New junction evidence
		seq id	position	reads (cov)	reads (cov)	score	skew	freq	annotation	gene	product
*	?	CP009273	= 1973068	9 (0.420)	9 (0.420)	8/272	NT	50.0%	intergenic (‑614/‑166)	flhD/uspC	flagellar class II regulon transcriptional activator, with FlhC/universal stress protein
	?	CP009273	3576788 =	NA (NA)					intergenic (+10/‑55)	yrhA/insA	pseudogene, interrupted by IS1E/IS1 repressor TnpA

GATAAGCTATTTTTAAACAGACACTTACCGCACAACAAACTAATTAAATACAAAGAAAGGCAACAATCAACTTAATGTTAATGAAATGTTTTACATATATTAACCACTTGTTTAATGCGGAGAATCAGTACACTATTTTCTTATAATTACATTTGAAATTATATGATCACCGGGAGTGATTGATTAATTATCTTTACTAATAATCAGACTAATATTTACCTGTTTGACCGAGTTGGGATTGCGTCGTTTCTCCATTAGGAGTAAAGCTTTAATGTCACCTGAAGTTCAC  >  CP009273/1972928‑1973216                                                                                                                                             |                                                                                                                                                     ctgaatctgaggcagcacctggcacggctgggacggaagtcgctgtcgttctcaaaatcggtggagctgcatgacaaagtcctccggcattatctgaacataaaacactatcaataagttggagacattaccCTATTTtctttt                                                                                                                                                   <  2:205117‑M1/12‑3 (MQ=255)   gaatctgaggcagcacctggcacggctgggacggaagtcgctgtcgttctcaaaatcggtggagctgcatgacaaagtcatcgggcattatctgaacataaaacactatcaataagttggagtcattaccCTATTTTCTTATAATTACa                                                                                                                                            <  1:20575‑M1/19‑1 (MQ=255)     atctgaggcagcacctggcacggctgggacggaagtcgctgtcgttctcaaaatcggtggagctgcatgacaaagtcatcgggcattatctgaacataaaacactatcaataagttggagtcattaccCTATTTTCTTATAAtt                                                                                                                                               <  2:346045‑M1/16‑1 (MQ=255)           ttttAAACAGACACTTACCGCACAACAAACTAATTAAATACAAAGAAAGGCAACAATCAACTTAATGTTAATGAAATGTTTTACATATATTAACCACTTGTTTAATGCGGAGAATCAGTACACTATTTTCTggtgatgctgcca                                                                                                                                         >  2:293674‑M1/1‑131 (MQ=255)                       acTTACCGCACAACAAACTAATTAAATACAAAGAAAGGCAACAATCAACTTAATGTTAATGAAATGTTTTACATATATTAACCACTTGTTTAATGCGGAGAATCAGTACACTATTTTCTTATAATTACATTTGAAATTATATGATCAcc                                                                                                                        >  1:339745/1‑149 (MQ=255)                        cTTACCGCACAACAAACTAATTAAATACAAAGAAAGGCAACAATCAACTTAATGTTAATGAAATGTTTTACATATATTAACCACTTGTTTAATGCGGAGAATCAGTACACTATTTTCTTATAATTACATTTGAAATTATATGATCACCg                                                                                                                       >  1:283664/1‑149 (MQ=255)                          tACCGCACAACAAACTAATTAAATACAAAGAAAGACAACAATCAACTTAATGTTAATGAAATGTTTTACATATATTAACCACTTGTTTAATGCGGAGAATCAGTACACTATTTTCTggtgatgctgccaacttactgatttagt                                                                                                                          <  2:179499‑M1/144‑29 (MQ=255)                               ggacggaagtcgctgtcgttctcaaaatcggtggagctgcatgacaaagtcatcgggcattatctgaacataaaacactatcaataagttggagtcattaccCTATTTTCTTATAATTACATTTGAAGTTAtatgatcaccaagagaga                                                                                                                <  1:72411‑M1/47‑9 (MQ=255)                                acaacaAACTAATTAAATACAAAGAAAGGCAACAATCAACTTAATGTTAATGAAATGTTTTACATATATTAACCACTTGTTTAATGCGGAGAATCAGTACACTATTTTCTTATAATTACATTTGAAATTATATGATCACCGGGa                                                                                                                    >  2:332378/1‑144 (MQ=255)                                       aCTAATTAAATACAAAGAAAGGCAACAATCAACTTAATGTTAATGAAATGTTTTACATATATTAACCACTTGTTTAATGCGGAGAATCAGTACACTATTTTCTggtgatgctgccaacttactgatttagtgtatgatggtgtt                                                                                                             <  