New junction evidence
		seq id	position	reads (cov)	reads (cov)	score	skew	freq	annotation	gene	product
*	?	CP009273	= 1973068	17 (0.590)	9 (0.310)	8/270	NT	34.6%	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

CCAGATAAGCTATTTTTAAACAGACACTTACCGCACAACAAACTAATTAAATACAAAGAAAGGCAACAATCAACTTAATGTTAATGAAATGTTTTACATATATTAACCACTTGTTTAATGCGGAGAATCAGTACACTATTTTCTTATAATTACATTTGAAATTATATGATCACCGGGAGTGATTGATTAATTATCTTTACTAATAATCAGACTAATATTTACCTGTTTGACCGAGTTGGGATTGCGTCGTTTCTCCATTAGGAGTAAAGCTTTAATGTCACCTGAA  >  CP009273/1972925‑1973210                                                                                                                                                |                                                                                                                                               ccAGATAAGCTATTTTTAAACAGACACTTACCGCACAACAAACTAATTAAATACAAAGAAAGGCAACAATCAACTTAATGTTAATGAAATGTTTTACATATATTAACCACTTGTTTAATGCGGAGAATCAATACAATATTTTCTTATaa                                                                                                                                           >  1:257/1‑149 (MQ=255)    ctgaatctgaagcagcacctggcacggctgggacggaagtcgcagtcgttctcaaaatcggtggagctgcatgacaaagtcatcgggcattatctgaacataaaacactatcaataggtgggagccaggaccCTATTTCCTta                                                                                                                                              >  2:98877‑M2/133‑143 (MQ=255)         tctgaggcagcacctggcacggctgggacggaagtcgctgtcgttctcaaaatcggtggagctgcatgacaaagtcatcgggcattatctgaacataaaacactatcaataagttggagtcattaccCTATTTTCTTATAAtt                                                                                                                                         <  2:344935‑M2/16‑1 (MQ=255)                ttAAACAGACACTTACCGCACAACAAACTAATTAAATACAAAGAAAGGCAACAATCAACTTAATGTTAATGAAATGTTTTACATATATTAACCACTTGTTTAATGAGGAGAATCAGTACACTATTTTCTggtgatgctgccaacttact                                                                                                                            >  1:347688‑M1/1‑129 (MQ=255)                  aaaCAGACACTTACCGCACAACAAACTAATTAAATACAAAGAAAGGCAACAATCAACTTAATGTTAATGAAATGTTTTACATATATTAACCACTTGTTTAATGCGGAGAATCAGTACACTATTTTCTggtgatgctgccaacttactga                                                                                                                          >  1:17650‑M1/1‑127 (MQ=255)                  aaaCAGACACTTACCGCACAACAAACTAATTAAATACAAAGAAAGGCAACAATCAACTGAATGTTAATGAAATGTTTTACATATATTAACCACTTGTTTAATGCGGAGAATCAGTACACTATTTTCTggtgatgctgccaacttacggg                                                                                                                          >  1:17703‑M1/1‑127 (MQ=255)                                     aacaaACTAATTAAATACAAAGAAAGGCAACAATCAACTTAATGTTAATGAAATGTTTTACATATATTAACCACTTGTTTAATGCGGAGAATCAGTACACTATTTTCTTATAATTACATTTGAAATTATATGATCACCGGGAGtgattg                                                                                                       >  1:472655/1‑149 (MQ=255)                                             aaTTAAATACAAAGAAAGGCAACAATCAACTTAATGTTAATGAAATGTTTTACATATATTAACCACTTGTTTAATGCGGAGAATCAGTACACTATTTTCTTATAATTACATTTGAAATTATATGATCACCGGGAGtgattgat                                                                                                     >  2:87588/1‑143 (MQ=255)                                             aaTTAAATACAAAGAAAGGCAACAATCAACTTAATGTTAATGAAATGTATTACATATATTAACCACTTGTTTAATGCGGAGAATCAGTACACTATTTTCTTATAATTACATTTGAAATTATATGATCACCGGGAGtgattgat                                                                                                     >  2:2095/1‑143 (MQ=255)                                               