Predicted mutation
evidence	seq id	position	mutation	annotation	gene	description
MC JC	NC_000913_3_pae_pgi	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_pgi	1978503	1979278	776	43 [0]	[1] 44	insB1–insA	insB1,insA

New junction evidence
		seq id	position	reads (cov)	reads (cov)	score	skew	freq	annotation	gene	product
*	?	NC_000913_3_pae_pgi	= 1978502	0 (0.000)	41 (0.980)	34/262	0.3	100%	intergenic (‑305/+16)	flhD/insB1	flagellar class II regulon transcriptional activator, with FlhC/IS1 transposase B
	?	NC_000913_3_pae_pgi	1979279 =	0 (0.000)					intergenic (‑64/‑474)	insA/uspC	IS1 repressor TnpA/universal stress protein

GTCTTTACACTTATCTAAGATTTTTCCTAAATCGACGCAACTGTACTCGTCACTACACGCACATACAACGGAGGGGGGCTGCGATTTTCAATAATGCGTGATGCAGATCACACAAAACACTCAATTACTTAACATAAATGGGTAATGACTCCAACTTATTGATAGTGTTTTATGTTCAGATAATGCCCGATGACTTTGTCATGCAGCTCCACCGATTTTGAGAACGACAGCGACTTCCGTCCCAGCCGTGCCAGGTGCTGCCTCAGATTCAGGTTATGCCGC  >  NC_000913_3_pae_pgi/1978363‑1978644                                                                                                                                            |                                                                                                                                               gTCTTTACACTTATCTAAGATTTTTCCTAAATCGACGCAACTGTACTCGTCACTACACGCACATACAACGGAGGGGGGCTGCGATTTTCAATAATGCGTGATGCAGATCACACAAAACACTCAATTACTTAACATAAATGtataagtca                                                                                                                                       >  2:192363‑M1/1‑140 (MQ=255)    tttACACTTATCTAAGATTTTTCCTAAATCGACGCAACTGTACTCGTCACTACACGCACATACAACGGAGGGGGGCTGCGATTTTCAATAATGCGTGATGCAGATCACACAAAACACTCAATTACTTAACATAAATGtataagtcatac                                                                                                                                    <  1:121354‑M1/149‑13 (MQ=255)        cacTTATCTAAGATTTTTCCTAAATCGACGCAACTGTACTCGTCACTACACGCACATACAACGGAGGGGGGCTGCGATTTTCAATAATGCGTGATGCAGATCACACAAAACACTCAATTACTTAACATAAATGtataagtcatactttt                                                                                                                                <  1:347302‑M1/149‑17 (MQ=255)        cacTTATCTAAGATTTTTCCTAAATCGACGCAACGGTACTCGTCACTACACGCACCTACAACGTAGGGGGGCTGCGATTTTCAATAATGCGTGATGCAGATCACACAAAACACTCAATTACTTAACATAAATGtataagtcatactttt                                                                                                                                <  1:699290‑M1/149‑17 (MQ=255)         acTTATCTAAGATTTTTCCTAAATCGACGCAACTGTGCTCGTCACTACACGCACATACAACGGAGGGGGGCTGCGATTTTCAATAATGCGTGATGCAGATCACACAAAAAACTCAATTACTTAACATAAATGtataagtcatacttttg                                                                                                                               >  1:416234‑M1/1‑132 (MQ=255)          cgatcaaaagagttttAATAAATCGACGCACCTGAACTCGACACAACACGCAGATACAACGGAGGGGGGCTGCGATTTTCAATAATGCGTGATGCAGATCACACAAAACACTCAATTACTTAACATAAATGtataagtcatacttttgt                                                                                                                              <  2:82891‑M1/142‑19 (MQ=255)               cTAAGATTTTTCCTAAATCGACGCAACTGTACTCGTCACTACACGCACATACAACGGAGGGGGGCTGCGATTTTCAATAATGCGTGATGCAGATCACACAAAACACTCAATTACTTAACATAAATGtataagtcatacttttgttttgg                                                                                                                         <  2:578108‑M1/149‑24 (MQ=255)                tAAGATTTTTCCTAAATCGACGCAACTGTACTCGTCACTACACACACATACAACGGAGGGGGGCTGCGATTTTCAATAATGCGTGATGCAGATCACACAAAACACTCAATTACTTAACATAAATGtataagtcatacttttgttttggg                                                                                                                        <  1:541047‑M1/149‑25 (MQ=255)                