56e876a710840529715cd8a5496f46e3e9d372cb max Fri Aug 21 03:57:10 2020 -0700 fixing general usage problems with chromToUcsc found by Matt, refs diff --git src/utils/chromToUcsc/tests/hg19.chromAlias.tsv src/utils/chromToUcsc/tests/hg19.chromAlias.tsv index 3170ef7..2abecab 100644 --- src/utils/chromToUcsc/tests/hg19.chromAlias.tsv +++ src/utils/chromToUcsc/tests/hg19.chromAlias.tsv @@ -1,890 +1,892 @@ -alias chrom source 1 chr1 assembly CM000663.1 chr1 genbank NC_000001.10 chr1 refseq 10 chr10 assembly CM000672.1 chr10 genbank NC_000010.10 chr10 refseq GL383543.1 chr10_gl383543_fix genbank HG544_PATCH chr10_gl383543_fix assembly NW_003315932.1 chr10_gl383543_fix refseq GL383544.1 chr10_gl383544_fix genbank HG995_PATCH chr10_gl383544_fix assembly NW_003315933.1 chr10_gl383544_fix refseq GL383545.1 chr10_gl383545_alt genbank HSCHR10_1_CTG2 chr10_gl383545_alt assembly NW_003315934.1 chr10_gl383545_alt refseq GL383546.1 chr10_gl383546_alt genbank HSCHR10_1_CTG5 chr10_gl383546_alt assembly NW_003315935.1 chr10_gl383546_alt refseq GL877873.1 chr10_gl877873_fix genbank HG905_PATCH chr10_gl877873_fix assembly NW_003571043.1 chr10_gl877873_fix refseq HG1211_PATCH chr10_jh591181_fix assembly JH591181.2 chr10_jh591181_fix genbank NW_003871068.1 chr10_jh591181_fix refseq HG311_PATCH chr10_jh591182_fix assembly JH591182.1 chr10_jh591182_fix genbank NW_003871069.1 chr10_jh591182_fix refseq HG339_PATCH chr10_jh591183_fix assembly JH591183.1 chr10_jh591183_fix genbank NW_003871070.1 chr10_jh591183_fix refseq HG871_PATCH chr10_jh636060_fix assembly JH636060.1 chr10_jh636060_fix genbank NW_003871071.1 chr10_jh636060_fix refseq HG1479_PATCH chr10_jh806580_fix assembly JH806580.1 chr10_jh806580_fix genbank NW_004070870.1 chr10_jh806580_fix refseq HG1074_PATCH chr10_kb663606_fix assembly KB663606.1 chr10_kb663606_fix genbank NW_004504302.1 chr10_kb663606_fix refseq HG979_PATCH chr10_ke332501_fix assembly KE332501.1 chr10_ke332501_fix genbank NW_004775432.1 chr10_ke332501_fix refseq 11 chr11 assembly CM000673.1 chr11 genbank NC_000011.9 chr11 refseq GL000202.1 chr11_gl000202_random genbank HSCHR11_RANDOM_CTG2 chr11_gl000202_random assembly NT_113921.2 chr11_gl000202_random refseq GL383547.1 chr11_gl383547_alt genbank HSCHR11_1_CTG1_1 chr11_gl383547_alt assembly NW_003315936.1 chr11_gl383547_alt refseq GL582973.1 chr11_gl582973_fix genbank HG281_PATCH chr11_gl582973_fix assembly NW_003571045.1 chr11_gl582973_fix refseq GL949744.1 chr11_gl949744_fix genbank HG536_PATCH chr11_gl949744_fix assembly NW_003571046.1 chr11_gl949744_fix refseq HG142_HG150_NOVEL_TEST chr11_jh159136_alt assembly JH159136.1 chr11_jh159136_alt genbank NW_003871073.1 chr11_jh159136_alt refseq HG151_NOVEL_TEST chr11_jh159137_alt assembly JH159137.1 chr11_jh159137_alt genbank NW_003871074.1 chr11_jh159137_alt refseq HG299_PATCH chr11_jh159138_fix assembly JH159138.1 chr11_jh159138_fix genbank NW_003871076.1 chr11_jh159138_fix refseq HG305_PATCH chr11_jh159139_fix assembly JH159139.1 chr11_jh159139_fix genbank NW_003871077.1 chr11_jh159139_fix refseq HG306_PATCH chr11_jh159140_fix assembly JH159140.1 chr11_jh159140_fix genbank NW_003871078.1 chr11_jh159140_fix refseq HG348_PATCH chr11_jh159141_fix assembly JH159141.2 chr11_jh159141_fix genbank NW_003871079.1 chr11_jh159141_fix refseq HG388_HG400_PATCH chr11_jh159142_fix assembly JH159142.2 chr11_jh159142_fix genbank NW_003871080.1 chr11_jh159142_fix refseq HG414_PATCH chr11_jh159143_fix assembly JH159143.1 chr11_jh159143_fix genbank NW_003871081.1 chr11_jh159143_fix refseq HG256_PATCH chr11_jh591184_fix assembly JH591184.1 chr11_jh591184_fix genbank NW_003871075.1 chr11_jh591184_fix refseq HG873_PATCH chr11_jh591185_fix assembly JH591185.1 chr11_jh591185_fix genbank NW_003871082.1 chr11_jh591185_fix refseq HG122_PATCH chr11_jh720443_fix assembly JH720443.2 chr11_jh720443_fix genbank NW_003871072.2 chr11_jh720443_fix refseq HG865_PATCH chr11_jh806581_fix assembly JH806581.1 chr11_jh806581_fix genbank NW_004070871.1 chr11_jh806581_fix refseq 12 chr12 assembly CM000674.1 chr12 genbank NC_000012.11 chr12 refseq GL383548.1 chr12_gl383548_fix genbank HG996_PATCH chr12_gl383548_fix assembly NW_003315937.1 chr12_gl383548_fix refseq GL383549.1 chr12_gl383549_alt genbank HSCHR12_1_CTG2 chr12_gl383549_alt assembly NW_003315938.1 chr12_gl383549_alt refseq