Predicted mutation
evidence	seq id	position	mutation	annotation	gene	description
MC JC	NC_000913_3_vch_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_vch_tpiA	1299499–1300697	1300697	1–1199	37 [0]	[0] 37	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_vch_tpiA	= 1299498	0 (0.000)	37 (1.340)	31/276	0.1	100%	noncoding (1299498/4641682 nt)	repeat_region	repeat region
	?	NC_000913_3_vch_tpiA	1300698 =	0 (0.000)					noncoding (1300698/4641682 nt)	repeat_region	repeat region

AAATTACAGTTAGTTATAAGGATTTCCTTAACTGCTTCTCCTCACCATCATGTTATTTTCGCCACATCATAATCCTGGGCTTGCTGAAGAATAATTGAAATGATATTATTAATTCCACTGCCTTTGGTAGAGGAAAGTGCTAAGGAAGGTGCGAACAAGTCCCTGATATGAGATCATGTTTGTCATCTGGAGCCATAGAACAGGGTTCATCATGAGTCATCAACTTACCTTCGCCGACAGTGAATTCAGCAGTAAGCGCCGTCAGACCAGAAAAGAGATTTTCTT  >  NC_000913_3_vch_tpiA/1299356‑1299640                                                                                                                                               |                                                                                                                                               acattACAGTTCGTTATAAGGATTTCCTTAACGTCTTGACCTCACCATCATGTTATTTTCGCCACATCATAATCCTAGGCTTGCTGAAGAATAATTGAAATGATATTATTAATTCCACTGCCTTTGGTAGAGGAAAGTGCTAAataata                                                                                                                                          >  2:297579‑M1/3‑143 (MQ=255)        agttagttATAAGGATTTCCTTAACTGCTTCTCCTCACCATCATGTTATTTTCGCCACATCATAATCCTGGGCTTGCTGAAGAATAATTGAAATGATATTATTAATTCCACTGCCTTTGTTAGAGGAAAGTGCTAAataataatcaatt                                                                                                                                   >  2:213016‑M1/1‑136 (MQ=255)          ttagttaTAAGGATTTCCTTAACTGCTTCTCCTCACCATCATGTTATTTTCGCCACATCATAATCCTGGGCTTGCTGAAGAATAATTGAAATGATATTATTAATTCCACTGCCTTTGGTAGAGGAAAGTGCTAAataataatcaattgt                                                                                                                                 >  1:304046‑M1/1‑134 (MQ=255)                ataAGGATTTCCTTAACTGCTTCTCCTCACCATCATGTTATTTTCGCCACATCATAATCCTGGGCTTGCTGAAGAATAATTGAAATGATATTATTAATTCCACTGCCTTTGGTAGAGGAAAGTGCTAAataataatcaattgttaaatt                                                                                                                           >  1:197158‑M1/1‑128 (MQ=255)                              aaCTGCTTCTCCGCACCACCACATTATTTTCGCCACATCATAATCCTGTGCTTGCTGAAGTATAATTGAAATGATATTATTAATTCCACTGCCTTTGGTACAGGAAAGTGCTAAatagtaatcaattgttaaattattgtgcatttcac                                                                                                             <  2:276996‑M1/149‑36 (MQ=255)                                        cctcACCATCATGTTATTTTCGCCACATCATAATCCTGGGCTTGCTGAAGAATAATTGAAATGATATTATTAATTCCACTGCCTTTGGTAGAGGAAAGTGCTAAataataatcaattgttaaattattgtgcatttcactactggaact                                                                                                   <  1:321496‑M1/149‑46 (MQ=255)                                             ccATCTTGTTGTTTTCGCCACATCATAATCCCGGGCTTGCTGAAGAATAATTGAAATGATATTATTAATTCCACTGCCTTTGGTAGAGGAAAGTGCTAAataataatcaattgttaaattattgtgcatttcactactggaactgtaat                                                                                              <  1:262051‑M1/149‑51 (MQ=255)                                             ccATCATGTTATTTTCGCCACATCATAATCCTGGGCTTGCTGAAGAATAATTGAAATGATATTATTAATTCCACTGCCTTTGGTAGAGGAAAGTGCTAAataataatcaattgttaaattattgtgca                                                                                                                   >  2:289939‑M1/1‑99 (MQ=255)                                             ccATCATGTTATTTTCGCCACATCATAATCCTGGGCTTGCTGAAGAATAATTGAAATGATATTATTAATTCCACTGCCTTTGGTAGAGGAAAGTGCTAAataataatcaattgttaaattattgtgca                                                                                                                   <  1:289939‑M1/128‑30 (MQ=255)                                                   tGTTATTTTCGCCACATCATAATCTTGGGCTTGCTGAAGAATAATTGAAATGATATTATTAATTCCACTGCCTTTGGTAGAGGAAAGTGCTAAataataatcaattgttaaattattgtgcatttcactactggaactgtaatcagaaa                                                                                        >  1:201320‑M1/1‑93 (MQ=255)                                                       aTTTTCGCCACATCATAATCCTGGGCTTGCTGAAGAATAATTGAAATGATATTATTAATTCCACTGCCTTTGGTAGAGGAAAGTGCTAAataataatcaattgttaaattattgtgcatttaactactggaactgtaatcagaaaagat                                                                                    >  2:282865‑M1/1‑89 (MQ=255)                                                                  atcatAATCCTGGGCTTGCTGAAGAATAATTGAAATGATATTATTAATTCCACTGCCTTTGGTAGAGGAAAGTGCTAAataataatcaattgttaaattattgtgcatttcactactggaactgtaatcagcaaagatagacatgctta                                                                         >  2:143421‑M1/1‑78 (MQ=255)                                                                  atcatAATCCTGGGCTTGCTGAAGAATAATTGAAATGATATTATTAATTCCACTGCCTTTGGTACACGAATGTGCTAAataataatcaattgttaaattattgtgcatttcactactggaactgtaatcagaaaagatagacatgctta                                                                         >  1:346996‑M1/1‑78 (MQ=255)                                                                    catAATCCTGGGCTTGCTGAAGAATAATTGAAATGATATTATTAATTCCACTGCCTTTGGTAGAGGAAAGTGCTAAataataatcaattgttaaattattgtgcatttcactactggaactgtaatcagaaaagatagacatgcttagc                                                                       >  1:140725‑M1/1‑76 (MQ=255)                                                                     atAATCCTGGGCTTGCTGAAGAATAATTGAAATGATATTATTAATTCCACTGCCTTTGGTAGAGGAAAGTGCTAAataataatcaattgttaaattattgtgcatttcactactggaactgtaatcagaaaagatagacatgcttagcc                                                                      >  2:464310‑M1/1‑75 (MQ=255)                                                                       aaTCCTGGGCTTGCTGAAGAATAATTGAAATGATATTATTAATTCCACTGCCTTTGGTAGAGGAAAGTGCTAAataataatcaattgttaaattattgtgcatttcgctactggaactgtaatcagaaaagatagacctgattagtcaa                                                                    >  2:15173‑M1/1‑73 (MQ=255)                                                                               gCTTGCTGAAGAATAATTGAAATGATATTATTAATTCCACTGCCTTTGGTAGAGGAAAGTGCTAAataataatcaattgttaaattattgtgcatttcactactggaactgtaatcagaaaagatagacatgcttagccaatctctatt                                                            >  2:173636‑M1/1‑65 (MQ=255)                                                                                cTTGCTGAAGAATAATTGAAATGATATTATTAATTCCACTGCCTTTGGTAGAGGAAAGTGCTAAataataatcaattgttaaattattgtgcatttcactactggaactgtaatcagaaaagatagacatgcttagccaatctctattt                                                           >  1:264105‑M1/1‑64 (MQ=255)                                                                                cTTGCTGAAGAATAATTGAAATGATATTATTAATTCCACTGCCTTTGGTAGAGGAAAGTGCTAAataataatcaattgttaaattattgtgcatttcactactggaactgtaatcagaaaagatagacatgcttagccaatctctattt                                                           >  1:264079‑M1/1‑64 (MQ=255)                                                                                  tGCTGAAGAATAATTGAAATGATATTATTAATTCCACTGCCTTTGGTCAAGGAAAGTGCTAAataataatcaattgttaaattattgtgcatttcactactggaactgtaatcagaaaagatagacatgcttagccaatctctatttga                                                         <  1:242017‑M1/149‑88 (MQ=255)                                                                                      gaagaaTAATTGAAATGATATTATTAATTCCACTGCCTTTGGTAGAGGAAAGTGCTAAataataatcaattgttaaattattgtgcatttcactactggaactgtaatcagaaaagatagacatgcttcgcaaatatctatttgcttga                                                     >  2:241846‑M1/1‑58 (MQ=255)                                                                                        agaaTAATTGAAATGATATTATTAATTCCACTGCCTTTGGTAGAGGAAAGTGCTAAataataatcaattgttaaattattgtgcatttcactactggaactgtaatcagaaaagatagacatgcttagccaatctctatttgattgaat                                                   <  2:264105‑M1/149‑94 (MQ=255)                                                                                        agaaTAATTGAAATGATATTATTAATTCCACTGCCTTTGGTAGAGGAAAGTGCTAAataataatcaattgttaaattattgtgcatttcactactggaactgtaatcagaaaagatagacatgcttagccaatctctatttgattgaat                                                   <  2:264079‑M1/149‑94 (MQ=255)                                                                                                   aaTGATATTATTAATTCCACTGCCTTTGGTAGAGGAAAGTGCTAAataataatcaattgttaaattattgtgcatttcactactggaactgtaatcagaaaagatagacatgcttagccaatctctatttgattgaattgaaagatgtt                                        >  2:106439‑M1/1‑45 (MQ=255)                                                                                                           tattaATTCCACTGCCTTTGGTAGAGGAAAGTGCTAAataataatcaattgttaaattattgtgcatttcactactggaactgtaatcagaaaagatagacatgcttagccaatctctatttgattgaattgaaagatgtttgttaagg                                <  1:391817‑M1/149‑113 (MQ=255)                                                                                                           tattaATTCCACTGCCTTTGGTAGAGGAAAGTGCTAAataataatcaattgttaaattattgtgcatttcactactggaactgtaatcagaaaagatagacatgcttagccaatctctatttgattgaattgaaagatgtttgttaaag                                >  1:209389‑M1/1‑37 (MQ=255)                                                                                                             ttaATTCCACTGCTTTTGGTAGAGGAAAGTGCTAAataataatcaattgttaaattattgtgcatttcactactggaactgtaatcagaaaagatagacatgcttagccaatctctatttgattgaattgaaagatgtttgttaaggca                              <  2:115807‑M1/149‑115 (MQ=255)                                                                                                               aaTTACACTGCTTTTGGTAGAGGAAAGTGATAAataataatcaattgttaaattattgtgcatttcactactggaactgtaatcagaaaatatagacatgcttagccaatctctatttgattgaattgaaagatgtttgttaaggcatg                            <  1:336441‑M1/149‑117 (MQ=255)                                                                                                                 ttCCACTGCCTTTGGTAGAGGAAAGTGCTAAataataatcaattgttaaattattgtgcatttcactactggaactgtaatcagaaaagatagacatgcttagccaatctctatttgattgaattgaaagatgtttgttaaggcatgga                          <  2:201320‑M1/149‑119 (MQ=255)                                                                                                                       tGCCTTTGGTAGAGGAAAGTGCTAAataataatcaattgttaaattattgtgcatttcactactggaactgtaatcagaaaagatagacatgcttagccaatctctatttgattgaattgaaagatgtttgttaaggcatggatgcaag                    <  1:106439‑M1/149‑125 (MQ=255)                                                                                                                          cTTTGGTAGAGGAAAGTGCTAAataataatcaattgttaaattattgtgcatttcactactggaactgtaatcagaaaagatagacatgcttagccaatctctatttgattgaattgaaagatgtttgttaaggcatggatgcaagcta                 >  1:76815‑M1/1‑22 (MQ=255)                                                                                                                           tttGGTAGAGGAAAGTGCTAAataataatcaattgttaaattattgtgcatttcactactggaactgtaatcagaaaagatagacatgcttagccaatctctatttgattgaattgaaagatgtttgttaaggcatggatgcaagctat                >  1:415144‑M1/1‑21 (MQ=255)                                                                                                                                tAGAGGAAAGTGCTAAataataatcaattgttaaattattgtgcatttcactactggaactgtaat                                                                                              >  2:125211‑M1/1‑16 (MQ=255)                                                                                                                                tAGAGGAAAGTGCTAAataataatcaattgttaaattattgtgcatttcactactggaactgtaat                                                                                              <  1:125211‑M1/66‑51 (MQ=255)                                                                                                                                  gagGAAAGTGCTAAataataataaattgttaaattattgtgcatttcactactggaactgtaatcagaaaagatagacatgcttagccaatctctatttgattgaattgaaagatgtttgttaaggcatggatgcaagctatagattct         <  1:157033‑M1/149‑136 (MQ=255)                                                                                                                                         gTGCTAAataataatcaattgttaaattattgtgcatttcactactggaactgtaatcagaaaagatagacatgcttagccaatctctatttgattgaattgaaagatgtttgttaaggcatggatgcaagctatagattctgatacgg  <  1:375290‑M1/149‑143 (MQ=255)                                                                                                                                         gTGCTAAataataatcaattgttaaattattgtgcatttcactactggaactgtaatcagaaaagatagacatgcttagccaatctctatttgattgaattgaaagatgtttgttaaggcatggatgcaagctatagattctgatacgg  <  1:374669‑M1/149‑143 (MQ=255)                                                                                                                                               |                                                                                                                                               AAATTACAGTTAGTTATAAGGATTTCCTTAACTGCTTCTCCTCACCATCATGTTATTTTCGCCACATCATAATCCTGGGCTTGCTGAAGAATAATTGAAATGATATTATTAATTCCACTGCCTTTGGTAGAGGAAAGTGCTAAGGAAGGTGCGAACAAGTCCCTGATATGAGATCATGTTTGTCATCTGGAGCCATAGAACAGGGTTCATCATGAGTCATCAACTTACCTTCGCCGACAGTGAATTCAGCAGTAAGCGCCGTCAGACCAGAAAAGAGATTTTCTT  >  NC_000913_3_vch_tpiA/1299356‑1299640

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: ‑