Predicted mutation
evidence	seq id	position	mutation	annotation	gene	description
JC JC	NC_000913	4,049,922	IS5 (–) +4 bp	noncoding (24‑27/109 nt)	spf →	Spot 42 sRNA antisense regulator of galK translation, Hfq‑dependent

New junction evidence
		seq id	position	reads (cov)	reads (cov)	score	skew	freq	annotation	gene	product
*	?	NC_000913	3652036 =	NA (NA)	77 (1.250)	55/284	0.1	100%	noncoding (1195/1195 nt)	IS5	repeat region
	?	NC_000913	= 4049925	0 (0.000)					noncoding (27/109 nt)	spf	Spot 42 sRNA antisense regulator of galK translation, Hfq‑dependent
*	?	NC_000913	= 3653230	NA (NA)	74 (1.200)	61/284	0.0	100%	noncoding (1/1195 nt)	IS5	repeat region
	?	NC_000913	4049922 =	0 (0.000)					noncoding (24/109 nt)	spf	Spot 42 sRNA antisense regulator of galK translation, Hfq‑dependent

TCTTTTCTGGTCTGACGGCGCTTACTGCTGAATTCACTGTCGGCGAAGGTAAGTTGATGACTCATGATGAACCCTGTTCTATGGCTCCAGATGACAAACATGATCTCATATCAGGGACTTGTTCGCACCTTCCTTAGGTGACACTATTTTTTTACATAAAGAACACCCTACCCCCAAATTATATAAAGATGGACAATATCTTGACAAACAAATCGAAGGTTTATTTTCAACATTATTAACCATTAATGACAACCTTTTACGAGCAAAAGCGGAAA  >  NC_000913/3653098‑3653372                                                                                                                                     |                                                                                                                                               tctTTTCTGGTCTGACGGCGCTTACTGCTGAATTCACTGTCGGCGAAGGTAAGTTGATGACTCATGATGAACCCTGTTCTATGGCTCCAGATGACAAACATGATCTCATATGAGGGACTTGATCGCACCTTCCTTAGGTGaca                                                                                                                                      >  1:202452/1‑143 (MQ=17) tctGTTCTGGGCTGACGGCGCTTACTGCTGAATTCACTGTCGGCGAAGGTAAGTTGATGACTCATGATGAACCCTGTTCTATGGCTCCAGATGACAAACATGATCTCATATCAGGGACTTGTTCGCACCTTCCTTAGGTGaca                                                                                                                                      <  1:441848/143‑1 (MQ=17)   ttttCTGGTCTGACGGCGCTTACTGCTGACTTCACTGTCGGCGAAGGTAAGTTGATGACTCATGATGAAACCTGTACTATGACTCCAGATGACAAACATGATCTCATATCAGGGACTTGTTCGCACCTTCCTTCGGTGACACt                                                                                                                                    >  1:966515/1‑143 (MQ=11)         ggTCTGACGGCGCTTACTGCTGAATTCACTGTCGGCGAAGGTAAGTTGATGACTCATGATGAACCCTGTTCTATGGCTCCAGATGACAAACATGATCTCATATCAGGGACTTGTTCGCACCTTCCTTAGGTGACACTAttttt                                                                                                                              <  2:109275/143‑1 (MQ=39)         ggTCTGACGGCGCTTACTGCTGAATTCACTGTCGGCGAAGGTAAGTTGATGACTCATGATGAACCCTGTTCTATGGCTCCAGATGACAAACATGATCTCATATCAGGGACTTGTTCGCACCTTCCTTAGGTGACACTAttttt                                                                                                                              >  2:181364/1‑143 (MQ=38)         ggTCTGACGGCGCTTACTGCTGAATTCACTGTCGGCGAAGGTAAGTTGATGACTCATGATGAACCCTGTTCTATGGCTCCAGATGACAAACATGATCTCATATCAGGGACTTGTTCGCACCTTCCTTAGGTGACACTAttttt                                                                                                                              <  2:564092/143‑1 (MQ=39)         ggTCTGACGGCGCTTACTGCTGAATTCACTGTAGGCGAAGGTAAGTTGATGACTCATGATGAACCCTGGTCTATGGCTCCAGGTGACAAACATGATCTCATATCAGGGACTTGTTCGCACCTTCCTCAGGTGGCTCTAtgttt                                                                                                                              >  