Description

These tracks show regions of this target genome (Human - Dec. 2013 (GRCh38/hg38) - GRCh38 Genome Reference Consortium Human Reference 38 (GCA_000001405.15)) that have alignments to other query genome assemblies, aligned with lastz or minimap2. The alignable parts are shown with thick blocks that look like exons. Non-alignable parts between these are shown like introns.

Query genome assemblies aligned to this target genome assembly:

The query assemblies are grouped by clade, from the NCBI taxonomy: each clade is named for the taxonomic group of the query just below the most recent group it shares with this target genome. The clades are listed from the closest to the most distant from the target, and within each clade, the assemblies are ordered by their mash distance to the target assembly, then by their chain coverage of the target genome.

The minimap2 alignments are intended for pairs of very similar same-species/same-individual assemblies, for example the haplotypes of a diploid assembly, or closely related strain assemblies, where minimap2's splice-free asm5/asm10/asm20 presets do a better job with the larger indels and structural differences seen between such assemblies than lastz's general-purpose scoring does.

Alignment coverage

percent of the target genome covered by each type of chain,
except quickLift: percent of the query genome covered by the quickLift chain
common
name		assemblymethodchainssyntenicreciprocal
best		lift
over		quickLift
(% of query)
Homo sapiens
Humanhs1lastz92.82192.73487.633 92.035
Humanhs1lastz (swap)   92.85792.063
Humanhs1minimap2 (swap)94.375  94.37292.895
Humanhs1minimap292.241  92.23993.016
humanGCA_054883265.1_H9_T2T.hap2lastz92.40892.28786.11292.39994.186
humanGCA_054883195.1_H9_T2T.hap1lastz92.39792.27386.09692.38993.479
humanGCA_018873775.2_hg01243.v3.0lastz92.76692.66086.832 91.980
humanGCA_018505845.1_HG03492.pri.mat.f1_v2lastz92.38992.24986.01092.381 
humanGCA_018852615.3_hg002v1.1.matlastz92.39792.27686.05092.38993.100
humanGCA_018505835.1_HG03492.alt.pat.f1_v2lastz88.50388.35082.19788.494 
humanGCA_018852605.3_hg002v1.1.patlastz88.49288.33782.21088.48392.085
humanGCA_018471345.1_HG01106.pri.mat.f1_v2lastz92.52292.38286.06992.512 
humanGCA_018506165.1_HG03098.pri.mat.f1_v2lastz92.47592.34786.04592.465 
humanGCA_018472715.1_HG00735.alt.pat.f1_v2lastz92.44192.31186.04592.432 
humanGCA_018469405.1_HG01258.pri.mat.f1_v2lastz92.43892.30185.98292.429 
humanGCA_018506965.1_HG005.pri.mat.f1_v2lastz92.42492.29086.00192.41593.712
humanGCA_018467165.1_HG01891.alt.pat.f1_v2lastz92.42092.28786.02192.410 
humanGCA_018506125.1_HG02055.pri.mat.f1_v2lastz92.42092.28485.99492.411 
humanGCA_018506975.1_HG00733.pri.mat.f1_v2lastz92.42092.27885.99092.411 
humanGCA_018467015.1_HG02486.pri.mat.f1_v2lastz92.41992.28586.02892.410 
humanGCA_018469425.1_HG03516.pri.mat.f1_v2lastz92.41892.29186.08992.409 
humanGCA_018470455.1_HG02886.pri.mat.f1_v2lastz92.41792.29686.14792.408 
humanGCA_018506955.1_HG00733.alt.pat.f1_v2lastz92.41792.29986.07892.409 
humanGCA_018469415.1_HG03516.alt.pat.f1_v2lastz92.41692.28086.07492.407 
humanGCA_018469925.1_HG02622.alt.pat.f1_v2lastz92.41392.29986.08392.404 
humanGCA_018470465.1_HG02886.alt.pat.f1_v2lastz92.41292.28186.06192.402 
humanGCA_018471095.1_HG00741.pri.mat.f1_v2lastz92.41292.27586.01192.403 
humanGCA_018472605.1_HG00621.pri.mat.f1_v2lastz92.41292.28485.96792.403 
humanGCA_018469665.1_HG01123.pri.mat.f1_v2.1lastz92.41192.28085.98192.403 
humanGCA_018466835.1_HG02257.alt.pat.f1_v2lastz92.41092.26685.96092.401 
humanGCA_018472765.1_HG00735.pri.mat.f1_v2lastz92.40992.27086.04792.400 
humanGCA_018504075.1_HG02723.alt.pat.f1_v2lastz92.40992.28986.04992.400 
humanGCA_018473305.1_HG03453.alt.pat.f1_v2lastz92.40792.27986.09092.397 
humanGCA_018472725.1_HG01071.alt.pat.f1_v2lastz92.40692.27486.00992.398 
humanGCA_018472855.1_HG03453.pri.mat.f1_v2lastz92.40692.27586.06892.397 
humanGCA_018471545.1_HG01952.pri.mat.f1_v2lastz92.40592.27086.03592.396 
humanGCA_018472595.1_HG00438.alt.pat.f1_v2lastz92.40392.28186.09992.395 
humanGCA_018466845.1_HG02257.pri.mat.f1_v2lastz92.40292.27586.01592.393 
humanGCA_018466985.1_HG02559.pri.mat.f1_v2lastz92.40292.26486.04692.392 
humanGCA_018469705.1_HG01361.alt.pat.f1_v2lastz92.40292.27986.00792.394 
humanGCA_018503285.1_NA18906.alt.pat.f1_v2lastz92.40292.26786.07892.393 
humanGCA_018471515.1_HG00438.pri.mat.f1_v2lastz92.40192.27386.01092.392 
humanGCA_018503255.1_NA18906.pri.mat.f1_v2lastz92.39992.27386.03492.390 
humanGCA_018504625.1_NA20129.alt.pat.f1_v2lastz92.39992.26686.03592.390 
humanGCA_018504055.1_HG02080.alt.pat.f1_v2lastz92.39892.26485.98992.389 
humanGCA_018472695.1_HG01928.pri.mat.f1_v2lastz92.39492.26485.98392.385 
humanGCA_018505825.1_HG02109.pri.mat.f1_v2lastz92.39492.26985.99892.385 
humanGCA_018472845.1_HG01978.alt.pat.f1_v2lastz92.39392.25685.97292.384 
humanGCA_018469685.1_HG01361.pri.mat.f1_v2lastz92.39292.23985.89892.383 
humanGCA_018469935.1_HG02717.pri.mat.f1_v2lastz92.39292.26385.90792.383 
humanGCA_018469695.1_HG01123.alt.pat.f1_v2.1lastz92.39192.25485.97992.382 
humanGCA_018471535.1_HG02148.pri.mat.f1_v2lastz92.39192.25485.96892.383 
humanGCA_018504085.1_HG02080.pri.mat.f1_v2lastz92.39192.26685.94992.383 
humanGCA_021951015.1_HG002.mat.cur.20211005lastz92.39192.26886.75392.38292.771
humanGCA_018503265.1_NA19240.alt.pat.f1_v2lastz92.39092.26286.01092.38193.459
humanGCA_018472565.1_HG00673.pri.mat.f1_v2lastz92.38792.25586.06592.378 
humanGCA_018503245.1_HG03486.alt.pat.f1_v2lastz92.38692.25786.03692.377 
humanGCA_018469955.1_HG02630.pri.mat.f1_v2lastz92.38592.24786.04492.376 
humanGCA_018471525.1_HG02148.alt.pat.f1_v2lastz92.38492.25485.91592.375 
humanGCA_018471065.1_HG01175.alt.pat.f1_v2lastz92.38292.25586.00792.374 
humanGCA_018469945.1_HG02630.alt.pat.f1_v2lastz92.38092.23886.01492.370 
humanGCA_018467155.1_HG01891.pri.mat.f1_v2lastz92.37992.23385.91992.369 
humanGCA_018504635.1_NA20129.pri.mat.f1_v2lastz92.37892.24486.03992.368 
humanGCA_018503575.1_HG02818.alt.pat.f1_v2lastz92.37792.24185.94392.367 
humanGCA_018504665.1_NA21309.alt.pat.f1_v2lastz92.37792.25286.00492.368 
humanGCA_018466855.1_HG02559.alt.pat.f1_v2lastz92.37592.24385.97892.366 
humanGCA_018469865.1_HG01358.pri.mat.f1_v2.1lastz92.37592.24086.02392.366 
humanGCA_018471105.1_HG00741.alt.pat.f1_v2lastz92.37492.25486.00392.365 
humanGCA_018472825.1_HG03579.pri.mat.f1_v2lastz92.37492.24986.03492.365 
