Predicted mutation
evidence	seq id	position	mutation	freq	annotation	gene	description
JC JC	CP009273	481,667	IS1 (–) +9 bp	100%	coding (451‑459/648 nt)	acrR →	transcriptional repressor

New junction evidence
		seq id	position	reads (cov)	reads (cov)	score	skew	freq	annotation	gene	product
*	?	CP009273	19796 =	NA (NA)	31 (1.200)	28/294	NT	100%	noncoding (768/768 nt)	IS1	repeat region
	?	CP009273	= 481675	0 (0.000)					coding (459/648 nt)	acrR	transcriptional repressor
*	?	CP009273	= 20563	NA (NA)	15 (0.580)	12/294	NT	100%	noncoding (1/768 nt)	IS1	repeat region
	?	CP009273	481667 =	0 (0.000)					coding (451/648 nt)	acrR	transcriptional repressor

AGTCCAGCGGTGCGTTAATCGGCAGCTCCCCCAAAGTTAAGGTGGGGGAGATAGATTAGTTGTACATTACCACGATTTTGACTCGGCTCATTATTTGCCCGCTTGAGACATTGTTTCCATATGTACGCGGGCGAATAAATAGAGGAATCTGATTACTTCCTTCATGGGGATGCTGAAAAGAGTAGTAATTGCTGGTAATGACTCCAACTTATTGATAGTGTTTTATGT‑TCAGATAATGCCCGATGACTTTGTCATGCAGCTCCACCGATTTTGAGAACGACAGCGACTTCCGTCCCAGCCGTGCCAGGTGCTGCCTCAGATTCAGGTTATGCCGCTCAATTCGCTGCGTATATCGCTTGCTGATTACGTGCAGCTTTCCCTTCAGGCGGGATTCATACAGCGGCCAGCCATCCGTCATCCATATCACCACGTCAAAGGGTGACAGCAGGCTCATAA  >  CP009273/19603‑20058                                                                                                                                                                                                  |                                                                                                                                                                                                                                                                        tgTCCTGCGTTGCGTTAATCGGCAGCTCCCCCATAGTTGAGGTGGGGGAGATAGATTAGTTGTACATTACCTCGATTTTGACTCGGCTCATTATTTGCCCGTTTGAGACATTGTTTCCATATGTACGCGGGCGAATAAATAGAGGAATCTGATTACTTCCTTCATGGGGATGCTGAAAAGAGTAGTAATTGCTGGTAATGACTCCAACTTATTGATAGTGTTTTATGT‑TCAGATAATGCCCGATGACTTTGTCATGCAGCTCCACCGATTTTgag                                                                                                                                                                                       <  1:60181/274‑1 (MQ=255)                                                   atttatTGGTTGTAAATTAGTAAGATTTTGACTCGGCTCATTANTTGCCCGCTTGATACATTGTTTCCATATGTACGCGGGCGAATAAATAGAGGAATCTGATTACTTCCTTCATGGGGATGCTGAAAAGAGTAGTAATTGCTGGTAATGACTCCAACTTATTGATAGTGTTTTATGT‑TCAGATAATGCCCGATGACTTTGTCATGCAGCTCCACCGATTTTGAGAACGACAGCGACTTCCGTCCCAGCCGTGCCAGGTGCTGCCTCAGAtt                                                                                                                                        <  2:313514/268‑1 (MQ=255)                                                          aGTTGTACATTACCATGATTTTGACTCGGCTCATTATTTGCCCGCTTGAGACATTGTTTCCATATGTACGCGGGCGAATAAATAGAGGAATCTGATTACTTCCTTCATGGGGATGCTGAAAAGAGTAGTAATTGCTGGTAATGACTCCAACTTATTGATAgt                                                                                                                                                                                                                                                >  1:343026/1‑162 (MQ=255)                                                              gTACATTACCACGATTTTGACTCGGCTCATTATTTGCCCGCTTGAGACATTGTTTCCATATGTACGCGGGCGAATAAATAGAGGAATCTGATTACTTCCTTCATGGGGATGCTGAAAAGAGTAGTAATTGCTGGTAATGACTCCAACTTATTGATAGTGttt                                                                                                                                                                                                                                            <  2:343014/162‑1 (MQ=255)                                                                      ccACGATTTTGACTCGGCTCATTATTTGCCCGCTTGAGACATTGTTTCCATATGTACGCGGGCGAATAAATAGAGGAATCTGATTACTTCCTTCATGGGGATGCTGAAAAGAGTAGTAATTGCTGGTAATGACt                                                                                                                                                                                                                                                                >  2:430547/1‑134 (MQ=255)                                                                      ccACGATTTTGACTCGGCTCATTATTTGCCCGCTTGAGACATTGTTTCCATATGTACGCGGGCGAATAAATAGAGGAAGCTGATTACTTCCTTCATGGGGATGCTGAAAAGAGTAGTAATTGCTGGTAATGACTCCAACTTATTGATAGTGTTTTATGT‑TCAGATAATGCCCGATGACTTTGTCATGCAGCTCCACCGATTTTGAGAACGACAGCGACTTCCGTCCCAGCCGTACCAGGTGCTGCCTCAGATTCACGTTATGCCGCTCAATTCGc                                                                                                                  >  1:8639/1‑275 (MQ=255)                                                                          