 1842 1.3% |X 550-599 2770 2.0% |X 600-649 4397 3.2% |XX 650-699 8671 6.3% |XXX 700-749 20029 14.5% |XXXXXXX 750-799 41114 29.7% |XXXXXXXXXXXXXXX 800-849 40337 29.2% |XXXXXXXXXXXXXXX 850-899 11008 8.0% |XXXX 900-949 316 0.2% | Number of reads: 138,240 Total bases: 123,817,120 Total Phred 20 bases: 102,597,872 Average length: 895.7 Phred average: 742.2 Phred average without failures: 746.4 Percent failed: 0.6% ALIGNMENT PROTOCOL ================== Quality-trimmed BAC end reads from the file GtomentellaD3_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 GtomentellaD3_BES.clipped.gff. ALIGNMENT STATISTICS ==================== Total Reads 135,828 Aligned Reads 105,575 Reads having alignments with >= 90% coverage & identity 23,982 Reads remaining after filtering those with more than 2 alignments and no alignments within a 1,000,000bp window of a mate's alignment 23,450 Number of alignments for remaining reads 31,164 ACKNOWLEDGEMENTS ================ This work was supported by the National Science Foundation under Grant No. 0822258-DFBI.