caagCTTTTACCTAAATCGACGCAACTGTGCTCGTCACTACACGCACATACAACGGAGGGGGGCTGCGATTTTCAATAATGCGTGATGCAGATCACACAAAACACTCAATTACTTAACATAAATGtataagtcatacttttgttttggg                                                                                                                        <  2:416234‑M1/148‑25 (MQ=255)                           ttaAATCGACGCAACTGTACTCGTTACTACACGCACATACAACGGAGGGGGGCTGCGATTTTCAATAATGCGTGATGCAGATCACACAAAACACTCAATTACTTAACATAAATGtataagtcatacttttgttttgggtgtatttcaat                                                                                                             <  1:182410‑M1/148‑36 (MQ=255)                             aaaTCGACGCAACTGTACTCGTCACTACACGCACATACAACGGAGGGGGGCTGCGATTTTCAATAATGCGTGATGCAGATCACACAAAACACTCAATTACTTAACATAAATGtataagtcatacttttgttttgggtgtatttcaatct                                                                                                           >  2:670805‑M1/1‑112 (MQ=255)                                     gCAACTGGACTCGTCACTACACGCACATACAACGGAGGGGGGCTGCGATTTTCAATAATGCGTGATGCAGATCACACAAAACACTCAATTACTTAACATAAATGtataagtcatacttttgttttgggtgtatttcaatctgttaaaaa                                                                                                   <  1:159249‑M1/149‑46 (MQ=255)                                       aaCTGTACTCGTCACTACACGCACATACAACGGAGGGGGGCTGCGATTTTCAATAATGCGTGATGCAGATCACACAAAACACTCAATTACTTAACATAAATGtataagtcatacttttgttttgggtgtatttcaatctgttaaaaagt                                                                                                 >  1:316125‑M1/1‑102 (MQ=255)                                            cacTCGTCACTACACGCAGATACAACGGAGGGGGGCTGCGATTTTCAATAATGCGTGATGCAGATCACATAAAACACTAAATTACTTAACATAAATGtataagtcatacttttgttttgggtgtatttcaatctgttaaaaagtttttc                                                                                            <  2:84598‑M1/148‑53 (MQ=255)                                             aCTCGTCACTACACGCACATACAACGGAGGGGGGCTGCGATTTTCAATAATGCGTGATGCAGATCACACAAAACACTCAATTACTTAACATAAATGtataagtcatacttttgttttgggtgtatttcaatctgttaaaaagtttttcg                                                                                           >  1:475006‑M1/1‑96 (MQ=255)                                                     cTACACGCACATACAACGGAGGGGGGCTGCGATTTTCAATAATGCGTGATGCAGATCACACAAAACACTCAATTACTTAACATAAATGtataagtcatacttttgttttgggtgtatttcaatctgttaaaaagtttttcgctacgcta                                                                                   <  1:670805‑M1/149‑62 (MQ=255)                                                         acGTACATACAACGGAGGGGGGCTGCGATTTTCAATAATGCGTGATGCAGATCACACAAAACACTCAATTACTTAACATAAATGtataagtcatacttttgttttgggtgtatttcaatctgttaaaaagtttttcgctacgctagcaa                                                                               <  2:737891‑M1/149‑66 (MQ=255)                                                         acGCACATACAACGGAGGGGGGCTGCGATTTTCAATAATGCGTGATGCAGATCACACAAAACACTCAATTACTTAACATAAATGtataagtcatacttttgttttgggtgtatttcaatctgttaaaaagtttttcgctacgctagcaa                                                                               >  2:728857‑M1/1‑84 (MQ=255)                                                               aTACAACGGAGGGGGGCTGCGATTTTCAATAATGCGTGATGCAGATCACACAAAACACTCAATTACTTAACATCAATGtataagtcatacttttgttttgggtgtatttcaatctgttaaaaagtttttcgctacgctagaaagcaaaa                                                                         >  1:675107‑M1/1‑78 (MQ=255)                                                               aTACAACGGAGGGGGGCTGCGATTTTCAATAATGCGTGATGCAGATCACACAAAACACTCAATTACTTAACATCAATGtataagtcatacatttgttttgggtgtatttcaatctgttaaaaagtttttcgctccgctcgcaagccaca                                                                         >  2:379615‑M1/1‑78 (MQ=255)                                                               aTACAACGGAGGGGGGCTGCGATTTTCAATAATGCGTGATGCAGATCACACAAAACACTCAATTACTTAACATAAATGtataagtcatacttttgttttgggtgtatttcaatctgttaaaaagtttttcgctacgctagcaggcaaaa                                                                         >  1:70088‑M1/1‑78 (MQ=255)                                                               aTACAACGGAGGGGGGCTGCGATTTTCAATAATGCGTGATGCAGATCACACAAAACACTCAATTACTTAACATAAATGtataagtcatacttttgttttgggtgtatttcaatctgttaaaaagtttttcgctacgctagcaagcaaaa                                                                         >  1:280898‑M1/1‑78 (MQ=255)                                                                       gAGGGGGGCTGCGATTTTCAATAATGCGTGATGCAGATCACACAAAACACTCAATTACTTAACATAAATGtataagtcatacttttgttttgggtgtatttcaatctgttaaaaagtttttcgctacgctagcaagcaaaaatgaaaca                                                                 <  1:504380‑M1/149‑80 (MQ=255)                                                                         ggggggCTGCGATTTTCAATAATGCGTGATGCAGATCACACAAAACACTCAATTACTTAACATAAATGtataagtcatacttttgttttgggtgtatttcaatctgttaaaaagtttttcgctacgctagcaagcaaaaatgaaacagg                                                               <  1:670210‑M1/149‑82 (MQ=255)                                                                          gggggATGCGATTTTCAATAATGCGTGATGCAGATCACACAAAACACTCAATTACTTAACATAAATGtataagtcatacttttgttttgggtgtatttcaatctgttaaaaagtttttcgctacgctagcaagcaaaaatgaaacagga                                                              <  1:168022‑M1/149‑83 (MQ=255)                                                                                tGCGATTTTCAATAATACGTGATGCAGATCACACAAAACACTCAATTACTTAACATAGATGtataagtcatacttttgttttgggtgtatttcaatctgttaaaaagtttttcgctacgctagcaagcaaaaatgaaacaggaataatc                                                        >  1:685519‑M1/1‑61 (MQ=255)                                                                                 gCGATTTTCAATAATGCGTGATGCAGATCACACAAAACACTCAATTACTTAACATAAATGtataagtcatacttttgttttgggtgtatttcaatctg                                                                                                          <  2:706702‑M1/98‑39 (MQ=255)                                                                                 gCGATTTTCAATAATGCGTGATGCAGATCACACAAAACACTCAATTACTTAACATAAATGtataagtcatacttttgttttgggtgtatttcaatctg                                                                                                          >  1:706702‑M1/1‑60 (MQ=255)                                                                                         cAATAATGCGTGATGCAGATCACACAAAACACTCAATTACTTAACATAAATGtataagttatacttttgttttgggtgtatttcaatctgttaaaaagtttttcgctacgctagcaagcaaagatgaaaaaggaatagtcgaaaggggc                                               >  1:135564‑M1/1‑52 (MQ=255)                                                                                         aaataattCGTGGTGCAGATTACACAAAACACTTAATTACTTAACATAAATGtataagtcatacttttgttttgggtgtatttcaatctgttaaaaagtttttcgctacgctagcaagcaaaaatgaaacaggcataatcgaaatggga                                               <  2:608404‑M1/148‑98 (MQ=255)                                                                                                  gTGATGCAGATCACACAAAACACTCAATTACTTAACATAAATGtataagtcatacttttgttttgggtgtatttcaatctgttaaaaagtttttcgc                                                                                          >  2:673142‑M1/1‑43 (MQ=255)                                                                                                  gTGATGCAGATCACACAAAACACTCAATTACTTAACATAAATGtataagtcatacttttgttttgggtgtatttcaatctgttaaaaagtttttcgc                                                                                          <  1:673142‑M1/97‑55 (MQ=255)                                                                                                      tGCAGATCACACAAAACACTCAATTACTTAACATAAATGtataagtcatacttttgttttgggtgtatttcaatctgttaaaaagtttttcgctacgctagcaagcaaaaatgaaacaggaataatcgaaatgggatgttgcgcacagt                                  >  1:11848‑M1/1‑39 (MQ=255)                                                                                                           acccaggaaagcactcaaTTACTTAACATAAATGtataagtcatacttttgttttgggtgtatttcaatctgttaaaaagtttttcgctacgctagcaagcaaaaatgaaacaggaataatcgaaatgggatgttgcgcacagtcaaaa                             >  2:7916‑M1/8‑34 (MQ=255)                                                                                                              acacaAAACACTCAATTACTTAAGATAAATGtataagtcatacttttgttttgggtgtatttcaatctgttaaaaagtttttcgctacgctagcaagcaaaaatgaaacaggaataatcgaaatgggatgttgcgcacagtcaaaataa                          <  2:785576‑M1/149‑119 (MQ=255)                                                                                                              acacaAAACACTCAATTACTTAACATAAATGtataagtcatacttttgttttgggtgtatttcaatctgttaaaaagtttttcgctacgctagcaagcaaaaatgaaacaggaataatcgaaatgggatgttgcgcacagtcaaaataa                          >  2:67813‑M1/1‑31 (MQ=255)                                                                                                                acaAAACACTCAATTACTTAACATAAATGtataagtcatacttttgttttgggtgtatttcaatctgttaaaaagtttttcgctacgctagcaagcaaaattgaaataggaataatcgaaatgggatgttgcgcacagtcagaataact                        >  1:440787‑M1/1‑29 (MQ=255)                                                                                                                    aaCGCTGAATTATTTAACATAAATGtataagtcatacttttgttttgggtgtatttcaatcttttaaaaagtttttcgctacgctagcaagcaaaaatgaaacaggaataatcgaaatgggatgttgcgcacagtcaaaataactcacc                    <  1:319291‑M1/149‑125 (MQ=255)                                                                                                                    aaCACTCAATTACTTAACATAAATGtataagtcatacttttgttttgggtgtatttcaatctgttaaaaagtttttcgctacgctagcaagcaaaaatgaaacaggaataatcgaaatgggatgttgcgcacagtcaaaataactcacc                    <  2:316125‑M1/149‑125 (MQ=255)                                                                                                                                cTTAACATAAATGtataagtcatacttttgttttgggtgtatttcaatctgttaaaaagtttttcgctacgctcgcaagcaaaaatgaaacaggaataatcgaaatgggatgttgcgcacagtcaaaataactcaccgtaaataatcat        >  2:371998‑M1/1‑13 (MQ=255)                                                                                                                                    aCATAAATGtataagtcatacttttgttttgggtgtatttcaatctgttaaaaagtttttcgctacgctagcaagcaaaaatgaaacaggaataatcgaaatgggatgttgcgcacagtcaaaataactcaccgtaaataatcatctgc    <  1:192363‑M1/149‑141 (MQ=255)                                                                                                                                      aTAAATGtataagtcatacttttgttttgggtgtatttcaatctgttaaaaagtttttcgctacgctagcaagcaaaaatggaacaggaataatcgaaatgggatgttgcgcacagtcaaaataactcaccgtaaataatcatctgcta  >  2:87241‑M1/1‑7 (MQ=255)                                                                                                                                      aTAAATGtataagtcatacttttgttttgggtgtatttcaatctgttaaaaagtttttcgctacgctagcaagcaaaaatgaaacaggaataatcgaaatgggatgttgcgcacagtcaaaataactcaccgtaaataatcatctgcag  >  1:754963‑M1/1‑7 (MQ=255)                                                                                                                                            |                                                                                                                                               GTCTTTACACTTATCTAAGATTTTTCCTAAATCGACGCAACTGTACTCGTCACTACACGCACATACAACGGAGGGGGGCTGCGATTTTCAATAATGCGTGATGCAGATCACACAAAACACTCAATTACTTAACATAAATGGGTAATGACTCCAACTTATTGATAGTGTTTTATGTTCAGATAATGCCCGATGACTTTGTCATGCAGCTCCACCGATTTTGAGAACGACAGCGACTTCCGTCCCAGCCGTGCCAGGTGCTGCCTCAGATTCAGGTTATGCCGC  >  NC_000913_3_pae_pgi/1978363‑1978644

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: ‑