All open Assembly Issues


  7 issues

Issue Version Chr Position Description Resolution Status
ASMBLY-3 RefGen_B73 v2 Chr1 unknown From Goettel and Messing PMID 19521498, the B73_v2 sequence on chr 1 is missing over 50% of the nearly identical tandem repeats of the B73 p1 gene, along with a chimeric 'gene'. Open
ASMBLY-1105 RefGen_B73 v4 Chr2 unknown Zm00001d000236, gene b1, is located on contig 44 in Zm-REFERENCE-GRAMENE-4.0, but was located on chromosome 2 as GRMZM2G172795 in B73 RefGen_v3. It should be placed on chromosome 2 instead. Open
ASMBLY-8 RefGen_B73 v3 Chr3 86,902,257 - 91,676,886 Per Ganal et al 2011 (PMID 22174790) Fig 6, this region is bracketed by 2 SNP: rs132018591 and rs132020236, on B73_V2 the region in bp: CHR3.86,902,257..91,676,886. The region is inverted in the assembly compared to genetic map data. Open
ASMBLY-1081 RefGen_B73 v2 Chr4 unknown There is an inversion in nongene sequence downstream of B73_V2 gene model GRMZM2G008913; based on Genbank sequence accession X58700 (Classical genes list, Schnable J & Freeeling M 2011 PLoS One 108:4069-74 ). Strand 1 Open
ASMBLY-5 RefGen_B73 v3 Chr6 unknown Chromosome 6 FPC contigs # 277 and 280 order should be reversed, based on 1. genetic map coordinate of chromosome anchors ctg277 umc1857 203.3 iCM on IBM2 6 ctg 280 pl1 211.5 iCM on IBM2 6 2. Fig 7, and Table 8 data for region 6.2 described in Ganal et al 2011 PUBMED ID 22174790; over 20,000 SNP mapped on high resolution IBM population, using the 55K SNP chip array from Illumina. The region for IBM map order not consistent with the assembly can be corrected if the 2 contigs were switched. Open
ASMBLY-11 RefGen_B73 v4 Chr6 unknown Chromosome 6 FPC contigs # 277 and 280 order should be reversed, based on: 1. genetic map coordinate of chromosome anchors ctg277 umc1857 203.3 iCM on IBM2 6 ctg 280 pl1 211.5 iCM on IBM2 6 2. Fig 7, and Table 8 data for region 6.2 described in Ganal et al 2011; PMID 22174790; over 20,000 SNP mapped on high resolution IBM population, using the 55K SNP chip array from Illumina. Open
ASMBLY-216 RefGen_B73 v3 Chr9 unknown Long arm of chromosome 9 has a ~1.8Mb nuclear mitochondrial DNA copy (NUMT) near the centromere that is largely absent from the B73 reference genome assembly. (K Newton personal communication; Lough AN et al 2008 Genetics 178:47-55; Lough AN et al 2015 G3 5:2229-2239) Open