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	53 [0]	[0] 53	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)	51 (0.900)	41/268	0.4	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

AAATGGGTCTTTACACTTATCTAAGATTTTTCCTAAATCGACGCAACTGTACTCGTCACTACACGCACATACAACGGAGGGGGGCTGCGATTTTCAATAATGCGTGATGCAGATCACACAAAACACTCAATTACTTAACATAAATGGGTAATGACTCCAACTTATTGATAGTGTTTTATGTTCAGATAATGCCCGATGACTTTGTCATGCAGCTCCACCGATTTTGAGAACGACAGCGACTTCCGTCCCAGCCGTGCCAGGTGCTGCCTCAGATTCAGGTTATGCCGCT  >  NC_000913_3_pae_tpiA/1978357‑1978645                                                                                                                                                  |                                                                                                                                                aactgggTCTTTACACTTATCTAAGAGTTTTCCTAAATCGACGCAACTGTACTCGTCACTACACGCACATACAACGGAGGGGGGCTGCGATTTTCAATAATGCGTGATGCAGATCACACAAAACACTCAATTACTTAACATAAATGtat                                                                                                                                              <  1:928445‑M1/146‑4 (MQ=255) aaaTGGGTCTTTACACTTATCTAAGATTTTTCCTAAATCGACGCAACTGTACTCGTCACTACACGCACATACAACGGAGGGGGGCTGCGATTTTCAATAATGCGTGATGCAGATCACACAAAACACTCAATTACTTAACATAAATGtat                                                                                                                                              <  2:799073‑M1/149‑4 (MQ=255)     gtgtcTTTACACTTAACTAAGATTGTTCCTAAATCGACGCAACTGTACTCGTCACTACACGCACATACAACGGAGGGGGGCTGCGATTTTCAATAATGCGTGATGCAGATCACACAAAACACTCAATTACTTAACATAAATGtataagt                                                                                                                                          <  2:669569‑M1/147‑8 (MQ=255)      tgtCTTTACACTTATCTAAGTTTTTTCATAAATCGACGCAACTGTACTCGTCACTACACGCACATACAACGGAGGGGGGCTGCGATTTTCAATAATGCGTGATGCAGATCACACAAAACACTCAATTACTTAACATAAATGtataagtc                                                                                                                                         <  2:7570‑M1/148‑9 (MQ=255)                      tAAGATTTTTCCTAAATCGACGCAACTGTACTCGTCACTACACGCACATACAACGGAGGGGGGCTGCGATTTTCAATAATGCGTGATGCAGATCACACAAAACACTCAATTACTTAACATAAATGtataagtcatact                                                                                                                                    >  1:340126‑M1/1‑125 (MQ=255)                      tAAGATTTTTCCTAAATCGACGCAACTGTACTCGTCACTACACGCACATACAACGGAGGGGGGCTGCGATTTTCAATAATGCGTGATGCAGATCACACAAAACACTCAATTACTTAACATAAATGtataagtcatact                                                                                                                                    <  2:340126‑M1/138‑14 (MQ=255)                       aaGATTTTTCCTAAATCGACGCAACTGTACTCGTCACTACACGCACATACAACGGAGGGGGGCTGCGATTTTCAATAATGCGTGATGCAGATCACACAAAACACTCAATTACTTAACATAAATGtataagtcatacttttgttttgggt                                                                                                                        >  1:226955‑M1/1‑124 (MQ=255)                       aaGATTTTTCCTAAATCGACGCAACTGTACTCGTCACTACACGCACATACAACGGAGGGGGGCTGCGATTTTCAATAATGCGTGATGCAGATCACACAAAACACTCAATTACTTAACATAAATGtataagtcatacttttgttttgggt                                                                                                                        >  1:12267‑M1/1‑124 (MQ=255)                       aaGAGTTTTTCCAAATTGACGCTACTGTACTCGTCACTACACGCACATACAACGGAGGGTGGCTGCGATTTTCAATAATGCGTGATGCATATCACACAAAACACTCAATTACTTAACATAAATGtataagtcatacttttgttttgggt                                                                                                                        <  2:1028274‑M1/149‑26 (MQ=255)                          ttttttcCTAAGTCGACGCAACTGTACGAGTCACTACACGCACATACAACGGTGGGGGGCTGCGATTTTCAGTAATGCGTGATGCAGATCACACAAAACACTCAATTACTTAACATAAATGtataagtcatgcttgggttttgggtgta                                                                                                                     <  2:125294‑M1/148‑29 (MQ=255)                                  gaaatCGACGCAACTGTACTCGTCACTACACGCACATACAACGGAGGGGGGCTGCGATTTTCAATAATGCGTGATGCAGATCACACAAAACACTCAATTACTTAACATAAATGtataagtcatacttttgttttgggtgtatttcaatc                                                                                                             >  1:741864‑M1/2‑113 (MQ=255)                                      tCGACTCAACTCTACGCGTCACTACACGCACATACAACGGAGGGGTGCTGCGATTTTCAATAATGCGTGATGCAGATCACACAAAACACTCAATTACTTAACATAAATGtataagtcatacttttgttttgggtgtatttcaatctgtt                                                                                                         <  1:11491‑M1/149‑41 (MQ=255)                                                         cACTACACGCACATACAACGGAGGGGGGCTGCGATTTTCAATAATGCGTGATGCAGATCACACAAAACACTCAATTACTTAACATAAATGtataagtcatacttttgttttgggtgtatttcaatctgttaaaaagtttttcgctacgc                                                                                      <  1:333229‑M1/149‑60 (MQ=255)                                                          aCTACACGCACATACAACGGAGGGGGGCTGCGATTTTCAATAATGCGTGATGCAGATCACACAAAACACTCAATTACTTAACATAAATGtataagtcatacttttgtgttgggtgtatttcaatctgttaaaaagtttttcgctacgct                                                                                     >  1:118230‑M1/1‑89 (MQ=255)                                                           cTACACGCACATACAACGGAGGGGGGCTGCGATTTTCAATAATGCGTGATGCAGATCACACAAAACACTCAATTACTTAACATAAATGtataagtcatacttttgttttgggtgtatttcaatctgttaaaaagtttttcgctacgcta                                                                                    >  1:838020‑M1/1‑88 (MQ=255)                                                              cacGCACATACAACGGAGGGGGGCTGCGATTTTCAATAATGCGTGATGCAGATCACACAAAACACTCAATTACTTAACATAAATGtataagtcatacttttgttttgggtgtatttcaatctgttaaaaagtttttcgctacgctagca                                                                                 >  2:571825‑M1/1‑85 (MQ=255)                                                               acGCACATACAACGGAGGGGGGCTGCGATTTTCAATAATGCGTGATGCAGATCACACAAAACACTCAATTACTTAACATAAATGtataagtcatacttttgttttgggtgtatttcaatctgttaaaaagtttttcgctacgctagcaa                                                                                >  1:59845‑M1/1‑84 (MQ=255)                                                               acGCACATACAACGGAGGGGGGCTGCGATTTTCAACCAGCCGAGGGGGAGATCACACAAAACACTCAATTACTTAACATAAATGtataagtcatacttttgttttgggtgtatttcaatctgttaaaaagtttttcgctacgctagcaa                                                                                <  1:459392‑M1/149‑66 (MQ=255)                                                                   acaTACAACGGAGGGGGGCTGCGATTTTCAATAATGCGTGATGCAGATCACACAAAACACTCAATTACTTAACATAAATGtataagtcatacttttgttttgggtgtatttcaatctgtaaaaaagtttttcgatacgctagcaagcaa                                                                            >  2:732564‑M1/1‑80 (MQ=255)                                                                       aCAACGGAGGGGGGCTGCGATTTTCAATAATGCGTGATGCAGATCACACAAAACACTCAATTACTTAACATAAATGgataagtcatacttttgttttgggtgtatttcaatctgttaaaaagtttttcgctacgctagcaagcaaaaat                                                                        <  2:641524‑M1/149‑74 (MQ=255)                                                                        