Turkey - Revision history

Dpuiu: /* Submission */

2010-01-20T19:32:42Z

Submission

← Older revision		Revision as of 19:32, 20 January 2010
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	* [https://netfiles.umn.edu/xythoswfs/webui/_xy-11544920_1-t_Tk0AQByW Nature draft]		* [https://netfiles.umn.edu/xythoswfs/webui/_xy-11544920_1-t_Tk0AQByW Nature draft]
	* [ftp://ftp.cbcb.umd.edu/pub/data/turkey/Assembly2.0/ CBCB ftp]		* [ftp://ftp.cbcb.umd.edu/pub/data/turkey/Assembly2.0/ CBCB ftp]
			* Local dirs:
			/fs/ftp-cbcb/pub/data/turkey/ # assemblies, FASTA, AGP ...
			/fs/ftp-cbcb/pub/data/turkey/Assembly2.0/final/Alignments/ # alignments to chicken

Dpuiu: /* Submission */

2010-01-20T18:25:46Z

Submission

← Older revision		Revision as of 18:25, 20 January 2010
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	* [https://netfiles.umn.edu/xythoswfs/webui/_xy-11544920_1-t_Tk0AQByW Nature draft]		* [https://netfiles.umn.edu/xythoswfs/webui/_xy-11544920_1-t_Tk0AQByW Nature draft]
			* [ftp://ftp.cbcb.umd.edu/pub/data/turkey/Assembly2.0/ CBCB ftp]

Dpuiu: /* Submition */

2009-12-14T15:05:36Z

Submition

← Older revision		Revision as of 15:05, 14 December 2009
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	15,704 - total number, protein and RNA gene loci.		15,704 - total number, protein and RNA gene loci.

	= ~~Submition~~ =		= Submission =

	* [https://netfiles.umn.edu/xythoswfs/webui/_xy-11544920_1-t_Tk0AQByW Nature draft]		* [https://netfiles.umn.edu/xythoswfs/webui/_xy-11544920_1-t_Tk0AQByW Nature draft]

Dpuiu at 15:04, 14 December 2009

2009-12-14T15:04:01Z

← Older revision		Revision as of 15:04, 14 December 2009
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	611 - noncoding RNA genes		611 - noncoding RNA genes
	15,704 - total number, protein and RNA gene loci.		15,704 - total number, protein and RNA gene loci.

			= Submition =

			* [https://netfiles.umn.edu/xythoswfs/webui/_xy-11544920_1-t_Tk0AQByW Nature draft]

Dpuiu: /* Table 13 */

2009-12-06T17:40:42Z

Table 13

← Older revision		Revision as of 17:40, 6 December 2009
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	* From the article		* From the article
	* 34 predicted rearrangements between the turkey and chicken genomes		* 34 predicted rearrangements between the turkey and chicken genomes ; 6 look wrong, 6 questionable, 22 probably right

	GGA GGA start GGA end MGA* Nature of the rearrangement Notes		GGA GGA start GGA end MGA* Nature of the rearrangement Notes

Dpuiu: /* Table 13 */

2009-12-06T17:36:31Z

Table 13

Dpuiu: /* Chr_112409 */

2009-12-03T20:24:40Z

Chr_112409

@@ Line 191: / Line 191: @@
    -1      22445
-Inverted scaffold examples:
+* Inverted scaffold examples:
   #scfid      alignDir alignCount AgpDir AgpCount  markerDir markerCount
   7180002103721    -1  602             1   395     -1        116  # flipped errorneously (395 ctg,3.3Mbp scaffold)
@@ Line 200: / Line 203: @@
   7180002103677    -1  246             1   186     -1,-1     53   # aligns in 2 separate regions of Chr1
   ...
 * Scaffolds don't seem to be interleaved any more

Dpuiu: /* Table 13 */

2009-12-03T18:24:15Z

Table 13

← Older revision		Revision as of 18:24, 3 December 2009
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	* From the article		* From the article
	* ~~Predicted~~ rearrangements between the turkey and chicken genomes		* 34 predicted rearrangements between the turkey and chicken genomes

