Predicted mutation
evidence	seq id	position	mutation	annotation	gene	description
JC JC	NC_000913	1,199,869	+GA :: IS3 (+) +4 bp	coding (935‑938/1128 nt)	intE ←	putative integrase

New junction evidence
		seq id	position	reads (cov)	reads (cov)	score	skew	freq	annotation	gene	product
*	?	NC_000913	315229 =	NA (NA)	39 (0.680) +TC	38/486	0.5	100%	noncoding (1/1255 nt)	IS3	repeat region
	?	NC_000913	= 1199872	0 (0.000)					coding (935/1128 nt)	intE	putative integrase
*	?	NC_000913	1094245 =	NA (NA)	55 (0.950)	47/490	0.3	100%	noncoding (1258/1258 nt)	IS3	repeat region
	?	NC_000913	1199869 =	0 (0.000)					coding (938/1128 nt)	intE	putative integrase

GCGAAAGCTTTAGCGGAAAGGATTCGGGAAAATGTTGAGCGTTTAACTGGCGATAATCCTGAATACGCTATACCACAAAAAGTGACGATTAGTATTGGCGCTGTTGTGACTCAGGAAAATGCGTTAAACCCAAATGAGATCTATCGACTGGCTGATAACGCACTTTACGAGGCGAAAGAGACCGGGCGTAATAAGGTGGTTGTGAGGGATGTGGTGAATTTTTGTGAGTCACCATAAAGCGGCATTTTGATCCTACCCACGTAATATGGACACAGGCCTAAGCGAGGTTCTTGTTTTCAAATTGTTCCGGACTGAGGCCGCCACACCAACTGTGCCGCCGCCACCGATTGTAATCACATTCGATATAATTAAACACCGTTGCCCGCATTATTTCCCGGCTGATAAAGTGTTCTCCATGGATACATTCCACTTTCAGCGAATGAAAGAAGCTTTCCACGCAGGCATTATCGTAGCAGCAACCTTTTGCGCTCAT  >  NC_000913/1093998‑1094490                                                                                                                                                                                                                                                        |                                                                                                                                                                                                                                                      gCGAAAGCTTTAGCGGAAAGGATTCGGGAAAATGTTGAGCGTTTAACTGGCGATAATCCTGAATACGCTATACCACAAAAAGTGACGATTAGTATTGGCGCTGTTGTGACTCAGGAAAATGCGTTAAACCCAAATTAGATCTATCGACTGGCTGATAACGCACTTTACGAGGCGAAAGAGACCGGGCGTAATAAGGTGGTTGTGAGGGATGTGGTGAATTTTTGTGAGTCACCATAAAGCGGCATTTTGa                                                                                                                                                                                                                                                     <  1:373060/250‑1 (MQ=255)            aGCGGAAAGGATTCGGGAAAATGTTGAGCGTTTAACTGGCGATAATCCTGAATACGCTATACCACAAAAAGTGACGATTAGTATTGGCGCTGTTGTGACTCAGGAAAATGCGTTAAACCCAAATGAGATCTATCGACTGGCTGATAACGCACTTTACGAGGCGAAAGAGACCGGGCGTAATAAGGTGGTTGTGAGGGATGTGGTGAATTTTTGTGAGTCACCATAAAGCGGCATTTTGATCCTACCCACg                                                                                                                                                                                                                                          <  1:36346/250‑1 (MQ=255)              cGGAAAGGATTCGGGAAAATGTTGAGCGTTTAACTGGCGATAATCCTGAATACGCTATACCACAAAAAGTGACGATTAGTATTGGCGCTGTTGTGACTCAGGAAAATGCGTTAAACCCAAATGAGATCTATCGACTGGCTGATAACGCACTTTACGAGGCGAAAGAGACCGGGCGTAATAAGGTGGTTGTGAGGGATGTGGTGAATTTTTGTGAGTCACCATAAAGCGGCATTTTGATCCTACCCACGTa                                                                                                                                                                                                                                        >  1:62674/1‑250 (MQ=255)                      