chr1 (reference) in projects: dports - OpenGrok search results

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Searched refs:chr1 (Results 1 – 25 of 1343) sorted by relevance

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/dports/biology/bedtools/bedtools2-2.30.0/test/intersect/sortAndNaming/bigTests/
H A D	qchr1.bed	`1 chr1 729 829 414466 100 - 2 chr1 3039 3139 129856 100 - 3 chr1 25777 25877 499279 100 + 4 chr1 32745 32845 213831 100 + 5 chr1 33890 33990 131543 100 - 6 chr1 44636 44736 162969 100 + 7 chr1 45868 45968 402049 100 + 8 chr1 53251 53351 368448 100 + 9 chr1 57216 57316 210380 100 + 10 chr1 59292 59392 106899 100 + [all …]`
H A D	dbchr1.bed	`1 chr1 22308 22408 440808 100 - 2 chr1 29666 29766 280807 100 + 3 chr1 41372 41472 384324 100 - 4 chr1 50746 50846 310420 100 + 5 chr1 53053 53153 271503 100 + 6 chr1 55872 55972 10776 100 - 7 chr1 59532 59632 66795 100 - 8 chr1 62461 62561 120603 100 + 9 chr1 68280 68380 66625 100 - 10 chr1 69568 69668 236014 100 + [all …]`
H A D	q500K.bed	`1 chr1 729 829 414466 100 - 2 chr1 3039 3139 129856 100 - 3 chr1 25777 25877 499279 100 + 4 chr1 32745 32845 213831 100 + 5 chr1 33890 33990 131543 100 - 6 chr1 44636 44736 162969 100 + 7 chr1 45868 45968 402049 100 + 8 chr1 53251 53351 368448 100 + 9 chr1 57216 57316 210380 100 + 10 chr1 59292 59392 106899 100 + [all …]`
H A D	db500K.bed	`1 chr1 22308 22408 440808 100 - 2 chr1 29666 29766 280807 100 + 3 chr1 41372 41472 384324 100 - 4 chr1 50746 50846 310420 100 + 5 chr1 53053 53153 271503 100 + 6 chr1 55872 55972 10776 100 - 7 chr1 59532 59632 66795 100 - 8 chr1 62461 62561 120603 100 + 9 chr1 68280 68380 66625 100 - 10 chr1 69568 69668 236014 100 + [all …]`
/dports/biology/gatk/gatk-4.2.0.0/src/test/resources/org/broadinstitute/hellbender/tools/walkers/coverage/DepthOfCoverage/expected/
H A D	testCoverageBehaviorWhenProvidedNoIntervalFile	`2 chr1:1570000,0,0.00,0,0,0,0,0,0 3 chr1:1570001,0,0.00,0,0,0,0,0,0 4 chr1:1570002,0,0.00,0,0,0,0,0,0 5 chr1:1570003,0,0.00,0,0,0,0,0,0 6 chr1:1570004,0,0.00,0,0,0,0,0,0 7 chr1:1570005,0,0.00,0,0,0,0,0,0 8 chr1:1570006,0,0.00,0,0,0,0,0,0 9 chr1:1570007,0,0.00,0,0,0,0,0,0 10 chr1:1570008,0,0.00,0,0,0,0,0,0 11 chr1:1570009,0,0.00,0,0,0,0,0,0 [all …]`
