The original fluorescence image files obtained from the X-ten platform were transformed to short reads (raw data) by base calling and the short reads were saved in FASTQ format, containing sequence information and corresponding sequencing quality information. Reads were filtered as follows: 1) Discard paired reads if either one read contained adapter contamination (>10 nucleotides aligned to the adapter, allowing ≤ 10% mismatches); 2) Discard paired reads if more than 10% of bases were uncertain in either one read; 3) Discard paired reads if the proportion of low quality (Phred quality <5) bases was over 50% in either one read. All the downstream bioinformatic analyses were performed on high-quality clean data.

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