	GGA GGA start GGA end MGA* Nature of the rearrangement Notes		GGA GGA start GGA end MGA* Nature of the rearrangement Notes

Dpuiu: /* Chr_112409 */

2009-12-03T18:22:42Z

Chr_112409

← Older revision		Revision as of 18:22, 3 December 2009
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	Inverted scaffold examples:		Inverted scaffold examples:
	#scfid alignDir alignCount AgpDir AgpCount markerDir markerCount		#scfid alignDir alignCount AgpDir AgpCount markerDir markerCount
	7180002103721 -1 602 1 395 -1 116		7180002103721 -1 602 1 395 -1 116 # flipped errorneously (395 ctg,3.3Mbp scaffold)
	7180002103327 -1 299 1 221 1 68		7180002103327 -1 299 1 221 1 68
	7180002103550 -1 298 1 241 1 65		7180002103550 -1 298 1 241 1 65

Dpuiu: /* Chr_112409 */

2009-12-03T17:57:57Z

Chr_112409

← Older revision		Revision as of 17:57, 3 December 2009
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	Inverted scaffold examples:		Inverted scaffold examples:
	#scfid alignDir alignCount AgpDir AgpCount		#scfid alignDir alignCount AgpDir AgpCount markerDir markerCount
	7180002103721 -1 602 1 395		7180002103721 -1 602 1 395 -1 116
	7180002103327 -1 299 1 221		7180002103327 -1 299 1 221 1 68
	7180002103550 -1 298 1 241		7180002103550 -1 298 1 241 1 65
	7180002103191 -1 280 1 258		7180002103191 -1 280 1 258 1 69
	7180002103618 -1 267 1 426		7180002103618 -1 267 1 426 -1,1 144 # half rev, half fwd
	7180002103677 -1 246 1 186		7180002103677 -1 246 1 186 -1,-1 53 # aligns in 2 separate regions of Chr1
	...		...

