Predicted mutation
evidence	seq id	position	mutation	annotation	gene	description
MC JC	NC_000913	1,978,503	Δ776 bp		insB5–insA5	insB5, insA5

Missing coverage evidence...
			seq id	start	end	size	←reads	reads→	gene	description
*	*	÷	NC_000913	1978503–1979270	1979278	9–776	36 [1]	[0] 35	insB5–insA5	insB5,insA5

New junction evidence
		seq id	position	reads (cov)	reads (cov)	score	skew	freq	annotation	gene	product
*	?	NC_000913	= 1978502	1 (0.020)	35 (0.690)	32/476	0.6	98.6%	intergenic (‑305/+16)	flhD/insB5	DNA‑binding transcriptional dual regulator FlhD/IS1 family protein InsB
	?	NC_000913	1979279 =	0 (0.000)					intergenic (‑64/‑474)	insA5/uspC	IS1 family protein InsA/universal stress protein C

AGCCCCGGTAAAAAATAATTAGCATTAGAATAGTTGCGATAAGCTGCAATAAGCAGAACCACCTTTTTGGTTTAATATGTCCTTACAAATAGAAATGGGTCTTTACACTTATCTAAGATTTTTCCTAAATCGACGCAACTGTACTCGTCACTACACGCACATACAACGGAGGGGGGCTGCGATTTTCAATAATGCGTGATGCAGATCACAC‑AAAACACTCAATTACTTAACATAAATGGGTAATGACTCCAACTTATTGATAGTGTTTTATGTTCAGATAATGCCCGATGACTTTGTCATGCAGCTCCACCGATTTTGAGAACGACAGCGACTTCCGTCCCAGCCGTGCCAGGTGCTGCCTCAGATTCAGGTTATGCCGCTCAATTCGCTGCGTATATCGCTTGCTGATTACGTGCAGCTTTCCCTTCAGGCGGGATTCATACAGCGGCCAGCCATCCGTCATCCATATCACCACGTCAAAGGGTGAC  >  NC_000913/1978265‑1978752                                                                                                                                                                                                                                               |                                                                                                                                                                                                                                                           aGCCCCGGTAAAAAATAATTAGCATTAGAATAGTTGCGATAAGCTGCAATAAGCAGAACCACCTTTTTGGTTTAATATGTCCTTACAAATAGAAATGGGTCTTTACACTTATCTAAGATTTTTCCTAAATCGACGCAACTGTACTCGTCACTACACGCACATACAACGGAGGGGGGCTGCGATTTTCAATAATGCGTGATGCAGATCACAC‑AAAACACTCAATTACTTAACATAAATGtataagtcatact                                                                                                                                                                                                                                               >  1:328971‑M1/1‑238 (MQ=255)    cccGGTAAAAAATAATTAGCATTAGAATAGTTGCGATAAGCTGCAATAAGCAGAACCACCTTTTTGGTTTAATATGTCCTTACAAATAGAAATGGGTCTTTACACTTATCTAAGATTTTTCCTAAATCGACGCAACTGTACTCGTCACTACACGCACATACAACGGAGGGGGGCTGCGATTTTCAATAATGCGTGATGCAGATCACAC‑AAAACACTCAATTACTTAACATAAATGtataagtcatactttt                                                                                                                                                                                                                                            <  1:34659‑M1/251‑17 (MQ=255)      cGGTAAAAAATAATTATCATTAGAATAGTTGCGATAAGCTGCAATAAGCAGAACCACCTTTTTGGTTTAATATGTCCTTACAAATAGAAATTGGTCTTTACACTTATCTAAGATTTTTCCTAAATCGACGCAACTGTACTCGTCACTACACGCACATACAACGGAGGGGGGCTGCGATTTTCAATAATGCGTGATGCAGATCACAC‑AAAACACTCAATTACTTAACATAAATGtataagtcatacttttgt                                                                                                                                                                                                                                          <  2:471520‑M1/251‑19 (MQ=255)      cGGTAAAAAATAATTAGCATTAGAAAAGTTGCGATAAGCTGCAATAAGCAGAACCACCTTTTTGGTTTAATATGTCCTTACAAATAGAAATGGGTCTTTACACTTATCTAAGATTTTTCCTAAATCGACGCAACTGTACTCGTCACTACACGCACATACAACGGAGGGGGGCTGCTATTTTCAATAATGCGTGATGCAGATCACAC‑AAAACACTCAATTACTTAACATAAATGtataagtcatacttttgt                                                                                                                                                                                                                                          <  1:156419‑M1/251‑19 (MQ=255)           aaaaaTAATTAGCATTAGAATAGTTGCGATAAGCTGCAATAAGCAGAACCACCTTTTTGGTTTAATATGTCCTTACAAATAGAAATGGGTCTTTACACTTATCTAAGATTTTTCCTAAATCGACGCAACTGTACTCGTCACTACACGCACATACAACGGAGGGGGGCTGCGATTTTCAATAATGCGTGATGCAGATCACAC‑AAAACACTCAATTACTTAACATAAATGtataagtcatacttttgttttgg                                                                                                                                                                                                                                     >  1:348295‑M1/1‑228 (MQ=255)            aaaaTAATTAGCATTAGAATAGTTGCGATAAGCTGCAATAAGAAGAATCACCTTTTTGGTTTAATATGTCCTTACAAATAGAAATGGGTCTTTACACTTATCTAAGATTTTTCCTAAATCGTCGCAACTGTACTCGTCACTACACGCACATACAACGGAGGGGGGCTGCGATTTTCAATAATGCGTGATGCAGATCACAC‑AAAATTCTCAATTACTTAACATAAATGtataagtaatacttttgttttggg                                                                                                                                                                                                                                    <  2:158918‑M1/251‑25 (MQ=255)                  atTAGCATTAGAATAGTTGCGATAAGCTGCAATAAGCAGAACCACCTTTTTGGTTTAATATGTCCTTACAAATAGAAATGGGTCTTTACACTTATCTAAGATTTTTCCTAAATCGACGCAACTGTACTCGTCACTACACGCACATACAACGGAGGGGGGCTGCGATTTTCAATAATGCGTGATGCAGATCACAC‑AAAACACTCAATTACTTAACATAAATGtataagtcatacttttgttttgggtgtatt                                                                                                                                                                                                                              >  2:145199‑M1/1‑221 (MQ=255)                                cgtTGCGATAAGCTGCAATAAGCAGAACCACCTTTTTGGTTTAATATGTCATTACAAATAGAAATGGGTCTTTACACTTATCTAAGATTTTTCCTAAATCGACGCAACTGTACTCGTCACTACACGCACATACAACGGAGGGGGGCTGCGATTTTCAATAATGCGTGATGCAGATCACAC‑AAAACACTCAATTACTTAACATAAATGtataagtcatacttttgttttgggtgtatttcaatctgttaaa                                                                                                                                                                                                                 >  2:102946‑M1/2‑207 (MQ=255)                                                aaTAAGCAGAACCACCTTTTTGGTTTAATATGTCCTTACAAATAGAAATGGGTCTTTACACTTATCTAAGATTTTTCCTAAATCGACGCAACTGTACTCGTCACTACACGCACATACAACGGAGGGGGGCTGCGATTTTCAATAATGCGTGATGCAGATCACAC‑AAAACACTCAATTACTTAACATAAATGtataagtcatacttttgttttgggtgtatttcaatctgttaaaaagtttttcgctacgct                                                                                                                                                                                                <  1:304152‑M1/251‑61 (MQ=255)                                                aaTAAGCAGAACCACCTTTTTGGTTTAATATGTCCTTACAAACAGAAATGGGTCTTTACACTTATCTAAGATTTTTCCTAAATCGACGCAACTGTACTCGTCACTACACGCACATACAACGGAGGGGGGCTGCGATTTTCAATAATGCGTGATGCAGATCACAC‑AAAACACTCAATTACTTAACATAAATGtataagtcatacttttgttttgggtgtatttcaatctgttaaaaagtttttcgctacgct                                                                                                                                                                                                <  1:452789‑M1/251‑61 (MQ=255)                                                       aGAACCACCTTTTTGGTTTAATATGTCCTTACAAATAGAAATGGGTCTTTACACTTATCTAAGATTTTTCCTAAATCGACGCAACTGTACTCGTCACTACACGCACATACAACGGAGGGGGGCTGCGATTTTCAATAATGCGTGATGCAGATCACAC‑AAAACACTCAATTACTTAACATAAATGtataagtcatacttttgttttgggtgtatttcaatctgttaaaaagtttttcgctacgctagcaagc                                                                                                                                                                                         <  1:468093‑M1/251‑68 (MQ=255)                                                             accTTTTTGGTTTAATATGTCCTTACAAATAGAAATGGGTCTTTACACTTATCTAAGATTTTTCCTAAATCGACGCAACTGTACTCGTCACTACACGCACATACAACGGAGGGGGGCTGCGATTTTCAATAATGCGTGATGCAGATCACAC‑AAAACACTCAATTACTTAACATAAATGtataagtcatacttttgttttgggtgtatttcaatctgttaaaaagtttttcgctacgctagcaagcaaaaat                                                                                                                                                                                   <  1:315168‑M1/251‑74 (MQ=255)                                                                  tttGGTTTAATATGTCCTTACAAATAGAAATGGGTCTTTACACTTATCTAAGATTTTTCCTAAATCGACGCAACTGTACTCGTCACTACACGCACATACAACGGAGGGGGGCTGCGATTTTCAATAATGCGTGATGCAGATCACAC‑AAAACACTCAATTACTTAACATAAATGtataagtcatacttttgttttgggtgtatttcaatctgttaaaaagtttttcgctacgctagcaagcaaaaatgaa                                                                                                                                                                                <  2:113167‑M1/249‑77 (MQ=255)                                                                   ttGGTTTAATATGACCTTACAAATAGAAATGATTCTTTACACTTATCTAAGATTTTTCCTAAATCGACGCAACTGTACTCGTCACTACCAGCACATACAACGGAGGGGGGCTGCGTTTTTCATTAATGCGTGATGAAGATCACCC‑AAAACACTCAATTACTTAACATACATGtataagtaatacttttgttttgggtgtatttcaatctgttaaacagtttttggctacactagcaagcaaaattaaaac                                                                                                                                                                              >  2:361921‑M1/1‑172 (MQ=255)                                                                       tttAATATGTCCTTACAAATAGAAATGGGTCTTTACACTTATCTAAGATTTTTCCTAAATCGACGCAACTGTACTCGTCACTACACGCACATACAACGGAGGGGGGCTGCGATTTTCAATAATGCGTGATGCAGATCACAC‑AAAACACTCAATTACTTAACATAAATGtataagtcatacttttgttttgggtgtatttcaatctgttaaaaagtttttcgctacgctagcaagcaaaaatgaaacagga                                                                                                                                                                          >  1:357030‑M1/1‑168 (MQ=255)                                                                                   ttACAAATAGAAATGGGTCTTTACACTTATCTTAGATTTTTCCTAAATCGAAGCAACTGTACTCGTCACTACACGCACATACAACGGAGGGGGGCTGCGATTTTCAATAATGCGTGATGCAGATCACAC‑AAAACACTCAATTACTTAACATAAATGtatacgtcatacttttgttttgggtgtatttcaatctgttaaaaagtttttcgctacgctagcaagcaacaatgaaacaggaataatcgaaatgg                                                                                                                                                             >  2:387269‑M1/1‑156 (MQ=255)                                                                                    tACAAATAGAAATGGGTCTTTACACTTATCTAAGATTTTTCCTAAATCGACGCAACTGTACTCGTCACTACACGCACATACAACGGAGGGGGGCTGCGATTTTCAATAATGCGTGATGCAGATCACAC‑‑AAACACTCAATTACTTAACATAAATGtataagtcatacttttgttttgggtgtatttcaatctgttaaaaagtttttcgctacgctagcaagcaaaaatgaaacaggaataatcgaaatggg                                                                                                                                                            <  1:322605‑M1/250‑97 (MQ=255)                                                                                           