New junction evidence
		seq id	position	reads (cov)	reads (cov)	score	skew	freq	annotation	gene	product
*	?	CP009273	= 1046001	22 (0.770)	14 (0.490)	13/270	NT	40.6%	intergenic (+15/+418)	insB1/cspH	IS1 transposase B/stress protein, member of the CspA‑family
	?	CP009273	1973060 =	19 (0.660)					intergenic (‑606/‑174)	flhD/uspC	flagellar class II regulon transcriptional activator, with FlhC/universal stress protein

GCAATACCAGATAAGCTATTTTTAAACAGACACTTACCGCACAACAAACTAATTAAATACAAAGAAAGGCAACAATCAACTTAATGTTAATGAAATGTTTTACATATATTAACCACTTGTTTAATGCGGAGAATCAGTACACTATTTTCTTATAATTACATTTGAAATTATATGATCACCGGGAGTGATTGATTAATTATCTTTACTAATAATCAGACTAATATTTACCTGTTTGACCGAGTTGGGATTGCGTCGTTTCTCCATTAGGAGTAAAGCTTTAAT  >  CP009273/1972919‑1973200                                                                                                                                              |                                                                                                                                             gCAATACCAGATAAGCTATTTTTAAACAGACACTTACCGCACAACAAACTAATTAAATACAAAGAAAGGCAACAATCAACTTAATGTTAATGAAATGTTTTACATATATTAACCACTTGTTTAATGCGGAGAATCAGTACACTATTTTc                                                                                                                                       >  1:319750/1‑149 (MQ=255)     ataacctgaatctgaggcagcacctggcacggctgggacggaagtcgctgtcgttctcaaaatcggtggagctgcatgacaaagtcatcgggcattatctgaacataaaacactatcaataagttggagtcattaccCTCttt                                                                                                                                         >  2:88349‑M2/138‑143 (MQ=255)       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                                          <  1:262817‑M2/101‑1 (MQ=255)                                                                                              gggcattatctgaacataaaacactatcaataagttggagtcattaccCTATTTTCTTATAATTACATTTGAAATTATATGATCACCGGGAGTGATTGATTAATTATCTTTACTAATAATCAGACTAATATTTACCTGTTTGACCGAGt                                          <  1:466890‑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)                                                                                                                                              |                                                                                                                                             GCAATACCAGATAAGCTATTTTTAAACAGACACTTACCGCACAACAAACTAATTAAATACAAAGAAAGGCAACAATCAACTTAATGTTAATGAAATGTTTTACATATATTAACCACTTGTTTAATGCGGAGAATCAGTACACTATTTTCTTATAATTACATTTGAAATTATATGATCACCGGGAGTGATTGATTAATTATCTTTACTAATAATCAGACTAATATTTACCTGTTTGACCGAGTTGGGATTGCGTCGTTTCTCCATTAGGAGTAAAGCTTTAAT  >  CP009273/1972919‑1973200

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.