Predicted mutation
evidence	seq id	position	mutation	annotation	gene	description
JC JC	NC_000913	618,513	IS5 (+) +4 bp	coding (260‑263/1134 nt)	fepE →	regulator of length of O‑antigen component of lipopolysaccharide chains

New junction evidence
		seq id	position	reads (cov)	reads (cov)	score	skew	freq	annotation	gene	product
*	?	NC_000913	273955 =	NA (NA)	44 (1.180)	38/284	0.1	100%	noncoding (1195/1195 nt)	IS5	repeat region
	?	NC_000913	618513 =	0 (0.000)					coding (260/1134 nt)	fepE	regulator of length of O‑antigen component of lipopolysaccharide chains
*	?	NC_000913	= 275149	NA (NA)	40 (1.080)	31/282	0.2	100%	noncoding (1/1195 nt)	IS5	repeat region
	?	NC_000913	= 618516	0 (0.000)					coding (263/1134 nt)	fepE	regulator of length of O‑antigen component of lipopolysaccharide chains

GAAAATCTCTTTTCTGGTCTGACGGCGCTTACTGCTGAATTCACTGTCGGCGAAGGTAAGTTGATGACTCATGATGAACCCTGTTCTATGGCTCCAGATGACAAACATGATCTCATATCAGGGACTTGTTCGCACCTTCCGGAGGCGTTATGAGCTGGCGGCCCTTTTTGTATCTGATTATTAATCCCCACCCGCTATTAAGCGCCCGGCGCGGGCATCTGCGTCTGGTGCAGGGTTGACTTTGCATTCTGTTAACAAACGCGGTATAACAAACCTTCTT  >  NC_000913/275010‑275289                                                                                                                                            |                                                                                                                                             gAAAATCTCTTTTCTGGTCTGACGGCGCTTACTGCTGAATTCACTGTCGGCGAAGGTAAGTTGATGACTCATGATGAACCCTGTTCTATGGCTCCAGATGACAAACATGATCTCATATCAGGGACTTGTTCGCACCTTACGGa                                                                                                                                           >  2:601685/1‑143 (MQ=14)    agtctcTTTTCTGGTCTGACGGCGCTTACTGCTGAATTCACTGTCGGCGAAGGTAAGTTGATGACTCATGATGAACCCTGTTCTATGGCTCCAGATGACAAACGTGATCTCATATCAGGGACTTGTTCGCACCTTCCGGAGGc                                                                                                                                        <  2:493445/141‑1 (MQ=21)       ctctTTTCTGGTCTGACGGCGATTACGGCTGATTTCACTGTCGGCGAAGGTCGGTGGGCGACCCAAGATCACACCTGGGCTGCGGCTCCAGATGACAAACATGATCTCATATCAGGGACTTGTTCGCACCTTCCGGAGGCGtt                                                                                                                                     >  2:477514/1‑143 (MQ=11)        tctTTTCTGGTCTGACGGCGCTTACTGCTGAATTCACTGTCGGCGAAGGTAAGTTGATGAATCATGATGAACAGTGTTCTATGGCTCCAGATGACAAACATGATCTCATATCAGGGACTTGTGCGCACCTTCCGGCGGCGtca                                                                                                                                    >  2:519278/1‑141 (MQ=11)        tctGTTGTGGTCTGGCGGCGCTTACTGCCGAATTCACTGTCGGCGAAGGTAAGTTGATGACTCATGATGAACCCTGTTCTATGGCTCCAGATGACAAACATGATCTCATATCAGGGACTTGTTCGCACCTTCCGGAGGCGTTa                                                                                                                                    <  2:129590/143‑1 (MQ=255)        tctGTTCTGGTCTGAGGGCGCGGACTGCTGAATTCACTGTCGGCGAAGGTAAGTTGATGACTCATGATGAACCCTGTTCTATGGCTCCAGATGACAAACATGATCTCATATCAGGGACTTGTTCGCACCTTCCGGAGGCGTTa                                                                                                                                    <  2:500844/143‑1 (MQ=255)          ttttCTGGTCTGACGGCGCTTACTGCTGAATTCACTGTCGGCGAAGGTAAGTTGATGACTCATGATGAACCCTGTTCTATGGCTCCAGATGACAAACTTGATCTCATCTCAGGTCCTTGTTCGCACCTTCCGGCGGCGTTacg                                                                                                                                  >  2:431930/1‑141 (MQ=11)          ttttCTGGTCTGACGGCGCTTACTGCTGAATTCACTGTCGGCGAAGGTAAGTTGATGACTCATGATGAACCCTGTTCTATGGCTCCAGATGACAAACTTGATCTCATATCAGGGACTTGTTCGCACCTTCCGGAGGCGTTATg                                                                                                                                  >  2:274468/1‑143 (MQ=255)                  tCTGACGGCGCTTACTGCTGAATTCACTGTCGGCGAAGGTAAGTTGATGACTCATGATGAACCCTGTTCTATGGCTCCAGATGACAAACATGATCTCATATCAGGGACTTGTTCGCACCTTCCGGAGGCGTTATGAGCTggcg                                                                                                                          >  1:474191/1‑143 (MQ=255)                          cgcTTACTGCTGAATTCACTGTCGGCGAAGGTAAGTTGATGACTCATGATGAACCCTGTTCTATGGCTCCAGATGACAAACATGATCTCATATCAGGGACTTGTTCGCACCTTCCGGAGGCGTTATGAGATGGCGGCCCtttt                                                                                                                  >  2:650173/1‑143 (MQ=255)                             ttACTGCTCAATTCACTGTCGGCGAAGGTAAGTTGATGACTCATGATGAACCCTGTTCTATGGCTCCAGATGACAAACATGATCTCATATCAGGGACTTGTTCGCACCTTCCGGAGGCGTTATGAGCTGGCGGCCCTTTTTGt                                                                                                               <  1:656927/143‑1 (MQ=255)                               aCTGCTGTATTCACTGTCGGGGAAGGTATGTTCATGTCTCATGATGAGCCCTCTTCTATGGCTCCAGATGACAAACAGGTTCTCATATCAGGGACTTGTTCGCACCTTCCGGAGGCGTTATGAGCTGGCGGCCCTTTTTGTAt                                                                                                             <  1:469639/143‑1 (MQ=18)                                 tgctgAATTCACTGTCGGCGAAGGTAAGTTGATGACTCATGATGAACCCTGTTCTATGGCTCCAGATGACAAACATGATCTCATATCAGGGACTTGTTCGCACCTTCCGGAGGCGTTATGAGCTGGCGGCCCTTTTTGTATCt                                                                                                           >  1:71543/1‑143 (MQ=255)                                 tgctgAATTCACTGTCGGCGAAGGTAAGTTGATGACTCATGATGAACCCTGTTCTATGGCTCCAGATGACAAACATGATCTCATATCAGGGACTTGTTCGCACCTTCCGGAGGCGTTATGAGCTGGCGGCCCTTTTTGTATCt                                                                                                           >  2:512634/1‑143 (MQ=255)                                   ctgAATTCACTGTCGGCGAAGGTAAGTTGATGACTCATGATGAACCCTGTTCTATGGCTCCAGATGACAAACATGATCTCATATCAGGGACTTGTTCGCACCTTCCGGAGGCGTTATGAGCTGGCGGCCCTTTTTGTATCTGa                                                                                                         <  1:185212/143‑1 (MQ=255)                                   ctgAATTCACTGTCGGCGAAGGTAAGTTGATGACTCATGATGAACCCTGTTCTATGGCTCCAGATGACAAACATGATCTCATATCAGGGACTTGTTCGCACCTTCCGGAGGCGTTATGAGCTGGCGGCCCTCTTTGTATCTGa                                                                                                         >  2:487130/1‑143 (MQ=255)                                             tGTCGGCGAAGGTAAGTTGATGACTCATGATGAACCCTGTTCTATGGCTCCAGATGACAAACATGATCTCATATCAGGGACTTGTTCGCACCTTCCGGAGGCGTTATGAGCTGGCGGCCCTTTTTGTATCTGATTATTAATcc                                                                                               >  2:27170/1‑143 (MQ=255)                                               tCGGCGAAGGTAAGTTGATGACTCATGATGATCCCTGTTCTATGGCTCCAGATGACAAACATGATCTCATATCAGGGACTTGTTCGCACCTTCCGGAGGCGTTATGAGCTGGCGGCCCTTTTTGTATCTGATTATTAATcccc                                                                                             <  2:53094/143‑1 (MQ=255)                                               tCGGCGAAGGTAAGTTGATGACTCATGATGAACCCTGTTCTATGGCTCCAGATGACAAACATGATCTCATATCAGGGACTTGTTCGCACCTTCCGGAGGCGTTATGAGCTGGTGGCCCTTTTTGTATCTGATTATTAATcccc                                                                                             <  1:65973/143‑1 (MQ=255)                                                 ggCGAGGGCAGGTTGATGCCTCCTCATGAAGCCTGTTATAGGGCTCCAGATGACAAACATGATCTCATATCAGGGACTGGTTCGCACCTTCCTGAGGCGTTATGAGCTGGCGGCCCTTTTTGTATCTGATTATTAATCCCCAc                                                                                           <  2:189867/143‑1 (MQ=21)                                                 ggCGAAGGTAAGTTGATGACTCATGATGAACCCTGTTCTATGGCTCCAGATGACAAACATGATCTCATATCCGGGACCTGTTCGCACCTTCCGGAGGCGTTATGAGCTGGCTGCCCTATTCGTATCCGCTTATGAATcccccc                                                                                           >  2:564064/1‑141 (MQ=17)                                                      aGGTAAGTTGATGACTCATGATGAACCCTGTTCTATGGCTCCAGATGACAAACATGATCTCATATCAGTGACTTGTTCGCACCTTCCGGAGGCGTTATGAGCTGGCGGCCCTTTTTGTATCTGATTATTAATCCCCACCCGCt                                                                                      <  1:406016/143‑1 (MQ=255)                                                      aGGGAAGTTGATGACTCATGATGAACCCTGTTCTATGGCTCCAGATGACAAACATGATCTCATATCAGAGACTTGTTCGCACCTTCCGGAGGCGTTATGAGCTGGCGGCCCTTTTTGTATCTGATTATTAATCCCCACCCGCt                                                                                      <  1:491716/143‑1 (MQ=255)                                                        gTAAGTTGATGACTCATGATGAACCCTGTTCTATGGCTCCAGATGACAAACATGATCTCATATCAGGGACTTGTTCGCACCTTCCGGAGGCGTTATGAGCTGGCGGCCCTTTTTGTATCTGATTATTAATCCCCACCCGCTAt                                                                                    >  1:9939/1‑143 (MQ=255)                                                         tAAGTTGATGACTCATGATGAACCCTGTTCTATGGCTCCAGATGACAAACATGATCTCATATCAGGGACTAGTTCGCACCTTCCGGAGGCGTTATGAGCTGGCGGCCCCTTTTGTATCTGATTATTAATCCCCACCCGCTAtt                                                                                   >  2:411047/1‑143 (MQ=255)                                                           aGTTGATGACTCATGATGAACCCTGTTCTATGGCTCCAGATGACAAACATGATCTCATATCAGGGACTTGTTCGCACCTTCCGGAGGCGTTATGAGCTGGCGGCCCTTTTTGTATCTGATTATTAATCCCCACCCGCTATTaa                                                                                 <  1:199812/143‑1 (MQ=255)                                                             ttGATGACTCATGATTAACCCTGTTCTATGGCTCCAGATGACAAACATGATCTCATATCAGGGACTTGTTCGCACCTTCCGGAGGCGTTATGAGCTGGCGACCCTTTTCGTATCTGATTATTAATACCCAACCGCGATTaaac                                                                               >  2:437351/1‑141 (MQ=21)                                                             ttGATGACTCATGATGAACCCTGTTCTATGGCTCCAGATGACAAACATGATCTCATATCAGGGACTTGTTCGCACCTTCCGGAGGCGTTATGAGCTGGCGGCCCTTTTTGTATCTGATTATTAATCCCGCCCCGCTATTAAgc                                                                               >  1:595969/1‑143 (MQ=255)                                                                     tCATGATGAACCCTGTTCTATGGCTCCAGATGACAAACATGATCTCATATCAGGGACTTGTTCGCACCTTCCGGAGGCGTTATGAGCTGGCGGCCCTTTTTGTATCTGATTATTAATCCCCACCCGCTCTTAAGCGCCCGgcg                                                                       >  1:344213/1‑143 (MQ=255)                                                                         gatgaACCCTGTTCTATGGCTCCAGATGACAAACATGATCTCATATCAGGGACTTGTTCGCACCTTCCGGAGGCGTTATGAGCTGGCGGCCCTTTTTGTATCTGATTATTAATCCCCACCCGCTATTAAGCGCCCGGCGCggg                                                                   >  1:609485/1‑143 (MQ=255)                                                                          atgaACCCTGTTCTATGGCTCCAGATGACAAACATGATCTCATATCAGGGACTTGTTCGCACCTTCCGGAGGCGTTATGAGCTGGCGGCCCTTTTTGTATCCGATTATTAATCCACACCCGCCATTACGCGCCCGGCGCAGGc                                                                  >  2:255351/1‑143 (MQ=25)                                                                               cccTGTTCTATGGCTCCAGATGACAAACATGATCTCATATCAGGGACTTGTTCGCACCTTCCGGAGGCGTTATGAGCTGGCGGCCCTTTTTGTATCTGATTATTAATCCCCACCCGCTATTAAGCGCCCGGCGCGGGCATCTg                                                             >  1:591355/1‑143 (MQ=255)                                                                                ccTGTTCTATGGCTCCAGATGACAAACATGATCTCATATCAGGGAATTGTTGGCACCTTCCGGAGGCGTTATGAGATGGCGTCCCTTTTTGTATGTGATTTTTAGTCCCCACCCGCTATTAAGCGCCCGGCGCGGGCATCTGc                                                            >  1:419755/1‑143 (MQ=37)                                                                                  tGTTCTATGGCTGCATATGACAAACATGAGCTCATATCAGGGACTTGTTCGCACCTTCCGGAGGCGTTATGAGCTGGCGGCCCTTTTTGTATCTGATTATTAATCCCCACCCGCTATTAAGCGCCCGGCGCGGGCATCTGCGt                                                          <  1:430389/143‑1 (MQ=255)                                                                                  tGTTCTATGGCTCCAGATGACAAACATGATCTCATATCAGGGACTTGTTCGCACCTTCCGGAGGCGTTATGAGCTGGCGGCCCTTTTTGTATCTGATTATTAATCCCCACCCGCTATTAAGCGCCCGGCGCGGGCATCTGCGt                                                          <  1:93549/143‑1 (MQ=255)                                                                                      cTATGGCTCCAGATGACAAACATGATCTCATATCAGGGACTTGTTCGCACCTTCCGGACGCGTTATAAGCTGGCGGCCCTTTTTGTATCTGATTATTAATCCCCACCCGCTATTAAGCGCCCGGCGCGGGCATCTGCGTCTgg                                                      >  1:252823/1‑143 (MQ=255)                                                                                        aTGGCTCCAGATGACAAACATGCTCTCATATCAGGGACTTGTTCGCACCTTCCGGAGGCGTTATGAGCTGGCGGCCCTTTTTGTATCTGATTATTAATCCCCACCCGCTATTAAGCGCCCGGCGCGGGCATCTGCGTCTGGTg                                                    <  1:576317/143‑1 (MQ=255)                                                                                        aTGGCTCCAGATGACAAACATGATCTCATATCAGGGACTTGTTCGCACCTTCCGGAGGTGTTATGAGCTGGCGGCCCTTTTTGTATCTGATGACTAATCCCCACCCGCTATTACGCGCCCGGCGCGGCCAGCCGCGCCTgggg                                                    >  2:205755/1‑141 (MQ=25)                                                                                        aTGGCTCCAGATGACAAACATGATCTCATATCAGGGACTTGTTCGCACCTTCCGAAGGCGTTATGCGCTGGCGGCCCTTTTTGTATCTGATTATTCCTCCCCACCCGCTATTAAGCGCCCGGCGCCGGCCTCTCCGCCCGGtc                                                    >  2:468968/1‑142 (MQ=25)                                                                                           gCTCCAGCTGACAAACATGATCTCATATCAGGGACTTGTTCGCAGGTTCCGGAGGCGTTATGAGCTGGCGGCCCTTTTTGTATCTGATTATTAATCCCCACCCGCTATTAAGCGCCCGGCGCGGGCATCTGCGTCTGGTGCAg                                                 <  2:474191/143‑1 (MQ=255)                                                                                           gCTCCAGATGACAAACATGATCTCATATCAGGGACTTGGTCGCACCTTCCGGAGCGGCAGTTAGCTGGCGGCCCTTTTTGTATCTGATTATTAATCCCCACCCGCTATTAAGCGCCCGGCGCGGGCATCTGCGTCTGGTGCAg                                                 <  1:668026/143‑1 (MQ=37)                                                                                             tCCAGATGACAAACATGATCTCATATCAGGGACTTGTTCGCACCTTCCGGAGGCGTTATGAGCTGGCGGCCCTTTTTGTATCTGACTCTTACTCCCCACCCGCTATTAAGCACCCGGCACGGGCCTCTGCGCCTCGTGCCggc                                               >  2:289821/1‑142 (MQ=37)                                                                                                aGATGACAAACATGATCTCATATCAGGGACTTGTTCGCACCTTCCGGAGGCGTTATGAGCTGGCGGCCCTTTTTGTATCTGATTATTAATCCACACCCGCTATTAAGCGCCCGGCGCGGGCATCTGCGTCTGGTGCAGGGTTg                                            >  2:494378/1‑143 (MQ=255)                                                                                                   tGACAAACATGATCTCATATCAGGGACTTGTTCGCACCTTCCGGAGGCGTTATGAGCTGGCGGCCCTTTTTGTATCTGATTATTAATCCCCACCCGCTATTAAGCGCCCGGCGCGGGCATCTGCGTCTGGTGCAGGGTTGACt                                         <  1:53121/143‑1 (MQ=255)                                                                                                   tGACAAACATGATCTCATATCAGGGACTTGTTCGCACCTTCCGGAGGCGTTATGAGCTGGCGGCCCTTTTTGTATCTGATTATTAATCCCCACCCGCTATTAAGCGCCCGGCGCGGGCATCTGCGTCTGGTGCAGGGTTGACt                                         >  1:659898/1‑143 (MQ=255)                                                                                                    gACAAACATGATCTCATATCAGGGACTTGTTCGCACCTTCCGGAGGCGTTATGAGCTGGCGGCCCTTTTTGTATCTGATTATTAATCCCCACCCGCTATTAAGCGCCCGGCGCGGGCATCTGCGTCTGGTGCAGGGTTGACtt                                        <  1:236930/143‑1 (MQ=255)                                                                                                                   