Predicted mutation
evidence	seq id	position	mutation	annotation	gene	description
MC JC	NC_000913	1,978,503	Δ776 bp		insB1–insA	insB1, insA

Missing coverage evidence...
			seq id	start	end	size	←reads	reads→	gene	description
*	*	÷	NC_000913	1978503–1979270	1979278	9–776	48 [0]	[0] 48	insB1–insA	insB1, insA

New junction evidence
		seq id	position	reads (cov)	reads (cov)	score	skew	freq	annotation	gene	product
*	?	NC_000913	= 1978502	0 (0.000)	47 (1.300)	38/268	0.0	100%	intergenic (‑305/+16)	flhD/insB1	flagellar class II regulon transcriptional activator, with FlhC/IS1 transposase B
	?	NC_000913	1979279 =	0 (0.000)					intergenic (‑64/‑474)	insA/uspC	IS1 repressor TnpA/universal stress protein

GTCTTTACACTTATCTAAGATTTTTCCTAAATCGACGCAACTGTACTCGTCACTACACGCACATACAACGGAGGGGGGCTGCGATTTTCAATAATGCGTGATGCAGATCACACAAAACACTCAATTACTTAACATAAATGGGTAATGACTCCAACTTATTGATAGTGTTTTATGTTCAGATAATGCCCGATGACTTTGTCATGCAGCTCCACCGATTTTGAGAACGACAGCGACTTCCGTCCCAGCCGTGCCAGGTGCTGCCTCAGATTCAGGTTATG  >  NC_000913/1978363‑1978640                                                                                                                                            |                                                                                                                                           gTCTTTACACTTATCTAAGATTTTTCCTAAATCGACGCAACTGTACTCGTCACTACACGCACATACAACGGAGGGGGGCTGCGATTTTCAATAATGCGTGATGCAGATCACACAAAACACTCAATTACTTAACATAAATGtat                                                                                                                                         <  2:637933‑M1/143‑4 (MQ=255)  tCTTTACACTTATCTAAGATTTTTCCTAAATCGACGCAACTGTACTCGTCACTACACGCACATACAACGGAGGGGGGCTGCGATTTTCAATAATGCGTGATGCAGATCACACAAAACACTCAATTACTTAACATAAATGtata                                                                                                                                        >  2:505528‑M1/1‑139 (MQ=255)  tCTTTACACTTATCTAAGATCTTTCCTAAATCGACGCAACTGTACTCGTCACTACACGCACATACAACGGAGGGGGGCTGCGATTTTCAATAATGAGTGATGCAGATCACACAAAACACTCAATTACTTAACATAAATGtata                                                                                                                                        <  1:276410‑M1/143‑5 (MQ=255)   cTTTACACTTATCTAAGATTTTTCCTAAATCGACGCAACTGTACTCGTCACTACACGCACATACAACGGAGGGGGGCTGCGATTTTCAATAATGCGTGATGCAGATCACACAAAACACTCAATTACTTAACATAAATGtataa                                                                                                                                       <  1:504110‑M1/143‑6 (MQ=255)   cTTTACACTTATCTAAGATTTGGCCCAAAGCGACGCAACTGTACTCGTCACTACACGCACATACAACGGAGGGGGGCTGCGATTTTCAATAATGCGTGATGCAGATCACACAAAACACTCAATTACTTAACATAAATGtataa                                                                                                                                       <  2:387520‑M1/143‑6 (MQ=255)              tcgaagatTTTTCCTAAATCGACGCAACTGTACTCGTCACTACACGCACATACAACGGAGGGGGGCTGCGATTTTCAATAATGCGTGATGCAGATCACACAAAACACTCAATTACTTAACATAAATGtataagtcatactttt                                                                                                                            <  1:324223‑M1/140‑17 (MQ=255)              tCTAAGATTTTTCCTAAATCGACGCAACTGTACTCGTCACTACACGCACATACAACGGAGGGGGGCTGCGATTTTCAATAATGCGTGATGCAGATCACACAAAACACTCAATTACTTAACATAAATGtataagtcatactttt                                                                                                                            <  2:433980‑M1/143‑17 (MQ=255)              tCTAAGATTTGTCCTAAATCGACGCAACTGTACTCGTCACTACACGCACATACAACGGAGGGGGGCTGCGATTTTCAATAATGCGTGATGCAGATCACACAAAACACTCAATTACTTAACATAAATGtataagtcatactttt                                                                                                                            <  1:452369‑M1/143‑17 (MQ=255)               cgaagaTTTTTCGTGAATCGACGCGGCTGGAGTCGTCAGTACACGCACGTACGGCGGAGGGGGGCTGCGATTTTCAATAATGCGTGATGCAGATCACACAAAACACTCAATTACTTAACATAAATGtataagtcatactgttg                                                                                                                           <  1:28491‑M1/141‑18 (MQ=255)                   