Index of /EvidentialGene/other/gnodes/gnodesdoc/gnodes_doc3tables
 Name Last modified Size
![[DIR]](/icons/back.gif) Parent Directory 21-Dec-2023 20:31 -
![[TXT]](/icons/text.gif) allspp_ncbiasmsize2020tab.txt 22-Aug-2023 13:27 71k
asm_cyto_size_equal_arthropods.txt 03-Jul-2023 16:03 10k
asm_cytosize_table_arthropods.txt 03-Jul-2023 16:06 68k
eukaryote_genoacsizes1a.txt 17-Dec-2023 17:44 32k
![[IMG]](/icons/image2.gif) genosize_allspp1a_paclogplot.png 16-Dec-2023 21:22 567k
gnodes23atasmquals.txt 17-Dec-2023 21:17 4k
gnodes23chrasm_dnatable.txt 07-Aug-2023 15:28 1k
gnodes23chrasm_idtable.txt 04-Jul-2023 16:28 2k
gnodes23chrasm_metadata.txt 22-Aug-2023 13:24 9k
gnodes23doctables_about.txt 04-Jul-2023 16:19 6k
gnodes23sizedisagree.txt 07-Aug-2023 20:51 2k
gnodes23tandrepts.txt 17-Dec-2023 21:16 7k
species23chrdna_gdupstr_sum2b.txt 03-Jul-2023 16:11 17k
gnodes23doctables/
gnodes23chrasm_idtable.txt
---------------------------------
Genome assembly IDs, size, date used per species
gnodes23chrasm_dnatable.txt
---------------------------------
SRA IDs of genomic DNA used for each species assembly, as tabled in species23chrdna_gdupstr_sum2b below.
gnodes23chrasm_metadata.txt
---------------------------------
Genome assembly meta data, including ID, Species, size, GenbankID or Asm URL, Date
asm_cyto_size_equal_arthropods.txt
---------------------------------
Summary of assembly and cyto-measured genome sizes of crustacean, insect of next table
Equal column counts number of assemblies that are 85% to 125% of median CytoMB size
AsmMB is range high>low of assembly sizes,
CytoMB is range low:high,count of cyto measures, and count of measures
#Class Species_name Equal_ga AsmMB CytoMB
C_Branchiopoda Daphnia_magna 0/6 161>122 235:518,10
C_Branchiopoda Daphnia_pulex 0/7 197>128 189:362,9
C_Copepoda Lep._salmonis 0/5 790>632 567:1506,3
..
Insecta Drosophila_melanogaster 5/116 190>109 117:205,12
Insecta Drosophila_virilis 0/6 206>168 333:401,4
..
Insecta Lucilia_cuprina 0/4 464>378 616:792,2
Insecta Solenopsis_invicta 0/7 413>349 460:753,3
Insecta Tribolium_castaneum 0/1 165 196:205,4
Sums:
Insecta 94/143,66% species with near-equal Asm and Cyto genome size, excluding Drosophila
Drosophila 40/71, 56% " near-equal "
Crustacea 2/15, 13% species with near-equal Asm and Cyto genome size
Assembled since 2020
Insecta 95/150, 63% (including Dros.), Crustacea 1/12, 8%
asm_cytosize_table_arthropods.txt
---------------------------------
Crustacean and Insect species, with corresponding cyto and assembly sizes,
from these sources:
Genome Cytometric sizes from Gregory, T.R. (2023). Animal Genome Size Database.
http://www.genomesize.com, with supplements from published reports below
Genome Assembly sizes from NCBI Genomes summary table
ftp://ftp.ncbi.nlm.nih.gov/genomes/GENOME_REPORTS/eukaryotes.txt of 2023june16
This table has one row for each NCBI genomes assembly of corresponding species.
Columns from genomesize:
Gsize = cyto measured size, median;
EqualGA = equal | DIFF if Asize and Gsize are same or not, by 15%
Class = species class
Mbases, C_value = cyto measured 1C pg value, and megabases as 978*C_value
Method = FC, FIA, FD or other cytometric measure
MBrange = range and count of cyto measures
Columns from NCBI
Asize and Size (Mb) = assembly size,
Assembly Accession = NCBI ID, Scaffolds, Release Date per NCBI table
#Species Gsize Asize EqualGA Class Mbases C_value Method MBrange Size (Mb) Assembly Accession Scaffolds Release Date
Daphnia_magna 362 148 DIFF_ga Branchiopoda 362 0.37 FD 235:518,10 148.4 GCA_927798105.1 1254 2022/01/29
Daphnia_magna 362 129 DIFF_ga Branchiopoda 362 0.37 FD 235:518,10 129.995 GCA_030254905.1 72 2023/06/12
Drosophila_virilis 381 206 DIFF_ga Insecta 381 0.39 FCM 333:401,4 206.027 GCA_000005245.1 13530 2006/04/11
Drosophila_virilis 381 182 DIFF_ga Insecta 381 0.39 FCM 333:401,4 182.303 GCA_016920725.1 564 2021/02/23
species23chrdna_gdupstr_sum2b.txt
---------------------------------
Summary table of major contents of assemblies and DNA in animals and plant genomes, calculated with Gnodes.
