New junction evidence
		seq id	position	reads (cov)	reads (cov)	score	skew	freq	annotation	gene	product
*	?	CP009273	1045234 =	24 (1.210)	15 (0.760)	14/270	NT	50.0%	intergenic (‑34/‑55)	gfcA/insA	O‑antigen capsule production threonine‑rich inner membrane protein/IS1 repressor TnpA
	?	CP009273	= 1973123	6 (0.300)					intergenic (‑669/‑111)	flhD/uspC	flagellar class II regulon transcriptional activator, with FlhC/universal stress protein

AAGAAAGGCAACAATCAACTTAATGTTAATGAAATGTTTTACATATATTAACCACTTGTTTAATGCGGAGAATCAGTACACTATTTTCTTATAATTACATTTGAAATTATATGATCACCGGGAGTGATTGATTAATTATCTTTACTAATAATCAGACTAATATTTACCTGTTTGACCGAGTTGGGATTGCGTCGTTTCTCCATTAGGAGTAAAGCTTTAATGTCACCTGAAGTTCACAGAATAAGGAACAGGTTATGAGCTATAGCAATATTCTTGTCGCTGTTGCGGTTA  >  CP009273/1972980‑1973270                                                                                                                                                |                                                                                                                                                    aacctgaatctgaggcagcacctggcacggctgggacggaagtcgctgtcgttctcaaaatcggtggagctgcatgacaaagtcatcgggcattatctgaacataaaacactatcaataagttggagtcattaccTTATCTTTACtaat                                                                                                                                                >  1:278404‑M1/136‑149 (MQ=255)  acctgaatctgaggcagcacctggcacggctgggacggaagtcgctgtcgttctcaaaatcggtggagctgcatgacaaagtcatcgggcattatctgaacataaaacactatcaataagttggagtcattaccTTATCTTTActaatc                                                                                                                                               <  1:356608‑M1/15‑2 (MQ=255)      gaaacctaggcagcacctggcacggctgggacggaagtcgctgtcgttctcaaaatcggtggagctgcatgacaaagtcatcgggcattatctgaacataaaacactatcaacaagttggagtcattaccTTATCTTTACTAATAATCa                                                                                                                                           >  1:81510‑M1/131‑149 (MQ=255)                    acctggcacggctgggacggaagtcgctgtcgttctcaaaatcggtggagctgcatgacaaagtcatcgggcattatctgaacataaaacactatcaataagttggagtcattaccTTATCTTTACTAATAATCAGACTAATATTTAcc                                                                                                                             <  1:126124‑M1/33‑1 (MQ=255)                         gttaatgAAATGGTTTACATATATTAACCACTTGTTTAATGCGGAGAATAAGTACACTATTTTCTTATAATTACATTTGAAATTATATGATCACCGGGAGCGATAGATTGATTATCATTAggggatgctgccaacttaccgat                                                                                                                              <  2:69465‑M2/143‑24 (MQ=255)                          ttaatgAAATGTTTTACATATATTAACCACTTGTTTAATGCGGAGAATCAGTACACTATTTTCTTATAATTACATTTGAAATTATATGATCACCGGGAGTGATTGATTAATTATGTTTAggtgatgctgccaacttactgatttagtgt                                                                                                                       <  1:31581‑M2/149‑31 (MQ=255)                          ttaatgAAATGTTTTACATATATTAACCACTTGTTTAATGCGGAGAATCAGTACACTATTTTCTTATAATTACATTTGAAATTATATGATCACCGGGAGTGATTGATTAATTATCTTTACTAATAATCAGACTAAAAtttcac                                                                                                                             >  2:119470/1‑140 (MQ=255)                               gAAATGTTTTACATATATTAACCACTTGTTTAATGCGGAGAATCAGTACACTATTTTCTTATAATTACATTTGAAATTATATGATCACCGGGAGTGATTGATTAATTATCTTTACTAATAATCAGACTAATATTTACCTGTTTGACCGa                                                                                                                  >  1:263265/1‑149 (MQ=255)                               