Predicted mutation
evidence	seq id	position	mutation	annotation	gene	description
MC JC	NC_000913	1,299,499	Δ1,199 bp	intergenic (+254/‑485)	ychE → / → oppA	UPF0056 family inner membrane protein/oligopeptide ABC transporter periplasmic binding protein

Missing coverage evidence...
			seq id	start	end	size	←reads	reads→	gene	description
*	*	÷	NC_000913	1299499–1300697	1300697	1–1199	59 [0]	[0] 60	ychE/oppA	UPF0056 family inner membrane protein/oligopeptide ABC transporter periplasmic binding protein

New junction evidence
		seq id	position	reads (cov)	reads (cov)	score	skew	freq	annotation	gene	product
*	?	NC_000913	= 1299498	0 (0.000)	57 (1.200)	48/274	0.0	100%	intergenic (+253/‑1684)	ychE/oppA	UPF0056 family inner membrane protein/oligopeptide ABC transporter periplasmic binding protein
	?	NC_000913	1300698 =	0 (0.000)					intergenic (+1453/‑484)	ychE/oppA	UPF0056 family inner membrane protein/oligopeptide ABC transporter periplasmic binding protein

ATTACAGTTAGTTATAAGGATTTCCTTAACTGCTTCTCCTCACCATCATGTTATTTTCGCCACATCATAATCCTGGGCTTGCTGAAGAATAATTGAAATGATATTATTAATTCCACTGCCTTTGGTAGAGGAAAGTGCTAAGGAAGGTGCGAACAAGTCCCTGATATGAGATCATGTTTGTCATCTGGAGCCATAGAACAGGGTTCATCATGAGTCATCAACTTACCTTCGCCGACAGTGAATTCAGCAGTAAGCGCCGTCAGACCAGAAAAGAGATTTTCT  >  NC_000913/1299358‑1299639                                                                                                                                             |                                                                                                                                              aTTACAGTTAGTTATAAGGATTTCCTTAACTGCTTCTCCTCACCATCATGTTATTTTCGCCACATCATAATCCTGGGCTTGCTGAAGAATAATTGAAATGATATTATTAATTCCACTGCCTTTGGTAGAGGAAAGTGCTAAat                                                                                                                                             <  1:421791‑M1/143‑3 (MQ=255)  ttccagtTAGTTATAAGGATTTCCTGAACCGCTTCTCCTCACCATCATGTTATTTTCGCCACATCATAATCCTGGGCTTGCTGAAGATTACTTGAGATGATATTATTAATTCCACTGCCTTTGGTAGAGGAAAGTGCTAAata                                                                                                                                            <  2:351656‑M1/140‑4 (MQ=255)     cAGTTAGTTATAAGGATTTCCTTAACTGCTTCTCCTCACCATCATGTTATTTTCGCCACCTCATAATCGTGGGCCTGCTGAAGAATAATTGAAATGATATTATTAATTCCACTGCCTTTGGTCGAGGAAAGTGCTAAataata                                                                                                                                         >  2:822210‑M1/1‑137 (MQ=255)      agttagttATAAGGATTTCCTTAACTGCTTCTCCTCACCATCATGTTATTTTCGCCACATCATAATCCTGGGCTTGCTGAAGAATAATTGAAATGATATTATTAATTCCACTGCCTTTGGTAGAGGAAAGTGCTAAataataa                                                                                                                                        >  2:294301‑M1/1‑136 (MQ=255)       tttagttatAAGGATTTCCTTAACTGCTTCTCCTCACCATCATGTTATTTTCGCCACATCATAATCCTGGGCTTGCTGAAGAATAATTGAAATGATATTATTAATTCCACTGCCTTTGGTAGAGGAAAGTGCTAAataataat                                                                                                                                       <  2:128120‑M1/142‑9 (MQ=255)        ttagttaTAAGGATTTCCTTAACTGCTTCTCCTCACCATCATGTTATTTTCGCCACATCATAATCCTGGGCTTGCTGAAGAATAATTGAAATGATATTATTAATTCCACTGCTTTTGGTAGAGGAAAGTGCTAAataataatc                                                                                                                                      >  1:790740‑M1/1‑134 (MQ=255)        ttagttaTAAGGATTTCCTTAACTGCTTCTCCTCACCATCATGTTATTTTCGCCACATCATAATCCTGGGCTTGCTGAAGAATAATTGAAATGATATTATTAATTCCACTGCCTTTGGTAGAGGAAAGTGCTAAataataatc                                                                                                                                      >  2:142166‑M1/1‑134 (MQ=255)        ttagttaTAAGGATTTCCTTAACTGCTTCTCCTCACCATCATGTTATTTTCGCCACATCATAATCCTGGGCTTGCTGAAGAATAATTGAAATGATATTATTAATTCCACTGCCTTTGGTAGAGGAAAGTGCTAAataataatc                                                                                                                                      >  1:436071‑M1/1‑134 (MQ=255)          