Confused with sam flags
I have a paired end rna sequence alignment. I have a pair of reads that one has the flag 103 and the other 147
103 means:
read paired
read mapped in proper pair
read unmapped
mate reverse strand
first in pair
147:
read paired
read mapped in proper pair
read reverse strand
second in pair
Why it says that read are mapped in propper pairs since they map in different transcripts? how can my first read be unmapped? Here are the sequence output
HWI-ST30398_7_64_11728_7000_0 103 isotig01097 3775 29 48S24M28S isotig03570 24 0 CTGTTCCAGAAATTGGTATTCAAAGAGTTCAATTTAAAACAAACGCCGAAGTGGCGCTTGAACCTATAAGTCCAGCGCCATTATCACCAATGTTATCATC gggggggfggggggggggggggfggggcgggggggfggggggggggggeggceegeeddgegdgcecggdaddc^dcdebggggegggag]edcfefggd XT:A:M NM:i:0 SM:i:29 AM:i:29 XM:i:0 XO:i:0 XG:i:0 MD:Z:24
HWI-ST30398_7_64_11728_7000_0 147 isotig03570 24 29 37M1I62M isotig01097 3775 0 CAGCGCCATTATCACCAATGTTATCATCTTCCAATATAAAAAAAATCTTCATCGAGATTATCGTCTTTTCGTAAAATGAAAGCCCAATCTGTTGGTGGAG dXXcbd]^cadeecegfaegdeeedeefdadgggggegggggggdffffegedggggggggggggggggggggggggfgggggggggegggggggfgggg XT:A:U NM:i:1 SM:i:29 AM:i:29 X0:i:1 X1:i:0 XM:i:0 XO:i:1 XG:i:1 MD:Z:99
103 means:
read paired
read mapped in proper pair
read unmapped
mate reverse strand
first in pair
147:
read paired
read mapped in proper pair
read reverse strand
second in pair
Why it says that read are mapped in propper pairs since they map in different transcripts? how can my first read be unmapped? Here are the sequence output
HWI-ST30398_7_64_11728_7000_0 103 isotig01097 3775 29 48S24M28S isotig03570 24 0 CTGTTCCAGAAATTGGTATTCAAAGAGTTCAATTTAAAACAAACGCCGAAGTGGCGCTTGAACCTATAAGTCCAGCGCCATTATCACCAATGTTATCATC gggggggfggggggggggggggfggggcgggggggfggggggggggggeggceegeeddgegdgcecggdaddc^dcdebggggegggag]edcfefggd XT:A:M NM:i:0 SM:i:29 AM:i:29 XM:i:0 XO:i:0 XG:i:0 MD:Z:24
HWI-ST30398_7_64_11728_7000_0 147 isotig03570 24 29 37M1I62M isotig01097 3775 0 CAGCGCCATTATCACCAATGTTATCATCTTCCAATATAAAAAAAATCTTCATCGAGATTATCGTCTTTTCGTAAAATGAAAGCCCAATCTGTTGGTGGAG dXXcbd]^cadeecegfaegdeeedeefdadgggggegggggggdffffegedggggggggggggggggggggggggfgggggggggegggggggfgggg XT:A:U NM:i:1 SM:i:29 AM:i:29 X0:i:1 X1:i:0 XM:i:0 XO:i:1 XG:i:1 MD:Z:99
