Predicted mutation
evidence	seq id	position	mutation	annotation	gene	description
MC JC	NC_000913_3_vch_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_vch_pgi	1299499–1300697	1300697	1–1199	24 [0]	[0] 24	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_pgi	= 1299498	0 (0.000)	22 (1.500)	20/282	0.0	100%	intergenic (+253/‑1684)	ychE/oppA	UPF0056 family inner membrane protein/oligopeptide ABC transporter periplasmic binding protein
	?	NC_000913_3_vch_pgi	1300698 =	0 (0.000)					intergenic (+1453/‑484)	ychE/oppA	UPF0056 family inner membrane protein/oligopeptide ABC transporter periplasmic binding protein

GCCTTAAATGGCGAAGAAACGGTCTAAATAGGCTGATTCAAGGCATTTACGGGAGAAAAAATCGGCTCAAACATGAAGAAATGAAATGACTGAGTCAGCCGAGAAGAATTTCCCCGCTTATTCGCACCTTCCCTAAATAATAATCAATTGTTAAATTATTGTGCATTTCACTACTGGAACTGTAATCAGAAAAGATAGACATGCTTAGCCAATCTCTATTTGATTGAATTGAAAGATGTTTGTTAAGGCATGGATGCAAGCTATAGA  >  NC_000913_3_vch_pgi/1300562‑1300828                                                                                                                                         |                                                                                                                                   agatggttataagcatttgcttaactccttctcctcaccatcatgttattttcgccacattataatcctgggcttgctgaagaataattgaaatgatattattaatttcacttcctttggtagaggaaagtgctaaATAATAATCAAtt                                                                                                                        <  2:178365‑M2/13‑1 (MQ=255)          taaggatttccttaactgcttctcctcaccatcatgttattttcgccacatcataatcctgggcttgctgaagaataattgaaatgatattattaattccactgcctttggtagaggaaagtgctaaataataat                                                                                                                             >  1:131345‑M2/128‑135 (MQ=255)          taaggatttccttaactgcttctcctcaccatcatgttattttcgccacatcataatcctgggcttgctgaagaataattgaaatgatattattaattccactgcctttggtagaggaaagtgctaaataataat                                                                                                                             <  2:131345‑M2/8‑1 (MQ=255)                 ttccttaactgcttctcctcaccatcatgttattttcgccacatcataatcctgggcttgctgaagaataattgaaatgatattattaattccaatgcctttgataaaggaaggtgctaaATAATAATCATTTGTTAAATTATTATGCa                                                                                                        >  2:142446‑M2/121‑149 (MQ=255)                   ccttaactgcttctcctcacgatcatgttattttcgccacatcataatcctgggcttgctgaagaataattgaaatgatattattaattccactgcctttggtagaggaaagtgctaaATAATAATCAATTGTTAAATTATTGTGCAtt                                                                                                      <  2:117506‑M2/31‑1 (MQ=255)                     ttaactgcttctcctcaccatcatgttattttcgccacatcataatcctgggcttgctgaagaataattgaaatgatattattaattccactgcctttggtaaaggaaagtgctaaATAATAATCAATTGTTAAATTGTTGTGCATTTc                                                                                                    >  1:188659‑M2/117‑149 (MQ=255)                        actgcttctcctcaccatcatgttattttcgccacatcataatcctgggcttgctgaagaataattgaaatgatattattaattccactgcctttggtagaggaaagtgctaaATAATAATCAATTGTTAAATTATTGTGCATTTCcct                                                                                                 >  1:219801‑M2/114‑149 (MQ=255)                         ctgcttctcctcaccatcatgttattttcgccacatcataatcctgggcttgctgaagaataattgaaatgatattattaattccactgcctttggtagaggaaagtgctaaATAATAATCAATTGTTAAATTATTGTGCATTTCacta                                                                                                >  2:95789‑M2/113‑149 (MQ=255)                                tcctcaccatcatgttattttcgccacatcataatcctgggcttgctgaagaataattgaaatgatattattaattccactgcctttggtagaggaaagtgctaaATAATAATCAATTGTTAAATTATTGTGCATTTCACTACTGGAAc                                                                                         <  2:34218‑M2/44‑1 (MQ=255)                                                attttcgccacatcataatcctgggcttgctgaagaataattgaaatgatattattaattccactgcctttggtagaggaaagtgctaaATAATAATCAATTGTTAAATTATTGTGCATTTCACTACTGGAACTGTAATCGGAAAAGAt                                                                         >  1:200698‑M2/90‑149 (MQ=255)                                                        cacatcataatcctgggcttgctgaagaataattgaaatgatattattaattccactgcctttggtagaggaaagtgctaaATAATAATCAATTGTTAAATTATTGTGCATTTCACTACTGGAACTGTAATCAGAAAAGATAGACATGc                                                                 >  1:137441‑M2/82‑149 (MQ=255)                                                         acatcataatcctgggcttgctgaagaataattgaaatgatattattaattccactgcctttggtagaggaaagtgctaaATAATAATCAATTGTTAAATTATTGTGCATTTCACTACTGGAACTGTAATCAGAAAAGATAGACATGCt                                                                <  1:95789‑M2/69‑1 (MQ=255)                                                                                 agaataattgaaatgatattattaattccactgcctttggtagaggaaagtgctaaATAATAATCAATTGTTAAATTATTGTGCATTTCACTACTGGAACTGTAATCAGAAAAGATAGACATGCTTAGCCAATCTCTATTTGattgaat                                        <  2:168828‑M2/93‑1 (MQ=255)                                                                                       attgaaatgatattattaattccactgcctttggtagaggaaagtgctaaATAATAATGATTTGGTAAATTATTGTGCATTTCACTACTGGAACTGTAATCAGAAAAGGTAGTCATGCGTAGCCAATCTCTGTTTGATGGATTTGAAAg                                  >  1:90263‑M2/51‑149 (MQ=255)                                                                                              tgatattattaattccactgcctttggtagaggaaagtgctaaATAATAATCAATTGTTAAATTATTGTGCATTTCACTACTGGAACTGTAATCAGAAAAGATAGGCATGCTTAGCCAATCTCTATTTGATTGAATTGAAAGAtgtttg                           <  1:263312‑M2/106‑1 (MQ=255)                                                                                                 tattattaattccactgcctttggtagaggaaagtgctaaATAATAATCAATTGTTAAATTATTGTGCATTTCACTACTGGAACTGTAATCAGAAAAGATAGACATGCTTAGCCAATCTCTATTTGATTGAATTGAAAGATGTTTGTTa                        >  1:17731‑M2/41‑149 (MQ=255)                                                                                                 tattattaattccactgcctttggtagaggaaagtgctaaATAATAATCAATTGTTAAATTATTGTGCATTTCACTACTGGAACTGTAATCAGAAAAGATAGACATGCTTAGCCAATCTCTATTTGATTGAATTGAAAGATGTTTGTTa                        >  1:17703‑M2/41‑149 (MQ=255)                                                                                                        aattcccctggctttggtagaggaaagtgctaaATAATAGTCAATTGTTAAATTATTGTGCATTGCGATATTGGGAGTGTAATCAGAAAAGATAGATATGCTTAGCAAATCTCTATTTGATTGAATTGAAAGATGTTTGTTAAGGAATg                 >  2:38532‑M2/34‑149 (MQ=255)                                                                                                           tccactgcttttggtagaggaaagtgctaaATAATAATCAATTGTTAAATTATTGTGCATTTCACTACTGGAACTGTAATCAGAAAAGATAGACATGCTTAGCCAATCTCTATTTGATTGAATTGAAAGATGTTTGTTAAGGCATGGAt              <  2:17703‑M2/119‑1 (MQ=255)                                                                                                           tccactgcctttggtagaggaaagtgctaaATAATAATCAATTGTTAAATTATTGTGCATTTCACTACTGGAACTGTAATCAGAAAAGATAGACATGCTTAGCCAATCTCTATTTGATTGAATTGATAGATGTTTGTTAAGGCATGGAt              <  2:17731‑M2/119‑1 (MQ=255)                                                                                                            ccactgcctttggtagaggaaagtgctaaATAATAATCAATTGTTAAATTATTGTGCATTTCACTACTGGAACTGTAATCAGAAAAGATAGACATGCTTTGCCAATCACTACTAGATTTAATTGAAGGATGTTTGTTAAGGCATGTATg             >  2:214436‑M2/30‑149 (MQ=255)                                                                                                                       ggtagaggaaagtgctaaATAATAATCAATTGTTAAATTATTGTGCATTTCACTACTGGAACTGTAATCAGAAAAGATAGACATGCTTAGCCAATCTCTATTTGATTGAATTGAAAGATGTTTGTTAAGGCATGGATGCAAGCTATAGa  <  2:137441‑M2/131‑1 (MQ=255)                                                                                                                                       aaATAATAATCAATTGTTAAATTATTGTGCATTTCACTACTGGAACTGTAATCAGAAAAGATAGACATGCTTAGCCAATCTCTATTTGATTGAATTGAAAGATGTTTGTTAAGGCatggtt              <  2:32946‑M2/119‑3 (MQ=255)                                                                                                                                       aaATAATAATCAATTGTTAAATTATTGTGCATTTCACTACTGGAACTGTAATCAGAAAAGATAGACATGCTTAGCCAATCTCTATTTGATTGAATTGAAAGATGTTTGTTAAGGCATGGAt              >  1:32946‑M2/3‑121 (MQ=255)                                                                                                                                         |                                                                                                                                   GCCTTAAATGGCGAAGAAACGGTCTAAATAGGCTGATTCAAGGCATTTACGGGAGAAAAAATCGGCTCAAACATGAAGAAATGAAATGACTGAGTCAGCCGAGAAGAATTTCCCCGCTTATTCGCACCTTCCCTAAATAATAATCAATTGTTAAATTATTGTGCATTTCACTACTGGAACTGTAATCAGAAAAGATAGACATGCTTAGCCAATCTCTATTTGATTGAATTGAAAGATGTTTGTTAAGGCATGGATGCAAGCTATAGA  >  NC_000913_3_vch_pgi/1300562‑1300828

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: ‑