[Bio-bwa-help] XS larger than AS ?

[Thomas N. P. <tn...@cb...>]

What does it mean when the 'XS' flag (sub-optimal alignment) is larger than AS (Alignment score)?

HWUSI-EAS664L:24:64FGCAAXX:4:11:3337:6807	99	gi|407955691|dbj|AP012495.1|	1359455	0	101M	=	1359704	351	CCAATGGCCGCTGCCAGTGGCGTTTTGTCGTGTCTTTCCGGGTTGGACTCAAGTTGATAGTTACC
GGATAAGGCGCAGCGGTCGGGCTGAACGGGGGGTTC	IIHGDIIIIGIIDIIIIEHIIIIGIIGHIIIIHHHIIIIIHIEIIIHIIIHGHIIIFGHIFIHHHIICIGHHHIIIBCGHGEGHGGDGHBEGGIGEFEAD?	NM:i:8	MD:Z:3G4T13A1A0A10A16A0C46	AS:i:62	XS:i:68