ttAAATACAAAGAAAGGCAACAATCAACTTAATGTTAATGAAATGTTTTACATATATTAACCACTTGTTTAATGCGGAGAATCAGTACACTATTTTCTTATAATTACATTTGAAATTATATGATCACCGGGAGTGATTGATTAATTATc                                                                                             >  1:68927/1‑149 (MQ=255)                                               tgtcgttctcaaaatcggtggagctgcatgacaaagtcatcgggcattatctgaacataaaacactatcaataagttggagtcattaccCTATTTTCTTATAATTAAATTTGAAATTATATGATCAACGGGAGTGATTGatta                                                                                                   >  2:464262‑M2/90‑143 (MQ=255)                                                    ttctcaaaatcggtggagctgcatgacaaagtcatcgggcattatctgaacataaaacactatcaataagttggagtcattaccCTATTTTCTTATAATTACATTTGAAATTATATGATCCCCGGGAGTGATTGATTAATTATCTTTAc                                                                                        >  1:238775‑M2/85‑149 (MQ=255)                                                     tctcaaaatcggtggagctgcatgacaaagtcatcgggcattatctgaacataaaacactatcaataagttggagtcattaccCTATTTTCTTATAATTACATTTGAAATTATATGATCACCGGGAGTGATTGATTAATTATc                                                                                             <  2:12412‑M2/60‑1 (MQ=255)                                                         agaaagGCAACAATCAACTTAATGTTAATGAAATGTTTTACATATATTAACCACTTGTTTAATGCGGCGAATCAGTACACTATTTTCTggtgatgctgccaacttactgatttagtgtatgatggtgtttttgaggtgctccagtggct                                                                                   >  1:138135‑M1/1‑88 (MQ=255)                                                            aagGCAACAATCAACTTAATGTTAATGAAATGTTTTACATATATTAACCACTTGTTTAATGCGGAGAATCAGTACACTATTTTCTTATAATTACATTTGAAATTATATGATCACCGGGAGTGATTGATTAATTATCTTTACTAATAATc                                                                                >  1:163348/1‑149 (MQ=255)                                                            aagGCAACAATCAACTTAATGTTAATGAAATGTGTTACATATATTAACCACTTGTTTAATGCGGAGAATCAGGACACTATTTTCTTATAATTACATTTCAACTTATATAATCACCGGGAGAGATTGATTAAGTAGCTTTACTAGTAATc                                                                                >  1:387373/1‑149 (MQ=255)                                                                gtggagctgcatgacaaagtcatcgggcattatctgaacataaaacactatcaataagttggagtcattaccCTATTTTCTTATAATTACATTTGAAATTATATGATCACCGGGAGTGATTGATTAATTATCTTTACTAATAATCAGAc                                                                            <  1:517411‑M2/77‑1 (MQ=255)                                                                caacaaTCAACTTAATGTTAATGAAATGTTTTACATATATTAACCACTTGTTTAATGCGGAGAATCAGTACACTATTTTCTggtgatgctgccaacttactgatttagtgtatgatggtgtttttgaggtgctccagtggctt                                                                                  <  2:245688‑M1/143‑63 (MQ=255)                                                                 aacaaTCAACTTAATGTTAATGAAATGTTTTACATATATTAACCACTTGTTTAATGCGGAGAATCAGTACACTATTTTCTTATAATTACATTTGAAATTATATGATCACCGGGAGTGATTGCTTAATGATCTTTaataataat                                                                                 >  2:360600/1‑143 (MQ=255)                                                                          cTTAATGTTAATGAAATGTTTTACATATATTAACCACTTGTTTAATGCGGAGAATCAGTACACTATTTTCTTATAATTACATTTGAAATTATATGATCACCGGGAGTGATTGATTAATTATCTTTACTAATAATCAGACTAat                                                                        <  2:117710/143‑1 (MQ=255)                                                                               tgttaatgAAATGTTTTACTTATATTAACCACTTGTTTAATGCGGAGAATCAGTACACTATTTTCTTATAATTACATTTGAAATTATATGATCACCGGGAGTGATTGATTAATTATCTTTACTAACAATCAGGCTCTTATTTa                                                                   <  2:437343/143‑1 (MQ=255)                                                                                