humanGCA_018504655.1_NA21309.pri.mat.f1_v2lastz92.37492.22385.98992.36493.471
humanGCA_018505865.1_HG02109.alt.pat.f1_v2lastz92.37492.23085.89092.364 
humanGCA_018472685.1_HG01071.pri.mat.f1_v2lastz92.37192.24085.98392.362 
humanGCA_018473295.1_HG03540.pri.mat.f1_v2lastz92.36892.23685.96892.358 
humanGCA_018852585.1_HG02145.pri.mat.f1_v2lastz92.36892.22385.98292.358 
humanGCA_018472865.1_HG01978.pri.mat.f1_v2lastz92.36792.23685.95292.357 
humanGCA_018503525.1_HG03486.pri.mat.f1_v2lastz92.36692.22686.00892.356 
humanGCA_018503275.1_NA19240.pri.mat.f1_v2lastz92.35792.22986.00992.34793.643
humanGCA_018503585.1_HG02818.pri.mat.f1_v2lastz92.35792.21585.93992.348 
humanGCA_018504065.1_HG02723.pri.mat.f1_v2lastz92.35792.22685.93892.347 
humanGCA_018469875.1_HG02622.pri.mat.f1_v2lastz92.35592.21885.97492.345 
humanGCA_018473315.1_HG03540.alt.pat.f1_v2lastz92.35192.19885.95392.341 
humanGCA_018470445.1_HG02572.pri.mat.f1_v2lastz92.34692.21686.02392.337 
humanGCA_018504375.1_HG01243.pri.mat.f1_v2lastz92.34492.21085.97492.335 
humanGCA_018504365.1_HG01109.pri.mat.f1_v2lastz92.32092.18985.92892.311 
humanGCA_018471085.1_HG01175.pri.mat.f1_v2lastz92.30692.16985.95392.297 
humanGCA_018472575.1_HG00621.alt.pat.f1_v2lastz88.53188.39582.14988.523 
humanGCA_018472705.1_HG01928.alt.pat.f1_v2lastz88.52988.38182.16488.521 
humanGCA_018506945.1_HG005.alt.pat.f1_v2lastz88.52888.37882.17288.52092.338
humanGCA_018471075.1_HG01106.alt.pat.f1_v2lastz88.52688.37982.19088.518 
humanGCA_018469675.1_HG01258.alt.pat.f1_v2lastz88.52588.36582.19288.516 
humanGCA_018469965.1_HG01358.alt.pat.f1_v2.1lastz88.51588.36482.22288.507 
humanGCA_018504645.1_HG01109.alt.pat.f1_v2lastz88.51388.37482.21388.504 
humanGCA_018470425.1_HG02717.alt.pat.f1_v2lastz88.51088.35582.16888.501 
humanGCA_018505855.1_HG02055.alt.pat.f1_v2lastz88.50988.36082.20988.499 
humanGCA_018472585.1_HG00673.alt.pat.f1_v2lastz88.49488.33782.07588.485 
humanGCA_021950905.1_HG002.pat.cur.20211005lastz88.48788.32182.79188.47991.615
humanGCA_018504045.1_HG01243.alt.pat.f1_v2lastz88.48388.31582.12588.474 
humanGCA_018467005.1_HG02486.alt.pat.f1_v2lastz88.48088.31382.13788.470 
humanGCA_018472835.1_HG03579.alt.pat.f1_v2lastz88.47988.33082.22888.469 
humanGCA_018852595.1_HG02145.alt.pat.f1_v2lastz88.47988.32282.14288.469 
humanGCA_018471555.1_HG01952.alt.pat.f1_v2lastz88.47188.31182.05188.463 
humanGCA_018470435.1_HG02572.alt.pat.f1_v2lastz88.45488.29482.01788.444 
humanGCA_018506155.1_HG03098.alt.pat.f1_v2lastz88.43988.27582.06788.429 
Pan
pygmy chimpanzeeGCA_029289425.2_NHGRI_mPanPan1-v2.0_prilastz90.90890.39183.959 85.429
BonobopanPan3lastz93.13592.58587.673 89.406
ChimppanTro6lastz95.45194.807  89.996
chimpanzeeGCA_028858775.2_NHGRI_mPanTro3-v2.0_prilastz90.90590.38683.936 87.208
GCF_028858775.2GCF_028858775.2lastz90.90590.38783.93690.86687.208
BonobopanPan1lastz92.929   92.477
BonobopanPan2lastz92.68591.496  80.754
ChimppanTro5lastz95.35594.413  84.774
ChimppanTro4lastz93.112   80.949
ChimppanTro3lastz93.11492.003  80.986
pygmy chimpanzeeGCF_029289425.1_NHGRI_mPanPan1-v1.1-0.1.freeze_prilastz90.77990.27683.880 84.647
Gorilla
GorillagorGor4lastz92.859   86.457
western lowland gorillaGCF_029281585.2_NHGRI_mGorGor1-v2.1_prilastz90.35989.78483.39990.33377.665
GorillagorGor6lastz93.95793.21687.012 88.526
GorillagorGor5lastz94.69194.077  87.959
GorillagorGor3lastz88.005   82.448
western lowland gorillaGCA_029281585.2_NHGRI_mGorGor1-v2.0_prilastz90.65890.03383.505 77.765
Ponginae
Bornean orangutanGCA_028885625.2_NHGRI_mPonPyg2-v2.0_prilastz88.41887.63180.917 82.944
Sumatran orangutanGCA_028885655.2_NHGRI_mPonAbe1-v2.0_prilastz88.44587.66980.920 81.963
OrangutanponAbe3lastz92.59391.851  86.172
OrangutanponAbe2lastz89.18786.134  73.679
Sumatran orangutanGCF_028885655.1_NHGRI_mPonAbe1-v1.1-hic.freeze_prilastz88.31887.54380.870 79.343
Bornean orangutanGCF_028885625.1_NHGRI_mPonPyg2-v1.1-hic.freeze_prilastz88.28987.49780.782 82.081
Hylobatidae
northern white-cheeked gibbonGCF_006542625.1_Asia_NLE_v1lastz83.81782.69576.11883.76188.342
GibbonnomLeu3lastz86.37984.538  82.470
siamangGCA_028878055.2_NHGRI_mSymSyn1-v2.0_prilastz83.99082.83776.485 77.374
siamangGCF_028878055.1_NHGRI_mSymSyn1-v1.1-hic.freeze_prilastz80.36179.21873.053 75.772
Cercopithecoidea
Crab-eating macaquemacFas5lastz85.67583.880  82.256
BaboonpapAnu4lastz87.39885.484  83.231
BaboonpapAnu3lastz86.33684.291   
BaboonpapAnu2lastz84.179   80.732
olive baboonGCF_008728515.1_Panubis1.0lastz79.96478.39172.768 83.694
crab-eating macaqueGCF_012559485.2_MFA1912RKSv2lastz (swap)80.59979.54273.789 86.245
RhesusrheMac8lastz84.50683.158  74.235
RhesusrheMac10lastz83.85582.82678.262 81.580
DrillmanLeu1lastz82.49881.096   
RhesusrheMac3lastz80.828   77.365
crab-eating macaqueGCF_037993035.2_T2T-MFA8v1.1lastz (swap)80.88479.71773.57280.81379.367
crab-eating macaqueGCA_011100615.1_Macaca_fascicularis_6.0lastz79.77278.55072.504 82.359
Golden snub-nosed monkeyrhiRox1lastz85.10983.245  82.832
Pig-tailed macaquemacNem1lastz83.52482.167   
Sooty mangabeycerAty1lastz83.84782.532   
RhesusrheMac2lastz80.513   80.180
Green monkeychlSab2lastz84.39383.224  85.964
Black snub-nosed monkeyrhiBie1lastz83.06580.466   
Angolan colobuscolAng1lastz81.64180.010   
Proboscis monkeynasLar1lastz74.54162.687  69.453
Platyrrhini
Ma's night monkeyaotNan1lastz70.62968.808   
White-faced sapajoucebCap1lastz70.68369.316   
Squirrel monkeysaiBol1lastz70.56568.741  76.183
white-tufted-ear marmosetGCA_011100555.2_mCalJa1.2.pat.Xlastz66.35765.10760.62066.27269.596
white-tufted-ear marmosetGCF_011100555.1_mCalJa1.2.pat.Xlastz66.35765.10760.620 69.597
white-tufted-ear marmosetGCF_049354715.1_calJac240_prilastz (swap)66.27765.08960.60366.20168.194
MarmosetcalJac4lastz75.17872.69969.007 74.113
MarmosetcalJac3lastz71.70969.500  69.314
Tarsiiformes
TarsiertarSyr2lastz56.02253.222  45.287
Strepsirrhini
Sclater's lemureulFla1lastz33.32631.924   
Ring-tailed lemurGCF_020740605.2_mLemCat1.prilastz31.26230.34628.954 42.553
Black lemureulMac1lastz33.70832.264   
Mouse lemurmicMur3lastz29.72828.692   
gray mouse lemurGCA_040939475.2_M.murinus_Inina_pat1.0lastz27.367  26.67835.745
Mouse lemurmicMur2lastz53.530   61.488
gray mouse lemurGCF_040939455.1_M.murinus_Inina_mat1.0lastz27.367  26.67736.234
Coquerel's sifakaproCoq1lastz32.46730.954   
Mouse lemurmicMur1lastz42.653   40.960
BushbabyotoGar3lastz53.19650.742  58.843
slow lorisGCF_027406575.1_mNycCou1.prilastz14.76913.81413.598 15.384