cAACGGAGGGGGGCTGCGATTTTCAATAATGCGTGATGCAGATCACACAAAACACTCAATTACTTAACATAAATGtataagtcatacttttgttttgggtgtatttcaatctgttaaaaagtttttcgctacgctagcaagcaaaaatg                                                                       >  1:655613‑M1/1‑75 (MQ=255)                                                                          accgaggGGGGCTGCGATTTTCAATAATGCGTGATGCAGATCACACAAAACACTCAATTACTTAACATAAATGtataagtcctactttcgttttgggtgtatttcaatctgttaaaaagtttttcgctacgctagcaagcaaaaatgaa                                                                     <  1:202460‑M1/146‑77 (MQ=255)                                                                             gAGGGGGGCTGCGATTTTCAATAATGCGTGATGCAGATCACACAAACCGATCAATTACTTAACATAAATGtataagtcatacttttgttttgggtgtatttcaatctgttaaaaagtttttcgctacgctagcaagcaaaaatgaaaca                                                                  >  1:994596‑M1/1‑70 (MQ=255)                                                                              aGGGTGGCTGCGATTTTCAATAATGCGTGATTCAGATCTCACAAAACACTCAATTACTTAACATAAATGtataagtcatacttttgttttgggtgtatttcaatctgttaaaaagtttttcgctacgctagcaagcaaaaatgaaacag                                                                 <  1:436377‑M1/149‑81 (MQ=255)                                                                                gggggCTGCGATTTTAAATAATTCGTGATGCAGATAACAAAAAACACTCAATTAGTTAAGATGAATGtataagtcatacttttgttatgggtgtatttcaatctgttaaaaagtttttcgctacgaaaaaaaacaaaaatgaaacagga                                                               <  2:401936‑M1/149‑83 (MQ=255)                                                                                   ggCTGCGATTTTCAATAATGCGTGATGCAGATCACACAAAACACTCAATTACTTAACATAAATGtataagtcatacttttgtttagggtgtatttcaatctgttaaaaagtttttcgctacgctagcaagcaaaaatgaaacaggaata                                                            <  1:913798‑M1/149‑86 (MQ=255)                                                                                     cTGTGATTTTCAATAAGGCGTGATGCAGATTACACAAAACATTCAATTACTTAACATAAATGtataagtcatacttttgttttgggtttatttcaatctgttaaaaagtttttcgctacgctagcaagcaaaaatgaaacaggaataat                                                          <  2:282658‑M1/149‑88 (MQ=255)                                                                                            tttCAATAATGCGTGATGCAGATCACACAAAACACTCAATTACTTAACATAAATGtataagtcatacttttgttttgggtgtatttcaatctgttaaaaagtttttcgctacgctagcaaccaaaaatgaaaaaggaatcatcgaaatg                                                   >  2:158724‑M1/1‑55 (MQ=255)                                                                                              tCAATAATGCGTGATGCAGATCACACAAAACACTCAATTACTTAACATAAATGtataagtcatacttttgttttgggtgtatttcgatctgttaaaaagtttttcgctacgctagcaagcaaaaatgaaacaggaataatagaaatggg                                                 >  1:933957‑M1/1‑53 (MQ=255)                                                                                                 ataatGCGTGATGCAGATCACACAAAACACTCAATTACTTAACATAAATGtataagtcatacttttgttttgggtgtatttcaatctgttaaaaagtttttcgctccgctagcaagcaanaatgaaacaggaataancgcaatgggatg                                              >  1:172893‑M1/1‑50 (MQ=255)                                                                                                      gCGTGATGCAGATCACACAAAACACTCAATTACTTAACATAAATGtataagtcatacttttgttttgggtgtatttcaatctgttaaaaagtttttcgctccgctagcaagcaaaaatgaaacaggaataatcgaaatgggatgttgcg                                         >  2:191340‑M1/1‑45 (MQ=255)                                                                                                        gTGATGCAGATCACACAAAACACTCAATTACTTAACATAAATGtataagtcatacttttgttttgggtgtatttcaatctgttaaaaagtttttcgctacgctagcaagcaaaaatgaaacaggaataatcgaaatgggatgttgcgca                                       >  1:328441‑M1/1‑43 (MQ=255)                                                                                                          gataaagatcaCACAAAACACTCCATTACTTAAAATAAATGtataagtcatacttttgttttgggtgtatttcaatctgttaaaaacgttttcgctacgctagcaagcaaaaatgaaacaggaataatcgaaatgggatgttgcgcaca                                     <  2:172893‑M1/144‑109 (MQ=255)                                                                                                          gATGCAGATCACACAAAACACTCAATTACTTAACATAAATGtataagtcatacttttgttttgggtgtatctcaatctgttaaaaagtttttcgctacgctagcaagcaaaaatgaaacaggaataatcgaaatgggatgttgcgcaca                                     <  1:970414‑M1/149‑109 (MQ=255)                                                                                                            tGCAGATCACACAAAACACTCAATTACTTAACATAAATGtataagtcatacttttgttttgggtgtatttcaatctgttaaaaagtttttcgctacgctagcaagcaaaaatgaaacaggaataatcgaaatgggatgttgcgcacagt                                   >  1:785032‑M1/1‑39 (MQ=255)                                                                                                            tGCAGATCACACAAAACACTCAATTACTTAACATAAATGtataagtcatacttttgattagggtgtatttcaatctgttaaaaagtttttcgctacgctagcaagcaaaaatgaaacaggaataatcgaaaggggatgttgcgcacagt                                   >  1:199919‑M1/1‑39 (MQ=255)                                                                                                             gCAGATCACACAAAACACTCAATTACTTAACATAAATGtataagtcatacttttgttttgggtgtatttcaatctgttaaaaagtttttcgctacgctagcaagcaaaaatgaaacaggaataatcgaaatgggatgttgcgcacagtc                                  <  2:328441‑M1/149‑112 (MQ=255)                                                                                                                 aTCACACAAAACACTCAATTACTTAACATAAATGtataagtcatacttttgttttgggtgtatttcaatctgttaaaaagtttttcgctacgctagcaagcaaaaatgaaacaggaataatcgaaatgggatgttgcgcacagtcaaaa                              >  2:340495‑M1/1‑34 (MQ=255)                                                                                                                 aTCACACAAAACACTCAATTACTTAACATAAATGtataagtcatacttttgttttgggtgtatttcaatctgttaaaaagtttttcgctacgctagcaagcaaaaatgaaacaggaataatcgaaatgggatgttgcgcacagtaaaaa                              >  2:1029689‑M1/1‑34 (MQ=255)                                                                                                                 aTCACACAAAACACTCAATTACTTAACATAAATGtataagtcatacttttgttttgggtgtatttcaatctgttaaaaagtttttcgctacgctagcaaacaaaaatgaaacaggaataatcgaattgggatgttgcgcacagtcaaaa                              >  1:140100‑M1/1‑34 (MQ=255)                                                                                                                      acaAAACACTCAATTACTTAACATAAATGtataagtcatacttttgttttgggtgtatttcaatctgttaaaaagtttttcgctacgctagcaagcaaaaatgaaacaggaataatcgaaatgggatgttgcgcacagtcaaaataact                         <  1:340495‑M1/149‑121 (MQ=255)                                                                                                                        agaacaCTCAATTACTTAACATAAAGGtataagtcatacttttgttttgcgtgtatttcaatctgttaaaaagtttttcgctacgctagcaagcaaaaatgaaaacagcataacagaaatgggatgttgcgcaaagtaaagataaatca                       >  2:745627‑M1/3‑27 (MQ=255)                                                                                                                        aaaaCACTCAATTACTTAACATAAATGtataagtcatacttttgttttgggtgtatttcaatctgttaaaaagtttttcgctacgctagcaagcaaaaatgaaacaggaataatcgaaatgggatgttgcgcacagtcaaaataactca                       >  1:249300‑M1/1‑27 (MQ=255)                                                                                                                           