GL383550.1 chr12_gl383550_alt genbank HSCHR12_1_CTG2_1 chr12_gl383550_alt assembly NW_003315939.1 chr12_gl383550_alt refseq GL383551.1 chr12_gl383551_alt genbank HSCHR12_1_CTG5 chr12_gl383551_alt assembly NW_003315940.1 chr12_gl383551_alt refseq GL383552.1 chr12_gl383552_alt genbank HSCHR12_2_CTG2_1 chr12_gl383552_alt assembly NW_003315941.1 chr12_gl383552_alt refseq GL383553.2 chr12_gl383553_alt genbank HSCHR12_3_CTG2_1 chr12_gl383553_alt assembly NW_003315942.2 chr12_gl383553_alt refseq GL582974.1 chr12_gl582974_fix genbank HG858_PATCH chr12_gl582974_fix assembly NW_003571048.1 chr12_gl582974_fix refseq GL877875.1 chr12_gl877875_alt genbank HSCHR12_1_CTG1 chr12_gl877875_alt assembly NW_003571049.1 chr12_gl877875_alt refseq GL877876.1 chr12_gl877876_alt genbank HSCHR12_2_CTG2 chr12_gl877876_alt assembly NW_003571050.1 chr12_gl877876_alt refseq GL949745.1 chr12_gl949745_alt genbank HG1133_PATCH chr12_gl949745_alt assembly NW_003571047.1 chr12_gl949745_alt refseq HG344_PATCH chr12_jh720444_fix assembly JH720444.2 chr12_jh720444_fix genbank NW_003871083.2 chr12_jh720444_fix refseq HG1595_PATCH chr12_kb663607_fix assembly KB663607.2 chr12_kb663607_fix genbank NW_004504303.2 chr12_kb663607_fix refseq 13 chr13 assembly CM000675.1 chr13 genbank NC_000013.10 chr13 refseq GL582975.1 chr13_gl582975_fix genbank HG531_PATCH chr13_gl582975_fix assembly NW_003571051.1 chr13_gl582975_fix refseq 14 chr14 assembly CM000676.1 chr14 genbank NC_000014.8 chr14 refseq HG1592_PATCH chr14_kb021645_fix assembly KB021645.1 chr14_kb021645_fix genbank NW_004166863.1 chr14_kb021645_fix refseq 15 chr15 assembly CM000677.1 chr15 genbank NC_000015.9 chr15 refseq GL383554.1 chr15_gl383554_alt genbank HSCHR15_1_CTG4 chr15_gl383554_alt assembly NW_003315943.1 chr15_gl383554_alt refseq GL383555.1 chr15_gl383555_alt genbank HSCHR15_1_CTG8 chr15_gl383555_alt assembly NW_003315944.1 chr15_gl383555_alt refseq HG971_PATCH chr15_jh720445_fix assembly JH720445.1 chr15_jh720445_fix genbank NW_003871084.1 chr15_jh720445_fix refseq 16 chr16 assembly CM000678.1 chr16 genbank NC_000016.9 chr16 refseq GL383556.1 chr16_gl383556_alt genbank HSCHR16_1_CTG3_1 chr16_gl383556_alt assembly NW_003315945.1 chr16_gl383556_alt refseq GL383557.1 chr16_gl383557_alt genbank HSCHR16_2_CTG3_1 chr16_gl383557_alt assembly NW_003315946.1 chr16_gl383557_alt refseq HG1208_PATCH chr16_jh720446_fix assembly JH720446.1 chr16_jh720446_fix genbank NW_003871085.1 chr16_jh720446_fix refseq 17 chr17 assembly CM000679.1 chr17 genbank NC_000017.10 chr17 refseq GL000258.1 chr17_ctg5_hap1 genbank HSCHR17_1_CTG5 chr17_ctg5_hap1 assembly NT_167251.1 chr17_ctg5_hap1 refseq GL000203.1 chr17_gl000203_random genbank HSCHR17_RANDOM_CTG1 chr17_gl000203_random assembly NT_113941.1 chr17_gl000203_random refseq GL000204.1 chr17_gl000204_random genbank HSCHR17_RANDOM_CTG2 chr17_gl000204_random assembly NT_113943.1 chr17_gl000204_random refseq GL000205.1 chr17_gl000205_random genbank HSCHR17_RANDOM_CTG3 chr17_gl000205_random assembly NT_113930.1 chr17_gl000205_random refseq GL000206.1 chr17_gl000206_random genbank HSCHR17_RANDOM_CTG4 chr17_gl000206_random assembly NT_113945.1 chr17_gl000206_random refseq GL383558.1 chr17_gl383558_fix genbank HG183_PATCH chr17_gl383558_fix assembly NW_003315947.1 chr17_gl383558_fix refseq GL383559.2 chr17_gl383559_fix genbank HG745_PATCH chr17_gl383559_fix assembly NW_003315948.2 chr17_gl383559_fix refseq GL383560.1 chr17_gl383560_fix genbank HG75_PATCH chr17_gl383560_fix assembly NW_003315949.1 chr17_gl383560_fix refseq GL383561.2 chr17_gl383561_fix genbank HG987_PATCH chr17_gl383561_fix assembly NW_003315950.2 chr17_gl383561_fix refseq GL383562.1 chr17_gl383562_fix genbank HG990_PATCH chr17_gl383562_fix assembly NW_003315951.1 chr17_gl383562_fix refseq GL383563.2 chr17_gl383563_alt genbank HSCHR17_1_CTG1 chr17_gl383563_alt assembly NW_003315952.2 chr17_gl383563_alt refseq GL383564.1 chr17_gl383564_alt genbank HSCHR17_1_CTG4 chr17_gl383564_alt assembly NW_003315953.1 chr17_gl383564_alt refseq GL383565.1 chr17_gl383565_alt genbank HSCHR17_2_CTG4 chr17_gl383565_alt assembly NW_003315954.1 chr17_gl383565_alt refseq GL383566.1 chr17_gl383566_alt genbank HSCHR17_3_CTG4 chr17_gl383566_alt assembly NW_003315955.1 chr17_gl383566_alt refseq GL582976.1 chr17_gl582976_fix genbank HG185_PATCH chr17_gl582976_fix