I want to browse the “QCed genomic constraint by 1kb regions” file included in the v3 Download tab to check the chromosomal coordinates of the 1kb bin over a gene in chromosome 19.
However, when I download the file, I can only see the rows and columns mentioned in the README file for chromosome 1 (the table has only 592 rows, when the file should include constraint Z scores of 1,984,900 tiling 1kb genomic windows).
Any ideas?
Thanks!!
Can you confirm which file you downloaded? I just downloaded https://storage.googleapis.com/gcp-public-data--gnomad/release/3.1/secondary_analyses/genomic_constraint/constraint_z_genome_1kb.qc.download.txt.gz and see that this file has 1984901 lines, including chr19, e.g.:
chr19 244000 245000 chr19-244000-245000 2408.0 165.2039039396319 181.0 1.0956157553403836 -1.2289652786964134
chr19 246000 247000 chr19-246000-247000 1362.0 173.42931486384606 190.0 1.0955471982874585 -1.2582855552151662
chr19 252000 253000 chr19-252000-253000 2942.0 203.37643403448465 206.0 1.0129000490050408 -0.1839677404413773
chr19 253000 254000 chr19-253000-254000 2786.0 186.8963559019949 172.0 0.920296167198646 1.0896314331745702
chr19 257000 258000 chr19-257000-258000 2677.0 194.65193521570941 150.0 0.7706062610360025 3.2004490889732597
chr19 260000 261000 chr19-260000-261000 2273.0 181.25848213659543 162.0 0.8937512776804434 1.4304506705326363
chr19 261000 262000 chr19-261000-262000 1798.0 137.73041493900166 133.0 0.9656545365009124 0.4030735585758758
chr19 262000 263000 chr19-262000-263000 2333.0 172.79295277129944 150.0 0.8680909585388756 1.73395402249621
chr19 264000 265000 chr19-264000-265000 2986.0 211.02595611180573 169.0 0.8008493510175613 2.8930081980135496
chr19 269000 270000 chr19-269000-270000 1271.0 92.13856986722307 77.0 0.8356977985545182 1.5771177368608176