acacTCAATTACTTAACATAAATGtataagtcatacttttgttttgggtgtatttcaatctgttaaaaagtttttcgctacgctagcaagcaaaaatgaaacaggaataatcgaaatgggatgttgcgcacagtcaaaataactcaccg                    >  1:866805‑M1/1‑24 (MQ=255)                                                                                                                                 aaTTACTTAACATAAATGtataagtcatacttttgttttgggtgtatttcaatctgttaaaaagtttttcgctacgctagcaagcaaaaatgaaacagtcataatcaaaatggtatgttgtgcacagtcaaaataactcaccgaaatta              >  2:238987‑M1/1‑18 (MQ=255)                                                                                                                                 aaTTACTTAACATAAATGtataagtcatacttttgttttgggtgtatttcaatctgttaaaaagtttttcgctacgctagcaagcaaaaatgaaacaggaataatcgaaatgggatgttgcgcacagtcaaaataactcaccgtaaata              >  1:233517‑M1/1‑18 (MQ=255)                                                                                                                                 aaTTACTTAACATAAATGtataagtcatacttttgttttgggtgtatttcaatctgttaaaaagtttttcgctacgctagcaagcaaaaatgaaacaggaataatcgaaatgggatgttgcgcacagtcaaaataactcaccgtaaata              >  1:727663‑M1/1‑18 (MQ=255)                                                                                                                                    taattaacATAAATGtataaggcatacttttgttttgggtgtatttcaatctgttaaaaagtttttcgctacgctagcaagcaaaaatgaaacaggaataatcgaaatgggatgttgcgcacagtcaaaataactcaccgtaaataatc           <  2:394828‑M1/146‑135 (MQ=255)                                                                                                                                       ttAACATAAATGtataagtcatacttttgttttgggtgtatttcaatctgttaaaaagtttttcgctacgctagcaagcaaaaatgaaacaggaataatcgaaatgggatgttgcgcacaggcaaaataactcaccgtaaataatcatc        >  1:161313‑M1/1‑12 (MQ=255)                                                                                                                                       ttAACATAAATGgataagtcatacttttgttttgggtgtatttcaatctgttaaaaagtttttcgctacgctagcaagcaaaaatgaaacaggaataatcgaaatgggatgttgcgcacagtcaaaataactcaccgtaaataatcatc        <  2:198275‑M1/149‑138 (MQ=255)                                                                                                                                        tAACATAAATGtataagtcatacttttgttttgggtgtatttcaatctgttaaaaagtttttcgctacgctagcaagcaaaaatgaaacaggaataatcgaaatgggatgttgcgcacagtcaaaataactcaccgtaaataatcatct       <  1:327732‑M1/149‑139 (MQ=255)                                                                                                                                            aTAAATGtataagtcatacttttgttctgggtgtatttcaatctgttaaaaagtttttcgctacgctagcaagcaaaaatgaaacaggaataatcgaaatgggatgttgcgcacagtcaaaataactcaccgtaaataatcatctgcta   <  2:77497‑M1/149‑143 (MQ=255)                                                                                                                                             tAAATGtataagtcatacttttgttttgggtgtactacaatctgttaaaaagtttttcgctacgctagcaagcaaaaatgaaacaggaataatcgaaatgggatgttgcgcacagtcaaaataaataaccgtaaataatcatctgctat  >  2:490416‑M1/1‑6 (MQ=255)                                                                                                                                                  |                                                                                                                                                AAATGGGTCTTTACACTTATCTAAGATTTTTCCTAAATCGACGCAACTGTACTCGTCACTACACGCACATACAACGGAGGGGGGCTGCGATTTTCAATAATGCGTGATGCAGATCACACAAAACACTCAATTACTTAACATAAATGGGTAATGACTCCAACTTATTGATAGTGTTTTATGTTCAGATAATGCCCGATGACTTTGTCATGCAGCTCCACCGATTTTGAGAACGACAGCGACTTCCGTCCCAGCCGTGCCAGGTGCTGCCTCAGATTCAGGTTATGCCGCT  >  NC_000913_3_pae_tpiA/1978357‑1978645

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: ‑