Chain Track

The chain tracks show alignments of the query genome assemblies to the target genome using a gap scoring system that allows longer gaps than traditional affine gap scoring systems. It can also tolerate gaps in both query and target genomes simultaneously. These "double-sided" gaps can be caused by local inversions and overlapping deletions in both species.

The chain track displays boxes joined together by either single or double lines. The boxes represent aligning regions. Single lines indicate gaps that are largely due to a deletion in the query assembly or an insertion in the target assembly. Double lines represent more complex gaps that involve substantial sequence in both species. This may result from inversions, overlapping deletions, an abundance of local mutation, or an unsequenced gap in one species. In cases where multiple chains align over a particular region of the target genome, the chains with single-lined gaps are often due to processed pseudogenes, while chains with double-lined gaps are more often due to paralogs and unprocessed pseudogenes.

In the "pack" and "full" display modes, the individual feature names indicate the chromosome, strand, and location (in thousands) of the match for each matching alignment.

The types of chains measured in the table above:

A (swap) alignment was made with the query as the target genome, and then swapped to this target genome coordinates.

Net Track

The lastz alignments also have a net track, which shows the best query chain for every part of the target genome.

Display Conventions and Configuration

Chain Track

By default, the chains to chromosome-based assemblies are colored based on which chromosome they map to in the aligning organism. To turn off the coloring, check the "off" button next to: Color track based on chromosome.

To display only the chains of one chromosome in the aligning organism, enter the name of that chromosome (e.g. chr4) in box next to: Filter by chromosome.

Net Track

In full display mode, the top-level (level 1) chains are the largest, highest-scoring chains that span this region. In many cases gaps exist in the top-level chain. When possible, these are filled in by other chains that are displayed at level 2. The gaps in level 2 chains may be filled by level 3 chains and so forth.

Individual items in the display are categorized as one of four types (other than gap):

Methods

lastz alignments

The query genome was aligned to the target genome with lastz. The resulting alignments were converted into PSL format and fed into axtChain, which organizes all alignments between a single query chromosome and a single target chromosome into a group and creates a kd-tree out of the gapless subsections (blocks) of the alignments. A dynamic program was then run over the kd-trees to find the maximally scoring chains of these blocks.

The chains were sorted with the highest-scoring chains in the genome ranked first. The program chainNet was then used to place the chains one at a time, trimming them as necessary to fit into sections not already covered by a higher-scoring chain. During this process, a natural hierarchy emerged in which a chain that filled a gap in a higher-scoring chain was placed underneath that chain. The program netSyntenic was used to fill in information about the relationship between higher- and lower-level chains, such as whether a lower-level chain was syntenic or inverted relative to the higher-level chain. The program netClass was then used to fill in how much of the gaps and chains contained Ns (sequencing gaps) in one or both species and how much was filled with transposons inserted before and after the two organisms diverged. The syntenic and lift over chains were extracted from the net with netChainSubset.

