Predicted mutation
evidence	seq id	position	mutation	annotation	gene	description
MC JC	NC_000913_3_bme_pgi	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_bme_pgi	1299499–1300697	1300697	1–1199	38 [0]	[0] 38	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_bme_pgi	= 1299498	0 (0.000)	35 (0.800)	33/278	0.4	100%	intergenic (+253/‑1684)	ychE/oppA	UPF0056 family inner membrane protein/oligopeptide ABC transporter periplasmic binding protein
	?	NC_000913_3_bme_pgi	1300698 =	0 (0.000)					intergenic (+1453/‑484)	ychE/oppA	UPF0056 family inner membrane protein/oligopeptide ABC transporter periplasmic binding protein

TTACAGTTAGTTATAAGGATTTCCTTAACTGCTTCTCCTCACCATCATGTTATTTTCGCCACATCATAATCCTGGGCTTGCTGAAGAATAATTGAAATGATATTATTAATTCCACTGCCTTTGGTAGAGGAAAGTGCTAAGGAAGGTGCGAACAAGTCCCTGATATGAGATCATGTTTGTCATCTGGAGCCATAGAACAGGGTTCATCATGAGTCATCAACTTACCTTCGCCGACAGTGAATTCAGCAGTAAGCGCCGTCAGACCAGAAAAGAGATTTTCTTGTCCCG  >  NC_000913_3_bme_pgi/1299359‑1299646                                                                                                                                            |                                                                                                                                                     ttACAGTTAGTTATAAGGATTTCCTTAACTGCTTCTCCTCACCATCATGTTATTTTCGCCACATCATAATCCTGGGCTTGCTGAAGAATAATTGAAATGATATTATTAATTCCACTGCCTTTGGTAGAGGAAAGTGCTAAataataatc                                                                                                                                             <  1:466280‑M1/149‑10 (MQ=255)   aCAGTTAGTGATAAGGAGTTCCGTAACTGCTTGTCCTCACCATCATGTTATTTTCGCCACATCATAATCCTGGGCTTGCTGAAGAATAATTGAAATGATATTATTAATTCCACTGCTTGTGGTAGAGGAAAGTGCTAAataataatcaa                                                                                                                                           <  2:170617‑M1/149‑12 (MQ=255)     agttagttATAAGGATTTCCTTAACTGCTTCTCCTCACCATCATGTTATTTTCGCCACATCATAATCCTGGGCTTGCTGAAGAATAATTGAAATGATATTATTAATTCCACTGCCTTTGGTAGAGGAAAGTGCTAAataataatcaatt                                                                                                                                         <  2:287430‑M1/149‑14 (MQ=255)           ttaTAAGGATTTCCTTAACTGCTTCTCCTCACCATCATGTTATTTTCGCCACATCATAATCCTGGGCTTGCTGAAGAATAATTGAAATGATATTATTAATTCCACTGCCTTTGGTAGAGGAAAGTGCTAAataataatcaattgttaaa                                                                                                                                   <  1:114877‑M1/149‑20 (MQ=255)                aGGATTTCCTTAACTGCTTCTCCTCACCATCATGTTATTTTCGCCACATCATAATCCTGGGCTTGCTGAAGAATAATTGAAATGATATTATTAATTCCACTGCCTTTGGTAGAGGAAAGTGCTAAataataatcaattgttaaattatt                                                                                                                              <  2:157899‑M1/149‑25 (MQ=255)                aGGATTTCCTTAACTGCTTCTCCTCACCATCATGTTATTTTCGCCACATCATAATCATGGGCTTGCTGAAGAATAATTGAAATGATATTATTAATTCCACTGCCTTTGGTAGAGGAAAGTGCTAAataataatcaattgttaaattatt                                                                                                                              <  2:359570‑M1/149‑25 (MQ=255)                          tAACTGCTTCTCCTCACCATCATGTTATTTTCGCCACATCATAATCCTGGGCTTGCTGAAGAATAATTGAAATGATATTATTAATTCCACTGCCTTTGGTAGAGGAAAGTGCTAAataataatcaattgttaaattattgtgcatttca                                                                                                                    <  1:22505‑M1/149‑35 (MQ=255)                             