assembly NW_003571052.1 chr17_gl582976_fix refseq HG747_PATCH chr17_jh159144_fix assembly JH159144.1 chr17_jh159144_fix genbank NW_003871088.1 chr17_jh159144_fix refseq HG883_PATCH chr17_jh159145_fix assembly JH159145.1 chr17_jh159145_fix genbank NW_003871090.1 chr17_jh159145_fix refseq HSCHR17_4_CTG4 chr17_jh159146_alt assembly JH159146.1 chr17_jh159146_alt genbank NW_003871091.1 chr17_jh159146_alt refseq HSCHR17_5_CTG4 chr17_jh159147_alt assembly JH159147.1 chr17_jh159147_alt genbank NW_003871092.1 chr17_jh159147_alt refseq HSCHR17_6_CTG4 chr17_jh159148_alt assembly JH159148.1 chr17_jh159148_alt genbank NW_003871093.1 chr17_jh159148_alt refseq HG748_PATCH chr17_jh591186_fix assembly JH591186.1 chr17_jh591186_fix genbank NW_003871089.1 chr17_jh591186_fix refseq HG271_PATCH chr17_jh636061_fix assembly JH636061.1 chr17_jh636061_fix genbank NW_003871087.1 chr17_jh636061_fix refseq HG1146_PATCH chr17_jh720447_fix assembly JH720447.1 chr17_jh720447_fix genbank NW_003871086.1 chr17_jh720447_fix refseq HG417_PATCH chr17_jh806582_fix assembly JH806582.2 chr17_jh806582_fix genbank NW_004070872.2 chr17_jh806582_fix refseq HG385_PATCH chr17_kb021646_fix assembly KB021646.2 chr17_kb021646_fix genbank NW_004166864.2 chr17_kb021646_fix refseq HG1591_PATCH chr17_ke332502_fix assembly KE332502.1 chr17_ke332502_fix genbank NW_004775433.1 chr17_ke332502_fix refseq 18 chr18 assembly CM000680.1 chr18 genbank NC_000018.9 chr18 refseq GL000207.1 chr18_gl000207_random genbank HSCHR18_RANDOM_CTG1 chr18_gl000207_random assembly NT_113947.1 chr18_gl000207_random refseq GL383567.1 chr18_gl383567_alt genbank HSCHR18_1_CTG1_1 chr18_gl383567_alt assembly NW_003315956.1 chr18_gl383567_alt refseq GL383568.1 chr18_gl383568_alt genbank HSCHR18_1_CTG2 chr18_gl383568_alt assembly NW_003315957.1 chr18_gl383568_alt refseq GL383569.1 chr18_gl383569_alt genbank HSCHR18_1_CTG2_1 chr18_gl383569_alt assembly NW_003315958.1 chr18_gl383569_alt refseq GL383570.1 chr18_gl383570_alt genbank HSCHR18_2_CTG1_1 chr18_gl383570_alt assembly NW_003315959.1 chr18_gl383570_alt refseq GL383571.1 chr18_gl383571_alt genbank HSCHR18_2_CTG2 chr18_gl383571_alt assembly NW_003315960.1 chr18_gl383571_alt refseq GL383572.1 chr18_gl383572_alt genbank HSCHR18_2_CTG2_1 chr18_gl383572_alt assembly NW_003315961.1 chr18_gl383572_alt refseq 19 chr19 assembly CM000681.1 chr19 genbank NC_000019.9 chr19 refseq GL000208.1 chr19_gl000208_random genbank HSCHR19_RANDOM_CTG1 chr19_gl000208_random assembly NT_113948.1 chr19_gl000208_random refseq GL000209.1 chr19_gl000209_random genbank HSCHR19_RANDOM_CTG2 chr19_gl000209_random assembly NT_113949.1 chr19_gl000209_random refseq GL383573.1 chr19_gl383573_alt genbank HSCHR19_1_CTG3 chr19_gl383573_alt assembly NW_003315962.1 chr19_gl383573_alt refseq GL383574.1 chr19_gl383574_alt genbank HSCHR19_1_CTG3_1 chr19_gl383574_alt assembly NW_003315963.1 chr19_gl383574_alt refseq GL383575.2 chr19_gl383575_alt genbank HSCHR19_2_CTG3 chr19_gl383575_alt assembly NW_003315964.2 chr19_gl383575_alt refseq GL383576.1 chr19_gl383576_alt genbank HSCHR19_3_CTG3 chr19_gl383576_alt assembly NW_003315965.1 chr19_gl383576_alt refseq GL582977.2 chr19_gl582977_fix genbank HG730_PATCH chr19_gl582977_fix assembly NW_003571053.2 chr19_gl582977_fix refseq GL949746.1 chr19_gl949746_alt genbank HSCHR19LRC_COX1_CTG1 chr19_gl949746_alt assembly NW_003571054.1 chr19_gl949746_alt refseq GL949747.1 chr19_gl949747_alt genbank HSCHR19LRC_COX2_CTG1 chr19_gl949747_alt assembly NW_003571055.1 chr19_gl949747_alt refseq GL949748.1 chr19_gl949748_alt genbank HSCHR19LRC_LRC_I_CTG1 chr19_gl949748_alt assembly NW_003571056.1 chr19_gl949748_alt refseq GL949749.1 chr19_gl949749_alt genbank HSCHR19LRC_LRC_J_CTG1 chr19_gl949749_alt assembly NW_003571057.1 chr19_gl949749_alt refseq GL949750.1 chr19_gl949750_alt genbank HSCHR19LRC_LRC_S_CTG1 chr19_gl949750_alt assembly NW_003571058.1 chr19_gl949750_alt refseq GL949751.1 chr19_gl949751_alt genbank HSCHR19LRC_LRC_T_CTG1 chr19_gl949751_alt assembly NW_003571059.1 chr19_gl949751_alt refseq GL949752.1 chr19_gl949752_alt genbank HSCHR19LRC_PGF1_CTG1 chr19_gl949752_alt assembly NW_003571060.1 chr19_gl949752_alt refseq GL949753.1 chr19_gl949753_alt genbank HSCHR19LRC_PGF2_CTG1 chr19_gl949753_alt assembly NW_003571061.1 chr19_gl949753_alt refseq HG729_PATCH chr19_jh159149_fix