File S1: Assembly breakpoints for 4,615 disease-associated OMIM genes, excluding genes on the X or Y chromosome, for either the Flye or Shasta-Hapdup assemblies. chromosome position num_samples_flye_breaks num_samples_shasta_hapdup_breaks region chr1 16725244 1 34 segdup_and_satellite_repeats chr1 16849163 24 0 segdup_and_satellite_repeats chr1 83489743 35 0 segdup chr1 108222544 0 20 segdup chr1 124932831 29 9 satellite_repeats chr1 143242868 4 26 segdup chr1 143242878 0 22 segdup chr1 149817485 0 31 segdup chr1 161472827 36 0 segdup chr1 161617430 36 0 segdup chr1 206409932 0 30 segdup chr1 223888834 26 0 segdup chr1 228556393 45 0 segdup chr1 228608364 57 0 segdup chr1 228647667 22 0 segdup chr1 228647668 29 0 segdup chr1 234776470 0 23 segdup chr1 243212175 24 0 segdup chr1 243212176 38 0 segdup chr1 248946422 30 4 segdup chr2 10174 45 14 segdup_and_satellite_repeats chr2 10845 25 24 segdup_and_satellite_repeats chr2 90379847 8 28 segdup_and_satellite_repeats chr2 91423156 82 63 segdup chr2 107825913 0 25 segdup chr2 109736878 0 29 segdup chr2 113410326 34 0 segdup chr2 113650608 0 21 segdup chr2 242119868 25 0 segdup chr3 10000 52 6 segdup chr3 90722454 26 5 satellite_repeats chr3 93705581 38 27 satellite_repeats chr3 188117521 14 76 None chr3 196000877 3 28 segdup_and_satellite_repeats chr3 198174527 21 3 segdup chr4 10000 31 0 segdup chr4 49120489 0 33 segdup_and_satellite_repeats chr4 49709070 32 29 segdup_and_satellite_repeats chr4 51107579 20 25 segdup_and_satellite_repeats chr4 51793951 29 25 satellite_repeats chr4 118578645 23 0 segdup chr5 10000 23 4 segdup chr5 17517000 25 8 segdup_and_satellite_repeats chr5 17598417 33 20 segdup_and_satellite_repeats chr5 34066027 36 0 segdup chr5 34407994 44 0 segdup_and_satellite_repeats chr5 46435885 18 30 segdup_and_satellite_repeats chr5 46435900 15 31 segdup_and_satellite_repeats chr5 50109824 73 66 segdup_and_satellite_repeats chr5 69533912 0 24 segdup chr5 175902481 0 27 segdup chr6 61177036 23 0 segdup_and_satellite_repeats chr6 160650609 30 1 segdup chr7 10238 67 0 segdup_and_satellite_repeats chr7 54233711 32 0 segdup_and_satellite_repeats chr7 54308696 31 0 satellite_repeats chr7 55763059 0 22 segdup chr7 58119653 23 17 segdup chr7 61015333 23 7 segdup_and_satellite_repeats chr7 61964167 30 7 segdup_and_satellite_repeats chr7 62456779 45 21 segdup chr7 74728287 0 36 segdup chr7 102480244 20 0 segdup chr7 128489636 21 0 segdup chr7 128658908 27 0 segdup chr7 144296174 45 14 segdup chr7 149931963 41 0 segdup chr7 153705621 24 0 segdup chr7 154164996 22 0 segdup chr7 154164997 21 0 segdup chr7 159335269 48 42 segdup_and_satellite_repeats chr8 12611662 0 23 segdup_and_satellite_repeats chr8 12667988 0 25 segdup_and_satellite_repeats chr8 85828675 26 0 segdup chr8 145076005 53 19 segdup chr8 145078636 23 12 segdup chr9 39964563 0 26 segdup_and_satellite_repeats chr9 40907581 27 0 segdup_and_satellite_repeats chr9 40907748 0 86 segdup_and_satellite_repeats chr9 41229378 29 2 segdup_and_satellite_repeats chr9 41333805 29 35 segdup_and_satellite_repeats chr9 41333838 13 42 segdup_and_satellite_repeats chr9 60518558 20 5 segdup_and_satellite_repeats chr9 63825923 22 1 segdup chr9 63825986 0 21 segdup chr9 63892463 35 71 segdup chr9 63918447 78 47 segdup chr9 66352193 0 30 segdup chr9 94306806 29 0 segdup chr9 94313318 0 20 segdup chr9 94438761 25 0 segdup chr9 96897114 26 0 segdup chr9 138192963 0 28 segdup chr10 10732 38 0 segdup_and_satellite_repeats chr10 60210 0 23 segdup chr10 38635051 40 84 segdup chr10 42066265 62 13 segdup chr10 42242897 0 77 segdup chr10 42242910 41 0 segdup chr10 48181624 0 33 segdup_and_satellite_repeats chr10 48181659 36 0 segdup_and_satellite_repeats chr10 49845538 26 0 segdup_and_satellite_repeats chr10 79650937 23 0 segdup chr10 133787422 26 0 segdup chr11 4321479 21 0 segdup chr11 50821348 20 0 satellite_repeats chr11 