H A D	testIntervalListOverlappingUniqueBehavior.sample_interval_summary	2 chr1:1656275-1656375,24298,240.57,4151,41.10,41,42,43,100.0,4862,48.14,48,49,51,100.0,4267,42.25,39… 3 chr1:1656285-1656385,24287,240.47,4164,41.23,41,42,43,100.0,4854,48.06,48,49,51,100.0,4157,41.16,38… 4 chr1:1656295-1656395,24249,240.09,4192,41.50,41,43,43,100.0,4822,47.74,48,49,50,100.0,4039,39.99,37… 5 chr1:1656305-1656405,24265,240.25,4239,41.97,41,43,45,100.0,4800,47.52,48,49,50,100.0,3931,38.92,36… 6 chr1:1656315-1656415,24289,240.49,4309,42.66,41,43,46,100.0,4764,47.17,48,48,49,100.0,3810,37.72,36… 7 chr1:1656325-1656425,24299,240.58,4370,43.27,41,44,47,100.0,4740,46.93,48,48,49,100.0,3713,36.76,36… 8 chr1:1656335-1656435,24327,240.86,4426,43.82,42,46,48,100.0,4716,46.69,47,48,48,100.0,3608,35.72,35… 9 chr1:1656345-1656445,24395,241.53,4443,43.99,42,46,48,100.0,4722,46.75,47,48,48,100.0,3537,35.02,35… 10 chr1:1656355-1656455,24522,242.79,4473,44.29,43,46,48,100.0,4734,46.87,47,48,49,100.0,3531,34.96,35… 11 chr1:1656365-1656465,24641,243.97,4524,44.79,44,46,48,100.0,4768,47.21,48,48,49,100.0,3555,35.20,35… [all …]
/dports/biology/bedtools/bedtools2-2.30.0/test/shuffle/
H A D	simrep.bed	`1 chr1 10000 10468 trf 789 2 chr1 10627 10800 trf 346 3 chr1 10757 10997 trf 434 4 chr1 11225 11447 trf 273 5 chr1 11271 11448 trf 187 6 chr1 11283 11448 trf 199 7 chr1 19305 19443 trf 242 8 chr1 20828 20863 trf 70 9 chr1 30862 30959 trf 79 10 chr1 44835 44876 trf 73 [all …]`
/dports/biology/ncbi-cxx-toolkit/ncbi_cxx--25_2_0/src/app/agp_validate/test/
H A D	runs_of_ns.agp	`5 chr1 1 150000 1 N 150000 telomere no 6 chr1 150001 208443 2 D AC229737.8 1 58443 + 7 chr1 208444 213443 3 N 5000 fragment yes 8 chr1 213444 216591 4 D AC202463.29 1 3148 + 9 chr1 216592 216691 5 N 100 fragment yes 11 chr1 220773 220872 7 N 100 fragment yes 13 chr1 225917 226016 9 N 100 fragment yes 15 chr1 233823 233922 11 N 100 fragment yes 17 chr1 235968 236067 13 N 100 fragment yes 19 chr1 240990 241089 15 N 100 fragment yes [all …]`
/dports/biology/bio-mocha/bcftools-1.14/test/
H A D	gvcfz.2.vcf	`30 ##contig=<ID=chr1,length=248956422> 1551 chr1 11519 . T . . . . GT:AD:DP ./.:0:0 1552 chr1 11520 . G . . . . GT:AD:DP ./.:0:0 1553 chr1 11521 . G . . . . GT:AD:DP ./.:0:0 1554 chr1 11522 . G . . . . GT:AD:DP ./.:0:0 1555 chr1 11523 . A . . . . GT:AD:DP ./.:0:0 1556 chr1 11524 . T . . . . GT:AD:DP ./.:0:0 1557 chr1 11525 . T . . . . GT:AD:DP ./.:0:0 1558 chr1 11526 . C . . . . GT:AD:DP ./.:0:0 1559 chr1 11527 . C . . . . GT:AD:DP ./.:0:0 [all …]`