1:64717/1‑143 (MQ=11)          gTCTGACGGCGCTTACTGCTGAATTCACTGTCGGCGAAGGTAAGTTGATGACTCATGATGAACCCTGTTCTATGGCTCCAGATGACAAACATGATCTCATATCAGGGACTTGTTCGCACCTTCCTTAGGTGACACTAtttttt                                                                                                                             <  1:1071929/143‑1 (MQ=40)               aCGGCGCTTACTGCTGAATTCACTGTCGGCGAAGGTAAGTTGATGACTCATGATGAACCCTGTTCTATGGCTCCAGATGACAAACATGATCTCATATCAGGGACTTGTTCGCACCTTACTTAGGTGACACTATTTTTTTACAt                                                                                                                        >  2:481831/1‑143 (MQ=255)                      tgacggctgAATTCACTGTCGGCCAAGGTAAGTTGATGACTCATGATGAACCCTGTTCTATGGCTCCAGATGACAAACATGATCTCATATCAGGGACTTGTTCGCACCTTCCTTAGGTGACACTATTTTTTTACATAAAGAac                                                                                                                 <  1:1029453/138‑1 (MQ=255)                          tgctgAATTCACTGTCGGCGAAGGTAAGTTGATGACTCATGATGAACCCTGTTCTATGGCTCCAGATGACAAACATGATCTCATATCAGGGACTTGTTCGCACCTTCCTTAGGTGACACTATTTTTTTACATAAAGAACAccc                                                                                                             >  1:110617/1‑143 (MQ=255)                               aaTTCACTGTCGGCGAAGGTAAGTTGATGACTCATGATGAACCCTGTTCTATGGCTCCAGATGACAAACATGATCTCATATCAGGGACTTGTTCGCACCTTCCTTAGGTGACACTATTTTTTTACATAAAGAACACCCTAccc                                                                                                        >  2:400784/1‑143 (MQ=255)                                 ttCACTGTGGGCGAAGGTAAGTTGATGACTCATGATGAACCCTGTTCTATGGCTCCAGATGACAAACATGATCTCATATCAGGGACTTGTTCGCACCTTCCTTAGGTGACACTATTTTTTTACATAAAGAACACCCTAccccc                                                                                                      >  1:948398/1‑143 (MQ=255)                                 ttCACTGTCGGCGAAGGTAAGTTGATGACTCATGATGAACCCTGTTCTATGGCTCCAGATGACAAACATGATCTCATATCAGGGACTTGTTCGCACCTTCCTTAGGTGACACTATTTTTTTACATAAAGAACACCCTAccccc                                                                                                      >  1:296229/1‑143 (MQ=255)                                    aCTGTCGGCGAAGGTAAGTTGATGACTCATGATGAACCCTGTTCTATGGCTCCAGATGACAAACATGATCTCATATCAGGGACTTGTTCGCACCTTCCTTAGGTGACACTATTTTTTTACATAAATAACACCCTACCCCCaaa                                                                                                   >  2:591512/1‑143 (MQ=255)                                       gTCGGCGAAGGTAAGTTGATGACTCATGATGAACCCTGTTCTATGGCTCCAGATGACAAACATGATCTCATATCAGGGACTTGTTCGCACCTTCCTTAGGTGACACTATTTTTTTACATAAAGAACACCCTACCCCCAAATta                                                                                                >  1:615206/1‑143 (MQ=255)                                             gAAGGTAAGTTGATGACTCATGATGAACCCTGTTCTATGGCTCCAGATGGCAAACATGATCTCATATCAGGGACTTGTTCGCACCTTCCTTAGGTGACACTATTTTTTTACATAAAGAACACACTACCCCCAAATTATATaaa                                                                                          >  1:494897/1‑143 (MQ=255)                                                  tAAGTTGATGACCCATGATGAACCCTGTTCTATGGCTCCAGATGACAAACATGATCTCATATCAGGGACTTGTTCGCACCTTCCTTAGGTGACACTATTTTTTTACATAAAGAACACCCTACCCCCAAATTATATAAAGATgg                                                                                     <  1:256514/143‑1 (MQ=255)                                                            