The format and meanings of each field are described in "cnt_file_description.txt" under RSEM directory.
http://deweylab.github.io/RSEM/rsem-calculate-expression.html#OUTPUT
https://github.com/bli25broad/RSEM_tutorial
Here is the transcript.
# '#' marks the start of comments (till the end of the line)
# *.cnt file contains alignment statistics based purely on the alignment results
# obtained from aligners
N0 N1 N2 N_tot
# N0, number of unalignable reads; N1, number of alignable reads; N2, number
#of filtered reads due to too many alignments; N_tot = N0 + N1 + N2
nUnique nMulti nUncertain
# nUnique, number of reads aligned uniquely to a gene; nMulti, number of reads
#aligned to multiple genes; nUnique + nMulti = N1;
# nUncertain, number of reads aligned to multiple locations in the given reference
#sequences, which include isoform-level multi-mapping reads
nHits read_type
# nHits, number of total alignments.
# read_type: 0, single-end read, no quality score; 1, single-end read, with quality
#score; 2, paired-end read, no quality score; 3, paired-end read, with quality score
# The next section counts reads by the number of alignments they have. Each line
#contains two values separated by a TAB character. The first value is number of
# alignments.
# 'Inf' refers to reads filtered due to too many alignments. The second value is the
#number of reads that contain such many alignments
0 N0
...
number_of_alignments number_of_reads_with_that_many_alignments
...
Inf N2
