Addi ional File 1
auN(A) and Misassemblies as compu ed by Quas
Fig. 1 (Le :) auN, (Middle:) misassemblies and (Righ :) auNA as compu ed by Quas o he new
sca olds p oduced by AncST.
Fig. 2 (Le :) auN, (Middle:) misassemblies and (Righ :) auNA as compu ed by Quas o he new
sca olds p oduced by n Join.
Fig. 3 (Le :) auN, (Middle:) misassemblies and (Righ :) auNA as compu ed by Quas o he new
sca olds p oduced by Ragou 2.
1
Fig. 4 (Le :) auN, (Middle:) misassemblies and (Righ :) auNA as compu ed by Quas o he new
sca olds p oduced by CSAR.
Fig. 5 (Le :) auN, (Middle:) misassemblies and (Righ :) auNA as compu ed by Quas o he new
sca olds p oduced by RagTag.
2
Addi ional File 2
Co e age o Main Human Ch omosomes wi h Quas Alignmen s o New
Sca olds
Fig. 6 Shown a e da a based on he esul s o sca olding he human genome wi h a leas 5
% ea anged sequence agains (le :) chimp and ( igh :) chimp and bonobo om AncST. Rela i e
co e age (X-axis) o 24 human ch omosomes (22+X+Y) (Y-axis) by all alignmen s p oduced by Quas .
Fi s , he o al leng h o all alignmen s o a e e ence ch omosome wi h any new sca olds is no ed.
Then each new sca old is assigned i s ela i e co e age as he p opo ion o he leng h o i s alignmen s
wi h he e e ence. Sca olds co e ing a leas 50 % o a e e ence a e colo ed and he es is g ay.
Rela i e co e age by one con ig is bo de ed by whi e e ical lines.
Fig. 7 Shown a e da a based on he esul s o sca olding he human genome wi h a leas 5 %
ea anged sequence agains (le :) chimp and ( igh :) chimp and bonobo om n Join. De ails can
be ound in cap ion o 6.
3
Fig. 8 Shown a e da a based on he esul s o sca olding he human genome wi h a leas 5 %
ea anged sequence agains (le :) chimp and ( igh :) chimp and bonobo om RagTag. De ails can
be ound in cap ion o 6.
Fig. 9 Shown a e da a based on he esul s o sca olding he human genome wi h a leas 5 %
ea anged sequence agains (le :) chimp and ( igh :) chimp and bonobo om CSAR. De ails can be
ound in cap ion o 6.
4
Fig. 10 Shown a e da a based on he esul s o sca olding he human genome wi h a leas 5 %
ea anged sequence agains chimp and bonobo om Ragou 2. De ails can be ound in cap ion o 6.
5
Addi ional File 3
D osophila Assemblies Used
Table 1 Genomes o D osophila species used. same in NCBI Re .(e ence) means ha he Con ig o Sca old le el
assembly used as a sca olding a ge is also ma ked as he e e ence ch omosome o his species on NCBI.
Accession Species Abb e ia ion Assembly Le el NCBI Re . Iden i ie
GCA 018904445.1 D. sechellia Dsec Sca old GCF 004382195.2 A
GCA 039725655.1 D. simulans Dsim Con ig GCF 016746395.2 B
GCA 000778455.1 D. melanogas e Dmel Con ig GCF 000001215.4 C
GCA 018904385.1 D. yakuba Dyac Con ig GCF 016746365.2 D
GCA 018904525.1 D. e ec a De e Sca old GCF 003286155.1 E
GCA 018904475.1 D. mau i iana Dmau Sca old GCF 004382145.1 F
GCA 018903625.1 D. eissie i D ei Con ig GCF 016746235.2 G
GCA 005876975.1 D. o ena Do e Con ig same H
GCF 018153835.1 D. eug acilis Deug Con ig same I
GCA 018148935.1 D. bia mipes Dbia Con ig GCF 025231255.1 J
GCA 018152695.1 D. akahashii D ak Con ig GCF 030179915.1 K
GCF 018152265.1 D. icusphila D ic Con ig same L
GCF 018152505.1 D. elegans Dele Con ig same M
GCF 018152115.1 D. hopaloa D ho Con ig same N
GCA 008042655.1 D. bu lai Dbu Sca old same O
GCA 018152535.1 D. kikkawai Dkik Con ig GCF 030179895.1 P
GCA 008042735.1 D. leon ia Dleo Sca old same Q
GCA 021223765.1 D. bipec ina a Dbip Sca old GCF 030179905.1 R
GCA 018153235.1 D. male ko liana Dmal Con ig same S
GCA 018148915.1 D. ananassae Dana Con ig same T
6
Addi ional File 4
Sca olding E alua ion o D osophilas
Fig. 11 auN as compu ed by Quas o 20 D osophila newly sca olded species. The new sca olds
o compu ed by RagTag o D osophila bia mipes (J) show an auN o a ound 180 million while
we se he uppe limi o he y-axis o 75 million o clea e display. Iden i ie co espondence and
u he de ails in Table 1.
7
Fig. 12 Numbe i misassemblies as compu ed by Quas o he 11 D osophila newly sca olded
species wi h a ch omosome- scale e e ence genome on NCBI. Fu he de ails in Table 1.
8
Addi ional File 5
Assessmen o Re e ence Ch omosome Co e age wi h New Sca olds
Fig. 13 Shown a e all e e ence ch omosomes o he D osophila bia mipes o icial e e ence assem-
bly on NCBI on he y-axis. Fo each e e ence ch omosome, he uppe ba displays esul s compu ed
wi h he AncST-based pipeline and he lowe ba he ones om RagTag. The ba s a e s acked acco ding
o he co e age o each e e ence ch omosome by new sca olds om he espec i e ool. The co e age
is es ima ed by he o al alignmen leng h o all minimap alignmen s eco ded in he ou pu o Quas .
Only con igs/sca olds co e ing a leas a hi d o he o al alignmen leng h a e d awn colo ed while
he es is kep g ay. Each colo ep esen s a di e en new sca old which a e indica ed in he legend.
9
Fig. 26 Le : auNA om Quas o each D osophila species wi h a ch omosome-le el e e ence as
in main ex . Righ : Same analysis as in main ex bu using AncST weigh s o RagTag and n Join.
16
