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RPCI-11 BES Pairs to Human Genome

RPCI-11 BES Pairs to Human Genome. Question how many RPCI-11 BES pairs can be placed on human genome? RPCI-11 BES Pairs Q20 bases >=350 bp, false negative by low quality sequences Unique bases >= 100 bp, false negative by repeats masking 30,030 BESs from 15,015 clones

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RPCI-11 BES Pairs to Human Genome

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  1. RPCI-11 BES Pairs to Human Genome • Question • how many RPCI-11 BES pairs can be placed on human genome? • RPCI-11 BES Pairs • Q20 bases >=350 bp, false negative by low quality sequences • Unique bases >= 100 bp, false negative by repeats masking • 30,030 BESs from 15,015 clones • Human GoldenPath 12dec2000 version • 3.25 Gb from assembled chromosomes • 83 Mb from random sequences • Two Step Searching • Human Genome vs. repeats-masked BES pairs (step 1) • Human Genome vs. unmasked copy of all ends from positive clones identified from step 1 • Identity >=95% & match length >= 0.5 BES read length

  2. RPCI-11 BES Paris to Human Genome Results • 99.5% average identity & 531 bp match length • 99.5% & 531 bp for assemblies, 98.3% & 484 bp for random reads • Total Clones Mapped: 14627 (97%) • Two ends: 11584 (77%) • One end: 3043 (20%) • 87% BESs have hits (83% unique hits), • 97% have unique chromosome hit • 93% have unique hit within one chromosome

  3. RPCI-11 BES Pairs to Human GenomeMore Searching • 87 % BESs placed on Genome • 13% not-mapped BES • Repeats Masking? • Searching unmasked BESs against the Genome • Identity & match length? false positives • Searching still goes on…

  4. RPCI-11 BES Pairs to Chromosomes 5, 16 & 19

  5. RPCI-11 BES Pairs to Chromosomes 20, 21 &22

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