View source for VGP Assembly gap analysis

==VGP assembly gap annotation vs. AGP file==

I'm curious about the lack of gap annotation in the VGP genome assemblies.  Looking at the AGP files supplied
with the assemblies, for example:

  [https://ftp.ncbi.nlm.nih.gov/genomes/all/GCA/007/474/595/GCA_007474595.1_mLynCan4_v1.p/GCA_007474595.1_mLynCan4_v1.p_assembly_structure/Primary_Assembly/assembled_chromosomes/AGP/  GCA_007474595.1_mLynCan4_v1.p]

the chr*.comp.agp.gz files have no references at all to the gaps in the assembly.  Of the 24 assemblies I have seen to date, only one has
any gap annotation in the AGP files:

  [https://ftp.ncbi.nlm.nih.gov/genomes/all/GCF/900/246/225/GCF_900246225.1_fAstCal1.2/GCF_900246225.1_fAstCal1.2_assembly_structure/Primary_Assembly/assembled_chromosomes/AGP/ GCF_900246225.1_fAstCal1.2]

with the following characteristics of the annotated gaps:

{| border='1' style='border-collapse:collapse'
|-
! style='text-align:left;'| Assembly ID
UCSC browser link
! style='text-align:right;'| assembly
size
! style='text-align:right;'| sequence
count
! style='text-align:right;'| number
of gaps
! total
gap size
! smallest
gap
! largest
gap
! median
size
! mean
size
! common name
VGP link
|-
| [https://genome.ucsc.edu/cgi-bin/hgTracks?hubUrl=https://hgdownload.soe.ucsc.edu/hubs/VGP/hub.txt&genome=GCF_900246225.1_fAstCal1.2&position=lastDbPos GCF_900246225.1_fAstCal1.2]
| style="text-align:right;"| 880,445,564
| style="text-align:right;"| 249
| style="text-align:right;"| 115
| style="text-align:right;"| 11,500
| style="text-align:right;"| 100
| style="text-align:right;"| 100
| style="text-align:right;"| 100
| style="text-align:right;"| 100.0
| [https://vgp.github.io/genomeark/Astatotilapia_calliptera/ eastern happy]
|}

The actual total gaps in this assembly are much more than indicated in these AGP file specifications.

The table below indicates the actual gaps (any sequence of unknown nucleotides) in the assemblies.  Clearly some of these assemblies have significant gaps and I suspect
some of them are ''non-bridged'' gaps.

