Predicted mutation
evidence	seq id	position	mutation	freq	annotation	gene	description
JC	CP000730	2,501,544	Δ108 bp	9.8%	coding (68‑175/2106 nt)	USA300HOU_2364 →	AraC transcriptional regulator

New junction evidence
		seq id	position	reads (cov)	reads (cov)	score	skew	freq	annotation	gene	product
*	?	CP000730	= 2501543	45 (0.700)	5 (0.080)	3/240	NT	9.8%	coding (67/2106 nt)	USA300HOU_2364	AraC transcriptional regulator
	?	CP000730	2501652 =	50 (0.840)					coding (176/2106 nt)	USA300HOU_2364	AraC transcriptional regulator

GATTTTAAAAATTTCCATGTTTTACATTTAAATGATAGATTTCAATATATATTAGGCAGGAGAGAGAAATATGACATGCCAACTTAAAATACATCATACATTATCGACAATACCAAGTCGTAATATTAATAATATTATGGTGCTATTTTCACTTACAAGTAAACTCAATATTACGATTAATGGTGAAACCAAAGACGTAAGTAATTATATTATCTTAATTAACCATGGTGATATTTATAATATTAACCACGGCGAAAATATAATCGAATTAA  >  CP000730/2501407‑2501678                                                                                                                                         |                                                                                                                                        gATTTTAAAAATTTCCATGTTTTCCTGAATTATGATAGATTTCAATATATATTAGGCAGGAGAGAGAAATATGACATGCCAACTTAAAATACATCATACATTATCGACAATACCAAGTCGTAATATTAATAATATTATgg                                                                                                                                      >  1:368061/1‑140 (MQ=255)        aaaaTTTCCATGTTTTACATTTAAATGATAGATTTCAATATATATTAGGCAGGGGAGAGAAATATGACATGCCAACTTAAAATACATCATACATTATCGACAATACCAAGTGGTAATATTAATAATATTAaccacagcaa                                                                                                                               >  2:379239‑M1/1‑130 (MQ=255)        aaaaTTTCCATGTTTTACATTTAAATGATAGATTTCAATATATATTAGGCAGGAGAGAGAAATATGACATGCCAACTTAAAATACATCATACATTATCGACAATACCAAGTCGTAATATTAATAATATTATGGTGCTAtt                                                                                                                               >  2:126562/1‑140 (MQ=255)        aaaaTTTCCATGTTTTACATTTAAATGATAGATTTCAATATATATTAGGCAGGAGAGAGAAATATGACATGCCAACTTAAAATACATCATACATTATCGAAAATACCAAGTCGTAATATTAAAAATATTATGGTGCTAtt                                                                                                                               >  1:611252/1‑140 (MQ=255)                      ttACATTTAAATGATAGATTTCAATATATATTAGGCAGGAGAGAGAAATATGACATGCCAACTTAAAATACATCATACATTATCGACCATACCCAGTCGTACTATTAATAATATTCTGGTGCTATTGTCACATACAAGTa                                                                                                                 >  1:301585/1‑140 (MQ=255)                      ttACATTTAAATGATAGATTTCAATATATATTAGGCAGGAGAGAGAAATATGACATGCCAACTTAAAATACATCATACATTATCGACAATACCAAGTCGTAATATTAATAATATTATGGTGCTATTTTCACTTACAAgca                                                                                                                 >  2:391860/1‑138 (MQ=255)                      ttACATTTAAATGATAGATTTCAATATATATTAGGCAGGAGAGAGAAATATGACATGCCAACTTAAAATACATCATACATTATCGACAATACCAAGTCGTAATATTAATAATATTATGGTGCTATTTTAACTTACAAGTa                                                                                                                 >  2:686389/1‑140 (MQ=255)                            ttAAATGATAGATTTTAATATATATTAGGCAGGAGAGAGAAATATGACATGCTAACTTAAAATACATCATACATTATCGACAATACCAAGTCGTAATATTAATAATATTATGGTGCTATTTTCACTTACAAGTAAACTCa                                                                                                           <  1:594747/140‑1 (MQ=255)                            