aCTCATGATGCACCCTGTTCTATGGCTCCAGATGACAAACATGATCTCATATCAGGAACTTGTTCGCACCTTCCTTAGGTGACACTATTTTTTTACATAAAGAACACCCTACCCCCAAATTATATAAAGATGGACAATATCtt                                                                           <  2:571374/143‑1 (MQ=255)                                                            aCTCATGATGAACCCTGTTCTATGGCTCCAGATGACAAACATGATCTCATATCAGGGACTTGTTCGCACCTTCCTTACGTGACACTATTTTTTTACATAAAGAACACCCTACCCCCAAATTATATAAAGATGGACAATATCtt                                                                           <  2:633338/143‑1 (MQ=255)                                                              tCATGATGTACCCTGTTCTATGGCTCCAGATGACAAACATGATCTCATATCAGGGACTTGTTCGCACCTTCCTTAGGTGACACTATTTTTTTACATAAAGAACACCCTACCCCCAAAGTATATAAAGATGGACAATGTCTTGa                                                                         <  2:193453/143‑1 (MQ=255)                                                              tCATGATGAACCCTGTTCTATGGCTCCAGATGACAAACATGATCTCATATCAGGGACTTGTTCGCACCTTCCTTAGGTGACACTATTTTTTTACATAAAGAACACCCTACCCCCAAATTCTATACAGATGGACAAGATCTTGa                                                                         >  1:472138/1‑143 (MQ=255)                                                              tCATGATGAACCCTGTTCTATGGCTCCAGATGACAAACATGATCTCATATCAGGGACTTGTTCGCACCTTCCTTAGGTGACACTATTTTTTTACATAAAGAACACCCTACCCCCAAATTATAGAAAGATGGACAATATCTTGa                                                                         >  1:35469/1‑143 (MQ=255)                                                              tCATGATGAACCCTGTTCTATGGCACCAGATGACAAACATGATCTCATATCAGGGACTTGTTCGCACCTTCCTTAGGTGACACTATTTTTTTACATAAAGAACACCCTACCCCCAAATTATATAAAGATGGACAATATCTTGa                                                                         <  2:563435/143‑1 (MQ=255)                                                                  gatgaACCCTGTTCTATGGCTCCAGATGACAAACATGATCTCATATCAGGGACTTGTTCGCACCTTCCTTAGGTGACACTATTTTTTTACATAAAGAACACCCTACCCCCAAATTATATAAAGCTGGACAATATCTTGacaaa                                                                     >  1:1089923/1‑143 (MQ=255)                                                                      aaCCCTGTTCTATGGCTCCAGATGACAAACAAGAGCTCATATCAGGGACTTGTTCGCCCCTTCCTTAGGTGACACTATTTTTTTACATAAAGAACACCCTACCCCCAAATTATATAAAGATTGACAATACCTTGAcaaacaaa                                                                 >  2:680545/1‑143 (MQ=37)                                                                                    gCTCCAGATGACAAACATGATCTCATATCAGGGACTTGTTCGCACCTTCCTTAGGTGACACTAttttt                                                                                                                              >  2:1062358/1‑68 (MQ=255)                                                                                    gCTCCAGATGACAAACATGATCTCATATCAGGGACTTGTTCGCACCTTCCTTAGGTGACACTAttttt                                                                                                                              <  1:1062358/68‑1 (MQ=255)                                                                                       cccgATGACAAACATGATCTCATATCAGGGACTTGTTCGCACCTTCCTTAGGTGACACTATTTTTTTACATAAAGAACACCCTACCCCCAAATTATATAAAGATGGACAATATCTTGACAAACAAATCGAAGGTTTATTTTCa                                                <  1:527528/140‑1 (MQ=255)                                                                                         aGATGACAAACATGATCTCATATCAGGGACTTGTTCGCACCTTCCTTAGGTGACACTATTTTTTTACATAAAGAACACCCTACCCCCAAATTATATAAAGATGGACAATATCTTGACAAACAAATCGAAGGTTTATTTTCAAc                                              >  2:634586/1‑143 (MQ=255)                                                                                          gATGACAAACATGATCTCATATCAGGGACTTGTTCGCACCTTCCTTAGGTGACACTATTTTTTTACATAAAGAACACCCTACCCCCAAATTATATAAAGATGGACAATATCTTGACAAACAAATCGAAGGTTTATTTTCAACa                                             >  1:735405/1‑143 (MQ=255)                                                                                                aaaCATGATCTCATATCAGGGACTTGTTCGCACCTTCCTTAGGTGACACTATTTTTTTACATAAAGAACACCCTACCCCCAAATTATATAAAGATGGACAATATCTTGACAAACAAATCGAAGGTTTATTTTCAACAttatta                                       >  2:162513/1‑143 (MQ=255)                                                                                                  acgtggtctcACATCAGGGACTTGTTCGCACCTTCCTTAGGTGACACTATTTTTTTACATAAAGAACACCCTACCCCCAAATTATCTAAAGATGGACAATATCTTGACAAACAAATCGAAGGTTTATTTTCAACATTATTAAc                                     <  2:266737/137‑1 (MQ=255)                                                                                                    aTGATCTCATATCAGGGACTTGTTCGCACCTTCCTTAGGTGACACTATTTTTTTACATAAAGAACACCCTACCCCCAAATTATATAAAGATGGACAATATCTTGACAAACAAATCGAAGGTTTATTTTCAACATTATTAACCa                                   <  2:868128/143‑1 (MQ=255)                                                                                                        tctcATATCAGGGACTTGTTCGCACCTTCCTTAGGTGACACTATTTTTTTACATAAAGAACACCCTACCCCCAAATTATATAAAGATGGACAATATCTTGACAAACAAATCGAAGGTTTATTTTCAACATTATTAACCATTaa                               >  1:634921/1‑143 (MQ=255)                                                                                                         ctcATATCAGGGACTTGTTCGCACCTTCCTTAGGTGACACTATTTTTTTACATAAAGAACACCCTACCCCCAAATTATATAAAGATGGACAATATCTTGACAAACAAATCGAAGGTTTATTTTCAACATTATTAACCATTAAt                              >  2:169300/1‑143 (MQ=255)                                                                                                          tcatcgcAGGGAGTTGTTCGCACCGTCCTTAGGTGACACTATTTTTTTACATAAAGAACACCCTACCCCCAAATTATATAAAGATGGACAATATCTTGACAAACAAATCGAAGGTTTATTTTCAACATTATTAACCATTAATg                             <  2:1007844/137‑1 (MQ=255)                                                                                                           cATATCAGGGACTTGTTCGCACCTTCCTTAGGTGACACTATTTTTTTACATAAAGAACACCCTACCCCCAAATTATATAAAGATGGACAATATCTTGACAAACAAATCGAAGGTTTATTTTCAACATTATTAACCATTAATGa                            <  2:296229/143‑1 (MQ=255)                                                                                                           cATATCAGGGACTTGTTCGCACCTTCCTTAGGTGACACTA‑TTTTTTACATAAAGAACACCCTACCCCCAAATTATATAAAGATGGACAATATCTTGACAAACAAATCGAAGGTTTATTTTCGACATTATTAACCATTAATGAc                           >  1:94437/1‑143 (MQ=255)                                                                                                            atatCAGGGACTTGTTCGCACCTTCCTTAGGTGACACTATTTTTTTACATAAAGAACACCCTACTCCCAAATTATATAAAGATGGACAATATCTTGACAAACAAATCGAAGGTTTATTTTCAACATTATTAAACATTAATGAc                           >  2:632755/1‑143 (MQ=255)                                                                                                              atCAGGGACTTGTTCGCACCCTCCTTAGGTGACACTATTTTTTTACATAAATAACACCCTACCTTCAAATTTTATAAAGTTGGACAATATCTTTACAAACAAATCAAATATTTATTTTAAACATTTTTAACCATTAATAACat                         >  2:585057/1‑142 (MQ=255)                                                                                                               