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:

 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:

 GCF_900246225.1_fAstCal1.2

with the following characteristics of the annotated gaps:

Assembly ID UCSC browser link	assembly size	sequence count	number of gaps	total gap size	smallest gap	largest gap	median size	mean size	common name VGP link
GCF_900246225.1_fAstCal1.2	880,445,564	249	115	11,500	100	100	100	100.0	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

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