hi, all
I don't understand what do the underlined reads mean output by samtools tview.
The alignment records for a pair of reads are as follows:
ST-E00205:55:HF5CYCCXX:8:1108:13647:27908 129 5 97912081
43 14S64M72S 10 126683038 0
GGGGGAACAGGTCACTGTACCAGGCACTGAGGGAAGGCACACGAGTTCACAGCGTGGAGCAGATTGGCGAGGTGGCCTCAGTAAAGGCCCGCATTCGTGGGGAGATATTGGGCCTCATCGGCTTCGGTCGCACGCAGCAGGAGGTTGCAG
><===>?<>==7=><>=;><=>=>=><<>;>>>>?>>>?=?=8>>1<>?=?>>8>><6=>?>><>>>>8>>>;??>??>?>>???>??=?9?>+2<6>????>?=:=;=???7<=<=9?7>=?@@:@>?:?A?/,>??,4?,=@=*+:;9
BD:Z:JJIILKLLJONMMMHMNIMMMKNMMOHMNNKMIIJKMMOHIHJKKNKJMHINOJKIKIKOONKMJLKMJKKMLIKMNMKMNNMLDKMMNHIKOKJJJKIKIIIKKMLLJLKINONLNLNKJNPLKKJMNKLPIKLQPQQPOKMNLJLNON
MD:Z:15T10G2G5G14G13 PG:Z:MarkDuplicates
RG:Z:Derm3235_DHG02696_HF5CYCCXX_L8
BI:Z:LLJJLMLMKOMNMOINMJNMLLNLMNINMNKLIKJLLMNIJIJKKNKJNIJNPIKJKKKPNNKNKMKMILLMNKLNNNKOOOOMGMMNNIIKOMLKJLKLJJLLLOMOMOMKOOOLPNPKJOQMLKJONKLQLMMQQSQQONNNNLNNOO
NM:i:5 AS:i:39 XS:i:20
ST-E00205:55:HF5CYCCXX:8:1108:13647:27908 65 10 126683038
20 3S144M3S 5 97912081 0
CATCTGCTTTATGGTAAAGTCATGGATAAGGTGGTAGTTTTGTTCGTTGAGATTGCAATGCAAGAAGACGCAGTCGTTCTGATACAGCAAATCCTGCTGGGTGTAGACCCTATGCACACCCAGGGACCGCTCGATCCCATCCTGCAAAGG
?>=>??>?>>?>>>>???>>>?>>>>>??>>>>>>?><;>>>>>>8>>>>>>>>>>??>>>??>>?>>=8>?>=>8>>>?>>>?=?>>???>>>?>>?>>>;>>???>??@=???@>@>??@?>??>?9?@?9<>>??@5??A???<==?
BD:Z:JJKMOQQQMEMMLKLMLDKNMMKKKIMLLJLLIKLMNNKDCKHJIIJJKMJJLIKMNJIJMNJJJIJJKIJNMMMJKKJKNNMLMINOOKDJMJMNNONKILIIMNKLMHMMLKNOHJINILONJJMNJLPLKMOOLJMMPMPQQRKDKM
MD:Z:20T3G7G3A17G6G11C20A13C5G29 PG:Z:MarkDuplicates
RG:Z:Derm3235_DHG02696_HF5CYCCXX_L8
BI:Z:LLMONPOQLGNOLKMNLFLNLNLLKKNLLLLMJKMNMNKFFMJKJIKKMNKKNKMMNLKLMNLLKJLKLJJNNNLIKKJKMNNLMJNPOMGLOKNNNPNLJNKKONLMMINOOMNPKLKNJNPNKMNNJLQMLNQQMLPPRNQPPPMGMM
NM:i:10 AS:i:94 XS:i:82
I used samtools tview to look at these two reads (the two pictures below), and
these two reads are underlined:
From the FLAG (65 and 129), these two reads are not multiple mapping, so they
are underlined because of they are orphan reads?
I searched the definition of orphan reads: (1) in paired end, the other pair
end is not mapped. (2) After quality or adapter trimming paired-end reads, one
of the pairs may be discarded and the remaining read is often referred to as an
orphaned read.
So, what is the exact definition for orphan reads? For a pair of reads, if each
maps to different chromosomes, is this pair should be considered as orphan
reads?
Best wishes!
Junhui
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