==Gap statistics==

{| border='1' style='border-collapse:collapse' class='wikitable sortable'
|-
! style='text-align:left;'| Assembly ID
UCSC browser link
! style='text-align:right;'| assembly
size
! style='text-align:right;'| sequence
count
! style='text-align:right;'| number
of gaps
! total
gap size
! smallest
gap
! largest
gap
! median
size
! mean
size
! common name
VGP link
|-
| [https://genome.ucsc.edu/cgi-bin/hgTracks?hubUrl=https://hgdownload.soe.ucsc.edu/hubs/VGP/hub.txt&genome=GCA_003957555.2_bCalAnn1_v1.p&position=lastDbPos GCA_003957555.2_bCalAnn1_v1.p]
| style="text-align:right;"| 1,059,706,240
| style="text-align:right;"| 160
| style="text-align:right;"| 429
| style="text-align:right;"| 16,096,800
| style="text-align:right;"| 1
| style="text-align:right;"| 664,828
| style="text-align:right;"| 100
| style="text-align:right;"| 37,521.7
| [https://vgp.github.io/genomeark/Calypte_anna/ Anna's hummingbird]
|-
| [https://genome.ucsc.edu/cgi-bin/hgTracks?hubUrl=https://hgdownload.soe.ucsc.edu/hubs/VGP/hub.txt&genome=GCA_003957565.2_bTaeGut1_v1.p&position=lastDbPos GCA_003957565.2_bTaeGut1_v1.p]
| style="text-align:right;"| 1,058,012,133
| style="text-align:right;"| 135
| style="text-align:right;"| 312
| style="text-align:right;"| 2,334,250
| style="text-align:right;"| 1
| style="text-align:right;"| 535,815
| style="text-align:right;"| 200
| style="text-align:right;"| 7,481.6
| [https://vgp.github.io/genomeark/Taeniopygia_guttata/ zebra finch]
|-
| [https://genome.ucsc.edu/cgi-bin/hgTracks?hubUrl=https://hgdownload.soe.ucsc.edu/hubs/VGP/hub.txt&genome=GCA_004027225.1_bStrHab1_v1.p&position=lastDbPos GCA_004027225.1_bStrHab1_v1.p]
| style="text-align:right;"| 1,165,639,803
| style="text-align:right;"| 100
| style="text-align:right;"| 362
| style="text-align:right;"| 27,568,500
| style="text-align:right;"| 1
| style="text-align:right;"| 9,491,740
| style="text-align:right;"| 500
| style="text-align:right;"| 76,156.1
| [https://vgp.github.io/genomeark/Strigops_habroptila/ owl parrot]
|-
| [https://genome.ucsc.edu/cgi-bin/hgTracks?hubUrl=https://hgdownload.soe.ucsc.edu/hubs/VGP/hub.txt&genome=GCA_004115265.2_mRhiFer1_v1.p&position=lastDbPos GCA_004115265.2_mRhiFer1_v1.p]
| style="text-align:right;"| 2,075,785,400
| style="text-align:right;"| 135
| style="text-align:right;"| 158
| style="text-align:right;"| 7,546,100
| style="text-align:right;"| 1
| style="text-align:right;"| 833,261
| style="text-align:right;"| 499
| style="text-align:right;"| 47,760.1
| [https://vgp.github.io/genomeark/Rhinolophus_ferrumequinum/ greater horseshoe bat]
|-
| [https://genome.ucsc.edu/cgi-bin/hgTracks?hubUrl=https://hgdownload.soe.ucsc.edu/hubs/VGP/hub.txt&genome=GCA_007364275.1_fArcCen1&position=lastDbPos GCA_007364275.1_fArcCen1]
| style="text-align:right;"| 932,947,025
| style="text-align:right;"| 189
| style="text-align:right;"| 744
| style="text-align:right;"| 16,903,500
| style="text-align:right;"| 1
| style="text-align:right;"| 1,459,710
| style="text-align:right;"| 100
| style="text-align:right;"| 22,719.7
| [https://vgp.github.io/genomeark/Archocentrus_centrarchus/ flier cichlid]
|-
| [https://genome.ucsc.edu/cgi-bin/hgTracks?hubUrl=https://hgdownload.soe.ucsc.edu/hubs/VGP/hub.txt&genome=GCA_007399415.1_rGopEvg1_v1.p&position=lastDbPos GCA_007399415.1_rGopEvg1_v1.p]
| style="text-align:right;"| 2,298,564,209
