Hello, This NNNs for this case represent ambiguity in the source contig used for this portion of the assembly. It is not a gap in the assembly.
To view this, open the first region in hg18, hide all tracks, then open Base Position, Assembly, and Gap as full. Thank you, Jennifer Jackson --------------------------------- Jennifer Jackson UCSC Genome Informatics Group http://genome.ucsc.edu/ On 6/7/10 7:24 AM, Qianqian Zhu wrote: > Hi Hiram, > I download the gap positions from tables browser. I found there are some > positions that are "N"s in the genome but didn't show up in the gap file. > For example: > chr2:31579444-31580294 > chr2:32945702-32946701 > chr2:32995197-32996196 > Do you know what are these regions if they are not gaps? > Thank you! > Sincerely, > Qianqian > > > On Sun, Jun 6, 2010 at 10:14 PM, Hiram Clawson<[email protected]> wrote: > >> From the public MySQL server: >> >> $ mysql --user=genome --host=genome-mysql.cse.ucsc.edu \ >> -A -e "select chrom,chromStart,chromEnd,type from gap;" hg18 >> >> Or, from the tables browser at genome.ucsc.edu >> Use the "gap" table. >> >> --Hiram >> >> Qianqian Zhu wrote: >> >>> Hi, >>> >>> I'm wondering where can I obtain the locations of assembly gaps in hg18. >>> Thank you! >>> >>> Sincerely, >>> Qianqian >>> _______________________________________________ >>> Genome maillist - [email protected] >>> https://lists.soe.ucsc.edu/mailman/listinfo/genome >>> >>> > _______________________________________________ > Genome maillist - [email protected] > https://lists.soe.ucsc.edu/mailman/listinfo/genome _______________________________________________ Genome maillist - [email protected] https://lists.soe.ucsc.edu/mailman/listinfo/genome
