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	1299499–1300693	1300697	5–1199	41 [0]	[0] 41	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)	41 (1.040)	38/276	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

GATAACGCCTTAAATGGCGAAGAAACGGTCTAAATAGGCTGATTCAAGGCATTTACGGGAGAAAAAATCGGCTCAAACATGAAGAAATGAAATGACTGAGTCAGCCGAGAAGAATTTCCCCGCTTATTCGCACCTTCCCTAAATAATAATCAATTGTTAAATTATTGTGCATTTCACTACTGGAACTGTAATCAGAAAAGATAGACATGCTTAGCCAATCTCTATTTGATTGAATTGAAAGATGTTTGTTAAGGCATGGATGCAAGCTATAGATTCTGA  >  NC_000913/1300556‑1300834                                                                                                                                               |                                                                                                                                         aattacagttagttataaggatttccttaactgcttctcctcaccatcacgttattttcgccacatcataatcctgggcttgctgaacaatattggaaatgatattattaattccactgcctttggtagaggaaagtgctaaa                                                                                                                                          >  2:710180‑M2/143‑143 (MQ=255)       agttagttataaggatttccttaactgcttctcctcaccatcatgttattttcgccacatcataatcccgggcttgctgaagaataattgaaaagatattattaattccactgcctttggtagaggaaagtgctaaataataa                                                                                                                                    <  1:308767‑M2/7‑1 (MQ=255)               ataaggatttccttaactgcttctcctcaccatcatgttattttcgccacatcataatcctgggcttgctgagtaataattgaaatgatattattaattccactgcctttggtagaggaaagtgctaaATAATAATCAGTTGt                                                                                                                            >  2:120276‑M2/129‑143 (MQ=255)                taaggatttccttaactgcttctcctcaccatcatgttattttcgccacatcataatcctgggcttgctgaagaataattgaaatgatattattaattccactccctttggtagaggaaagtgctaaATAATAATCAATTGtt                                                                                                                           >  1:67122‑M2/128‑143 (MQ=255)                taaggacttccttaactgcttctcctcaccatcatgttattttcgccacatcataatcctgggcttgctgaagaataattgaaatgatattattaattccactgcctttggtagaggaaagtgctaaATAATAATCAATTGtt                                                                                                                           <  2:220864‑M2/16‑1 (MQ=255)                      tttccttaactgcttctcctcaccatcatgttattttcacaacatcataatcctgggcttgatgaagaataattgaaatgatagtattaattacactgcctttggtagaggaaagtggtaaATAATAATCAATTGTTAAatta                                                                                                                     >  2:105268‑M2/122‑143 (MQ=255)                        tccttaactgcttctcctcaccatcatgttattttcgccacatcataatcctgggcttgctgaagaataattgaaatgatattattaattccactgcctttggtagaggaaagtgctaaATAATAATCAATTGTTAAattatt                                                                                                                   <  1:669152‑M2/24‑1 (MQ=255)                           ttaactgcttctcctcaccatcatgttattttcgccacatcataatcctgggcttgctgaagaataattgaaatgatattattaattccactgcctttggtagaggaaagtgctaaATAATAATCAATTGTTAAATTATtgtg                                                                                                                <  1:681407‑M2/27‑1 (MQ=255)                           ttaactgctcatcctcgccatcatgttattttcgccacatcataatcctgggcttgctgaagaataattgaaatgatattattaattccactgcctttggtagaggaaagtgctaaATAATAATCAATTGTTAAATTATtgtg                                                                                                                <  2:90304‑M2/27‑1 (MQ=255)                            taactgcttctcctcatcatcatgttattttcgccacatcataatcctgggcttgctgaagaataattgaaatgatattattaattccactgcctttggtagaggaaagtgctaaATAATAATCAATTGTTAAATTATTGTGc                                                                                                               <  2:613037‑M2/28‑1 (MQ=255)                             aacatcttctccttaccatgatgttattttcgccacatcataatcctgggcttgatgaataataattgaaatcatattattaattccattgcacttgggataggaaattgctaaATAATAATCAATTGTTAAATTATTGTGCa                                                                                                              <  2:399702‑M2/29‑1 (MQ=255)                               ctgcttctcctcaccatcatgttattttcgccacatcataatcctgggcttgctgaagaataattgcaatgatattattaattccactgcctttggtagaggaaaatgctaaATAATAATCAATTGTTCAGTTACTGTGCAtt                                                                                                            >  2:181817‑M2/113‑143 (MQ=255)                                  cttctcctcaccatcatgttattttcgccacatcataatcctgggcttgctgaagaataattgaaatgatattattaattccactgcctttggtagaggaaagtgctaaATAATAATCAATTGTTAAATTATTGTGCATTTCa                                                                                                         >  1:439646‑M2/110‑143 (MQ=255)                                    tctcctcaccatcatgttattttcgcaacaaaacaagcccgggcttgctgaagaataattgaaatgatattattaattccactgcctttggtagaggaaagtgctaaATAATAATCAATTGTTAAATTATCGTGCATTTCact                                                                                                       >  2:401823‑M2/108‑143 (MQ=255)                                       cctcaccatcatgttattttcgccacatcataatcctgggcttgctgaagaataattgaaacgatattattaattccactgcctttggtagaggaaagtgctaaATAATAATCAATTGTTAAATTATTGTGCATTTCactact                                                                                                    <  2:607073‑M2/39‑1 (MQ=255)                                           accagcatgttattttcgccacatcataatcctgggcttgctgaagaataattgaaatgatattattaattccactgcctttggtagaggaaagtgctaaATAATAATCAATTGTTAAATTATTGTGCATTTCACTACTGGaa                                                                                                <  2:617146‑M2/43‑1 (MQ=255)                                              atcatgttattttcgccacatcataatcctgggcttgctgaagaataattgaaatgatattattaattccactgcctttggtagaggaaagtgctaaATAATAATCAATTGTTAAATTATTGTGCATTTCACTACTGGAACTg                                                                                             >  2:533168‑M2/98‑143 (MQ=255)                                               tcatggtattttcgccacatcataatcctgggcttgctgaagaataattgaaatgatattattaattccactgcctttggtagaggaaagtgctaaATAATAATCAATTGTTAAATTATTGTGCATTTCACTACTGGAACTGt                                                                                            <  1:622320‑M2/47‑1 (MQ=255)                                                     tattttcgccacatcataatcctgggcttgctgaagaataattgaaatgatattattaattccactgcctttggtagaggaaagtgctaaATAATAATCAATTGTTAAATTATTGTGCATTTCACTACTGGAACTGTAATCAg                                                                                      >  2:438636‑M2/91‑143 (MQ=255)                                                         ttctccacatcataatcctgggcttgctgaagaataattgaaatgatattattaattccactgcctttagtagaggaaagtgctaaATAATAATCAATTGTTAAATTATTGTGCATTTCACTACTGGAACTGTAATCAGaaaa                                                                                  <  2:711768‑M2/57‑1 (MQ=255)                                                          tcgccacatcataatcctgggcttgctgaagaataattgaaatgatattattaattccactgcctttggtagaggaaagtgataaATAATAATCAATTGTTAAATTATTGTGCATTTCAATAATGGAAATGTAATCAGAAAAg                                                                                 >  2:511724‑M2/86‑143 (MQ=255)                                                             ccacatcatagtcctgggcttgctgaagaataattgaaatgatattattaattccactgcctttggtagaggaaagtgctaaATAATAATCAATTGTTAAATTATTGTGCATTTCACTACTGGAACTGTAATCAGAAAAGATa                                                                              <  1:719496‑M2/61‑1 (MQ=255)                                                             ccacatcataatcctgggcttgctgaagaataattgaaatgatattattaattccactgcatttggtagagaaaagtgctaaATAATAATCAATTGTTAAATTATTGTGCATTTCAATACTGGAACTGTCATCAGAAAAGATa                                                                              >  2:229718‑M2/83‑143 (MQ=255)                                                             ccacatcataatcctgggcttgctgaagaataattgaaatgatattattaattcaactgcctttggtagaggaaagtgctaaATAATAATCAATTGTTAAATTATGGTGAATTTCACTACTGGAACTATAATAAGAAAagaaa                                                                              >  2:403355‑M2/83‑141 (MQ=255)                                                               acatcataatcctgggcttgctgaagaataattgaaatgatattattaattccactgcctttggtagaggaaagtgctaaATAATAATCAATTGTTAAATTATTGTGCATTTCACTACTGGAACTGTAATCAGAAAAGATAGa                                                                            <  1:25246‑M2/63‑1 (MQ=255)                                                                     taatcctgggcttgctgaagaataattgaaatgatattattaattccactgcctttggtagaggaaagtgctaaATAATAATCAATTGTTAAATTATTGTGCATTTCACTACTGGAACTGTAATCAGAAAGGATAGACATGCt                                                                      >  1:469504‑M2/75‑143 (MQ=255)                                                                           tgggcttgctaaagaataattgaaatgatattattacttccactgcctttggtagaggaaagtgctaaATAATAATCAATTGTTAAATTATTGTGCATTTCACTACTGGAACTGTAATCAGAAAAGATAGACACCCTTAGCCa                                                                >  2:113209‑M2/69‑143 (MQ=255)                                                                                    tgaagaataattgaaatgatattattaattccactgcctttggtagaggaaagtgctaaATAATAATCAATTGTTAAATTATTGTGCATTTCACTACTGGAACTGTAATCAGAAAAGATAGACATGCTTAGCCAATCTCTAtt                                                       >  2:295177‑M2/60‑143 (MQ=255)                                                                                    tgaagaataattgaaatgatattattaattccactgcctttggtagaggaaagtgctaaATAATAATCAATTGTTAAATTATTGTGCATTTCACTACTGGAACTGTAATCAGAAAAGATAGACATGCTTAGCCAATCTCTAtt                                                       >  1:179480‑M2/60‑143 (MQ=255)                                                                                     gaagaataattgaaatgatattattaattccactgcctttggtagaggaaagtgctaaATAATAATCAATTGTTAAATTATTGTGCATTTCACTACTGGAACTGTAATCAGAAAAGATAGACATGCTTAGCCAATCTCTAttt                                                      >  1:230237‑M2/59‑143 (MQ=255)                                                                                           gagttgaaacgctattattaattccactggcttttgtagatgaaagtgctaaATAATAATCAATTGTTAAATTAGTGTGCATTTCACTACTGGAACTGTAATCAGAAAAGATAGACATGCTTAGCCAATCTCCATttgattga                                                <  2:536749‑M2/91‑1 (MQ=255)                                                                                              ttgaaatgatattattaattccactgcctttggtagaggaaagtgctaaATAATAATCAATTGTTAAATTATTGTGCATTTCACTACTGGAACTGTAATCAGAAAAGATAGACATGCTTAGCCAATCTCTATTTGattgaatt                                             >  2:167904‑M2/50‑143 (MQ=255)                                                                                                    tgatattattaattccactgcctttggtagaggaaagtgctaaATAATAATCAATTGTTAAATTCTTGTGCATTTCACTACTGGAACTATAATCAGAAAAGATAGACAAGATTAGAAAAAATCAATTTGATTGAATAGAAAGa                                       >  1:93209‑M2/44‑143 (MQ=255)                                                                                                     gatattattaattccactgcctttggtagaggaaagtgctaaATAATAATCAATTGTTAAATTATTGTGCATTTCACTACTGGAACTGTAATCAGAAAAGATAGACATGCTTAGCCAATCTCTATTTGATTGAATTGAAAGAt                                      >  1:478330‑M2/43‑143 (MQ=255)                                                                                                          tattaattccactgcctttggtagaggaaagtgctaaATAATAATCAATTGTTAAATTATTGTGCATTTCACTACTGGAACTGTAATCAGAAAAGATAGACATGCTTAGCCAATCTCTATTTGATTGAATTGAAAGAtgtttg                                 <  1:616802‑M2/106‑1 (MQ=255)                                                                                                           attaattccactgcctttggtagaggaaagtgctaaATAATAATCAATTGTTAAATTATTGTGCATTTCACTACTGGAACTGTAATCAGAAAAGATAGACATGCTTAGCCAATCTCTATTTGATTGAATTGAAAGAtgtttgt                                <  1:604060‑M2/107‑1 (MQ=255)                                                                                                            ttaattccactgcctttggtagaggaaagtgctaaATAATAATCAATTGTTAAATTATTGTGCATTTCACTACTGGAACTGTAATCAGAAAAGATAGACATGCTTAGCCAATCTCTATTTGATTGAATTGAAAGAtgtttgtt                               >  2:208372‑M2/36‑143 (MQ=255)                                                                                                             taattccactgcctttggtagaggaaagtgctaaATAATAATCAATTGTTAAATTATTGTGCATTTCACTACTGGAACTGTAATCAGAAAAGATAGACATGCTTAGCCAATCTCTATTTGATTGAATTGAAGGATGATTGGTa                              >  1:430216‑M2/35‑143 (MQ=255)                                                                                                                  ccactgcctttggtagaggaaagtgctaaATAATAATCAATTGTTTAATTATTGTGCCTTTCAATAGTGGCATTGTGCTCAGATATGATAGCCATGCTTAGCCAGTCTCTATTTGATTGAATTGAAAGATGTTTGTTAAGGCa                         >  1:124011‑M2/30‑143 (MQ=255)                                                                                                                                    gaaagtgctaaATAATAATCAATTGTTAAATTATTGTGCATTTCACTACTGGAACTGTAATCAGAAAAGATAGACATGCTTAGCCAATCTCTATTTGATTGAATTGAAAGATGTTTGTTAAGGCATGGATGCAAGCTATAGAt       >  1:570975‑M2/12‑143 (MQ=255)                                                                                                                                         tgctaaATAATAATCAATTGTTAAATTATTGTGCATTTCACTACTGGAACTGTAATCAGAAAAGATAGACATGCTTAGCCAATCTCTATTTGATTGAATTGAAAGATGTTTGTTAAGGCATGGATGCAAGCTATAGATTCTGa  >  1:471059‑M2/7‑143 (MQ=255)                                                                                                                                               |                                                                                                                                         GATAACGCCTTAAATGGCGAAGAAACGGTCTAAATAGGCTGATTCAAGGCATTTACGGGAGAAAAAATCGGCTCAAACATGAAGAAATGAAATGACTGAGTCAGCCGAGAAGAATTTCCCCGCTTATTCGCACCTTCCCTAAATAATAATCAATTGTTAAATTATTGTGCATTTCACTACTGGAACTGTAATCAGAAAAGATAGACATGCTTAGCCAATCTCTATTTGATTGAATTGAAAGATGTTTGTTAAGGCATGGATGCAAGCTATAGATTCTGA  >  NC_000913/1300556‑1300834

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 12 ≤ ATCG/ATCG < 13 ≤ ATCG/ATCG < 27 ≤ ATCG/ATCG < 41 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