Predicted mutation
evidence	seq id	position	mutation	freq	annotation	gene	description
MC JC	NC_000913_3_pae_tpiA	1,978,503	Δ776 bp	100%		insB1–insA	insB1, insA

Missing coverage evidence...
			seq id	start	end	size	←reads	reads→	gene	description
*	*	÷	NC_000913_3_pae_tpiA	1978503	1979278	776	50 [0]	[0] 51	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)	47 (0.960)	34/256	NT	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

GAAATGGGTCTTTACACTTATCTAAGATTTTTCCTAAATCGACGCAACTGTACTCGTCACTACACGCACATACAACGGAGGGGGGCTGCGATTTTCAATAATGCGTGATGCAGATCACACAAAACACTCAATTACTTAACATAAATGGGTAATGACTCCAACTTATTGATAGTGTTTTATGTTCAGATAATGCCCGATGACTTTGTCATGCAGCTCCACCGATTTTGAGAACGACAGCGACTTCCGTCCCAGCCGTGCCAGGTGCTGCCTCAGATTCAGGTTATGCCGCTCAAT  >  NC_000913_3_pae_tpiA/1978356‑1978649                                                                                                                                                   |                                                                                                                                                    gAAATGGGTCTTTACACTTATCTAAGATTTTTCCTAAATCGACGCAACTGTACTCGTCACTACACGCACATACAACGGAGGGGGGCTGCGATTTTCAATAATGCGTGATGCAGATCACACAAAACACTCAATTACTTAACATAAATGta                                                                                                                                                   <  1:826506‑M1/149‑3 (MQ=255)       ggTCTTTACACTTATCTAAGATTTTTCCTAAATCGACGCAACTGTACTCGTCACTACACGCACATACAACGGAGGGGGGCTGCGATTTTCAATAATGCGTGATGCAGATCACACAAAACACTCAATTACTTAACATAAATGtataagtc                                                                                                                                             >  1:814633‑M1/1‑141 (MQ=255)       ggTCTTTACACTTATCTAAGATTTTTCCTAAATCGACGCAACTGTACTCGTCACTACACGCACATACAACGGAGGGGGGCTGCGATTTTCAATAATGCGTGATGCAGATCACACAAAACACTCAATTACTTAACATAAATGtataagtc                                                                                                                                             >  1:546923‑M1/1‑141 (MQ=255)            ttACACTTATCTAAGATTTTTCCTAAATCGACGCAACTGTACTCGTCACTACACGCACATACAACGGAGGGGGGCTGCGATTTTCAATAATGCGTGATGCAGATCACACAAAACACTCAATTACTTAACATAAATGtataagtcatact                                                                                                                                        >  1:523131‑M1/1‑136 (MQ=255)            ttACACTTATCTAAGATTTTTCCTAAATCGACGCAACTGTACTCGTCACTACACGCACATACAACGGAGGGGGGCTGCGATTTTCAATAATGCGTGATGCAGATCACACAAAACACTCAATTAATTAACATAAATGtataagcactact                                                                                                                                        >  2:934445‑M1/1‑136 (MQ=255)                gctTATCCAAGATTTTTCCTAAATCGACGCAACTGTACTCGTCACTACACGCACATACAACGGAGGGGGGCTGCGATTTTCAATAATGCGTGATGCAGATCACACAAAACACTCAATTACTTAACATAAATGtataagtcatacttttg                                                                                                                                    <  1:189334‑M1/148‑18 (MQ=255)                acTTATCTAAGATTTTTCCTAAATCGACGCAACTGTACTCGTCACTACACGCACATACAACGGAGGGGGGCTGCGATTTTCAATAATGCGTGATGCAGATCACACAAAACACTCAATTACTTAACATAAATGtataagtcatacttttg                                                                                                                                    >  1:900544‑M1/1‑132 (MQ=255)                acTTATCTAAGATTTTTCCTAAATCGACGCAACTGTACTCGTCACTACACGCACATACAACGGAGGGGGGCCGCGATTTTCAATAATGCGTGATGCAGATCACACAAAACACTCAATTACTTAACATAAATGtataagtcatacgtttg                                                                                                                                    >  2:685018‑M1/1‑132 (MQ=255)                      cTAAGATTTTTCCTAAATCGACGCAACTGTACTCGTCACTACACGCACATACAACGGAGGGGGGCTGCGATTTTCAATAATGCGTGAGCCAGATCACACAAAACACTCAATTACTTAACATAAAGGtataggggatacttgtgttttcg                                                                                                                              >  1:48536‑M1/1‑126 (MQ=255)                      cTAAGATATTTCCTAAATCGACGCAACTGTACTCGTCACTACACGCACATACAACGGAGGGGTGCTGCGATTTTCAATAATGCGTGATGCATATCACACAAAACACTCAATTACTTAACATAAATGtataagtcatacttttgttttgg                                                                                                                              <  2:914684‑M1/149‑24 (MQ=255)                       tAAGATTTTTCCTAAATCGACGCAACTGTACTCGTCACTACACGCACATACAACGGAGGGGGGCTGCGATTTTCAATAATGCGTGATGCAGATCACACAAAACACTCAATTACTTAACATAAATGtataagtcatactttttgtttggg                                                                                                                             >  2:711838‑M1/1‑125 (MQ=255)                              tttCCTAAATCGACGCAACTGTACTCGTCACTACACGCACATACAACGGAGGGGGGCTGCGATTTTCAATAATGCGTGATGCAGATCACACAAAACACTCAATTACTTAACATAAATGtataagtcatacttttgttttgggtgtattt                                                                                                                      >  1:188253‑M1/1‑118 (MQ=255)                                   tAAATCGACGCAACTGTACTCGTCACTACACGCACATACAACGGAGGGGGGCTGCGATTTTCAATAATGCGTGATGCAGATCACACAAAACACTCAATTACTTAACATAAATGtataagtcatacttttgttttgggtgtatttcaatc                                                                                                                 >  1:587189‑M1/1‑113 (MQ=255)                                   tAAATCGACGCAACTGTACTCGTCACTACACGCACATACAACGGAGGGGGGCTGCGATTTTCAATAATGCGTGATGCAGATCACACAAAACACTCAATTACTTAACATAAATGtataagtcatacttttgttttgggtgtatttcaatc                                                                                                                 >  1:775932‑M1/1‑113 (MQ=255)                                      aTCGACGCAACTGTACTCGTCACTACACGCACATACAACGGAGGGGGGCTGCGATTTTAAATACAACGTGAAGCAGAACACACAAGACACTCAATTACTTAACGTAAATGtataaggcatacttttgttttgggtgtatgtaaatattt                                                                                                              >  1:464399‑M1/1‑110 (MQ=255)                                       tCGACGCAACTGTACTCGTCACTACACGCACATACAACGGAGGGGGGCTGCGATTTTCAATAATGCGTAATGCAGATCACACAAAACACTCAATTACTTAACATAAATGgataagtcatacttttgttttgggtgtatttcaatctgtt                                                                                                             >  1:898926‑M1/1‑109 (MQ=255)                                         gACGCAACTGTACTCGTCACTACACGCACATACAACGGAGGGGGGCTGCGATTTTCAATAATGCGTGATGCAGATCACACAAAACACTCAATTACTTCACATAAATGtataagtcatacttttgttttgggtgtatttcaatctgttaa                                                                                                           >  1:597032‑M1/1‑107 (MQ=255)                                              aaCTGTACTCGTCACTACACGCACATACAACGGAGGGGGGCTGCGATTTTCAATAATGCGTGATGCAGATCACACAAAACACTCAATTACTTAACATAAATGtataagtcatacttttgttttgggtgtatttcaatctgttaaaaagt                                                                                                      >  1:471707‑M1/1‑102 (MQ=255)                                               aCTGTACTCGTCACTACACGCACATACAACGGAGGGGGGCTGCGATTTTCAATAATGCGTGATGCAGATCACACAAAACACTCAATTACTTAACATAAATGtataagtcatacttttgttttgggtgtatttcaatctgttaaaaagtt                                                                                                     >  2:599427‑M1/1‑101 (MQ=255)                                                     cTCGTCACTACACGCACATACAACGGAGGGGGGCTGCGATTTTCAATAATGCGTGATGCAGATCACACAAAACACTCAATTACTTAACATAAATGtataagtcatacttttgttttgggtgtatttcaatctgttaaaaagtttttcgc                                                                                               >  1:726571‑M1/1‑95 (MQ=255)                                                         tCACCACACGCACATACAACGGAGTGGGGCTGTGATTTTCAATAATGCGTGATGCAGATCACACAAAACACTCAATTACTTAACATAAATGtataagtcatacttttgttttgggtgtatttcaatctgttaaaaagtttttcgctact                                                                                           <  2:63785‑M1/149‑59 (MQ=255)                                                                     caTACAACGGAGGGGGGCTGCGATTTTCAATAATGCGTGATGCAGATCACACAAAACACTCAATTACTTAACATAAATGtataagtcatacttttgttttgggtgtatttcaatctgttaaaaagtttttcgctacgctagcaagcaaa                                                                               >  2:73135‑M1/1‑79 (MQ=255)                                                                      aTACAACGGAGGGGGGCTGCGATTTTCAATAATGCGTGATGCAGATCACACAAAACACTCAATTACTTAACATAAATGtataagtcatacttttgttttgggtgtatttcaatctgttaaaaagtttttcgctacgctagcaagcaaaa                                                                              >  2:904395‑M1/1‑78 (MQ=255)                                                                            cGGAGGGGGGCTGCGATTTTCAATAATGCGTGATGCAGATCACACAAAACACTCAATTACTTAACATAAATGtataagtcatacttttgttttgggtgtatttcaatctgttaaaaagtttttcgctacgctagcaagcaaaaatgaaa                                                                        <  2:788274‑M1/149‑78 (MQ=255)                                                                            cGGAGGGGGGCTGCGATTTTCAATAATGCGTGATGCAGATCACACAAAACACTCAATTACTTAACATAAATGtataagtcatacttttgttttgggtgtatttcaatctgttaaaaagtttttcgctacgctagcaagcaaaaatgaaa                                                                        <  2:775932‑M1/149‑78 (MQ=255)                                                                            aggaGGGGGGCTGCGATTTTCAATAATGCGTGATGCAGATCACACAAAACTCTCAATTACTTAACATAAATGtataagtcatacttttgttttgggtgtatttcaatctgttaaaaagtttttcgctacgctagcaagcaaaaatgaaa                                                                        <  2:322986‑M1/148‑78 (MQ=255)                                                                               aGGGGGGCTGCGATTTTCAATAATGCGTGATGCAGATCACACAAAACACTCAATTACTTAACATAAATGtataagtcatacttttgttttgggtgtatttcaatatgttaaaaagtttttcgctacgctagcaagcaaaaatgaaacag                                                                     >  1:724263‑M1/1‑69 (MQ=255)                                                                                 gggggCTGCGATTTTCAATAATGCGTGATGCAGATCACACAAAACACTCAATTACTTAACATAAATGtataagtcatacttttgttttgggtgtatttcaatctgttaaaaagtttttcgctacgctagcaagcaaaaatgaaacagga                                                                   >  2:311339‑M1/1‑67 (MQ=255)                                                                                  ggggCTGCGATTTTCAATAATGCGTGATGCAGATCACACAAAACACTCAATTACTTAACATAAATGtataagtcatacttttgttttgggtgtatttcaatctgttaaaaagtttttcgctacgctagcaagcaaaaatgaaacaggaa                                                                  <  2:90534‑M1/149‑84 (MQ=255)                                                                                     gCTGCGATTTTCAATAATGCGTGATGCAGATCACACAGAACACTCAATTACTTAACATAAATGtataagtcatacttttgttttgggtgtatttcaatctgttaaaaagtttttcgctacgctagcaagcaaaaatgaaacaggaataa                                                               >  1:326672‑M1/1‑63 (MQ=255)                                                                                     gCTGCGATTTTCAATAATGCGTGATGCAGATCACACAAAACACTCAATTACTTAACATAAATGtataagtcatacttttgttttgggtgtatttcaatctgttaaaaagtttttcgctacgcttgcaagcaaaaatgaaacaggaataa                                                               >  1:547237‑M1/1‑63 (MQ=255)                                                                                     gCTGCGATTTTCAATAATGCGTGATGCAGATCACACAAAACACTCAATTACTTAACATAAATGtataagtcatacttttgttttgggtgtatttcaatctgttaaaaagtttttcgctacgctagcaaccaaaaatgaaacaggaaaaa                                                               >  1:546310‑M1/1‑63 (MQ=255)                                                                                       tGCGATTTTCAATAATGCGTGATGCAGATCACACAAAACACTCAATTACTTAACATAAATGtataagtcatacttttgttttggttgtatttcaatctgttaaaaagtttttctctacgctagcaagcaaaaatgaaacaggcataatc                                                             >  2:69117‑M1/1‑61 (MQ=255)                                                                                       tGCGATTTTCAATAATGCGTGATGCAGATCACACAAAACACTCAATTACTTAACATAAATGtataagtcatacttttgttttgggtgtatttcaatctgttaaaaagtttttcgctacgttagcaagcaaaattgaaacaggaataatc                                                             >  1:160501‑M1/1‑61 (MQ=255)                                                                                       tGCGATTTTCAATAATGCGTGATGCAGATCACACAAAACACTCAATTACTTAACATAAATGtataagtcatacttttgttttgggtgtatttcaatctgttaaaaagtttttcgctacgctagcaagcaaaaatgaaacaggaataatc                                                             >  1:712341‑M1/1‑61 (MQ=255)                                                                                            ttttCAATAATGCGTGATGCAGATCACACAAAACACTCAATTACTTAACATAAATGtataagtcatacttttgttttgggtgtatttcaatctgttaaaaagtttttcgctacgctagcaagcaaaaatgaaacaggaataatcgaaat                                                        >  1:544164‑M1/1‑56 (MQ=255)                                                                                                   taatGCGTGATGCAGATCACACAAAACACTCAATTACTTAACATAAATGtataagtcatacttttgttttgggtgtatttcaatctgttaaaaagtttttcgctacgctagcaagcaaacatgaaacaggaataatagaaatgggattt                                                 >  2:127161‑M1/1‑49 (MQ=255)                                                                                                         gTGATGCAGATCACACAAAACACTCAATTACTTAACATAAATGtataagtcatacttttgttttgggtgtatttcaatctgttaaaaagtttttcgctacgctagcaagcaaaaatgaaacagaaataatcgaaatgggatgttgcgca                                           >  1:727965‑M1/1‑43 (MQ=255)                                                                                                         gTGATGCAGAACACACAAAACACTCAATTACTTAACATAAATGtataagtcatacttttgttttgggtgtatttcaatctgttaaaaagtttttcgctacgctagcaagcaaaaatgaaacaggaataatcgaaatgggatgttgcgca                                           <  2:145076‑M1/149‑107 (MQ=255)                                                                                                           gATGCAGATCACACAAAACTCTCGATTACTTAACATAAATGtataagtcatacttttgttttgggtgtatttcaatctgttaaaaagtttttcgctacgctagcaagcaaaaatgaaacaggaataatcgaaatgggatgttgcgcaca                                         <  2:756387‑M1/149‑109 (MQ=255)                                                                                                           gATGCAGATCACACAAAACACTCAATTACTTAACATAAATGtataagtcatacttttgttttgggtgtatttcaatctgttaaaaagtttttcgctacgctagcaagcaaaaatgaaacaggaataatcgaaatgggatgttgcgcaca                                         <  1:796071‑M1/149‑109 (MQ=255)                                                                                                           gATGCAGATCACACAAAACACTCAATTACTTAACATAAATGtataagtcatacttttgttttgggtgtatttcaatctgttaaaaagtttttcgctacgctagcaagcaaaaatgaaacaggaataatcgaaatgggatgttgcgcaca                                         <  1:703833‑M1/149‑109 (MQ=255)                                                                                                                   tCACACAAAACCCTCAATTACTTAATATAAATGtataagtcatactgttgttttgggtgtatttcaatctgttaaaaagtttttcgctacgctagcaagcaaaaatgaaacaggaataatcgaaatgggatgttgcgcacagtcaaaat                                 <  1:726334‑M1/149‑117 (MQ=255)                                                                                                                        caAAACACTCAATTACTTAACATAAATGtataagtcatacttttgttttgggtgtatttcaatctgttaaaaagtttttcgctacgctagcaagcaaaaatgaaacaggaataatcgaaatgggatgttgcgcacagtcaaaataacat                            >  2:368650‑M1/1‑28 (MQ=255)                                                                                                                         aaaaCACTCAATTACTTAACATAAATGtataagtcatacttttgttttgggtgtatttcaatctgttaaaaagtttttcgctacgctagcaagcaaaaatgaaacaggaataatcgaaatgggatgttgcgcacagtcaaaataactca                           >  1:521300‑M1/1‑27 (MQ=255)                                                                                                                            acacTCAATTACTTAACATAAATGtataagtcatacttttgttttgggtgtatttcaatctgttaaaaagtttttcgctacgctagcaagcaaaaatgaaacaggaataatcgaaatgggatgttgcgcacagtcaaaataactcaccg                        >  1:316023‑M1/1‑24 (MQ=255)                                                                                                                              acTCAATTACTTAACATAAATGtataagtcatacttttgttttgggtgtatttcaatctgttaaaaagtttttcgctacgctagcaagcaaaaatgaaacaggaataatcgaaatgggatgttgcgcacagtcaaaataactcaccgta                      >  2:623979‑M1/1‑22 (MQ=255)                                                                                                                                  aaTTACTTAACATAAATGtataagtcatacttttgttttgggtgtatttcaatctgttaaaaagtttttcgctacgctagcaagcaaaaatgaaacaggaataatcgaaatggcatgttgcgcacagtcaaaataactcaccgtaaata                  >  1:639918‑M1/1‑18 (MQ=255)                                                                                                                                                aaTGtatacgtcatacttttgttttgggtgtatttcaatctgttaaaaagtttttcgctacgctagcaagaaaaaatgaaacaggaatagtcgaaatgggatgtttcgcacagtcaaaataaataaccgtgaataatcatttgctatat    >  2:280341‑M1/1‑4 (MQ=255)                                                                                                                                                  tGtataagtcatacttttgttttgggtgtatttcaatctgttaaaaagtttttcgctacgctagcaagcaaaaatgaaacaggaataatcgaaatgggatgttgcgcacagtcaaaataactcaccgtaaataatcatctgctataaat  <  2:188253‑M1/149‑148 (MQ=255)                                                                                                                                                   |                                                                                                                                                    GAAATGGGTCTTTACACTTATCTAAGATTTTTCCTAAATCGACGCAACTGTACTCGTCACTACACGCACATACAACGGAGGGGGGCTGCGATTTTCAATAATGCGTGATGCAGATCACACAAAACACTCAATTACTTAACATAAATGGGTAATGACTCCAACTTATTGATAGTGTTTTATGTTCAGATAATGCCCGATGACTTTGTCATGCAGCTCCACCGATTTTGAGAACGACAGCGACTTCCGTCCCAGCCGTGCCAGGTGCTGCCTCAGATTCAGGTTATGCCGCTCAAT  >  NC_000913_3_pae_tpiA/1978356‑1978649

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: ‑