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	55 [0]	[0] 55	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)	55 (1.020)	48/270	0.1	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

ATGGGTCTTTACACTTATCTAAGATTTTTCCTAAATCGACGCAACTGTACTCGTCACTACACGCACATACA‑ACGGAGGGGGGCTGCGATTTTCAATAATGCGTGATGCAGATCACACAAAACACTCAATTACTTAACATAAATGGGTAATGACTCCAACTTATTGATAGTGTTTTATGTTCAGATAATGCCCGATGACTTTGTCATGCAGCTCCACCGATTTTGAGAACGACAGCGACTTCCGTCCCAGCCGTGCCAGGTGCTGCCTCAGATTCAGGTTATGCC  >  NC_000913_3_pae_tpiA/1978359‑1978642                                                                                                                                                 |                                                                                                                                             aTGTGTCCTTACACTTATCCAATATTTTTCCTAACTCGACGCAACTGTACCCGTCACTACACACACATACA‑ACGGAGGGGGGCAGCGATTTTCAATAACGCGTGATGCAGATCACACAAAACACTCAATTACTTAACATAAATGtataa                                                                                                                                         <  1:162339‑M1/149‑6 (MQ=255) aTGGGTCTTTACACTTATCTAAGATTTTTCCTAAATCGACGCAACTGTACTCGTCACTACACGCACATACA‑ACGGAGGGGGGCTGCGATTTTCAATAATGCGTGATGCAGATCACACAAAACACTCAATTACTTAACATAAATGtataa                                                                                                                                         <  2:174165‑M1/149‑6 (MQ=255)      tCTTTACACTTATCTAAGATTTTTCCTAAATCGACGCAACTGTACTCGTCACTAAACG‑ACACCCACACGGAGGGGGGCTGCGATTTTCAATAATGCGTGATGCAGAACACACAAAACACTCAATTACTTAACATAAATGtataagtgat                                                                                                                                    >  1:746162‑M1/1‑139 (MQ=255)             acTTATCTAAGATTTTTCCTAAATCGACGCAACTGTACTCGTCACTACACGCACCTAAA‑ACGGAGGGGGGCTGCGATTTTCAATAATGCGTGATGCAGATCACACAAAACACTCAATTACTTAACCTACATGtctaagtcatacttttg                                                                                                                             >  2:833640‑M1/1‑132 (MQ=255)                   cTAAGATTTTTCCTAAATCGACGCAACTGTACTCGTCACTACACGCACATACA‑ACGGAGGGGGGCTGCGATTTTCAATAATGCGTGATGCAGATCACACAAAACACTCAATTACTTAACATAAATGtataagtcatacttttgttttgg                                                                                                                       <  1:920175‑M1/149‑24 (MQ=255)                    tAAGATTTTTCCTAAATCGACGCAACTGTACTCGTCACTACACGCACATACA‑ACGGAGGGGGGCTGCGATTTTCAATAATGCGTGATGCAGATCACACAAAACACTCAATTACTTAACATAAATGtcaaattcatacttttgttttggg                                                                                                                      >  2:204305‑M1/1‑125 (MQ=255)                    tAAGATTTTTCCTAAATCGACGCAACTGTACTCGTCACTACACGCACATACA‑ACGGAGGGGGGCTGCGATTTTCAATAATGCGTGATGCAGATCACACAAAACACTCAATTACTTAACATAAATGtataagtcatacttttgttttggg                                                                                                                      >  2:981508‑M1/1‑125 (MQ=255)                     aaGATTTTTCCTAAATCGACGCAACTGTACTCGTCACTACACGCACATACA‑ACGGAGGGGGGCTGCGATTTTCAATAATGCGTGATGCAGATCACACAAAACACTCAATTACTTAACATAAATGtataagtcatacttttgttttgggt                                                                                                                     <  1:645220‑M1/149‑26 (MQ=255)                       gATTTTTCCTAAATCGACGCAACTGTACTCGTCACTACACGCACATACA‑ACGGAGGGGGGCTGCGATTTTCAATAATGCGTGATGCAGATCACACAAAACACTCAATTACTTAACATAAATGtataagtcatacttttgttttgggtgt                                                                                                                   >  1:262866‑M1/1‑122 (MQ=255)                         