ctgggacggaagtcgctgtcggtctcaaaatcggtggagctgcatgacaaagtcatcgggcattatctgaacataaaacactatcaataagttggagtcattaccTTATCTTTACTAATAATCAGACTAATATTTACCTGttt                                                                                                                        >  2:94646‑M1/106‑143 (MQ=255)                                        tACATATATTAACCACTTGTTTAATGCGGAGAATCAGTACACTATTTTCTTATAATTACATTTGAAATTATATGATCACCGGGAGTGATTGATTAATTATCTTTAggtgatgctgccaacttactgatttagtgtatgatggtgttttt                                                                                                         >  1:258472‑M2/1‑105 (MQ=255)                                            cgctgtcgttctcaaaatcggtggagctgcatgacaaagtcatcgggtattatctgaacataaaacactatcaataagttggagtcattaccTTATCTTTACTAATAATCAGACTAATATTTACCTGTTTGACCGAGTTGGGATTGcgt                                                                                                     >  1:56606‑M1/93‑149 (MQ=255)                                                gtcgttctcaaaatcggtggagctgcatgacaaagtcatcgggcattatctgaacataaaacactatcaataagttggagtcattaccTTATCTTTACTAATAATCCGACTAATATTTACCTGTTTGACCGAGTTCGGAATGc                                                                                                       <  2:94421‑M1/55‑1 (MQ=255)                                                 gcgttctcaaaatcggtggagctgcatgacaaagtcatcgggcattatctgaacataaaacactatcaataagttggagtcattaccTTATCTTTACTAATAATCAGACTAATATTTACCTGTTTGACCGAGTTGGGATTGCGTCGttt                                                                                                >  1:59775‑M1/88‑149 (MQ=255)                                                  aaCCACTTGTTTAATGCGTAGAATCAGTACACTATTTTCTTATCATTACAGTTGAAATTATATGATCACCGCGAGTGATTGATTAATTATCTTTAggtgatgctgccaacttactgatttagtgtatgatggtgtttttgagg                                                                                                     >  2:147914‑M2/1‑95 (MQ=255)                                                  aaCCACTTGTTGAATGCGGAGAATCAGTACCCGACATTCTTATAATTACATTTGAAATTATATGATCACCGGGAGTTATTGATTAATTATCTTTACTAATAATCAGACTAATATTTACCTGTTTGACCGAGTTGGGATTGcgt                                                                                                     <  2:148731/143‑1 (MQ=255)                                                   ggtctcaaaatcggtggagctgcatgacaaagtcatcgggcattatctgaacataaaacactatcaataagttggagtcattaccTTATCTTTACTAATAATCAGACTAATATTTACCCGTTTCACCGAGTTGGGATTGCGTCGTTtct                                                                                              >  1:190736‑M1/86‑149 (MQ=255)                                                          aaatcggtggagctgcatgacaaagtcatcgggcattatctgaacataaaacactatcaataagttggagtcattaccTTATCTTTACTAATAATCAGACTAATATTTACCTGTTTGACCGAGTTGGGATTGCGTCGTTtctc                                                                                             <  2:147753‑M1/65‑1 (MQ=255)                                                                      ctgcatgacaaagtcatcgggcattatctgaacataaaacactatcaataagttggagtcattaccTTATCTTTACTAATAATCAGACTAATATTTACCTGTTTGACCGAGTTGGGATTGCGTCGTTTCTCCATTAGGAGtag                                                                                 <  2:288998‑M1/77‑2 (MQ=255)                                                                          cAGTACACTATTTTCTTATAATTACATTTGAAATTATATGATCACCGGGAGTGATTGATTAATTATCTTTAggtgatgctgccaacttactgatttagtgtatgatggtgttttttttgtttttctgtggcttctgtttctat                                                                             <  2:270017‑M2/143‑73 (MQ=255)                                                                          