Table 5 5meDIP-seq alignment statistics.

From: Analysis of diet-induced differential methylation, expression, and interactions of lncRNA and protein-coding genes in mouse liver

Sample

Number of reads

Number of alignments

Number of unique alignments

Number of unique alignments without duplicate reads

HFD A

33550731

31488970

15502775

10051886

HFD B

33370167

31294850

16434763

10894779

HFD C

36995355

34708215

19888168

14948873

STD A

37931887

35475014

19716455

13654052

STD B

39045552

36407892

20167366

14222042

STD C

36576656

34298870

19934085

14208816

Average

36245058

33945635

18607269

12996741

Average HFD (n = 3 pools)

34638751

32497345

17275235

11965179

Average STD (n = 3 pools)

37851365

35393925

19939302

14028303

  1. 5-methylcytosine DNA immunoprecipitates (n = 3 pools of 2 livers/diet) were single-end sequenced. The number of alignments is the number of reads that aligned with no more than 2 mismatches to the mouse genome. The number of unique alignments refers to the number of reads that aligned to a unique site of the mouse genome with no more than 2 mismatches. The number of unique alignments without duplicate reads is the number of reads that aligned to a unique site of the mouse genome with less than 2 mismatches and were not exact duplicates produced by PCR amplification of the sequencing libraries. Of these, exactly 10 million reads were used for methylation analysis.
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