New junction evidence
		seq id	position	reads (cov)	reads (cov)	score	skew	freq	annotation	gene	product
*	?	CP000731	= 1623	1236 (0.920)	11 (0.020)	6/272	0.8	1.9%	intergenic (+408/‑448)	repA/USA300HOU_pUSA300HOUMR0003	replication protein A/hypothetical protein
	?	NC_012417	= 1066	15 (0.840)					coding (129/192 nt)	USA300HOU_RS15665	hypothetical protein
Rejected: Frequency below/above cutoff threshold.

AGAAGAAAAAGCACATTCAATTACCGCAATTTGGAATTTCGAAAAGCAAAATTATTATTTAAGACATTAGTGTTGACTAATGTCTTTTTTG‑TTGATTTTTTATAAAAAAGTACTGTCTTATTTTTGTGACAAATGCTGTATGTAGTGTCACAAAAATAAGACAAACGCAATATATTGTGTCACAAAAATAAGACAGTACAGCTTTGTATGATATCACTTTAAAATACCTTAAAACCCCTGGAATTTCTGGCTTTGCCAGACCTATCATTTTTGAATGATAGCA  >  NC_012417/927‑1209                                                                                                                                             |                                                                                                                                                agaagaaAAAGCACATTCAATTACCGCAATTTGGAATTTCGAAAAGCAAAATTATTATTTAAGACATTAGTGTTGACTAATGTCTTTTTTG‑TTGATTTTTTATAAAAAAGTACTGTCTTATTTTTGTGACAAATGCTGTAtgtagtgtc                                                                                                                                        <  2:1742916‑M2/149‑10 (MQ=255)       aaaaGCACATTCAATTACCGCAATTTGGAATTTCGAAAAGCAAAATTATTATTTAAGACATTAGTGTTGACTAATGTCTTTTTTG‑TTGATTTTTTATAAAAAAGTACTGTCTTATTTTTGTGACAAATGCTGTATGTAGTGTCACaaaa                                                                                                                                  >  2:841024/1‑149 (MQ=255)        aacgCACATGTAACTAGCGCAATTTGGAATTTTCAAAAACAAAATTATTATTTAAGACATTAGTGTTGACTAATGTCTTGTTTG‑TTGATTTTTTAGAAAAAAGTACTGTCTTATTTTTGTGACAAATGCTGTATGTAGTGTCACaaaaa                                                                                                                                 <  1:343966/146‑1 (MQ=17)        aaaGCACATTCAATTACCGCAATTTGGAATTTCGAAAAGCAAAATTATTATTTAAGACATTAGTGTTGACTAATGTCTTTTTTG‑TTGATTTTTTATAAAAAAGTACTGTCTTATTTTTGTGACAAATGCTGTATGTAGTGTCACaaaaa                                                                                                                                 >  2:796497/1‑149 (MQ=255)        aaaGCACATTCAATTACCGCAATTTGGAATTTCGAAAAGCAAAATTATTATTTAAGACATTAGTGTTGACTAATGTCTTTTTTG‑TTGATTTTTTATAAAAAAGTACTGTCTTATTTTTGTGACAAATGCTGTATGTAGTGTCACaaaaa                                                                                                                                 <  2:713439/149‑1 (MQ=255)        aaaGCACATTCAATTACCGCAATTTGGAATTTCGAAAAGCAAAATTATTATTTAAGACATTAGTGTTGACTAATGTCTTTTTTG‑TTGATTTTTTATAAAAAAGTACTGTCTTATTTTTGTGACAAATGCTGTATGTAGTGTCACaaaaa                                                                                                                                 >  2:362045/1‑149 (MQ=255)        aaaGCACATTCAATTACCGCAATTTGGAATTTCGAAAAGCAAAATTATTATTTAAGACATTAGTGTTGACTAATGTCTTTTTTG‑TTGATTTTTTATAAAAAAGTACTGTCTTATTTTTGTGACAAATGCTGTATGTAGTGTCACaaaaa                                                                                                                                 >  2:1361990/1‑149 (MQ=255)                                     tttCGAAAAGCAAAATTATTATTTAAGACATTAGTGTTGACTAATGTCTTTTTTG‑TTGATTTTTTATAAAAAAGTACTGTCTTATTTTTGTGACAAATGCTGTATGTAGTGTCACAAAAATAAGACAAACGCAATATATTGTGTCACaa                                                                                                    <  1:1739522/149‑1 (MQ=255)                                                 aaaTTATTATTTAATCAATTAGTGATAACTGATGTCTTTTTTTATTGTTTTTCTGTAAAAAAGTGCTGTCTTATTTTTGTGACAAATGCTGTAtgtagtgtcacacttttgtgacactacatacagcatttgtcacaaaaataagacag                                                                                         >  1:1249708‑M2/1‑93 (MQ=255)                                                        tattTAAGACATTAGTGTTGACTAATGTCTTTTTTG‑TTGATTTTTTATAAAAAAGTACTGTCTTATTTTTGTGACAAATGCTGTATGTAGTGTCACCAAAATAAGACAAACGCAATATATTGTGTCACAAAAATAAGACAGTACAGCtt                                                                                 <  2:1412126/149‑1 (MQ=255)                                                        tatgTAAGACATTAGTGTTGACTAATGTCTTTTTTG‑TTGATTTTTTATAAAAAAGTACTGTCTTATTTTTGTGACAAATGCTGTATGTAGTGTCACAAAAATAAGACAAACGCAATATATTGTGTCACAAAAATAAGACAGTACAGCtt                                                                                 <  1:344611/149‑1 (MQ=255)                                                            tAAGACATTAGTGTTGACTAATGTCTTTTTTG‑TTGATTTTTTATAAAAAAGTGCTGTCTTATTTTTGTGACAAATGCTGTATGTAGTGTCACAAAAATAAGACAAACGCAATATATTGTGTCACAAAAATAAGACAGTACAGCTTTCTa                                                                             >  2:1066877/1‑149 (MQ=255)                                                               gACATTAGTGATAACTGATGTCTTTTTTTATTGTTTTTCTGTAAAAAAGTGCTGTCTTATTTTGGTGACAAATGCTGTAtgtagtgtcacacttttgtgacactacatacagcatttgtcacaaaaataagacagcacttttttacaga                                                                           >  2:167583‑M2/1‑79 (MQ=255)                                                                aCATTAGTGTTGACTAATGTCTTTTTTG‑TTGATTTTTTATAAAAAAGTACTGTCTTATTTTTGTGACAAATGCTGTATGTAGTGTCACAAAAATAAGACAAACGCAATATATTGTGTCACAAAAATAAGACAGTACAGCTTTGTATGat                                                                         <  1:362045/149‑1 (MQ=255)                                                                       tgtTGACTAATGTCTTTTTTG‑TTGATTTTTTATAAAAAAGTACTGTCTTATTTTTGTGACAATTGCTGTATGTAGTGTCACAAAAATAAGACAAACGCAATATATTGTGTCACAAAAATAAGACAGTACAGCTTTGTATGATATCACtt                                                                  >  1:1330154/1‑149 (MQ=255)                                                                       tgtTGACTAATGTCTTTTTTG‑TTGATTTTTTATAAAAAAGTACTGTCTTATTTTTGTGACAAATGCTGTATGTAGTGTCACAAAAATAAGACAAACGCAATATATTGTGTCACAAAAATAAGACAGTACAGCTTTGTATGATATCACtt                                                                  >  1:141059/1‑149 (MQ=255)                                                                                                      tataAAAAAGTACTGTCTTATTTTTGTGACAAATGCTGTATGCAGTGTCACAAAAATAAGACAAACGCAATATATTGTGTCACAAAAATAAGACAGTACAGCTTTGTATGATATCACTTTAAAATACCTTAAAACCCCTGGAATTTCTg                                    <  1:384884/149‑1 (MQ=255)                                                                                                                  cTGTCTTATTTTTGTGACAAATGCTGTAtgtagtgtcacaaaagtgtgacactacatacagcatttgtcacaaaaataagacagcacttttttacagaaatacaataaaaaaagacatcagttataactaatttctttaataataaatt                        <  1:343190‑M2/149‑122 (MQ=255)                                                                                                                  