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	51 [0]	[0] 52	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)	49 (0.870)	40/274	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

ATGGGTCTTTACACTTATCTAAGATTTTTCCTAAATCGACGCAACTGTACTCGTCACTACACGCACATACAACGGAGGGGGGCTGCGATTTTCAATAATGCGTGATGCAGATCACACAAAACACTCAATTACTTAACATAAATGGGTAATGACTCCAACTTATTGATAGTGTTTTATGTTCAGATAATGCCCGATGACTTTGTCATGCAGCTCCACCGATTTTGAGAACGACAGCGACTTCCGTCCCAGCCGTGCCAGGTGCTGCCTCAGATTCAGGTTATGCCGCTCAA  >  NC_000913_3_pae_tpiA/1978359‑1978648                                                                                                                                                |                                                                                                                                                   aTGGGTCTTTACACTTATCTAAGATTTTTCCTAAATCGACGCAACTGTACTCGTCACTACACGCACATACAACGGAGGGGGGCTGCGATTTTCAATAATGCGTGATGCAGATCACACAAAACACTCAATTACTTAACATAAATGtataa                                                                                                                                               <  1:507405‑M1/149‑6 (MQ=255)             acTTATCTAAGATTTTTCCTAAATCGACGCAACTGTACTCGTCACTCCACGCACATACAACGGAGGGGGGCTGCGATTTTCAATAATGCGTGATGCAGATCACACAAAACACTCAATTACTTAACATAAATGtataagtcatacttttg                                                                                                                                   >  1:440957‑M1/1‑132 (MQ=255)                 aTCTAAGATTTTTCCTAAATCGACGGAACTGTACTCGTCACTACACGCACATACAACGGAGGGGGGCTGCGATTTTCAATAATGCGTGATGCAGATCACACAAAACACTCAATTACTTAACATAAATGtataagtcatacttttgtttt                                                                                                                               <  2:182979‑M1/149‑22 (MQ=255)                   cTAAGATTTTTCCTAAATCGACGCAACTGTACTCGTCACTACACGCACATACAACGGAGGGGGGCTGCGATTTTCAATAATGCGTGATGCAGATCACACAAAACACTCAATTACTTAACATAAATGtataagtcatacttttgttttgg                                                                                                                             >  1:751479‑M1/1‑126 (MQ=255)                   cTAAAATTTTACTTAATTCGACGCAACTGTACTCGTCACTACACGCACATACAACGGAGGGGGGCTGCGATTTTCAATAATGCGTGATGCAGATCACACAAAACACTCAATTACTTAACATAAATGtataagtcatacttttgttttgg                                                                                                                             <  2:161443‑M1/149‑24 (MQ=255)                               cTAAATCGACGCAACTGTACTCGTCACTACACGCACATACAACGGAGTGGGGCTGCGATTTTCAATAATGCGTGATGCAGATCACACAAAACACTCAATTACTTAAAATAAATGtataaggcatacttttgttttgggtgtatttcaat                                                                                                                 >  2:363421‑M1/1‑114 (MQ=255)                               cTAAATCGACGCAACTGTACTCGTCACTACACGCACATACAACGGAGGGGGGCTGCGATTTTCAATAATGCGTGATGCAGATCACACAAAACACTCAATTACTTAACATAAATGtataagtcatacttttgttttgggtgtatttcaat                                                                                                                 <  2:985319‑M1/149‑36 (MQ=255)                               cTAAATCGACGCAACTGTACTCGTCACTACACGCACATACAACGGAAGGGGGCTGCGATTTTCAATAATGCTTGATGCAGATCACGCAAAACACTCAATTACTTAACATAAATGtataacgcatattttcactttgggtgtatttcaat                                                                                                                 >  2:205142‑M1/1‑114 (MQ=255)                               cTAAATCGACGCAACTGTACTCGTCACTACAAGCACATACAACGGAGGGTGGCTGCGATTTTCAATAATGCGTGATGCAGATCACACAAAACACTCAATTACTTAACATAAATGtataagtcatacttttgttttgggtgtatttcaat                                                                                                                 <  1:734478‑M1/149‑36 (MQ=255)                                   aTCGACGCAACTGTACTCGTCACTACACGCACATACAACGGAGGGGGGCTGCGATTTTCAATAATGCGTGATGCAGATCACACAAAACACTCAATTACTTAACATAAATGtataagtcatacttttgttttgggtgtatttcaatctgt                                                                                                             <  2:342595‑M1/149‑40 (MQ=255)                                         gcatttgtactCGTCACTCAACGCACATAGAACGGAGGGGGGCTGCGATTTTCAATAATGCGTGATGCAGATCACACAAAACACTCAATTACTTAACATAAATGtataagtcatacttttgttttgggtgtatttcaatctgttaaaaa                                                                                                       <  2:803099‑M1/144‑46 (MQ=255)                                         ccaACTGTACTCACCACTACACGCACATACAACAGAGGGGGGCTGCGACTATCCACAATGCGTGATGCAGATCACACAAAACACTCAATTACTTAACATAAATGtataagtcatacttttgttttgggtgtatttcaatctgttaaaaa                                                                                                       <  2:896240‑M1/148‑46 (MQ=255)                                              tGTACTCGTCACTACACGCACATACAACGGAGGGGGGCTGCGATGTTCAATAATACGTGATGCAGATCACACAAAACACTCAATTACTTAACAAAAATGaaaaaatcatactattgttataggtgtaattcaaactgttaaaaagtttt                                                                                                  >  1:43199‑M1/1‑99 (MQ=255)                                               gTACTCGTAACTACACGCACATACAACGGAGGGGGGCTGCGATTTTCAATAATGCGTGATGCAGATCACACAAAACACTCAATTACTTAACATAAATGtataagtcatacttttgttttgggtgtatttcaatctgttaaaaagttttt                                                                                                 <  1:753121‑M1/149‑52 (MQ=255)                                                 aCTCGTCACTACACGCACATACAACGGAGGGGGGCTGCGATTTTCAATAATGCGTGATGCAGATCACACAAAACACTCAATTACTTAACATAAATGtataagtcatacttttgttttgggtgtatttcaatctgttaaaaagtttttcg                                                                                               >  2:778880‑M1/1‑96 (MQ=255)                                                   tCGTCACTACGCGCACATACAACGGAGGGGGGCTGCGATTTTCAATAATGCGTGATGCAGATCACACAAAACACTCAATTACTTAACATAAATGtataagtcatacttttgttttgggtgtatttcaatctgttataaagtttttcgac                                                                                             >  1:1017083‑M1/1‑94 (MQ=255)                                                   tCGTCACTACACGCACATACAACGGAGGGGGGCTGCGATTTTCAATAATGCGTGATGCAGATCACCCAAAACACTCAATTACTTAACATAAATGtataagtcatacttttgtcttggctgtatttcaatctgataaaaaattattcgct                                                                                             >  1:231667‑M1/1‑94 (MQ=255)                                                   tCGTCACTACACGCACATACAACGGAGGGGGGCTGCGATTTTCAATAATGCGTGATGCAGATCACACAAAACACTCAATTACTTAACATAAATGtataagtcatacttttgttttgggtgtatttcaatctgttaaaaagtttttcgct                                                                                             >  1:494788‑M1/1‑94 (MQ=255)                                                   tCGTCACTACACGCACATACAACGGAGGGGGGCTGCGATTTTCAATAATGCGTGATGCAGATCACACAAAACACTCAATTACTTAACATAAATGtataagtcatacttttgttttgggagtatttcaatctgttaaaaagtttttcgtt                                                                                             >  1:704019‑M1/1‑94 (MQ=255)                                                       tacTACACGCACAATCAACGGAGGGGGGCTTCGATTTTAAATAATGCGTGATGCAGATCACACAAAACACTCAATTACTTAACATAAATGtataagtcatacttttgttttgggtgtatttcaatctgttaaaaagtttttcgctacgc                                                                                         <  2:769704‑M1/148‑60 (MQ=255)                                                              cGCACATCCAACGGAGGTGTGTTGCGATTTTCAATAATGCGTTATGCAGATCACACAAAACACTCAATTACTTAACATAAATGtataagtcatacttttgttttgggtgtatttcaatctgttaaaaagtttttcgctacgctagcaag                                                                                  <  1:352560‑M1/149‑67 (MQ=255)                                                                cacaTACAACGGAGGGGGGCTGCGATTTTCAATAATGCGTGATGCAGATCACACAAAACACTCAATTACTTAACATAAATGtataagtcatacttttgttttgggtgtatttcaatctgttaaaaagtttttcgctacgctagcaagaa                                                                                >  1:822733‑M1/1‑81 (MQ=255)                                                                         cGGAGGGGAGCTGCGATTTTCAATAATGCGTGATGCAGATCACACAAAACACTCAATTACTTAACATAAATGtataagtcatacttttgttttgggtgtatttcaatctgttaataacgtttgcgctacgctagcaagcaaaaatgaaa                                                                       <  2:224695‑M1/149‑78 (MQ=255)                                                                           gAGGGGGGCTGCGATTTTCAATAATGCGTGATGCAGATCACACAAAACACTCAATTACTTAACATAAATGtataagtcatacttttgttttgggtgtatttcaatctgttaaaaagtttttcgctacgctagcaagcaaaaatgaaaca                                                                     <  2:974968‑M1/149‑80 (MQ=255)                                                                                    tgttattttCAATAATGCGTGATTCAGATCTCATAAAACATTCAAATACTTAACATAAATGtataagtcatacttttgttttgggtgtatttcaatctgttaaaaagtttttcgctacgctagcaagcaaaaatgaaacaggaataatc                                                            <  1:233153‑M1/145‑89 (MQ=255)                                                                                    tGCGATTTTCAATAATGCGTGATGCAGATCACACAAAACACTCAATTACTTAACATAAATGtataagtcatacttttgttttgggtgtatttcaatctgttaaaaagtttttcgctacgctagcaagcaaaaatgaaacaggaataatc                                                            >  2:515422‑M1/1‑61 (MQ=255)                                                                                             cAATAATGCGTGATGCAGATCACACAAAACACTCAATTACTTAACATAAATGaatacgtcatacttttgttttgggtgtatttcaatatgttaaaaagtttttcgctacgctagcaagccaaaatgaaacaggaataatcgaaatggga                                                   >  2:118351‑M1/1‑52 (MQ=255)                                                                                              aataatGCGTGATGCAGATCACACAAAACACTCAATTACTTAACATAAATGtataagtcatacttttgttttgggtgtatttcaatctgttaaaaagtttttcgctacgctagcaagcaaaaatgaaacaggaataatcgaaatgggat                                                  >  2:277175‑M1/1‑51 (MQ=255)                                                                                                    gCGTGATGCAGATCACACAAAACACTCAATTACTTAACATAAATGtataagtcatacttttgttttgggtgtatttcaatctgttaaaaagtttttcgctacgctagcaagcaaaaatgaaacaggaataatcgaaatgggatgttctg                                            >  2:421995‑M1/1‑45 (MQ=255)                                                                                                        gATGCAGATCACACAAAACACTAAATTACTTAACATAAATGtataagtcatacttttgttttgggtgtatttcaatctgttaaaaagtttttctctacgctagcaagcaaaaatgaaacaggaataatcgaaatgggatgttgcgcaca                                        <  2:122638‑M1/149‑109 (MQ=255)                                                                                                            cAGATCACACAAAACACTCAATTACTTAACATAAATGtataaatcatacttgtgttttgggtgtatttcaatctgttaaaaagtttttcgctacgctagcaagcaaaaatgaaacaggaataatcgaaatgggatgttgcgcacagtca                                    >  2:526977‑M1/1‑37 (MQ=255)                                                                                                             aGATCACAAAAAACACTCAATTACTTAACATAAATGtataagtcatacttttgttttgggtgtatttcaatctgttaaaaagtttttcgctacgctagcaagcaaaaatgaaacaggaataatcgaaatgggatgttgcgcacagtcaa                                   <  1:351623‑M1/149‑114 (MQ=255)                                                                                                              gATCACACAAAACACTCAATTACTTAACATAAATGtataagtcatacttttgttttgggtgtatttcaatctgttaaaaagtttttcgctacgctagcaagcaaaaatgaaacaggaataattgaaatgggatgttgcgcacagtcaaa                                  >  2:48818‑M1/1‑35 (MQ=255)                                                                                                                tCACACAAAACACTCAATTACTTAACATAAATGtataagtcatacttttgttttgggtgtatttcaatctgttaaaaagtttttcgctacgctagcaagcaaaaatgaaacaggaataatcgaaatgggatgttgcgcacagtcaaaat                                >  1:593038‑M1/1‑33 (MQ=255)                                                                                                                 cacacaAAACACTCAATTACTTAACATAAATGtataagtcatacttttgttttgggtgtatttcaatctgttaaaaagtttttcgctacgctagcaagcaaaaatgaaacaggaataatcgaaatgggatgttgcgcacagtcaaaata                               >  2:1035125‑M1/1‑32 (MQ=255)                                                                                                                  acaaaAAACACTCTATTACTAAACATAAATGtataagtcatacttttcttttgggtgtacttcaatctgttaaaaagtttttcgctacgctagcaagcaaaaatgaaacaggaataatcgaaatgggatgttgcgcacagtcaaaataa                              <  2:199251‑M1/149‑119 (MQ=255)                                                                                                                    acaAAACACTCAATTACTTAACATAAATGtataagtcatacttttgttttgggtgtatttcaatctgtgaaaaagtttttcgctacgctagcaagcaaaaatgaaacaggaataatcgaaatgggatgttgcgcacagtcaaaataaca                            >  1:198972‑M1/1‑29 (MQ=255)                                                                                                                      aaaaCACTCAATTACTTAACAAAAATGtataagtcatacttttgttttgggtgtatttcaatctgttaaaaagtttttcgctacgctagcaagcaaaaatgaaacaggaataatcgaaatgggatgttgcgcacagtcaaaataactca                          <  2:649680‑M1/149‑123 (MQ=255)                                                                                                                       aaaCACTCAATGACTTAGCATAAATGtataagtcatacttttgttttgggtgtatttcaatctgttaaaaagtttttcgctacgctagcaagcaaaaatgaaacaggaataatcgaaatgggatgttgcgcacagtcaaaataactcac                         <  1:161036‑M1/149‑124 (MQ=255)                                                                                                                        aatcatcaattATTTAACATATACTtataagtcatacttttgttttgggtgtatttcaatcggttaaaaagtgtttcgctgcgctagcaagcaaaaatgaaacaggaataatcgaaatgggatgttgcgcacagtcaaaataactcacc                        <  1:983198‑M1/144‑125 (MQ=255)                                                                                                                        aaCACTCAATTACTTAACATAAATGtataagtcatacttttgttttgggtgtatttcaatctgttaaaaagtttttcgctacgctagcaagcaaaaatgaaacaggaataatcgaaatgggatgttgcgcacagtcaaaataactcacc                        >  2:561402‑M1/1‑25 (MQ=255)                                                                                                                        aaCACTCAATTACTTAACATAAATGtataagtcatacttttgttttgggtgtatttcaatctgttaaaaagtttttcgctacgctagcaagcaaaaatgaaacaggaataatcgaaatgggatgttgcgcacagtcaaaataactcacc                        >  2:766408‑M1/1‑25 (MQ=255)                                                                                                                        