Predicted mutation
evidence	seq id	position	mutation	freq	annotation	gene	description
JC JC	CP009273	1,613,458	IS2 (+) +5 bp	100%	coding (82‑86/435 nt)	marR →	transcriptional repressor of multiple antibiotic resistance

New junction evidence
		seq id	position	reads (cov)	reads (cov)	score	skew	freq	annotation	gene	product
*	?	CP009273	1462167 =	NA (NA)	27 (0.990)	22/226	NT	100%	noncoding (1331/1331 nt)	IS2	repeat region
	?	CP009273	1613458 =	0 (0.000)					coding (82/435 nt)	marR	transcriptional repressor of multiple antibiotic resistance
*	?	CP009273	= 1613462	0 (0.000)	17 (0.630)	14/222	NT	100%	coding (86/435 nt)	marR	transcriptional repressor of multiple antibiotic resistance
	?	CP009273	= 2063752	NA (NA)					noncoding (1/1331 nt)	IS2	repeat region

CATTGAACAAAACTTGAACCGATTTAGCAAAACGTGGCATCGGTCAATTCATTCATTTGACTTATACTTGCCTGGGCAATATTATCCCCTGCAACTAATTACTTGCCAGGGCAACTAATGTGAAAAGTACCAGCGATCTGTTCAATGAAATTATTCCATTGGGTCGCTTAATCCATATGGTTAATCAGAAGAAAGATCGCCTGCTTAACGAGTATCTGTCTCCGCTGGATATTACCGCGGCACAGTTTAAGGTGCTCTGCTCTATCCGCTGCGCGGCGTGTATTACTCCGGTTGAACTGAAAAAGGTATTGTCGGTCGACCTGGGAGCACTGACCCGTATGCTGGATCGCCTGGTCTGTAAAGGCTGGGTGGAAAGGTTGCCGAACCCGAATGACAAGCGCGGCGTACTGGTAAAACTTACCACCGGCGGCGCGGCAATATGTGAACAATGCCATC  >  CP009273/1613258‑1613713                                                                                                                                                                                                             |                                                                                                                                                                                                                                                            cATTGAACAAAACTTGAACCGATTTAGCAAAACGTGGCATCGGTCAATTCATTCATTTGACTTATACTTGCCTGGGCAATATTATCCCCTGCAACTAATTACTTGCCAGGGCAACTAATGTGAAAAGTACCAGCGATCTGTTCAATGAAATTATTCCATTGGGTCGCTTAATCCATATGGTTAATCAGAAGAAAGATCGCCTGCTtagactggccccctgaatatccagacaaccaaaatcacta                                                                                                                                                                                                                     >  2:182792‑M1/1‑205 (MQ=255)     gAACAAAACTTGAACCGATTTAGCAAAACGTGGCATCGGTCAATTCATTCATTTGACTTATACTTGCCTGGGCAATATTATCCCCTGCAACTAATTACTTGCCAGGGCAACTAATGTGAAAAGTACCAGCGATCTGTTCAATGAAATTATTCCATTGGGTCGCTTAATCCATATGGTTAATCAGAAGAAAGATCGCCTGCTtagactggccccctgaatctccagacaaccaatatcacttaaat                                                                                                                                                                                                                 <  1:182796‑M1/245‑45 (MQ=255)                                                                    aggcgttcgagcattataacgaatggcatccgcatagtgcgctgggttatcgctcgccacgggaatatctgcggcagcgggcttgtaatgggttaagtgataacagatgtctggaaatataggggcaaatccaCTGCTTAACGAGTATCTGTCTCAGCTGGATATTACcg                                                                                                                                                                                                                             >  2:553072‑M2/134‑170 (MQ=255)                                                                        gttcgagcattataacgaatggcatccgcatagtgcgctgggttatcgctcgccacgggaatatctgcggcagcgggcttgtaatgggttaagtgataacagatgtctggaaatataggggcaaatccaCTGCTTAACGAGTATCTGTCTCAGCTGGATATTACCGCGGc                                                                                                                                                                                                                         <  1:553083‑M2/41‑1 (MQ=255)                                                                         ttcgagcattataacgaatggcatccgcatagtgcgctgggttctcgctcgccacgggaatatctgcggcagcgggcttgtaatgggttaagtgataacagatgtctggaaatataggggcaaatccaCTGATTAACGAGTATCTGTCTCCGCTGGACATTACCGCGGCACAGTTTAAgg                                                                                                                                                                                                              >  1:368922‑M2/129‑180 (MQ=255)                                                                           ggCAATATTATCCCCTGCAACTAATTACTTGCCAGGGCAACTAATGTGAAAAGTACCAGCGATCTGTTCAATGAAATTATTCCATTGGGTCGCTTAATCCATATGGTTAATCAGAAGAAAGATCGCCTGCTtagactggccccctgaatctccagacaaccaatatcacttaaataagtgatagtcttaatactagtttttagactagtcattggagaacagatgattgatgtcttagggc                                                                                                                                               >  1:141193‑M1/1‑131 (MQ=255)                                                                                   ataacgaatggcatccgcatagtgctctgggttatcgctcgccacgggaatatctgcggcagcgggcttgtaatgggttaagtgataacagatgtctggaaatataggggcaaatccaCTGCTTAACGAGTATCTGTCTCCGCTGGATATTACCGCGGCACAGTTTAAGGTGCTCTGCTCTATCCGCTGCGCGGCGTGTATTACTCCGGTTGAACTGAAAAAGGTATTGTCGGTCGACCTGGGAGCACTGACCCGTATGCTGGATCGCCTgg                                                                                                        <  1:359683‑M2/154‑1 (MQ=255)                                                                                     tCCCCTGCAACTAATTACTTGCCAGGGCAACTAATGTGAAAAGTACCAGCGATCTGTTCAATGAAATTATTCCATTGGGTCGCTTAATCCATATGGTTAATCAGAAGAAAGATCGCCTGCTtagactggccc                                                                                                                                                                                                                                                  >  1:533382‑M1/1‑121 (MQ=255)                                                                                         cTGCAACTAATTACTTGCCAGGGCAACTAATGTGAAAAGTACCAGCGATCTGTTCAATGAAATTATTCCATTGGGTCGCTTAATCCATATGGTTAATCAGAAGAAAGATCGCCTGCTtagactggccccctg                                                                                                                                                                                                                                              <  2:533371‑M1/132‑16 (MQ=255)                                                                                          tGCAACTAATTACTTGCCAGGGCAACTAATGTGAAAAGTACCAGCGATCTGTTCAATGAAATTATTCCATTGGGTCGCTTAATCAATATGGTTAATCAGAAGAAAGATCGCCTGCTtagactggccccct                                                                                                                                                                                                                                               >  1:78605‑M1/1‑116 (MQ=255)                                                                                              aCTAATTACTTGCCATGGCAACTAATGTGAAAACTACCAGCGATCGATTCAATGAAATTATTCCATTGGGTCGCTTAATCCATATGGTTAATCAGAAGAAAGATCGCCTGCTtagccgggccccctgtaa                                                                                                                                                                                                                                           <  2:78605‑M1/130‑19 (MQ=255)                                                                                                         tgcgctgggttatcgctcgccacgggaatatctgcggcagcgggcttgtaatgggttaagggataacagatgtctgggaatataggggcaaatccaCTGCTTAACGAGTATCTGTCTCCGCTGGATATTACCGCGGCACAGTTTAAGGTGCTCTGATCTATCCGCTGCGCGGCGTGCATTACTCCGGTTGTACTGCAAAAGGTATGGTCGGTAGACCTGGGAg                                                                                                                                   >  2:93495‑M2/97‑223 (MQ=255)                                                                                                             ctgggttatcgctcgccacgggaatatctgcggcagcgggcttgtaatgggttaagtgataacagatgtctggaaatataggggcaaatccaCTGCTTAACGAGTATCTGTCTCCGCTGGATATTACCGCGGCACAGTTTAAGGTGCTCTGCTCTATCCGCTGCGCGGCGTGTATTACTCCGGTTGAACTGAAAAAGGTATTGTCGGTCGACCTGGGAGCACt                                                                                                                               <  1:93495‑M2/131‑1 (MQ=255)                                                                                                              tgggttatcgctcgccacgggaatatctgcggcagcgggcttgtaatgggttaagtgataacagatgtctggaaatataggggcaaatccaCTGCTTAACGAGTATCTGtc                                                                                                                                                                                                                                              >  2:207861‑M2/92‑111 (MQ=255)                                                                                                               gCAACTAATGTGAAAAGTACCAGCGATCTGTTCAATGAAATTATTCCATTGGGTCGCTTAATCCATATGGTTAATCAGAAGAAAGATCGCCTGCTta                                                                                                                                                                                                                                                           <  2:229709‑M1/97‑3 (MQ=255)                                                                                                                  ttatcgctcgccacgggaatatctgcggcagcgggcttgtaatgggttaagtgataacagatgtctggaaatataggggcaaatccaCTGCTTAACGAGTATCTGTCTCCg                                                                                                                                                                                                                                          <  1:207865‑M2/24‑1 (MQ=255)                                                                                                                          cgccacgggaatatctgcggcagcgggcttgtaatgggttaagtgataacagatgtctggaaatataggggcaaatccaCTGCTTAACGAGTATCTGTCTCCGCTGGATATTACCGCGGCACAGTTTAAGGTGCTCTGCTCTATCCGCTgcg                                                                                                                                                                                         >  1:175048‑M2/80‑152 (MQ=255)                                                                                                                            ccacgggaatatctgcggcagcgggcttgtaatgggttaagtgataacagatgtctggaaatataggggcaaatccaCTGCTTAACGAGTATCTGTCTCCGCTGGATATTACCGCGGCACAGTTTAAGGTGCTCTGCTCTATCCGCTGCGCGGCGTGTATTACTCCGGTTGAACTGAAAAAGGTATTGTCGGTCGACCTGGGa                                                                                                                                    >  2:588790‑M2/78‑203 (MQ=255)                                                                                                                              acgggaatatctgcggcagcgggcttgtaatgggttaagtgataacagatgtctggaaatataggggcaaatccaCTGCTTAACGAGTATCTGTCTCCGCTGGATATTACCGCGGCACAGTTTAAGGTGCTCTGCTCTATCCGCTGCgcggc                                                                                                                                                                                     <  2:175044‑M2/77‑1 (MQ=255)                                                                                                                                gggaatatctgcggcagcgggcttgtaatgggttaagtgataacagatgtctggaaatataggggcaaatccaCTGCTTAACGAGTATCTGTCTCCGCTGGATATTACCGCGGCACAGTTTAAGGTGCTCTGCTCTATCCGCTGCGCGGCGTGTATTACTCCGGTTGAACTGAAAAAGGTATTGTCGGTCGACCTGGGAGCAc                                                                                                                                <  1:588801‑M2/130‑1 (MQ=255)                                                                                                                                     gCGATCTGTTCAATGAAATTATTCCATTGGGTCGCTTAATCCATATGGTTAATCAGAAGAAAGATCGCCTGCTtagactggccccctgaatct                                                                                                                                                                                                                                         >  2:552288‑M1/1‑73 (MQ=255)                                                                                                                                         tCTGTTCAATGAAATTATTCCATTGGGTCGCTTAATCCATATGGTTAATCAGAAGAAAGATCGCCTGCTtagactggccccctgaatctccag                                                                                                                                                                                                                                     <  1:552299‑M1/93‑25 (MQ=255)                                                                                                                                                              ggttaagtgataacagatgtctggaaatataggggcaaatccaCTGCTTAACGAGTATCTGTCTCCGCTGGATATTACCGCGGCACAGTTTAAGGTGCTCTGCTCTATCCGCTgcgc                                                                                                                                                                                        >  2:16831‑M2/44‑117 (MQ=255)                                                                                                                                                              ggttaagtgataacagatgtctggaaatataggggcaaatccaCTGCTTAACGAGTATCTGTCTCCGCTGGATATTACCGCGGCACAGTTTAAGGTGCTCTGCTCTATCCGCTGCGCGGCGTGTATTACTCCGGTTGAACTGAAAAAGGTATTgt                                                                                                                                                  >  1:24614‑M2/44‑155 (MQ=255)                                                                                                                                                              gggtaagtgctaacagatgtctggaaatataggggcaaatcaaCTGCTTAACGAGTATCTGTCTCCGCTAGATATTACCGCGGCCCAGTTTAAGGTGATCTGCTCTATCCGCTGCGCGGCGTGTATTACTCAGGTAGAACTGAAAAAGGTATTgtcggtc                                                                                                                                             >  2:72571‑M2/44‑160 (MQ=255)                                                                                                                                                                ttaagtgataacagatgtctggaaatataggggcaaatccaCTGCTTAACGAGTATCTGTCTCCGCTGGATATTACCGCGGCACAGTTTAAgg                                                                                                                                                                                                              >  2:499024‑M2/42‑93 (MQ=255)                                                                                                                                                                  aagtgataacagatgtctggaaatataggggcaaatccaCTGCTTAACGAGTATCTGTCTCCGCTGGATATTACCGCGGCACAGTTTAAGGTGCTCTGCTCTATCCGCTGCgcggcg                                                                                                                                                                                    <  1:16831‑M2/78‑1 (MQ=255)                                                                                                                                                                   agtgataacagatgtctggaaatataggggcaaatccaCTGCTTAACGAGTATCTGtc                                                                                                                                                                                                                                              >  2:613407‑M2/39‑58 (MQ=255)                                                                                                                                                                   agtgataacagatgtctggaaatataggggcaaatccaCTGCTTAACGAGTATCTGTCTCCGCTGGATATTACCGCGGCACAGTTTAAGGTGCTCTGCTCTATCCGCTgcg                                                                                                                                                                                         >  1:505087‑M2/39‑111 (MQ=255)                                                                                                                                                                    gtgataacagatgtctggaaatataggggcaaatccaCTGCTTAACGAGTATCTGTCGCCGCTGCATATTACCGCGGCACAGTTTACGGtgct                                                                                                                                                                                                          <  1:499033‑M2/56‑1 (MQ=255)                                                                                                                                                                       cTTAATCCATATGGTTAATCAGAAGAAAGATCGCCTGCTtagactggccccctgaatctccagacaaccaatatcacttaaataagtgatagtcttaatactagtttttagactagtcattggagaacagatgattgatgtcttagggccggagaaacgcagacggcgt                                                                                                                           >  1:8055‑M1/1‑39 (MQ=255)                                                                                                                                                                       ataacagatgtctggaaatataggggcaaatccaCTGCTTAACGAGTATCTGTCTCCg                                                                                                                                                                                                                                          <  1:613418‑M2/24‑1 (MQ=255)                                                                                                                                                                       ataacagatgtctggaaatataggggcaaatccaCTGCTTAACGAGTATCTGTCTCCGCTGGATATTACCGCGGCACAGTTTAAGGTGCTCTGCTCTATCCGCTGCgcggc                                                                                                                                                                                     <  2:505077‑M2/77‑1 (MQ=255)                                                                                                                                                                         aacagatgtctggaaatataggggcaaatccaCTGCTTAACGAGTATCTGTCTCCGCTGGATATTACCGCGGCACAGTTTAAGGTGCTCTGCTCTATCCGCTGCGCGGCGTGTATTACTCCGGTTGAACTGAAAAAGGTATTgt                                                                                                                                                  >  1:89626‑M2/33‑144 (MQ=255)                                                                                                                                                                           aTCCATATGGTTAATCAGAAGAAAGATCGCCTGCTtagactggccccctgaatctccagacaaccaatatcacttaaataagtgatagtcttaatactagtttttagactagtcattggagaacagatgattgatgtcttagggccggagaaacgcagacggcgtacca                                                                                                                       <  2:8055‑M1/169‑135 (MQ=255)                                                                                                                                                                             gatgtctggaaatataggggcaaatccaCTGCTTAACGAGTATCTGTCTCCGCTGGATATTACCGCGGCACAGTTTAAGGTGCTCTGCTCTATCCGCTGCGCGGCGTGTATTACTCCGGTTGAACTGAAAAAGGTATTgtcggt                                                                                                                                              <  2:89626‑M2/116‑1 (MQ=255)                                                                                                                                                                                 atGGTTAATCGGAAGAAAGATCGCCTGCTtagactggccccctgaatctccagacaaccaatatcacttaaataagtgatagtcttaatactagtttttagactagtcattggagaacagatgattgatgtcttagggccggagaaacgcagacggcgtaccacacaggaaaagatcgcaattgttcagcagagctttgaaccggggatgaaggtctccctcgttgcccggcaacat                                             >  2:190906‑M1/1‑29 (MQ=255)                                                                                                                                                                                 atGGTTAATCAGAAGAAAGATCGCCTGCTtagactggccccctgaatctc                                                                                                                                                                                                                                        >  2:621151‑M1/1‑29 (MQ=255)                                                                                                                                                                                  tGGTTAATCAGAAGAAAGATCGCCTGCTtagactggccccctgaatctccagacaaccaa                                                                                                                                                                                                                             >  1:526104‑M1/1‑28 (MQ=255)                                                                                                                                                                                     ttAATCAGAAGAAAGATCGCCTGCTtagactggccccctgaatctccagacaaccaatatcacttaaataagtgatagtcttaatactagtttttagactagtcattggagaacagatgattgatgtcttagggccggagaaacgcagacggcgtaccacacaggaaaagatcgcaattgttcagcagagctttgaaccggggatgacggtctccctcgttgcccggcaacatggtg                                         <  1:190910‑M1/237‑213 (MQ=255)                                                                                                                                                                                      tactcagAAGAAAGATCGCCTGCTtagactggccccctgaatctccagacaaccaatatcacttaaataagtgatagtcttaatactagtttttagactagtcattggagaacagatgattgatgtcttagggcaggagcaacgcagccggcgtaccacacagcaaaagatcgcagttgttcagcagagatttgaaccgtggaggacggactccctgggacgccggcaaccaggtggagcagctagccggttatttctctggcgttctcaaccac  >  2:4859‑M1/4‑24 (MQ=255)                                                                                                                                                                                      tAATCAGAAGAAAGATCGCCTGCTtagactggccccctgaatctccagacaaccaatatc                                                                                                                                                                                                                         <  2:526093‑M1/60‑37 (MQ=255)                                                                                                                                                                                           taggggcaaatccaCTGCTTAACGAGTATCTGTCTCCGCTGGATATTACCGCGGCACAGTTTAAGGTGCTCTGCTCTATCCGCTGCGCGGCGTGTATTACTCCGGTTGAACTGAAAAAGGTATTGTCGGTCGACCTggg                                                                                                                                     >  1:244734‑M2/15‑139 (MQ=255)                                                                                                                                                                                               ggcaaatccaCTGCTTAACGAGTATCTGTCTCCGCTGGATATTACCGCGGCACAGTTTAAGGTGCTCTGCTCTATCCGCTGCGCGGCGTGTATTACTCCGGTTGAACTGAAAAAGGTATTGTCGGTCGACCTGGGAGCa                                                                                                                                 <  2:244730‑M2/129‑1 (MQ=255)                                                                                                                                                                                                   aatccaCTGCTTAACGAGTATCTGTCTCCGCTGGATATTACCGCGGCACAGTTTAAGGTGCTCTGCTCTATCCGCTGCGCGGCGTGTATTACTCCGGTTGAACTGAAAAAGGTATTGTCGGTCGACCTGGGAGCACTg                                                                                                                              >  1:239331‑M2/7‑138 (MQ=255)                                                                                                                                                                                                       caCTGCTTAACGAGTATCTGTCTCCGCTGGATATTACCGCGGCACAGTTTAAGGTGCTCTGCTCTATCCGCTGCGCGGCGTGTATTACTCCGGTTGAACTGAAAAAGGTATTGTCGGTCGACCTGGGAGCACTGAccc                                                                                                                          <  2:239327‑M2/136‑1 (MQ=255)                                                                                                                                                                                                        aCTGCTTAACGAGTATCTGTCTCCGCTGGATATTACCGCGGCACAGTTTAAGGTGCTCTGCTCTATCCGCTGCGCGGCGTGTATTACTCCGGTTGAACTGAAAAAGGTATTGTCGGTCGACCTGGGAGCACTGACCCGTATGCTGGATCGCCTGGTCTGTAAAGGCTGGGTGGAAAGGTTGCCGAACCCGAATGACAAGCGCGGCGTACt                                                 >  1:188126‑M2/2‑210 (MQ=255)                                                                                                                                                                                                            cTTAACGAGTATCTGTCTCCGCTGGATATTACCGCGGCACAGTTTAAGGTGCTCTGCTCTATCCGCTGCGCGGCGTGTATTACTCCGGTTGAACTGAAAAAGGTATTGTCGGTCGACCTGGGAGCACTGACCCGTATGCTGGATCGCCTGGTCTGTAAAGGCTGGGTGGAAAGGTTGCCGAACCCGAATGACAAGCGCGGCGTACTGGTa                                             <  2:188122/210‑1 (MQ=255)                                                                                                                                                                                                             ttagactggccccctgaatctccagacaaccaatatcacttaaataagtgatagtcttaatactagtttttagactagtcattggagaacagatgattgatgtcttagggccggagaaacgcagacggcgtaccacacaggaaaagatcgcaattgttctgcagagctttgaaccggggatgacggtctccctcgttgcccggcaac                                               <  2:271952‑M1/207‑207 (MQ=255)                                                                                                                                                                                                             |                                                                                                                                                                                                                                                            CATTGAACAAAACTTGAACCGATTTAGCAAAACGTGGCATCGGTCAATTCATTCATTTGACTTATACTTGCCTGGGCAATATTATCCCCTGCAACTAATTACTTGCCAGGGCAACTAATGTGAAAAGTACCAGCGATCTGTTCAATGAAATTATTCCATTGGGTCGCTTAATCCATATGGTTAATCAGAAGAAAGATCGCCTGCTTAACGAGTATCTGTCTCCGCTGGATATTACCGCGGCACAGTTTAAGGTGCTCTGCTCTATCCGCTGCGCGGCGTGTATTACTCCGGTTGAACTGAAAAAGGTATTGTCGGTCGACCTGGGAGCACTGACCCGTATGCTGGATCGCCTGGTCTGTAAAGGCTGGGTGGAAAGGTTGCCGAACCCGAATGACAAGCGCGGCGTACTGGTAAAACTTACCACCGGCGGCGCGGCAATATGTGAACAATGCCATC  >  CP009273/1613258‑1613713

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 11 ≤ ATCG/ATCG < 26 ≤ ATCG/ATCG < 37 ≤ ATCG/ATCG < 38 ≤ 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.