tttttCCTAAATCGACGCAACTGTACTCGTCACTACACGCACATACA‑ACGGAGGGGGGCTGCGATTTTCAATAATGCGTGATGCAGATCACACAAAACACTCAATTACTTAACATAAATGtataagtcatacttttgttttgggtgtat                                                                                                                 >  2:950237‑M1/1‑120 (MQ=255)                                  aaTCGACGCAACTGTACTCGTCACTACACGCACATACA‑ACGGAGGGGGGCTGCGATTTTCAATAATGCGTGATGCAGATCACACAAAACACTCAATTACTTAACATAAATGtataagtcatacttttgttttgggtgtatttcactctg                                                                                                        >  1:251113‑M1/1‑111 (MQ=255)                                   aTCGACGCAACTGTACTCGTCACTACACGCACATACA‑ACGGAGGGGGGCTGCGATTTTCAATAATGCGTGATGCAGATCACACAAAACACTCAATTACTTAACATAAATGtataagtcatacttttgttttgggtgtatttcaatctgt                                                                                                       <  2:746162‑M1/149‑40 (MQ=255)                                   aTCGACGCAACTGTACTCGTCACTACACGCACATACA‑ACGGAGGGGGGCTGCGATTTTCAATAATGCGTGATGCAGATCACACAAAACACTCAATTACTTAACATAAATGtataagtcatacttttgttttgggtgtatttcaatctgt                                                                                                       <  2:565000‑M1/149‑40 (MQ=255)                                    tCGACGCAAGTGTACTGGTCACTACACGCACATAGA‑ACGGAGGGGGGCTGCGATTTTCAATAATGCGTGATGCAGTTCACACAAAACACTCAATTACTTAACATAAATGtatatgtcatacttttgttttgggtgtatttcaatctgtt                                                                                                      <  2:490667‑M1/149‑41 (MQ=255)                                         gCAACTGTACTCGTCACTACACGCACATACA‑ACGGAGGGGGGCTGCGATTTTCAATAATGCGTGATGCAGATCACACAAAACACTCAATTACTTAACATAAATGtataagtcatacttttgttttgggtgtatttcaatctgttaaaaa                                                                                                 <  1:935646‑M1/149‑46 (MQ=255)                                         gCAACTGTACTCGTCACTACACGCACATACA‑ACGGAGGGGGGCTGCGATTTTCAATAATGCGTGATGCAGATCACACAAAACACTCAATTACTTAACATAAATGtataagtaatactattgttttgggtgtatttcaatctgttaaaaa                                                                                                 >  1:943258‑M1/1‑104 (MQ=255)                                               gTACTCGTCACTACACGCACATACA‑ACGGAGGGGGGCTGCGATTTTCAATAATGCGTGATGCAGATCACACAAAACACTCAATTACTTAACATAAATGtataagtcatacttttgttttgggtgtatttcaatctgttaaaaagttttt                                                                                           <  1:124099‑M1/149‑52 (MQ=255)                                                tACTCGTCACTACACGCACATACA‑ACGGAGGGGGGCTGCGATTTTCAATAATGCGTGATGCAGATCACACAAAACACTCAATTACTTAACATAAATGtataagtcatacttttgttttgggtgtatttcaatctgttaaaaagtttttc                                                                                          >  1:348583‑M1/1‑97 (MQ=255)                                                   tCGTCACTACACGCACATACA‑ACGGAGGGGGGCTGCGATTTTCAATAATGCGTGATGCAGATCACACAAAACACTCAATTACTTAACATAAATGtataagtcatacttttgttttgggtgtattttaatctgttaaaaagtttttcgct                                                                                       >  1:685591‑M1/1‑94 (MQ=255)                                                   tCGTCACTACACGCACAAACA‑ACGGAGGGGGGCTGCGATTTTCAATAATGCGTGATGCAGATCACACAAAACACTCAATTACTTAACATAAATGtataagtcatacttttgttttgggtgtatttcaatctgttaaaaagtttttcgct                                                                                       <  2:138253‑M1/149‑56 (MQ=255)                                                            cacGCACATACA‑ACGGAGGGGGGCTGCGATTTTCAATAATGCGTGATGCAGATCACACAAAACACTCAATTACTTAACATAAATGtataagtcatacttttgttttgggtgtatttcaatctgttaaaaagtttttcgctacgctcgca                                                                              >  1:422677‑M1/1‑85 (MQ=255)                                                             