Predicted mutation
evidence	seq id	position	mutation	freq	annotation	gene	description
JC	USA300TCH1516_ALE	1,441,097	+TGTTG	22.2%	coding (122/624 nt)	USA300HOU_RS07160 →	hypothetical protein

New junction evidence
		seq id	position	reads (cov)	reads (cov)	score	skew	freq	annotation	gene	product
*	?	USA300TCH1516_ALE	= 1441097	25 (0.580)	7 (0.160) +TGTTG	6/238	NT	22.2%	coding (122/624 nt)	USA300HOU_RS07160	hypothetical protein
	?	USA300TCH1516_ALE	1441098 =	25 (0.560)					coding (123/624 nt)	USA300HOU_RS07160	hypothetical protein

AATAAAGGAAGATGACAGTGAGATATAATATTTCTCATATATTTGGGGTGTTAGTGGGAATTCCTGTAGCGTTTTTAACAAGCATATTTGGGATGATTGCACTTGATGTATCTTTTTTAATTGATATGTCTATTGGTAT‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑  >  USA300TCH1516_ALE/1440959‑1441097 ‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑TGTTGGCTTTTTAATGACATACCTACCGATACAAAAACTCACTTCACGCAAATATTTAAACGAAATTGGTTTGACTAGAAAAGACTATCGCTATATTCGAAATCAGTTAAATCATACACACCAAAAACTT  >  USA300TCH1516_ALE/1441098‑1441227                                                                                                                                            |||||                                                                                                                                   AATCAAGGAAGAGGATAGTGAGGTATAATATTTCTCTTATATTTGGGGTGTTAGTGGGAATTCCTGTAGCGTTTTTAACAAGCATATTTGGGATGATTGCACTTGATTTATCTTTTTTAATTGATATGTCTATTGGTATT                                                                                                                                        <  2:98001/140‑1                    GAGATATAATATTTCTCATATATTTGGGGTGTTAGTGGGAATTCCTGTAGCGTTTTTAACAAGCATATTTGGGATGATTGCACTTGATGTATCTTTTTTAATTGATATGTCTATTGGTATTGTTGTGTTGGCTTTTTAAT                                                                                                                     >  2:344088/1‑140                    GAGATATAATATTTCTCATATATTTGGGGTGTTAGTGGGAATTCCTGTAGCGTTTTTAACAAGCATATTTGGGATGATTGCACTTGATGTATCTTTTTTAATTGATATGTATATTGGTATTGGTGTGTTGGCTTTTTAAT                                                                                                                     >  2:410397/1‑140                                  CTCATATATTTGGGGTGTTAGTGGGAATTCCTGTAGCGTTTTTAACAAGCATATTTGGGATGATTGCACTTGATGTATCTTTTTTAATTGATATGTCTATTGGTATTGTTGTGTTGGCTTTTTAATGACATACCTACCGA                                                                                                       <  2:221630/140‑1                                      TATATTTGGGGTGTTAGTGGGAATTCCTGTAGCGTTTTTAACAAGCATATTTGGGATGATTGCACTTGATGTATCTTTTTTAATTGATATGTCTATTGGTATTGTTGTGTTGGCTTTTTAATGACATACCTACCGATACA                                                                                                   <  2:393118/140‑1                                                      GTGGGAATTCCTGTAGCGTTTTTAACAAGCATATTTGGGATGATTGCACTTGATGTATCTTTTTTAATTGATATGTCTATTGGTATTGTTGTGTTGGCTTTTTAATGACATACCTACCGATACAAAAACTCACTTCACGC                                                                                   >  1:224498/1‑140                                                      GTGGGAATTCCTGTAGCGTTTTTAACAAGCATATTTGGGATGATTGCACTTGATGTATCTTTTTTAATTGATATGTCTATTGGTATTGTTGTGTTGGCTTTTTAATGACATACCTACCGATACAAAAACTCACTTCACGC                                                                                   >  1:435268/1‑140                                                                                                                CTTTTTTAATTGATATGTCTATTGGGATTGTTGTGTTGGCTTTTTAATGACATACCTACCGATACAAAAACTCACTTCACGCAAATATTTAAACGAAATTGGTTTGACTAGAAAAGACTATCGCTATATTCGAAATCAGT                         <  2:378428/140‑1                                                                                                                               tggCTATTGGTATTGTTGTGGTGGCTTTTTAATGACATACCTACCGATACAAAAACTCACTTCACGCAAATATTTAAACGAAATTGGTTTGACTAGAAAAGACTATCGCTATATTCGAAATCAGTTAAATCATACACACC          <  1:385613/137‑1                                                                                                                                       GGTATTGTTGTGTTGGCTTTTTAATGACATACCTACCGATACAAAAACTCACTTCACGCAAATATTTAAACGAAATTGGTTTGACTAGAAAAGACTATCGCTATATTCGAAATCAGTTAAATCATACACACCAAAAACTT  >  2:106027/1‑140                                                                                                                                            |||||                                                                                                                                   AATAAAGGAAGATGACAGTGAGATATAATATTTCTCATATATTTGGGGTGTTAGTGGGAATTCCTGTAGCGTTTTTAACAAGCATATTTGGGATGATTGCACTTGATGTATCTTTTTTAATTGATATGTCTATTGGTAT‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑  >  USA300TCH1516_ALE/1440959‑1441097 ‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑TGTTGGCTTTTTAATGACATACCTACCGATACAAAAACTCACTTCACGCAAATATTTAAACGAAATTGGTTTGACTAGAAAAGACTATCGCTATATTCGAAATCAGTTAAATCATACACACCAAAAACTT  >  USA300TCH1516_ALE/1441098‑1441227

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 12 ≤ ATCG/ATCG < 13 ≤ ATCG/ATCG < 32 ≤ ATCG/ATCG < 41 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑
Reads not counted as support for junction
read_name Not counted due to insufficient overlap past the breakpoint.
read_name Not counted due to not crossing MOB target site duplication.