ttAAATGATAGATTTCAATATATATTAGGCAGGAGAGAGAAATATGACATGCCAACTTAAAATACATCATACATTATCGACAATACCAAGTCGTAATATTAATAATATTATGGTGCTATTTTCACTTACAAGTAAACTCa                                                                                                           <  1:408168/140‑1 (MQ=255)                            ttAAATGATAGATTTCAATATATATTAGGCAGGAGAGAGAAATATGACATGCCAACTTAAAATACATCATACATTATCGACAATACCAAGTCGTAATATTAATAATATTATGGTGCTATTTTCACTTACAAGTAAACTCa                                                                                                           >  2:671611/1‑140 (MQ=255)                            ttAAATGATAGATTTCAATATATATTAGGCAGGAGAGAGAAATATGACATGCCAACTTAAAATACATCATACATTATCGACAATACCAAGTCGTAATATTAATAATATTATGGTGATATTTTCACTTACAAGTAAACtac                                                                                                           >  2:604091/1‑138 (MQ=255)                             tAAATGATAGATTTCAATATTTATTAGGCAGGAGAGAGAAATATGACATGCCTACTTAAATTACTTCATTCATTTTCGACAATACCAAGTCGTAATATTAATAATATTATGGTGCTATTTTCACTTACAAGTAAACTCaa                                                                                                          <  1:702516/140‑1 (MQ=255)                             tAAATGAGAGATTTCAATATATATTAGGCAGGAGAGAGAAATATGACATGCCAACTTAAAATACATCATACATTATCGACAATACCAAGTCGTAATATTAATAATATTATGGTGCTATTTTCACTTACAAGTAAACTCaa                                                                                                          <  2:91661/140‑1 (MQ=255)                                      gATTTCAATATATATTAGGCAGGAGAGAGAAATATGACATGCCAACTTAAAATACATCATACATTATCGACAATACCAAGTCGTAATATTAATAATATTATGGTGCTATTTTCACTTACAAGTAAACTCAATATTACGAt                                                                                                 <  2:53650/140‑1 (MQ=255)                                       aTTTCAATATATATTAGGCAGGAGAGAGAAATATGACATGCCAACTTAAAATACATCATACATTATCGACAATACAAAGTCGTAATATTAATGATATTATGGTGCTATTTTCACTTACAAGTAAACTCAATATTACGAtt                                                                                                >  1:82898/1‑140 (MQ=255)                                              tatatatTAGGCAGGAGAGAGAAATATGACATGCCAACTTAAAATACATCATACATTATCGACAATACCAAGTCGTAATATTAATAATATTATGGTGCTATTTTCACTTACAAGTAAACTCAATATTACGATTAATGGTg                                                                                         >  1:7810/1‑140 (MQ=255)                                              tatatatTAGGCAGGAGAGAGAAATATGACATGCCAACTTAAAATACATCATACATTATCGACAATACCAAGTCGTAATATTAATAATATTATGGTGCTATTTTCACTTACAAGTAAACTCAATATTACGATTAATGGTg                                                                                         <  2:242114/140‑1 (MQ=255)                                                tatatTAGGCAGGAGAGAGAAATATGACATGCCAACTTAAAATACATCATACATTATCGACAATACCAAGTCGTAATATTAATAATATTATGGTGCTATTTTCACTTACAAGTAAACTCAATATTCCGATTAATGGTGaa                                                                                       >  2:525661/1‑140 (MQ=255)                                                tatatTAGGCAGGAGAGAGAAATATGACATGCCAACTTAAAATACATCATACATTATCGACAATACCAAGTCGTAATATTAATAATATTATGGTGCTATTTTCACTTACAAGTAAACTCAATATTACGATTAATGGTGaa                                                                                       >  2:620371/1‑140 (MQ=255)                                                    ttAGGCATGAGAGAGAAATATGACATGCCAACTTAAAATACATCATACATTATCGACAATACCAAGTCGTAATATTAATAATATTATGGTGCTATTTTCACTTACAAGTAAACTCAATATTACGATTAATGGTGAAACCa                                                                                   <  1:115089/140‑1 (MQ=255)                                                      