New junction evidence
		seq id	position	reads (cov)	reads (cov)	score	skew	freq	annotation	gene	product
*	?	CP000730	368774 =	28 (1.180)	4 (0.180)	4/258	1.6	14.3%	intergenic (+208/+70)	nagC/USA300HOU_0337	possible transcriptional regulator/possible RpiR family transcriptional regulator
	?	CP000730	368825 =	21 (0.920)					intergenic (+259/+19)	nagC/USA300HOU_0337	possible transcriptional regulator/possible RpiR family transcriptional regulator
Rejected: Frequency below/above cutoff threshold.

TCCACACATCACACTCTATCTAGGACCAATCTAAACTATATCAACCAACAGTGTGCCACGGGCAAATTAAATTGAAGAAGCTGAGATATTAAAATTTTAGAAAATGTAAAAAAATATTTGGTATTGAAATTAAAAAAGCACCTAGCAACTCGTTGGGACAATCACGATGATTGTCTACAGTTGCAGGTGGATTTGAATATACTACTAGTTATTTGTTGTCTAGGATAATAGATTTAGTATGTTGATAAGTTTGACTCAGATTCGTATTTTCTAATAA  >  CP000730/368636‑368912                                                                                                                                           |                                                                                                                                           tcaacacacaaattgcgacactctttttaatcgatatcgtgagttatcatttattagaaaatacgaatctgagtcaaacttatcaacatactaaatctattatcctagacaacaaataactagtagtatattcaaatcCAc                                                                                                                                          <  2:218382‑M1/3‑1 (MQ=255)         tCACACTCTATCTAGGACCAATCTAAACTATATCAACCAACAGTGTGCCACGGGCAAATTAAATTGTTGAAGCTGGGATATGAAAATTTTAGAAAATGTAAAAAAATATTTGGTATTGAAATTAAAAAAGCACCTAGCAAc                                                                                                                                  >  1:195135/1‑141 (MQ=255)                   tctaGGACCAATCTAAACTATATCAACCAACAGTGTGCCACGGGCAAATTAAATTGAAGAAGCTGAGATATTAAAATTTTAGAAAATGTAAAAAAATATTTGGTATTGAAATTAAAAAAGCACCTAGCAACTCGTTGGGAc                                                                                                                        >  1:218382/1‑141 (MQ=255)                          tttaatcgatatcgtgagttatcatttattagaaaatacgaatctgagtcaaacttatcaacatactaaatctattatcctagacaacaaataactagtagtatattcaaatcCACCTAGCAACTCGTTGGGACAATCACg                                                                                                                 <  1:46144‑M1/28‑1 (MQ=255)                              tCTAAACTATATCAACCAACAGTGTGCCACGGGCAAATTAAATTGAAGAAGCTGAGATATTAAAATTTTAGAAAATGTAAAAAAATATTTGGTATTGAAATTAAAAAAGCACCTAGCAACTCGTTGGGACAATCACgatga                                                                                                             >  2:232102/1‑141 (MQ=255)                                    cTATATCAACCAACAGTGTGCCACGGGCAAATTAAATTGAAGAAGCTGAGATATTAAAATTTTAGAAAATGTAAAAAAATATTTGGTATTGAAATTAAAAAAGCACCTAGCAACTCGTTGGGACAATCACGATGATTGTCt                                                                                                       >  2:252387/1‑141 (MQ=255)                                         tCAACCAACAGTGTGCCACGGGCAAATTAAATTGAAGAAGCTGAGATATTAAAATTTTAGAAAATGTAAAAAAATATTTGGTATTGAAATTAAAAAAGCACCTAGCAACTCGTTGGGACAATCACGATGATTGTCTACAGt                                                                                                  <  1:112051/141‑1 (MQ=255)                                         tCAACCAACAGTGTGCCACGGGCAAATTAAATTGAAGAAGCTGAGATATTAAAATTTTAGAAAATGTAAAAAAATATTTGGTATTGAAATTAAAAAAGCACCTAGCAACTCGTTGGGACAATCACGATGATTGTCTACAGt                                                                                                  <  1:112108/141‑1 (MQ=255)                                         tCAACCAACAGTGTGCCACGGGCAAATCAAATTGAAGAAGCTGAGATATTAAAATTTAAGATAATTTAAAAAAATATTTGGTATTGAAATTAAAAAAGCACCTAGCAACTCGTTGGAACAATCACGATGATTGTCTACAGt                                                                                                  >  2:18811/1‑141 (MQ=255)                                            