I am using SRA-FASTQ-to-bam-kit in on windows to allign large human WGS fastq files [100-150gb], BWA has latest version. Kit works through .bat file and it uses -t 4 option by default. My laptop has i5 7300HQ processor which has 2 cores but works as 4 core [like most of intel processors]. When i change to -t 1 it makes bamfile 2-3 times faster than with -t 4 or -t 2, and there is no difference in bam file size that it outputs, its the same with any options, it just works faster with -t 1. My question is - should i stay with 1 thread option or i can loose "quallity" of bam file using it, i want maximal quality no matter what time it will take. When i switch to 1 thread it shows that it reads 10000043 bp, with 4 - 40000043 bp, is it really affects bam file?