← Older revision		Revision as of 17:36, 6 December 2009
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	1 75,800,000 76,000,000 MGA1 small inversion possible unequal recombination within KCN gene cluster		1 75,800,000 76,000,000 MGA1 small inversion possible unequal recombination within KCN gene cluster
	1 104,450,000 104,459,439 MGA1 possible very small intrachromosomal translocation the genetic map places this short segment near 1q telomere		1 104,450,000 104,459,439 MGA1 possible very small intrachromosomal translocation the genetic map places this short segment near 1q telomere
	1 125,900,000 126,300,000 MGA1 small interchromosomal translocation insertion of GGA4:25,500,000-25,550,000 at repetitive locus (see also below)		#1 125,900,000 126,300,000 MGA1 small interchromosomal translocation insertion of GGA4:25,500,000-25,550,000 at repetitive locus (see also below)
	1 156,600,000 156,600,001 MGA1 small interchromosomal translocation may be misplacement of Ctg13.1004 in GGA seq or LINE-based translocation of a small segment from GGA4:73,089,000-73,090,000 1 172,822,000 172,900,000 MGA1 possible small inversion may be mis-assembly of GGA ctg3.1161		#1 156,600,000 156,600,001 MGA1 small interchromosomal translocation may be misplacement of Ctg13.1004 in GGA seq or LINE-based translocation of a small segment from GGA4:73,089,000-73,090,000 1 172,822,000 172,900,000 MGA1 possible small inversion may be mis-assembly of GGA ctg3.1161
	2 54,870,224 56,560,442 MGA3 inversion with 56.560 Mb coordinate being telomeric in MGA3 (together one inversion and two translocations or assembly errors)		2 54,870,224 56,560,442 MGA3 inversion with 56.560 Mb coordinate being telomeric in MGA3 (together one inversion and two translocations or assembly errors)
	2 54,398,341 54,413,232 MGA3 small translocation or mis-assembly of GGA seq., inverted rel. to GGA seq. coord. (together one inversion and two translocations or assembly errors)		2 54,398,341 54,413,232 MGA3 small translocation or mis-assembly of GGA seq., inverted rel. to GGA seq. coord. (together one inversion and two translocations or assembly errors)
	2 54,641,337 54,845,268 MGA3 probably inverted relative to GGA sequence coordinates (together one inversion and two translocations or assembly errors)		2 54,641,337 54,845,268 MGA3 probably inverted relative to GGA sequence coordinates (together one inversion and two translocations or assembly errors)
	2 54,290,000 54,330,000 MGA3 small translocation or mis-assembly of GGA seq., orientation uncertain (together one inversion and two translocations or assembly errors)		#2 54,290,000 54,330,000 MGA3 small translocation or mis-assembly of GGA seq., orientation uncertain (together one inversion and two translocations or assembly errors)
	2 54,452,395 54,545,188 MGA3 probably inverted relative to GGA sequence coordinates (together one inversion and two translocations or assembly errors)		#2 54,452,395 54,545,188 MGA3 probably inverted relative to GGA sequence coordinates (together one inversion and two translocations or assembly errors)
	2 53,804,240 54,263,147 MGA3 inverted relative to GGA seq. coordinates with 53.8 Mb joined to 56.6 Mb in MGA (together one inversion and two translocations or assembly errors)		2 53,804,240 54,263,147 MGA3 inverted relative to GGA seq. coordinates with 53.8 Mb joined to 56.6 Mb in MGA (together one inversion and two translocations or assembly errors)
	3 6,218 2,344,838 MGA2 inversion, telomeric FISH CONFIRMED, order is telo-cen-[2.4-0.0Mb]-[2.4-5.6Mb]-[11.605-5.605Mb]-[13.16Mb-------]		3 6,218 2,344,838 MGA2 inversion, telomeric FISH CONFIRMED, order is telo-cen-[2.4-0.0Mb]-[2.4-5.6Mb]-[11.605-5.605Mb]-[13.16Mb-------]
	3 5,605,686 11,605,484 MGA2 inversion, (agrees with genetic map) FISH CONFIRMED, order is telo-cen-[2.4-0.0Mb]-[2.4-5.6Mb]-[11.605-5.605Mb]-[13.16Mb-------]		3 5,605,686 11,605,484 MGA2 inversion, (agrees with genetic map) FISH CONFIRMED, order is telo-cen-[2.4-0.0Mb]-[2.4-5.6Mb]-[11.605-5.605Mb]-[13.16Mb-------]
	4 25,500,000 25,550,000 MGA4 small interchromosomal translocation to about 125.90 Mb orthologous coord. on MGA1 see also chr1:125900000		#4 25,500,000 25,550,000 MGA4 small interchromosomal translocation to about 125.90 Mb orthologous coord. on MGA1 see also chr1:125900000
	4 35,150,000 35,160,000 MGA4 likely small duplication part of this segment duplicated at around 35,828,000 may be misplacement of Ctg13.1004 in seq or		?4 35,150,000 35,160,000 MGA4 likely small duplication part of this segment duplicated at around 35,828,000 may be misplacement of Ctg13.1004 in seq or