acGCACATACA‑ACGGAGGGGGGCTGCGATTTTCAATAATGCGTGATGCAGATCACACAAAACACTCAATTACTTAACATAAATGtataagtcatacttttgttttgggtgtatttcaatctgttaaaaagtttttcgatacgctagcaa                                                                             >  2:622004‑M1/1‑84 (MQ=255)                                                               gCACATACA‑ACGGAGGGGGGCTGCGATTTTCAATAATGCGTGATGCAGATCACACAAAACACTCAATTGCTTAACATAAATGtttaggtcatacttttgcgttgggtgtatttcaatctgttaaaccgtttttcgctaccctagcatgc                                                                           >  2:619510‑M1/1‑82 (MQ=255)                                                                 acaTACA‑ACGGAGGGGGGCTGCGATTTTCAATAATGCGTGATGCAGATCACACAAAACACTCAATTACTTAACATAAATGtataagtcatacttttgttttgggtgtatttcaatctgttaaaacgtttttaactacgctagtaagcac                                                                         >  2:402030‑M1/1‑80 (MQ=255)                                                                 acaTACA‑ACGGAGGGGGGCTGCGATTTTCAATAATGCGTGATGCAGATCACACAAAACACTCAATTACTTAACATAAATGtataagtcatactttt                                                                                                                              <  2:822467‑M1/96‑17 (MQ=255)                                                                 acaTACA‑ACGGAGGGGGGCTGCGATTTTCAATAATGCGTGATGCAGATCACACAAAACACTCAATTACTTAACATAAATGtataagtcatactttt                                                                                                                              >  1:822467‑M1/1‑80 (MQ=255)                                                                   aTACA‑ACGGAGGGGGGCTGCGATTTTCAATAATGCGTGATGCAGATCACACAAAACGCTCAATTGCTTAACATAAATGtataagtcatacttttggtttgggtttatttcactgtgtaaaaaagtttttcgctacgctagcaagcaaaa                                                                       >  1:87918‑M1/1‑78 (MQ=255)                                                                   aTACA‑ACGGAGGGGGGCTGCGATTTTCAATAATGCGTGATGCAGATCACACAAAACACTCAATTACTTAACATAAATGtataagtcatacttttgttttgggtgtatttcaatctgttaaaaagtttttcgctacgctagcaagcaaaa                                                                       >  2:756586‑M1/1‑78 (MQ=255)                                                                       a‑aCGGAGGGGGGCTGCGATTTTCAATAATGCGTGATGCAGATCACACAAAACACTCAATTACTTAACGTAAATGtataagtcatacttttgttttgggtgtatttcaatctgttaaaaagtctttcgctacgctagcgatcaaagataa                                                                   >  1:449626‑M1/1‑74 (MQ=255)                                                                       a‑aCGGAGGGGGGCTGCGATTTTCAATAATGCGTGATGCAGATCACACAAAACACTCAATTACTTAACATAAATGtataagtcatacttttgttttgggtgtatttcaatctgttaaaaagtttttcgctacgctagcaagcaaaaatga                                                                   >  1:391168‑M1/1‑74 (MQ=255)                                                                             aGGGGGGCTGCGATTTTCAATAATGCGTGATGCAGATCACACAAAACACTCAATTACTTAACATAAATGtataagtcatacttttgttttgggtgtatttcaatctgttaaaaagtttttcgctacgctagcaagcaaaaatgaaacag                                                              <  1:950237‑M1/149‑81 (MQ=255)                                                                                ggggCTGCGATTTTCAATAATGCGTGATGCAGATCACACAAAACACTCAATTACTTAACATAAATGtataagtcatacttttgttttgggtgtatttcaatctgttaaaaagtttttcgctacgctagcaagcaaaaatgaaacaggaa                                                           <  2:962525‑M1/149‑84 (MQ=255)                                                                                    cTGCGATTTTCAATAATGCGTGATGCAGATCACACAAAACACTCAATTACTTAACATAAATGtataagtcatacttttgttttgggtgtatttcaatctgttaaaaagtttttcgctacgctagcaagcaaaaatgaaacaggaataat                                                       <  1:722067‑M1/149‑88 (MQ=255)                                                                                           