atatCAGGGACTTGTTCGCACCTTCCGGAGGCGTTATGAGCTGGCGGCCCTTTTTGTATATGATAATTTTTACTCGCCCGCTATTAAGCGCCCGGCGCGGGCATCTGCGTCTGGTGCAGGGTTGACTTTGCATTCTGTTAACa                         >  1:422543/1‑143 (MQ=255)                                                                                                                     atCAGGGACTTGTTCGCACCTTCCGGAGGCGTTATGAGCTGGCGGCCCTTTTTGTATCTGATTATTAATCCCCACCCGCTATTAAGCGCCCGGCGCGGGCATCTGCGTCTGGTGCAGGGTTGACTTTGCATTCTGTTAACaaa                       <  1:233938/143‑1 (MQ=255)                                                                                                                     atCAGGGACTTGTTCGCACCTTCCGGAGGCGTTATGAGCTGGCGGCCCTGTTTGTATCTGATTATTAATCCCCACCCGCAATTTGTCACCCGTCGCGGGCATCTGCGTCTGGTGCAGGGTTGACTTGGCATCGTGTTatccaa                       >  2:583383/1‑138 (MQ=255)                                                                                                                            aCTTGTTCGCACCTTCCGGAGGCGTTATGAGCTGGCGGCCCTTTTTGTAACTGATTAGGAATACACAACAGCTCGTAGGCGCCCGGCGCGGGCATCTGCGTATGGTGCAGGGGGGACTTTGCATGCTGTTGACAGAAGCGGta                >  2:80373/1‑143 (MQ=255)                                                                                                                              ttGTTCGCACCTTCCGGAGGCGTTATGAGCTGGCGGCCCTTTTTGTATCTGATTATTAATCCCCACCCGCTATTAAGCGCCCGGCGCGGGCATCTGCGTCTGGTGCAGGGTTGACTTTGCATTCTGTTAACAAACGCGGtata              >  1:267900/1‑143 (MQ=255)                                                                                                                                   cGCACCTTCCGGAGGCGTTATGAGCTGGCGGCCCTTTTTGTATCTGATTATTAATCCCCACCCGCTATTAAGCGCCCGGCGCGGGCATCTGCGTCTGGTGCAGGGTTGACTTTGCATTCTGTTAACAAACGCGGTATAACaaa         <  2:378567/143‑1 (MQ=255)                                                                                                                                    gCACCTTCCGGAGGCGTTATGAGCTGGCGGCCCTTTTTGTATCTGATTATTAATCCCCACCCGCTATTAAGCGCCCGGCGCGGGCATCTGCGTCTGGTGCAGGGTTGACTTTGCATTCTGTTAACAAACGCGGTATAACAAAc        <  1:477514/143‑1 (MQ=255)                                                                                                                                          gccGGCGGCGTTATGAGCTGGCGGCCCTTTTTGTATCTGATTATTAATCCCCACCCGCTATTAAGCGCCCGGCGCGGGCATCTGCGTCTGGTGCAGGGTTGACTTTGCATTCTGTTAACAAACGCGGTATAACAAACcttctt  <  1:95742/142‑1 (MQ=255)                                                                                                                                            |                                                                                                                                             GAAAATCTCTTTTCTGGTCTGACGGCGCTTACTGCTGAATTCACTGTCGGCGAAGGTAAGTTGATGACTCATGATGAACCCTGTTCTATGGCTCCAGATGACAAACATGATCTCATATCAGGGACTTGTTCGCACCTTCCGGAGGCGTTATGAGCTGGCGGCCCTTTTTGTATCTGATTATTAATCCCCACCCGCTATTAAGCGCCCGGCGCGGGCATCTGCGTCTGGTGCAGGGTTGACTTTGCATTCTGTTAACAAACGCGGTATAACAAACCTTCTT  >  NC_000913/275010‑275289

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 8 ≤ ATCG/ATCG < 12 ≤ ATCG/ATCG < 27 ≤ 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.