Discovery of new PT sites using deep resequencing and the inconsistency between extensive PT modified sites and the PT linked dinucleotides abundance of the <i>E</i>. <i>coli</i> B7A genome.

(A) Plotted PT modified sites detected with the increase of sequencing depth. (B) The PT abundances quantified by LC-MS/MS. Error bars are calculated as the s. d. of three biological replicates. (C) Accumulation of sequencing depth contributed to the revealing of more PT-modified sites. Here, one loci are chosen for each case as an example to illustrate each situation: some sites like loci 33670, the ended reads number of which reached 50 at 200 × was detected as PT modified sites, while some sites like 3865 loci only be regarded as PT modified site when the sequencing depth increase up to 400 ×. In other word, if the sequencing depth is only 200 ×, they would be identified as non-PT modified sites. Similar phenome can be seen at the sites like 19366 loci (600 ×), 5390 loci (800 ×) and 1138 loci (1000 ×). Also, some sites like 301 loci, the ended reads number of which could not reach 50 even the sequencing depth increased up to 1000 ×. While, some GAAC/GTTC sites like 614 loci and some randomly selected non GAAC/GTTC sites like 2024 loci, the ended reads number could not be detected at each five gradient sequence depth. (D) The schematic molecular PT modification. The specific GAAC/GTTC site is partially modified and with different modification frequency. High frequency sites are easy to detected and low frequency sites need further sequencing depth.