Table 7 Number of variants detected for each maize line as compared to inbred line B73.

From: High-quality chromosome-scale genome assemblies of 29 maize inbred lines of European breeding relevance

Inbred line

Number of SNPs

Number of indels

Number of SVs

A632

8,831,074

993,629

85,074

B14

7,370,699

889,197

73,610

B37

11,061,066

1,151,188

89,875

CM174

9,976,071

1,088,490

90,590

CO255

15,072,571

1,505,472

118,730

DK3IIH6

12,979,891

1,322,942

108,468

DKFBLL

3,100,121

434,673

31,717

DKMM501D

13,317,829

1,374,340

110,652

DKPB80

1,601,782

311,382

19,480

EA1197

14,376,326

1,435,168

125,021

F120

15,352,014

1,525,832

122,866

F2

15,823,786

1,570,288

119,594

F252

13,405,714

1,391,609

108,710

F283

14,712,732

1,457,867

121,289

F331

13,264,044

1,333,745

115,224

F353

12,055,207

1,261,391

112,471

F4

16,050,744

1,598,782

119,325

F7130

14,307,725

1,448,508

117,640

GF111

15,148,796

1,492,753

123,741

LH123Ht

11,161,491

1,208,926

104,891

LH82

12,255,189

1,285,313

105,323

Lo3

14,238,292

1,426,952

124,129

MBS847

12,026,058

1,260,694

106,079

PHG35

12,564,429

1,305,163

106,186

PHG39

9,345,231

965,746

94,057

PHN82

11,649,929

1,224,619

104,339

PHP02

12,203,337

1,260,503

104,832

PHR03

11,593,591

1,195,478

104,471

PHW52

7,035,096

800,381

66,397

  1. SNPs: Single Nucleotide Polymorphisms, indels: insertion/deletions shorter than 50 bp, SVs: structural variants longer than 50 pb. Counts were obtained using the –snps and –indels flag of bcftools, for SNPs and indels respectively with the condition of a least one alternative allele (COUNT(GT =“alt”) > 0), and simply using this condition for the number of SVs on the associated structural variants vcf files.
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