Hi friends,
I have made a de novo transcriptome assembly, followed by mapping back read to the assembly using bowtie2 with this command:
bowtie2 -x assembly_4 -1 file_1.fq -2 file_2.fq --local --no-unal -p 8 -S assembly_4.sam
the output of bowtie2 is here:
182786653 reads; of these:
182786653 (100.00%) were paired; of these:
6674426 (3.65%) aligned concordantly 0 times
125631460 (68.73%) aligned concordantly exactly 1 time
50480767 (27.62%) aligned concordantly >1 times
----
6674426 pairs aligned concordantly 0 times; of these:
978106 (14.65%) aligned discordantly 1 time
----
5696320 pairs aligned 0 times concordantly or discordantly; of these:
11392640 mates make up the pairs; of these:
8790860 (77.16%) aligned 0 times
1476379 (12.96%) aligned exactly 1 time
1125401 (9.88%) aligned >1 times
97.60% overall alignment rate
when I used the flagstat with samtools (./samtools flagstat assembly_4.bam > report.stats), the its report was:
356782446 + 0 in total (QC-passed reads + QC-failed reads)
0 + 0 secondary
0 + 0 supplementary
0 + 0 duplicates
356782446 + 0 mapped (100.00%:-nan%)
356782446 + 0 paired in sequencing
178733950 + 0 read1
178048496 + 0 read2
352224454 + 0 properly paired (98.72%:-nan%)
355623980 + 0 with itself and mate mapped
1158466 + 0 singletons (0.32%:-nan%)
2758204 + 0 with mate mapped to a different chr
2576765 + 0 with mate mapped to a different chr (mapQ>=5)
I want to know how the properly paired is 98.72% while based on bowtie2 the percentage of aligned concordantly is 96.35%. Why there is such a difference?