ttatcatttattagaaaatacgaatctgagtcaaacttatcaacatactaaatctattatcctagacaacaaataactagtagtatattcaaatcCACCTAGCAACTCGTTGGGACAATCACGATGATTGTCTACAGTTGc                                                                                               >  2:46144‑M1/96‑141 (MQ=255)                                                acAGTGTGCCACGGGCAAATTAAATTGAAGAAGCTGAGATATTAAAATTTTAGAAAATGTAAAAAAATATTTGGTATTGAAATTAAAAAAGCACCTAGCAACTCGTTGGGACAATCACGATGATTGTCTACAGTTGCAGGt                                                                                           <  1:254716/141‑1 (MQ=255)                                                   gtgtGCCACGGGCAAATTAAATTGAAGAAGCTGAGATATTAAAATTTTAGAAAATGTAAAAAAATATTTGGTATTGAAATTAAAAAAGTACATAGACACTAATTGGGACAATCACGATGATTGTCTACAGTTGCAGGTGGa                                                                                        >  1:110555/1‑141 (MQ=255)                                                       gCCACGGGCAAAGTAAATTGAAGAAGCTGAGATATTAAAATTTTAGAAAATGTAAAAAAATATTTGGTATTGAAATTAAAAAAGCACCTAGCAACTCGTTGGGACAATCACGATGATTGTCTACAGTTGCAGGTGGATTTg                                                                                    >  2:56763/1‑141 (MQ=255)                                                           cGGGCAAATTAAATTGAAGAAGCTGAGATATTAAAATTTTAGAAAATGTAAAAAAATATTTGGTATTGAAATTAAAAAAGCACCTAGCAACTCGTTGGGACAATCACGATGATTGTCTACAGTTGCAGGTGGATTTGAata                                                                                >  2:258111/1‑141 (MQ=255)                                                                    taaattGAAGAAGCTGAGATATTAAAATTTTAGAAAATGTAAAAAAATATTTGGTATTGAAATTAAAATAGCACCTAGCAACTCGTTGGGACAATCACGATGATTGTCTACAGTTGCAGGTGGATTTGAATATACTACTAg                                                                       <  1:208746/141‑1 (MQ=255)                                                                                    agaTATTAAAATTTTAGAAAATGTAAAAAAATATTTGGTATTGAAATTAAAAAAGCACCTAGCAACTCGTTGGGACAATCACga                                                                                                                >  2:197192/1‑84 (MQ=255)                                                                                    agaTATTAAAATTTTAGAAAATGTAAAAAAATATTTGGTATTGAAATTAAAAAAGCACCTAGCAACTCGTTGGGACAATCACga                                                                                                                <  1:197192/84‑1 (MQ=255)                                                                                            aaaTTTTAGAAAATGTAAAAAAATATTTGGTATTGAAATTAAAAAAGCACCTAGCAACTCGTTGGGACAATCACGATGATTGTCTACAGTTGCAGGTGGATTTGAATATACTACTAGTTATTTGTTGTCTAGGATAATAGa                                               >  2:140165/1‑141 (MQ=255)                                                                                               ttttAGAAAATGTAAAAAAATATTTGGTATTGAAATTAAAAAAGCACCTAGCAACTCGTTGGGACAATCACGATGATTGTCTACAGTTGCAGGTGGATTTGAATATACTACTAGTTATTTGTTGTCTAGGATAATAGAttt                                            >  1:52648/1‑141 (MQ=255)                                                                                               ttttAGAAAATGTAAAAAAATATTTGGTATTGAAATTAAAAAAGCACCTAGCAACTCGTTGGGACAATCACGATGATTGTCTACAGTTGCAGGTGGATTTGAATATACTACTAGTTATTTGTTGTCTAGGATAATAGAttt                                            >  1:25067/1‑141 (MQ=255)                                                                                                  tAGAAAATGTAAAAAAATATTTGTTATTGAAATTAAAAAAGCACCTAGCAACTCGTTGGGACAATCACGATGATTGTCTACAGTTGCAGGTGGATTTGTATATACTACTAGTTATTGGTTGTCTAGGATGATAGATTTAGt                                         >  2:214638/1‑141 (MQ=255)                                                                                                             aaaaaaTATTTGGTATTGAAATTAAAAAAGCACCTAGCAACTCGTTGGGACAATCACGATGATTGTCTACAGTTGCAGGTGGATTTGAATATACTACTAGTTAttt                                                                 >  2:177848/1‑106 (MQ=255)                                                                                                             