H A D	gvcfz.vcf	33 ##contig=<ID=chr1,length=248956422> 1554 chr1 11519 . T . . . . GT:AD:DP:RGQ ./.:0:0:0 1555 chr1 11520 . G . . . . GT:AD:DP:RGQ ./.:0:0:0 1556 chr1 11521 . G . . . . GT:AD:DP:RGQ ./.:0:0:0 1557 chr1 11522 . G . . . . GT:AD:DP:RGQ ./.:0:0:0 1558 chr1 11523 . A . . . . GT:AD:DP:RGQ ./.:0:0:0 1559 chr1 11524 . T . . . . GT:AD:DP:RGQ ./.:0:0:0 1560 chr1 11525 . T . . . . GT:AD:DP:RGQ ./.:0:0:0 1561 chr1 11526 . C . . . . GT:AD:DP:RGQ ./.:0:0:0 1562 chr1 11527 . C . . . . GT:AD:DP:RGQ ./.:0:0:0 [all …]
H A D	overlap.vcf	`3 ##contig=<ID=chr1> 11 chr1 98 outd1 AT A . . . 12 chr1 98 d2 ATT A . . . 14 chr1 99 outs1 A T . . . 15 chr1 99 d3 AT A . . . 18 chr1 100 s1 A T . . . 19 chr1 100 d4 AT A . . . 21 chr1 101 s2 A T . . . 22 chr1 101 i2 A AT . . . 24 chr1 199 s3 A T . . . [all …]`
/dports/biology/bcftools/bcftools-1.14/test/
H A D	gvcfz.2.vcf	`30 ##contig=<ID=chr1,length=248956422> 1551 chr1 11519 . T . . . . GT:AD:DP ./.:0:0 1552 chr1 11520 . G . . . . GT:AD:DP ./.:0:0 1553 chr1 11521 . G . . . . GT:AD:DP ./.:0:0 1554 chr1 11522 . G . . . . GT:AD:DP ./.:0:0 1555 chr1 11523 . A . . . . GT:AD:DP ./.:0:0 1556 chr1 11524 . T . . . . GT:AD:DP ./.:0:0 1557 chr1 11525 . T . . . . GT:AD:DP ./.:0:0 1558 chr1 11526 . C . . . . GT:AD:DP ./.:0:0 1559 chr1 11527 . C . . . . GT:AD:DP ./.:0:0 [all …]`
H A D	gvcfz.vcf	33 ##contig=<ID=chr1,length=248956422> 1554 chr1 11519 . T . . . . GT:AD:DP:RGQ ./.:0:0:0 1555 chr1 11520 . G . . . . GT:AD:DP:RGQ ./.:0:0:0 1556 chr1 11521 . G . . . . GT:AD:DP:RGQ ./.:0:0:0 1557 chr1 11522 . G . . . . GT:AD:DP:RGQ ./.:0:0:0 1558 chr1 11523 . A . . . . GT:AD:DP:RGQ ./.:0:0:0 1559 chr1 11524 . T . . . . GT:AD:DP:RGQ ./.:0:0:0 1560 chr1 11525 . T . . . . GT:AD:DP:RGQ ./.:0:0:0 1561 chr1 11526 . C . . . . GT:AD:DP:RGQ ./.:0:0:0 1562 chr1 11527 . C . . . . GT:AD:DP:RGQ ./.:0:0:0 [all …]
H A D	overlap.vcf	`3 ##contig=<ID=chr1> 11 chr1 98 outd1 AT A . . . 12 chr1 98 d2 ATT A . . . 14 chr1 99 outs1 A T . . . 15 chr1 99 d3 AT A . . . 18 chr1 100 s1 A T . . . 19 chr1 100 d4 AT A . . . 21 chr1 101 s2 A T . . . 22 chr1 101 i2 A AT . . . 24 chr1 199 s3 A T . . . [all …]`
/dports/biology/gatk/gatk-4.2.0.0/src/test/resources/org/broadinstitute/hellbender/tools/funcotator/validationTestData/