89742445 0 23 segdup chr11 90097478 0 23 segdup chr11 135076382 84 48 satellite_repeats chr12 55557 28 0 segdup chr12 55736 21 0 segdup chr12 2757767 0 25 segdup chr12 34719407 23 9 segdup_and_satellite_repeats chr12 133265306 29 15 segdup chr12 133265309 29 14 segdup chr13 114354328 46 5 segdup chr14 16113238 1 20 segdup_and_satellite_repeats chr14 90445694 4 39 satellite_repeats chr14 106883718 44 9 segdup_and_satellite_repeats chr15 17000000 2 22 segdup_and_satellite_repeats chr15 22308242 56 0 segdup chr15 23276874 49 19 segdup_and_satellite_repeats chr15 28567133 20 3 segdup chr15 30077908 38 0 segdup chr15 74060678 0 20 segdup chr15 75304763 0 20 segdup chr16 18073571 0 21 segdup_and_satellite_repeats chr16 18782412 0 20 segdup_and_satellite_repeats chr16 22699406 0 29 segdup chr16 22699430 22 28 segdup chr16 34584622 53 14 segdup_and_satellite_repeats chr16 46381024 48 28 segdup_and_satellite_repeats chr16 74430260 0 20 segdup chr17 113093 20 0 segdup chr17 16853577 0 24 segdup_and_satellite_repeats chr17 19189332 53 1 segdup_and_satellite_repeats chr17 20374791 23 0 segdup_and_satellite_repeats chr17 20374794 34 0 segdup_and_satellite_repeats chr17 21290406 39 8 segdup chr17 21602817 47 6 segdup chr17 26940994 76 51 segdup_and_satellite_repeats chr17 36458149 24 0 segdup_and_satellite_repeats chr17 43323824 33 0 segdup chr17 43323830 21 8 segdup chr17 83247136 59 0 segdup chr18 10928 28 0 segdup_and_satellite_repeats chr18 20603247 22 2 segdup chr18 80262862 45 15 segdup_and_satellite_repeats chr19 8740450 31 0 segdup chr19 24448980 71 37 segdup_and_satellite_repeats chr19 27240874 62 64 segdup_and_satellite_repeats chr19 36265220 26 1 segdup_and_satellite_repeats chr19 36309962 38 8 segdup_and_satellite_repeats chr19 37268642 28 16 segdup_and_satellite_repeats chr19 37306174 24 5 segdup_and_satellite_repeats chr19 47903486 19 26 segdup_and_satellite_repeats chr19 47959655 22 0 segdup_and_satellite_repeats chr19 47959659 30 2 segdup_and_satellite_repeats chr19 50091196 29 7 segdup_and_satellite_repeats chr19 50140065 24 23 segdup_and_satellite_repeats chr19 58607614 21 3 segdup_and_satellite_repeats chr20 60000 92 0 segdup chr20 60226 0 41 segdup chr20 60291 0 47 segdup chr20 26386232 24 5 segdup_and_satellite_repeats chr20 28557053 50 50 segdup chr20 28646195 3 44 segdup chr20 28728974 52 84 segdup chr20 28754818 0 23 segdup_and_satellite_repeats chr20 28779772 0 22 segdup_and_satellite_repeats chr20 29204768 27 8 segdup chr20 29256197 20 0 segdup_and_satellite_repeats chr20 29340263 37 0 segdup chr20 29368733 3 41 segdup chr20 29701190 28 0 segdup_and_satellite_repeats chr20 29865042 1 32 segdup_and_satellite_repeats chr20 30503328 33 0 segdup chr20 30880755 3 69 segdup chr20 30882875 28 0 segdup chr20 30931318 0 37 segdup_and_satellite_repeats chr20 31001508 72 46 segdup chr20 31051508 22 3 segdup chr20 64334159 47 4 segdup chr21 5216450 7 53 segdup chr21 5315292 25 1 segdup_and_satellite_repeats chr21 5499012 23 2 segdup chr21 7550890 0 26 segdup chr21 7638396 21 0 segdup chr21 7934784 0 61 segdup chr21 7968008 2 24 segdup_and_satellite_repeats chr21 8756715 26 0 segdup chr21 10814560 79 100 None chr21 46699983 41 2 segdup_and_satellite_repeats chr22 11016724 20 11 segdup_and_satellite_repeats chr22 11211025 38 13 satellite_repeats chr22 11211032 21 6 satellite_repeats chr22 11215415 0 28 satellite_repeats chr22 11269739 0 34 segdup_and_satellite_repeats chr22 11713770 22 6 segdup_and_satellite_repeats chr22 12641730 17 89 segdup_and_satellite_repeats chr22 12693136 21 3 segdup_and_satellite_repeats chr22 16065440 22 2 segdup_and_satellite_repeats chr22 18896989 25 0 segdup_and_satellite_repeats chr22 18896990 52 18 segdup_and_satellite_repeats chr22 50760299 0 21 segdup_and_satellite_repeats chr22 50807273 30 0 segdup_and_satellite_repeats chr22 50808468 23 0 segdup_and_satellite_repeats