agttaTAAGGATTTCCTTAACTGCTTCTCCTCACCATCATGTTATTTTCGCCACATCATAATCCTGGGCTTGCTGAAGAATAATTGAAATGATATTATTAATTCCACTGCCCTTTGTAGAGGAAAGTGCTAAataataatcaa                                                                                                                                    >  2:20879‑M1/1‑132 (MQ=255)              ataAGGATTTCCTTAACTGCTTCTCCTCACCATCATGTTATTTTCGCCACATCATAATACTGGGCTTGCTGAAGAATAATTGAAATGATATTATTAATTCCACTGCCTTTGGTAGAGGAAAGTGCTAAataataatcaattgt                                                                                                                                <  2:168811‑M1/143‑16 (MQ=255)               taAGGATTTCCTTAACTGCTTCTCCTCACCATCATGTTATTTTCGCCACATCATAATCCTGGGCTTGCTGAAGAATAATTGAAATGATATTATTAATTCCACTGCCTTTGGTAGAGGAAAGTGCTAAataataattaattgtt                                                                                                                               >  1:366872‑M1/1‑127 (MQ=255)               taAGGATTTCCTTAACTGCTTCTCCTCACCATCATGTTATTTTCGCCACATCATAATCCTGAGCTTGCTGAAGAATAATTGAAATGATATTATTAATTCCACTGCCTTTGGTAGAGGAAAGTGCTAAataataatcaattgtt                                                                                                                               >  2:120873‑M1/1‑127 (MQ=255)                  ggATTTCCTTAACTGCTTCTCCTCACCATCATGTTATTTTCGCCACATCATAATCCTGGGCTTGCTGAAGAATAATTGAAATGATATTATTAATTCCACTGCCTTTGGTAGAGGAAAGTGCTAAataataatcaattgttaaa                                                                                                                            <  1:351440‑M1/143‑20 (MQ=255)                       tCCTTAACTGCTTCTCCTCACCATCATGTTATTTTCGCCACATCATAATCCTGGGCTTGCTGAAGAATAATTGAAATGATATTATTAATTCCACTGCCTTTGGTAGAGGAAAGTGCTAAataataatcaattgttaaattatt                                                                                                                       <  1:427747‑M1/143‑25 (MQ=255)                       tCCTTAACTGCTTCTCCTCACCATCATGTTATTTTCGCCACATCATAATCCTGGGCTTGCTGAAGAATAATTGAAATGATATTATTAATTCCACTGCCTTTGGTAGAGGAAAGTGCTAAataataatcaattgttaaattatt                                                                                                                       <  2:429754‑M1/143‑25 (MQ=255)                       tCCCTAACTGCTTCCCCTGCACAGCATGTTATTTTCGCCACATCATAATACTTAGCTTGCTGAAGAATAATTGAAATGATATTATTAATTCCACTGCCTTTGGTAGAGGAAAGTGCTAAataataatcaattgttaaattatt                                                                                                                       <  2:144258‑M1/143‑25 (MQ=255)                              cTGCTTCTCCTCACCATCATGTTATTTTCGCCACATCATAATCCTGGGCTTGCTGAAGAATAATTGACATGATATTATTAATTCCACTGCCTTTGGTAGAGGAAAGTGCTAAataataatcaattgttaaattattgtgcatt                                                                                                                >  2:168117‑M1/1‑112 (MQ=255)                                 cTTCTCCTCACCATCATGTTATTTTCGCCACATCATAATCCTGGGCTTGCTGAAGAATAATTGAAATGATATTATTAATTCCACTGCCTTTGGTAGAGGAAAGTGCTAAataataatcaattgttaaattattgtgcatttca                                                                                                             <  1:207753‑M1/143‑35 (MQ=255)                                       ctcACCATCATGTTATTTTCGCCACATCATAATCCTGGGCTTGCTGAAGAATAATTGAAATGATATTATTACTTCCACTGCCTTTGGTAGAGGAAAGTGCTAAataataatcaattgttaaattattgtccatttcactactg                                                                                                       >  2:370967‑M1/1‑103 (MQ=255)                                             atcatGTTATTTTCGCCACATCATAATCCTGGGCTTGCTGAAGAATAATTGAAATGATATTATTACTTCCACTGCCTTTGGTAGAGGAAAGTGCTACctgctcgccgagttgtaaattattgtgcatttcactactggaactg                                                                                                 <  2:537039‑M1/143‑47 (MQ=255)                                             atcatGTTATTTTCGCCACATCATAATCCTGGGCTTGCTGAAGAATAATTGAAATGATATTATTAATTCCACTGCCTTTGGTAGAGGAAAGTGCTAAataataatcaattgttaaattattgtgcatttcactactggaactg                                                                                                 >  1:23163‑M1/1‑97 (MQ=255)                                                  