assembly JH159149.1 chr19_jh159149_fix genbank NW_003871094.1 chr19_jh159149_fix refseq HG1079_PATCH chr19_kb021647_fix assembly KB021647.1 chr19_kb021647_fix genbank NW_004166865.1 chr19_kb021647_fix refseq HG1350_HG959_PATCH chr19_ke332505_fix assembly KE332505.1 chr19_ke332505_fix genbank NW_004775434.1 chr19_ke332505_fix refseq GL000191.1 chr1_gl000191_random genbank HSCHR1_RANDOM_CTG5 chr1_gl000191_random assembly NT_113878.1 chr1_gl000191_random refseq GL000192.1 chr1_gl000192_random genbank HSCHR1_RANDOM_CTG12 chr1_gl000192_random assembly NT_167207.1 chr1_gl000192_random refseq GL383516.1 chr1_gl383516_fix genbank HG999_1_PATCH chr1_gl383516_fix assembly NW_003315903.1 chr1_gl383516_fix refseq GL383517.1 chr1_gl383517_fix genbank HG999_2_PATCH chr1_gl383517_fix assembly NW_003315904.1 chr1_gl383517_fix refseq GL383518.1 chr1_gl383518_alt genbank HSCHR1_1_CTG31 chr1_gl383518_alt assembly NW_003315905.1 chr1_gl383518_alt refseq GL383519.1 chr1_gl383519_alt genbank HSCHR1_2_CTG31 chr1_gl383519_alt assembly NW_003315906.1 chr1_gl383519_alt refseq GL383520.1 chr1_gl383520_alt genbank HSCHR1_3_CTG31 chr1_gl383520_alt assembly NW_003315907.1 chr1_gl383520_alt refseq GL949741.1 chr1_gl949741_fix genbank HG989_PATCH chr1_gl949741_fix assembly NW_003571030.1 chr1_gl949741_fix refseq HG1287_PATCH chr1_jh636052_fix assembly JH636052.4 chr1_jh636052_fix genbank NW_003871055.3 chr1_jh636052_fix refseq HG1292_PATCH chr1_jh636053_fix assembly JH636053.3 chr1_jh636053_fix genbank NW_003871056.3 chr1_jh636053_fix refseq HG1293_PATCH chr1_jh636054_fix assembly JH636054.1 chr1_jh636054_fix genbank NW_003871057.1 chr1_jh636054_fix refseq HG1471_PATCH chr1_jh806573_fix assembly JH806573.1 chr1_jh806573_fix genbank NW_004070863.1 chr1_jh806573_fix refseq HG1472_PATCH chr1_jh806574_fix assembly JH806574.2 chr1_jh806574_fix genbank NW_004070864.2 chr1_jh806574_fix refseq HG1473_PATCH chr1_jh806575_fix assembly JH806575.1 chr1_jh806575_fix genbank NW_004070865.1 chr1_jh806575_fix refseq 2 chr2 assembly CM000664.1 chr2 genbank NC_000002.11 chr2 refseq 20 chr20 assembly CM000682.1 chr20 genbank NC_000020.10 chr20 refseq GL383577.1 chr20_gl383577_alt genbank HSCHR20_1_CTG1 chr20_gl383577_alt assembly NW_003315966.1 chr20_gl383577_alt refseq GL582979.2 chr20_gl582979_fix genbank HG506_HG507_HG1000_PATCH chr20_gl582979_fix assembly NW_003571063.2 chr20_gl582979_fix refseq HG144_PATCH chr20_jh720448_fix assembly JH720448.1 chr20_jh720448_fix genbank NW_003871095.1 chr20_jh720448_fix refseq HG944_PATCH chr20_kb663608_fix assembly KB663608.1 chr20_kb663608_fix genbank NW_004504304.1 chr20_kb663608_fix refseq 21 chr21 assembly CM000683.1 chr21 genbank NC_000021.8 chr21 refseq GL000210.1 chr21_gl000210_random genbank HSCHR21_RANDOM_CTG9 chr21_gl000210_random assembly NT_113950.2 chr21_gl000210_random refseq GL383578.1 chr21_gl383578_alt genbank HSCHR21_1_CTG1_1 chr21_gl383578_alt assembly NW_003315967.1 chr21_gl383578_alt refseq GL383579.1 chr21_gl383579_alt genbank HSCHR21_2_CTG1_1 chr21_gl383579_alt assembly NW_003315968.1 chr21_gl383579_alt refseq GL383580.1 chr21_gl383580_alt genbank HSCHR21_3_CTG1_1 chr21_gl383580_alt assembly NW_003315969.1 chr21_gl383580_alt refseq GL383581.1 chr21_gl383581_alt genbank HSCHR21_4_CTG1_1 chr21_gl383581_alt assembly NW_003315970.1 chr21_gl383581_alt refseq HG237_PATCH chr21_ke332506_fix assembly KE332506.1 chr21_ke332506_fix genbank NW_004775435.1 chr21_ke332506_fix refseq 22 chr22 assembly CM000684.1 chr22 genbank NC_000022.10 chr22 refseq GL383582.2 chr22_gl383582_alt genbank HSCHR22_1_CTG1 chr22_gl383582_alt assembly NW_003315971.2 chr22_gl383582_alt refseq GL383583.1 chr22_gl383583_alt genbank HSCHR22_1_CTG2 chr22_gl383583_alt assembly NW_003315972.1 chr22_gl383583_alt refseq HG329_PATCH chr22_jh720449_fix assembly JH720449.1 chr22_jh720449_fix genbank NW_003871096.1 chr22_jh720449_fix refseq HG1486_PATCH chr22_jh806583_fix assembly JH806583.1 chr22_jh806583_fix genbank NW_004070873.1 chr22_jh806583_fix refseq HG1487_PATCH chr22_jh806584_fix assembly JH806584.1 chr22_jh806584_fix genbank NW_004070874.1 chr22_jh806584_fix refseq HG1488_PATCH chr22_jh806585_fix assembly JH806585.1 chr22_jh806585_fix genbank NW_004070875.1 chr22_jh806585_fix refseq HG497_PATCH chr22_jh806586_fix assembly JH806586.1 chr22_jh806586_fix