Hi, I am a newbie for NGS, I was experimenting with chip-seq analysis with galaxy-bowtie. Question is: what does the XM:i:N mean in the bowtie file? Reason I ask is: My research shows it means (from bowtie manual) : "For a read with no reported alignments, <N> is 0 if the read had no alignments. If [-m] was specified and the read's alignments were supressed because the [-m] ceiling was exceeded, <N> equals the [-m] ceiling + 1, to indicate that there were at least that many valid alignments (but all were suppressed). In [-M] mode, if the alignment was randomly selected because the [-M] ceiling was exceeded, <N> equals the [-M] ceiling + 1, to indicate that there were at least that many valid alignments (of which one was reported at random)." I've pasted few lines from the bowtie output. I noticed when there is a unique match, the XM:I field is not shown. When XM:i:1 or XM:i:0, there is no match. Problem is shouldn't XM:i:1 mean there is a match???? Here is the bowtie parameters: ID:Bowtie VN:0.12.7 CL:"bowtie -q -p 6 -S -n 2 -e 70 -l 28 --maxbts 125 -k 1 -m 1 --phred33-quals /galaxy/data/hg19/hg19full/bowtie_index/hg19full /galaxy-repl/main/files/019/148/dataset_19148014.dat"

QNAME   FLAG    RNAME   POS MAPQ    CIGAR   MRNM    MPOS    ISIZE   SEQ QUAL    OPT
SRR4237722.115 HS38_18889:1:1101:10918:1975 length=50   4   *   0   0   *   *   0   0   GGGTCNCACTCTGTCACCCAGGCTGGAGTGCAGTGGCCGTGATCTCGGCT  BCCDF!2AAFFHHIJJIJIJFHIIDGIGFCEGGHIIJGIDHIIJIEEHHH  XM:i:1
SRR4237722.108 HS38_18889:1:1101:10120:1993 length=50   4   *   0   0   *   *   0   0   ATTCCATTCCACTCCATTCCATTCCAATCCTTTCCGCTCGGGTTGATTCC  CCCFFEFFGHHHGJIJJIIIIIJJJJJJIJJJIJJJJJJJII?FHIIJJJ  XM:i:0
SRR4237722.168  0   chr13   75065209    255 50M *   0   0   CACTGGAGCCTCTGATATCTTTTTTCTTTTTCCTGCTGACACAGGACTGC  CCCFFFDEHHHHHIIJJJJJJJJJJIJIGGJIJJIIJJJJJIJJJIJIJJ  XA:i:0 MD:Z:50 NM:i:0
SRR4237722.94   0   chr3    121413904   255 50M *   0   0   TGATGNAACCGATTCTGAACATGTAGGTCTTGTGCTCATACTCAGAGAGT  @@?DD!2=CFHHHFHIIF>GHIIHCGI*@FGHFGIIIIHIIHGIIIGIID  XA:i:1 MD:Z:5G44 NM:i:1