Predicted mutation
evidence	seq id	position	mutation	annotation	gene	description
MC JC	NC_000913_3_pae_tpiA	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_3_pae_tpiA	1299499–1300697	1300697	1–1199	33 [0]	[0] 33	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_3_pae_tpiA	= 1299498	0 (0.000)	32 (1.130)	31/274	0.1	100%	intergenic (+253/‑1684)	ychE/oppA	UPF0056 family inner membrane protein/oligopeptide ABC transporter periplasmic binding protein
	?	NC_000913_3_pae_tpiA	1300698 =	0 (0.000)					intergenic (+1453/‑484)	ychE/oppA	UPF0056 family inner membrane protein/oligopeptide ABC transporter periplasmic binding protein

ATTACAGTTAGTTATAAGGATTTCCTTAACTGCTTCTCCTCACCATCATGTTATTTTCGCCACATCATAATCCTGGGCTTGCTGAAGAATAATTGAAATGATATTATTAATTCCACTGCCTTTGGTAGAGGAAAGTGCTAAGGAAGGTGCGAACAAGTCCCTGATATGAGATCATGTTTGTCATCTGGAGCCATAGAACAGGGTTCATCATGAGTCATCAACTTACCTTCGCCGACAGTGAATTCAGCAGTAAGCGCCGTCAGACCAGAAAAGAGATTTTCTTGT  >  NC_000913_3_pae_tpiA/1299358‑1299642                                                                                                                                             |                                                                                                                                                 aTTACTGTTAGGTATATGGATTTCCTTAACTGCTTCTCCTCACCATCATGTTATTTTCGCCACATCATAATCCTGGGCTTGCTGAAGAATAATTGAAATGATATTATTAATTCCACTGCCTTTGGTAGAGGAAAGTGCTAAataataat                                                                                                                                          <  2:49677‑M1/149‑9 (MQ=255)        ttagttaTAAGGATTTCCTTAACTGCTTCTCCTCACCATCATGTTATTTTCGCCACATCATAATCCTGGGCTTGCTGAAGAATAATTGAAATGATATTATTAATTCCACTGCCTTTGGTAGAGGAAAGTGCTAAataataatcaattgt                                                                                                                                   >  1:363098‑M1/1‑134 (MQ=255)        ttagttaTAAGGATTTCCTTAACTGCTTCTCCTCACCATCATGTTATTTTCGCCACATCATAATCCTGGGCTTGCTGAAGAATAATTGAAATGACATTATTAATTCCACTGCCTTTGGTAGAGGAAAGTGCTAAataataatcaattgt                                                                                                                                   >  1:404940‑M1/1‑134 (MQ=255)          agttaTAAGGATTTACTTAACTGCTTCTCCTCACCATCATGTTATTTTCGCCACATCATAATCCTGAGCTTGCTGAAGAATAATTTTAATGATATTATTAATTCTACTGCCTTTGGTACAGGAAATTGCTAAataatactcaattgtta                                                                                                                                 >  2:338576‑M1/1‑132 (MQ=255)            ttaTAAGGATTTCCTTAACTGCTTCTCCTCACCATCATGTTATTTTCGCCACATCATAATCCTGGGCTTGCTGAAGAATAATTGAAATGATATTATTAATTCCACTGCCTTTGGTAGAGGAAAGTGCTAAataataatcaattgttaaa                                                                                                                               <  2:408731‑M1/149‑20 (MQ=255)                          ttAACTGCTTCTCCTCACCATCATGTTATTTTCGCCACATCATAATGCTGGGCTTGCTGAAGAATAAGTGAAATGATATTATTAATTCCACTGCCTTTGGTAGAGGAAAGTGCTAAataatatcgaattgttgaattattgtgcattta                                                                                                                 >  1:465538‑M1/1‑116 (MQ=255)                              cTGCTTCTCCTCACCATCATGTTATTTTCGCCACATCATAATCCTGGGCTTGCTGAAGAATAATTGAAATGATATTATTAATTCCACTGCCTTTGGTAGAGGAAAGTGCTAAataataatcaattgttaaattattgtgcatttcacta                                                                                                             >  2:112517‑M1/1‑112 (MQ=255)                                gCTTCTCCTCACCATCATGTTATTTTCGCCACATCATAATCCTGGGCTTGCTGAAGAATAATTGAAATGATATTATTAATTCCACTGCCTTTGGTAGAGGAAAGTGCTAAataataatcaattgttaaattattgtgcatttcactact                                                                                                           >  2:165264‑M1/1‑110 (MQ=255)                                 cTTCTCCTCACCATCATGTTATTTTCGCCACATCATAATCCTGGGCTTGCTGAAGAATAATTGAAATGATATTATTAATTCCACTGCCTTTGGTAGAGGAAAGTGCTAAataataatcaattgttaaattattgtgcatttcactactg                                                                                                          <  2:473174‑M1/149‑41 (MQ=255)                                           