lastz and axtChain parameters, lastz settings not listed here are the lastz defaults
assemblymethodlastz
version		lastz settingsaxtChain
minScore		axtChain
linearGap
hs1lastz1.04.03T=2 O=600 E=150 M=254 K=4500 Y=15000 Q=human_chimp.v2.q5000medium
GCA_054883265.1_H9_T2T.hap2lastz1.04.03T=2 O=600 E=150 M=254 K=4500 Y=15000 Q=human_chimp.v2.q5000medium
GCA_054883195.1_H9_T2T.hap1lastz1.04.03T=2 O=600 E=150 M=254 K=4500 Y=15000 Q=human_chimp.v2.q5000medium
GCA_018873775.2_hg01243.v3.0lastz1.04.03T=2 O=600 E=150 M=254 K=4500 Y=15000 Q=human_chimp.v2.q5000medium
GCA_018505845.1_HG03492.pri.mat.f1_v2lastz1.04.03T=2 O=600 E=150 M=254 K=4500 Y=15000 Q=human_chimp.v2.q5000medium
GCA_018852615.3_hg002v1.1.matlastz1.04.03T=2 O=600 E=150 M=254 K=4500 Y=15000 Q=human_chimp.v2.q5000medium
GCA_018505835.1_HG03492.alt.pat.f1_v2lastz1.04.03T=2 O=600 E=150 M=254 K=4500 Y=15000 Q=human_chimp.v2.q5000medium
GCA_018852605.3_hg002v1.1.patlastz1.04.03T=2 O=600 E=150 M=254 K=4500 Y=15000 Q=human_chimp.v2.q5000medium
GCA_018471345.1_HG01106.pri.mat.f1_v2lastz1.04.03T=2 O=600 E=150 M=254 K=4500 Y=15000 Q=human_chimp.v2.q5000medium
GCA_018506165.1_HG03098.pri.mat.f1_v2lastz1.04.03T=2 O=600 E=150 M=254 K=4500 Y=15000 Q=human_chimp.v2.q5000medium
GCA_018472715.1_HG00735.alt.pat.f1_v2lastz1.04.03T=2 O=600 E=150 M=254 K=4500 Y=15000 Q=human_chimp.v2.q5000medium
GCA_018469405.1_HG01258.pri.mat.f1_v2lastz1.04.03T=2 O=600 E=150 M=254 K=4500 Y=15000 Q=human_chimp.v2.q5000medium
GCA_018506965.1_HG005.pri.mat.f1_v2lastz1.04.03T=2 O=600 E=150 M=254 K=4500 Y=15000 Q=human_chimp.v2.q5000medium
GCA_018467165.1_HG01891.alt.pat.f1_v2lastz1.04.03T=2 O=600 E=150 M=254 K=4500 Y=15000 Q=human_chimp.v2.q5000medium
GCA_018506125.1_HG02055.pri.mat.f1_v2lastz1.04.03T=2 O=600 E=150 M=254 K=4500 Y=15000 Q=human_chimp.v2.q5000medium
GCA_018506975.1_HG00733.pri.mat.f1_v2lastz1.04.03T=2 O=600 E=150 M=254 K=4500 Y=15000 Q=human_chimp.v2.q5000medium
GCA_018467015.1_HG02486.pri.mat.f1_v2lastz1.04.03T=2 O=600 E=150 M=254 K=4500 Y=15000 Q=human_chimp.v2.q5000medium
GCA_018469425.1_HG03516.pri.mat.f1_v2lastz1.04.03T=2 O=600 E=150 M=254 K=4500 Y=15000 Q=human_chimp.v2.q5000medium
GCA_018470455.1_HG02886.pri.mat.f1_v2lastz1.04.03T=2 O=600 E=150 M=254 K=4500 Y=15000 Q=human_chimp.v2.q5000medium
GCA_018506955.1_HG00733.alt.pat.f1_v2lastz1.04.03T=2 O=600 E=150 M=254 K=4500 Y=15000 Q=human_chimp.v2.q5000medium
GCA_018469415.1_HG03516.alt.pat.f1_v2lastz1.04.03T=2 O=600 E=150 M=254 K=4500 Y=15000 Q=human_chimp.v2.q5000medium
GCA_018469925.1_HG02622.alt.pat.f1_v2lastz1.04.03T=2 O=600 E=150 M=254 K=4500 Y=15000 Q=human_chimp.v2.q5000medium
GCA_018470465.1_HG02886.alt.pat.f1_v2lastz1.04.03T=2 O=600 E=150 M=254 K=4500 Y=15000 Q=human_chimp.v2.q5000medium
GCA_018471095.1_HG00741.pri.mat.f1_v2lastz1.04.03T=2 O=600 E=150 M=254 K=4500 Y=15000 Q=human_chimp.v2.q5000medium
GCA_018472605.1_HG00621.pri.mat.f1_v2lastz1.04.03T=2 O=600 E=150 M=254 K=4500 Y=15000 Q=human_chimp.v2.q5000medium
GCA_018469665.1_HG01123.pri.mat.f1_v2.1lastz1.04.03T=2 O=600 E=150 M=254 K=4500 Y=15000 Q=human_chimp.v2.q5000medium
GCA_018466835.1_HG02257.alt.pat.f1_v2lastz1.04.03T=2 O=600 E=150 M=254 K=4500 Y=15000 Q=human_chimp.v2.q5000medium
GCA_018472765.1_HG00735.pri.mat.f1_v2lastz1.04.03T=2 O=600 E=150 M=254 K=4500 Y=15000 Q=human_chimp.v2.q5000medium
GCA_018504075.1_HG02723.alt.pat.f1_v2lastz1.04.03T=2 O=600 E=150 M=254 K=4500 Y=15000 Q=human_chimp.v2.q5000medium
GCA_018473305.1_HG03453.alt.pat.f1_v2lastz1.04.03T=2 O=600 E=150 M=254 K=4500 Y=15000 Q=human_chimp.v2.q5000medium
GCA_018472725.1_HG01071.alt.pat.f1_v2lastz1.04.03T=2 O=600 E=150 M=254 K=4500 Y=15000 Q=human_chimp.v2.q5000medium
GCA_018472855.1_HG03453.pri.mat.f1_v2lastz1.04.03T=2 O=600 E=150 M=254 K=4500 Y=15000 Q=human_chimp.v2.q5000medium
GCA_018471545.1_HG01952.pri.mat.f1_v2lastz1.04.03T=2 O=600 E=150 M=254 K=4500 Y=15000 Q=human_chimp.v2.q5000medium
GCA_018472595.1_HG00438.alt.pat.f1_v2lastz1.04.03T=2 O=600 E=150 M=254 K=4500 Y=15000 Q=human_chimp.v2.q5000medium
GCA_018466845.1_HG02257.pri.mat.f1_v2lastz1.04.03T=2 O=600 E=150 M=254 K=4500 Y=15000 Q=human_chimp.v2.q5000medium
GCA_018466985.1_HG02559.pri.mat.f1_v2lastz1.04.03T=2 O=600 E=150 M=254 K=4500 Y=15000 Q=human_chimp.v2.q5000medium
GCA_018469705.1_HG01361.alt.pat.f1_v2lastz1.04.03T=2 O=600 E=150 M=254 K=4500 Y=15000 Q=human_chimp.v2.q5000medium
GCA_018503285.1_NA18906.alt.pat.f1_v2lastz1.04.03T=2 O=600 E=150 M=254 K=4500 Y=15000 Q=human_chimp.v2.q5000medium