H A D	regressionTestHg19Large.vcf	`206 chr1 861349 exm41 C T . PASS . 209 chr1 865584 exm44 G A . PASS . 210 chr1 865625 exm46 G A . PASS . 211 chr1 865628 exm47 G A . PASS . 212 chr1 865662 exm51 G A . PASS . 213 chr1 865665 exm53 G A . PASS . 214 chr1 865694 exm55 C T . PASS . 215 chr1 865700 exm56 C T . PASS . 216 chr1 866429 exm60 C T . PASS . 217 chr1 866438 exm63 G A . PASS . [all …]`
/dports/biology/biolibc-tools/biolibc-tools-0.1.1/Test/
H A D	test.vcf	`4 chr1 548 . T G 18 . . GT:AD:DP 0\|1:16,15:31 5 chr1 1362 . G C 0 . . GT:AD:DP 1\|0:27,22:49 6 chr1 2163 . C G 30 . . GT:AD:DP 0\|1:29,5:34 7 chr1 2352 . C G 37 . . GT:AD:DP 0\|1:18,0:18 8 chr1 2994 . G T 22 . . GT:AD:DP 0\|1:12,7:19 9 chr1 3104 . G A 16 . . GT:AD:DP 0\|1:25,0:25 10 chr1 3833 . G A 36 . . GT:AD:DP 0\|1:26,18:44 12 chr1 4662 . C A 30 . . GT:AD:DP 1\|0:20,4:24 15 chr1 6338 . C A 55 . . GT:AD:DP 1\|0:1,1:2 20 chr1 7450 . G A 4 . . GT:AD:DP 0\|1:1,1:2 [all …]`
/dports/biology/iqtree/IQ-TREE-2.0.6/example/
H A D	example.cf	3 chr1 869378 0,0,0,6 0,0,0,2 0,0,0,54 0,0,0,6 0,0,0,12 0,0,0,26 0,0,0,20 0,0,0,12 0,0,0,8 0,0,0,10 0… 4 chr1 877254 6,0,0,0 2,0,0,0 54,0,0,0 6,0,0,0 12,0,0,0 26,0,0,0 20,0,0,0 12,0,0,0 8,0,0,0 10,0,0,0 1… 5 chr1 887074 0,0,6,0 0,0,2,0 0,0,54,0 0,0,6,0 0,0,12,0 0,0,26,0 0,0,20,0 0,0,12,0 0,0,8,0 0,0,10,0 0… 6 chr1 891852 6,0,0,0 2,0,0,0 54,0,0,0 6,0,0,0 12,0,0,0 26,0,0,0 20,0,0,0 12,0,0,0 8,0,0,0 10,0,0,0 1… 7 chr1 939520 0,0,6,0 0,0,2,0 0,0,54,0 0,0,6,0 0,0,12,0 0,0,26,0 0,0,20,0 0,0,12,0 0,0,8,0 0,0,10,0 0… 8 chr1 967305 0,0,6,0 0,0,2,0 0,0,54,0 0,0,6,0 0,0,12,0 0,0,26,0 0,0,20,0 0,0,12,0 0,0,8,0 0,0,10,0 0… 9 chr1 969594 0,0,6,0 0,0,2,0 0,0,54,0 0,0,6,0 0,0,12,0 0,0,26,0 0,0,20,0 0,0,12,0 0,0,8,0 0,0,10,0 0… 10 chr1 971686 0,0,6,0 0,0,2,0 0,0,54,0 0,0,6,0 0,0,12,0 0,0,26,0 0,0,20,0 0,0,12,0 0,0,8,0 0,0,10,0 0… 11 chr1 979769 0,0,6,0 0,0,2,0 0,0,54,0 0,0,6,0 0,0,12,0 0,0,26,0 0,0,20,0 0,0,12,0 0,0,8,0 0,0,10,0 0… 12 chr1 1106011 0,6,0,0 0,2,0,0 0,54,0,0 0,6,0,0 0,12,0,0 0,26,0,0 0,20,0,0 0,12,0,0 0,8,0,0 0,10,0,0 … [all …]
/dports/biology/bedtools/bedtools2-2.30.0/docs/content/tools/
H A D	unionbedg.rst	`41 chr1 1000 1500 10 42 chr1 2000 2100 20 45 chr1 900 1600 60 46 chr1 1700 2050 50 53 chr1 5000 159 chr1 0 1 A/G 160 chr1 5 6 C/T 163 chr1 0 1 C/C 164 chr1 7 8 T/T 167 chr1 0 1 A/G [all …]`
H A D	genomecov.rst	`99 chr1 1000 142 chr1 1000 148 chr1 6 0 149 chr1 7 0 150 chr1 8 0 151 chr1 9 0 152 chr1 10 0 153 chr1 11 1 154 chr1 12 1 155 chr1 13 1 [all …]`
/dports/biology/p5-Bio-GFF3/Bio-GFF3-2.0/t/data/
