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On the mm6 assembly, Ive found duplicate contigs that are placed on both chrY and chrY_random. Is this intentional?

April 26, 2017assembly contigs duplicate intentional mm6 Placed

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On the mm6 assembly, Ive found duplicate contigs that are placed on both chrY and chrY_random. Is this intentional?

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Response: On the mm6 assembly, chrY_random erroneously contains a region duplicated from chrY. Because NCBI discovered this assembly problem after the UCSC Genome Browser was processed, we were not able to remove it from mm6 prior to the browser’s release. The duplicated section occupies chrY:1-696,521 and chrY_random:29,615,053-30,311,573 (the end of the chromosome) and includes the following repeated fragments: • AC139318.5 • AC134433.3 • AC145392.2 • AC148319.2 • AC145571.3 • AC145393.4 The fragments are assembled into the contig NT_111995 for chrY_random and also appear (under different names) as regions on contigs MmY_110865_34, MmY_78990_34 and NT_078925.