aGAAATGGGTCTTTACACTTATCTAAGATTTTTACTAAATCGACGCAACTGTACTCGTCACTACACGCACATACAACGGAGGGGGGCTGAGATTTTCAATAATGCGTGATGCAGATCACAC‑AAAACACTCAATTACTTAACATAAATGtataagtcatacttttgttttgggtgtatttcaatctgttaaaaagtttttcgctacgctagcaagcaaaaatgaaacaggaataatcgaaatgggatgttgc                                                                                                                                                     >  2:489368‑M1/1‑148 (MQ=255)                                                                                             aaaTGGGTCTTTACACTTATCTAAGATTTTACCTAAATCGACGCAACTGTACTCGTCACTACTCGCACATACAACGGAGGGGGGCTGCGATTTTCAATAATGCGTGATGCAGATCACAC‑AAAACTCTCAATTACTTAACATAAATTtataagtcatacttttgttttgggtgtatttcaatctgttaaaaagtttttcgctacgctagcaagcaaaaatgaaacaggaataatcgcaatggtatgttgcgc                                                                                                                                                   <  2:531206‑M1/251‑106 (MQ=255)                                                                                              aaTGGGTCTTTACACTTATCTAAGATTTTTCCTAAATCGACGCAACTGTACTCGTCACTACACGCACATACAACGGAGGGGGGCTGCGATTTTCAATAATGCGTGATGCAGATCACAC‑AAAACACTCAATTACTTAACATAAATGtataagtcatacttttgttttgggtgtatttcaatctgttaaaaagtttttcgctacgctagcaagcaaaaatgaaacaggaataatcgaaatgggatgttgcgc                                                                                                                                                   >  1:369829‑M1/1‑145 (MQ=255)                                                                                                  ggTCTTTTCACTTATCTAAGATTTTTCCTAAAGCGACGCAACTGTACTCGTCACTACACGCACATACAACAGAGGGGGGCTGCGATTTTCAATAATGCGGGATGCAGATCA‑ACTAAAACACTCAATTACTTAACATAAATGtataagtcatacttttgttttgggtgtatgtcaatctgttaaaaagtgtttcgcgacgctagcaagcaaaaatgaaacaggaataaccgaaatgggatgttgcgcacagt                                                                                                                                              <  2:16267‑M1/251‑111 (MQ=255)                                                                                                       ttACACTTATCTAAGATTTTTCCTAAATCGACGCAACTGTACTCGTCACTACACGCACATACAACGGAGGGGGGCTGCGATTTTCAATAATGCGTGATGCAGATCACAC‑AAAACACTCAATTACTTAACATAAATGtataagtcatacttttgttttgggtgtatttcaatctgttaaaaagtttttcgctacgctagcaagcaaaaatgaaacaggaataatcgaaatgggatgttgcgcacagtca                                                                                                                                            <  1:54061‑M1/248‑113 (MQ=255)                                                                                                         acacTTATCTAAGATTTTTCCTAAATCGACGCAACTGTACTCGTCACTACACGCACATACAACGGAGGGGGGCTGCGATTTTCAATAATGCGTGATGCAGATCACAC‑AAAACACTCAATTACTTAACATAAATGtataagtcatacttttggtttgggtgtatttcaatctgttaaaaagtttttcgctacgctagcaagcaaaaatgaaacaggaataatcgaaatgggatgttgcgcacagtcaaaat                                                                                                                                        <  2:328971‑M1/250‑117 (MQ=255)                                                                                                              tATCTAAGATTTTTCCTAAATCGACGCAACTGTACTCGTCACTACACGCACATACAACGGAGGGGGGCTGCGATTTTCAATAATGCGTGATGCAGATCACAC‑AAAACACTCAATTACTTAACATAAATGtataagtcatacttttgttttgggtgtatttcaatctgttaaaaagtttttcgctacgctagcaagcaaaaatgaaacaggaataatcgaaatgggatgttgcgcacagtcaaaataactc                                                                                                                                   <  1:174688‑M1/250‑122 (MQ=255)                                                                                                                