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	38 [0]	[0] 37	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)	36 (1.090)	30/268	0.2	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

ATGGGTCTTTACACTTATCTAAGATTTTTCCTAAATCGACGCAACTGTACTCGTCACTACACGCACATACAACGGAGGGGGGCTGCGATTTTCAATAATGCGTGATGCAGATCACACAAAACACTCAATTACTTAACATAAATGGGTAATGACTCCAACTTATTGATAGTGTTTTATGTTCAGATAATGCCCGATGACTTTGTCATGCAGCTCCACCGATTTTGAGAACGACAGCGACTTCCGTCCCAGCCGTGCCAGGTGCTGCCTCAGATTCAGGTTATGCCGC  >  NC_000913_3_pae_tpiA/1978359‑1978644                                                                                                                                                |                                                                                                                                               aTGGGTCTTTACACTTATCTAAGATTTTTCCTAAATCGACGAAACTGTACTCGTCACTCAACGCACATAAAACGGAGGGGGGCTGCGATTATACATAATGCGTAATTCAGCACACACAAAACAACACATTACTTAACAACAATgtctaa                                                                                                                                           >  2:73108/1‑144 (MQ=255)        tttACACTTATCTAAGATTTTTCCTAAATCGACGCAACTGTACTCGTCACTACACGCACATACAACGGAGGGGGGCTGCGATTTTCAATAATGCGTGATGCAGATCACACAAAACACTCAATTACTTAACATAATTGtataagtcatac                                                                                                                                    >  2:199202‑M1/1‑137 (MQ=255)             acTTATCTAAGATTTTTCCTAAATCGACGCAACTGTACTCGTCACTACACGCACATACAACGGAGGGGGGCTGCGATTTTCAATAATGCGTGATGCAGATCACACAAAACACTCAATTACTTAACATAAATGtataagtcatacttttg                                                                                                                               >  2:219965‑M1/1‑132 (MQ=255)             acTTATCTAAGATTTTTCCTAAATCGACGCAACTGTACTCGTCACTACACGCACATACAACGGAGGGGGGCTGCGATTTTCAATAATGCGTGATGCAGATCACACAAAACACTCAATTACTTAACATAAATGtataagtcatacttttg                                                                                                                               >  1:291114‑M1/1‑132 (MQ=255)               ttATCTAAGATTTTTCCTAAATCGACGCAACTGTACTCGTCACTACACGCACATACAACGGAGGGGGGCTGCGATTTTCAATAATGCGTGATGCAGATCACACAAAACACTCAATTACTTAACATAAATGtataagtcatacttttgtt                                                                                                                             >  1:620237‑M1/1‑130 (MQ=255)                 gtgagttatttttccTAAATCGACGCAACTGTACTCGTCACTACACGCACATACAACGGAGGGGGGCTGCGATTTTCAATAATGCGTGATGCAGATCACACAAAACACTCAATTCCTTAACATAAATGtataagtcatacttttgtttt                                                                                                                           >  2:194111‑M1/8‑128 (MQ=255)                    gaagATTTTTCCTAAATCGACGCAACTGTACTCGTCACTACACGCACATACAACGGAGGGGGGCTGCGATTTTCAATAATGCGTGATGCAGATCACACAAAACACTCAATTACTTAACATAAATGtataagtcatacttttgttttggg                                                                                                                        <  1:266298‑M1/148‑25 (MQ=255)                                         ttttttgtactTGTCACTACACGCACATACAACTGAGGGGGGCTGCGACTTTAAATAATGCGTGATGCAGATCACACAAACCACTCAATTACTTAACATAAATGtataagtcatacttttgttttggttgtatttcaatctgttaaaaa                                                                                                   <  2:274506‑M1/144‑46 (MQ=255)                                              tGTACTCGTCACTACACGCACATACAACGGAGGGGGGCTGCGATTTTCAATAATGCGTGATGCAGATCACACAAAACACTCAATTACTTAACATAAATGtataagtcatacttttgttttgggtgtatttcaatctgttaaaaagtttt                                                                                              >  1:502569‑M1/1‑99 (MQ=255)                                                    cGTCACTACACGCACATACAACGGAGGGGGGCTGCGATTTTCAATAATGCGTGATGCAGATCACACAAAACACTCAATTACTTAACATAAATGtataagtcatacttttgttttgggtgtatttcaatctgttaaaaagtttttcgcta                                                                                        <  2:183554‑M1/149‑57 (MQ=255)                                                           acacGCACATACAACGGAGGGGGGCTGCGATTTTCAATAATGCGTGATGCAGATCACACAAAACACTCAATTACTTAACATAAAGGtataagtcatacttttgttttgggtgtatttcaatctgttaaaaagtttttcgctacgctagc                                                                                 <  1:199202‑M1/149‑64 (MQ=255)                                                                 acaTACAACGGAGGGGGGCTGCGATTTTCAATAATGCGTGATGCAGATCACACAAAACACTCAATTACTTAACATAAATGtataagtcatacttttgttttgggtgtatttcaat                                                                                                             >  2:112635‑M1/1‑80 (MQ=255)                                                                 acaTACAACGGAGGGGGGCTGCGATTTTCAATAATGCGTGATGCAGATCACACAAAACACTCAATTACTTAACATAAATGtataagtcatacttttgttttgggtgtatttcaat                                                                                                             <  1:112635‑M1/115‑36 (MQ=255)                                                                       aaCGGAGGGGGGCTGCGATTTTCAATAATGCGTGATGCAGATCACACAAAACACTCAATTACTTAACATAAATGtataagtcatacttttgttttgggtgtatttcaatctgttaaaaagtttttcgctacgctagcaagcaaaaatga                                                                     >  1:378095‑M1/1‑74 (MQ=255)                                                                       aaCGGAGGGGGGCTGCGATTTTCAATAATGCGTGATGCAGATCACACAAAACACTCAATTACTTAACATAAATGtataagtcatacttttgttttgggtgtatttcaatctgttaaaaagtttttcgctacgctagcaagcaaaaatga                                                                     >  2:126910‑M1/1‑74 (MQ=255)                                                                                  gCTGCGATTTTCAATAATGCGTGATGCAGATCACACAAAACACTCAATTACTTAACATAAATGtataagtcatacttttgttttgggtgtatttcaatctgttaaaaagtttttcgctacgcta                                                                                   <  1:270501‑M1/124‑62 (MQ=255)                                                                                  gCTGCGATTTTCAATAATGCGTGATGCAGATCACACAAAACACTCAATTACTTAACATAAATGtataagtcatacttttgttttgggtgtatttcaatctgttaaaaagtttttcgctacgcta                                                                                   >  2:270501‑M1/1‑63 (MQ=255)                                                                                   cTGCGATTTTCAATAATGCGTGATGCAGATCACACAAAACACTCAATTACTTAACATAAATGtataagtcatacttttgttttgggtgtatttcaatctgttaaaaagtttttcgctacgctagcaagcaaaaatgaaacaggaataat                                                         >  2:351244‑M1/1‑62 (MQ=255)                                                                                    tGCGATTTTCAATAATGCGTGATGCAGATCACACAAAACACTCAATTACTTAACATAAATGtataagtcatacttttgttttgggtgtatttcaatctgttaaaaagtttttcgctacgctagcaagcaaaaatgaaaaaggaataatc                                                        >  1:322946‑M1/1‑61 (MQ=255)                                                                                       gATTTTCAATAATGCGTGATGCAGATCACACAAAACACTCAATTACTTAACATAAATGtataagtcatacttttgttttgggtgtatttcaatctgttaaaaagtttttcgctacgctagcaagcaaaaatgaaacaggaataatcgaa                                                     <  2:378095‑M1/149‑92 (MQ=255)                                                                                          tttAAATAATGCGTGATGCAGATCACACAAAACACTCAATTACTTAACATAAATGtataagtcatacttttgttttgggtgtatttcaatctgttaaaaagtttttcgctacgctagcaagcaaaaatgaaacaggaataatcgaaatg                                                  >  1:493425‑M1/1‑55 (MQ=255)                                                                                              aataatGCGTGATGCAGATCACACAAAACACTCAATTACTTAACATAAATGtataagtcatacttttgttttgggtgtatttcaatctgttaaaaagtttttcgctacgctagcaagcaaaaataaaacaggaataatcgaaatgggat                                              >  1:268243‑M1/1‑51 (MQ=255)                                                                                                              gATCACACAAAACACTCAATTACTTAACATAAATGtataagtcatacttttgttttgggtgtatttcaatctgttaaaaagtttttcgctatgctagcaagcaaaaatgaaacaggaatagtcaaaatatgctcttgcgaccagttaaa                              >  2:117342‑M1/1‑35 (MQ=255)                                                                                                              gATCACACAAAACACTCAATTACTTAACATAAATGcataagtcatacttttgttttgggtgtatttcaatctgttaaaaagtttttcgctacgctagcaagcaaaaatgaaacaggaataatcgaaatgggatgttgcgcacagtcaaa                              >  2:132286‑M1/1‑35 (MQ=255)                                                                                                                    gcaaAACACTCAATTACTTAACATAAATGtataagtcatacttttgttttgggtgtatttcaatctgttaaaaagtttttcgctacgctagcaagcaaaaatgaaacaggaataatcgaaatgggatgttaggcacagtaaaaataact                        >  2:321585‑M1/2‑29 (MQ=255)                                                                                                                      aaaaCACTCAATTACTTAACATAAATGtataagtcatacttttgttttgggtgtatttcaatctgttaaaaagtttttcgctacgctagcaagcaaaaatgaaacaggaataatcgaaatgggatgttgcgcacagtcaaaataactca                      <  1:126910‑M1/149‑123 (MQ=255)                                                                                                                       aaaCACTCAATTACTTAACATAAATGtataagtcatacttttgttttgggtgtatttcaatctgttaaaaagtttttcgctacgctagcaagcaaaaatgaaacaggaataatcgaaatgggatgttgcgcacagtcaaaataactcac                     <  1:194111‑M1/149‑124 (MQ=255)                                                                                                                        aaCACTCAATTCCTTATCATAAATGtataagtcatactgttgttttgggtgtatttcaatctgttaaaaagtttttcgctgcgctagcaacccaaaatgaaacaggaataatcgaaatgcgatgttgcgcacagtcaaaataactcacc                    <  2:179044‑M1/149‑125 (MQ=255)                                                                                                                           acTCAATTACTTAACATAAATGtataagtcatacttttgttttgggtgtatttcaatctgttaaaaagtttttcgctacgctagcaagcaaaaatgaaacaggaataatcgaaatgggatgttgcgcacagtcaaaataactcaccgta                 >  1:555220‑M1/1‑22 (MQ=255)                                                                                                                             tCAATTACTTAACATAAATGtataagtcatacttttgttttgggtgtatttcaatctgttaaaaagtttttcgctacgctagcaagcaaaaatgaaacaggaataatcgaaatgggatgttgcgcacagtcaaaataactcaccgtaa                >  1:552770‑M1/1‑20 (MQ=255)                                                                                                                             tCAATTACTTAACATAAATGtataagtcatacttttgttttgggtgtatttcaatctgttaaaaagtttttcgctacgctagcaagcaaaaatgaaacaggaataatcgaaatgggatgttgcgcacagtcaaaataactcaccgtaa                <  2:552770‑M1/148‑129 (MQ=255)                                                                                                                                 ttACTTAACATAAATGtataagtcatacttttgttttgggtgtatttcaatctgttaaaaagtttttcgctacgctagcaagcaaaaatgaaacaggaataatcgaaatgggatgttgcgcacagtcaaaataactcaccgtaaataat           >  2:526608‑M1/1‑16 (MQ=255)                                                                                                                                     ttAACATAAATGtataagtcatacttttgttttgggtgtatttcaatctgttaaaaagtttttcgctacgctagcaagcaaaaatgaaacaggaataatcgaaatgggatgttgcgcacagtcaaaataactcaccgtaaataatcatc       <  2:190826‑M1/149‑138 (MQ=255)                                                                                                                                     ttAACATAAATGtataagtcatacttttgttttgggtgtatttcaatctgttaaaaagtttttcgctacgctagcaagcaaaaatgaaacaggaataatcgaaataggatgttgcgcacagtcaaaataactcaccttaaataatcatc       >  2:455893‑M1/1‑12 (MQ=255)                                                                                                                                     ttAACATAAATGtataagtcatacttttgttttgggtgtatttcaatctgttaaaaagtttttcgctacgctagcaagcaaaaatgaaacaggaataat                                                         >  1:575633‑M1/1‑12 (MQ=255)                                                                                                                                     ttAACATAAATGtataagtcatacttttgttttgggtgtatttcaatctgttaaaaagtttttcgctacgctagcaagcaaaaatgaaacaggaataat                                                         <  2:575633‑M1/99‑88 (MQ=255)                                                                                                                                       aaCATAAATGtataagtcatacttttgttttgggtgtatttcaatctgttaaaaagtttttcgctacgctagcaagcaaaaatgaaacaggaataatcgaaatgggatgttgcgcacagtcaaaataactcaccgtaaataatcatctg     <  1:219965‑M1/149‑140 (MQ=255)                                                                                                                                          aTAAATGtataagtcatacttttgttttgggtgtatttcaatctgttaaaaagtttttcgctacgctagcaagcaaaaatgaaacaggaataatcgaaatgggatgttgcgcaccgtcaaaataacttacatgaaataatcatctgcta  >  1:116522‑M1/1‑7 (MQ=255)                                                                                                                                                |                                                                                                                                               ATGGGTCTTTACACTTATCTAAGATTTTTCCTAAATCGACGCAACTGTACTCGTCACTACACGCACATACAACGGAGGGGGGCTGCGATTTTCAATAATGCGTGATGCAGATCACACAAAACACTCAATTACTTAACATAAATGGGTAATGACTCCAACTTATTGATAGTGTTTTATGTTCAGATAATGCCCGATGACTTTGTCATGCAGCTCCACCGATTTTGAGAACGACAGCGACTTCCGTCCCAGCCGTGCCAGGTGCTGCCTCAGATTCAGGTTATGCCGC  >  NC_000913_3_pae_tpiA/1978359‑1978644

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: ‑