cTGCTTCTCCTCACCATCATGTTATTTTCGCCACATCATAATCCTGGGCTTGCTGAAGAATAATTGAAATGATATTATTAATTCCACTGCCTTTGGTAGAGGAAAGTGCTAAataataatcaattgttaaataattgtgcatttcacta                                                                                                                 <  1:684475‑M1/149‑38 (MQ=255)                               gCTTCTCCTCACCATCATGTTATTTTCGCCACATCATAATCCTGGGCTTGCTGAAGAATAATTGAAATGATATTATTAATTCCACTGCCTTTGGTAGAGGAAAGTGCTAAataataatcaattgttaaattattgtgcatttcactact                                                                                                               >  2:625725‑M1/1‑110 (MQ=255)                                cTTCTCCTCACCATCCTGTTATTTTCGCCACCTCACAATCATGGGCTTGCTGAAGAATAATTGAAATGATATTATTAATTCCACTGCTTTTGGGAGAGGAAAGTGCTAAataataatcaattgttaaattattgtgcatttcactactg                                                                                                              <  1:657799‑M1/149‑41 (MQ=255)                                 ttCTCCTCACCATCATGTTATTTTCGCCACATCATAATCCTGGGCTTGCTGAAGAATAATTGAAATGATATTATTAATTCAACTGCCTTTGGTAGAGGAAAGTGCTAAataataatcaattgttaaattattgtgcttttcactactgg                                                                                                             >  2:75268‑M1/1‑108 (MQ=255)                                   ctcctcACCATCATGTTATTTTCGCCACATCATAATCCTGGGCTTGCTGAAGAATAATTGAAATGATATTATTAATTCCACTGCCTTTGGTAGAGGAAAGTGCTAAataataatcaattgttaaattattgtgcatttcactactggaa                                                                                                           <  1:328346‑M1/149‑44 (MQ=255)                                   ctcctcACCATCATGTTATTTTCGCCACATCATAATCCTGGGCTTGCTGAAGAATAATTGAAATGATATTATTAATTCCACTGCATTTGGTAGAGGAAAGTGCTAAataataatcaatttttaaattattgtacatttcacgacttgaa                                                                                                           >  2:235064‑M1/1‑106 (MQ=255)                                      ctcACCATCATGTTATTTTCGCCACATCATAATCCTGGGCTTGCTGAAGAATAATTGAAATGATATTATTAATTCCACTGCCTTTGGTAGAGGAAAGTGCTAAataataatcaattgttaaattattgtgcatttcactactggaactg                                                                                                        >  1:513707‑M1/1‑103 (MQ=255)                                       tcACCATCATGTTATTTTCGCCACATCATAATCCTGGGCTTGCTGAAGAATAATTGAAATGATATTATTAATTCCACTGCCTTTGGTAGAGGAAAGTGCTAAataataatcaattgttaaattattgtgcatttcactactgtaactgt                                                                                                       >  2:173821‑M1/1‑102 (MQ=255)                                         aCCATCATGTTATTTTCGCCACATAATCATTTTGGGCTTGCTGAAGAATAATTGAAATGATATTATTAATTCCACTGCCTTTGGTAGAGGAAAGTGCTAAataataatcaattgttaaattattgtgcatttcactactggaactgtaa                                                                                                     >  2:370989‑M1/1‑100 (MQ=255)                                          ccATCATGTTATTTTCGCCACATCATAATCCTGGGCTTGCTGAAGAATAATTGAAATGATATTATTAATTCCACTGCCTTTGGTAGAGGAAAGTGCTAAataataatcaattgttaaattattgtgcatttcactactggaactgtaat                                                                                                    <  1:677697‑M1/149‑51 (MQ=255)                                                          gCCACATCATAATCCTGGGCTTGCTGAAGAATAATTGAAATGATATTATTAATTCCACTGCCTTTGGTAGAGGAAAGTGCTAAataataatcaattgttaaattattgtgcatttcactactggaactgtaatcagaaaagatagacat                                                                                    >  1:313174‑M1/1‑83 (MQ=255)                                                          