Predicted mutation
evidence	seq id	position	mutation	annotation	gene	description
MC JC	NC_000913_3_pae_tpiA	1,978,503	Δ776 bp		insB1–insA	insB1, insA

Missing coverage evidence...
			seq id	start	end	size	←reads	reads→	gene	description
*	*	÷	NC_000913_3_pae_tpiA	1978503	1979278	776	42 [0]	[0] 43	insB1–insA	insB1,insA

New junction evidence
		seq id	position	reads (cov)	reads (cov)	score	skew	freq	annotation	gene	product
*	?	NC_000913_3_pae_tpiA	= 1978502	0 (0.000)	41 (0.820)	40/268	0.3	100%	intergenic (‑305/+16)	flhD/insB1	flagellar class II regulon transcriptional activator, with FlhC/IS1 transposase B
	?	NC_000913_3_pae_tpiA	1979279 =	0 (0.000)					intergenic (‑64/‑474)	insA/uspC	IS1 repressor TnpA/universal stress protein

GAAATGGGTCTTTACACTTATCTAAGATTTTTCCTAAATCGACGCAACTGTACTCGTCACTACACGCACATACAACGGAGGGGGGCTGCGATTTTCAATAATGC‑GTGATGCAGATCACACAAAACACTCAATTACTTAACATAAATGGGTAATGACTCCAACTTATTGATAGTGTTTTATGTTCAGATAATGCCCGATGACTTTGTCATGCAGCTCCACCGATTTTGAGAACGACAGCGACTTCCGTCCCAGCCGTGCCAGGTGCTGCCTCAGATTCAGGTTATGCCG  >  NC_000913_3_pae_tpiA/1978356‑1978643                                                                                                                                                    |                                                                                                                                              gAAATGGGTCTTTACACTTATCTAAGATTTTTCCTAAATCGACGCAACTGTACTCGTCACTACACGCACATACAACGGAGGGGGCCTGCCA‑CTACACACATCCGGTGATGCAGATCACACAAAACACTCAATTACTTAACATAAATGta                                                                                                                                             <  2:478545‑M1/149‑3 (MQ=255)  aaaTGGGTCTTTACACTTATCTAAGATTTTTCCTAAATCGACGCAACTGTACTCGTCACTACACGCACATACAACGGAGGGGGGCTGCGATTTTCAATAATGC‑GTGATGCAGATCACACAAAACACTCAATTACTTAACATAAATGtat                                                                                                                                            <  2:913293‑M1/149‑4 (MQ=255)                     tCTAAGATTTTTCCTAAATCGACGCAACTGTACTCGACACTACACGCACATACAACGGAGGGGGGCTGCGATTTTCAATAATGC‑GTGATGCAGATCACACAAAACACTCAATTACTTAACATAAATGtataagtcatacttttgttttg                                                                                                                         <  1:494570‑M1/149‑23 (MQ=255)                      cTAAGATTTTTCCTAAATCGACGCAACTGTACTCGTCACTACACGCACATACAACGGAGGGGGGCTGCGATTTTCAATAATGC‑GTGATGCAGATCACACAAAACACTCAATTACTTAACATAAATGtataagtcatacttttgttttgg                                                                                                                        <  2:481304‑M1/149‑24 (MQ=255)                                tCCTAAATCGACGCAACTGTTCTCGTCACTACACGCACATACAACGGAGGGGGGCTGCGAGTTTCAATAATGC‑GTGATGCAGATTTCACAAAACACTTAATTACTTAACATAAATGtataagtcatacttttgttttgggtgtatttca                                                                                                              <  2:53563‑M1/149‑34 (MQ=255)                                  cTAAATCGACGCAACTGTACTCGTCACTACACGCACATACAACGGAGGGGGGCTGCGATTTTCAATAATGC‑GTGATGCAGATCACACAAAACACTCAATTACTTAACATAAATGtataagtcatacttttgttttgggtgtttttcaat                                                                                                            >  2:531234‑M1/1‑114 (MQ=255)                                   tAAATCGACGCAACTGTACTCGTCACTACACGCACATACAACGGAGGGGGGCTGCGATTTTCAATAATGC‑GTGATGCAGATCACACAAAACACTCAATTACTTAACATAAATGtatcagtcatacttttgttttgggtgtatttcaatc                                                                                                           >  1:752636‑M1/1‑113 (MQ=255)                                     aaTCGACGCAACTGTACTCGTCACTACACGCACATACAACGGAGGGGGGCTGCGATTTTCAATAATGC‑GTGATGCAGATCACACAAAACACTCAATTACTTAACATAAATGtataagtcatacttttgttttgggtgtatttaaatgtg                                                                                                         >  2:191609‑M1/1‑111 (MQ=255)                                      accgaCGGAACTGTACTCGGCACTACACGCACATACAACGGAGGGGGGCTGCGATTTTCAATAATGC‑GTGATGCAGAGCACACAAAACACTCAATTACTTAACATAAATGtataagtcatacttttgttttgggtgtatttcaatctgt                                                                                                        <  1:211361‑M1/147‑40 (MQ=255)                                       tCGACGCAACTGTACTCGTCACTACACGCACATACAACGGAGGGGGGCTGCGATTTTCAATAATGC‑GTGATGCAGATCACACAAAACACTCAATTACTTAACATAAATGta                                                                                                                                             >  2:508490‑M1/1‑109 (MQ=255)                                       tCGACGCAACTGTACTCGTCACTACACGCACATACAACGGAGGGGGGCTGCGATTTTCAATAATGC‑GTGATGCAGATCACACAAAACACTCAATTACTTAACATAAATGta                                                                                                                                             <  1:508490‑M1/111‑3 (MQ=255)                                          aCGCAACTGTACTCGTCACTACACGCACATACAACGGAGGGGGGCTGCGATTTTCAATAATGC‑GTGATGCAGATCACACAAAACACTCAATTACTTAACATAAATGtataagtcatacttttgttttgggtgtatttcaa                                                                                                             <  1:554666‑M1/140‑35 (MQ=255)                                          aCGCAACTGTACTCGTCACTACACGCACATACAACGGAGGGGGGCTGCGATTTTCAATAATGC‑GTGATGCAGATCACACAAAACACTCAATTACTTAACATAAATGtataagtcatacttttgttttgggtgtatttcaa                                                                                                             >  2:554666‑M1/1‑106 (MQ=255)                                            gCAACTGTACTCGTCACTACACGCACATACAACGGAGGGGGGCTGCGATTTTCAATAATGC‑GTGATGCAGATCACACAAAACACTCAATTACTTAACATAAATGtataagtcatacttttgttttgggtgtatttcaatctgttaaaaa                                                                                                  <  1:484839‑M1/149‑46 (MQ=255)                                               aCTGTACTCGTCACTACACGCACATACAACGGAGGGGGGCTGCGATTTTCAATAATGC‑GTGATGCAGATCACACAAAACACTCAATTACTTAACATAAATGtataagtcatacttttgttttgggtgtatttcaatctgttaaaaagtt                                                                                               <  2:242293‑M1/149‑49 (MQ=255)                                                 tGTACTCGTCACTACACGCACATACAACGGAGGGGGGCTGCGATTTTCAATAATGC‑GTGATGCAGATCACCCAAAACACTCAATTACTTAACATAAATGtataagtcatacttttgtcttgggtgtatttcacactgttaccaagtttt                                                                                             >  2:913987‑M1/1‑99 (MQ=255)                                                      tCGTCACTACACGCACATACAACGGAGGGGGGCTGCGATTTTCAATAATGC‑GTGATGCAGATCACACAAAACACTCAATTACTTAACATAAATGtataagtcatacttttgttttgggtgtatttcaatctgttaaaaagtttttcgct                                                                                        >  1:505047‑M1/1‑94 (MQ=255)                                                            cTACACGCACATACAACGGAGGGGGGCTGCGATTTTCAATAATGC‑GTGATGCAGATCACACAAAAAACTCAATTACTTAACATAAATGtataagtcatacttttgttttgggtgtatttcaatctgttaaacagtttttcgctgcgcta                                                                                  >  2:872724‑M1/1‑88 (MQ=255)                                                              acacGCACATACAACGGAGGGGGGCTGCGATTTTCAATAATGC‑GTGATGCAGATCACACAAAACACTCAATTACTTAACATAAATGtataagtcatacttttgttttgggtgtatttcaatctgttaaaaagtttttcgctacgctagc                                                                                <  1:460844‑M1/149‑64 (MQ=255)                                                                    acaTACAACGGAGGGGGGCTGCGATTTTCAATAATGC‑GTGATGCAGATCACACAAAACACTCAATTACTTAACATGAATGtataagtcatacttttgttttgggtgtatttcaatctgttaaaaagtttttcgctacgctagcaagcaa                                                                          <  