Ficedula albicollis (ID 11872) - Genome

Ficedula albicollis
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Organism Overview ; Genome Assembly and Annotation report

Ficedula albicollis (Collared flycatcher)

Collared flycatcher RefSeq Genome

Lineage: Eukaryota[15557]; Metazoa[7782]; Chordata[3579]; Craniata[3544]; Vertebrata[3544]; Euteleostomi[3500]; Archelosauria[1076]; Archosauria[1039]; Dinosauria[1034]; Saurischia[1034]; Theropoda[1034]; Coelurosauria[1034]; Aves[1034]; Neognathae[1009]; Passeriformes[351]; Muscicapidae[13]; Ficedula[1]; Ficedula albicollis[1]

Summary

Submitter:

Uppsala University

Assembly level:

Chromosome

Assembly:

GCA_000247815.2 FicAlb1.5 scaffolds: 21,836 contigs: 30,843 N50: 410,964 L50: 771

BioProjects:

PRJNA208061

Whole Genome Shotgun (WGS):

INSDC: AGTO00000000.2

Statistics:

total length (Mb): 1118.34

protein count: 26464

GC%: 44.2999

Publications (limited to 20 most recent records)

A high-density linkage map enables a second-generation collared flycatcher genome assembly and reveals the patterns of avian recombination rate variation and chromosomal evolution. Kawakami T, et al. Mol Ecol 2014 Aug
Patterns of sequencing coverage bias revealed by ultra-deep sequencing of vertebrate mitochondria. Ekblom R, et al. BMC Genomics 2014 Jun 12
The genomic landscape of species divergence in Ficedula flycatchers. Ellegren H, et al. Nature 2012 Nov 29
tRNAscan-SE: a program for improved detection of transfer RNA genes in genomic sequence. Lowe TM, et al. Nucleic Acids Res 1997 Mar 1

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Replicon Info

Type	Name	RefSeq	INSDC	Size (Mb)	GC%	Protein	rRNA	tRNA	Other RNA	Gene	Pseudogene
Chr	1	NC_021671.1	CM001988.1	120	41.1	1,966	-	15	148	1,188	-

Chr	1A	NC_021672.1	CM001989.1	74.95	41.8	1,500	-	4	133	963	6

Chr	2	NC_021673.1	CM001990.1	157.56	40.8	2,330	-	43	190	1,461	4

Chr	3	NC_021674.1	CM001991.1	115.84	41.2	1,907	-	11	153	1,193	3

Chr	4	NC_021675.1	CM001992.1	70.44	40.6	1,266	-	-	81	734	4

Chr	5	NC_021677.1	CM001994.1	64.72	43.0	1,725	-	5	101	1,011	5

Chr	4A	NC_021676.1	CM001993.1	21.18	46.6	565	-	2	49	355	2

Chr	6	NC_021678.1	CM001995.1	37.23	43.9	1,037	-	1	55	562	1

Chr	7	NC_021679.1	CM001996.1	39.41	43.1	915	-	15	51	530	3

Chr	8	NC_021680.1	CM001997.1	32.1	44.3	954	-	3	71	552	-

Chr	9	NC_021681.1	CM001998.1	26.79	45.4	793	-	1	54	459	-

Chr	10	NC_021682.1	CM001999.1	21.35	46.0	674	-	6	46	421	1

Chr	11	NC_021683.1	CM002000.1	21.73	45.5	585	-	14	28	400	-

Chr	12	NC_021684.1	CM002001.1	21.94	46.2	611	-	1	41	376	2

Chr	13	NC_021685.1	CM002002.1	18.64	47.5	580	-	-	43	339	2

Chr	14	NC_021686.1	CM002003.1	17.37	48.4	715	-	2	41	420	-

Chr	15	NC_021687.1	CM002004.1	14.94	49.5	642	-	5	39	377	-

Chr	17	NC_021688.1	CM002005.1	12.38	52.1	544	-	1	22	296	-

Chr	18	NC_021689.1	CM002006.1	13.16	50.9	522	-	8	40	358	1

Chr	19	NC_021690.1	CM002007.1	11.93	50.5	561	-	1	35	348	-

Chr	20	NC_021691.1	CM002008.1	15.68	49.3	600	-	2	43	372	1

Chr	21	NC_021692.1	CM002009.1	8.07	52.0	368	-	1	22	251	-

Chr	22	NC_021693.1	CM002010.1	5.73	55.7	227	-	1	11	170	-

Chr	23	NC_021694.1	CM002011.1	7.94	55.7	382	-	-	30	253	1

Chr	24	NC_021695.1	CM002012.1	8.01	53.1	294	-	-	14	187	-

Chr	25	NC_021696.1	CM002013.1	2.8	60.7	247	-	1	12	182	1

Chr	26	NC_021697.1	CM002014.1	7.65	57.3	411	-	2	25	271	1

Chr	27	NC_021698.1	CM002015.1	5.57	57.0	348	-	2	8	257	1

Chr	28	NC_021699.1	CM002016.1	6.18	58.1	402	-	4	18	272	-

Chr	Z	NC_021700.1	CM002017.1	59.86	41.8	1,027	-	-	77	667	9

group	LG34	NC_021701.1	CM002018.1	0.48	67.1	17	-	-	2	19	-

group	LG35	NC_021702.1	CM002019.1	0.25	62.1	4	-	-	-	4	-

group	LGE22	NC_021703.1	CM002020.1	2.15	65.4	130	-	-	2	106	1

	MT	NC_021621.1	KF293721.1	0.02	48.4	13	2	22	-	35	-

Un	-	.	-	74.26	53.2	1,602	-	28	224	1,491	33

Chromosomes

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Genome Region

Ficedula albicollis mitochondrion, complete genome	Go to nucleotide:Graphics FASTA GenBank

Genome

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