ctatcatgtTGTTTTCGTCCAATCATTATCCTGGGCTTGGTGGATAAGAATTGAAGTGATAGTATTAATTCCACTGCCTTTGGTAGAGGAAAGTGTTAAataataatcaattgttaaattattgtgcatttcactactggaactgtaat                                                                                                <  2:313360‑M1/147‑51 (MQ=255)                                               catGTTATTTTCGCCACATCATAATCCTGGGCTTGCTGAAGAATAATTGAAATGATATTATTAATTCCACTGCCTTTGGTAGAGGAAAGTGCTAAataataatcaattgttaaattattgtgcatttcactactggaactgtaatcaga                                                                                            >  2:48377‑M1/1‑95 (MQ=255)                                                atGTTATTTTCGCCACATCATAATCCTGGGCTTGCTGAAGAATAATTGAAATGATATTATTAATTCCACTGCCTTTGGTAGAGGAAAGTGCTAAataataatcaattgttaaattattgtgcatttcactactggaactgtaatcagaa                                                                                           >  1:199180‑M1/1‑94 (MQ=255)                                                    tATTTTCGCCACATCATAATCCTGGGCTTGCTGAAGAATAATTGAAATGATATTATTAATTCCACTGCCTTTGGTAGAGGAAAGTGCTAAataataatcaattgttaaattattgtgcatttcactactggaactgtaatcagaaaaga                                                                                       <  1:425201‑M1/149‑60 (MQ=255)                                                             cacaTCATAATCCTGGGCTTGCTGAAGAATAATTGAAATGATATTATTAATTCCACTGCCTTTGGTAGAGGAAAGTGCAAAataataatcatttggtaaattagtgtgcagttcactactggaactgtaatcagaaaagatagacatgc                                                                              <  2:189522‑M1/149‑69 (MQ=255)                                                                 tcatAATCCTGGGCTTGCTGAAGAATAATTGAAATGATATTATTAATTCCACTGCCTTTGGTAGAGGAAAGTGCTAAataataatcaattgttaaattattgtgcatttcactactggaactgtaatcagaaaagatagacatgcttag                                                                          <  1:165264‑M1/149‑73 (MQ=255)                                                                             gCTTGCTGAAGAATAATTGAAATGATATTATTAATTCCACTGCCTTTGGTAGAGGAAAGTGCTAAataataatcaattgttaaattattgtgcatttcactactggaactgtaatcagaaaagatagacatgcttagccaatctctatt                                                              <  2:357027‑M1/149‑85 (MQ=255)                                                                                  cTGAAGAATAATTGAAATGATATTATTAATTCCACTGCCTTTGGTAGAGGAAAGTGCTAAataataatcaattgttaaattattatgcatttcactactggaactgtaatcagaaaagatagacatgcttagccaatctctatttgatt                                                         >  2:512142‑M1/1‑60 (MQ=255)                                                                                     aagaaTAATTGAAATGATATTATTAATTCCACTGCCTTTGGTAGAGGAAAGTGCTAAataataatcaattgttaaattattctgacaaagattactggaactgtaatcagaaaagatagacatgcttagccaatctctatttgattgaa                                                      >  1:120559‑M1/1‑57 (MQ=255)                                                                                       gaaTAATTGAAATGATATTATTAATTCAACTGCATTTGGTAGAGGAAAGTGCTAAataataatcaattgttaaattattgtgcatttcactactggaactgtaatcagaaacgatagacatgcctagccaatctctatttgattgaata                                                    >  2:279308‑M1/1‑55 (MQ=255)                                                                                                aaaTGATATTATTAATTCCACTGCCTTTGGCGGGCGGGAGTTCTAAataataatcaattgttaaattattgtgcatttcactactggaactgtaatcagaaaagatagacatgcttagccaatctctatttgattgaatggaaagatgt                                           >  1:383525‑M1/1‑46 (MQ=255)                                                                                                   tgctattattaaTTCAACTGTCTTTGCGAGAGGAAAGTGCTAAataataatcaattgttaaattattgtgtatttcagtactggaactgtaatcagaaaagatagacatgcttagccagtctctattttattgaattgaaagatgtttg                                        <  2:300724‑M1/146‑107 (MQ=255)                                                                                                    gATATTATTAATTCCACTGCCTTTGGTAGAGGAAAGTGCTAAataataatcaattgttaaattattgtgcatttcactactggaactgtgatcagaaaagatagacatgcttagccaatctctatttgattgaattgaacaatgtttgt                                       >  2:474850‑M1/1‑42 (MQ=255)                                                                                                            taATTCCACTGCCTTTGGTAGAGGAAAGTGCTAAataataatcaattgttaaattattgtgcatttcactactggaactgtaatcagaaaagatagacatgcttagccaatctctatttgattgaattgaaagatgtttgttaaggcat                               <  1:279308‑M1/149‑116 (MQ=255)                                                                                                             aaTTCCAGTGCCTTGTGTAGAGGGAAGTGGTAAataataatcaattgttaaattattgtgcatttcactactgtaactgtaatcagaaaagatagacatgattagcaaatgtctatttgattgaattgaaagatgtttgttaaggcatg                              <  2:159759‑M1/149‑117 (MQ=255)                                                                                                              aTTCCACTGCCTTTGGTAGAGGAAAGTGCTAAataataatcaattgttaaattattgttcctttcactactggaactgtaatcagaaaagataaacatgcttagccaatctctatttgattaaattgaaagatgttttttaaggcatgg                             >  1:454411‑M1/1‑32 (MQ=255)                                                                                                               ctcCATTGCCTGTGGTAGATGAAAGTGTTAAataataatcaattgttaaattattgtgcatttcactactggaactgtaatcagaaaagatagacatgcttagccaatctctattttattgaattgaaagatgtttgttaaggcatgga                            <  2:155518‑M1/148‑119 (MQ=255)                                                                                                                  cACTGCCTTTGGTTGAGGAAAGTGCTAAataataatcaattgttaaattattgtgcatttcactactggaactgtaatcagaaaagatagacatgcttagccaatctctatttgattgaattgaaagatgtttgttaaggcatggatgc                         <  2:129644‑M1/149‑122 (MQ=255)                                                                                                                     tGCCTTTGGTAGATGAAAGTGCTAAataataatcaattgttaaattattgtgcatttcactactggaactgtaatcagaaaagatagacaggcttagccaatctctatttgattgaattgaaagatgtttgttaaggcatggatgcaag                      <  1:100544‑M1/149‑125 (MQ=255)                                                                                                                         tttGGTAGAGGAAAGTGCTAAataataatcaattgttaaattattgtgcatttcactactggaactgtaatcagaaaagatagacatgcttagccaatctctatttgattgaattgaaagatgtttgttaaggcatggatgcaagctat                  <  1:112517‑M1/149‑129 (MQ=255)                                                                                                                              tAGAGGAAAGTGCTAAataataatcaattgttaaattattgtgcatttcactactggaactgtaatcagaaaagatagacattcttagccaatctctatttgattgaattgaaagatgtttgttaagtcatggatgcaagctatatatt             >  2:206694‑M1/1‑16 (MQ=255)                                                                                                                               agagGAAAGTGCTAAataataatcaattgttaaattattgtgcatttcactactggaactgtaatcagaaaagatagacatgcttagccaatccctatttgaattacttgaacgatgttcgttaaggcatggatgcaagctatagattt            >  1:327408‑M1/1‑15 (MQ=255)                                                                                                                                  ggAAAGTGTGAAataataatcaattgttaaattattgtgcatttcactactggaactgtaatcagaaaagatagacatgcttagccaatctctatttgattgaattgaaagatgtttgttaaggcatggatgcaagctatagattctga         <  2:174280‑M1/149‑138 (MQ=255)                                                                                                                                         tctAAataataatcaattgttaaattattgtgcatttcactactggaactgtaatcagaaaagatagacatgcttagccaatctctatttgattgaattgaaagatgtttgttaaggcatggatgcaagctatagattctgatacggtc  <  2:363098‑M1/148‑145 (MQ=255)                                                                                                                                             |                                                                                                                                                 ATTACAGTTAGTTATAAGGATTTCCTTAACTGCTTCTCCTCACCATCATGTTATTTTCGCCACATCATAATCCTGGGCTTGCTGAAGAATAATTGAAATGATATTATTAATTCCACTGCCTTTGGTAGAGGAAAGTGCTAAGGAAGGTGCGAACAAGTCCCTGATATGAGATCATGTTTGTCATCTGGAGCCATAGAACAGGGTTCATCATGAGTCATCAACTTACCTTCGCCGACAGTGAATTCAGCAGTAAGCGCCGTCAGACCAGAAAAGAGATTTTCTTGT  >  NC_000913_3_pae_tpiA/1299358‑1299642

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: ‑