| style="text-align:right;"| 383
| style="text-align:right;"| 562
| style="text-align:right;"| 29,560,300
| style="text-align:right;"| 1
| style="text-align:right;"| 3,059,780
| style="text-align:right;"| 100
| style="text-align:right;"| 52,598.4
| [https://vgp.github.io/genomeark/Gopherus_evgoodei/ Goodes thornscrub tortoise]
|-
| [https://genome.ucsc.edu/cgi-bin/hgTracks?hubUrl=https://hgdownload.soe.ucsc.edu/hubs/VGP/hub.txt&genome=GCA_007474595.1_mLynCan4_v1.p&position=lastDbPos GCA_007474595.1_mLynCan4_v1.p]
| style="text-align:right;"| 2,408,900,816
| style="text-align:right;"| 67
| style="text-align:right;"| 848
| style="text-align:right;"| 2,778,740
| style="text-align:right;"| 1
| style="text-align:right;"| 378,177
| style="text-align:right;"| 100
| style="text-align:right;"| 3,276.8
| [https://vgp.github.io/genomeark/Lynx_canadensis/ Canada lynx]
|-
| [https://genome.ucsc.edu/cgi-bin/hgTracks?hubUrl=https://hgdownload.soe.ucsc.edu/hubs/VGP/hub.txt&genome=GCA_900324465.2_fAnaTes1.2&position=lastDbPos GCA_900324465.2_fAnaTes1.2]
| style="text-align:right;"| 555,641,398
| style="text-align:right;"| 50
| style="text-align:right;"| 266
| style="text-align:right;"| 3,606,500
| style="text-align:right;"| 25
| style="text-align:right;"| 482,892
| style="text-align:right;"| 100
| style="text-align:right;"| 13,558.3
| [https://vgp.github.io/genomeark/Anabas_testudineus/ climbing perch]
|-
| [https://genome.ucsc.edu/cgi-bin/hgTracks?hubUrl=https://hgdownload.soe.ucsc.edu/hubs/VGP/hub.txt&genome=GCA_900324485.2_fMasArm1.2&position=lastDbPos GCA_900324485.2_fMasArm1.2]
| style="text-align:right;"| 591,935,101
| style="text-align:right;"| 122
| style="text-align:right;"| 238
| style="text-align:right;"| 13,231,300
| style="text-align:right;"| 2
| style="text-align:right;"| 607,827
| style="text-align:right;"| 300
| style="text-align:right;"| 55,593.9
| [https://vgp.github.io/genomeark/Mastacembelus_armatus/ zig-zag eel]
|-
| [https://genome.ucsc.edu/cgi-bin/hgTracks?hubUrl=https://hgdownload.soe.ucsc.edu/hubs/VGP/hub.txt&genome=GCA_901699155.1_bStrTur1.1&position=lastDbPos GCA_901699155.1_bStrTur1.1]
| style="text-align:right;"| 1,178,928,410
| style="text-align:right;"| 357
| style="text-align:right;"| 894
| style="text-align:right;"| 3,876,370
| style="text-align:right;"| 2
| style="text-align:right;"| 156,350
| style="text-align:right;"| 100
| style="text-align:right;"| 4,336.0
| [https://vgp.github.io/genomeark/Streptopelia_turtur/ turtle dove]
|-
| [https://genome.ucsc.edu/cgi-bin/hgTracks?hubUrl=https://hgdownload.soe.ucsc.edu/hubs/VGP/hub.txt&genome=GCA_901709675.1_fSynAcu1.1&position=lastDbPos GCA_901709675.1_fSynAcu1.1]
| style="text-align:right;"| 324,331,233
| style="text-align:right;"| 87
| style="text-align:right;"| 43
| style="text-align:right;"| 13,700
| style="text-align:right;"| 100
| style="text-align:right;"| 500
| style="text-align:right;"| 200
| style="text-align:right;"| 318.6
| [https://vgp.github.io/genomeark/Syngnathus_acus/ greater pipefish]
|-
| [https://genome.ucsc.edu/cgi-bin/hgTracks?hubUrl=https://hgdownload.soe.ucsc.edu/hubs/VGP/hub.txt&genome=GCA_901765095.1_aMicUni1.1&position=lastDbPos GCA_901765095.1_aMicUni1.1]
| style="text-align:right;"| 4,685,923,413
| style="text-align:right;"| 1,080
| style="text-align:right;"| 2,452
| style="text-align:right;"| 47,437,300
| style="text-align:right;"| 1