aTTCGGGAAAATGTTGAGCGTTTAACTGGCGATAATCCTGAATACGCTATACCACAAAAAGTGACGATTAGTATTGGCGCTGTTGTGACTCAGGAAAATGCGTTAAACCCAAATGAGATCTATCGACTGGCTGATAACGCACTTTACGAGGCGAAAGAGACCGGGCGTAATAAGGTGGTTGTGAGGGATGTGGTGAATTTTTGTGAGTCACCATAAAGCGGCATTTTGATCCTACCCACGTAATATGGaca                                                                                                                                                                                                                               <  1:148545/251‑1 (MQ=255)                                aTGTTGAGCGTATAACTGGCGATAATCCTGAATACGCTATACCACAAAAAGTTACGATTAGTATTGGCGCTGTTGTGACTCAGGAAAATGCGTTAAACCCAAATGAGATCTATCGACTGGCTGATAACGCACTTTACGAGGCGAAAGAGACCGGGCGTAATAAGGTGGTTGCGAGGGATGTGGTGAATTTTTGTGAGTCACCAGAAAGCGGCATTTTTATCCTACCCACGTAATATGGACACAGGCCTAAg                                                                                                                                                                                                                     <  1:526520/251‑1 (MQ=255)                                        cGTTTAACTGGCGATAATCCTGACTACGCTATACCCCAAAAAGTGACGATTCGTATTGGCGCTGTTGTGACTCAGGAAAATACGTTAAACCCAAATGAGATCTATCGACTGGCTGATAACGCACTTTACGAGGCGAAAGAGACCGGGCGTAATAAGGAGGTTGTGAGGGATGTGGTGAATTTTTGTGAGTCACCATAACGCGGCATTTTGATCCTACCCACGTAATATGGACACAGGACTAAGCGAGGTTc                                                                                                                                                                                                             >  2:431835/1‑251 (MQ=255)                                            tAACTGGCGATAATCCTGAATACGCTATACCACAAAAAGTGACGATTAGTATTGGCGCTGTTGTGACTCAGGAAAATGCGTTAAACCCAAATGAGATCTATCGACTGGCTGATAACGTACTTTACGAGGCGAAAGAGACCGGGCGTAATAAGGTGGTTGTGAGGGATGTGGTGAATTTTTGTGAGTCACCATAAAGCGGCATTTTGATCCTACCCACGTAATATGGACACAGGCCTAAGCGAGGTTCTTg                                                                                                                                                                                                          <  2:237393/250‑1 (MQ=255)                                              aCTGGCGATAATCCTGAATACGCTATACCACAAAAAGTGACGATTAGTATTGGCGCTGTTGTGACTCAGGAAAATGCGTTAAACCCAAATGAGATCTATCGACTGGCTGATAACGCACTTTACGAGGCGAAAGAGACCGGGCGTAATAAGGTGGTTGTGAGGGATGTGGTGAATTTTTGTGAGTCACCATAAAGCGGCATTTTGATCCTACCCACGTAATATGGACACAGGCCTAAGCGAGGTTCTTGttt                                                                                                                                                                                                       <  1:510762/251‑1 (MQ=255)                                                  gCGATAATCCTGAATACGCTATACCACAAAAAGTGACGATTAGTATTGGCGCTGTTGTGACTCAGGAAAATGCGTTAAACCCAAATGAGATCTATCGACTGGCTGTTAACGCACTTTACGAGGCGAAAGAGACCGGGCGTAATACGGTGGTGGTGAGGGATGTGGTGAATTTTTGTGAGTCACCATAAAGCGGCATTTTGATCATACCCACGTAATATGGATACAGGCCTAAGCGAGGTTCTTGTTTTCa                                                                                                                                                                                                    >  1:589270/1‑250 (MQ=255)                                                              