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eweitz / ideogram

Chromosome visualization for the web
https://eweitz.github.io/ideogram
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Add yeast centromeres, and refine centromere rendering #229

Closed eweitz closed 4 years ago

eweitz commented 4 years ago

This adds centromere position data for the genome of baker's yeast, using data from the Saccharomyces Genome Database (SGD, https://www.yeastgenome.org). This enhancement was motivated by #223.

It also refines handling of centromere rendering. Classification of a centromere position as "telocentric" (which entails special rendering) now uses relative centromere position instead of absolute base pair coordinate. Now, centromeres within 5% of a chromosome's length from its end are considered telocentric. Before, it was within 2 million base pairs from a chromosome end -- problematic if the chromosome is smaller than 2 Mbp, like all yeast chromosomes.

Before

yeast_genome_without_centromeres_ideogram

After

yeast_genome_with_centromeres_ideogram

Data and sources

Chromosome Centromere range Centromere midpoint Source
I 151465 - 151582 151524 https://www.yeastgenome.org/locus/S000006463
II 238207 - 238323 238265 https://www.yeastgenome.org/locus/S000006464
III 114385 - 114501 114443 https://www.yeastgenome.org/locus/S000006465
IV 449711 - 449821 449766 https://www.yeastgenome.org/locus/S000006466
V 151987 - 152104 152046 https://www.yeastgenome.org/locus/S000006467
VI 148510 - 148627 148569 https://www.yeastgenome.org/locus/S000001896
VII 496920 - 497038 496979 https://www.yeastgenome.org/locus/S000006468
VIII 105586 - 105703 105645 https://www.yeastgenome.org/locus/S000006469
IX 355629 - 355745 355687 https://www.yeastgenome.org/locus/S000006470
X 436307 - 436425 436366 https://www.yeastgenome.org/locus/S000006471
XI 440129 - 440246 440188 https://www.yeastgenome.org/locus/S000006472
XII 150828 - 150947 150888 https://www.yeastgenome.org/locus/S000006473
XIII 268031 - 268149 268090 https://www.yeastgenome.org/locus/S000006474
XIV 628758 - 628875 628817 https://www.yeastgenome.org/locus/S000006475
XV 326584 - 326702 326643 https://www.yeastgenome.org/locus/S000006476
XVI 555957 - 556073 556015 https://www.yeastgenome.org/locus/S000006477
coveralls commented 4 years ago

Coverage Status

Coverage decreased (-0.005%) to 89.665% when pulling d1ea7c25206ab9419c6d85d080014569005ea1da on yeast-centromeres into 7669122b8d49e850a0a8b4c96745a1c99add2117 on master.