GCA_018471515.1_HG00438.pri.mat.f1_v2lastz1.04.03T=2 O=600 E=150 M=254 K=4500 Y=15000 Q=human_chimp.v2.q5000medium
GCA_018503255.1_NA18906.pri.mat.f1_v2lastz1.04.03T=2 O=600 E=150 M=254 K=4500 Y=15000 Q=human_chimp.v2.q5000medium
GCA_018504625.1_NA20129.alt.pat.f1_v2lastz1.04.03T=2 O=600 E=150 M=254 K=4500 Y=15000 Q=human_chimp.v2.q5000medium
GCA_018504055.1_HG02080.alt.pat.f1_v2lastz1.04.03T=2 O=600 E=150 M=254 K=4500 Y=15000 Q=human_chimp.v2.q5000medium
GCA_018472695.1_HG01928.pri.mat.f1_v2lastz1.04.03T=2 O=600 E=150 M=254 K=4500 Y=15000 Q=human_chimp.v2.q5000medium
GCA_018505825.1_HG02109.pri.mat.f1_v2lastz1.04.03T=2 O=600 E=150 M=254 K=4500 Y=15000 Q=human_chimp.v2.q5000medium
GCA_018472845.1_HG01978.alt.pat.f1_v2lastz1.04.03T=2 O=600 E=150 M=254 K=4500 Y=15000 Q=human_chimp.v2.q5000medium
GCA_018469685.1_HG01361.pri.mat.f1_v2lastz1.04.03T=2 O=600 E=150 M=254 K=4500 Y=15000 Q=human_chimp.v2.q5000medium
GCA_018469935.1_HG02717.pri.mat.f1_v2lastz1.04.03T=2 O=600 E=150 M=254 K=4500 Y=15000 Q=human_chimp.v2.q5000medium
GCA_018469695.1_HG01123.alt.pat.f1_v2.1lastz1.04.03T=2 O=600 E=150 M=254 K=4500 Y=15000 Q=human_chimp.v2.q5000medium
GCA_018471535.1_HG02148.pri.mat.f1_v2lastz1.04.03T=2 O=600 E=150 M=254 K=4500 Y=15000 Q=human_chimp.v2.q5000medium
GCA_018504085.1_HG02080.pri.mat.f1_v2lastz1.04.03T=2 O=600 E=150 M=254 K=4500 Y=15000 Q=human_chimp.v2.q5000medium
GCA_021951015.1_HG002.mat.cur.20211005lastz1.04.03T=2 O=600 E=150 M=254 K=4500 Y=15000 Q=human_chimp.v2.q5000medium
GCA_018503265.1_NA19240.alt.pat.f1_v2lastz1.04.03T=2 O=600 E=150 M=254 K=4500 Y=15000 Q=human_chimp.v2.q5000medium
GCA_018472565.1_HG00673.pri.mat.f1_v2lastz1.04.03T=2 O=600 E=150 M=254 K=4500 Y=15000 Q=human_chimp.v2.q5000medium
GCA_018503245.1_HG03486.alt.pat.f1_v2lastz1.04.03T=2 O=600 E=150 M=254 K=4500 Y=15000 Q=human_chimp.v2.q5000medium
GCA_018469955.1_HG02630.pri.mat.f1_v2lastz1.04.03T=2 O=600 E=150 M=254 K=4500 Y=15000 Q=human_chimp.v2.q5000medium
GCA_018471525.1_HG02148.alt.pat.f1_v2lastz1.04.03T=2 O=600 E=150 M=254 K=4500 Y=15000 Q=human_chimp.v2.q5000medium
GCA_018471065.1_HG01175.alt.pat.f1_v2lastz1.04.03T=2 O=600 E=150 M=254 K=4500 Y=15000 Q=human_chimp.v2.q5000medium
GCA_018469945.1_HG02630.alt.pat.f1_v2lastz1.04.03T=2 O=600 E=150 M=254 K=4500 Y=15000 Q=human_chimp.v2.q5000medium
GCA_018467155.1_HG01891.pri.mat.f1_v2lastz1.04.03T=2 O=600 E=150 M=254 K=4500 Y=15000 Q=human_chimp.v2.q5000medium
GCA_018504635.1_NA20129.pri.mat.f1_v2lastz1.04.03T=2 O=600 E=150 M=254 K=4500 Y=15000 Q=human_chimp.v2.q5000medium
GCA_018503575.1_HG02818.alt.pat.f1_v2lastz1.04.03T=2 O=600 E=150 M=254 K=4500 Y=15000 Q=human_chimp.v2.q5000medium
GCA_018504665.1_NA21309.alt.pat.f1_v2lastz1.04.03T=2 O=600 E=150 M=254 K=4500 Y=15000 Q=human_chimp.v2.q5000medium
GCA_018466855.1_HG02559.alt.pat.f1_v2lastz1.04.03T=2 O=600 E=150 M=254 K=4500 Y=15000 Q=human_chimp.v2.q5000medium
GCA_018469865.1_HG01358.pri.mat.f1_v2.1lastz1.04.03T=2 O=600 E=150 M=254 K=4500 Y=15000 Q=human_chimp.v2.q5000medium
GCA_018471105.1_HG00741.alt.pat.f1_v2lastz1.04.03T=2 O=600 E=150 M=254 K=4500 Y=15000 Q=human_chimp.v2.q5000medium
GCA_018472825.1_HG03579.pri.mat.f1_v2lastz1.04.03T=2 O=600 E=150 M=254 K=4500 Y=15000 Q=human_chimp.v2.q5000medium
GCA_018504655.1_NA21309.pri.mat.f1_v2lastz1.04.03T=2 O=600 E=150 M=254 K=4500 Y=15000 Q=human_chimp.v2.q5000medium
GCA_018505865.1_HG02109.alt.pat.f1_v2lastz1.04.03T=2 O=600 E=150 M=254 K=4500 Y=15000 Q=human_chimp.v2.q5000medium
GCA_018472685.1_HG01071.pri.mat.f1_v2lastz1.04.03T=2 O=600 E=150 M=254 K=4500 Y=15000 Q=human_chimp.v2.q5000medium
GCA_018473295.1_HG03540.pri.mat.f1_v2lastz1.04.03T=2 O=600 E=150 M=254 K=4500 Y=15000 Q=human_chimp.v2.q5000medium
GCA_018852585.1_HG02145.pri.mat.f1_v2lastz1.04.03T=2 O=600 E=150 M=254 K=4500 Y=15000 Q=human_chimp.v2.q5000medium
GCA_018472865.1_HG01978.pri.mat.f1_v2lastz1.04.03T=2 O=600 E=150 M=254 K=4500 Y=15000 Q=human_chimp.v2.q5000medium
GCA_018503525.1_HG03486.pri.mat.f1_v2lastz1.04.03T=2 O=600 E=150 M=254 K=4500 Y=15000 Q=human_chimp.v2.q5000medium
GCA_018503275.1_NA19240.pri.mat.f1_v2lastz1.04.03T=2 O=600 E=150 M=254 K=4500 Y=15000 Q=human_chimp.v2.q5000medium
GCA_018503585.1_HG02818.pri.mat.f1_v2lastz1.04.03T=2 O=600 E=150 M=254 K=4500 Y=15000 Q=human_chimp.v2.q5000medium
GCA_018504065.1_HG02723.pri.mat.f1_v2lastz1.04.03T=2 O=600 E=150 M=254 K=4500 Y=15000 Q=human_chimp.v2.q5000medium
GCA_018469875.1_HG02622.pri.mat.f1_v2lastz1.04.03T=2 O=600 E=150 M=254 K=4500 Y=15000 Q=human_chimp.v2.q5000medium