tCTAAGTTTTTTCCTAAATCGACGCAACTGTACTCGTCACTACACGCACATACAACGGAGGGGGGCTGCGATTTTCAATAATGCGTGATGCAGATCACAC‑AAAACACTCAATTACTTAAAATAAATGtctaagtcatacttttgttttgggtgtatttcaatctgttaaaaagtttttcgttacgctagcgagcaaaaatgaaacaggaataatcgaaatgggatgttgcgcacagtcaaaataactcacc                                                                                                                                >  2:488402‑M1/1‑127 (MQ=255)                                                                                                                   aaGATTTTTCCTAAATCGACGCAACTGTACTCGTCACTACACGCACATACAACGGAGGGGGGCTGCGATTTTCAATAATGCGTGATGCAGATCACAC‑AAAACACTCAATTACTTAACATAAATGtataagtcatacttttgttttgggtgtatttcaatctgttaaaaagtttttcgctacgctagcaagcaaaaatgaaacaggaataatcgaaatgggatgttgcgcacagtcaaaataactcac                                                                                                                                 <  1:453663‑M1/247‑124 (MQ=255)                                                                                                                                        cAACTGTACTCGTCACTACACGCACATACAACGGAGGGGGGCTGCGATTTTCAATAATGCGTGATGCAGATCACAC‑AAAACACTCAATTACTTAACATAAATGtataagtcatacttttgttttgggtgtatttcaatctgttaaaaagtttttcgctacgctagcaagcaaaaatgaaacaggaataatcgaaatgggatgttgcgcacagtcaaaataactcaccgtaaataatcatctgctataaata                                                                                                        <  1:135578‑M1/251‑149 (MQ=255)                                                                                                                                             gTACTCGTCACTACACGCACATACAACGGAGGGGGGCTGCGATTTTCAATAATGCGTGATGCAGATCACAC‑AAAACACTCAATTACTTAACATAAATGtataagtcatacttttgttttgggtgtatttcaatctgttaaaaagtttttcgctacgctagcaagcaaaaatgaaacaggaataatcgaaatgggatgttgcgcacagtcaaaataactcaccgtaaataatcatctgctataaataatcac                                                                                                   <  1:331108‑M1/251‑154 (MQ=255)                                                                                                                                               aCTCGTCACTACACGCACATACAACGGAGGGGGGCTGCGATTTTCAATAATGCGTGATGCAGATCACAC‑AAAACTCTCAATTACTTAACATAAATGtataagtcatacttttgttttgggtgtatttcaatctgttaaaaagttgttcgctacgctagcaagcaaaaatgaaacaggaataatcgaaatgggatgttgcgcacagtcaaaataactcaccgtaaataatcatctgctataaataatcact                                                                                                  <  2:502054‑M1/250‑155 (MQ=255)                                                                                                                                                            cGCACATACAACGGAGGGGGGCTGCGATTTTCAATAATGCGTGATGCAGATCACAC‑AAAACACTCAATTACTTAACATAAATGtataagtaatacttttgttttgggtgtatttcaatctgttaaaaagtttttcgctacgctagcaagcaaaaatgaaacaggaataatcgaagtgggatgttgcacacagtcaacataactcacagtaaataatcatcttctaaaaataatcactttcatgcaacaccc                                                                                    >  2:79340‑M1/1‑83 (MQ=255)                                                                                                                                                                   aCAACGGAGGGGGGCTGCGATTTTCAATAATGCGTGATGCAGATCACAC‑AAAACACTCAATTACTTAACATAAATGtataagtcatacttttgttttgggtgtatttcaatctgttaaaaagtttttcgctacgctagcaagcaaaaatgaaacaggaataatcgaaatgggatgttgcgcacagtcaaaataactcaccgtaaataatcatctgctataaataatcactttcatgcaataccagataagc                                                                             >  1:539751‑M1/1‑76 (MQ=255)                                                                                                                                                                                        