aGGCAGGAGAGAGAAATATGACATGCCAACTTAAAATACATCATACATTATCGACAATACCAGGTCGTAATATTAATAATATTATGGTGCTATTTTCACTTACAAGTAAACTAAATATTAAGATTAATGGTGAAAACaaa                                                                                 >  1:596532/1‑140 (MQ=255)                                                      aGGCAGGAGAGAGAAATATGACATGCCAACTTAAAATACATCATACATTATCGACAATACCAAGTCGTAATATTAATAATATTATGGTGCTATTTTCACTTACAAGTAAACTCAATATTACGATTAATGGTGAAACCaaa                                                                                 >  1:759949/1‑140 (MQ=255)                                                           ggAGAGAGAAATATGACATGCCAACTTAAAATACATCATACATTATCGACAATACCAAGTCGTCATATTAATAATATTATGGTGCTATTTTCACTTACAAGTAAACTCAATATTACGATTAATGGTGAAACCAAAGACgt                                                                            >  1:341973/1‑140 (MQ=255)                                                           ggAGAGAGAAATATGACATGCCAACTTAAAATACATCATACATTATCGACAATACCAAGTCGTAATATTAATAATATTATGTTGCTATTTTCACTTACAAGTAAACTCAATATTACGATTAATGGTGAAACCAAAGACgt                                                                            <  1:844/140‑1 (MQ=255)                                                           ggAGAGAGAAATATGACATGCCAACTTAAAATACATCATACATTATCGACAATACCAAGTCGTAATATTAATAATATTATGGTGCTATTTTCACTTACAAGTAAACTCAATATTACGATTAATGGTGAAACCAAAGCCgt                                                                            >  2:317363/1‑140 (MQ=255)                                                           ggAGAGAGAAATATGACATGCCAACTTAAAATACATCATACATTATCGACAATACCAAGTCGTAATATTAATAATATTATGGTGCTATTTTCACTTACAAGTAAACTCAATATTACGATTAATGGTGAAACCAAAAACgt                                                                            >  1:756828/1‑140 (MQ=255)                                                               agagaAATATGACATGCCAACTTAAAATACATCATACATTATCGACAATACCAAGTCGTAATATTACTAAAATTATGGTGCTATTTTCACTTACAAGTAAACTCAATATTACGATTAATGGTGAAACCAAAGACgtaagt                                                                        >  2:650990/1‑140 (MQ=255)                                                                          aCATGCCAACTTAAAATACATCATACATTATCGACAATACCAAGTCGTAATATTAATAATATTAaccacggcgaaaatataatcgaattaatgaaaaccgttttttatttttatcaacaagatgatgatttctttaatgg                                                             >  1:317044‑M1/1‑64 (MQ=255)                                                                           cATGACAACTTAAAATACATCATACATTATCGACAATACCAAGTCGTAATATTAATAATATTATGGTGCTATTTTCACTTACAAGTAAACTCAATATTACGATTAATGGTGAAACCAAAGACGTAAGTAATTATATTATc                                                            <  1:353118/140‑1 (MQ=255)                                                                            aTGCCAACTTAAAATACATCATACATTATCGACAATACCAAGTCGTAATATTAATAATATTATGGTGCTATTTTCACTTACAAGTAAACTCAATATTACGATTAATGGTGAAACCAAAGACGTAAGTAATTATATTATCt                                                           >  2:601611/1‑140 (MQ=255)                                                                              gctaacttAAAATACATCATACATTATCGACAATACCAAGTCGTAATATTAATAATATTAaccacggcgaaaatataatcgaattaatgatacccgttttttatttttatcaacaagatgatgatttctttaattgttat                                                         <  2:383107‑M1/137‑81 (MQ=255)                                                                              gCCAACTTAAAATACATTAAACAATATATACAATAAAAAATCGTAATATACATAATATAATAATGCTACTGAAAATTAAAACTAGAATCAAGACTCGGATTAAAGGAGAAACAAAAGCCGTAAGTAATTATATTATCtta                                                         >  2:304074/1‑140 (MQ=255)                                                                              