aaCACTCAATTACTTAACATAAATGtataagtcatacttttgttttgggtgtatttcaatctgttaaaaagtttttcgctacgctagcaagcaaaaatgaaacaggaataatcgaaatgggatgttgcgcacagtcaaaataactcaac                        >  1:1004921‑M1/1‑25 (MQ=255)                                                                                                                            cTCAATTACTTAACATTAATGtataagtcatacttttgttttgggtgtatttcaatctgttaaaaagtttttcgctacgctagcaagcaaaaatgaaacaggaataatcgaaatgggatgttgcgcacagtcaaaataactcaccgtaa                    <  1:531192‑M1/149‑129 (MQ=255)                                                                                                                             tCAATTACTTAACATAAATGtataagtcatacttttgttttgggtgtatttcaatctgttaaaaagtttttcgctacgctagcaagcaaaaatgaaacaggaataatcgaaatgggatgttgcgcacagtcaaaataactcaccgtaaa                   >  2:1019691‑M1/1‑20 (MQ=255)                                                                                                                               aaTTACTTAACATAAATGtataagtcatacttttgttttgggtgtatttcaatctgttaaaaagtttttcgctacgctagcaagcaaaaatgaaacaggaataatctaaatgggatgttgcgcacagtcaaaataactcaccgtcaata                 >  2:52322‑M1/1‑18 (MQ=255)                                                                                                                               aaTTACTTAACATAAATGtataagtcatacttttgttttgggtgtatttcaatctgttaaaaagtttttcgctacgctagcaagcaaaaatgaaacaggaataatcgaaatgggatgttgcgcacagccaaaacaactcaccgtaaata                 >  1:643128‑M1/1‑18 (MQ=255)                                                                                                                                aTTACTTAACATAAATGtataagtcatacttttgttttgggtgtatttcaatctgttaaaaagtttttcgctacgctagcaagcaaaaatgaaacaggaataatcgaaatgggatgttgcgcacagtcaaaataactcaccgtaaataa                >  1:252574‑M1/1‑17 (MQ=255)                                                                                                                                        aCATAAATGtataagtcatacttttgttttgggtgtatttcaatctgttaaaaagtttttcgctacgctagcaagcaaaaatgaaacaggaataatcgaaatgggatgttgcgcacagtcaaaataactcaccgtaaatactcatctgc        >  1:380447‑M1/1‑9 (MQ=255)                                                                                                                                              aTGtataagtcatacttttgttttgggtgtatttcaatctgttaaaaagtttttcgctacgctagcaagcaaaaatgaaacaggaataatcgaaatgggatgttgcgcacagtcaaaataactcaccgtaaataatcatctgctataaa  >  1:226586‑M1/1‑3 (MQ=255)                                                                                                                                              aTGtataagtcatacttttgttttgggtgtatttcaatctgttaaaaagtttttcgctacgctagcaagcaaaaatgaaacaggaataatcgaaatgggatgttgcgcacagtcaaaataactcaccgtaaataatcatctgctataaa  <  2:252574‑M1/149‑147 (MQ=255)                                                                                                                                                |                                                                                                                                                   ATGGGTCTTTACACTTATCTAAGATTTTTCCTAAATCGACGCAACTGTACTCGTCACTACACGCACATACAACGGAGGGGGGCTGCGATTTTCAATAATGCGTGATGCAGATCACACAAAACACTCAATTACTTAACATAAATGGGTAATGACTCCAACTTATTGATAGTGTTTTATGTTCAGATAATGCCCGATGACTTTGTCATGCAGCTCCACCGATTTTGAGAACGACAGCGACTTCCGTCCCAGCCGTGCCAGGTGCTGCCTCAGATTCAGGTTATGCCGCTCAA  >  NC_000913_3_pae_tpiA/1978359‑1978648

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 12 ≤ ATCG/ATCG < 13 ≤ ATCG/ATCG < 27 ≤ ATCG/ATCG < 41 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