Table 2:

A comparison of mapping procedures and filters used in mRNA methylation studies

	Edelheit, S., et al., PLoS Genet, 2013[11]	Amort, T., et al., Genome Biol, 2017[13]	Yang, X, et al., Cell Res, 2017[14]	Huang, T., et al., 2019[17]
Mapping tool	Novoalign	meRanGs (STAR)	Bismark (Bowtie2)	HISTA2/Bowtie2
Reference	Genome/Transcriptome	Genome	Genome → Transcriptome → exon-exon junctions	Genome → Transcriptome
Reads filters	Identical reads were considered as a single read to eliminate PCR duplicate in the genome-based analysis; 40-nt long reads with ≥ 3 unconverted cytosines were eliminated	Potential PCR duplicates were filtered by defining at most five identical reads	Reads with > 30% unconverted cytosines were eliminated	Gini coefficient was used to determine C-cutoff to remove the reads with unconverted cytosines
Sites filters	Coverage depth ≥ 5; Methylation level ≥ threshold; Base quality >20; P value < 0.01	Coverage depth ≥ 10; Methylation level≥ 0.2; Base quality ≥35 for single-end reads; Base quality ≥30 for paired-end reads; FDR < 0.01	Coverage depth ≥ 30; Methylation level≥ 0.1; Methylated cytosine depth ≥ 5	Coverage depth ≥ 20; Methylation level ≥0.1; Methylated cytosine depth ≥ 3; Base quality ≥ 30; P value <0.001
Other filters	Candidate methylation sites within 10 nt from an additional candidate site were discarded	10 bases on the 5’ end of forward reads and 7 bases on the 5’ end of reverse reads were excluded from methylation calling; RNA secondary stmcture was conducted with RNA fold to discard base-paired sites; The presence of candidate site in all three replicates was required	The presence of candidate site in two replicates was required	Signal ratio filter was used to further remove sites in conversion resistant regions; Excluded genes with low conversion rate; The presence of candidate site in the biological replicates was required