genbank NW_004070876.1 chr22_jh806586_fix refseq HSCHR22_2_CTG1 chr22_kb663609_alt assembly KB663609.1 chr22_kb663609_alt genbank NW_004504305.1 chr22_kb663609_alt refseq GL383521.1 chr2_gl383521_alt genbank HSCHR2_1_CTG1 chr2_gl383521_alt assembly NW_003315908.1 chr2_gl383521_alt refseq GL383522.1 chr2_gl383522_alt genbank HSCHR2_1_CTG12 chr2_gl383522_alt assembly NW_003315909.1 chr2_gl383522_alt refseq GL582966.2 chr2_gl582966_alt genbank HSCHR2_2_CTG12 chr2_gl582966_alt assembly NW_003571033.2 chr2_gl582966_alt refseq GL877870.2 chr2_gl877870_fix genbank HG1007_PATCH chr2_gl877870_fix assembly NW_003571031.1 chr2_gl877870_fix refseq GL877871.1 chr2_gl877871_fix genbank HG686_PATCH chr2_gl877871_fix assembly NW_003571032.1 chr2_gl877871_fix refseq HG953_PATCH chr2_kb663603_fix assembly KB663603.1 chr2_kb663603_fix genbank NW_004504299.1 chr2_kb663603_fix refseq 3 chr3 assembly CM000665.1 chr3 genbank NC_000003.11 chr3 refseq GL383523.1 chr3_gl383523_fix genbank HG186_PATCH chr3_gl383523_fix assembly NW_003315910.1 chr3_gl383523_fix refseq GL383524.1 chr3_gl383524_fix genbank HG280_PATCH chr3_gl383524_fix assembly NW_003315911.1 chr3_gl383524_fix refseq GL383525.1 chr3_gl383525_fix genbank HG991_PATCH chr3_gl383525_fix assembly NW_003315912.1 chr3_gl383525_fix refseq GL383526.1 chr3_gl383526_alt genbank HSCHR3_1_CTG2_1 chr3_gl383526_alt assembly NW_003315913.1 chr3_gl383526_alt refseq HG1091_PATCH chr3_jh159131_fix assembly JH159131.1 chr3_jh159131_fix genbank NW_003871058.1 chr3_jh159131_fix refseq HG325_PATCH chr3_jh159132_fix assembly JH159132.1 chr3_jh159132_fix genbank NW_003871059.1 chr3_jh159132_fix refseq HSCHR3_1_CTG1 chr3_jh636055_alt assembly JH636055.1 chr3_jh636055_alt genbank NW_003871060.1 chr3_jh636055_alt refseq HG957_PATCH chr3_ke332495_fix assembly KE332495.1 chr3_ke332495_fix genbank NW_004775426.1 chr3_ke332495_fix refseq 4 chr4 assembly CM000666.1 chr4 genbank NC_000004.11 chr4 refseq GL000257.1 chr4_ctg9_hap1 genbank HSCHR4_1_CTG9 chr4_ctg9_hap1 assembly NT_167250.1 chr4_ctg9_hap1 refseq GL000193.1 chr4_gl000193_random genbank HSCHR4_RANDOM_CTG2 chr4_gl000193_random assembly NT_113885.1 chr4_gl000193_random refseq GL000194.1 chr4_gl000194_random genbank HSCHR4_RANDOM_CTG3 chr4_gl000194_random assembly NT_113888.1 chr4_gl000194_random refseq GL383527.1 chr4_gl383527_alt genbank HSCHR4_1_CTG12 chr4_gl383527_alt assembly NW_003315914.1 chr4_gl383527_alt refseq GL383528.1 chr4_gl383528_alt genbank HSCHR4_1_CTG6 chr4_gl383528_alt assembly NW_003315915.1 chr4_gl383528_alt refseq GL383529.1 chr4_gl383529_alt genbank HSCHR4_2_CTG9 chr4_gl383529_alt assembly NW_003315916.1 chr4_gl383529_alt refseq GL582967.1 chr4_gl582967_fix genbank HG706_PATCH chr4_gl582967_fix assembly NW_003571035.1 chr4_gl582967_fix refseq GL877872.1 chr4_gl877872_fix genbank HG1032_PATCH chr4_gl877872_fix assembly NW_003571034.1 chr4_gl877872_fix refseq HG174_HG254_PATCH chr4_ke332496_fix assembly KE332496.1 chr4_ke332496_fix genbank NW_004775427.1 chr4_ke332496_fix refseq 5 chr5 assembly CM000667.1 chr5 genbank NC_000005.9 chr5 refseq GL339449.2 chr5_gl339449_alt genbank HSCHR5_1_CTG1 chr5_gl339449_alt assembly NW_003315917.2 chr5_gl339449_alt refseq GL383530.1 chr5_gl383530_alt genbank HSCHR5_1_CTG2 chr5_gl383530_alt assembly NW_003315918.1 chr5_gl383530_alt refseq GL383531.1 chr5_gl383531_alt genbank HSCHR5_1_CTG5 chr5_gl383531_alt assembly NW_003315919.1 chr5_gl383531_alt refseq GL383532.1 chr5_gl383532_alt genbank HSCHR5_2_CTG1 chr5_gl383532_alt assembly NW_003315920.1 chr5_gl383532_alt refseq GL949742.1 chr5_gl949742_alt genbank HSCHR5_3_CTG1 chr5_gl949742_alt assembly NW_003571036.1 chr5_gl949742_alt refseq HG1063_PATCH chr5_jh159133_fix assembly JH159133.1 chr5_jh159133_fix genbank NW_003871061.1 chr5_jh159133_fix refseq HG1082_HG167_PATCH chr5_ke332497_fix assembly KE332497.1 chr5_ke332497_fix genbank NW_004775428.1 chr5_ke332497_fix refseq 6 chr6 assembly CM000668.1 chr6 genbank NC_000006.11 chr6 refseq GL000250.1 chr6_apd_hap1 genbank HSCHR6_MHC_APD_CTG1 chr6_apd_hap1 assembly NT_167244.1 chr6_apd_hap1 refseq GL000251.1 chr6_cox_hap2 genbank HSCHR6_MHC_COX_CTG1 chr6_cox_hap2 assembly NT_113891.2 chr6_cox_hap2 refseq GL000252.1 chr6_dbb_hap3 genbank HSCHR6_MHC_DBB_CTG1 chr6_dbb_hap3 assembly NT_167245.1 chr6_dbb_hap3 refseq GL383533.1 