Oxytricha trifallax small RNA sequencing mapping statistics.

Small RNA libraries were prepared from 11 different biological samples indicated under “Library name”. veg02 is vegetative ALXC2 and veg09 is from vegetative ALXC9. mat## libraries were made from matings between ALXC2 with ALXC9, and the time in hours after mixing of the strains that the RNA for the library was isolated is indicated (mat24 RNA was extracted 24 hours after mixing mating strains). “Raw Reads” are the number of bidirectionally sequenced reads for each library (M = million). “Bidirectional Identical Reads” are the number of reads that were identical in both directions. These were used as high confidence sequences for further mapping. The bidirectional identical reads were filtered through a collection of Oxytricha trifallax non-coding RNAs (ncRNAs). “Matches to ncRNA Filter” are the number of sequences that match ncRNAs, and ncRNA% are the percentage of bidirectional identical reads that match the ncRNA filter. “Not ncRNA” are reads that did not match the ncRNA filter, and “Not ncRNA%” are the percentage of Bidirectional Identical Reads that are not a match to ncRNA. Bowtie was used to align the Not ncRNA reads to the macronuclear genome chr1 and chr2, as well as the 70 kb mitochondrial genome (chrM). “No macronuclear match” is the number of reads that did not match to the macronuclear sequences. “Mapped to Macronucleus” indicates the number of reads that mapped to the macronuclear sequences, and “Mapped to Macronucleus %” shows the fraction of “not ncRNA” reads that are macronuclear in origin. “> = 10 Map Sites” are the number of reads that map to 10 or more places in the macronuclear sequence assembly, “