understanding bamtobed output

Question

[sumithrasank75]

I am new to bedtools. I have an alignment file from bowtie2: op.sam. In order to convert it to bed, I did the following

samtools view -bSq 25 -h -F 260 op.sam | samtools sort - -o sorted_read.bam

samtools index sorted_read.bam

bedtools bamtobed -i sorted_read.bam > sorted_read.bed

The sorted bed file looks like

chr1 6811028 6811203 M00181:330:000000000-ANP8N:1:1106:13069:9454_TTATGCTAAGTATC 44 -

chr1 6811028 6811203 M00181:330:000000000-ANP8N:1:1108:14515:6525_TTATGCTAAGTATC 44 -

chr1 6811028 6811203 M00181:330:000000000-ANP8N:1:1114:27695:8423_TTATGCTAAGTATC 44 -

The first 4 columns are chr,start,end and read id and the last column is strand. I don't understand what the 5th column represents? The bed format says that it is score, but I don't know what it represents. Please help me understand this. thanks

Answer 1

[ben.kunfang]

I think its represent to MAPQ score, see detail in this thread:How to interpret the outputs generated from bamtobed using BedTools?