The high-quality reads from each sample were aligned against the gene catalog by SOAP2.21 with the criterion of identity > 90% [63]. In our sequence-based profiling analysis, the alignments that met one of the following criteria as previously described could be accepted [67]: (i) an entire of a paired-end read can be mapped onto a gene with the correct insert-size and (ii) only when the one end of paired-read was mapped outside the genic region; the other end of reads can be mapped onto the end of a gene. In both cases, the mapped read was counted as one copy. The formula used in this study for calculating gene relative abundance is similar to RPKM/FPKM (reads per kilobase of exon model per million mapped reads/fragments per kilobase of exon model per million mapped fragments) value. Accordingly, for any sample 푆, we calculated the abundance as follows:

Step 1: Calculation of the copy number of each gene:

Step 2: Calculation of the relative abundance of gene i:

ai: The relative abundance of gene i in sample S

Li: The length of gene i

xi: The times which gene i can be detected in sample S (the number of mapped reads)

bi: The copy number of gene i in the sequenced data from S.

j: The iHSMGC gene number.

The value of bi standardizes the effect of gene length in Step 1. The value of bijbi standardizes the effect of sequencing depth in Step 2.

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