cTGGCTTATTTTTGTGACAAATGCTGTAtgtagtgtcacaaaagtgtgacactacatatagcatttgtcacaaaaataagacagcacttttttacagaaaaacaataaaaaaaaacatcagatatcactaatgtcttaaataataaatt                        <  2:1474026‑M2/149‑122 (MQ=255)                                                                                                                          tttttGTGACAAATGCTGTAtgtagtgtcacaaaagtgtgacactacatacagcatttgtcacaaaaataagacagcccttttttacagaaaaacaataaaaaaagacatcagatatcaataatgtgttaaataataattttgcttttc                <  1:457689‑M2/149‑130 (MQ=255)                                                                                                                          tttttGTGACAAATGCTGTAtgtagtgtcacaaaagtgtgacactacatacagcatttgtcacaaaaataagacagcactttttttcattaattcaataaaaaaagacatcagttattactaatgtcttaaataatatttttgattttt                <  2:1357609‑M2/149‑130 (MQ=255)                                                                                                                            tttGTGACAAATGCTGTAtgtagtgtcacaaaagtgtgacactacatacagcatttgtcacaaaaataagacagcacttttttacagaaaaacaatcattaaaaacatcagttatcactcataacttaaataatacttttgcttttcga              <  1:1446889‑M2/149‑132 (MQ=255)                                                                                                                              tgtgACAAATGCTGTATGTAGTGTCACAAAAATAAGACAAACGCAATATATTGTGTCACAAAAATAAGACAGTACAGCTTTGTATGATATCACTTTAAAATACCTTAAAACCCCTGGAATTTCTGGCTTTGCCAGACCTATCATTTTTg            <  1:1742916/149‑1 (MQ=255)                                                                                                                                tgACAAATGCTGTAtgtagtgtcacaaaagtgtgacactacatacagcatttgtcacaaaaataagacagcacttttttccagaaaaacaataaaaaaagacatcagttatcactaatgtcttaaataataattttgcttttcgaaatt          <  2:66262‑M2/149‑136 (MQ=255)                                                                                                                                     aaTGCTGTAtgtagtgtcacacttttgtgacactacatacagcatttgtcacaaaaataagacagcacttttttacagaaaaacaataaaaaaagacatcagttatcactaatgtcttaaataataattttgcttttcgacattccaaa     <  1:670221‑M2/149‑141 (MQ=255)                                                                                                                                     aaTGCTGTAtgtagtgtcacacttttgtgacactacatacagcatttgtcacaaaaataagacagcacttttttacagaaaaacaataaaaaaagacatcagttatcactaatgtcttaaataataattttgcttttcgaaattccaaa     <  2:1232351‑M2/149‑141 (MQ=255)                                                                                                                                        gCTGTAtgtagtgtcacaaaagtgtgacactacatacagcatttgtcacaaaaataagacagcacttttttacagaaaaacaataaaaaaagacatcagttatcactaatgtcttaaataataattttgcttttcgaaattccaaattg  <  2:1899624‑M2/149‑144 (MQ=255)                                                                                                                                             |                                                                                                                                                AGAAGAAAAAGCACATTCAATTACCGCAATTTGGAATTTCGAAAAGCAAAATTATTATTTAAGACATTAGTGTTGACTAATGTCTTTTTTG‑TTGATTTTTTATAAAAAAGTACTGTCTTATTTTTGTGACAAATGCTGTATGTAGTGTCACAAAAATAAGACAAACGCAATATATTGTGTCACAAAAATAAGACAGTACAGCTTTGTATGATATCACTTTAAAATACCTTAAAACCCCTGGAATTTCTGGCTTTGCCAGACCTATCATTTTTGAATGATAGCA  >  NC_012417/927‑1209

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.