aaaaaaTATTTGGTATTGAAATTAAAAAAGCACCTAGCAACTCGTTGGGACAATCACGATGATTGTCTACAGTTGCAGGTGGATTTGAATATACTACTAGTTAttt                                                                 <  1:177848/106‑1 (MQ=255)                                                                                                                  atatTTGGTATTGAAATTAAAAAAGCACCTAGCAACTCGTTGGGACAATCACGATGATTGTCTACAGTTGCAGGTGGATTTGAATATACTACTAGTTATTTGTTGTCTAGGATAATAGATTTAGTATGTTGATAAGTTTGa                         <  2:52648/141‑1 (MQ=255)                                                                                                                     tttGGTATTGAAATTAAAAAAGCACCTAGCAACTCGTTGGGACAATCACGATGATTGTCTACAGTTGCAGGTGGATTTGAATATACTACTAGTTATTTGTTGTCTAGGATAATAGATTTAGTATGTTGATAAGTTTGACTc                      <  1:232102/141‑1 (MQ=255)                                                                                                                        ctagtagtatattcaaatcCACCTAGCAACTCGTTGGGACAATCACGATGATTGTCTACAGTTGCAGGTGGATTTGAATATACTACTAg                                                                       >  1:263549‑M1/20‑89 (MQ=255)                                                                                                                        ctagtagtatattcaaatcCACCTAGCAACTCGTTGGGACAATCACGATGATTGTCTACAGTTGCAGGTGGATTTGAATATACTACTAg                                                                       <  2:263549‑M1/70‑1 (MQ=255)                                                                                                                            ttGAAATTAAAAAAGCACCTAGCAACTCGTTGGGACAATCACGATGATTGTCTACAGTTGCAGGTGGATTTGAATATACTACTAGTTATTTGTTGTCTAGGATAATAGATTTAGTATGTTGATAAGTTTGACTCAGATTCg               <  1:258111/141‑1 (MQ=255)                                                                                                                                 aTTAAAAAAGCACCTAGCAACTCGTTGGGACAATCACGATGATTGTCTACAGTTGCAGGTGGATTTGAATATACTACTAGTTATTTGTTGTCTAGGATAATAGATTTAGTATGTTGATAAGTTTGACTCAGATTCGTAttt          >  1:57952/1‑141 (MQ=255)                                                                                                                                 aTTAAAAAAGCACCTAGCAACTCGTTGGGACAATCACGATGATTGTCTACAGTTGCAGGTGGATTTGAATATACTACTAGTTATTTGTTGTCTAGGATAATAGATTTAGTATGTTGATAAGTTTGACTCAGATTCGTAttt          <  2:28784/141‑1 (MQ=255)                                                                                                                                  ttAAAAAAGCACCTAGCAACTCGTTGGGACAATCACGATGATTGTCTACAGTTGCAGGTGGATTTGAATATACTACTAGTTATTTGTTGTCTAGGATAATAGATTTAGTATGTTGATAAGTTTGACTCAGATTCGTAtttt         <  1:108647/141‑1 (MQ=255)                                                                                                                                        aaGCACCTAGCAACTCGTTGGGACAATCACGATGATTGTCTACAGTTGCAGGTGGATTTGAATATACTACTAGTTATTTGTTGTCTAGGATAATAGATTTAGTATGTTGATAAGTTTGACTCAGATTCGTATTTTCtaata   <  2:195135/141‑1 (MQ=255)                                                                                                                                         aGCACCTAGCAACTCGTTGGGACAATCACGATGATTGTCTACAGTTGCAGGTGGATTTGAATATACTACTAGTTATTTGTTGTCTAGGATAATAGATTTAGTATGTTGATAAGTTTGACTCAGATTCGTATTTTCtaataa  >  1:246043/1‑141 (MQ=255)                                                                                                                                           |                                                                                                                                           TCCACACATCACACTCTATCTAGGACCAATCTAAACTATATCAACCAACAGTGTGCCACGGGCAAATTAAATTGAAGAAGCTGAGATATTAAAATTTTAGAAAATGTAAAAAAATATTTGGTATTGAAATTAAAAAAGCACCTAGCAACTCGTTGGGACAATCACGATGATTGTCTACAGTTGCAGGTGGATTTGAATATACTACTAGTTATTTGTTGTCTAGGATAATAGATTTAGTATGTTGATAAGTTTGACTCAGATTCGTATTTTCTAATAA  >  CP000730/368636‑368912

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 12 ≤ ATCG/ATCG < 27 ≤ 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.