gCCAACTTAAAATACATCATACATTATCGACAATACCAAGTCGTAATATTAATAATATTAaccacggcgaaaatataatcgaattaatgatacccgttttttatttttatcaacaagatgatgatttctttaatggttat                                                         <  2:99695‑M1/140‑81 (MQ=255)                                                                              actaacttAATATACAACATACATTAGCTACAAGACCAAGTCGTAATATTAATAATATTAaccacggcgaaaatataatcgaattaatgatacccgttttttatttttatcaacaagatgatgatttctttaatggttat                                                         <  2:593578‑M1/137‑81 (MQ=255)                                                                                cAACTTAAAATACATCATACATTATCGACAATACCAAGTCGTAATATTAATAATATTATGGTGCTATTTTCACTTACAAGTAAACTCAATATTACGATTAATGGTGAAACCAAAGACGTAAGTAATTATATTATCttaat                                                       >  2:319884/1‑140 (MQ=255)                                                                                cAACTTAAAATACATCATACATTATCGACAATACCAAGTCGTAATATTAATAATATTATGGTGCTATTTTCACTTACAAGTAAACTCAATATTACGATTAATGGTGAAACCAAAGACGTAAGTAATTATATTATCttaat                                                       >  1:470012/1‑140 (MQ=255)                                                                                   cTTAAAATACATCCTACATTATCGACAATACCAAGTCGTAATGTTAATAATATTATGGTGCTATTTTCACTTACAAGTAAACTCAATATTACGATTAATGGTGAAACCAAAGACGGAAGTAATTATATTATCttgattaa                                                    >  1:599153/1‑140 (MQ=255)                                                                                    ttATAATACATCATACATTATCGACAATACCAAGTCGTAATATTAATAATATTATGGTGCTATTTTCACTTACAAGTAAACTCAATATTACGATTAATGGTGAAACCAAAGACGTAAGTAATTATATTATCTTAATTAAc                                                   <  2:360317/140‑1 (MQ=255)                                                                                    ttAAAATACATCATACATTATCGACAATACCAAGTCGTAATATTAATAATATTATGGTGCTATTTTCACTTACAAGTAAACTCAATATTACGATTAATGGTGAAACCAAAGACGTAAGTAATTATATTATCTTAATTAAc                                                   >  1:296877/1‑140 (MQ=255)                                                                                    ttAAAATACATCATACATTATCGACAATACCAAGTCGTAATATTAATAATATTATGGTGCTATTTTCACTTACAAGTAAACTCAATATTACGATTAATGGTGAAACCAAAGACATAAGTAATTATATTATCTTAATTAAc                                                   <  2:471402/140‑1 (MQ=255)                                                                                     tAAAATACATCATACATTATCGACAATACCAAGTCGTAATATTAATAATATTATGGTGCTATTTTCACTTACAAGTAAACTCAATATTACGATTAATGGTGAAACCAAAGACGTAAGTAATTATATTATCTTATTTAAcc                                                  >  1:434256/1‑140 (MQ=255)                                                                                        aaTACATCATATCTTATCGACAATACCAAGTCGTAATATTAATAATATTATGGTGCTATTTTCACTTACAAGTAAACTCAATATTACGATTAATGGTGAAACCAAAGACGTAAGTAATTATATTATCTTAATTAACCATg                                               <  1:604091/140‑1 (MQ=255)                                                                                        aaTACATCATACATTATCGACAATACCAAGTCGTAATATTAATAATATTATGGTGCTATTTTCACTTACAAGTAAACTCAATATTACGATTAATGGTGAAACCAAAGACGTAAGTAATTATATTATCTTAATTAACCATg                                               <  1:671611/140‑1 (MQ=255)                                                                                            catcatACATTATCGACCATACCTAGTCGTAATATTAATAATTTTATGGTGCTATTTTCACTTACAAGTAAACTCAATATTACGATTAATGGTGAAACCAAAGACGTAAGTAATTATATTATCTTAATTAACCATGGTGa                                           <  1:359546/140‑1 (MQ=255)                                                                                              