H A D	refGene_excerpt.gff3	1 chr1 ngsutils gene 10490158 10502872 . + . ID=APITD1 6 chr1 ngsutils CDS 10490574 10490625 . + 0 Parent=NM_199294 7 chr1 ngsutils CDS 10493898 10494022 . + 0 Parent=NM_199294 8 chr1 ngsutils CDS 10494713 10494747 . + 1 Parent=NM_199294 9 chr1 ngsutils CDS 10500403 10500470 . + 2 Parent=NM_199294 10 chr1 ngsutils CDS 10502321 10502462 . + 0 Parent=NM_199294 13 chr1 ngsutils gene 10490158 10512060 . + . ID=APITD1-CORT 19 chr1 ngsutils CDS 10490574 10490625 . + 0 Parent=NM_198544 20 chr1 ngsutils CDS 10493898 10494022 . + 0 Parent=NM_198544 21 chr1 ngsutils CDS 10494713 10494747 . + 1 Parent=NM_198544 [all …]
/dports/biology/gatk/gatk-4.2.0.0/src/test/resources/org/broadinstitute/hellbender/tools/calculatecontamination/
H A D	small_gene_panel.pileups	`3 chr1 985826 1 0 0 0.0112655 4 chr1 985900 3 0 0 0.0147823 5 chr1 985999 1 0 0 0.0140709 6 chr1 986010 1 0 0 0.0111126 7 chr1 1021408 1 0 0 0.0157902 8 chr1 1222267 2 0 0 0.17354 9 chr1 1229114 1 0 0 0.0364279 10 chr1 1247555 1 0 0 0.0155276 11 chr1 1247588 1 0 0 0.0277505 13 chr1 1336006 1 0 0 0.035275 [all …]`
/dports/biology/py-crossmap/CrossMap-0.5.4/test/
H A D	test00_hg19.bed3	`1 chr1 65886334 66103176 2 chr1 120454175 120612317 3 chr1 210502249 210849638 4 chr1 229577043 229644088 5 chr1 763177 794826 6 chr1 1571099 1655775 7 chr1 16576558 16678948 8 chr1 25943958 26111258 9 chr1 44173203 44396837 10 chr1 65613849 65697828 [all …]`
/dports/biology/gatk/gatk-4.2.0.0/src/test/resources/org/broadinstitute/hellbender/tools/funcotator/
H A D	FILTER_test.vcf	`9 …chr1:11869-14412 --intervals chr1:14363-29806 --intervals chr1:29554-31109 --intervals chr1:69091-…`
/dports/biology/ncbi-cxx-toolkit/ncbi_cxx--25_2_0/src/objtools/writers/unit_test/bedwriter_test_cases/
H A D	mss-603.annot.asn	`21 id local str "chr1" 61 id local str "chr1" 67 id local str "chr1" 73 id local str "chr1" 79 id local str "chr1" 85 id local str "chr1" 91 id local str "chr1" 97 id local str "chr1" 103 id local str "chr1" 221 id local str "chr1" [all …]`
/dports/biology/bedtools/bedtools2-2.30.0/test/closest/kclosest/
H A D	d3.bed	`1 chr1 10 20 3.1 20 - 2 chr1 30 40 3.2 20 + 3 chr1 45 60 3.3 20 - 4 chr1 50 60 3.4 20 - 5 chr1 55 60 3.5 20 - 6 chr1 70 80 3.6 20 + 7 chr1 75 80 3.65 20 + 8 chr1 90 105 3.7 20 + 9 chr1 95 110 3.8 20 - 10 chr1 110 115 3.9 20 + [all …]`

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