chr6_gl383533_alt genbank HSCHR6_1_CTG5 chr6_gl383533_alt assembly NW_003315921.1 chr6_gl383533_alt refseq HG1304_PATCH chr6_jh636056_fix assembly JH636056.1 chr6_jh636056_fix genbank NW_003871062.1 chr6_jh636056_fix refseq HG1322_PATCH chr6_jh636057_fix assembly JH636057.1 chr6_jh636057_fix genbank NW_003871063.1 chr6_jh636057_fix refseq HG27_PATCH chr6_jh806576_fix assembly JH806576.1 chr6_jh806576_fix genbank NW_004070866.1 chr6_jh806576_fix refseq HSCHR6_2_CTG5 chr6_kb021644_alt assembly KB021644.1 chr6_kb021644_alt genbank NW_004166862.1 chr6_kb021644_alt refseq HG357_PATCH chr6_kb663604_fix assembly KB663604.1 chr6_kb663604_fix genbank NW_004504300.1 chr6_kb663604_fix refseq HG193_PATCH chr6_ke332498_fix assembly KE332498.1 chr6_ke332498_fix genbank NW_004775429.1 chr6_ke332498_fix refseq GL000253.1 chr6_mann_hap4 genbank HSCHR6_MHC_MANN_CTG1 chr6_mann_hap4 assembly NT_167246.1 chr6_mann_hap4 refseq GL000254.1 chr6_mcf_hap5 genbank HSCHR6_MHC_MCF_CTG1 chr6_mcf_hap5 assembly NT_167247.1 chr6_mcf_hap5 refseq GL000255.1 chr6_qbl_hap6 genbank HSCHR6_MHC_QBL_CTG1 chr6_qbl_hap6 assembly NT_167248.1 chr6_qbl_hap6 refseq GL000256.1 chr6_ssto_hap7 genbank HSCHR6_MHC_SSTO_CTG1 chr6_ssto_hap7 assembly NT_167249.1 chr6_ssto_hap7 refseq 7 chr7 assembly CM000669.1 chr7 genbank NC_000007.13 chr7 refseq GL000195.1 chr7_gl000195_random genbank HSCHR7_RANDOM_CTG1 chr7_gl000195_random assembly NT_113901.1 chr7_gl000195_random refseq GL383534.2 chr7_gl383534_alt genbank HSCHR7_1_CTG6 chr7_gl383534_alt assembly NW_003315922.2 chr7_gl383534_alt refseq GL582968.1 chr7_gl582968_fix genbank HG115_PATCH chr7_gl582968_fix assembly NW_003571037.1 chr7_gl582968_fix refseq GL582969.1 chr7_gl582969_fix genbank HG14_PATCH chr7_gl582969_fix assembly NW_003571038.1 chr7_gl582969_fix refseq GL582970.1 chr7_gl582970_fix genbank HG736_PATCH chr7_gl582970_fix assembly NW_003571039.1 chr7_gl582970_fix refseq GL582971.1 chr7_gl582971_fix genbank HG7_PATCH chr7_gl582971_fix assembly NW_003571040.1 chr7_gl582971_fix refseq GL582972.1 chr7_gl582972_fix genbank HG946_PATCH chr7_gl582972_fix assembly NW_003571041.1 chr7_gl582972_fix refseq HG1257_PATCH chr7_jh159134_fix assembly JH159134.2 chr7_jh159134_fix genbank NW_003871064.1 chr7_jh159134_fix refseq HG1308_PATCH chr7_jh636058_fix assembly JH636058.1 chr7_jh636058_fix genbank NW_003871065.1 chr7_jh636058_fix refseq HG444_PATCH chr7_ke332499_fix assembly KE332499.1 chr7_ke332499_fix genbank NW_004775430.1 chr7_ke332499_fix refseq 8 chr8 assembly CM000670.1 chr8 genbank NC_000008.10 chr8 refseq GL000196.1 chr8_gl000196_random genbank HSCHR8_RANDOM_CTG1 chr8_gl000196_random assembly NT_113909.1 chr8_gl000196_random refseq GL000197.1 chr8_gl000197_random genbank HSCHR8_RANDOM_CTG4 chr8_gl000197_random assembly NT_113907.1 chr8_gl000197_random refseq GL383535.1 chr8_gl383535_fix genbank HG104_HG975_PATCH chr8_gl383535_fix assembly NW_003315923.1 chr8_gl383535_fix refseq GL383536.1 chr8_gl383536_fix genbank HG243_PATCH chr8_gl383536_fix assembly NW_003315924.1 chr8_gl383536_fix refseq GL949743.1 chr8_gl949743_fix genbank HG19_PATCH chr8_gl949743_fix assembly NW_003571042.1 chr8_gl949743_fix refseq HG418_PATCH chr8_jh159135_fix assembly JH159135.2 chr8_jh159135_fix genbank NW_003871066.2 chr8_jh159135_fix refseq HG1699_PATCH chr8_ke332500_fix assembly KE332500.1 chr8_ke332500_fix genbank NW_004775431.1 chr8_ke332500_fix refseq 9 chr9 assembly CM000671.1 chr9 genbank NC_000009.11 chr9 refseq GL000198.1 chr9_gl000198_random genbank HSCHR9_RANDOM_CTG1 chr9_gl000198_random assembly NT_113914.1 chr9_gl000198_random refseq GL000199.1 chr9_gl000199_random genbank HSCHR9_RANDOM_CTG2 chr9_gl000199_random assembly NT_113916.2 chr9_gl000199_random refseq GL000200.1 chr9_gl000200_random genbank HSCHR9_RANDOM_CTG4 chr9_gl000200_random assembly NT_113915.1 chr9_gl000200_random refseq GL000201.1 chr9_gl000201_random genbank HSCHR9_RANDOM_CTG5 chr9_gl000201_random assembly NT_113911.1 chr9_gl000201_random refseq GL339450.1 chr9_gl339450_fix genbank HG79_PATCH chr9_gl339450_fix assembly NW_003315925.1 chr9_gl339450_fix refseq GL383537.1 chr9_gl383537_fix genbank HG998_1_PATCH chr9_gl383537_fix assembly NW_003315926.1 chr9_gl383537_fix refseq GL383538.1 chr9_gl383538_fix genbank HG998_2_PATCH chr9_gl383538_fix assembly NW_003315927.1 chr9_gl383538_fix