[Samtools-help] are pair-end reads considered as orphan reads by samtools tview?

[杨俊辉 <yan...@16...>]

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