GCA_018473315.1_HG03540.alt.pat.f1_v2lastz1.04.03T=2 O=600 E=150 M=254 K=4500 Y=15000 Q=human_chimp.v2.q5000medium
GCA_018470445.1_HG02572.pri.mat.f1_v2lastz1.04.03T=2 O=600 E=150 M=254 K=4500 Y=15000 Q=human_chimp.v2.q5000medium
GCA_018504375.1_HG01243.pri.mat.f1_v2lastz1.04.03T=2 O=600 E=150 M=254 K=4500 Y=15000 Q=human_chimp.v2.q5000medium
GCA_018504365.1_HG01109.pri.mat.f1_v2lastz1.04.03T=2 O=600 E=150 M=254 K=4500 Y=15000 Q=human_chimp.v2.q5000medium
GCA_018471085.1_HG01175.pri.mat.f1_v2lastz1.04.03T=2 O=600 E=150 M=254 K=4500 Y=15000 Q=human_chimp.v2.q5000medium
GCA_018472575.1_HG00621.alt.pat.f1_v2lastz1.04.03T=2 O=600 E=150 M=254 K=4500 Y=15000 Q=human_chimp.v2.q5000medium
GCA_018472705.1_HG01928.alt.pat.f1_v2lastz1.04.03T=2 O=600 E=150 M=254 K=4500 Y=15000 Q=human_chimp.v2.q5000medium
GCA_018506945.1_HG005.alt.pat.f1_v2lastz1.04.03T=2 O=600 E=150 M=254 K=4500 Y=15000 Q=human_chimp.v2.q5000medium
GCA_018471075.1_HG01106.alt.pat.f1_v2lastz1.04.03T=2 O=600 E=150 M=254 K=4500 Y=15000 Q=human_chimp.v2.q5000medium
GCA_018469675.1_HG01258.alt.pat.f1_v2lastz1.04.03T=2 O=600 E=150 M=254 K=4500 Y=15000 Q=human_chimp.v2.q5000medium
GCA_018469965.1_HG01358.alt.pat.f1_v2.1lastz1.04.03T=2 O=600 E=150 M=254 K=4500 Y=15000 Q=human_chimp.v2.q5000medium
GCA_018504645.1_HG01109.alt.pat.f1_v2lastz1.04.03T=2 O=600 E=150 M=254 K=4500 Y=15000 Q=human_chimp.v2.q5000medium
GCA_018470425.1_HG02717.alt.pat.f1_v2lastz1.04.03T=2 O=600 E=150 M=254 K=4500 Y=15000 Q=human_chimp.v2.q5000medium
GCA_018505855.1_HG02055.alt.pat.f1_v2lastz1.04.03T=2 O=600 E=150 M=254 K=4500 Y=15000 Q=human_chimp.v2.q5000medium
GCA_018472585.1_HG00673.alt.pat.f1_v2lastz1.04.03T=2 O=600 E=150 M=254 K=4500 Y=15000 Q=human_chimp.v2.q5000medium
GCA_021950905.1_HG002.pat.cur.20211005lastz1.04.03T=2 O=600 E=150 M=254 K=4500 Y=15000 Q=human_chimp.v2.q5000medium
GCA_018504045.1_HG01243.alt.pat.f1_v2lastz1.04.03T=2 O=600 E=150 M=254 K=4500 Y=15000 Q=human_chimp.v2.q5000medium
GCA_018467005.1_HG02486.alt.pat.f1_v2lastz1.04.03T=2 O=600 E=150 M=254 K=4500 Y=15000 Q=human_chimp.v2.q5000medium
GCA_018472835.1_HG03579.alt.pat.f1_v2lastz1.04.03T=2 O=600 E=150 M=254 K=4500 Y=15000 Q=human_chimp.v2.q5000medium
GCA_018852595.1_HG02145.alt.pat.f1_v2lastz1.04.03T=2 O=600 E=150 M=254 K=4500 Y=15000 Q=human_chimp.v2.q5000medium
GCA_018471555.1_HG01952.alt.pat.f1_v2lastz1.04.03T=2 O=600 E=150 M=254 K=4500 Y=15000 Q=human_chimp.v2.q5000medium
GCA_018470435.1_HG02572.alt.pat.f1_v2lastz1.04.03T=2 O=600 E=150 M=254 K=4500 Y=15000 Q=human_chimp.v2.q5000medium
GCA_018506155.1_HG03098.alt.pat.f1_v2lastz1.04.03T=2 O=600 E=150 M=254 K=4500 Y=15000 Q=human_chimp.v2.q5000medium
GCA_029289425.2_NHGRI_mPanPan1-v2.0_prilastz1.04.03T=2 O=600 E=150 M=254 K=4500 Y=15000 Q=human_chimp.v2.q5000medium
panPan3lastz1.04.03T=2 O=600 E=150 M=254 K=4500 L=4500 Y=15000 Q=human_chimp.v2.q3000medium
panTro6lastz1.04.00T=2 O=600 E=150 M=254 K=4500 L=4500 Y=15000 Q=human_chimp.v2.q5000medium
GCA_028858775.2_NHGRI_mPanTro3-v2.0_prilastz1.04.03T=2 O=600 E=150 M=254 K=4500 Y=15000 Q=human_chimp.v2.q5000medium
GCF_028858775.2lastz1.04.03T=2 O=600 E=150 M=254 K=4500 Y=15000 Q=human_chimp.v2.q5000medium
panPan1lastz1.03.54T=2 O=400 E=30 M=254 X=1000 Y=3400 Q=hg38.panPan1.tuning.Q.txt3000medium
panPan2lastz1.03.66T=2 O=600 E=150 M=254 K=4500 L=4500 Y=15000 Q=human_chimp.v2.q3000medium
panTro5lastz1.03.66T=2 O=600 E=150 M=254 K=4500 L=4500 Y=15000 Q=human_chimp.v2.q5000medium
panTro4lastz1.03.52O=600 E=150 M=254 T=2 Y=15000 K=4500 Q=human_chimp.v2.q5000medium
panTro3lastz1.03.66T=2 O=600 E=150 M=254 K=4500 L=4500 Y=15000 Q=human_chimp.v2.q5000medium
GCF_029289425.1_NHGRI_mPanPan1-v1.1-0.1.freeze_prilastz1.04.03T=2 O=600 E=150 M=254 K=4500 Y=15000 Q=human_chimp.v2.q5000medium
gorGor4lastz1.03.66T=2 O=600 E=150 M=254 K=4500 Y=15000 Q=human_chimp.v2.q3000medium
GCF_029281585.2_NHGRI_mGorGor1-v2.1_prilastz1.04.03T=2 O=600 E=150 M=254 K=4500 Y=15000 Q=human_chimp.v2.q5000medium
gorGor6lastz1.04.00T=2 O=600 E=150 M=254 K=4500 Y=15000 Q=human_chimp.v2.q3000medium
gorGor5lastz1.03.66T=2 O=600 E=150 M=254 K=4500 Y=15000 Q=human_chimp.v2.q3000medium
gorGor3lastz1.03.54T=2 O=400 E=30 M=254 X=1000 Y=3400 Q=hg38.gorGor3.tuning.Q.txt3000medium
GCA_029281585.2_NHGRI_mGorGor1-v2.0_prilastz1.04.03T=2 O=600 E=150 M=254 K=4500 Y=15000 Q=human_chimp.v2.q5000medium
GCA_028885625.2_NHGRI_mPonPyg2-v2.0_prilastz1.04.03T=2 O=600 E=150 M=254 K=4500 Y=15000 Q=human_chimp.v2.q5000medium
GCA_028885655.2_NHGRI_mPonAbe1-v2.0_prilastz1.04.03T=2 O=600 E=150 M=254 K=4500 Y=15000 Q=human_chimp.v2.q5000medium