aaTACGCTATACCACAAAAAGTGACGATTAGTATTGGCGCTGTTGTGACTCAGGAAAATGCGTTAAACCCAAATGAGATCTATCGACTGGCTGATAACGCACTTTACGAGGCGAAAGAGACCGGGCGTAATAAGGTGGTTGTGAGGGATGTGGTGAATTTTTGTGAGTCACCATAAAGCGGCATTTTGATCCTACCCACGTAATATGGACACAGGCCTAAGCGAGGTTCTTGTTTTCAAATTGTTCCGGAc                                                                                                                                                                                       <  2:110676/251‑1 (MQ=255)                                                                    cTATACCACAAAAAGTGACGATTAGTATTGGCGCTGTTGTGACTCAGGAAAATGCGTTAAACCCAAATGAGATCTATCGACTGGCTGATAACGCACTTTACGAGGCGAAAGAGACCGGGCGTAATAAGGTGGTTGTGAGGGATGTGGTGAATTTTTGTGAGTCACCATAAAGCGGCATTTTGATCCTACCCACGTAATATGGACACAGGCCTAAGCGAGGTTCTTGTTTTCAAATTGATCCGGACTGAGgc                                                                                                                                                                                 >  2:25450/1‑251 (MQ=255)                                                                      ataCCATAAAAAGAGACGAAAAGTCTTGGCGCTGTTGTGACTCAGGAAAATGCGTTAACCCCACAGGAGATCTATCGACTATCTGCTAACGCACTTTACGCGGCGAAAGCGACCGGGCGTAATAAGGTGGTTGTGAGGGCTGTGGTGAATTTTTGTGAGTCACCATAAAGCGGCATTTTGATCCTACGCACGTAATATGGACACACGCCTAAGCGAGGTTCTTGTTTTCAAATAGTTCCGGACTGAGcccg                                                                                                                                                                               >  2:412236/1‑251 (MQ=255)                                                                              aaaaGTGACGATTAGTATTGGCGCTGTTGTGACTCAGGAAAATGCGTTAAACCCAAATGAGATCTATCGACTGGCTGATAACGCACTTTACGAGGCGAAAGAGACCGGGCGTAATAAGGTGGTTGTGAGGGATGTGGTGAATTTTTGTGAGTCACCATAAAGCGGCATTTTGATCCTACCCACGTAATATGGACACAGGCCTAAGCGAGGTTCTTGTTTTCAAATTGTTCCGGACTGAGGCCGCCACAcc                                                                                                                                                                        >  1:183550/1‑250 (MQ=255)                                                                                            gTATTGGCGCTGTTGTGACTCAGGAAAATGCGTTAAACCCAAATGAGATCTCTCGACTGGCTGATAACGCACTTTACGAGGCGAAAGAGAAAGAGCGTAATAAGGTGGTTGTGAGGGATGTGGTGAATTTTTGTGAGTCACCATAAAGCGGCATTTTGATCCTACCCACGCAATATGCACAAAGGCCTAAGCGAGGTTCTTGTTTTCAAATTGTTCCGGACTGAGGCCGCCACACCAACTGTgccgccgcc                                                                                                                                                         >  1:235803/1‑251 (MQ=38)                                                                                                                     aaaTGCGTTAAACCCAAATGAGATCTATCGACTGGCTGATAACGCACTTTACGAGGCGAAAGAGACCGGGCGTAATAAGGTGGTTGTGAGGGATGTGGTGAATTTTTGTGAGTCACCATAAAGCGGCATTTTGATCCTACCCACGTAATATGGACACAGGCCTAAGCGAGGTTCTTGTTTTCAAATTGTTCCGGACTGAGGCCGCCACACCAACTGTGCCGCCGCCACCGATTGTAATCACATTCGatat                                                                                                                                 >  1:321435/1‑250 (MQ=255)                                                                                                                          cGTTAAACCCAAATGAGATCTATCGACTGGCTGATAACGCACTTTACGAGGCGAAAGAGACCGGGCGTAATAAGGTGGTTGTGAGGGATGTGGTGAATTTTTGGGAGTCACCATAAAGCGGCATTTTGCTCCTACCCACGTAATATGGACACAGGCCTAAGCGAGGCTCTTGTTTTCAAATTGTTCCGTACTGAGGCCGCCACACCAACTGTGCCGCCGCCACCGATTGTAATCACATTCGATATAATTa                                                                                                                            >  2:441799/1‑250 (MQ=255)                                                                                                                                                          gATAACGCACTTTACGAGGCGAAAGAGACCGGGAGTAATAAGGAGGTTGTGAGGGATGTGGTGAATTTTTGTGAGTCACCATAAAGCGGCATTTTGATCCTACCCACGTAATATGGACACAGGCCTAAGCGAGGTTCTTGTTTTCAAATTGTTCCGGACTGAGGCCGCCACACCAACTGTGCCGCCGCCACCGATTGTAATCACATTCGATATAATTAAACACCGTTGCCCGCATTATTTCCCGGCTGAt                                                                                            >  2:563470/1‑250 (MQ=255)                                                                                                                                                                gCACTTTACGAGGCGAAAGAGACCGGGCGTAATAAGGTGGTTGTGAGGGATGTGGTGAATTTTTGTGAGTCACCATAAAGCGGCATTTTGATCCTACCCACGTAATATGGACACAGGCCTAAGCGAGGTTCTTGTTTTCAAATTGTTCCGGACTGAGGCCGCCACACCAACTGTGCCGCCGCCACCGATTGTAATCACATTCGATATAATTAAACACCGTTGCCCGCATTATTTCCCGGCTGATAAAgtgt                                                                                     >  2:350170/1‑251 (MQ=255)                                                                                                                                                                gCACTTTACGAGGCGAAAGAGACCGGGCGTAATAAGGTGGTTGTGAGGGATGTGGTGAATTTTTGTGAGTCACCATAAAGCGGCATTTTGATCCTACCCACGTAATATGGACACAGGCCTAAGCGAGGTTCTTGTTTTCAAATTGTTCCGGACTGAGGCCGCCACACCAACTGTGCCGCCGCCACCGATTGTAATCACATTCGATATAATTAAACACCGTTGCCCGCATTATTTCCCGGCTGATAAAgtgt                                                                                     >  1:296126/1‑251 (MQ=255)                                                                                                                                                                 cACTTTACGAGGCGAAAGAGACCGGGCGTAATAAGGTGGTGGTGAGGGATTTGGTGAATTTTTGTGAGTCACCATAAAGCGGCATTTTGATCCTACCCACGTAATATGGACACAGGCCTAAGCGAGGTTCTTGTTTTCAAATGGTTCCGGACTGAGGCCGCCACACCAACTGTGCCGCCGCCACCGATTGTAATCACATTCGATATAATTAAACACCGTTGCCCGCATTATTTCCCGGCTGATAAAGTGtt                                                                                    <  2:217441/251‑1 (MQ=255)                                                                                                                                                                               aaaGAGACCGGGCGTAATAAGGTGGTTGTGAGGGATGTGGTGAATTTTTGTGAGTCACCATAAAGCGGCATTTTGATCCTACCCACGTAATATGGACACAGGCCTAAGCGAGGTTCTTGTTTTCAAATTGTTCCGGACTGAGGCCGCCACACCAACTGTGCCGCCGCCACCGATTGTAATCACATTCGATATAATTAAACACCGTTGCCCGCATTATTTCCCGGCTGATAAAGTGTTCTCCATGGATACAt                                                                      >  1:108360/1‑251 (MQ=255)                                                                                                                                                                                aaGAGACCGGGCGTAATAAGTTGGTTGGGAGGGAGGTGGTGAAGTTTTGGGATTCACCATAAGGCGGCATTTTGATCCTGCCCCCTTAAGATGGACACAGGCCTAAGCGAGGTGCTTTTTTGCAAGTTGTTCCGGGCTGAGGGCGCCTCACCAACTGTGCCGCCGCCTCCTATTGTAATCACATTCGATATAATTAAACACCGTTGCCCGCATTATTTCCCGGCTGATAAAGTGTTCTCCATGGATACAtt                                                                     <  1:572622/251‑1 (MQ=17)                                                                                                                                                                                  gagaCCGGGCGTAATAAGGTGGTTGTGAGGGATGTGGTGAATTTTTGTGAGTCACCATAAAGCGGCATTTTGATCCTACCCACGTAATATGGACACAGGACTAAGCGAGGTTCTTGTTTTCAAATTGTTCCGGACTGAGGCCGCCACACCAACTGTGCCGCCGCCACCGATTGTAATCACATTCGATATAATTAAACACCGTTGCCCGCATTATTTCCCGGCTGATAAAGTGTTCTCCATGGATACATTcc                                                                   >  1:65163/1‑251 (MQ=255)                                                                                                                                                                                      ccGGGCGTAATAAGGGGGTTGTGAGGGATGTGGTGAATTTTTGTGAGTCACCATAAAGCGGCATTTTGATCCTACCCACGTAATATGGACACAGGCCTAAGCGAGGTTCTTGTTTTCAAATTGTTCCGGACTGAGGCCGCCACACCAACTGTGCCGCCGCCACCGATTGTAATCACATTCGATATAATTAAACACCGTTGCCCGCATTATTTCCCGGCTGATAATGTGTTCTCCATGGATCCATTACACtt                                                               >  2:133633/1‑251 (MQ=255)                                                                                                                                                                                                  aGGTGGTTGTGAGGGATGGGGTGAATTTTTGTGAGTAACCATAAAGCGGCATTGTGATCCTACCCACGTAATATGGACTCAGGCCTAAGCGAGGTTCTTGTTTGCAAATTGTTCCGGACTGAGGCCGCCACACCAACTGTGCCGCCGCCACCGATTGTAATCACATTCGATATAATTAAACACCGTTGCCCGCATTATTTCCCGGCTGATAAAGTGTTCTCCATGGATACATTCCACTTTCAGCGAATGaa                                                   <  2:107385/251‑1 (MQ=255)                                                                                                                                                                                                   ggtggtTGTGAGGGATGTGGTGAATTTTTGTGAGTCACCATAAAGCGGCATTTTGATCCTACCCACTTAATATGGACACAGGCCTAAGCGAGGTTCTTGTTTTCAAATTGTTCCGGACTGAGGCCGCCACACCa                                                                                                                                                                       <  2:300236/134‑1 (MQ=255)                                                                                                                                                                                                   ggtggtTGTGAGGGATGTGGTGAATTTTTGTGAGTCACCATAAAGCGGCATTTTGATCCTACCCACGTAATATGGACACAGGCCTAAGCGAGGTTCTTGTTTTCAAATTGTTCCGGACTGAGGCCGCCACACCa                                                                                                                                                                       >  1:300236/1‑134 (MQ=255)                                                                                                                                                                                                                            ttttGTGAGTCACCAAAAAGCGGCATTTTGATCCTACCCACGTAATATGGACACAGGCCTAAGCGAGGTTCTTGTTTTCAAATTGTTCCGGACTGAGGCCGCCACACCAACTGTGCCGCCGCCACCGATTGTAATCACATTCGATATAATTAAACACCGTTGCCCGCATTATTTCCCGGCTGATAAAGTGTTCTCCATGGATACATTCCACTTTCAGCGAATGAAAGAAGCTTTCCACGCAGGCATTATc                          <  2:371732/250‑1 (MQ=255)                                                                                                                                                                                                                                