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	51 [0]	[0] 51	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)	45 (0.840)	41/276	0.3	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

GGGGATAACGCCTTAAATGGCGAAGAAACGGTCTAAATAGGCTGATTCAAGGCATTTACGGGAGAAAAAATCGGCTCAAACATGAAGAAATGAAATGACTGAGTCAGCCGAGAAGAATTTCCCCGCTTATTCGCACCTTCCCTAAATAATAATCAATTGTTAAATTATTGTGCATTTCACTACTGGAACTGTAATCAGAAAAGATAGACATGCTTAGCCAATCTCTATTTGATTGAATTGAAAGATGTTTGTTAAGGCATGGATGCAAGCTATAGATTCTGATACGGTCAA  >  NC_000913_3_pae_tpiA/1300553‑1300843                                                                                                                                                  |                                                                                                                                                  tcaaattacagttagttataaggatttccttaactgcttctcctcaccatcatgttattttcgccacatcataatcctgggcttgctgaagaataattgaaatgatattattaattccactgcctttggtaaaggaaaatgctaaataa                                                                                                                                                >  2:575544‑M2/146‑149 (MQ=255)    aaatacagttagttataaggatttccttaactgcttctcctcaccatcatgttattttcgccacatcataatcctgggcttgctgaagaataattgaaatgatattatgaattccactgcctttggtagaggaaagtgctaaataataa                                                                                                                                             <  2:360513‑M2/7‑1 (MQ=255)                   taaggatttccttaactgcttctcctcaccatcatgttattttcgccacatcataatcctgggcttgctgaagaataatggaaatgatattattaattcaactgcatttggtagaggaaagtgctaaATAATAATAAATTGTTAGatta                                                                                                                              >  2:17179‑M2/128‑149 (MQ=255)                    aaggatttccttaactgcttctcctcaccatcatgttattttcgccacatcataatcctgggcttgctgaagaataattgaaatgatattattaattccactgcctttggtagaggaaagtgctaaATAATAATCAATTGTTAAattat                                                                                                                             >  1:907776‑M2/127‑149 (MQ=255)                     aggttttcgttaactgcttctcctcaccattatgttattttcgccacatcataatcctgggcttgctgaagaataattgaaatgatattattaattccactgtctttggtagaggaaagtgctaaATAATAATCAATTGTTAAattatt                                                                                                                            <  2:442539‑M2/24‑1 (MQ=255)                           tccttaactgcttctcctcaccatcatgttattttggccatatcataatcctgggcttgctgaagaataattgaaatgatattattaattccactgcctttggtagaggaaagtgctaaTTAATAATCAATTGTTAATTTATTTtgctt                                                                                                                      >  2:706266‑M2/120‑147 (MQ=255)                           tccttaactgcttctcctcaccatcatgttattttcgccacatcataatcctgggcttgctgaagaataattgaaatgatattattaattccactgccttttgtagaggaaagtgctaaCTAGTAATCAATTTTTAAAtttttgttaat                                                                                                                      >  1:175622‑M2/120‑145 (MQ=255)                             cttaactgcttctcctcaccatcatgttattttcgccacatcataatcctgggcttgctgaagaataattgaaatgatattattaattccactgcctttggtagaggaaagtgctaaATAATAATCAATTGTTAATTTATtatgcgtgt                                                                                                                    >  2:255450‑M2/118‑145 (MQ=255)                              ttaactgcttctcctcaccatcatggtattttcgccacatcataatcctgggcttgctgaagaataattaaaatgatattattaattccactgcctttggtagaggaaagtgctaaATAATAATCAATTGCTAAATTATTGTGCATTTc                                                                                                                   >  1:751124‑M2/117‑149 (MQ=255)                               tgagtgcttctccgaaccagcatgttatttacgccacatcataatcctgggcttgctgaagaataattgagatgatattattaattccactgcttttggtagaggaaagtgctaaATAATAATCAATTGTTAAATTATTGTGCATTTCa                                                                                                                  <  2:344971‑M2/34‑1 (MQ=255)                                 actgcttctcctcaccatcatgttattttcgccacatcataatcctgggcttgctgaagactaattgaaatgatattattaattccactgcctttggtagaggaaagtgctaaATAATAATCAATTGTTAAATTATTCTCCATTTCcct                                                                                                                >  2:46740‑M2/114‑149 (MQ=255)                                   tgcttctcctcaccatcatgttattttcgccacatcataatcctgggcttgctgaagaataattgaaatgatattattaattccactgcctttggtagaggaaagtgctaaATAATAATCAATTGTTAAATTATTGTGCATTTCactac                                                                                                              <  2:649249‑M2/38‑1 (MQ=255)                                     cttcacctctccattatgttattttcgccacattataatcctgggtttgctgaagaataattgaaatgatattattaattccactgcctttggtagaggaaagtgctaaATAATAATCAATTGTTAAATTATTGTGCATTTCACTACTg                                                                                                            <  2:798680‑M2/40‑1 (MQ=255)                                            tcaccatcatgttattttcgccacatcataatcctgggcttgctgaagaataattgaaatgatattattaattccactgcctttggtagaggaaagtgctaaATAATAATCAATTGTTAAATTATTGTGCATTTCACTACTGGAACTGt                                                                                                     >  1:902296‑M2/103‑149 (MQ=255)                                                 atcatgttattttcgccacatcataatcctgggcttgctgaagaataattgaaatgatattattaattccactgcctttggtagaggaaagtgctaaATAATAATCAATTGTTAAATTATTGTGCATTTCACTACTGGAACTGTAATCa                                                                                                <  1:810106‑M2/52‑1 (MQ=255)                                                 atcatgttattttcgccacatcataatcctgggcttgctgaagaataattgaaatgatattattaattccactgcctttggtagaggaaagtgctaaATAATAATCAATTGTTAAATTATTGTGCATTTCACTACTGGAACTGTAATCa                                                                                                <  2:240908‑M2/52‑1 (MQ=255)                                                         attttcgccacatcataatcctgggcttgctgaagaataattgaaatgatattattaattccactgcctttggtagaggaaagtgctaaATAATAATCAATTGTTAAATTATTGTGCATTTCACTACTGGAACTGTAATCAGAAAAGAt                                                                                        >  2:79393‑M2/90‑149 (MQ=255)                                                               gccacatcataatcctgggcttgctgaagaataattgaaatgatattattaattccactgcctttggtagaggaaagtgctaaATAATAATCAATTGTTAAATTATTGTGCATTTCACTACTGGAACTGTAATCAGAAAAGATAGACAt                                                                                  >  1:643424‑M2/84‑149 (MQ=255)                                                               gccacatcataatcctgggcttgctgaagaataattgaaatgatattattaattccactgcctttggtagaggaaagtgctaaATAATAATCAATTGTTAAATTATTGTGCATTTCACTACTGGAACTGTAATCAGAAAAGATAGACAt                                                                                  >  2:389389‑M2/84‑149 (MQ=255)                                                                ccacatcataatcctgggcttgctgaagaataattgaaatgatattattaattccactgcctttggtagaggaaagtgctaaATAATAATCAATTGTTAAATTATTGTGCATTTCACTACTGGCACTGTAATCAGAAAAGATAGACATg                                                                                 >  2:392043‑M2/83‑149 (MQ=255)                                                                 cacatcacaatccctgtctggctgaagaataattgaaatgatattattaattccactgcctttggtagaggaaagtgctaaATAATAATCAATTGTTAAATTATTGTGCATTTCACTACTGGAACTGTAATCAGAAAAGATAGACATGc                                                                                <  2:402708‑M2/68‑1 (MQ=255)                                                                  acatcataatcctgggcttgctgaagaataattgaaatgatattattaattccactgcctttggtagaggaaagtgctaaATAATAATCAATTGTTAAATTATTGTGCATTTCACTACTGGAACTGTAATCAGAAAAGATAGACATGCt                                                                               >  1:646238‑M2/81‑149 (MQ=255)                                                                  acatcataatcctgcgcttgctgaagaataattgaaatgatattattaattccactgcctttggtagaggaaagtgctaaATAATAATCAATTGTTAAATTATTGTGCATTTCACTACTGGCACTGTAATCAGAAAAGATAGACATGCt                                                                               <  2:968306‑M2/69‑1 (MQ=255)                                                                       ataatcctgggcttgctgaagaataattgaaatgatattattaattccactgcctttggtagaggaaagtgctaaATAATAATCAATTGTTAAATTATGGTGCATTTCACTACTGGAACTGTAATCATAAAAGATAGAAAGGTTTAGcc                                                                          >  1:976735‑M2/76‑149 (MQ=255)                                                                         aatcctgggcttgctgaagaataattgaaatgatattattaattccactgcctttggtagaggaaagtgctaaATAATAATCAATTGTTAAATTATTGTGCATTTCACTACTGGAACTGTAATCAGAAAAGATAGACATGCTTAGCCaa                                                                        >  2:273038‑M2/74‑149 (MQ=255)                                                                             ctgggcttgctgaagaataattgaaatgatattattaattccactgcctttggtagaggaaagtgctaaATAATAATCAATTGTTAAATTATTGTGCATTTCACTACTGGAACTGTAATCAGAAAAGATAGACATGCTTAGCCACtctc                                                                    >  2:544428‑M2/70‑149 (MQ=255)                                                                             ctgggcttgctgaagaataattgaaatgatattattaattccactgcctttggtagaggaaagtgctaaATAATAATCAATTGTTAAATTATTGTGCATTTCACTACTGGAACTGTAATCAGAAAAGATAGACATGCTTAGCCAAtctc                                                                    <  1:389389‑M2/80‑1 (MQ=255)                                                                                  cttgctgaagaataattgaaatgatattattaattccactgcctttggtagaggaaagtgctaaATAATAATCAATTGTTAAATTATTGTGCATTTCACTACTGGAACTGTAATCAGAAAAGATAGACATGCTTCGCAAATCTCTAttt                                                               >  1:120657‑M2/65‑149 (MQ=255)                                                                                     gctgaagaataattgaaatgatattattaagtccacactgcttgttagaggaaagtgctaaATAATAATCAATTGTTAAATTATTGTGCATTTCACTACTGGAACTGTAATCAGAAAAGCTAGACATGATTAGCAAATCTCTATttgat                                                            <  2:454287‑M2/88‑1 (MQ=255)                                                                                      ctgaagaataattggaatgatattattagttccactgcctgtggtagaggaaagtgctaaATAATAATCAATTGTTAAACTATTGTGCATTTCACTACTGGACCTGTAATCAGAACAGATAGACATGCTTAGCCAATCTCTATttgatt                                                           <  2:338304‑M2/89‑1 (MQ=255)                                                                                        gaagaataattgaaatgatattattaattccactgcctttggtagaggaaagtgctaaATAATAATCATTTGTTAAATTATTGTGCATTTCACTACTGGAACAGTAGTCAGAAAAGATAGACATGCTTAGCCAATCTCTATttgattga                                                         >  2:850424‑M2/59‑149 (MQ=255)                                                                                             ataattgaaatgatattattaattccactgcctttggtagaggaaagtgctaaATAATAATCAATTGTTAAATTATTGTGCATTTCACTACTGGAACTGTAATCAGAAAAGATAGACATGCTTAGCCAATCTCTATTTGattgaattga                                                    <  2:248376‑M2/96‑1 (MQ=255)                                                                                                 ttgaaatgatattattaattccactgcctttggtagaggaaagtgctaaATAATAATCAATTGTTAAATTATTGTGCATTTCACTCATGGAACTGTAATCAGAAAAGATAGACATGCTTCGCCAATCTGTATATGATGGAATTGAAAGa                                                >  2:686364‑M2/50‑149 (MQ=255)                                                                                                     aatgatattaataattccactgcctttcgtagaggaaagtgctaaATAATAATCAATTGTTAAATTATTGTGCAGTTCTCTACTGTAACTGTAATCAGAAAAGATAGACATGCTTAGCCAATCTCTATTTGATTGAATTGAAAGAtgtt                                            <  2:727154‑M2/104‑1 (MQ=255)                                                                                                           attattaattccactgcctttggtagaggaaagtgctaaATAATAATCAATTGTTAAATTATTGTGCATTTCACTACTGGAACTGTAATCAGAAAAGATAGACATGCTTAGCCAATCTCTATTTGATTGAATTGAAAGATGTTTGTTaa                                      <  2:643424‑M2/110‑1 (MQ=255)                                                                                                                    tacactgcctttggtagaggaaagtgctaaATAATAATCAATTGTTAAATTATTGTGCATTTCACTACTGGAACTGTAATCAGAAAAGATAGACATGCTTAGCCAATCTCTATTTGATTGAATTGAAAGATGTTTGTTAAGGCATGGAt                             <  2:327731‑M2/119‑1 (MQ=255)                                                                                                                             tttggtagaggaaagtgctaaATAATAATCAATTGTTAAATTATTGTGCATTTCACTACTGGAACTGTAATCAGAAAAGATAGACATGCTTAGCCAATCTCTATTTGATTGAATTGAAAGAtgttt                                           >  2:502231‑M2/22‑126 (MQ=255)                                                                                                                             tttggtagaggaaagtgctaaATAATAATCAATTGTTAAATTATTGTGCATTTCACTACTGGAACTGTAATCAGAAAAGATAGACATGCTTAGCCAATCTCTATTTGATTGAATTGAAAGAtgttt                                           <  1:502231‑M2/105‑1 (MQ=255)                                                                                                                             tttggtagaggaaagtgctaaATAATAATCAATTGTTAAATTATTGTGCATTTCACTACTGGAACTGTAATCAGAAAAGATAGACATGCTTAGCCAATCTCTATTTGATTGAATTGAAAGATGTTTGTTAAGGCATGGATGCAAGCtat                    >  2:316481‑M2/22‑149 (MQ=255)                                                                                                                               tggtagaggaaagtgctaaATAATAATCAATTGTTAAATTATTGTGCATTTCACTAGTGGAACTGTAATCAGAAAAGATAGACATGCTTAGACAATCCCTAGTTGATTGAATTGAAAGATGTTTGTTAAGGCATGGATGCGAGATAAAg                  >  2:647499‑M2/20‑149 (MQ=255)                                                                                                                                   agagggaagtgctaaATAATAATCGATTGTTTAATTATTGGGTATTGCACTACTGGAACTGTAATCAGAAAAGGTAGCAATGCTTAGCGAAGCTCTATTTGATTGAATTGAAAGATGTTTGTTAAGGCATGGATGCAAGCTATAGATTc              <  2:410848‑M2/134‑1 (MQ=255)                                                                                                                                     aggaaagtgctaaATAATAATCAATTGTTAAATTATTGTGCATTTCACTACTGGAACTGTAATCAGAAAAGATAGACATGCTTAGCCAATCTCTATTTGATTGAATTGAAAGATGTTTGTTAAGGCATGGATGCAAGCTATAGATTCTg            >  1:583276‑M2/14‑149 (MQ=255)                                                                                                                                          agtgccaaATAATAAGCAATTGTGAAATTATTGTGCATTTCACTACTGGAACTGTAATCAGAAAAGATAGACATGCTTAGCCAATCTCTATTTGATTGAATTGAAAGATGTTTGTTAAGGCATGGATGCAAGCTATAGATTCTGATACg       <  2:372820‑M2/141‑1 (MQ=255)                                                                                                                                           gtgctaaATAATAATCAATTGTTAAATTATTGTGCATTTCACTACTGGAACTGTAATCAGAAAAGATAGACATGCTTAGCCAATCTCTATTTGATTGAATTGAAAGATGTTTGTTAAGGCATGGATGCAAGCTATAGATTCTGATACgg      <  1:708314‑M2/142‑1 (MQ=255)                                                                                                                                            tgctaaATAATAATCAATTGTTAAATTATTGTGCATTTAACTACTGGAACTGTAATCAGAAAAGATAGACATGCTTAGCCAATCTCTATTTGATTGAATTGAAAGATGTTTGTTAAGGCATGGATGCAAGCTATAGATTCTGATACGGt     <  2:515228‑M2/143‑1 (MQ=255)                                                                                                                                              ctaaATAATAATCAATTGTTAAATTATTGTGCATTTCACTACTGGAACTGTAATCAGAAAAGATAGACATGCTTAGCCAATCTCTATTTGATTGAATTGAAAGATGTTTGTTAAGGCATGGATGCAAGCtata                   >  1:758561‑M2/5‑133 (MQ=255)                                                                                                                                              ctaaATAATAATCAATTGTTAAATTATTGTGCATTTCACTACTGGAACTGTAATCAGAAAAGATAGACATGCTTAGCCAATCTCTATTTGATTGAATTGAAAGATGTTTGTTAAGGCATGGATGCAAGCtata                   <  2:758561‑M2/129‑1 (MQ=255)                                                                                                                                               taaATAATAATCAATTGTTAAATTATTGTGCATTTCACTACTGGAACTGTAATCATAAAAGATAGACATGCTTAGCTAATCTCTATTTGATCGAATTAAATGATGTTTGTTAATGAATGGTTGCAAGCTAATTATTCTGATACCGTCaa  >  2:464874‑M2/4‑149 (MQ=255)                                                                                                                                               taaATAATAATCAATTGTTAAATTATTGTGCATTTCACTACTGGAACTGTAATCAGAAAAGATAGACATGCTTAGCCAATCTCTATTTGATTGAATTGAAAGAt                                               >  1:162572‑M2/4‑104 (MQ=255)                                                                                                                                               taaATAATAATCAATTGTTAAATTATTGTGCATTTCACTACTGGAACTGTAATCAGAAAAGATAGACATGCTTAGCCAATCTCTATTTGATTGAATTGAAAGAt                                               <  2:162572‑M2/101‑1 (MQ=255)                                                                                                                                               taaATAATAATCAATTGTTAAATTATTGTGCATTTCACTACTGGAACTGTAATCAGAAAAGATAGACATGCTTAGCCAATCTCTATTTGATTGAATTGAAAGATGTTTGTTAAGGCATGGATGCAAGCTATAGATTCTGATACGGTCaa  <  1:414129‑M2/146‑1 (MQ=255)                                                                                                                                                  |                                                                                                                                                  GGGGATAACGCCTTAAATGGCGAAGAAACGGTCTAAATAGGCTGATTCAAGGCATTTACGGGAGAAAAAATCGGCTCAAACATGAAGAAATGAAATGACTGAGTCAGCCGAGAAGAATTTCCCCGCTTATTCGCACCTTCCCTAAATAATAATCAATTGTTAAATTATTGTGCATTTCACTACTGGAACTGTAATCAGAAAAGATAGACATGCTTAGCCAATCTCTATTTGATTGAATTGAAAGATGTTTGTTAAGGCATGGATGCAAGCTATAGATTCTGATACGGTCAA  >  NC_000913_3_pae_tpiA/1300553‑1300843

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: ‑