ponAbe3lastz1.04.00T=2 O=600 E=150 M=254 K=4500 L=4500 Y=15000 Q=human_chimp.v2.q5000medium
ponAbe2lastz1.03.52O=600 E=150 M=254 T=2 Y=15000 K=4500 Q=human_chimp.v2.q5000medium
GCF_028885655.1_NHGRI_mPonAbe1-v1.1-hic.freeze_prilastz1.04.03T=2 O=600 E=150 M=254 K=4500 Y=15000 Q=human_chimp.v2.q5000medium
GCF_028885625.1_NHGRI_mPonPyg2-v1.1-hic.freeze_prilastz1.04.03T=2 O=600 E=150 M=254 K=4500 Y=15000 Q=human_chimp.v2.q5000medium
GCF_006542625.1_Asia_NLE_v1lastz1.04.03T=2 O=600 E=150 M=254 K=4500 Y=15000 Q=human_chimp.v2.q5000medium
nomLeu3lastz1.03.54T=2 O=400 E=30 M=254 X=1000 Y=3400 Q=hg38.nomLeu3.tuning.Q.txt3000medium
GCA_028878055.2_NHGRI_mSymSyn1-v2.0_prilastz1.04.03T=2 O=600 E=150 M=254 K=4500 Y=15000 Q=human_chimp.v2.q5000medium
GCF_028878055.1_NHGRI_mSymSyn1-v1.1-hic.freeze_prilastz1.04.03T=2 O=600 E=150 M=254 K=4500 Y=15000 Q=human_chimp.v2.q5000medium
macFas5lastz1.03.54T=2 O=400 E=30 M=254 X=1000 Y=3400 Q=hg38.macFas5.tuning.Q.txt3000medium
papAnu4lastz1.03.66M=2543000medium
papAnu3lastz1.03.66M=2543000medium
papAnu2lastz1.03.54T=2 O=400 E=30 M=254 X=1000 Y=3400 Q=hg38.papAnu2.tuning.Q.txt3000medium
GCF_008728515.1_Panubis1.0lastz1.04.03T=2 O=600 E=150 M=254 K=4500 Y=15000 Q=human_chimp.v2.q5000medium
GCF_012559485.2_MFA1912RKSv2lastz (swap)1.04.03T=2 O=600 E=150 M=254 K=4500 Y=15000 Q=human_chimp.v2.q5000medium
rheMac8lastz1.03.66M=254 Q=human_chimp.v2.q O=600 E=150 K=4500 Y=15000 T=25000medium
rheMac10lastz1.04.00M=254 Q=human_chimp.v2.q O=600 E=150 K=4500 Y=15000 T=25000medium
manLeu1lastz1.03.66M=254 Q=human_chimp.v2.q O=600 E=150 K=4500 Y=15000 T=25000medium
rheMac3lastz1.03.66M=254 Q=human_chimp.v2.q O=600 E=150 K=4500 Y=15000 T=25000medium
GCF_037993035.2_T2T-MFA8v1.1lastz (swap)1.04.03T=2 O=600 E=150 M=254 K=4500 Y=15000 Q=human_chimp.v2.q5000medium
GCA_011100615.1_Macaca_fascicularis_6.0lastz1.04.03T=2 O=600 E=150 M=254 K=4500 Y=15000 Q=human_chimp.v2.q5000medium
rhiRox1lastz1.03.54T=2 O=400 E=30 M=254 X=1000 Y=3400 Q=hg38.rhiRox1.tuning.Q.txt3000medium
macNem1lastz1.03.66M=254 Q=human_chimp.v2.q O=600 E=150 K=4500 Y=15000 T=25000medium
cerAty1lastz1.03.66M=254 Q=human_chimp.v2.q O=600 E=150 K=4500 Y=15000 T=25000medium
rheMac2lastz1.03.52M=254 Q=human_chimp.v2.q O=600 E=150 K=4500 Y=15000 T=25000medium
chlSab2lastz1.03.52M=254 Q=human_chimp.v2.q O=600 E=150 K=4500 Y=15000 T=25000medium
rhiBie1lastz1.03.66M=254 Q=human_chimp.v2.q O=600 E=150 K=4500 Y=15000 T=25000medium
colAng1lastz1.03.66M=254 Q=human_chimp.v2.q O=600 E=150 K=4500 Y=15000 T=25000medium
nasLar1lastz1.03.54T=2 O=400 E=30 M=254 X=1000 Y=3400 Q=hg38.nasLar1.tuning.Q.txt3000medium
aotNan1lastz1.03.66M=254 Q=human_chimp.v2.q O=600 E=150 K=4500 Y=15000 T=25000medium
cebCap1lastz1.03.66M=254 Q=human_chimp.v2.q O=600 E=150 K=4500 Y=15000 T=25000medium
saiBol1lastz1.03.54T=2 O=400 E=30 M=254 X=1000 Y=3400 Q=hg38.saiBol1.tuning.Q.txt3000medium
GCA_011100555.2_mCalJa1.2.pat.Xlastz1.04.03T=2 O=600 E=150 M=254 K=4500 Y=15000 Q=human_chimp.v2.q5000medium
GCF_011100555.1_mCalJa1.2.pat.Xlastz1.04.03T=2 O=600 E=150 M=254 K=4500 Y=15000 Q=human_chimp.v2.q5000medium
GCF_049354715.1_calJac240_prilastz (swap)1.04.03T=2 O=600 E=150 M=254 K=4500 Y=15000 Q=human_chimp.v2.q5000medium
calJac4lastz1.04.03M=2543000medium
calJac3lastz1.03.54T=2 O=400 E=30 M=254 X=1000 Y=3400 Q=hg38.calJac3.tuning.Q.txt3000medium
tarSyr2lastz1.03.54T=2 O=400 E=30 M=50 X=1000 Y=3400 Q=hg38.tarSyr2.tuning.Q.txt3000medium
eulFla1lastz1.03.66M=254 Q=human_chimp.v2.q O=600 E=150 K=4500 Y=15000 T=25000medium
GCF_020740605.2_mLemCat1.prilastz1.04.03T=2 O=600 E=150 M=254 K=4500 Y=15000 Q=human_chimp.v2.q5000medium
eulMac1lastz1.03.66M=254 Q=human_chimp.v2.q O=600 E=150 K=4500 Y=15000 T=25000medium
micMur3lastz1.03.66M=254 Q=human_chimp.v2.q O=600 E=150 K=4500 Y=15000 T=23000medium
GCA_040939475.2_M.murinus_Inina_pat1.0lastz1.04.03T=2 O=600 E=150 M=254 K=4500 Y=15000 Q=human_chimp.v2.q 
micMur2lastz1.03.66T=2 O=400 E=30 M=254 X=1000 Y=3400 Q=hg38.micMur2.tuning.Q.txt3000medium
GCF_040939455.1_M.murinus_Inina_mat1.0lastz1.04.03T=2 O=600 E=150 M=254 K=4500 Y=15000 Q=human_chimp.v2.q 
proCoq1lastz1.03.66M=254 Q=human_chimp.v2.q O=600 E=150 K=4500 Y=15000 T=25000medium
micMur1lastz1.03.54T=2 O=400 E=30 M=254 X=1000 Y=3400 Q=hg38.micMur1.tuning.Q.txt3000medium
otoGar3lastz1.03.66T=2 O=400 E=30 M=2543000medium
GCF_027406575.1_mNycCou1.prilastz1.04.03T=2 O=600 E=150 M=254 K=4500 Y=15000 Q=human_chimp.v2.q5000medium

