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	55 [0]	[0] 56	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)	54 (1.230)	44/274	0.1	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

ACGCCTTAAATGGCGAAGAAACGGTCTAAATAGGCTGATTCAAGGCATTTACGGGAGAAAAAATCGGCTCAAACATGAAGAAATGAAATGACTGAGTCAGCCGAGAAGAATTTCCCCGCTTATTCGCACCTTCCCTAAATAATAATCAATTGTTAAATTATTGTGCATTTCACTACTGGAACTGTAATCAGAAAAGATAGACATGCTTAGCCAATCTCTATTTGATTGAATTGAAAGATGTTTGTTAAGGCATGGATGCAAGCTATAGATTCTGATACGGT  >  NC_000913/1300560‑1300840                                                                                                                                           |                                                                                                                                               gcagtgagttataaggatttccttaactgcttctcctcaccatcatgttattttcgccacatcataatcctgggcttgctgaagaataattgaaatgatattattaattccactgcctttggtagaggaaagtgctaaataat                                                                                                                                            <  2:154727‑M2/5‑1 (MQ=255)     ttcgttataaggatttccttaactgcttctcctcaccatcatgttattttcgccacatcataatcctgggcttgctgaagaataattgaaatgatattattaattccactgcctttggtagaggaaagtgctaaATAATAATc                                                                                                                                        <  1:702553‑M2/9‑1 (MQ=255)           ataaggatttccttaactgcttctcctcaccattttgttatcaccgccacaccataatcctgggcttgctgaagaataattgaaatgatattattatttccactgcctttgttagtggcaagtgctaaATAAtaaccatcctt                                                                                                                                  >  2:590240‑M2/129‑138 (MQ=255)            taaggatttccttaactgcttctcctcagcatcatgttattttcgccacatcataatcctgggcttgctgaagaataattgaaatgatattattaattccactgcctttggtagaggaaagtgctaaATAATAATCAATTGtt                                                                                                                                 >  2:60882‑M2/128‑143 (MQ=255)                gatttccttaactgcttctcctcaccatcatgttattttcgccacatcataatcctgggcttgctgaagaataattgaaatgatattattaattccactgcctttggtagaggaaagtgctaaATAATAATCAATTGTTAAat                                                                                                                             >  1:64394‑M2/124‑143 (MQ=255)                  tttccttaactgcttctcctcaccatcatgttattttcgccacatcataatcctgggcttgctgaagaataattgaaatgatattattaattccactgcctttggtagaggaaagtgctaaATAATAATCAATTGTTAAatta                                                                                                                           >  1:64029‑M2/122‑143 (MQ=255)                    gccttcactgcgtctccgccgcaacatggtactctcgctacatcataatcctgggggtgctgaagaataattgaaatgatattattaattccactgcctttggtagaggaaagtgctaaACAATAATCAATTGTTAAattatt                                                                                                                         <  1:105902‑M2/24‑1 (MQ=255)                         aactgcttctcctcaccatcatgttattttcgccacatcataatcctgggcttgctgaagaataattgaaatgatattattaattccactgcctttggtagaggaaagtgctaaATAATAATAAATTGTTAAATGATTGTGCa                                                                                                                    >  1:43001‑M2/115‑143 (MQ=255)                           ctgcttctcctcaccatcatgttattttcgccacatcataatcctgggcttgctgaagaataattgaaatgatattattaattccactgcctttggtagaggaaagtgctaaATAATACTCAATTGTTAAATTATTGTGAAtt                                                                                                                  >  2:108920‑M2/113‑143 (MQ=255)                            tgcttctcctcaccatcatgttattttcgccacatcataatcctgggcttgctgaagaataattgaaatgatattattaattccactgcctttggtagaggaaagtgctaaATAATAATCAATTGTTAAATTATTGTGCAttt                                                                                                                 >  1:775550‑M2/112‑143 (MQ=255)                                 ctcctcaccatcatgttattttcgccacatcataatcctgggcttgctgaagaataattgaaatgatattattaattccactgcctttggtagaggaaagtgctaaATAATAATCAATTGTTAAATTATTGTGCATTTCacta                                                                                                            <  2:766663‑M2/37‑1 (MQ=255)                                                   ttttcgccacatcataatcctgggcttgctgaagaataattgaaatgatattattaattccactgcctttggtagaggaaagtgctaaATAATAATCAATTGTTAAATTATTGTGCATTTCACTACTGGAACTGTAATCAGaa                                                                                          >  1:351745‑M2/89‑143 (MQ=255)                                                   ttttcgccacatcataatcctgggcttgctgaagaataattgaaatgatattattaattccactgcctttggtagaggaaagtgctaaATAATAATCAATTGTTAAATTATTGTGCATTTCACGACTGTAACTGTAATCGGaa                                                                                          >  1:141094‑M2/89‑143 (MQ=255)                                                    tttcgccacctcataatcctgggcttgctgaagaataattgaaatgatattattaattccactgcctttggtagaggaaagtgctaaATAATAATCAATTGTTAAATTATTGTGCATTTCACTACTGGAACTGTAATCAGaaa                                                                                         <  1:660591‑M2/56‑1 (MQ=255)                                                        gccacttcataatcctgggtttgcttaagaataattgaaaagatattattaattccactgcctttggtagaggaaagtgctaaATAATAATCAATTGTTAAATTATTGTGCATTTCACTACTGGAACTGTAATCAGAAAAGAt                                                                                     <  2:50598‑M2/60‑1 (MQ=255)                                                        gccacaccataagcctgggcttgatgaagaataattgaaatgatattattaattccactgcctttggtagaggaaagtgctaaATAAGAATCAATGGTTAAATTAGTGTGCATTTCACTACTGGAACTGTAATCAGAAAAGAt                                                                                     <  1:331134‑M2/60‑1 (MQ=255)                                                         ccacatcataatcctgggcttgctgaagaataattgaaatgatattattaattccactgcctttggtagaggaaagtgctaaATAATAATCAATTGTTAAATTATTGTGCATTTCACTACTGGAACTGTAATCAGAAAAGATa                                                                                    >  2:664810‑M2/83‑143 (MQ=255)                                                          cacatcataatcctgggcgtgctgaagaataattggaatgatattattaattccactgcctttggtagaggaaagtgctaaATAATAATCAATTGTTAAATTATTGTGCATTTCACTACTGGAACTGTAATCAGAAAAGATAg                                                                                   <  2:342080‑M2/62‑1 (MQ=255)                                                            catcataatcctgggcttgctgaagaataattgaaatgatattattaattccactgcctttggtagaggaaagtgctaaATAATAATCAATTGTTAAATTATTGTGCATTTCACTACTGGAACTGTAATCAGAAAAGATAGAc                                                                                 <  1:307655‑M2/64‑1 (MQ=255)                                                                ataatcctgggcttgctgaagaataattgaaatgatattattaattccactgcctttggtagaggaaagtgctacATAATAATCAATTGTTAAATTATTGTGCATTTCGCTACTGGAACTGTAATCAGAAACGATAGACATGc                                                                             >  1:758235‑M2/76‑143 (MQ=255)                                                                 taatcctgggcttgctgaaggataatggaaatgatattattaattccactgcctttggtagaggaaagtgctaaATAATAATCAATTGTTAAATTATTGTGCATTTCACTACTGGAACTGTAATCAGAAAAGATAGACATGCt                                                                            >  2:504343‑M2/75‑143 (MQ=255)                                                                 taatcctgggcttgctgaagaataattgaaatgatattattgattccactgcagttggtagaggaaagtgataaTTAATAATCAATTGTTAAATTATTGTGCATTTAACTACTGGACAGGTAATTAGAAAAGATAGAAATACt                                                                            >  2:382251‑M2/75‑143 (MQ=255)                                                                 taatcctgggcttgctgaagaataattgaaatgatattattaattccactgcctttggtagaggaaagtgctaaATAATAATCAATTGTTAAATTATTGTGCATTTCACTACTGGAACTGTAATCAGAAAAGATAGACATGCt                                                                            >  2:825957‑M2/75‑143 (MQ=255)                                                                     cctgggcttgctgaagaataattgaaatgatattattaattccactgcctttggtagaggaaagtgctaaATAATAATCAATTGTTAAATTATTGTGCATTTCACTACTGGAACTGTAATCAGAAAAGATAGACATGCTTAGc                                                                        <  2:700856‑M2/73‑1 (MQ=255)                                                                     cctgggcttgctgaagaataattgaaatgatattattaattccactgcctttggtagaggaaagtgctaaATAATAATCAATTGTTAAATTATTGTGCATTTCACTACTGGAACTGTAATCAGAAAAGATAGACATGCTTAGc                                                                        >  2:36037‑M2/71‑143 (MQ=255)                                                                         ggcgtgcggaagaagaagtgaaatgagattatacactccactgcctttggtagaggaaagtgctaaATAAGAATCAATTGTTAAATAACTGTGCTGTCCACTACTGGAACTGTAATCAGAAAAGATAGACATGCTTAGCCAAt                                                                    <  2:176760‑M2/77‑1 (MQ=255)                                                                              gttgaagaataattgaaatgatattattaattccactgcctttggtagaggaaagtgctaaATAATAATCAATTGTTAAATTATTGTGCATTTCACTACTGGAACTGTAATCAGAAAAGATAGACATGCTTAGCCAATCTCTa                                                               <  1:44881‑M2/82‑1 (MQ=255)                                                                               ctgaagaataattgaaatgatattattaattccactgcctttggtagaggaaagtgctaaATATTAATCAATTGTTAAATTATTGTGTATTTCACTACTGGAACTGTAATCAGAAAGGATAGACATGCTTAGCCAATCTCTAt                                                              <  2:789844‑M2/83‑1 (MQ=255)                                                                                tgaagaataattgaaatgatattattaattccactgcctttggtagaggaaagtgctaaATAATAATCAATTGTTAAATTATTGTGCATTTCACTACTGGAACTGTAATCAGAAAAGATAGACATGCTTAGCCAATCTCTAtt                                                             >  2:137241‑M2/60‑143 (MQ=255)                                                                                  aagaataattgaaatgatattattaattccactgcctttggtagaggaaagtgctaaATAATAATCAATTGTTAAATTATTGTGCATTTCATTACTGGAACTGTAATCAGAACGGATCCTTATGCTTAGCCAATCTCTATttg                                                           >  1:738005‑M2/58‑143 (MQ=255)                                                                                  aagaataattgaaatgatattattaattccactgcctttggtagaggaaagtgctaaATAATAATCAATTGTTAAATTATTGTGCATTTCACTACTGGAACTGTAATCAGAAAAGATAGACATGCTTAGCCAATCTCTATttg                                                           >  1:771365‑M2/58‑143 (MQ=255)                                                                                   agaataattgaaatgatattattaattccactgcctttggtagaggaaagtgctaaATAATAATCAATTGTTAAATTATTGTGCATTTCACTACTGGAACTGTAATCAGAAAAGATAGACATGCTTAGCCAATCTCTATttga                                                          <  1:399476‑M2/87‑1 (MQ=255)                                                                                    gaataattgaaatgatattattaattccactgcctttggtagaggaaagtgctaaATAATAATCAATTGTTAAATTATTGTGCATTTCACTACTGGAACTGTAATCAGAAAAGATAGACATGCTTAGCCAATCTCTATttgat                                                         <  1:452644‑M2/88‑1 (MQ=255)                                                                                            gaaattgtattattaattccactgcctttggtagaggaaagtgctaaATAATAATCAATTGTTAAATTATTGTGCATTTCACTACTGGAACTGTAATCAGAAAAGATAGACATGCTTAGCCAATCTCTATTTGattgaattga                                                 <  2:195875‑M2/96‑1 (MQ=255)                                                                                                tgatattattaatgccactgcgtttggtagaggaaagtgctaaATAATAATCAATTGTTAAATTATTGTGCATTTCACTACTGGAACTGTAATCAGAAAAGATAGACATGCTTAGCCAATCTCTATTTGATTGAATTGAAAGa                                             <  2:655275‑M2/100‑1 (MQ=255)                                                                                                     ttattacttcccctgcctttggtagaggaaagttctaaATAATAACCAATTGTTAAATTATTCTGCATTTCACTACTGGAACTTTAATCAGAAAAGATAGACATGCTTAGCCAATCTCTATTTGATTGAATTGAAAGAtgttt                                        <  1:241115‑M2/105‑1 (MQ=255)                                                                                                     ttattaattccacttcctttggtagaggaaagtgctaaATAATAATCAATTGTTAAATTATTGTGCATTTCACTACTGGAACTGTAATCAGAAAAGATAGACATGCTTAGCCAATCTCTATTTGATTGAATTGAAAGAtgttt                                        <  1:5649‑M2/105‑1 (MQ=255)                                                                                                     ttattaattccactgcctttggtagaggaaagtgctaaATAATAATCAATTGTTAAATTATTGTGCATTTCACTACTGGAACTGTAATCAGAAAAGATAGACATGCTTAGCCAATCTCTATTTGATTGAATTGAAAGAtgttt                                        >  1:740810‑M2/39‑143 (MQ=255)                                                                                                     ttattaattccactgcctttggtagaggaaagtgctaaATAATAATCAATTGTTAAATTATTGTGCATTTCACTACTGGAACTGTAATCAGAAAAGATAGACATGCTTAGCCAATCTCTATTTGATTGAATTGAAAGAtgttt                                        <  1:423260‑M2/105‑1 (MQ=255)                                                                                                      tattaattccactgcctttggtagaggaaagtgctaaATAATAATCAATTGTTAAATTATTGTGCATTTCACTCCTGGAACTGTAATCAGAAAAGATAGACATGCTTAGCCAATCTCTATTTGATTGAATTGAAAGAtgtttg                                       >  1:92949‑M2/38‑143 (MQ=255)                                                                                                      tattaattccactgcctttggtagaggaaagtgctaaATAATAATCAATTGTTAAATTATTGTGCATTTCACTACTGGAACTGTAATCAGAAAAGATAGACATGCTTAGCCAATCTCTATTTGATTGAATTGAAAGAtgtttg                                       >  1:486724‑M2/38‑143 (MQ=255)                                                                                                        ttaattccactgcctttggtagaggaaagtgctaaATAATAATCAATTGTTAAATTATTGTGCATTTCACTACTGGAACTGTAATCAGAAAAGATAGACATGCTTAGCCAATCTCTATTTGATTGAATTGAAAGAtgtttgtt                                     >  1:493431‑M2/36‑143 (MQ=255)                                                                                                           attccactgcctttggttgaggaaagtgctaaATAATAATCAATTGTTAAATTATTGTGCATTTAACTAGTGGGACTGTAATCAGAAAAGATAGACATGCTTAGCCAATGTCTATTGGATTGAATTGAAAGAGGTTTGTTAAg                                  >  2:260402‑M2/33‑143 (MQ=255)                                                                                                             tccactgcctttggtagaggaaagtgctaaATAGTAATCAATTGTTAAATTATTGTGCATTTCACTACTGGAACTGTAATCAGAAAAGATAGACATGCTTAGCCAATCTCTATTTGATTGAATTGAAAGATGTTTGTTAAGGc                                <  2:365401‑M2/113‑1 (MQ=255)                                                                                                                actgcctttggtagaggaaagtgctaaATAATAATCAATTGTTAAATTATTGTGCATTTCACTACTGGAACTGTAATCAGAAAAGATAGACATGCTTAGCCAATCTCTATTTGATTGAATTGAAAGATGTTTGTTAAGGCATg                             >  2:270310‑M2/28‑143 (MQ=255)                                                                                                                actgcctttggtagaggaaagtgctaaATAATAATCAATTGTTAAATTATTGTGCATTTCACTACTGGAACTGTAATCAGAAAAGATAGACATGCTTAGCCAATCTCTATTTGATTGAATTGAAAGATGTTTGTTAAGGCATg                             >  1:815179‑M2/28‑143 (MQ=255)                                                                                                                 ctgcctttggtagaggaaagtgctaaATAATAATCAATTGTTAAATTATTGTGCATTTCACTACTGGAACTGTAATCAGAAAAGATAGACATGCTTAGCCAATCTCTATTTGATTGAATTGAAAGATGTTTGTTAAGGCATgg                            >  1:739747‑M2/27‑143 (MQ=255)                                                                                                                     ctttggtagaggaaagtgctaaATAATAATCAATTGTTAAATTATTGTGCACTTCACTACTGGAACTGTAATCAGAAAAGATAGACATGCTTAGCCAATCTCTATTTGCTTGAGTTGAAAGATGTTTGTTAAGGCATGGATGc                        >  2:693145‑M2/23‑143 (MQ=255)                                                                                                                      tttggtagaggaaagtgctaaATAATAATCAATTGTTAAATTATTGTGCATTTCACTACTGGAACTGTAATCAGAAAAGATAGACATGCTTAGCCAATCTCTATTTGATTGAATTGAAAGATGTTTGTTAAGGCATGGATGCa                       >  2:148314‑M2/22‑143 (MQ=255)                                                                                                                       ttgggagaggaaagtgctaaATAATAATCAATTGTTAAATTATTGTGCATTTCACTACTGGAACTGTAATCAGAAAAGATAGACATGCTTAGCCAATCTCTATTTGATTGAATTGAAAGATGTTTGTTAAGGCATGGATGCaa                      <  1:771947‑M2/123‑1 (MQ=255)                                                                                                                          gtagaggaaagtgctaaATAATAATCAATTGTTAAATTATTGTGCATTTCACTACTGGAACTGTAATCAGAAAAGATAGACATGGTTAGACAATCTCTATTTGATTGAATTGAGAGATGTTTGTTAAGGGATGGATGCAAGCt                   >  1:182729‑M2/18‑143 (MQ=255)                                                                                                                          gtagaggaaagtgctaaATAATAATCAATTGTTAAATTATTGTGCATTTCACTACTGGAACTGTAATCAGAAAAGATAGACATGCTTAGCCAATCTCTATTTGATTGAATTGAAAGATGTTTGTTAAGGCATGGATGCAAGCt                   >  1:105013‑M2/18‑143 (MQ=255)                                                                                                                           tagaggaaagtgctaaATAATAATCAATTGTTAAATTATTGTGCATTTCACTACTGGAACTGTAATCAGAAAAGATAGACATGCTTAGCCAATCTCTATTTGATTGAATTGAAAGATGTTTGTTAAGGCATGGATGCAAGCta                  >  1:704841‑M2/17‑143 (MQ=255)                                                                                                                                  aagtgctaaATAATAATCAATTGTTAAATTATTGTGCATTTCACTACTGGAACTGTAATCAGAAAAGATAGACATGCTTAGCCAATCTCTATTTGATTGAATTGAAAGATGTTTGTTAAGGCATGGATGCAAGCTATAGATTc           <  2:815179‑M2/134‑1 (MQ=255)                                                                                                                                         aaAGAATAATCAATTGTTAAATTATTGTGCATTTCACTACTGGAACTGTAATCAGAAAAGATAGACATGCTTAGCCAATCTCTATTTGATTGAATTGAAAGATGTTTGTTAAGGCATGGATGCAAGCTATAGATTCTGATACg    <  1:730873‑M2/141‑1 (MQ=255)                                                                                                                                           ataataatCAATTGTTAAATTATTGTGCATTTCACTACTGGAACTGTAATCAGAAAAGATAGACATGCTTAGCCAATCTCTATTTGATTGAATTGAAAGATGTTTGTTAAGGCATGGATGCAAGCTATAGATTCTGATACGGt  <  2:568477/143‑1 (MQ=255)                                                                                                                                           |                                                                                                                                               ACGCCTTAAATGGCGAAGAAACGGTCTAAATAGGCTGATTCAAGGCATTTACGGGAGAAAAAATCGGCTCAAACATGAAGAAATGAAATGACTGAGTCAGCCGAGAAGAATTTCCCCGCTTATTCGCACCTTCCCTAAATAATAATCAATTGTTAAATTATTGTGCATTTCACTACTGGAACTGTAATCAGAAAAGATAGACATGCTTAGCCAATCTCTATTTGATTGAATTGAAAGATGTTTGTTAAGGCATGGATGCAAGCTATAGATTCTGATACGGT  >  NC_000913/1300560‑1300840

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: ‑