Columns are
ChrMBob = Chr assembly Megabases, observed, i.e. assembly size
ChrMBes = Genomic DNA Megabases (estimated) from mapping DNA to assembly, measured w/ Gnodes
CDSann, CDSbus, CDSdup : size of gene CDS, all annotated, uniq conserved (bus) and duplicated
RPTann, RPTsat : repeat content, and Satellite subset, measured with RepeatMasker, RepeatModeler, TandemRepeatFinder, and SatelliteRepeatFinder
TEann : transposon content, measured with RepeatMasker, RepeatModeler, or from NCBI reference genome repmask output table.
NOann : unannotated as one of above.
allasm, dupasm are subset measures of Gnodes, not used here.
Last column is name of assembly.DNAsample
# ChrMBob : Assembly measured sizes
arathgnd export doe=0 pct=0;
ChrMBob allasm dupasm CDSann CDSbus CDSdup RPTann RPTsat TEann NOann
117 117 21 43 2.9 0.9 7.4 3.7 18 52 arath18tair_chr.ERR8666067
131 131 35 43 2.9 0.9 20 16 19 53 at22vlr_ncbi_chrs.ERR8666067
144 144 48 43 2.9 1.0 30 21 19 55 at22vcan2d_chrs.ERR8666067
# ChrMBes : DNA measured sizes
arathgnd export doe=1 pct=0;
ChrMBes allasm dupasm CDSann CDSbus CDSdup RPTann RPTsat TEann NOann
151 151 51 46 3.1 1.5 33 23 20 57 at22vcan2d_chrs.ERR8666067
151 151 56 45 3.0 1.3 36 28 18 57 at22vcan2d_chrs.ERR8666125
142 142 13 45 3.0 1.1 26 19 19 56 at22vcan2d_chrs.SRR16841688
#============
# Cytometric measures not in www.genomesize.com
# 9991 = Routtu et al. BMC Genomics 2014, http://www.biomedcentral.com/1471-2164/15/1033
# 9992 = https://cdnsciencepub.com/doi/full/10.1139/gen-2013-0004
# 9993 = Journal of Plankton Research, https://doi.org/10.1093/plankt/19.12.2031
# 9994 = Vergilino et al., 2009, Bio. J. Linnean Society, doi: 10.1111/j.1095-8312.2008.01185.x
# 9995 = Lepeophtheirus_salmonis cytology measures, Sci. Rept. 2022, doi:10.1038/s41598-022-10585-2
Branchiopoda Cladocera Daphniidae Daphnia_magna Water_flea 0.246 FCM Xinb GD 9991
Branchiopoda Cladocera Daphniidae Daphnia_magna Water_flea 0.240 FCM Iinb GD 9991
Branchiopoda Cladocera Daphniidae Daphnia_magna Water_flea 0.302 FCM LL4 GD 9992
Branchiopoda Cladocera Daphniidae Daphnia_magna Water_flea 0.37 FCM WB GD 9993
#
Branchiopoda Cladocera Daphniidae Daphnia_pulex Water_flea 0.193 FCM WB GD 9991
Branchiopoda Cladocera Daphniidae Daphnia_pulex Water_flea 0.225 FCM WB GD 9992
Branchiopoda Cladocera Daphniidae Daphnia_pulex Water_flea 0.32 FCM WB GD 9993
Branchiopoda Cladocera Daphniidae Daphnia_pulex Water_flea 0.245 FCM WB GD 9994
#
Branchiopoda Cladocera Daphniidae Daphnia_arenata Water_flea 0.193 FCM WB GD 9991
Branchiopoda Cladocera Daphniidae Daphnia_arenata Water_flea 0.24 FCM WB GD 9994
#
Copepoda Siphonostomatoida Caligidae Lepeophtheirus_salmonis Salmon_louse 1.54 FCM WB GD 9995
Copepoda Siphonostomatoida Caligidae Lepeophtheirus_salmonis Salmon_louse 1.35 FD CT GD 9995
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