gttaatgAAATGTTTTACATATATTAACCACTTGTTTAATGCGGAGAATCAGTACACTATTTTCTTATAATTACATTTGAAATTATATGATCACCGGGAGTGATTGATTAATTATCTTTACTAATAATCAGACTAATATTTACCTGttt                                                            <  1:246844/149‑1 (MQ=255)                                                                                  gtcatcgggcattatctgaacataaaacaccatcaataagtgggagtcattaccCTATTTTCTTATAATTACATTTGAAATTATATGATCACCGGGAGTGATTGATTAATTATCTTTACTAATAATCAGACTAATATTTACCTGTTTGa                                                          <  1:98652‑M2/95‑1 (MQ=255)                                                                                      gAAATGTTTTACATATATTAACCACTTGTTTAATGCGGAGAATCAGTACACTATTTTCTTATAATTACATTTGAAATTATATGATCACCGGGAGTGATTGATTAATTATCTTTACTAATAATCAGACTAATATTTACCTGTTTGACCGa                                                      >  1:392986/1‑149 (MQ=255)                                                                                        gggcattatctgaacataaaacactatcaataagttggagtcattaccCTATTTTCTTATAATTACATTTGAAATTATATGATCACCGGGAGTGATTGATTAATTATCTTTACTAATAATCAGACTAATATTTACCTGTTTGACCGAGt                                                    <  1:466890‑M2/101‑1 (MQ=255)                                                                                        gggcattatctgaacataaaacactatcaataagttggagtcattaccCTATTTTCTTATAATTACATTTGAAATTATATGATCACCGGGAGTGATTGATTAATTATCTTTACTAATAATCAGACTAATATTTACCTGTTTGACCGAGt                                                    <  1:262817‑M2/101‑1 (MQ=255)                                                                                          gcattatctgaacataaaacactatcaataagttggagtcattaccCTATTTTCTTATAATTACATTTGAAATTATATGATCACCGGGAGTGATTAATTAATTATATTTACTAATAATCAGACTAATATTTACCTATTTGAcc                                                        >  2:232513‑M2/47‑143 (MQ=255)                                                                                                      atTAACCACTTGTTTAATGCGGAGAATCAGTACACTATTTTCTggtgatgctgccaacttactgatttagtgtatgatggtgtttttgaggtgctccagtggcttctgtttctattcgctgtccctcctgttcagctactgac                                            >  2:181920‑M1/1‑43 (MQ=255)                                                                                                       ttAACCACTTGTTTAATGCGGAGAATCAGTACACTATTTTCTTATAATTACATTTGAAATTATATGATCACCGGGAGTGATTGATTAATTATCTTTACTAATAATCAGACTAATATTTACCTGTTTGACCGAGTTGGGATTGCGTCGtt                                     <  1:425727/149‑1 (MQ=255)                                                                                                         aaaacactatcaataagttggagtcattaccCTATTTTCTTATAATTACATTTGAAATTATATGATCACCGGGAGTGATTGATTAATTATCTTTACTAATAATCAGACTAATATTTACCTGTTTGACCGAGTTGGGATTGCGTCGTTtc                                   <  1:216607‑M2/118‑1 (MQ=255)                                                                                                          aCCACTTGTTTAATGCGGAGAATCAGTACACTATTTTCTTATAATTACATTTGAAATTATATGATCACCGGGAGTGATTGATTAATTATCTTTACTAATAATCAGACTAATATTTACCTGTTTGACCGAGTTGGGATTGCGTCGTTtct                                  >  1:254860/1‑149 (MQ=255)                                                                                                          aCCACTTGTTTAATGCGGAGAATCAGTACACTATTTTCTTATAATTACATTTGAAATTACATGATCACCGGGAGTGATTGATTAATTATCTTTACTAATAATCAGACTAATATTTACCTGTTTGACCGAGTTGGGATTGcgtc                                        <  2:359038/143‑1 (MQ=255)                                                                                                                 atcaataagttggagtcattaccCTATTTTCTTATAATTACATTTGAAATTATATGATCACCGGGAGTGATTGATTAATTATCTTTACTAATAATCAGACTAATATTTACCTGTTTGACCGAGTTGGGCTTGCGTCGTTtctc                                 >  2:202770‑M2/24‑143 (MQ=255)                                                                                                                     aaTGCGGAGAATCAGTACACTATTTTCTTATAATTACATTTGAAATTATATGATCACCGGGAGTGATTGATTAATTATCTTTACTAATAATCAGACTAATATTTACCTGTTTGACCGAGTTGGGATTGCGTCGTTTCTCCAtt                             >  2:421846/1‑143 (MQ=255)                                                                                                                      taattgggactcattaccCTATTTTCTTATAATTACACTTCAAATTATATGATCACCGGTAGTTATTGATTAATTATCTTTACTAATAATCAGACTAATATTTACCTGTTTGACCGAGTTGGGATTGCGTCGTTTCTCCATTa                            <  2:88884‑M2/125‑1 (MQ=255)                                                                                                                      aTGCGGAGAATCAGTACACTATTTTCTTATAATTACATTTGAAATTATATGATCACCGGGAGTGATTGATTAATTATCTTTACTAATAACAAGAAACATACGTACCTGTTTGACCGAGTTGGGATTGCGTCGTTTCTCCATTAGGAGTa                      >  1:101308/1‑149 (MQ=255)                                                                                                                         cGGAGAATCAGTACACTATTTTCTTATAATTACATTTGAAATTATATGATCACCGGGAGTGATTGATTAATTATCTTTACTAATAATCAGACTAATATTTACCTGTTTGACCGAGTTGGGATTGCGTCGTTTCTCCATTAGGAGTAAAg                   >  1:507131/1‑149 (MQ=255)                                                                                                                                tCAGTACACTATTTTCTggtgatgctgccaacttactgatttagtgtatgatggtgtttttgaggtgctccagtggcttctgtttctatcagctgtccctcctgttcagctactgacggggtggtgcgtaacggcaaaagcaccgccgg            >  1:102565‑M1/1‑17 (MQ=255)                                                                                                                                tCAGTACACTATTTTCAggtgatgctgccaacttactgatttagtgtatgatggtgtttttgaggtgctccagtggcttctgtttctatcagctgtccctcctgtccagctagtaacggggtggtgcgtaacggcaaaagcac                  <  2:216342‑M1/143‑127 (MQ=255)                                                                                                                                    tACACTATTTTCTggtgatgctgccaacttactgatttagtgtatgatggtgttttcgaggtgctccagtggcttctgtttctgtcagctgtccctcctgttcagctactgccggggtggtgcgtaacggcaaaagcaccgcc              >  2:305820‑M1/1‑13 (MQ=255)                                                                                                                                          agtttCTTATAATTACATTTGAAATTATATGATCACCGGGAGTGATTGATTAATTATCTTTACTAATAATCAGACTAATATTTACCTGTTTGACCGAGTTGGGATTGCGTCGTTTCTCCATTAGGAGTAAAGCTTTAATGTCACCTGaa  <  1:472903/147‑1 (MQ=255)                                                                                                                                             ttCTTATAATTACATTTGAAATTATATGATTAACTTTGTGGATTGATTAATTATCTTTACTAATAATCAGACTAATATTTACCTGTTTGACCGATGTGGGATTGCGTCGTTTCCCCATTAGGAGTACAGCTTTAATGTCACCt     >  2:335844/1‑143 (MQ=255)                                                                                                                                               cTTATAATTACATTTGAAATTATATGATCACCGGGAGTGATTGATTAATTATCTTTACTAATAATCAGACTAATATTTACCTGTTTGACCGAGTTGGGATTGCGTCGTTTCTCCATTAGGAGTAAAGCTTTAATGTCACCTGa   >  2:246546/1‑143 (MQ=255)                                                                                                                                                |                                                                                                                                               CCAGATAAGCTATTTTTAAACAGACACTTACCGCACAACAAACTAATTAAATACAAAGAAAGGCAACAATCAACTTAATGTTAATGAAATGTTTTACATATATTAACCACTTGTTTAATGCGGAGAATCAGTACACTATTTTCTTATAATTACATTTGAAATTATATGATCACCGGGAGTGATTGATTAATTATCTTTACTAATAATCAGACTAATATTTACCTGTTTGACCGAGTTGGGATTGCGTCGTTTCTCCATTAGGAGTAAAGCTTTAATGTCACCTGAA  >  CP009273/1972925‑1973210

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.