New junction evidence
		seq id	position	reads (cov)	reads (cov)	score	skew	freq	annotation	gene	product
*	?	CP009273	1973060 =	9 (0.420)	14 (0.650)	14/272	NT	60.9%	intergenic (‑606/‑174)	flhD/uspC	flagellar class II regulon transcriptional activator, with FlhC/universal stress protein
	?	CP009273	= 3577555	NA (NA)					intergenic (+15/‑1)	insB1/yrhA	IS1 transposase B/pseudogene, interrupted by IS1E

ATGCAATACCAGATAAGCTATTTTTAAACAGACACTTACCGCACAACAAACTAATTAAATACAAAGAAAGGCAACAATCAACTTAATGTTAATGAAATGTTTTACATATATTAACCACTTGTTTAATGCGGAGAATCAGTACACTATTTTCTTATAATTACATTTGAAATTATATGATCACCGGGAGTGATTGATTAATTATCTTTACTAATAATCAGACTAATATTTACCTGTTTGACCGAGTTGGGATTGCGTCGTTTCTCCATTAGGAGTAAAGCTTTAAT  >  CP009273/1972917‑1973200                                                                                                                                                |                                                                                                                                             agcggcataacctgaatctgaggcagcacctggcacggctgggacggaagtcgctgtcgttctcaaaatcggtggagctgcatgaccaagtcggcaggcattatctgaacataaaacactatcaataagttggaggcattaccCTAttt                                                                                                                                         <  1:388821‑M1/6‑1 (MQ=255)            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)                                                                                                                                                |                                                                                                                                             ATGCAATACCAGATAAGCTATTTTTAAACAGACACTTACCGCACAACAAACTAATTAAATACAAAGAAAGGCAACAATCAACTTAATGTTAATGAAATGTTTTACATATATTAACCACTTGTTTAATGCGGAGAATCAGTACACTATTTTCTTATAATTACATTTGAAATTATATGATCACCGGGAGTGATTGATTAATTATCTTTACTAATAATCAGACTAATATTTACCTGTTTGACCGAGTTGGGATTGCGTCGTTTCTCCATTAGGAGTAAAGCTTTAAT  >  CP009273/1972917‑1973200

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