gTTATTTTCGCCACATCATAATCCTGGGCTTGCTGAAGAATAATTGAAATGATATTATTAATTCCACTGCCTTTGGTAGAGGAAAGTGCTAAataataatcaattgttaaattattgtgcatttcactactggaactgtaatc                                                                                            >  1:752030‑M1/1‑92 (MQ=255)                                                   ttATTTTCGCCACTTCAGAATCCTGGGCTTGATGAAGAATAATTGAAATGATATTATGAATTCCACTGCCTTTGGTATAGGAAAGTGCTAAataataatcaattgttaaattattgtgcatttcactactggaactgtaatca                                                                                           <  2:226830‑M1/143‑53 (MQ=255)                                                     aTTTTCGCCACATCATAATCCTGGGCTTGCTGAAGAATAATTGAAATGATATTATTAATTCCACTGCCTTTGGTAGAGGAAAGTGCTAAataataatcaattgttaaattattttgcatttcactactggaactgtaatcaga                                                                                         >  2:636900‑M1/1‑89 (MQ=255)                                                       tttCGTCACATCATAATCCTGGGCTTGATGAAGAATAATTGAAATGATATTATTAATTCCACTGCCTTTGGTAGAGGAAAGTGCTAAataataatcaattgttaaattattgtgcatttcactactggaactgtaatcagaaa                                                                                       <  1:639416‑M1/143‑57 (MQ=255)                                                          cggtatatcataattctGGGCTTGATGAAGATTAATTGAAATGATATTATGAATTCCAGTGCGTTTGGTAGAGGAAAGTGTTAAataataatcaattgttaaattattgtgcatttcactactggaactgtaatcagaaaaga                                                                                    <  2:486705‑M1/137‑60 (MQ=255)                                                           gCCACATCATAATCCTGGGCTTGCTGAAGAATAATTGAAATGATATTATTAATTCCACTGCCTTTGGTAGAGGAAAGTGCTAAataataatcaattgttaaattattgtgcatttcactactggaactgtaatcagaaaagat                                                                                   >  1:512904‑M1/1‑83 (MQ=255)                                                            ccACATCATAATCCTGGGCTTGCTGAAGAATAATTGAAATGATATTATTAATTCCACTGCCGTTGGTAGAGGAAAGTGCTAAacaataatcaattgttaaattatggtgcatttcactactggaactgtaatcaaaaaagata                                                                                  >  2:436482‑M1/1‑82 (MQ=255)                                                              acaTCATAATCCTGGGCTTGCTGAAGAATAATTGAAATGATATTATTAATTCCACTGCCTTTGGTAGAGGAAAGTGCTAAataataatcaattgttaaattattgtgcatttcactactggaactgtaatcagaaaagataga                                                                                >  2:289569‑M1/1‑80 (MQ=255)                                                              acaTCATAATCCTGGGCTTGCTGAAGAATAATTGAAATGATATTATTAATTCCACTGCCTTTGGTAGAGGAAAGTGCTAAataataatcaattgttaaattattgtgcatttcactactggaactgtaatcagaaaagataga                                                                                <  1:674812‑M1/143‑64 (MQ=255)                                                                 tcatAATCCTGGGCTTGCTGAAGAATAATTGAAATGATATTATTAATTCCACTGCCTTTGGTAGCGGAAAGTGCTAAataataatcaattgttaaattattgtgcatttcactactggaactgtaatcagaaaagatagacat                                                                             >  1:52876‑M1/1‑77 (MQ=255)                                                                 tcatAATCCTGGGCTTGCTGAAGAATAATTGAAATGATATTATTAATTCCACTGCCTTTGGTAGAGGAAAGTGCTAAataataatcaattgttaaattattgtgcatttcactactggcactgtaagcagaaaagatagacat                                                                             >  2:4667‑M1/1‑77 (MQ=255)                                                                 tcatAATCCTGGGCTTGCTGAAGAATAATTGAAATGATATTATTAATTCCACTGCCTTTGGTAGAGGAAAGTGCTAAataataatcaattgttaaattattgtgcatttcactactggaactgtaatcagaaaagatagacat                                                                             >  1:504533‑M1/1‑77 (MQ=255)                                                                   atAATCCTGGGCTTGCTGAAGAATAATTGAAATGATATTATTAATTCCACTGCCTTTGGTAGAGGAAAGTGCTAAataataatcaattgttaaattattgtgcatttcactactggaactgtaatcagaaaagatagacatgc                                                                           <  1:384955‑M1/143‑69 (MQ=255)                                                                   atAATCCTGGGCTTGCTGAAGAATAATTGAAATGATATTATTAATTCCACTGCCTTTGGTAGAGGAAAGTGCTAAataataatcaattgttaaattattgtgcatttcactactggaactgtaatcagaaaagatagacatgc                                                                           >  2:370746‑M1/1‑75 (MQ=255)                                                                    tAATCCTGGGCTTGCTGAAGAATAATTGAAATGATATTATTAATTCCACTGCCTTTGGTAGAGGAAAGTGCTAAataataatcaattgttaaattattgtgcatttcactactggaactgtaatcagaaaagatagacatgct                                                                          >  1:251118‑M1/1‑74 (MQ=255)                                                                     aaTCCTGGGCTTGCTGAAGAATAATTGAAATGATATTATTAATTCCACTGCCTTTGGTAGAGGAAAGTGCTAActaataatcaattgttaaattgttgtgcatctcactactggaactgtcatccgaaccgctagacatgctt                                                                         >  1:14200‑M1/1‑73 (MQ=255)                                                                        ccTGGGCTTGCTGAAGAATAATTGAAATGATATTATTAATTCCACTGCCTTTGGTAGAGGAAAGTGCTAAataataatcaattgttaaattattgtgcatttcactactggaactgtaatcagaaaagatagacatgcttagc                                                                      <  1:294301‑M1/143‑74 (MQ=255)                                                                                  cTGAAGAATAATTGAAATGATATTATTAATTTCACTGCCTTTGGTAGAGGAAAGTGCTAAataataatcaattgttaaattattgtgcatttcactactggaactgtaatcagaaaagatagacatgcttagccaatctctat                                                            <  2:460980‑M1/143‑84 (MQ=255)                                                                                   tGAAGAATAATTGAAATGATATTATTAATTCCACTGCCTTTGGTAGAGGAAAGTGCTAAataataatcaattgttaaattattgtgcatttcactactggaactgtaatcagaaaagatagacatgcttagccaatcactaat                                                           >  2:15237‑M1/1‑59 (MQ=255)                                                                                       gaaTAATTGAAATGATATTATTAATTCCACTGCCTTTGGTAGAGGAAAGTGCTAAataataatcaattgttaaattattgtgcatttcactactggaactgtaatcagaaaagatagacatgcttagccaatctctgtttgat                                                       >  1:48315‑M1/1‑55 (MQ=255)                                                                                            atTGAAATGATATTATTAATTCCACTGCCTTTGGTAGAGGAAAGTGCTAAataataatcaattgttaaattattgtgcatttcactactggaactgtaatcagaaaagatagacatgcttagccaatctctatttgattgaat                                                  >  1:256648‑M1/1‑50 (MQ=255)                                                                                               gAAATGATATTATTAATTCCACTGCCTTTGGTAGAGGAAAGTGCTAAataataatcaattgttaaattattgtgcatttcactactggaactgtaatcagaaaagatagacatgcttagccaatctctatttgattgaattga                                               >  1:814457‑M1/1‑47 (MQ=255)                                                                                                   tGATATTATTAATTCCACTGCCTTTGGTAGAGGAAAGTGCTAAataataatcaattgttaaattattgtgcatttcactactggaactgtaatcagaaaagatagacatgcttagccaatctctatttgattgaattgaaaga                                           <  1:142166‑M1/143‑101 (MQ=255)                                                                                                    gATATTATTAATTCCACTGCCTTTGGTAGAGGAAAGTGCTAAataataatcaattgttaaattattgtgcatttcactactggaactgtaatcagaaaagatcgacatgcttagccaatctctatttgattgaattgaaagat                                          >  2:182973‑M1/1‑42 (MQ=255)                                                                                                    gATATTATTAATTCCACTGCCTTTGGTAGAGAAAAGTGCTAAataataatcaattgttaaattattgtgcatttcactactggaactgtaatcagaaaagatagacatgcttagccaatctctatttgattgaattgaaagat                                          >  1:209506‑M1/1‑42 (MQ=255)                                                                                                      tattatTAATTCCACTGCCTTTGGTAGAGGAAAGTGCTAAataataatcaattgttaaattattgtgcatttcactactggaactgtaataagaatagatagacatgcttagccaatctctatttgattgaattgaaagatgt                                        >  1:605065‑M1/1‑40 (MQ=255)                                                                                                          attaATTCCACTGCCTTTGGTAGAGGAAAGTGCTAAataataatcaattgttaaattattgtgcatttcactactggaactgtaatcagaaaagatagacatgcttagccactctctatttgcttgacttgaaagatgtttgt                                    >  1:40365‑M1/1‑36 (MQ=255)                                                                                                                        ccttggTAGAGGAAAGTGCTAAataataatcaattgttcaattattgtgcatttcactactggaactgtaatcacaaaagatagacatgcttagccaatctctatttgattgaattgaaagatgtttgttaaggcatggatgc                      <  1:706591‑M1/141‑122 (MQ=255)                                                                                                                        cTTTGGTAGAGGAAAGTGTTAAataataatcaattgttaaattattgtgcatttcactactggaactgtaatcagaaaagatagacatgcttagccaatctctatttgattgaattgaaagatgtttgttaaggcatggatgc                      <  1:20879‑M1/143‑122 (MQ=255)                                                                                                                          ttGGTAGAGGAAAGTGCTAAataataatcaattgttaaattattgtgcatttcactactggaactgtaatcagaaacgatagacatgcttagccagtctctatttgattgaattgaaagctgtttgttaagccagggatgcga                    >  1:390774‑M1/1‑20 (MQ=255)                                                                                                                              tAGAGGAAAGTGCTAActaataatcaattgttaaattattgtgcatttcactactggaactgtaatcagaaaagatagacatgcttagccaatctctatttgattgaattgaaagctgtttgttaaggcatggatgcaagcta                <  2:339119‑M1/143‑128 (MQ=255)                                                                                                                               agagGAAAGTGCTAAataataatcaattgttaaattattgtgcatttcactactggaactgtaatcagaaaagatagacatgcttagccaatctctatttgattgaattgaaagatgtttgttaaggcatggatgcaagctat               <  2:202436‑M1/143‑129 (MQ=255)                                                                                                                                gagGAAAGTGCGAAataacaagcaagggttaacgtattgtgccttgcactactggaactgtaatcagaaaagatagacatgcttagccaatctctatttgattgaattgaaagatgtttgttaaggcatggatgcaagctata              <  1:493808‑M1/143‑130 (MQ=255)                                                                                                                                   gAAAGTGCTAAataataatcaattgttaaattattgtgcatttcactactggaactgtaatcagaaaagatagacatgcttagccaatctctatttgattgaattgaaagatgtttgttaaggcatggatgcaagctatagat           <  1:423807‑M1/143‑133 (MQ=255)                                                                                                                                      aGTGCTAAataataatcaattgttaaattattgtgcatttcactactggaactgtaatcagaaaagatagacatgcttagccaatctctatttgattgaattgaaagatgtttgttaaggcatggatgcaagctatagattct        <  2:256648‑M1/143‑136 (MQ=255)                                                                                                                                      aGTGCTAAataataatcaattgttaaattattgtgcatttcactactggaactgtaatcagaaaagatagacatgcttagccaatctctatttgattgaattgaaagatgtttgttaaggcatggatgcaagctatagattct        >  1:271133‑M1/1‑8 (MQ=255)                                                                                                                                           tAAataataatcaattgttaaattattgtgcatttcactactggaactgtaatcagaaaagatagacatgcttagccaatctctatttgattgaattgaaagatgtttgttaaggcatggatgcaggctatagattctgatac   >  2:687474‑M1/1‑3 (MQ=255)                                                                                                                                            aaataataatcaattgttaaattattgtgcatttcactactggaactgtaatcagaaaagatagacatgcttagccaatctctatttgattgaattgaaagatgtttgttaaggcatggatgcaagctatagattctgatacg  >  2:837367‑M1/1‑2 (MQ=255)                                                                                                                                             |                                                                                                                                              ATTACAGTTAGTTATAAGGATTTCCTTAACTGCTTCTCCTCACCATCATGTTATTTTCGCCACATCATAATCCTGGGCTTGCTGAAGAATAATTGAAATGATATTATTAATTCCACTGCCTTTGGTAGAGGAAAGTGCTAAGGAAGGTGCGAACAAGTCCCTGATATGAGATCATGTTTGTCATCTGGAGCCATAGAACAGGGTTCATCATGAGTCATCAACTTACCTTCGCCGACAGTGAATTCAGCAGTAAGCGCCGTCAGACCAGAAAAGAGATTTTCT  >  NC_000913/1299358‑1299639

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: ‑