2:191120‑M1/144‑42 (MQ=255)                                        tcgctgtcgttctcaaaatcggtggagctgcatgacaaagtcatcgggcattatctgaacataaaacactatcaataagttggagtcattaccCTATTTTCTTATAATTACATTTGAAATTATATGATCACCGGGAGtgattga                                                                                                            <  2:216108‑M1/51‑1 (MQ=255)                                            ttAAATACAAAGAAAGGCAACAATCAACTTAATGTTAATGAAATGTTTTACATATATTAACCACGTGTTTAATGCGGAGAATCAGTACACTATTTTCTggtgatgctgccaacttactgatttagtgtatgatgcggtttttga                                                                                                        >  2:261409‑M1/1‑98 (MQ=255)                                                         atcggtggagctgcatgacaaagtcatcgggcattatctgaacattaaacagtatcaataagttggagtcattaccTTATTTTCTTATAATTACATTTGAAATTATATGATCACCGGGAGTGATTGATTAATTATCTTTACTAATAATc                                                                                      >  1:91568‑M1/77‑149 (MQ=255)                                                            ggtggagctgcatgacaaagtcatcgggcattatctgaacataaaacactatcaataagttggagtcattaccCTATTTTCTTATAATTACATTTGAAATTATATGATCACCGGGAGTGATTGATTAATTATCTTTACTAATAATCAGa                                                                                   >  1:39228‑M1/74‑149 (MQ=255)                                                                caaTCAACTTAATGTTAATGAAGTGTTTTACATATATTAACCACTTGTTTAATGCGGAGAATCAGTACACTATTTTCCTATAATTACATTTGAAATTATATGATCACCGGGAGTGATTGATTAATTATCTTTACTAATAATCAGACTaa                                                                               <  1:108389/149‑1 (MQ=255)                                                                       cTTAATGTTAATGAAATGTTTTACATATATTAACCACTTGTTTAATGCGGAAAATCAGTACACTATTTTCTTATAATTACATTTGAAATTATATGATCACCGGGAGTGATTGATTAATTATCTTTACTAATAATCAGACTAATATTTAc                                                                        <  1:130750/149‑1 (MQ=255)                                                                                  atcgggcattatctgaacataaaacgctatcaataagttggagtcattaccCTATTTTCTTATAATTACATTTGAAATTATCTGATCACCGGGAGTGATTGATTAATTATCTTTACTAATAATCAGACTAATATTTACCTGTTTGACCg                                                             >  1:243889‑M1/52‑149 (MQ=255)                                                                                            atctgaacataaaacactatcaataagttggagtcattaccCTATTTTCTTATAATTACATTTGAAATTATATGATCACCGGGAGTGATTGATTAATTATCTTTACTAATAATCAGACTAATATTTACCTGTTTGACCGAGTTg                                                        >  2:247496‑M1/42‑144 (MQ=255)                                                                                                     taaaacactatcaataagttggagtcattaccCTATTTTCTTATAATTACATTTGAAATTATATGATCACCGGGAGTGATTGATTAATTATCTTTACTAATAATCAGACTAATATTTACCTGTTTGACCGAGTTGGGATTGCGTCGttt                                          <  1:297090‑M1/117‑1 (MQ=255)                                                                                                         cagttgttTAATGCGGAGAATCAGTACACTATTTTCTggtgatgctgccaacttactgatttagtgtatgatggtgtttttgaggtgctccagtggcttctgtttctatcagctgtccctcctggtcagctactgacggtgtgg                                           <  2:206440‑M1/141‑108 (MQ=255)                                                                                                            ttGTTTAATGCGGAGAATCAGTACACTATTTTCTTATAATTACATTTGAAATTATATGATCACCGGGAGTGATTGATTAATTATCTTTACTAATAATCAGACTAATATTTACCTGTTTGACCGAGTTGGGATTGCGTCGTTTCTCCAtt                                   <  1:368749/149‑1 (MQ=255)                                                                                                             tGTTTAATGCTGAGAATCAGTACACTATTTTCTggtgatgctgccaacttactgatttagtgtatgatggtgtttttgaggtgctccagtggcttctgtttctatcagctgtccctcctgttcagctactgacggggtggtgcgtaacg                                  <  1:166732‑M1/149‑117 (MQ=255)                                                                                                             tGTTTAATGCGGAGAATCAGTACACTATTTTCTggtgatgctgccaacttactgatttagtgtatgatggtgtttttgaggtgctccagtggcttctgtttctatcagctgtccctcctgttcagctactgacggggtggtgcgtaacg                                  <  1:363740‑M1/149‑117 (MQ=255)                                                                                                                    tGCGGAGAATCAGTACCCTATTTTCTggagatgctgtcaacgtatttatttagtgtatgatggtgtttttgaggtgctccagtggcttctgtttctatcagctgtccctcctgttcagctactgacggggtggtgcgtaacggcaaaag                           <  1:269951‑M1/149‑124 (MQ=255)                                                                                                                      gttggagtcattaccCTATTTTCTTATAATTACATTTGAAATTATATGATCACCGGGAGTGATTGATTAATTATCTTTACTAATAATCAGACTAATATTTACCTGTTTGACCGAGTTGGGATTGCGTCGTTTCTCCATTAGGAg                              >  2:18069‑M1/16‑144 (MQ=255)                                                                                                                      cGGAGAATCAGTACACTATTTTCTTATAATTACATTTGAAATTATATGATCACCGGGAGTGATTGATTAATTATCTTTACTAATAATCAGACTAATATTTACCTGTTTGACCGAGTTGGGATGGCGTCGTTTCCCCATTAGGac                              >  2:227820/1‑143 (MQ=255)                                                                                                                        gagaATCAGTACACTATTTTCTTATAATTACAGTTGAAATTATATGATCACCGGGTGTGCTCTATTAATCATCTTTACTAATAATCAGACTAATATTTACCTGTTTGACCGAGTTGGGATTGCGTCGTTTCTCCATTAGGAGTa                            <  2:305481/144‑1 (MQ=255)                                                                                                                             tcattaccCTATTTTCTTATAATTAAATTTGAAATTATATGATCACCGGGAGTGATTGATTAATTATCTTTACTAATAATCAGACTAATATTTACCTGTTTGACCGAGTTGGGATTGCGTCGTTTCTCCATTAGGAGGAAAGCTTTAAt                  <  1:205440‑M1/141‑1 (MQ=255)                                                                                                                             tCAGTACACTATCTTCCTATAATTACATTTGAAATTATATGATCACCGGGAGTGATTGATTAATTATCTTTACTAATAATCAGACTAATATTTACCTGTTTGACCGAGTTGGGATTGCGTCGTTTCTCCATTAGGAGTAAAGCTTTAAt                  <  1:197511/149‑1 (MQ=255)                                                                                                                             gcatcaccCTGTTTTCTGATAATTACATTTGAAATTATATGATCACCGGGAGTGATTGATTAATTATCTTTACGAATAATCAGACTAATATTTACCTGTTTGACCGAGTTGGGATTGCGTCGTATCTCCATTAGGAGTAAAGCTTTAAt                  >  1:199484‑M1/9‑149 (MQ=255)                                                                                                                              cAGGACACTATTTTCTggggatgctgccaacttactgatttagtgtatgatggtgtttttgaggtgctccagtggcttctgtttctatcagctgtccctcctgttcagctactgacggggtggtgcgtaacggcaaaagcaccg                      <  2:82491‑M1/144‑129 (MQ=255)                                                                                                                                           tCTTATAATTACATTTGAAATTATATGATCACCGGGAGTGATTGATTAATTATCTTTACTAATAATCAGACTAATATTTACCTGTTTGACCGAGTTGGGATTGCGTCGTTTCTCCATTAGGAGTAAAGCTTTAATGTCACCTGAAGTTc    >  1:139512/1‑149 (MQ=255)                                                                                                                                           tCTTATAATTACATTTGAAATCATATGATCTCCGGGAGTGATTGATTAATTATCTTTACTAATAATCAGACTAATATTTACCTGTTTGACCGAGTTGGGATTGCGTCGTTTCTCCATTAGGGGTAAAGCTTTAATGTCACCTGAAGTTc    >  1:207515/1‑149 (MQ=255)                                                                                                                                             ttATAATTACATTTGAAATTATATGATCACCGGGTGTGATGGATTAATTATCTTTACTAATAATTAGACTAATATTTACCTGTTTGACCGAGTTGGGATTGCGTCGTTTCTCCATTAGGAGTAAAGCTTTAATGTCACCTGCAGTTctc  >  1:392588/1‑147 (MQ=255)                                                                                                                                             |                                                                                                                                                     GATAAGCTATTTTTAAACAGACACTTACCGCACAACAAACTAATTAAATACAAAGAAAGGCAACAATCAACTTAATGTTAATGAAATGTTTTACATATATTAACCACTTGTTTAATGCGGAGAATCAGTACACTATTTTCTTATAATTACATTTGAAATTATATGATCACCGGGAGTGATTGATTAATTATCTTTACTAATAATCAGACTAATATTTACCTGTTTGACCGAGTTGGGATTGCGTCGTTTCTCCATTAGGAGTAAAGCTTTAATGTCACCTGAAGTTCAC  >  CP009273/1972928‑1973216

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.