1:273434‑M1/149‑70 (MQ=255)                                                                       tACAACGGAGGGGGGCTGCGATTTTCAATAATGC‑GTGATGCAGATCACACAAAACACTCAATTACTTAACATAAATGtataagtcatacttttgttttgggtgtatttcaatctgttaaaaagtttttcgctacgctagcaagcaaaac                                                                       >  2:372775‑M1/1‑77 (MQ=255)                                                                       tACAACGGAGGGGGGCTGCGATTTTCAATAATGC‑GTGATGCAGATCACACAAAACACTCAATTACTTAACATAAATGtataagtcatacttttgttttgggtgtatttcaatctgttaaaaagtttttcgctacgctagcaagcaaaaa                                                                       <  2:102310‑M1/149‑73 (MQ=255)                                                                          aaCGGAGGGGGGCTGCGATTTTCAATAATGC‑GTGATGCAGATCACACAAAACACTCAATTACTTAACATAAATGtataagtcatacttttgttttgggtgtatttcaatctgttaaaaagtttttcgctacgctagcaagcaaaaagga                                                                    >  1:191099‑M1/1‑74 (MQ=255)                                                                          aaCGGAGGGGGGCTGCGATTTTCAATAATGC‑GTGATGCAGATCACACAAAACACTCAATTACTTAACATAAATGtataagtcatactgtggttttgggtgtatttcaatctgttaaaaagtttttcgctacgctagcaagcaaaaatga                                                                    <  1:179675‑M1/149‑76 (MQ=255)                                                                            cGGAGGGGGGCTGCGATTTTCAATAATGC‑GTGATGCAGATCACACAAAACACTCAATTACTTAACATAAATGtataagtcatacttttgttttgggtgtatttcaatctgttaaaaagtttttcgctacgctagcaagcaaaaatgaaa                                                                  <  2:809037‑M1/149‑78 (MQ=255)                                                                                 gggggCTGCGATTTTCAATAATGC‑GTGATGCAGATCACACAAAACACTCAATTACTTAACATAAATGtataagtcatacttttgttttgggtgtatttcaatctgttaaaaagtttttcgctacgctagcaagcaaaaatcgaacagga                                                             >  2:369490‑M1/1‑67 (MQ=255)                                                                                  ggggCTGCGATTTTCAATAATGC‑GTGATGCAGATCACACAAAACACTCAATTACTTAACATAAATGtataagtcatacttttgttttgggtgtatttcaatctgttaaaaagttttttgttatttttgcaagaaaaaatgaaacaggat                                                            >  2:563392‑M1/1‑66 (MQ=255)                                                                                       tGCGATTTTCAATAATGC‑GTGATGCAGATCACACAAAACACTCAATTACTTAACATAAATGtataagtcatacttttgttttgggtgtatttcaatctgttaaaaagtttttcgctacgctagcaagcaaaaatgaaacagggataatc                                                       >  2:477776‑M1/1‑61 (MQ=255)                                                                                                 aataatGC‑GTGATGCAGATCACACAAAACACTCAATTACTTAACATAAATGtataagtcatacttttgttttgggtgtatttcaatctgttaaaaagtttttcgctacgctagcaagcaaaaatgaaacaggaataatcgaaatgggat                                             >  1:573912‑M1/1‑51 (MQ=255)                                                                                                    aatGC‑GTGATGCAGATCACACAAAACACTCAATTACTTAACATAAATGtataagtcatacttttgttttgggtgtatttcaatctgttaaaaagtttttcgctacgctagcaagcaaaaatgaaacaggaataatcgaaatgggatgtt                                          <  2:661022‑M1/149‑102 (MQ=255)                                                                                                      tGC‑GTGATGCAGATCACACAAAACACTCAATTAATTAACATAAATGtataagtcatacttttgttttgggtgtatttcaatctgttaaaaagtttttcgctacgctagcaagcaaaaatgaaacaggaataatcgaaatgggatgttgc                                        <  1:729132‑M1/149‑104 (MQ=255)                                                                                                                   aTCACACAAAACACTCAATTACTTAACATAAATGtataagtcatacttttgttttgggtgtatttcaatctgttaaaaagtttttcgctacgctagcaagcaaaaatgaaacaggaataatcgaaatgggatgttacgcacagtcaaaa                            >  1:87898‑M1/1‑34 (MQ=255)                                                                                                                      acacaAAACACTCAATTACTTAACATAAATGtataagtcatacttttgttttgggtgtatttcaatctgttaaaaattttttcgctacgcgcgccagcaaaaatgaaacaggaatgatcgaaatgggatgttgcccacagtcaaaataa                         <  2:376711‑M1/149‑119 (MQ=255)                                                                                                                        acaAAACACTCAATTACTTAACATAAATGtataagttatacttttgttttgggtgtatttcaatctgttaaaaagtttttcgctacgctagcaagcaaaaatgaaacaggaataatcgaaatgggatgttgcgcacagtcaaaataact                       >  2:596850‑M1/1‑29 (MQ=255)                                                                                                                            atcacgtaattacttaACATAAATGtataagtcatacttttgttttccatcttcttcaatctgttaaatagtttttcgctacgatcgcaagcaaaaatgaaacaggaataatcgaaatgggatgttgcgtacagtcaaaataactcacc                   <  2:53963‑M1/142‑125 (MQ=255)                                                                                                                             accatcaatTACTTAACATAAATGtataagtcatacttttgttttgggtgtatttcaatctgttaaaaagtttttcgctacgctagcaagcaaaaatgaaacaggaataatcgaaatgggatgttgcgcacagtcaaaataactcaccg                  <  2:505047‑M1/145‑126 (MQ=255)                                                                                                                                      cgcttAACACAAATGtacaagtcatacttttgttttgggtgtatttcaatctgttaaaaagggtttcgcgacgctagcaagcaaaaatgaaacaggaataatcgaaatgggatgttgcgcacagtcaaaataactcaccgtaaataatc         <  2:421632‑M1/147‑135 (MQ=255)                                                                                                                                        cggaacatAAATGtataagtcatacttttgttttgggtgtatttcaatctgttaaaaagtttttcgctacgctagcaagcaaaaatgaaacaggaataatcgaaatgggatgttgcgcacagtcaaaataactcaccgtaaataatcat       <  2:725534‑M1/146‑137 (MQ=255)                                                                                                                                        cTTAACATAAATGtataagtcatacttttgttttgggtgtatttcaatctgttaaaaagtttttcgctacgctagcaagcaaaaatgaaacaggaataatcgaaatgggatgttgcgcacagtcaaaataactcaccgtaaataatcat       >  1:839834‑M1/1‑13 (MQ=255)                                                                                                                                         ttAACATAAATGtataagtcatacttttgttttgggtgtatttcaatctgttaaaaagtttttcgctacgctagcaagcaaaaatgaaacaggaataatcgaaatgggatgttgcgcacagtcaaaat                           <  1:88645‑M1/128‑117 (MQ=255)                                                                                                                                         ttAACATAAATGtataagtcatacttttgttttgggtgtatttcaatctgttaaaaagtttttcgctacgctagcaagcaaaaatgaaacaggaataatcgaaatgggatgttgcgcacagtcaaaat                           >  2:88645‑M1/1‑12 (MQ=255)                                                                                                                                             cATAAATGtataagtcatacttttgttttgggtgtatttcaatctgttaaaaagtttttcgctacgctagcaagcaaaaatgaaacaggaataatcgaaattggatgttgcgcacagtcaaattaactcaccttaaatattcatcttct  >  2:420452‑M1/1‑8 (MQ=255)                                                                                                                                                    |                                                                                                                                              GAAATGGGTCTTTACACTTATCTAAGATTTTTCCTAAATCGACGCAACTGTACTCGTCACTACACGCACATACAACGGAGGGGGGCTGCGATTTTCAATAATGC‑GTGATGCAGATCACACAAAACACTCAATTACTTAACATAAATGGGTAATGACTCCAACTTATTGATAGTGTTTTATGTTCAGATAATGCCCGATGACTTTGTCATGCAGCTCCACCGATTTTGAGAACGACAGCGACTTCCGTCCCAGCCGTGCCAGGTGCTGCCTCAGATTCAGGTTATGCCG  >  NC_000913_3_pae_tpiA/1978356‑1978643

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: ‑