This work was supported by the National Science Foundation under Grant No. 0822258-DFBI
Name Last modified Size Description
Parent Directory - Gcyrtoloba_BES.qual.bz2 2010-07-22 09:04 45M quality scores for Gcyrtoloba_BES.fasta Gcyrtoloba_BES.fasta.bz2 2010-07-22 09:01 39M Glycine cyrtoloba BAC-end sequence Gcyrtoloba_BES.clipped.gff.bz2 2012-08-08 16:43 876K Gcyrtoloba_BES.clipped aligned to G. max Gcyrtoloba_BES.clipped.bz2 2010-07-22 09:04 34M quality-trimmed Gcyrtoloba_BES.fasta
Glycine cyrtoloba BAC-end sequence from the SoyMap II project ============================================================= CONTENTS ======== Gcyrtoloba_BES.clipped.bz2 - quality-trimmed Gcyrtoloba_BES.fasta Gcyrtoloba_BES.clipped.gff.bz2 - Gcyrtoloba_BES.clipped aligned to G. max Gcyrtoloba_BES.fasta.bz2 - Glycine cyrtoloba BAC-end sequence Gcyrtoloba_BES.qual.bz2 - quality scores for Gcyrtoloba_BES.fasta README.txt - This README file BAC LIBRARY INFORMATION ======================= SOH AGI constructed library GC_Bb HindIII cut 147kb average insert size 12x genome coverage Complete set 288 plates Sequenced 200 Sequencing stats: Phred20 Reads %ofReads 0- 49 1804 1.2% |X 50- 99 1185 0.8% | 100-149 802 0.5% | 150-199 702 0.5% | 200-249 716 0.5% | 250-299 827 0.5% | 300-349 859 0.6% | 350-399 993 0.6% | 400-449 1294 0.8% | 450-499 1683 1.1% |X 500-549 2383 1.6% |X 550-599 3679 2.4% |X 600-649 6168 4.0% |XX 650-699 11801 7.7% |XXXX 700-749 23001 15.0% |XXXXXXX 750-799 38305 24.9% |XXXXXXXXXXXX 800-849 44642 29.1% |XXXXXXXXXXXXXXX 850-899 12427 8.1% |XXXX 900-949 329 0.2% | Number of reads: 153,600 Total bases: 138,204,169 Total Phred 20 bases: 112,184,554 Average length: 899.8 Phred average: 730.4 Phred average without failures: 738.0 Percent failed: 1.1% ALIGNMENT PROTOCOL ================== Quality-trimmed BAC end reads from the file Gcyrtoloba_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 Gcyrtoloba_BES.clipped.gff. ALIGNMENT STATISTICS ==================== Total Reads 150,528 Aligned Reads 113,422 Reads having alignments with >= 90% coverage & identity 20,869 Reads remaining after filtering those with more than 2 alignments and no alignments within a 1,000,000bp window of a mate's alignment 20,470 Number of alignments for remaining reads 27,472 ACKNOWLEDGEMENTS ================ This work was supported by the National Science Foundation under Grant No. 0822258-DFBI.