gtgAGTCACCATAAAGCGGCATTTTGATCCTACCCACGTAATATGGACACAGGCCTAAGCGAGGTTCTTGTTTTCAAATTGTTCCGGACTGAGGCCGCCACACCAACTGTGCCGCCGCCACCGATTGTAATCACATTCGATATAATTAAACACCGTTGCCCGCATTATTTCCCGGCTGATAAAGTGTTCTCCATGGATACATTCCACTTTCAGCGAATGAAAGAAGCTTTCCACGCAGGCATTATCGTag                      <  1:351787/250‑1 (MQ=40)                                                                                                                                                                                                                                          aTAAAGCGGCATTTTGATCCTACCCACTTAATATGGACACAGGCTGAAGCGAGGTTCTTGTTTTCAAATTGTTCCGGACTGATGCCGCCACACCAACTGTGCCGCCGCCACCGATTGTAATCACATTCGATATAATTAAACACCGTTGCCCGCATTATTTCCCGGCTGATAAAGTGTTCTCCATGGATACATTCCACTTTCAGCGAATGAAAGAAGCTTTCCACGCAGTCATTATCGTAGCAGCAACCttt           <  1:407523/251‑1 (MQ=255)                                                                                                                                                                                                                                             aaGCGGCATTTTGATCCAACCCACGTAATATGGACACAGCCCTAAGCGAGGTTCTTTTTTTCAATTTGTTCCGGACTGAGGCCGCCACACCAACTTTGCCGCCGCCACCGATTGTAATCACATTCGATATAATTAAACACCGTTGCCCGCATTATTTCCCGGCTGATAAATTGGTCTCCATTGATACATTCCACGTTCAGCGAATGAAAGAAGCTGTCCACGCAGGGATTATCGTAGCAGCAATCTTTTgc        <  2:300234/251‑1 (MQ=11)                                                                                                                                                                                                                                                   cATTTTGCTCCTACCCACGTAATATGGACACAGGCCTAAGCGAGGTTCTTGTTTTCAAATTGTTCCGGACTGAGGCCGCCACACCAACTGTGCCGCCGCCACCGATTGTAATCACATTCGATATAATTAAACACCGTTGCCCGCATTATTTCCCGGCTGATAAAGTGTTCTCCATGGATACATTCCACTTTCAGCGAATGAAAGAAGCTTTCCACGCAGGCATTATCGTAGCAGCACCCTTTTGCGCTCAt  >  2:372714/1‑251 (MQ=14)                                                                                                                                                                                                                                                        |                                                                                                                                                                                                                                                      GCGAAAGCTTTAGCGGAAAGGATTCGGGAAAATGTTGAGCGTTTAACTGGCGATAATCCTGAATACGCTATACCACAAAAAGTGACGATTAGTATTGGCGCTGTTGTGACTCAGGAAAATGCGTTAAACCCAAATGAGATCTATCGACTGGCTGATAACGCACTTTACGAGGCGAAAGAGACCGGGCGTAATAAGGTGGTTGTGAGGGATGTGGTGAATTTTTGTGAGTCACCATAAAGCGGCATTTTGATCCTACCCACGTAATATGGACACAGGCCTAAGCGAGGTTCTTGTTTTCAAATTGTTCCGGACTGAGGCCGCCACACCAACTGTGCCGCCGCCACCGATTGTAATCACATTCGATATAATTAAACACCGTTGCCCGCATTATTTCCCGGCTGATAAAGTGTTCTCCATGGATACATTCCACTTTCAGCGAATGAAAGAAGCTTTCCACGCAGGCATTATCGTAGCAGCAACCTTTTGCGCTCAT  >  NC_000913/1093998‑1094490

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 13 ≤ ATCG/ATCG < 14 ≤ ATCG/ATCG < 32 ≤ ATCG/ATCG < 39 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑
Reads not counted as support for junction
read_name Not counted due to insufficient overlap past the breakpoint.
read_name Not counted due to not crossing MOB target site duplication.