minimap2 alignments

The query genome was aligned to the target genome with minimap2, one job per target sequence against the whole query genome. The minimap2 alignment preset was selected from the mash distance between the two assemblies. The resulting PAF alignments were converted into PSL format using the pafToPsl program, and fed into axtChain to construct the chains in the same way as for the lastz alignments. The chain was placed with chainNet, and the program netChainSubset was used to extract the best/longest syntenic part of that net back out of the chain, giving the lift over chain.

minimap2 version, mash distance between the target and query assemblies, the minimap2 alignment preset selected from that distance, and the minimap2 command used for each target sequence job
assemblymethodminimap2
version		mash
distance		presetcommand
hs1minimap22.31-r13020.000984402asm5minimap2 -cx asm5 -N 5 -p 0.8 -t 8 target.fa query.fa > out.paf

Data Access

The lift over chain files are available in the liftOver directory of our download server, for use with the liftOver command line tool, available from the utilities download directory. The complete lastz chain and net files are in the vsHs1, vsGCA_054883265.1, vsGCA_054883195.1, vsGCA_018873775.2, vsGCA_018505845.1, vsGCA_018852615.3, vsGCA_018505835.1, vsGCA_018852605.3, vsGCA_018471345.1, vsGCA_018506165.1, vsGCA_018472715.1, vsGCA_018469405.1, vsGCA_018506965.1, vsGCA_018467165.1, vsGCA_018506125.1, vsGCA_018506975.1, vsGCA_018467015.1, vsGCA_018469425.1, vsGCA_018470455.1, vsGCA_018506955.1, vsGCA_018469415.1, vsGCA_018469925.1, vsGCA_018470465.1, vsGCA_018471095.1, vsGCA_018472605.1, vsGCA_018469665.1, vsGCA_018466835.1, vsGCA_018472765.1, vsGCA_018504075.1, vsGCA_018473305.1, vsGCA_018472725.1, vsGCA_018472855.1, vsGCA_018471545.1, vsGCA_018472595.1, vsGCA_018466845.1, vsGCA_018466985.1, vsGCA_018469705.1, vsGCA_018503285.1, vsGCA_018471515.1, vsGCA_018503255.1, vsGCA_018504625.1, vsGCA_018504055.1, vsGCA_018472695.1, vsGCA_018505825.1, vsGCA_018472845.1, vsGCA_018469685.1, vsGCA_018469935.1, vsGCA_018469695.1, vsGCA_018471535.1, vsGCA_018504085.1, vsGCA_021951015.1, vsGCA_018503265.1, vsGCA_018472565.1, vsGCA_018503245.1, vsGCA_018469955.1, vsGCA_018471525.1, vsGCA_018471065.1, vsGCA_018469945.1, vsGCA_018467155.1, vsGCA_018504635.1, vsGCA_018503575.1, vsGCA_018504665.1, vsGCA_018466855.1, vsGCA_018469865.1, vsGCA_018471105.1, vsGCA_018472825.1, vsGCA_018504655.1, vsGCA_018505865.1, vsGCA_018472685.1, vsGCA_018473295.1, vsGCA_018852585.1, vsGCA_018472865.1, vsGCA_018503525.1, vsGCA_018503275.1, vsGCA_018503585.1, vsGCA_018504065.1, vsGCA_018469875.1, vsGCA_018473315.1, vsGCA_018470445.1, vsGCA_018504375.1, vsGCA_018504365.1, vsGCA_018471085.1, vsGCA_018472575.1, vsGCA_018472705.1, vsGCA_018506945.1, vsGCA_018471075.1, vsGCA_018469675.1, vsGCA_018469965.1, vsGCA_018504645.1, vsGCA_018470425.1, vsGCA_018505855.1, vsGCA_018472585.1, vsGCA_021950905.1, vsGCA_018504045.1, vsGCA_018467005.1, vsGCA_018472835.1, vsGCA_018852595.1, vsGCA_018471555.1, vsGCA_018470435.1, vsGCA_018506155.1, vsGCA_029289425.2, vsPanPan3, vsPanTro6, vsGCA_028858775.2, vsGCF_028858775.2, vsPanPan1, vsPanPan2, vsPanTro5, vsPanTro4, vsPanTro3, vsGCF_029289425.1, vsGorGor4, vsGCF_029281585.2, vsGorGor6, vsGorGor5, vsGorGor3, vsGCA_029281585.2, vsGCA_028885625.2, vsGCA_028885655.2, vsPonAbe3, vsPonAbe2, vsGCF_028885655.1, vsGCF_028885625.1, vsGCF_006542625.1, vsNomLeu3, vsGCA_028878055.2, vsGCF_028878055.1, vsMacFas5, vsPapAnu4, vsPapAnu3, vsPapAnu2, vsGCF_008728515.1, vsGCF_012559485.2, vsRheMac8, vsRheMac10, vsManLeu1, vsRheMac3, vsGCF_037993035.2, vsGCA_011100615.1, vsRhiRox1, vsMacNem1, vsCerAty1, vsRheMac2, vsChlSab2, vsRhiBie1, vsColAng1, vsNasLar1, vsAotNan1, vsCebCap1, vsSaiBol1, vsGCA_011100555.2, vsGCF_011100555.1, vsGCF_049354715.1, vsCalJac4, vsCalJac3, vsTarSyr2, vsEulFla1, vsGCF_020740605.2, vsEulMac1, vsMicMur3, vsGCA_040939475.2, vsMicMur2, vsGCF_040939455.1, vsProCoq1, vsMicMur1, vsOtoGar3, vsGCF_027406575.1 download directories.

Credits

lastz was developed by Robert Harris, Pennsylvania State University.

minimap2 was developed by Heng Li.

The mash program, used to estimate the divergence between the target and query assemblies and automatically select the minimap2 alignment preset, was developed by Brian Ondov, Todd Treangen, and colleagues at the National Biodefense Analysis and Countermeasures Center and the University of Maryland.

The axtChain program was developed at the University of California at Santa Cruz by Jim Kent with advice from Webb Miller and David Haussler.

The browser display and database storage of the chains and nets were created by Robert Baertsch and Jim Kent.

The chainNet, netSyntenic, and netClass programs were developed at the University of California Santa Cruz by Jim Kent.

References

Harris RS. Improved pairwise alignment of genomic DNA. Ph.D. Thesis. Pennsylvania State University, USA. 2007.

Chiaromonte F, Yap VB, Miller W. Scoring pairwise genomic sequence alignments. Pac Symp Biocomput. 2002:115-26. PMID: 11928468

Schwartz S, Kent WJ, Smit A, Zhang Z, Baertsch R, Hardison RC, Haussler D, Miller W. Human-mouse alignments with BLASTZ. Genome Res. 2003 Jan;13(1):103-7. PMID: 12529312; PMC: PMC430961

Li H. Minimap2: pairwise alignment for nucleotide sequences. Bioinformatics. 2018 Sep 15;34(18):3094-3100. PMID: 29750242; PMC: PMC6137996

Ondov BD, Treangen TJ, Melsted P, Mallonee AB, Bergman NH, Koren S, Phillippy AM. Mash: fast genome and metagenome distance estimation using MinHash. Genome Biol. 2016 Jun 20;17(1):132. PMID: 27323842; PMC: PMC4915045

Kent WJ, Baertsch R, Hinrichs A, Miller W, Haussler D. Evolution's cauldron: duplication, deletion, and rearrangement in the mouse and human genomes. Proc Natl Acad Sci U S A. 2003 Sep 30;100(20):11484-9. PMID: 14500911; PMC: PMC208784