Table 1.

Reinterpretation of GCs by Yang et al. from sequencing data for two F₂ plants (C94 and C95) and listed for various sizes

Factors	2 Kb ∼10 Kb	20 bp ∼2 Kb	2 bp ∼20 bp	1 bp
Transpositions, %	14.10	2.91	0.15	—
Copy number variants, %	30.77	12.56	0.30	—
Other type of SVs, %	7.69	1.79	0.45	—
Misplacement of reads,* %	8.97	16.14	4.69	2.64
HDRs,† %	19.23	6.95	1.06	—
Failure of gap-opening, %	2.56	32.96	87.44	32.90
Incorrect SNPs,‡ %	_	3.36	2.12	1.98
Correct SNPs but no GCs,§ %	12.82	19.73	3.78	62.46
Other factors,¶ %	3.85	3.59	—	—
Sum, %	100	100	100	99.98
Total reported GCs	78	446	661	9,924

^*To distinguish from the type based on CNVs, this phrase refers to wrongly placing of a few reads, usually insufficient to contribute an extra coverage.

^†HDRs refer to highly divergent regions with insufficient identities between two ecotypes resulting in low read coverage of Ler. SNPs predicted in these regions lack enough support from sequencing data.

^‡SNPs predicted by Yang et al. (32) are not supported by sufficient Col/Ler genotypic reads.

^§SNPs predicted by Yang et al. are either consistent with those from 1001 Genomes (35, 36), or supported by resequencing reads of Col/Ler. However, reads from the corresponding F₂ plants do not support GCs in these SNP loci.

^¶Refers to false positive “GCs” due to incorrect prediction of CO borders, or the absence of reads mapped to the regions of GCs from the corresponding F₂ plant.