New junction evidence
		seq id	position	reads (cov)	reads (cov)	score	skew	freq	annotation	gene	product
*	?	CP000730	= 2693372	26 (0.850)	6 (0.210)	5/254	3.5	19.2%	intergenic (+43/+34)	USA300HOU_2547/USA300HOU_2548	TetR family transcriptional regulator/hypothetical protein
	?	CP000730	= 2693412	26 (0.910)					coding (162/168 nt)	USA300HOU_2548	hypothetical protein
Rejected: Coverage evenness skew score above cutoff.
Rejected: Frequency below/above cutoff threshold.

AGGTTTTATACATTGGATAAAAGATGAAAAAATTGATTGGCCTGGCGAAGATATTGATAACATTTTCCATAGATTAATCAATATTAAGATTAAATAGTAGATGAGAAACTCATGAGCGTTACCAACATTCATAATAAAAACGATAGTGTACACGTTAATGAATTCGTGTACTACTATCGTTTTTTATTTTTATCGTGCTTATCGCTATTAAAACAACTGATACACAACACATAAACTATGAAGAAAAAAATAAATCCGCTATCTAAATGAC  >  CP000730/2693233‑2693503                                                                                                                                            |                                                                                                                                    aGGTTTTATACATTGGATAAAAGATGAAAAAATTGATTGGCCTGGCGAAGATATTGATAACATTTTCCATAGATTAATCAATATTAAGATTAAATAGTAGATGAGAAACTCATGAGCGTTACCAACATTCATAATAAAAAc                                                                                                                                    >  1:17040/1‑141 (MQ=255)       tataCATTGGATAAAAGATGAAAAAATTGATTGGCCTGGCGAAGATATTGATAACATTTTCCATAGATTAATCAATATTAAGATTAAATAGTAGATGAGAAACTCATGAGCGTTACCAACATTCATAATAAAAACGATAgt                                                                                                                              >  1:287328/1‑141 (MQ=255)                gATAAAAGATGAAAAAATTGATTGGCCTGGCGAAGATATTGATAACATTTTCCATAGATTAATCAATATTAAGATTAAATAGTAGATGAGAAACTCATGAGCGTTACCAACATTCATAATAAAAACGATAGTGTACACGtt                                                                                                                     <  2:132834/141‑1 (MQ=255)                                   gattgGCCTGGCGAAGATATTGATAACATTTTCCATAGATTAATCAATATTAAGATTAAATAGTAGATGAGAAACTCATGAGCGTTACCAACATTCATAATAAAAACGATAGTGTACACGTTAATGAATTCGTGTactact                                                                                                  >  2:95964/1‑141 (MQ=255)                                     ttgGCCTGGCGAAGATATTGATAACATTTTCCATAGATTAATCAATATTAAGATTAAATAGTAGATGAGAAACTCATGAGCGTTACCAACATTCATAATAAAAACGATAGTGTACACGTTAATGAATTCGTGTACTACTAt                                                                                                <  2:245785/141‑1 (MQ=255)                                             gCGAAGATATTGATAACATTTTCCATAGATTAATCAATATTAAGATTAAATAGTAGATGAGAAACTCATGAGCGTTACCAACATTCATAATAAAAACGATAGTGTACACGTTAATGAATTCGTGTACTACTATCGtttttt                                                                                        <  2:309512/141‑1 (MQ=255)                                                 aGATATTGATAACCTTTTCCATAGATTAATCAATATTAAGATTAAATAGTAGATGAGAAACTCATGAGCGTTACCAACATTCATAATAAAAACGATAGTGTACACGTTAATGAATTCGTGTACTACTATCGTtttttattt                                                                                    <  2:313552/141‑1 (MQ=255)                                                   atatTGATAACATTTTCCATAGATTAATCAATATTAAGATTAAATAGTAGATGAGAAACTCATGAGCGTTACCAACATTCATAATAAAAACGATAGTGTACACGTTAATGAATTCGTGTACTACTATCGTtttttattttt                                                                                  <  2:207081/141‑1 (MQ=255)                                                          tAACATTTTCCATAGATTAATCAATATTAAGATTAAATAGTAGATGAGAAACTCATGAGCGTTACCAACATTCATAATAAAAACGATAGTGTACACGTTAATGAATTCGTGTACTACTATCGTTTTTTATTTTTATCGTGc                                                                           <  1:64547/141‑1 (MQ=255)                                                          tAACATGTTCCAGAGATTAATCAATATTAAGATTAAATAGTAGTTGAGAAACTCATGAGCGTTGCCAACATTCATAATAAAAACGATAGTGTACACGTTAATGAATTCGTGTACTACTATCGTTTTTTATTTTTATCGTGc                                                                           <  1:115801/141‑1 (MQ=255)                                                               ttttCCATAGATTAATCAATATTAAGATTAAATAGTAGATGAGAAACTCATGAGCGTTACCAACATTCATAATAAAAACGATAGTGTACACGTTAATGAATTCGTGTACTACTATCGTTTTTTATTTTTATCGTGCTTATc                                                                      <  1:41371/141‑1 (MQ=255)                                                                tggccgcataTTTATCAATATTAAGATTAAATAGTATATGGGAAACTCGTGAGCTTTACCAACATTCATAATAAAAACGATAGTGTACACGCTAATGAATTCGTGTACTACTATCGTTTTTTATTTTTATCGTGCTTATCg                                                                     <  2:297039/132‑1 (MQ=255)                                                                   