tttCAATAATGCGTGATGCAGATCACACAAAACACTCAATTACTTAACATAAATGtataagtcatccttttgttttgggtgtatttcaatctgttaaaaagtttttcgctacgctagcaagcaaaaatgaaacaggaataatcgaaatg                                                >  1:140700‑M1/1‑55 (MQ=255)                                                                                            ttaaataatgcgTGATGCAGATCACACAAAACACTCAAATACTTAACATAAATGtataagtcatacttttgttttgggtgtatttcaatctgttaaaaagtttttcgctacgctagcaagcaaaaatgaaacaggaataatcgaaatgg                                               <  2:17261‑M1/146‑96 (MQ=255)                                                                                             tCAATAATGCGTGATGCAGATCACACAAAACACTCAATTACTTAACATAAATGtataagtcatacttttgttttgggtgtatttcaatctgttaaaaagtttttcgctacgctagcaagcaaaaatgaaacaggaataatcgaaatggg                                              >  1:245310‑M1/1‑53 (MQ=255)                                                                                                  aatGCGAGATGCAGATCACACAAAACACTCAATCAGATAACATAAATGtagacatcatactcttgtcttgggtgtatttcaatctgttaaaaagtttttcgctacgctagcaagcaaaaatgaaacaggaataatcgaaatgggatgtt                                         <  2:813259‑M1/149‑102 (MQ=255)                                                                                                        tGATGCAGATCACACAAAACACTCAATTACTTAACATACATGtataagtcatacttttgttttgggtgtatttcaatctgttaaaaagtttttcgctacgctagcaagcaaaaatgaaacaggaataatcgaaatggtatgttgcgcac                                   >  2:679720‑M1/1‑42 (MQ=255)                                                                                                         gATGCAGATCACACAAAAAACTCAATTACTTACCATAAATGtataagtcatacttttgttttgggtgtatttcaatctgttaaaaagtttttcgctacgctagcaagcaaaaatgaaacaggaataatcgaaatgggatgttgcgcaca                                  <  1:204305‑M1/149‑109 (MQ=255)                                                                                                          aTGCAGATCACACACAACACTCAATTACTTAACATAAATGtataagtcatacttttgttttgggtgtatttcaatctgttaaaaagtttttcgctacgctagcaagcaaaaatgaaacaggaataatcgaaatgggatgttgcgcacag                                 <  1:781946‑M1/149‑110 (MQ=255)                                                                                                            gCAGATCACACAAAACACTCAATTACTTAACATAAATGtataagtcatacttttgttttgggtgtatttcaatctgttaaaaagtttttcgctacgctagcaagcaaaaatgaaacaggaataatcgaaatgggaagttgcgcacagtc                               >  1:255154‑M1/1‑38 (MQ=255)                                                                                                            gCAGATCACACAAAACACTCAATTACTTAACATAAATGtataagtcatacttttgttttgggtgtatttacatctgttaaaaagtttttcgctacgctagcaagcaaaaatgaaacaggaataatcgaaatgggatgttgcgcacaatc                               >  2:265782‑M1/1‑38 (MQ=255)                                                                                                                aTCACACAAAACACTCAATTACTTAACATAAATGtataagtcatacttttgttttgggtgtatttcaatctgttaaaaagtttttcgctacgctagcaagcaaaaatgaaacaggaataatcgaaatgggatgttgcgcacagtcaaaa                           >  1:574585‑M1/1‑34 (MQ=255)                                                                                                                   acacaAAACACTCAATTACTTAACATAAATGtataagtcatacttttgttttgggtgtatttcaatctgttaaaaagtttttcgctacgctagcaagcaaaaatgaaacaggaataatcgaaatgggatgttgcgcacagtcaaaataa                        >  1:253416‑M1/1‑31 (MQ=255)                                                                                                                     acaAAACACTCAATTACTTAACATAAATGtataagtcatacttttgttttgggtgtatttcaatctgttaaaaagtttttcgctacgctagcaagcaaaaatgaaacaggaataatcgaaatgggatgttgcgcacagtcaaaataact                      >  1:216638‑M1/1‑29 (MQ=255)                                                                                                                       