gATTTTTCCTAAATCGACGCAACTGTACTCGTCACTACACGCACATACAACGGAGGGGGGCTGCGATTGTCAATAATGCGTAATCCACATCACACAAAACACTCAATTACTTAACATCAATGtataagtcatacttttgcttt                                                                                                                       >  1:365391‑M1/1‑122 (MQ=255)                     tttttCCTAAATCGACGCAACTGTACTCGTCACTACACGCACATACAACGGAGGGGGGCTGCGATTTTCAATAATGTGTGATGCAGAACACAATAAACACTAAATTACTTAACATAAATGtataagtcatacttttgttttgg                                                                                                                     >  2:248962‑M1/1‑120 (MQ=255)                     tttttCCTAAATCGACGCAACTGTACTCGTCACTACACGCACATACAACGGAGGGGGGCTGCGATTTTCAATAATGCGTGATGCAGATCACACAAAACACTCAATTACTTAACATAAATGtataagtcatacttttgttttgg                                                                                                                     <  1:316092‑M1/143‑24 (MQ=255)                          ccTAAATCGACGCAACTGTACTCGTCACTACACGCACATACAACGGAGGGGGGCTGCGATTTTCAATAATGCGTGATGCAGATCACACAAAACACTCAATTACTTAACATAAATGtataagtcatacttttgttttgggtgta                                                                                                                <  2:275404‑M1/143‑29 (MQ=255)                            tAAATCGACGCAACTGTACTCGTCACTACACGCACATACAACGGAGGGGGGCTGCGATTTTCAATAATGCGTGATGCAGATCACACAAAACACTCAATTACTTAACATAAATGtataagtcatacttttgttttgggtgtatt                                                                                                              >  2:567177‑M1/1‑113 (MQ=255)                             aaaTCGACGCAACTGTACTCGTCACTACACGCACATACAACGGAGGGGGGCTGCGATTTTCAATAATGCGTGATGCAGATCACACAAAACACTCAATTACTTAACATAAATGtataagtcatacttttgctttgggtgcattt                                                                                                             >  1:56688‑M1/1‑112 (MQ=255)                               aTCGACGCAACTGTACTCGTCACTACACGCACATACAACGGAGGGGGGCTGCGATTTTCAATAATGCGTGATGCAGATCACACAAAACACTCAATTACTTAACATAAATGtataagtcatacttttgtcttgggtgtatttcc                                                                                                           >  2:31147‑M1/1‑110 (MQ=255)                                  gACGCAACTGTACTCGTCACTACACGCACATACAACGGAGACAGGCTGCGATTTTCAATAACGCGCGAGCCAGATCACACAAAACACTCAATTACTTAACATAAATGtataagtcatacttttgttttgggtgtatttcaatc                                                                                                        <  2:217727‑M1/143‑37 (MQ=255)                                      cAACTGTTCGCGTCCCTACACACACATACAACGGAGGGGGGCTGCGATTTTCAATAATGCGTGATGCAGATCACACAAAACACTCAATTACTTAACATAAATGtataagtcatacttttgttttgggtgtatttcaatctgtt                                                                                                    <  2:88683‑M1/143‑41 (MQ=255)                                       aaCTGCACTCGTCACTACACGCACATACAACGGAGGGGGGCTGCGATTTTCAATAATGCGTGATGCAGATCACACAAAACACTCAATTACTTAACATAAATGtataagtcatacttttgttttgggtgtatttcaatctgtta                                                                                                   >  2:273648‑M1/1‑102 (MQ=255)                                          tGTACTCGTCACTACACGCACATACAACGGAGGGGGGCTGCGATTTTCAATAATGCGTGATGCAGATCACACATAACACTCAATTACTTAACATAAATGtataagtcatacttttgttttgggtgtatttcaatctgttaaaa                                                                                                >  1:355393‑M1/1‑99 (MQ=255)                                          tGTACTCGTCACTACACGCACATACAACGGAGGGGGGCTGCGATTTTCAATAATGCGTGATGCAGATCACACAAAACCCTCAATTACTTAACATAAATGtataagtcatacttctgttttggctgtatttacatgtgttaaaa                                                                                                >  1:381332‑M1/1‑99 (MQ=255)                                           gTACTCGTCACTACACGCACATACAACGGAGGGGGGCTGCGATTTTCAATAATGCGTGATGCAGATCACACAAAACACTCAATTACTTAACATAAATGtataagtcatacttttgctttgggtgtatttcaatctgttacaaa                                                                                               >  2:632798‑M1/1‑98 (MQ=255)                                               tCGTCACTACACGCACATACAACGGAGGGGGGCTGCGATTTTCAATAATCCGTGATGCAGATCACACAAAACACTCAATTACTTAACATACATGcaaaagtcatacttttgttttgggtgtatttcaatctgttaaaaagttt                                                                                           >  1:656042‑M1/1‑94 (MQ=255)                                                  tCACTACACGGACATACAACGGAGGGGGGCTGCGATTTTCAATAATGCGTGATGCAGATCACACAAAACACTTATTTACTTAACATAAATGtataagtcatacttttgttttgggtgtatttcaatctgttaaaaagtttttc                                                                                        <  1:84611‑M1/143‑53 (MQ=255)                                                      tagacccacatacaacGGAGGGGGGCTGCGATTTTCAATAATGAGTGATGCAGATCACACAAAACACTCAATTACTTAACATAAATGtataagtcatacttttgttttgggtgtatttcaatctgttaaaaagtttttcgcta                                                                                    <  1:239113‑M1/137‑57 (MQ=255)                                                          cgctcctacatcgGAGGGGGGCTGCGATTTTCAATAATGCGTGATGCAGATCACACAAAACACTCAATTACTTAACTTAAATCtataagtcatacttttgttttgggtgtatttcaatctgttaaaaagtttttcgctacgct                                                                                <  1:79880‑M1/137‑61 (MQ=255)                                                                tACAACGGAGGGGGGCTGCGATTTTCAATAATGCGTGATGCAGATCACACAAAACACTCAATTACTTAACATAAATGtataagtcatacttttgttttgggtcacatgcgctcaggtaaaaagtttttcgctacgctagcaag                                                                          >  1:294896‑M1/1‑77 (MQ=255)                                                                 aCAACGGAGGGGGGCTGCGATTTTCAATAATGCGTGATGCAGATCACACAAAACACTCAATTACTTAACATAAATGtataagtcatacttttgtggttggagtatttcaatctgttaaaaagtttttcgccacgctagcaagc                                                                         >  2:125692‑M1/1‑76 (MQ=255)                                                                 aCAACGGAGGGGGGCTGCGATTTTCAATAATGCGTGATGCAGATCACACAAAACACTCAATTACTTAACATAAATGtataagtcatactattgttttgggtgtatttcaatctgataaaaagtttttcgctacgctagcaagc                                                                         >  1:54001‑M1/1‑76 (MQ=255)                                                                      ggAGGGGGGCTGCGATTTTTAATATGTCGTGATGAAGATCACACAAAACACTCAATTACTTAACATAAATGtataagtcatacttttgttttgggtgtatttcaatctgttaaaaagtttttcgctacgctagcaagcaaaaa                                                                    <  1:537402‑M1/143‑73 (MQ=255)                                                                           ggggCTGCGATTTTCAATAATGCGTGATGCAGATCACACAAAACACTCAATTACTTAACATAAATGtataagtcatacttttgttttgggtgtatttcaatctgttaaaaagtttttcgctacgctagcaagcaaaaatgaaa                                                               <  2:574780‑M1/143‑78 (MQ=255)                                                                                            taagGCGTGATGCTGATCACACAAAACCCTCAATTACTTACCATAAATGtataagtcatacttttgttttgggtgtatttcaatctgttaaaaagtttttcgctacgctagcaagcaaaaatgaaacaggaataatcgaaatg                                              <  2:629974‑M1/143‑95 (MQ=255)                                                                                             catgCGTGATGCAGATCACACAAAACACTCAATTACTTAACATAAATGtataagtcatacttttgttatgggtgtatttcaatctgttaaaaagtttttcgctacgctagcaagcaaaaatgaaacaggaataatcgaaatgg                                             <  2:538974‑M1/142‑96 (MQ=255)                                                                                                     aTGCAGATCACACAAAACACTCAGTTACGTAACGTAAAGGtgtaagtcatacttttgttttgggtgtatttcaatctgttaaaaagtttttcgctacgctagcaagcaaaaatgaaaaaggtataatcgaaatgggatgttgc                                     <  1:554679‑M1/143‑104 (MQ=255)                                                                                                        cAGATCACACAAAACACTCAATTACTTAACATAAATGtataagtcatacttttgttttgggtgtatttcaatctgttaaaaagtttttcgctacgctagcaagcaaaaatgaaacaggaataatcgaaatgggatgttgcgca                                  <  2:358251‑M1/143‑107 (MQ=255)                                                                                                           aTCACACAAAACACTCAATTACTTAACATAAATGtataagtcatacttttgttttgggtgtatttcaatctgttaaaaagtttttcgctacgctagcaagcaaaaatgaaacaggaataatcgaaatgggatgttgcgcacag                               <  2:173901‑M1/143‑110 (MQ=255)                                                                                                            