tcatACATTATCGACAATACCAAGTCGTAATATTAATCATATTATGGTGCTATTTTCACTTACAAGTAAACTCAATATTACGATTAATGGTGAAACCAAAGACGTAAGAAATTATATTAAATTAATTAACCATGGTGata                                         >  2:531024/1‑140 (MQ=255)                                                                                                           aCAATACCAAGTCGTAATATTACTAATATCATGGGGCTATTTTCACTTACAAGTAAACTCAATATTACGATTAATGGTGAAACCAAAGACGTAAGTAATTATATTATCTTAATTAACCATGGTGATATTTATAATATTaa                            >  2:162234/1‑140 (MQ=255)                                                                                                           aCAATACCAAGTCGTAATATTAATAATATTATGGTGCTATTTTCACTTACAAGTAAACTCAATATTACGATTAATGGTGAAACCAAAGACGTAAGTAATTATATTATCTTAATTAACCATGGTGATATTTATAATATTac                            >  2:674470/1‑139 (MQ=255)                                                                                                            ccaaaCCAAGTCGTAATATTAATAATACTATGGTGCTATTATCACTTACAAGTAAACTCAATATTACGATTAATGGTGAAACCAAAGACGTAAGTAATTATATTAGCTTAATTAACCATGGTTATATTTATAATATTAAc                           <  2:747802/136‑1 (MQ=255)                                                                                                                aCCAAGTCGTAATATTAATAATATTATGGTGCTATTTTCACTTACAAGTAAACTCAATATTACGATTAATGGTGAAACCAAAGACGTAAGTAATTATATTATCTTAATTAACCATGGTGATATTTATAATATTAACCACg                       >  2:126648/1‑140 (MQ=255)                                                                                                                 ccAAGTCGTAATATTAATAATATTATGGTGCTATTTTCACGTACAAGTAAACTCAATATTACGATTAATGGTGAAACCAAAGACGTAAGTAATTATATTATCTTAATTAACCATGGTGATATTTATAATATTAACCACgg                      >  2:493774/1‑140 (MQ=255)                                                                                                                 ccAAGTCGTAATATTAATAATATTATGGTGATATTTTCACTTACAAGTAAACTCAATATTACGATTAATGGTGAAACCAAAGACGTAAGTAATTATATTATCTTAATTAACCATGGTGATATTTATAATATTAACCACgg                      >  2:403747/1‑140 (MQ=255)                                                                                                                                  taatattaaccacggcgaaaatataatcgaattaatgatacccgttttttatttttattaacaagatgatgatttctttaattgttatttagatcgtcatttattacaatcaattaattatatgaattcattaattgcca     >  2:75380‑M1/1‑8 (MQ=255)                                                                                                                                  taatattaaccacggcgaaaatataatcgaattaatgatacccgttttttatttttatcaacaagatgatgatttctttaattgttatttagatcgtcatttattacaatcaagtaattatattaagtcattaattgcct     >  2:485232‑M1/1‑8 (MQ=255)                                                                                                                                     tattaaccacggctaatatataatcgaattaatgttacccgttttttatttttatcaacaagatgatgatttctttaatggttatttagatcgtcatttattacaatcaagtaattatattaagtcattaattgccgatt  <  2:434256‑M1/140‑136 (MQ=255)                                                                                                                                         |                                                                                                                                        GATTTTAAAAATTTCCATGTTTTACATTTAAATGATAGATTTCAATATATATTAGGCAGGAGAGAGAAATATGACATGCCAACTTAAAATACATCATACATTATCGACAATACCAAGTCGTAATATTAATAATATTATGGTGCTATTTTCACTTACAAGTAAACTCAATATTACGATTAATGGTGAAACCAAAGACGTAAGTAATTATATTATCTTAATTAACCATGGTGATATTTATAATATTAACCACGGCGAAAATATAATCGAATTAA  >  CP000730/2501407‑2501678

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: ‑
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.