aaaaCACTCAATTACTTAACATAAATGtataagtcatacttttgttttgggtgtatttcaatctgttaaaaagtttttcgctacgctagcaagcaaaaatgaaacaggaataatcgaaatggggtgttgcgcacagtcaaaataactca                    >  2:399811‑M1/1‑27 (MQ=255)                                                                                                                        aaaCACTCAATTACTTAACATAAATGtataagtcatacttttggtttgggtgtatttcaatctgttaaaaagtttttcgctacgctagcaagcaaaaatgaaacaggaataatcgaaatgggatgttgcgcacagtcaaaataactcac                   <  1:318490‑M1/149‑124 (MQ=255)                                                                                                                           cacTCAATTACTTAACATAAATGtataagtcatacttttgttttgggtgtagttcaatatgttaaaaagtttttggctacgctagcaagcaaaaatgaaacaggaataatcgacatgggatgttacgcacagtcaaaataactcaccga                >  2:312402‑M1/1‑23 (MQ=255)                                                                                                                            acTCAATTACTTAACATAAATGtataagtcatacttttgttttgggtgtatttcaatctgttaaaaagtttttcgctacgctagcaagccaaaatgaaacaggaataatcgaaatgggatgttaggcacagtcaaaataaatcgcagga               >  1:1008506‑M1/1‑22 (MQ=255)                                                                                                                                aaTTACTTAACATAAATAtataagtcatacttttgttttgggtgtatttcaatctgttaaaaagtttttcgctacgctggcaagcaaaaatgaaacaggaataatcgaaattggatgttgccaacagacaaaataactaacagtaaata           >  2:586593‑M1/1‑18 (MQ=255)                                                                                                                                     cTTAACATAAATGtataagtcatacttttgttttgggtgtatttcaatctgttaaaaagtttttcgctacgctagcaagcaaaaatgaaacaggaataatcgaaatgggatgttgcgcacagtcaaaataactcaccgtaaataatcat      <  1:978993‑M1/149‑137 (MQ=255)                                                                                                                                      ttAACATAAATGtataagtcatacttttgttttgggtgtatttcaatctgttaaaaagtttttcgctacgctagcaagcaaaaatgaaacaggaataatcgaaatgggatgttgcgcacagtcaaaataactc                     <  2:100306‑M1/133‑122 (MQ=255)                                                                                                                                      ttAACATAAATGtataagtcatacttttgttttgggtgtatttcaatctgttaaaaagtttttcgctacgctagcaagcaaaaatgaaacaggaataatcgaaatgggatgttgcgcacagtcaaaataactc                     >  1:100306‑M1/1‑12 (MQ=255)                                                                                                                                       tAACATAAATGtataagtcatacttttgttttgggtgtatttcaatctgttaaaaagtttttcgctacgctagcaagcaaaaatgaaacaggaataatcgacatggggtgttgcgcacagtgaaaataactcaccgtaaataatcatct    <  1:399811‑M1/149‑139 (MQ=255)                                                                                                                                         aCATAAATGtataagtcatacttttgttttgggtgtatttcaatctgttaaaaagtttttcgctacgctagcaagcaaaaatgaaacaggaataatcgaaatgggatgttgcgcacagtcaaaataactcaccgtaaataatcatctgc  >  1:163758‑M1/1‑9 (MQ=255)                                                                                                                                                 |                                                                                                                                             ATGGGTCTTTACACTTATCTAAGATTTTTCCTAAATCGACGCAACTGTACTCGTCACTACACGCACATACA‑ACGGAGGGGGGCTGCGATTTTCAATAATGCGTGATGCAGATCACACAAAACACTCAATTACTTAACATAAATGGGTAATGACTCCAACTTATTGATAGTGTTTTATGTTCAGATAATGCCCGATGACTTTGTCATGCAGCTCCACCGATTTTGAGAACGACAGCGACTTCCGTCCCAGCCGTGCCAGGTGCTGCCTCAGATTCAGGTTATGCC  >  NC_000913_3_pae_tpiA/1978359‑1978642

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: ‑