cAGTACACTATTTTCTTATAATTACATTTGAAATTATATGATCACCGGGAGTGATTGATTAATTATCTTTAggtgatgctgccaacttactgatttagtgtatgatggtgtttttgaggttctccagtggcttctgtttctatcagctg                                                                       <  1:353772‑M2/149‑79 (MQ=255)                                                                                         tggcgtatctgaacattaaacactttctatgtgttggagtcattaccTTATCTTTACTAATAATCAGACTAATATTTACCTGTTGGACCGAGTTGGGATTGCGTCGTTTCTCCATTAGGAGTAAAGCTTTAATGTCACCTGaa                                                              >  2:272542‑M1/48‑143 (MQ=255)                                                                                             aaTTACATTTGAAATTATATGATCACCGGGAGTGATTGATTAATTATCTTTACTAATAATCAGACTAATATTTACCTGTTTGACCGAGTTGGGATTGCGTCGTTTCTCCATTAGGAGTAAAGCTTTAATGTCGCCTGAAGTTCACAGaa                                                    >  1:13067/1‑149 (MQ=255)                                                                                                    tttGAAATTATATGATCACCGGGAGTGATTGATTAATTATCTTTAggtgatgctgccaacttactgatttagtgtatgatggtgtttttgaggttctccagtggcttctgtttctatcagctgtccctcctgttcagctactg                                                   <  2:322227‑M2/143‑99 (MQ=255)                                                                                                    atcataaaacactatctataagttggagtcattaccTTATCTTTACTAATAATCAGACTAATATTTACCTGTTTGACCGAGTTGGGATTGCGTCGTTTCTCCATTAGGAGTAAAGCTTTAATGTCACCTGAAGTTCACAGAATAAGGaa                                             >  1:255547‑M1/37‑149 (MQ=255)                                                                                                     tggaaATTATATGATCACCGGGAGTCATTGATTAATTATCTTTAggtgatgctgccaacttactgatttagtgtctgatggtgtttttgaggttctccagtggcttctgtttctatcagctgtccctcctgttcagctactgacggggt                                            >  1:77388‑M2/3‑44 (MQ=255)                                                                                                       gAAATTATATGATCACCGGGGGTTATTGATTAATTATCTTTAggtgatgctgccaacttactgatttagtgtatgatggtgtttttgaggttctccagtggcttctgtttctatcagctgtccctcctgttcagctactgacggggtgg                                          >  1:30044‑M2/1‑42 (MQ=255)                                                                                                       gAAATTATATGATCACCGGGAGTGATTGATTAATTATCTTTAggtgatgctgccaacttactgatttagtgtatgatggtgtttttgaggttctccagtggcttctgtttctatcagctgtccctcctgttcagctactgacggggtgg                                          <  1:21756‑M2/149‑108 (MQ=255)                                                                                                           aacactatcaatatgttggagtcattaccTTATCTTTACTAATAATCAGACTAATATTTACCTGTTTGACCGAGTTGGGATTGCGTCGTTTCTCCATTAGAAGTAAAGCTTTAATGTCACCTGAAGTTCACAGAATAAGGAAc                                            <  2:199289‑M1/114‑1 (MQ=255)                                                                                                                tatcaataagttggagtcattaccTTATCTTTACTAATAATCAGACTAATATTTACCTGTTTGACCGAGTTGGGATTGCGTCGTTTCTCCATTAGGAGTAAAGCTTTAATGTCACCTGAAGTTCACAGAATAAGGAACAGGTTATGAGc                                 <  1:263632‑M1/125‑1 (MQ=255)                                                                                                                  aTCACCGGGAGTGATTGATTAATTATCTTTAggtgatgctgccaacttactgatttagtgtatgatggtgtttttgaggttctccagtggcttctgtttctatcagctgtccctcctgttcagctactgacggggtggtgcgtaacggc                               >  1:313201‑M2/1‑31 (MQ=255)                                                                                                                             ggattgattaAGTATCTTTAtgtggtgccctcaacttactgatttagtgtatgatggtgttctcgaggttctccagtggcttctgttgctatcagctgtccctcctgttcagctactgacggggtggtgcgtaacggcaaaag                          >  2:10575‑M2/2‑20 (MQ=255)                                                                                                                                ttgattAATTATCTTTAggtgatgctgccaacttactgatttagtgtatgatggtgtttttgaggttctccagtggcttctgtttctatcagctgtccctcctgttcagctactgacggggtggtgcgtaacggcaaaagcac                       <  2:59780‑M2/143‑127 (MQ=255)                                                                                                                                   attaattaTCTTTACTAATAATCAGACTAATATTTACCTGTTTGACCGAGTTGGGATTGCGTCGTTTCTCCATTAGGAGTAAAGCTTTAATGTCACCTGAAGTTCACAGAATACGGAACAGCTTATGAGCTATAGCCATATTc                    >  2:23053/1‑143 (MQ=255)                                                                                                                                       attaTCTTTAggtgatgctgccaacttactgatttagtgtatgatggtgtttttgaggttctccagtggcttctgtttctatcagctgtccctcctgttcagctactgacggggtggtgcgtaacggcaaaagcactgccggacatcag          >  1:20554‑M2/1‑10 (MQ=255)                                                                                                                                        ttaTCTTTACTAATAATCAGACTAATATTTACCTGTTTGACCGAGTTGGGATTGCGTCGTTTCTCCATTAGGAGTAAAGCTTTAATGTCACCTGAAGTTCACAGAATAAGGAACAGGTTATGAGCTATAGCAATATTCTTGTc               <  2:111869/143‑1 (MQ=255)                                                                                                                                         taTCTTTAggtgatgctgccaacttactgatttagtgtatgatggtgtttttgaggttctccagtggcttctgtttctatcagctgtccctcctgttcagctactgacggggtggtgcgtaacggcaaaagcactgccggaca              >  2:185537‑M2/1‑8 (MQ=255)                                                                                                                                              ttACTAGTAATCAGACGAAGATTTACCTGGTTGACCGAGTTGGGAATGCGTCGGTTCTCCATTAGGAGTAAAGCTTTAATGTCACCTGAAGTGCACAGAATAAGGAACAGGTTATGAGCTATAGCAATATTCTTGTCGCTGTTGCGGtt   <  1:63560/149‑1 (MQ=255)                                                                                                                                              ttACTAATAATCAGACTAATATTTACCTGTTTGACCGAGTTGGGATTGCGTCGTTTCTCCATTAGGAGTAAAGCTTTAATGTCACCTGAAGTTCACAGAATAAGGAACAGGTTATGAGCTATAGCAATATTCTTGTCGCTGTTGCGGtc   >  1:154919/1‑148 (MQ=255)                                                                                                                                               tAggtgatgctgccaacttactgatttagtgtatgatggtgtttttgaggttctccagtggcttctgtttctatcagctgtccctcctgttcagctactgacggggtggtgcgtaacggcaaaagcactgccggacatcagcgctatct  >  1:95790‑M2/1‑2 (MQ=255)                                                                                                                                               caggtgatgctgccaacttactgatttagtgtatgatggtgtttttgaggttctccagtggcttctgtttctatcagctgtccctcctgttcagctactgacggggtggtgcgtaacggcaaaagcactgccggacatcagcgctatct  >  1:291672‑M2/2‑2 (MQ=255)                                                                                                                                                |                                                                                                                                                    AAGAAAGGCAACAATCAACTTAATGTTAATGAAATGTTTTACATATATTAACCACTTGTTTAATGCGGAGAATCAGTACACTATTTTCTTATAATTACATTTGAAATTATATGATCACCGGGAGTGATTGATTAATTATCTTTACTAATAATCAGACTAATATTTACCTGTTTGACCGAGTTGGGATTGCGTCGTTTCTCCATTAGGAGTAAAGCTTTAATGTCACCTGAAGTTCACAGAATAAGGAACAGGTTATGAGCTATAGCAATATTCTTGTCGCTGTTGCGGTTA  >  CP009273/1972980‑1973270

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 12 ≤ ATCG/ATCG < 13 ≤ 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.