gATTTTGACTCGGCTCATTATTTGCCCGCTTGAGACATTGTTTCCATATGTACGCGGGCGAATAAATAGAGGAATCTGATTACTTCCTTCATGGGGATGCTGAAAAGAGTAGTAATTGCTGGTAATGACTCCaa                                                                                                                                                                                                                                                            <  1:430560/134‑1 (MQ=255)                                                                                                 gCCCGCTTGAGACATTGTTTCCATATGTACGCGGGCGAATAAATAGAGGAATCTGATTACTTCCTTCATGGGGATGCTGAAAAGAGTAGTAATTGCTGGTAATGACTCCAACTTATTGATAGTGTTTTATGT‑TCAGATAATGCCCGATGACTTTGTCATGCAGCTCCACCGATTTTGAGAACGACAGCGACTTCCGTCCCAGCCGTGCCAGGTGCTGCCTCAGATTCAGGTTATGCCGCTCAATTCGCTGCGTATATCGCNTTCTGTGTACGttc                                                                                       >  2:361605/1‑273 (MQ=255)                                                                                                      cTTGAGACATTGTTTCCATATGTACGCGGGCGAATAAATAGAGGAATCTGATTACTTCCTTCATGGGGATGCTGAAAAGAGTAGTAATTGCTGGTAATGACTCCAACTTAtt                                                                                                                                                                                                                                                      >  2:199500/1‑112 (MQ=255)                                                                                                          agaCATTGTTTCCATATGTACGCGGGCGAATAAATAGAGGAATCTGATTACTTCCTTCATGGGGATGCTGAAAAGAGTAGTAATTGCTGGTAATGACTCCAACTTATTGATa                                                                                                                                                                                                                                                  <  1:199506/112‑1 (MQ=255)                                                                                                               ttGTTTCCATATGTACGCGGGCGAATAAATAGAGGAATCTGATTACTTCCTTCATGGGGATGCTGAAAAGAGTAGTAATTGCTGGTAATGACTCCAACTTATTGATAGTGTTTTATGT‑TCAGATAATGCCCGATGACTTTGTCATGCAGCTCCCCCGATTTTGAGAACGACAGCGACTTCCGTCCTAGCCGTGCCAGGTGCTGCCTAAGATTCAGGTGATGCCGCTCAATTCGCTGCGCATATCGCTTGCGGATTACGTGCAGCTGTcccggcaa                                                                         >  2:27848/1‑270 (MQ=255)                                                                                                                 gTTTCCATATGTACGCGGGCGAATAAATAGAGGAATCTGATTACTTCCTTCATGGGGATGCTGAAAAGAGTAGTAATTGCTGGTAATGACTNCAACTTATTGATAGTGTTTTATGT‑TCAGATAATGCCCGATGACTTTGTCATGCAGCTCCACCGATTTTGAGAACGACAGCGACTTCCGTCCCAGCCGTGCCAGGTGCTGCCTCAGATTCAGGTTATGCCGCTCAATTCAATGCGTATATCGCTTGCTGATTACGTGCAGCTTTCCCTTCAGGc                                                                       <  1:361617/275‑1 (MQ=255)                                                                                                                                    cGAATAAATAGAGGAATCTGATTACTTCCTTCATGGGGATGCTGAAAAGAGTAGTAATTGCTGGTAATGa                                                                                                                                                                                                                                                                  >  2:45229/1‑70 (MQ=255)                                                                                                                                        taaataGAGGAATCTGATTACTTCCTTCATGGGGATGCTGAAAAGAGTAGTAATTGCTGGTAATGACTcc                                                                                                                                                                                                                                                              <  1:45231/70‑1 (MQ=255)                                                                                                                                               agGAATCTGATTACTTCCTTCATGGGGATGCTGAAAAGAGTAGTAATTGCTGGTAATGACTCCAACTTAtt                                                                                                                                                                                                                                                      >  1:85280/1‑71 (MQ=255)                                                                                                                                                   aTCTGATTACTTCCTTCATGGGGATGCTGAAAAGAGTAGTAATTGCTGGTAATGACTCCAACTTATTGATa                                                                                                                                                                                                                                                  <  2:85278/71‑1 (MQ=255)                                                                                                                                                      tGATTACTTCCTTCATGGGGATGCTGAAAAGAGTAGTAATTGCTGGTAATGACTCCAACTTATTGATAgtg                                                                                                                                                                                                                                               >  1:70656/1‑71 (MQ=255)                                                                                                                                                         ttACTTCCTTCATGGGGATGCTGAAAAGAGTAGTAATTGCTGGTAATGACTCCAACTTATTGATAGTGTTTTATGT‑TCAGATAATGCCCGATGACTTTGTCATGCAGCTCCACCGATTTTGAGAACGACAGCGACTTCCGTCCCAGCCGTGCCAGGTGCTGCCTCAGATTCAGGTTATGCCGCTCAATTCGCTGCGTATATCGCTTGCTGATTACGTGCAGCTTTCCCTTCAGGCGGGATTCATACAGCGGCCAGCCCTcctgtctcttatccc                                >  1:4166/1‑261 (MQ=255)                                                                                                                                                          tACTTCCTTCATGGGGATGCTGAAAAGAGTAGTAATTGCTGGTAATGACTCCAACTTATTGATAGTGtttt                                                                                                                                                                                                                                           <  2:70654/71‑1 (MQ=255)                                                                                                                                                                       gggATGCTGAAAAGAGTAGTAATTGCTGGTAATGACTCCCACTTATTGATAGTGTTTTATGT‑TCAGATAATGCCCGATGACTTTGTCATGCAGCTCCACCGATTTTGAGAACGACAGCGACTTCCGTCCCAGCCGTTCCAGGTGCTGCCTCAGATTCAGGTTATGCCGCTCAATTCGTTGCGTATATCGCTTGCTGAt                                                                                              >  1:276627/1‑198 (MQ=255)                                                                                                                                                                       gggATGCTGAAAAGAGTAGTAATTGCTGGTAATGACTCCAACTTATTGATAGTGTTTTATGT‑TCAGATAATGCCCGATGACTTTGTCATGCAGCTCCACCGATTTTGAGAACGACAGCGACTTCCGTCCCAGCCGTGCCAGGTGCTGCCTCAGATTCAGGTTATGCCGCTCACTTCGCTGCGTATATCGCTTGCTGATTCCGTGCAGCTTTCCCTTCAGGCGGGATTCATACAGCGGCCAGCCATCCGTCATCCATATCACCACGTCcaattt                   >  2:415517/1‑270 (MQ=255)                                                                                                                                                                             cTGTAAAGAGTAGTAATTGCTGGTAATGACTCCAACTTATTGATAGTGTTTTATGT‑TCAGATAATGCCCGATGACTTTGTCATGCAGCTCCACCGATTTTGAGAACGACAGCGACTTCCGTCNCAGCCGTGCCAGATGCTGCCTCAGATTCAGGTTATGCCGCTCAATTCGCTGCGTATATCGCTTGCTGATTACGTGCAGCTTTCCCTTCAGGCGGGATTCATACAGCGGCCAGCCATCCGTCATCCATATCACCACGTCAAAGGGTGAcagca           <  1:415530/275‑1 (MQ=37)                                                                                                                                                                                     agtagtAATTGCTGGTAATGACTCCAACTTATTGCTAGTGTTTTATGT‑TCAGATAATGCCCGATGACTTTGTCATGCAGCTCCACCGATTTTGAGAACGACAGCGACTTCCGTCCCAGCCGTGCCAGGTGCTGCCTCAGATTCAGGTTATGCCGCTCAATTCGCTGCGTATATCGCTTGCTGATTACGTGCAGCTTTCCCTTCAGGCGGGATTCATACAGCGGCCAGCCATCCGTCATCCATATCACCACGTCAAAGGGTGACAGCAGGCTCAt    >  1:222147/1‑274 (MQ=21)                                                                                                                                                                                     agtagtAATTGCTGGTAATGACTCCAACTTATTGATAGTGTTTTATGT‑TCAGATAATGCCCGATGACTTTGTCATGCAGCTCCACCGATTTTGAGAACGACAGCGACTTCCGTCCCAGCCGTGCCAGGTGCTGCCTCAGATTCAGGTTATGCCGCTCAATTCGCTGCGTATATCGCTAGCTGATTACGTGCAGCTTTCCCTTCa                                                                          >  1:256963/1‑204 (MQ=37)                                                                                                                                                                                      tgagtaATTGCTGGTAATGACTCCAATCTATTTAAAGGGTTTTTTGTGTGAG‑TAATGCCGGATGACTTTGTGCTGCAGCGTAACCGATTTTGAGAACGACAGCGACGTCCTGTCCAGCCGTGCCAGGTGCTGCCTCAGAGTCAGGTTATGCCGCTCAATTCGCTGCGTATATCGCTTGCTGATTACGTGCATCTTTCCAGGCGGACGGGATTCATACAGCGGCCAGCCATCCGTCATCCATATCACCACGTCAAAGGGTGACGGCAGGCTCATaa  <  2:8639/273‑1 (MQ=11)                                                                                                                                                                                      