tCAGGGACTTGTTCGCACCTTCCTTAGGTGACACTATTTTTTTACATAAAGAACACCCTACCTCCAAATTATATAAAGATGGACAATATCTTGACAAACAAATCGAAGGTTTATTTTCAACATTATTAACCATTAATGACAAc                        <  1:560657/143‑1 (MQ=255)                                                                                                                 aGGGACTTGTTCGCACCTTCCTTAGGTGACACTATTTTTTTACATAAAGAACACCCTACCCCCAAATTATATAAAGATGGACAATATCTTGACAAACACATCGAAGGTTTATTTTCAACCTTATTAACCTTTAATGACAAccg                      >  1:354534/1‑142 (MQ=255)                                                                                                                  gggACTTGTTCGCACCTTCCTTAGGTGACACTATTTTTTTACATAAAGAACACCCTACCCCCAAATTATATAAAGATGGACAATATCTTGACAAACAAATCGAAGGTTTATTTTCAACATTAATAACCATTAATGACAACCtt                     >  1:260543/1‑143 (MQ=255)                                                                                                                    gACTTGTTCGCACCTTCCTTAGGTGACACTATTTTTTTACATAAAGAACACCCTACCCCCAAATTATATTAAGATGGACAATATCTTGACAAACAAATCGAAGGTTTATTTTCAACATTATTAACCATTAATGACAACCtttt                   <  2:183000/143‑1 (MQ=255)                                                                                                                     aCTTGTTCGCACCTTCCTTAGGTGACACTATTTTTTTACATAAAGAACACCCTACCCCCAAAGTATATAAAGATGGACAATATCTTGACAAACAAATCGAAGGTTTATTTTCAACATTATTAACCATTAATGACAACCTTTTa                  <  1:740806/143‑1 (MQ=255)                                                                                                                     aCTTGTGCGCACCCGTCTTAGGTGACACTATTTTTTTACATAAAGAACACCCTACCCCCAAATTATATAAAGATGGACAATATCTTGACAAACAAATCGAAGGTTTATTTTCAACATTATTAACCATTAATGACAACCTTTTa                  <  2:722708/143‑1 (MQ=255)                                                                                                                       ttGTTCGCACCTTCCTTAGGTGACACTATTTTTTTACATAAAGAACACCCTACCCCCAAATTATATAAAGATGGACAATATCTTGACAAACAAATCGAAGGTTTATTTTCAACATTATTAACCATTAATGACAACCTTTTACg                >  1:986822/1‑143 (MQ=255)                                                                                                                       ttGTTCGCACCTTCCTTAGGTGACACTATTTTTTTACATAAAGAACACCCTACCCCCAAATTATATAAAGATGGACAATATCTTGACAAACAAATCGAAGGTTTATTTTCAACATTATTAACCATTAATGACAACCTTTTACg                >  2:1113274/1‑143 (MQ=255)                                                                                                                         gTTCGCACCTTCCTTAGGTGACACTATTTTTTTTTTTTTTTTACACCCTACCCCCGACTTCTATATAGATTTCCATTATCTTGACTAACACATCGTCGCTTTCTTTTCTTCATTATTTACCATTAATGACAACCTTTTACgtt              >  2:880366/1‑141 (MQ=255)                                                                                                                          ttCGCACCTTCCTTAGGTGACACTATTTTTTTACATAAAGAACACCCTACCCCCAAATTATATAAAGATGGACAATATCTTGACAAACAAATCGAAGGTTTATTTTCAACATTATTAACCATTAATGACAACCTTTTACGAGc             <  2:110617/143‑1 (MQ=255)                                                                                                                          ttCGCACCTTCCTTAGGTGACACTATTTTTTTACATAAAGAACACCCTACCCCCAAATTATATAAAGATGGACAATATCTTGACAAACAAATCGAAGGTTTATTTTCAACATTATTAACCATTAATGACAACCTTTTACGAGc             <  1:181364/143‑1 (MQ=255)                                                                                                                          atCGCACCTTCCGTAGGTGACACTATTTTTTTACATAAAGAACACCCTACCCCCAAATTATATAAAGATCGACAATATCTTGACAAACAAATCGAAGGTTTATTTTCAACATTATTAACCATTAATGACAACCTTTTACGAGc             <  2:64717/142‑1 (MQ=255)                                                                                                                            cGCACCTTCCTTAGGTGACACTATTTTTTTACATAAAGAACACCCTACCCCCAAATTATATAAAGATGGACAATATCTTGACAAACAAATCGAAGGTTTATTTTCAACATTATTAACCATTCATGACAACCTTTTACCAGCac           >  2:47303/1‑142 (MQ=255)                                                                                                                               aCCTTCCTTAGGTGACACTATTTTTTTACATAAAGAACACCCTACCCCCAAATTATATAAAGATTTACAATATCTTGACAAACAAATCGAAGGTTTATTTTCACCATTATTAACCATTAATCACAACCTTTTACTAGCCAAAg        >  2:452490/1‑143 (MQ=255)                                                                                                                                ccttccttAGGTGACACTATTTTTTTACATAAAGAACACCCTACCCCCAAATTATATAAAGATGGACAATATCTTGACAAACAAATCGAAGGTTTATTTTCAACGTTATTAACCATTAATGACAACCTTTTACGAGCAAAAGc       >  1:358350/1‑143 (MQ=255)                                                                                                                                ccttccttAGGTGACACTATTTTTTTACATAAAGAACACCCTACCCCCAAATTATATAAAGATGGACAATATCTTGACAAACAAATCGAAGGTTTATTTTCAACATTATTAACCATTAATGACAACCTTTTACGAGCAAAAGc       <  1:957551/143‑1 (MQ=255)                                                                                                                                ccagcctgAGGGGACACTATTGTTTTACATAAAGAACACCCTACCCCCAAATTATATAAAGATGGACAATATCTTGACAAACAAATCGCAGGTTTATTTTCAACATTATTAACCATTAATGACAACCTTTTACGAGCAAAAGc       <  1:580919/139‑1 (MQ=255)                                                                                                                                 cttccttAGGTGACACTATTTTTTTACATAAAGAACACCCTACCCCCAAATTATATAAAGATGGACAATATCTTGACAAACAAATCGAAGGTTTATTTTCAACATTATTAACAATTAATTAAAACATTTTACGAGCAAAAGCg      >  2:243016/1‑143 (MQ=255)                                                                                                                                  ttccttAGGTGACACTATTTTTTTACATAAAGAACACCCTACCCCCAAATTATATAAAGATGGACAATATCTTGACAAACAAATCGAAGGTTTATTTTCAACATTATTAACCATTAATGACAACCTTTTACGAGCAAAAGCgg     <  2:246634/143‑1 (MQ=255)                                                                                                                                  ttccttAAGTGACACTATGTGTTTACATAAAGAACACCCTACCCCCAAATTATATAAAGATGGACAATATAGTGACAAACAAATCGAAGGTTTATTTTCAACATTATTAACCATTAATGACAACCTTTTACGAGCAAAAGCgg     <  1:781913/143‑1 (MQ=255)                                                                                                                                     cttAGGTGACACTATTTTTTTACATAAAGAACACCCTACCCCCAAATTATATAAAGATGGACAATATCTTGACAAACAAATCGAAGGTTTATTTTCAACATTATTAACCATTAATGACAACCTTTTACGAGCAAAAGCGGaaa  <  2:220573/143‑1 (MQ=255)                                                                                                                                     |                                                                                                                                               TCTTTTCTGGTCTGACGGCGCTTACTGCTGAATTCACTGTCGGCGAAGGTAAGTTGATGACTCATGATGAACCCTGTTCTATGGCTCCAGATGACAAACATGATCTCATATCAGGGACTTGTTCGCACCTTCCTTAGGTGACACTATTTTTTTACATAAAGAACACCCTACCCCCAAATTATATAAAGATGGACAATATCTTGACAAACAAATCGAAGGTTTATTTTCAACATTATTAACCATTAATGACAACCTTTTACGAGCAAAAGCGGAAA  >  NC_000913/3653098‑3653372

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.