gCCACATCATAATCCTGGGCTTGCTGAAGAATAATTGAAATGATATTATTAATTCCACTGCCTTTGGTAGAGGAAAGTGCTAAataataatcaattgttaaattattgtgcatttcactactggaactgtaatcagaaaagatagacat                                                                                    >  2:517509‑M1/1‑83 (MQ=255)                                                           ccACATCATAATCCTGGGCTTGCTGAAGAATAATTGAAATGATATTATTAATTCCACTGCCTTTGGTAGAGGAAAGTGCTAAataataatcaattgttaaattattgtgcatttcactactggaactgtaatcagaaaagatagacatg                                                                                   >  1:746001‑M1/1‑82 (MQ=255)                                                            cacaTCATAATCCTGGGCTTGCTGAAGAATAATTGAGATGATATTATTAATTCCACTGCCTTTGGTAGAGGAAAGTGCTAAataataatcaattgttaaattattgtgcatttcactactggaactgtactcagaaaagatagacatgc                                                                                  >  2:396586‑M1/1‑81 (MQ=255)                                                            cacaTCATAATCCTGGGCTTGCTGAAGAATAATTGAAATGATATTATTAATTCCACTGCCTTTGGTAGAGGAAAGTGCTAAataataatcaattgttaaattattgtgcatttcactactggaactgtaatcagaaaagatagacatgc                                                                                  <  1:625725‑M1/149‑69 (MQ=255)                                                                     aTCCTGGGCTTGCTGAAGAATAATGGAAATGATATTATTAATTCCACTGCCTTTGGTAGAGGAAAGTGCTAAataataatcaattgttaaattattgtgcatttcactactggaactgtaatcagaaaagatagacatgcttagccaat                                                                         <  2:617315‑M1/149‑78 (MQ=255)                                                                           ggCTTGCTGAAGAATAATTGAAATTATATTATTAATTCCACTGCCTTTGGTAGAGGAAAGTGCTAAataataatcaattgttaaattattgtgcatttcactactggaactgtaatcagaaaagatagacatgcttagccaatctctat                                                                   <  1:397512‑M1/149‑84 (MQ=255)                                                                            gCTTGCTGAAGAATAATTGAAATGATATTATTAATTCCACTGCCTTTGGTAGAGGAAAGTGCTAAataataatcaattgttaaattattgtgcatttcactactggaactgtaatcagaaaagatagacatgcttagccaatctctatt                                                                  <  1:387547‑M1/149‑85 (MQ=255)                                                                            gCTTGCTGAAGAATAATTGAAATGATATTATTAATTCCACTGCCTTTGGTAGAGGAAAGTGCTAAataataatcaattgttaaattattgtgcatttcactactggaactgtaatcagaaaagatagacatgcttagccaatctctatt                                                                  >  1:30570‑M1/1‑65 (MQ=255)                                                                             cTTGCTGAAGAATAATTGAAATGATATTATTAATTCCACTGCCTTTGGTAGAGGAAAGTGCTAAataataatcaattgttaaattattgtgcatttcactactggaactgtaatcagaaaagatagacatgcttagccaatctctattt                                                                 <  2:417775‑M1/149‑86 (MQ=255)                                                                                  tGAAGAATAATTGAAATGATATTATTAATTCCACTGCCTTTGGTAGAGGAAAGTGCTAAataataatcaattgttaaattattgtgcatttcactactggaactgtaatcagaaaagatagacatgcttagccaatctctatttgattg                                                            >  1:241678‑M1/1‑59 (MQ=255)                                                                                          aatTGAAATGATATTATTAATTCCACTGCCTTTGGTAGAGGAAAGAAATCCaaagtaatcaattgttaaattattgtgcatttcactactggaactgtaatcagaaaagatagacatgcttagccaatctctatttgattgaattgaaa                                                    <  1:23337‑M1/149‑99 (MQ=255)                                                                                            