tccccgaagttactcacttacttcACATAAATGtataagtcatacttttgttttgtgtgtatttcaatcgtgtaaagagtttttcgctacgctagcaagcaaaaatgaaacaggaataatcgtaatgggatgttgcgcacagt                              <  1:220117‑M1/132‑111 (MQ=255)                                                                                                                 caAAACACTCAATTACTTAACATAAATGtataagtcatacttttgttttgggtgtatttcaatctgttaaaaagtttttcgctacgctagcaagcaaaaatgaaacaggaataatcgaaatgggatgttgcgcacagtcaaaa                         <  1:273648‑M1/143‑116 (MQ=255)                                                                                                                     tcacttcattaattaacataaaTGtataagtcatacttttgttttgggtggatttcaatctgttaaaaagtggttcgctacgctagcaagcaaaaatgaaacaggaataatcgaaatgggatgttgcgcacagtcaaaataac                     <  2:374769‑M1/136‑120 (MQ=255)                                                                                                                         tCAATTGCTTAACATAAATGtataagtcatactgttgttttgggtgtatttcaatctgttaaagagtttttcgctacgctagcaagcaaaaatgaaacaggaatagtcgaaatgggaggtggcacacagtcaaaataagtcgc                 >  1:317361‑M1/1‑20 (MQ=255)                                                                                                                         tCAATTACTTAACATAAATGtataagtcatacttttgttttgggtgtatttcaatctgttaaaaagtttttcgctacgctagcaagcaaaaatgaaacaggaataatcgaaatggggtgttgcgcacagtcgaaataactcac                 >  2:200698‑M1/1‑20 (MQ=255)                                                                                                                         tCAATTACTTAACATAAATGtataagtcatacttttgttttgggtgtatttcaatctgttaaaaagtttttcgctacgctagcaagcaaaaatgaaacaggaataatcgaaatgggatgttgcgcacagtcaaaataactcac                 >  2:389826‑M1/1‑20 (MQ=255)                                                                                                                          cAATTACTTAACATAAATGtataagttatacttttgttttgggtgtatttcaatctgttaaaaagtttttcgctacggtagcaagcaaaaatgaaacaggaataatcgaaaagggatgttgcgcacagtcaaaataactcacc                >  1:551719‑M1/1‑19 (MQ=255)                                                                                                                          cAATTACTTAACATAAATGtataagtcatacttttgttttgggtgtatttcaatctgttaaaaagtttttcgctacgctagcaagcaaaaatgaaacaggaataatcgaaatgggatgttgcgcacagtcaaaataactcacc                <  2:296644‑M1/143‑125 (MQ=255)                                                                                                                           aaTTACTTAACATAAATGtataagtcatacttttgttttgggtgtatttcaatctgttaaaaagtttttcgctacgctagcaagcaaaaatgaaacaggaataatcgaaatgggatgttgcgcacagtcaaaataactcaccg               >  2:499446‑M1/1‑18 (MQ=255)                                                                                                                                 ttAACATAAATGtataagtcatacttttgttttgggtgtatttcaatctgttaaaaactttctctctacgctagcaagcaaaaatgaaacaggaataatcgaaatgggatgttgctcacagtcaaaatacctcaccgtaaata         >  1:451678‑M1/1‑12 (MQ=255)                                                                                                                                  tAAAATAAATGtataagtcatacttttgttttgcgtgtatttcaatctgttaaaaagtttttcgttacgctagcaagcaaaaatgaaacaggaataatcgaaatgggatgttgcgcacagtcaaaataactcaccgtaaataa        <  2:548837‑M1/143‑133 (MQ=255)                                                                                                                                        aaaTGtataagtcatacttttgttttgggtgtatttcaatctgttaaaaagtttttcgctacgctagcaagcaaaaatgaaacaggaataatcgaaatgggatgttgcgcacagtcaaaataactcaccgtaaataatcatct  <  2:513040‑M1/143‑139 (MQ=255)                                                                                                                                            |                                                                                                                                           GTCTTTACACTTATCTAAGATTTTTCCTAAATCGACGCAACTGTACTCGTCACTACACGCACATACAACGGAGGGGGGCTGCGATTTTCAATAATGCGTGATGCAGATCACACAAAACACTCAATTACTTAACATAAATGGGTAATGACTCCAACTTATTGATAGTGTTTTATGTTCAGATAATGCCCGATGACTTTGTCATGCAGCTCCACCGATTTTGAGAACGACAGCGACTTCCGTCCCAGCCGTGCCAGGTGCTGCCTCAGATTCAGGTTATG  >  NC_000913/1978363‑1978640

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: ‑