[Samtools-help] questions on "samtools mpileup count of reads"

[<lit...@fo...>]

Hi there,


I use samtools mpileup to check reads alignment around a position 20763685 and find a strange thing.


I first check 20763685 position, it has 491 reads, and one read is at its end. Then I check 20763686 position, but only got 172 reads. Where are the 318 reads that should appear? Anyone has any idea why this happens?


the 20763685 position result is as follows:
-> % samtools mpileup -r chr13:20763685-20763685 -f hg19.fa ID096.realign.sorted.bam
[mpileup] 1 samples in 1 input files
<mpileup> Set max per-file depth to 8000
chr13	20763685	A	491	......,,-1c,.-1C..+1C....+1C....+1C..+1C........+1C..+1C...........-1C......+1C.....+1C...+1C...-1C......+1C...........+1C..+1C..-1C.+1C....+1C..+1C....+1C.+1C.+1C...+1C..+1C....-1C..+1C.....-1C.....+1C....-1C..+1C...-1C......-1C........+1C......-1C....-1C......+1C........+1C......-1C.-1C....-1C.......-1C..+1C....+1C....-1C..+1C..+1C.......-1C.-1C..-1C,,,,-1cg,-1c,,+1c,+1c,,,,,,,,,,,,,,,,,,,,,,,,,,,,-1c,,,,,,g,,-1c,,,-1c,-1c,,,,,,,,,,,,,,,,,,,-1c,,,,,,,,,,,,,,,,,-1c,,,,,,,-1c,,,,,,,-1c,-1c,,-1c,,,,-1c,,-1c,,,,,,,,,,,,,,,-1c,,,,,,,,,,,-1c,+1c,,,,,,,,,,-1c,+1c......+1C..,,,,,,,+1c,,,,,,,,,+1c....,,,.+1C.,,,,.,,,,+1c,,.+1C,,,,..+1C,,..-1C,,,,,,,,+1c,,,..,,,...+1C,,,,,,,,,,$,-1c,,,,.,,-1c,,,-1c,,,,,,-1c,,,,,,,,,-1c,-1c,,,,,,,,,,,,,,-1c,-1c,,,-1c,+1c,-1c,,,,,,,,,	:989:6;<5:;6:<65:55585=::=1=67=667<3<965894:=><>:=:=66618886575=:5=5:<6:5=7<<6:=::;4<6866=4667589=7=:8=4=897?6<<585::<7<;56686==:8685=3<<=59:=:65:=<<3>565675=5;:6832=:3638;437=5<53778E<7=7<78<85;699563<5;7<=696<04;76=67=:;77::8:8::<==766:<;:==<8=::>878.76@<::77<<=<7:9<7<756==7:<8<:98:<=788:::<7<7<;:<<7<=:7<7;55.<=87:6::<:=?=:7:65:9::=6;508=<;:6;;=8177537698=9=6==.<8<=;==84=48=5:=7;8=><<8<746<:/;<.:6=:8=676:7<:3:=9643:75===7.=7.6;<;67:497;88:87=8<:65:77<53635>;=<<:<<5;5=55<88.05..:3<:=.5



the 20763686 position result is as follows:
-> % samtools mpileup -r chr13:20763686-20763686 -f hg19.fa ID096.realign.sorted.bam     
[mpileup] 1 samples in 1 input files
<mpileup> Set max per-file depth to 8000
chr13	20763686	C	172	....................................................................................................................................................................,.......	;9<:;6::>5:558>::>3=6@6:>5<86589:==>><:>96988576=;6=5:<5;6>8<5>;4=86=78><;25898?<=58:=<;576>=:8:7<8;<5<:<:6?=<4>56675<5<:832=:5><67=5=8<8===7<88;58:?67=67<7=5;>:<:>08646B81




 
Best Regards!


Tuan