ttGAAATGATATTATTAATTCCACTGCCTTTGGTAGAGGAAAGTGCTAAataataatcaattgttaaattattgtgcatttcactactggaactgtaatcagaaaagatagacatgcttagccaatctctatttgattgaattgaaaga                                                  >  2:333454‑M1/1‑49 (MQ=255)                                                                                              gAAATGATATTATTAATTCCACAGCCTTTGGTAGAGGAAAGTGCTAAataataatcaattgttaaagtattgtgcatttcactactggatctgtaatcagaaaagatagacatgcttagccaatctctatttgattgaattgaaagatg                                                <  1:173821‑M1/149‑103 (MQ=255)                                                                                                             aTTCCACTGCCTTTGGTAGAGGAAAGTGCTAAataataatcaattgttaaattattgtgcatttcactactggaactgtaatcagaaaagatagacatgcttagccaatctctatttgattgaattgaaagatgtttgttaaggcatgg                                 <  1:346509‑M1/149‑118 (MQ=255)                                                                                                                      ccTTTGGTAGAGGAAAGTGCTAAataataatcaattgttaaattattgtgcatttcactactggaactgtaatcagaaaagatagacatgcttagcgaatgttttggttgttgtattgaaagatgtttgttaaggcatggatgcaagct                        >  1:61916‑M1/1‑23 (MQ=255)                                                                                                                                 ggAAAGTGCTAAataataatcaattgttaaattattgtgcatttcactactggaactgtaatcagaaaagatagacatgcttagccaatctctatttgattgaattgaaagatgtttgttaaggcatggatgcaagctatagattctga             <  1:370989‑M1/149‑138 (MQ=255)                                                                                                                                       tGCTAAataataatcaattggtaaattattgtgcatttcactactggaactgtaatcagaaaagatagacatgcttagccaatctctatttgattgaattgaaagatgtttgttaaggcatggatgcaagctatagattctgatacggt       <  2:311007‑M1/149‑144 (MQ=255)                                                                                                                                          tAAataataatcaattgttaaattattgtgcatttcactactggaactgtaatcagaaaagatagacatgcttagccaatccctatttgattgaattgaaagatgtttgttaaggcatggatgcaagctatagattctgatacggtcaa    >  1:495769‑M1/1‑3 (MQ=255)                                                                                                                                            aataataatcaattgttaaattattgtgcatttcactactggaactgtaatcagaaaagatagacatgcttagccaatctctatttgattgaattgaaagatgtttgttaaggcatggatgcaagctatagattctgataggttcaata  >  2:274653‑M1/1‑1 (MQ=255)                                                                                                                                            aataataatcaattgttaaattattgtgcatttcactactggaactgtaatcagaaaagatagacatgcttagccaatctctatttgattgaattgaaagatgtttgttaaggcatggatgcaagcgatagattctgatacggtcacca  >  1:144462‑M1/1‑1 (MQ=255)                                                                                                                                            |                                                                                                                                                     TTACAGTTAGTTATAAGGATTTCCTTAACTGCTTCTCCTCACCATCATGTTATTTTCGCCACATCATAATCCTGGGCTTGCTGAAGAATAATTGAAATGATATTATTAATTCCACTGCCTTTGGTAGAGGAAAGTGCTAAGGAAGGTGCGAACAAGTCCCTGATATGAGATCATGTTTGTCATCTGGAGCCATAGAACAGGGTTCATCATGAGTCATCAACTTACCTTCGCCGACAGTGAATTCAGCAGTAAGCGCCGTCAGACCAGAAAAGAGATTTTCTTGTCCCG  >  NC_000913_3_bme_pgi/1299359‑1299646

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 12 ≤ ATCG/ATCG < 22 ≤ ATCG/ATCG < 37 ≤ ATCG/ATCG < 41 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