	4 73,080,000 73,090,000 MGA4 small interchromosomal translocation to about 156.60 Mb orthologous coord. on MGA1 LINE-based translocation of a small segment, see also GGA1:156,600,000		#4 73,080,000 73,090,000 MGA4 small interchromosomal translocation to about 156.60 Mb orthologous coord. on MGA1 LINE-based translocation of a small segment, see also GGA1:156,600,000
	5 1 270,229 MGA5 local small inversion with respect to p arm which as a whole is inverted local inversion with respect to p arm which as a whole is inverted		5 1 270,229 MGA5 local small inversion with respect to p arm which as a whole is inverted local inversion with respect to p arm which as a whole is inverted
	5 1 7,248,180 MGA5 inversion of p arm p arm likely inverted based on genetic map of Nte0897, MNT-193		5 1 7,248,180 MGA5 inversion of p arm p arm likely inverted based on genetic map of Nte0897, MNT-193
	6 1,576,787 13,080,207 MGA8 multiple inversions: predicted order is ... can be explained by a series of 4-5 consecutive inversions, including possible unequal recombination between SLC16A9 or, less likely, protocadherin genes		6 1,576,787 13,080,207 MGA8 multiple inversions: predicted order is ... can be explained by a series of 4-5 consecutive inversions, including possible unequal recombination between SLC16A9 or, less likely, protocadherin genes
	7 1 7,248,180 MGA7 inversion of p arm		7 1 7,248,180 MGA7 inversion of p arm
	8ran 64,951 407,592 MGA10 GGA8_random sequences likely telomeric on MGA10 (and probably GGA8)		?8ran 64,951 407,592 MGA10 GGA8_random sequences likely telomeric on MGA10 (and probably GGA8)
	8 44,817 10,199,568 MGA10 inversion of p arm possible unequal recombination between AMY genes		8 44,817 10,199,568 MGA10 inversion of p arm possible unequal recombination between AMY genes
	8 8,992,540 9,170,000 MGA10 local small inversion with respect to p arm which as a whole is inverted probable inversion but might be mis-orientation of GGA sequence contigs		8 8,992,540 9,170,000 MGA10 local small inversion with respect to p arm which as a whole is inverted probable inversion but might be mis-orientation of GGA sequence contigs
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	11 75,337 3,280,000 MGA13 no internal centromere observed in turkey inversion of GGA 11p, FISH CONFIRMED		11 75,337 3,280,000 MGA13 no internal centromere observed in turkey inversion of GGA 11p, FISH CONFIRMED
	12 95,816 940,546 MGA14 may be inverted, orientation uncertain may be fused to a repeat of 2.15-2.3 Mb region of GGA12		12 95,816 940,546 MGA14 may be inverted, orientation uncertain may be fused to a repeat of 2.15-2.3 Mb region of GGA12
	12 1,050,000 1,100,000 MGA14 possible small intrachromosomal translocation to telomere small segment may be now at MGA telomere		?12 1,050,000 1,100,000 MGA14 possible small intrachromosomal translocation to telomere small segment may be now at MGA telomere
	12 1,128,610 1,134,284 MGA14 possible very small intrachromosomal translocation small segment now between about 2,632,117-2,703,753 in GGA coordinates on q arm		?12 1,128,610 1,134,284 MGA14 possible very small intrachromosomal translocation small segment now between about 2,632,117-2,703,753 in GGA coordinates on q arm
	12 1,164,577 1,399,694 MGA14 inversion (1164577 joined to 1599552) centromere either misplaced in GGA or moved telomeric or between 940,546 and 1,399,694		12 1,164,577 1,399,694 MGA14 inversion (1164577 joined to 1599552) centromere either misplaced in GGA or moved telomeric or between 940,546 and 1,399,694
	13 8,233,861 8,511,782 MGA15 small inversion		13 8,233,861 8,511,782 MGA15 small inversion
	14 14,370,000 15,070,000 MGA16 inversion FISH CONFIRMED		14 14,370,000 15,070,000 MGA16 inversion FISH CONFIRMED
	18 5,062,096 9,882,412 MGA20 inversion unequal recombination between NME paralogs, FISH confirmed		18 5,062,096 9,882,412 MGA20 inversion unequal recombination between NME paralogs, FISH confirmed
	28 1,550,000 1,620,000 MGA30 apparent duplication with extra copy at about 1.05 Mb in MGA unclear if these are rearrangements or assembly errors		?28 1,550,000 1,620,000 MGA30 apparent duplication with extra copy at about 1.05 Mb in MGA unclear if these are rearrangements or assembly errors

	= Scaffold alignment to chicken =		= Scaffold alignment to chicken =