refseq GL383539.1 chr9_gl383539_alt genbank HSCHR9_1_CTG1 chr9_gl383539_alt assembly NW_003315928.1 chr9_gl383539_alt refseq GL383540.1 chr9_gl383540_alt genbank HSCHR9_1_CTG35 chr9_gl383540_alt assembly NW_003315929.1 chr9_gl383540_alt refseq GL383541.1 chr9_gl383541_alt genbank HSCHR9_2_CTG35 chr9_gl383541_alt assembly NW_003315930.1 chr9_gl383541_alt refseq GL383542.1 chr9_gl383542_alt genbank HSCHR9_3_CTG35 chr9_gl383542_alt assembly NW_003315931.1 chr9_gl383542_alt refseq HG962_PATCH chr9_jh636059_fix assembly JH636059.1 chr9_jh636059_fix genbank NW_003871067.1 chr9_jh636059_fix refseq HG1500_PATCH chr9_jh806577_fix assembly JH806577.1 chr9_jh806577_fix genbank NW_004070867.1 chr9_jh806577_fix refseq HG1501_PATCH chr9_jh806578_fix assembly JH806578.1 chr9_jh806578_fix genbank NW_004070868.1 chr9_jh806578_fix refseq HG1502_PATCH chr9_jh806579_fix assembly JH806579.1 chr9_jh806579_fix genbank NW_004070869.1 chr9_jh806579_fix refseq HG50_PATCH chr9_kb663605_fix assembly KB663605.1 chr9_kb663605_fix genbank NW_004504301.1 chr9_kb663605_fix refseq NC_001807.4 chrM genbank +J01415.2 chrMT genbank +MT chrMT assembly +NC_012920.1 chrMT refseq GL000211.1 chrUn_gl000211 genbank HSCHRUN_RANDOM_CTG1 chrUn_gl000211 assembly NT_113961.1 chrUn_gl000211 refseq GL000212.1 chrUn_gl000212 genbank HSCHRUN_RANDOM_CTG2 chrUn_gl000212 assembly NT_113923.1 chrUn_gl000212 refseq GL000213.1 chrUn_gl000213 genbank HSCHRUN_RANDOM_CTG3 chrUn_gl000213 assembly NT_167208.1 chrUn_gl000213 refseq GL000214.1 chrUn_gl000214 genbank HSCHRUN_RANDOM_CTG4 chrUn_gl000214 assembly NT_167209.1 chrUn_gl000214 refseq GL000215.1 chrUn_gl000215 genbank HSCHRUN_RANDOM_CTG5 chrUn_gl000215 assembly NT_167210.1 chrUn_gl000215 refseq GL000216.1 chrUn_gl000216 genbank HSCHRUN_RANDOM_CTG6 chrUn_gl000216 assembly NT_167211.1 chrUn_gl000216 refseq GL000217.1 chrUn_gl000217 genbank HSCHRUN_RANDOM_CTG7 chrUn_gl000217 assembly NT_167212.1 chrUn_gl000217 refseq GL000218.1 chrUn_gl000218 genbank HSCHRUN_RANDOM_CTG9 chrUn_gl000218 assembly NT_113889.1 chrUn_gl000218 refseq GL000219.1 chrUn_gl000219 genbank HSCHRUN_RANDOM_CTG10 chrUn_gl000219 assembly NT_167213.1 chrUn_gl000219 refseq GL000220.1 chrUn_gl000220 genbank HSCHRUN_RANDOM_CTG11 chrUn_gl000220 assembly NT_167214.1 chrUn_gl000220 refseq GL000221.1 chrUn_gl000221 genbank HSCHRUN_RANDOM_CTG13 chrUn_gl000221 assembly NT_167215.1 chrUn_gl000221 refseq GL000222.1 chrUn_gl000222 genbank HSCHRUN_RANDOM_CTG14 chrUn_gl000222 assembly NT_167216.1 chrUn_gl000222 refseq GL000223.1 chrUn_gl000223 genbank HSCHRUN_RANDOM_CTG15 chrUn_gl000223 assembly NT_167217.1 chrUn_gl000223 refseq GL000224.1 chrUn_gl000224 genbank HSCHRUN_RANDOM_CTG16 chrUn_gl000224 assembly NT_167218.1 chrUn_gl000224 refseq GL000225.1 chrUn_gl000225 genbank HSCHRUN_RANDOM_CTG17 chrUn_gl000225 assembly NT_167219.1 chrUn_gl000225 refseq GL000226.1 chrUn_gl000226 genbank HSCHRUN_RANDOM_CTG19 chrUn_gl000226 assembly NT_167220.1 chrUn_gl000226 refseq GL000227.1 chrUn_gl000227 genbank HSCHRUN_RANDOM_CTG20 chrUn_gl000227 assembly NT_167221.1 chrUn_gl000227 refseq GL000228.1 chrUn_gl000228 genbank HSCHRUN_RANDOM_CTG21 chrUn_gl000228 assembly NT_167222.1 chrUn_gl000228 refseq GL000229.1 chrUn_gl000229 genbank HSCHRUN_RANDOM_CTG22 chrUn_gl000229 assembly NT_167223.1 chrUn_gl000229 refseq GL000230.1 chrUn_gl000230 genbank HSCHRUN_RANDOM_CTG23 chrUn_gl000230 assembly NT_167224.1 chrUn_gl000230 refseq GL000231.1 chrUn_gl000231 genbank HSCHRUN_RANDOM_CTG24 chrUn_gl000231 assembly NT_167225.1 chrUn_gl000231 refseq GL000232.1 chrUn_gl000232 genbank HSCHRUN_RANDOM_CTG25 chrUn_gl000232 assembly NT_167226.1 chrUn_gl000232 refseq GL000233.1 chrUn_gl000233 genbank HSCHRUN_RANDOM_CTG26 chrUn_gl000233 assembly NT_167227.1 chrUn_gl000233 refseq GL000234.1 chrUn_gl000234 genbank HSCHRUN_RANDOM_CTG27 chrUn_gl000234 assembly NT_167228.1 chrUn_gl000234 refseq GL000235.1 chrUn_gl000235 genbank HSCHRUN_RANDOM_CTG28 chrUn_gl000235 assembly NT_167229.1 chrUn_gl000235 refseq GL000236.1 chrUn_gl000236 genbank HSCHRUN_RANDOM_CTG29 chrUn_gl000236 assembly NT_167230.1 chrUn_gl000236 refseq GL000237.1 chrUn_gl000237 genbank HSCHRUN_RANDOM_CTG30 chrUn_gl000237 assembly NT_167231.1 chrUn_gl000237 refseq GL000238.1 chrUn_gl000238 genbank HSCHRUN_RANDOM_CTG31 chrUn_gl000238 assembly NT_167232.1 chrUn_gl000238 refseq