tttCAATAATGCGTGATGCAGATCACAC‑AAAACACTCAATTACTTAACATAAATGtataagtcatacttttgttttgggtgtatttcaatctgttaaaaagtttttcgctacgctagcaagcaaaaatgaaacaggaataatcgaaatgggatgttgcgcacagtcaaaataactcaccgtaaataatcatctgctataaataatcactttcatgcaataccagataagctatttttaaacagacactta                                                         <  1:489368‑M1/250‑196 (MQ=255)                                                                                                                                                                                                               cacac‑aAAACACTCAATTACTTAACATAAATGtataagtcatacttttgttttgggtgtatttcaatctgttaaaaagtttttcgctacgctagcaagcaaaaatgaaacaggaataatcgaaatgggatgttgcgcacagtcaaaataactcaccgtaaataatcatctgctataaataatcactttcatgcaataccagataagctatttttaaacagacacttaccgcacaacaaactaattaaata                                  <  1:475924‑M1/250‑219 (MQ=255)                                                                                                                                                                                                                acac‑aAAACACTCAATTACTTAACATAAATGtataagtcatacttttgttttgggtgtatttcaatctgttaaaaagtttttcgctacgctagcaagcaaaaatgaaacaggaataatcgaaatgggatgttgcgcacagtcaaaataactcaccgtaaataatcatctgctataaataatcactttcatgcaataccagataagctatttttaaacagacacttaccgcacaacaaactaattaaatac                                 >  1:190772‑M1/1‑31 (MQ=255)                                                                                                                                                                                                                                     tAACATAAATGtataagtcatacttttgttttgggtgtatttcaatctgttaaaaagtttttcgctacgctagcaagcaaaaatgaaacaggaataatcgaaatgggatgttgcgcacagtcaaaataactcaccgtaaataatcatctgctataaataatcactttcatgcaataccagataagctatttttaaacagacacttaccgcacaacaaactaattaaatacaaagaaaggcaacaatcaac             <  1:131402‑M1/250‑240 (MQ=255)                                                                                                                                                                                                                                               gggTAATTACTCCAACTTATTGATATTGTTTTATGTTCAGATAATGCCCGATGACTTTGTCATGCAGCTCCACCGATTTTGAGAACGACAGCGACTTCCGTCCCAGCCGTGCCAGTTGCTGCCTCAGATTCAGGTTATGCCGCTCAATTCGCTGCGTATATCGCTTGCTGATTACGTGCAGCTTTCCCTTCAGGCTGGATTCATACAGCGGCCAGCCATCCGTCATCCATATCACCACGTCAAAGGGTGAc  <  2:228132/251‑1 (MQ=2)                                                                                                                                                                                                                                               |                                                                                                                                                                                                                                                           AGCCCCGGTAAAAAATAATTAGCATTAGAATAGTTGCGATAAGCTGCAATAAGCAGAACCACCTTTTTGGTTTAATATGTCCTTACAAATAGAAATGGGTCTTTACACTTATCTAAGATTTTTCCTAAATCGACGCAACTGTACTCGTCACTACACGCACATACAACGGAGGGGGGCTGCGATTTTCAATAATGCGTGATGCAGATCACAC‑AAAACACTCAATTACTTAACATAAATGGGTAATGACTCCAACTTATTGATAGTGTTTTATGTTCAGATAATGCCCGATGACTTTGTCATGCAGCTCCACCGATTTTGAGAACGACAGCGACTTCCGTCCCAGCCGTGCCAGGTGCTGCCTCAGATTCAGGTTATGCCGCTCAATTCGCTGCGTATATCGCTTGCTGATTACGTGCAGCTTTCCCTTCAGGCGGGATTCATACAGCGGCCAGCCATCCGTCATCCATATCACCACGTCAAAGGGTGAC  >  NC_000913/1978265‑1978752

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 14 ≤ ATCG/ATCG < 17 ≤ ATCG/ATCG < 34 ≤ ATCG/ATCG < 39 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