ccATAGATTAATCAATATTAAGATTAAATAGTAGATGAGAAACTCATGAGCGTTACCAACATTCATAATAAAAACGATAGTGTACACGTTAATGAATTCGTGTACTACTATCGTTTTTTATTTTTATCGTGCTTATCGCTa                                                                  >  1:154035/1‑141 (MQ=255)                                                                             aTCAATATTAAGATTAAATAGTAGATGAGAAACTCATGAGCGTTACCAACATTCATAATAAAAACGATAGTGTACACGTTAATGAATTCGTGTACTACAATCGTTTTTTATTTTTATCGTGCTTATCGCTATTAAaacaac                                                        >  1:17003/1‑141 (MQ=255)                                                                              tCAATATTAAGATTAAATAGTAGATGAGAAACTCATGAGCGTTACCAACATTCATAATAAAAACGATAGTGTACACGTTAATGAATTCGTGTACTACTATCGTTTTTTATTTTTATCGTTCTTATCGCTATTAAAACAACt                                                       >  1:134487/1‑141 (MQ=255)                                                                              tCAATATTAAGATTAAATAGTAGATGAGAAACTCATGAGCGTTACCAACATTCATAATAAAAACGATAGTGTACACGTTAATGAATTCGTGTACTACTATCGTTTTTTATTTTTATCGTGCTTATCGCTATTAAAACAACt                                                       <  2:224741/141‑1 (MQ=255)                                                                                        gATTAAATAGTAGATGAGAAACTCATGAGCGTTACCAACATTCATAATAAAAACGATAGTGTACACGATAATGAATTCGTGTACTACTATCGTTTTTTATTTTTATCGTGCTTATCGCTATTAAAACAACTGATacacaac                                             >  1:89528/1‑141 (MQ=255)                                                                                          taaaataataaagaagaAACTCATTAGCGTTACCAACATTCATAATAAAAACGATAGTGTACACGTTAATGAATTCGTTTACTACTATCGTTTTTTATTTGTATCTTGCGTAACGCTATTAAAACAACTGATacacaacac                                           <  2:217976/127‑1 (MQ=255)                                                                                                      tGAGAAACTCATGAGCGTTACCAACATTCATAATAAAAACGATAGTGTACACGTTAATGAATTCGTGTACTACTATCGTTTTTTATTTTTATCGTGCTTATCGCTATTAAAACAACTGATACACAACACATAAACTATgaa                               >  1:331560/1‑141 (MQ=255)                                                                                                       gagaAACTCATGAGCGTTACCAACATTCATAATAAAAACGATAGTGTACACGTTAATGAATTCGTGTACTACTATCGTTTTTTATTTTTATCGTGCTTATCGCTATTAAAACAACTGATACACAACACATAAACTATgaag                              >  1:296718/1‑141 (MQ=255)                                                                                                              acATGAGCGTTACCAACATTCATAATAAAAACGATAGTGTACACGTTAATGAATTCGTGTACTACTATCGTTTTTTATTTTTATCGTGCCTATCGCTCTTACAACAACTGATCCACAACACATCACCCATGAAGtaaaaaa                       >  2:93306/2‑141 (MQ=255)                                                                                                                       ttACCAACATTCATAATAAAAACGATAGTGTACACGTTAATGAATTCGTGTACTACTATCGTTTTTTATTTTTATCGTGCTTATCGCTATTAAAACAACTGATACACAACACATAAACTATGAAGAAAAAAATAAATCCGc              <  1:222773/141‑1 (MQ=255)                                                                                                                            aaCATTCATAATAAAAACGATAGTGTACACGTTAATGAATTCGTGTACTACTATCGTTTTTTATTTTTATCGTGCTTa                                                                        <  1:56500/78‑1 (MQ=255)                                                                                                                            aaCATTCATAATAAAAACGATAGTGTACACGTTAATGAATTCGTGTACTACTATCGTTTTTTATTTTTATCGTGCTTa                                                                        >  2:56500/1‑78 (MQ=255)                                                                                                                             aCATTCATAATAAAAACGATAGTGTACACGTTAATGAATTCGTGTACTACTATCGTTTTTTATTTTTATCGTGCTTATCGCTATTAAAACAACTGATACACAACACATAAACTATGAAGAAAAAAATAAATCCGCTATCTa        >  1:51832/1‑141 (MQ=255)                                                                                                                                   ataataAAAACGATAGTGTACACGTTAATGAATTCGTGTACTACTATCGTTTTTTATTTTTATCGTGCTTATCGCTATTAAAACAACTGATACACAACACATAAACTATGAAGAAAAAAATAAATCCGCTATCTAAATGAc  <  1:207932/141‑1 (MQ=255)                                                                                                                                            |                                                                                                                                    AGGTTTTATACATTGGATAAAAGATGAAAAAATTGATTGGCCTGGCGAAGATATTGATAACATTTTCCATAGATTAATCAATATTAAGATTAAATAGTAGATGAGAAACTCATGAGCGTTACCAACATTCATAATAAAAACGATAGTGTACACGTTAATGAATTCGTGTACTACTATCGTTTTTTATTTTTATCGTGCTTATCGCTATTAAAACAACTGATACACAACACATAAACTATGAAGAAAAAAATAAATCCGCTATCTAAATGAC  >  CP000730/2693233‑2693503

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 12 ≤ ATCG/ATCG < 22 ≤ ATCG/ATCG < 37 ≤ 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.