GL000239.1 chrUn_gl000239 genbank HSCHRUN_RANDOM_CTG32 chrUn_gl000239 assembly NT_167233.1 chrUn_gl000239 refseq GL000240.1 chrUn_gl000240 genbank HSCHRUN_RANDOM_CTG33 chrUn_gl000240 assembly NT_167234.1 chrUn_gl000240 refseq GL000241.1 chrUn_gl000241 genbank HSCHRUN_RANDOM_CTG34 chrUn_gl000241 assembly NT_167235.1 chrUn_gl000241 refseq GL000242.1 chrUn_gl000242 genbank HSCHRUN_RANDOM_CTG35 chrUn_gl000242 assembly NT_167236.1 chrUn_gl000242 refseq GL000243.1 chrUn_gl000243 genbank HSCHRUN_RANDOM_CTG36 chrUn_gl000243 assembly NT_167237.1 chrUn_gl000243 refseq GL000244.1 chrUn_gl000244 genbank HSCHRUN_RANDOM_CTG37 chrUn_gl000244 assembly NT_167238.1 chrUn_gl000244 refseq GL000245.1 chrUn_gl000245 genbank HSCHRUN_RANDOM_CTG38 chrUn_gl000245 assembly NT_167239.1 chrUn_gl000245 refseq GL000246.1 chrUn_gl000246 genbank HSCHRUN_RANDOM_CTG39 chrUn_gl000246 assembly NT_167240.1 chrUn_gl000246 refseq GL000247.1 chrUn_gl000247 genbank HSCHRUN_RANDOM_CTG40 chrUn_gl000247 assembly NT_167241.1 chrUn_gl000247 refseq GL000248.1 chrUn_gl000248 genbank HSCHRUN_RANDOM_CTG41 chrUn_gl000248 assembly NT_167242.1 chrUn_gl000248 refseq GL000249.1 chrUn_gl000249 genbank HSCHRUN_RANDOM_CTG42 chrUn_gl000249 assembly NT_167243.1 chrUn_gl000249 refseq CM000685.1 chrX genbank NC_000023.10 chrX refseq X chrX assembly GL877877.2 chrX_gl877877_fix genbank HG480_HG481_PATCH chrX_gl877877_fix assembly NW_003571064.2 chrX_gl877877_fix refseq HG1497_PATCH chrX_jh159150_fix assembly JH159150.3 chrX_jh159150_fix genbank NW_003871103.3 chrX_jh159150_fix refseq HG1423_PATCH chrX_jh720451_fix assembly JH720451.1 chrX_jh720451_fix genbank NW_003871098.1 chrX_jh720451_fix refseq HG1424_PATCH chrX_jh720452_fix assembly JH720452.1 chrX_jh720452_fix genbank NW_003871099.1 chrX_jh720452_fix refseq HG1425_PATCH chrX_jh720453_fix assembly JH720453.1 chrX_jh720453_fix genbank NW_003871100.1 chrX_jh720453_fix refseq HG1426_PATCH chrX_jh720454_fix assembly JH720454.3 chrX_jh720454_fix genbank NW_003871101.3 chrX_jh720454_fix refseq HG375_PATCH chrX_jh720455_fix assembly JH720455.1 chrX_jh720455_fix genbank NW_003871102.1 chrX_jh720455_fix refseq HG1433_PATCH chrX_jh806587_fix assembly JH806587.1 chrX_jh806587_fix genbank NW_004070877.1 chrX_jh806587_fix refseq HG1434_PATCH chrX_jh806588_fix assembly JH806588.1 chrX_jh806588_fix genbank NW_004070878.1 chrX_jh806588_fix refseq HG1435_PATCH chrX_jh806589_fix assembly JH806589.1 chrX_jh806589_fix genbank NW_004070879.1 chrX_jh806589_fix refseq HG1436_HG1432_PATCH chrX_jh806590_fix assembly JH806590.2 chrX_jh806590_fix genbank NW_004070880.2 chrX_jh806590_fix refseq HG1437_PATCH chrX_jh806591_fix assembly JH806591.1 chrX_jh806591_fix genbank NW_004070881.1 chrX_jh806591_fix refseq HG1438_PATCH chrX_jh806592_fix assembly JH806592.1 chrX_jh806592_fix genbank NW_004070882.1 chrX_jh806592_fix refseq HG1439_PATCH chrX_jh806593_fix assembly JH806593.1 chrX_jh806593_fix genbank NW_004070883.1 chrX_jh806593_fix refseq HG1440_PATCH chrX_jh806594_fix assembly JH806594.1 chrX_jh806594_fix genbank NW_004070884.1 chrX_jh806594_fix refseq HG1441_PATCH chrX_jh806595_fix assembly JH806595.1 chrX_jh806595_fix genbank NW_004070885.1 chrX_jh806595_fix refseq HG1442_PATCH chrX_jh806596_fix assembly JH806596.1 chrX_jh806596_fix genbank NW_004070886.1 chrX_jh806596_fix refseq HG1443_HG1444_PATCH chrX_jh806597_fix assembly JH806597.1 chrX_jh806597_fix genbank NW_004070887.1 chrX_jh806597_fix refseq HG1453_PATCH chrX_jh806598_fix assembly JH806598.1 chrX_jh806598_fix genbank NW_004070888.1 chrX_jh806598_fix refseq HG1458_PATCH chrX_jh806599_fix assembly JH806599.1 chrX_jh806599_fix genbank NW_004070889.1 chrX_jh806599_fix refseq HG1459_PATCH chrX_jh806600_fix assembly JH806600.2 chrX_jh806600_fix genbank NW_004070890.2 chrX_jh806600_fix refseq HG1462_PATCH chrX_jh806601_fix assembly JH806601.1 chrX_jh806601_fix genbank NW_004070891.1 chrX_jh806601_fix refseq HG1463_PATCH chrX_jh806602_fix assembly JH806602.1 chrX_jh806602_fix genbank NW_004070892.1 chrX_jh806602_fix refseq HG1490_PATCH chrX_jh806603_fix assembly JH806603.1 chrX_jh806603_fix genbank NW_004070893.1 chrX_jh806603_fix refseq HG29_PATCH chrX_kb021648_fix assembly KB021648.1 chrX_kb021648_fix genbank NW_004166866.1 chrX_kb021648_fix refseq CM000686.1 chrY genbank NC_000024.9 chrY refseq Y chrY assembly