| style="text-align:right;"| 2,824,530
| style="text-align:right;"| 100
| style="text-align:right;"| 19,346.4
| [https://vgp.github.io/genomeark/Microcaecilia_unicolor/ tiny Cayenne caecilian]
|-
| [https://genome.ucsc.edu/cgi-bin/hgTracks?hubUrl=https://hgdownload.soe.ucsc.edu/hubs/VGP/hub.txt&genome=GCF_004115215.1_mOrnAna1.p.v1&position=lastDbPos GCF_004115215.1_mOrnAna1.p.v1]
| style="text-align:right;"| 1,858,552,590
| style="text-align:right;"| 305
| style="text-align:right;"| 522
| style="text-align:right;"| 15,159,800
| style="text-align:right;"| 1
| style="text-align:right;"| 1,622,070
| style="text-align:right;"| 100
| style="text-align:right;"| 29,041.8
| [https://vgp.github.io/genomeark/Ornithorhynchus_anatinus/ platypus]
|-
| [https://genome.ucsc.edu/cgi-bin/hgTracks?hubUrl=https://hgdownload.soe.ucsc.edu/hubs/VGP/hub.txt&genome=GCF_004126475.1_mPhyDis1_v1.p&position=lastDbPos GCF_004126475.1_mPhyDis1_v1.p]
| style="text-align:right;"| 2,117,764,065
| style="text-align:right;"| 141
| style="text-align:right;"| 831
| style="text-align:right;"| 22,966,500
| style="text-align:right;"| 1
| style="text-align:right;"| 1,480,060
| style="text-align:right;"| 500
| style="text-align:right;"| 27,637.1
| [https://vgp.github.io/genomeark/Phyllostomus_discolor/ pale spear-nosed bat]
|-
| [https://genome.ucsc.edu/cgi-bin/hgTracks?hubUrl=https://hgdownload.soe.ucsc.edu/hubs/VGP/hub.txt&genome=GCF_900246225.1_fAstCal1.2&position=lastDbPos GCF_900246225.1_fAstCal1.2]
| style="text-align:right;"| 880,445,564
| style="text-align:right;"| 249
| style="text-align:right;"| 490
| style="text-align:right;"| 1,186,660
| style="text-align:right;"| 19
| style="text-align:right;"| 211,000
| style="text-align:right;"| 25
| style="text-align:right;"| 2,421.8
| [https://vgp.github.io/genomeark/Astatotilapia_calliptera/ eastern happy]
|-
| [https://genome.ucsc.edu/cgi-bin/hgTracks?hubUrl=https://hgdownload.soe.ucsc.edu/hubs/VGP/hub.txt&genome=GCF_900634415.1_fCotGob3.1&position=lastDbPos GCF_900634415.1_fCotGob3.1]
| style="text-align:right;"| 609,391,784
| style="text-align:right;"| 322
| style="text-align:right;"| 445
| style="text-align:right;"| 2,553,980
| style="text-align:right;"| 9
| style="text-align:right;"| 500,417
| style="text-align:right;"| 100
| style="text-align:right;"| 5,739.3
| [https://vgp.github.io/genomeark/Cottoperca_gobio/ channel bull blenny]
|-
| [https://genome.ucsc.edu/cgi-bin/hgTracks?hubUrl=https://hgdownload.soe.ucsc.edu/hubs/VGP/hub.txt&genome=GCF_900634625.1_fParRan2.1&position=lastDbPos GCF_900634625.1_fParRan2.1]
| style="text-align:right;"| 551,012,959
| style="text-align:right;"| 156
| style="text-align:right;"| 1,523
| style="text-align:right;"| 10,561,500
| style="text-align:right;"| 1
| style="text-align:right;"| 153,246
| style="text-align:right;"| 4,304
| style="text-align:right;"| 6,934.7
| [https://vgp.github.io/genomeark/Parambassis_ranga/ Indian glassy fish]
|-
| [https://genome.ucsc.edu/cgi-bin/hgTracks?hubUrl=https://hgdownload.soe.ucsc.edu/hubs/VGP/hub.txt&genome=GCF_900634775.1_fGouWil2.1&position=lastDbPos GCF_900634775.1_fGouWil2.1]
| style="text-align:right;"| 937,150,793
| style="text-align:right;"| 441
| style="text-align:right;"| 1,160
| style="text-align:right;"| 14,353,500
| style="text-align:right;"| 1
| style="text-align:right;"| 2,682,550
| style="text-align:right;"| 100