gtagtaATTGCTGGTAATGACTCAAACTTATTGATAGTGTTTTATGT‑TCAGATAATGCCCGATGACTTTGTCATGCAGCTCCACCGATTTTGAGAACGACAGCGACTTcc                                                                                                                                                                       >  1:212901/1‑110 (MQ=255)                                                                                                                                                                                       tagtaATTGCTGGTAATGACTCCAACTTATTGATAGTGTTTTATGT‑TCAGATAATGCCCGATGACTTTGTCATGCAGCTCCACCGa                                                                                                                                                                                              >  2:208423/1‑86 (MQ=255)                                                                                                                                                                                       tagtaATTGCTGGTAATGACTCCAACTTATTGATAGTGTTTTATGT‑TCAGATAATGCCCGATGACTTTGTCATGCAGCTCCACCGATTTTGAGAACGACAGCGACTTCCGTCCCAGCCGTGCCAGGTGCTGCCTCAGATTCAGGTTATGCCGCTCAATTCGCTGCGTATATCGCTTGCTGATTACGTGCCGCTTTCCCTTCAGGCGGGATTCACACAGCGGACAGCCATCCGTCAGCCATATCCCCCCGTCAAAGTATGACCGCGGGccccgaa  >  2:137614/1‑268 (MQ=11)                                                                                                                                                                                         gtaATTGCTGGTAATGACTCCAACTTATTGATAGTGTTTTATGT‑TCAGATAATGCCCGATGACTTTGTCATGCAGCTCCACCGATTTTGAGAACGACAGCGACTTCCGTCCCAGCCGTGCCAGGTGCTGCCTCAGATTCAGGTTATGCCGCTCAATTCGCTGCGTATATCGCTTGCTGATTACGTGCAGCTTTCCCTTCAGGCg                                                                      <  2:256955/204‑1 (MQ=34)                                                                                                                                                                                          taATTGCTGGTAATGACTCCAACTTATTGATAGTGTTTTATGT‑TCAGATAATGCCCGATGACTTTGTCATGCAGCTCCACCGATTTTGAGAACGACAGCGACTTCCGTcc                                                                                                                                                                   <  2:212894/110‑1 (MQ=38)                                                                                                                                                                                           aaTTGCTGTTAATGACTCCAACTTATTGATAGTGTTTTATGT‑TCAGATAATGCCCGATGACTTTGTCATGCAGCTCCACCGATTTTGAGAACGACAGCGACTTCCGTCCCAGCCGTGCCAGGTGCTGCCTCAGATTCAGGTTATGCCGCTCAATTCGCTGCGTATATCGCTTGCTGATTACGTGCAGCTTTCCCTTCAGGCGGGATTCATACAGCGGCCAGCCATCCGTCATCCATATCACCACGTCAAAGGGTGAcagca           <  1:137620/261‑1 (MQ=17)                                                                                                                                                                                           aaTTGCTGGTAATGACTCCAACTTATTGATAGTGTTTTATGT‑TCAGATAATGCCCGATGACTTTGTCATGCAGCTCCACCGAtttt                                                                                                                                                                                          <  1:208430/86‑1 (MQ=39)                                                                                                                                                                                               gCTGGTAATGACTCCAACTTATTGATAGTGTTTTATGT‑TCAGATAATGCCCGATGACTTTGTAATGCAGCTCCACCGATTTTGAGAACGACAGCGACTTCCGTCCCAg                                                                                                                                                                >  2:143265/1‑108 (MQ=17)                                                                                                                                                                                                  |                                                                                                                                                                                                                                                                        AGTCCAGCGGTGCGTTAATCGGCAGCTCCCCCAAAGTTAAGGTGGGGGAGATAGATTAGTTGTACATTACCACGATTTTGACTCGGCTCATTATTTGCCCGCTTGAGACATTGTTTCCATATGTACGCGGGCGAATAAATAGAGGAATCTGATTACTTCCTTCATGGGGATGCTGAAAAGAGTAGTAATTGCTGGTAATGACTCCAACTTATTGATAGTGTTTTATGT‑TCAGATAATGCCCGATGACTTTGTCATGCAGCTCCACCGATTTTGAGAACGACAGCGACTTCCGTCCCAGCCGTGCCAGGTGCTGCCTCAGATTCAGGTTATGCCGCTCAATTCGCTGCGTATATCGCTTGCTGATTACGTGCAGCTTTCCCTTCAGGCGGGATTCATACAGCGGCCAGCCATCCGTCATCCATATCACCACGTCAAAGGGTGACAGCAGGCTCATAA  >  CP009273/19603‑20058

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 10 ≤ ATCG/ATCG < 17 ≤ ATCG/ATCG < 33 ≤ 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.