| style="text-align:right;"| 12,373.7
| [https://vgp.github.io/genomeark/Gouania_willdenowi/ blunt-snouted clingfish]
|-
| [https://genome.ucsc.edu/cgi-bin/hgTracks?hubUrl=https://hgdownload.soe.ucsc.edu/hubs/VGP/hub.txt&genome=GCF_900700375.1_fDenClu1.1&position=lastDbPos GCF_900700375.1_fDenClu1.1]
| style="text-align:right;"| 567,401,054
| style="text-align:right;"| 460
| style="text-align:right;"| 464
| style="text-align:right;"| 4,648,390
| style="text-align:right;"| 13
| style="text-align:right;"| 518,837
| style="text-align:right;"| 100
| style="text-align:right;"| 10,018.1
| [https://vgp.github.io/genomeark/Denticeps_clupeoides/ denticle herring]
|-
| [https://genome.ucsc.edu/cgi-bin/hgTracks?hubUrl=https://hgdownload.soe.ucsc.edu/hubs/VGP/hub.txt&genome=GCF_900747795.1_fErpCal1.1&position=lastDbPos GCF_900747795.1_fErpCal1.1]
| style="text-align:right;"| 3,811,038,701
| style="text-align:right;"| 1,885
| style="text-align:right;"| 5,614
| style="text-align:right;"| 238,295,000
| style="text-align:right;"| 3
| style="text-align:right;"| 1,733,650
| style="text-align:right;"| 5,046
| style="text-align:right;"| 42,446.5
| [https://vgp.github.io/genomeark/Erpetoichthys_calabaricus/ reedfish]
|-
| [https://genome.ucsc.edu/cgi-bin/hgTracks?hubUrl=https://hgdownload.soe.ucsc.edu/hubs/VGP/hub.txt&genome=GCF_900963305.1_fEcheNa1.1&position=lastDbPos GCF_900963305.1_fEcheNa1.1]
| style="text-align:right;"| 544,229,245
| style="text-align:right;"| 38
| style="text-align:right;"| 140
| style="text-align:right;"| 599,356
| style="text-align:right;"| 13
| style="text-align:right;"| 248,230
| style="text-align:right;"| 100
| style="text-align:right;"| 4,281.1
| [https://vgp.github.io/genomeark/Echeneis_naucrates/ live sharksucker]
|-
| [https://genome.ucsc.edu/cgi-bin/hgTracks?hubUrl=https://hgdownload.soe.ucsc.edu/hubs/VGP/hub.txt&genome=GCF_900964775.1_fSclFor1.1&position=lastDbPos GCF_900964775.1_fSclFor1.1]
| style="text-align:right;"| 784,563,014
| style="text-align:right;"| 72
| style="text-align:right;"| 145
| style="text-align:right;"| 41,360
| style="text-align:right;"| 13
| style="text-align:right;"| 14,756
| style="text-align:right;"| 100
| style="text-align:right;"| 285.2
| [https://vgp.github.io/genomeark/Scleropages_formosus/ Asian bonytongue]
|-
| [https://genome.ucsc.edu/cgi-bin/hgTracks?hubUrl=https://hgdownload.soe.ucsc.edu/hubs/VGP/hub.txt&genome=GCF_901000725.2_fTakRub1.2&position=lastDbPos GCF_901000725.2_fTakRub1.2]
| style="text-align:right;"| 384,126,662
| style="text-align:right;"| 128
| style="text-align:right;"| 402
| style="text-align:right;"| 3,688,530
| style="text-align:right;"| 10
| style="text-align:right;"| 428,276
| style="text-align:right;"| 100
| style="text-align:right;"| 9,175.5
| [https://vgp.github.io/genomeark/Takifugu_rubripes/ torafugu]
|-
| [https://genome.ucsc.edu/cgi-bin/hgTracks?hubUrl=https://hgdownload.soe.ucsc.edu/hubs/VGP/hub.txt&genome=GCF_901001135.1_aRhiBiv1.1&position=lastDbPos GCF_901001135.1_aRhiBiv1.1]
| style="text-align:right;"| 5,319,239,201
| style="text-align:right;"| 1,330
| style="text-align:right;"| 3,573
| style="text-align:right;"| 33,955,800
| style="text-align:right;"| 4
| style="text-align:right;"| 771,063
| style="text-align:right;"| 100
| style="text-align:right;"| 9,503.5
| [https://vgp.github.io/genomeark/Rhinatrema_bivittatum/ two-lined caecilian]
|}