New junction evidence
		seq id	position	reads (cov)	reads (cov)	score	skew	freq	annotation	gene	product
*	?	CP009273	19796 =	NA (NA)	10 (0.200)	10/276	NT	21.7%	noncoding (768/768 nt)	IS1	repeat region
	?	CP009273	3649844 =	36 (0.720)					coding (257/333 nt)	hdeA	stress response protein acid‑resistance protein

TGCTTTTAAAGAAGATATTCCGGCCTGTTCAATATGCAAGGAAGTACGATGTAACGCATTCCCGGAATTACATATCTTTCTTAATTTTGTCCCATTCGCCTTTAACTTTATCTTTAAAGTTGGCTTGTTTATCCTGAGTACAAGCCTGAACGATAGCTGGGGTTACGGTTGCAATACCCTGAACATCTAAAACCGCATCTTCTGGTTTATCTTTGTTGTTCAGCGCTTCAGCAAAACCAACTGCAGTTGGCTGGAAGGATTCGTCCACAGCCAGGAAATCTTCAC  >  CP009273/3649701‑3649985                                                                                                                                                |                                                                                                                                              tgctTTTAAAGAAGATATTCCGGCCTGTTCAATATGAAATGATGTACGATGTAACGCATTCCCGGAATTACATATCTTTCTTAATTTTGTCCCATTCGCCTTTAACTTTATCTTTAAAGTTGGCTTGTTTATCCTGAGTACAAGCCTGa                                                                                                                                          <  1:611273/149‑1 (MQ=255)  gcggcataacctgaatctgaggcagcacctggcacggctgggacggaagtcgctgtcgttctcaaaatcggtggagctgcatgacaaagtcatcgggcattatctgaacataaaacactatcaataagttggagtcattaccGCCTGaa                                                                                                                                         <  1:732145‑M2/7‑1 (MQ=255)   ctTTTAAAGAAGATAGTCCGGCCTGTTCAATATGCAAGGAAGTACGATGTAACGCATTCCCGGAATTACATATCTTTCTTAATTTTGTCCCATTCGCCTTTAACTTTATCTCTAAAGTCGGCCTGCTTAACCTGAGTACAAGCCTGAAc                                                                                                                                        <  2:822682/149‑1 (MQ=255)           gaagaTATTCCGGCCTGTTCAATATGCAAGGAAGTACGATGTAACGCATTCCCGGAATTACATATCTTTCTTAATTTTGTCCCATTCGCCTTTAACTTTATCTTTAAAGTTGGCTTGTTTATCCTGAGTACAAGCCTGAACGATAGCTg                                                                                                                                >  1:670017/1‑149 (MQ=255)              gaTATTCCGGCCTGTTCAATATGCAAGGAAGTACGATGTAACGCATTCCCGGAATTACATATCTTTCTTAATTTTGTCCCATTCGCCTTTAACTTTATCTTTAAAGTTGGCTTGTTTATCCTGAGTACAAGCCTGAACGATAGCTgggg                                                                                                                             <  1:179969/149‑1 (MQ=255)                  ttCCGGCCTGTTCAATATGCAAGGAAGTACGATGTAACGTAGTCCCGGAATTACATATCTTTCTTAATTTTGTCCCATTCGCCTTTAACTTTATCTTTAAAGTTGGCTTGTTTATCCTGAGTACAAGCCTGAACGATAGCTGGGGTTAc                                                                                                                         <  1:590521/149‑1 (MQ=255)                          tGTTCAATATGCAAGGAAGTACGATGTAACGCATTCCCGGAATTACATATCTTTCTTAATTTTGTCCCATTCGCCTTTAACTTTATCTTTCACGCTGGCTTGTTTATCCTGAGTACAAGCCTGAACGATAGCTGGGGTTACGGTTGCaa                                                                                                                 <  2:598883/149‑1 (MQ=255)                          tGTTCAATATGCAAGGAAGTACGATGTAACGCATTCCCGGAATTACATATCTTTCTTAATTTTGTCCCATTCGCCTTTAACTTTATCTTTAAAGTTGGCTTGTTTATCCTGAGTACAAGCCTGAACGATAGCTGGGGTTACGGTTGCaa                                                                                                                 <  1:845253/149‑1 (MQ=255)                          tGTTCAATATGCAAGGAAGTACGATGTAACGCATTCCCGGAATTACATATCTTTCTTAATTTTGTCCCATTCGCCTTTAACTTTATCTTTAAAGTTGGCTTGTTTATCCTGAGTACAAGCCTGAACGATAGCTGGGGTTACGGTTGCaa                                                                                                                 <  1:771589/149‑1 (MQ=255)                                    gCAAGGAAGTACGATGTAACGCATTCCCGGAATTACATATCTTTCTTAATTTTGTCCCATTCGCCTTTAACTTTATCTTTAAAGTTGGCTTGTTTATCCTGAGTACAAGCCTGAACGATAGCTGGGGTTACGGTTGCAATACCCTGAAc                                                                                                       <  1:279347/149‑1 (MQ=255)                                                gATGTAACGCATTCCCGGAATTACATATCTTTCTTAATTTTGTCCCATTCGCCTTTAACTTTATCTTTAAAGTTGGCTTGTTTATCCTGAGTACAAGCCTGAACGATAGCTGGGGTTACGGTTGCAATACCCTGAACATCTAAAACCGc                                                                                           <  2:289096/149‑1 (MQ=255)                                                   gTAACGCATTCCCGGAATTACATATCTTTCTTAATTTTGTCCCATTCGCCTTTAACTTTATCTTTAAAGTTGGCTTGTTTATCCTGAGTACAAGCCTGAACGATAGCTGGGGTTACGGTTGCAATACCCTGAACATCTAAAACCGCAtc                                                                                        <  2:744125/149‑1 (MQ=255)                                                      ctgtcgttctcaaaatcggtggagctgcatgacaaagtcatcgggcattatctgaacataaaacactatcaataagttggagtcattaccGCCTGAACGATAGCTGGGGTTACGGTTGCAATACCCTGCACATCTAAAACCGCAtcttc                                                                                     >  1:11705‑M2/91‑149 (MQ=255)                                                      aCGCATTCCCGGAATTACATATCTTTCTTAATTTTGTCCCATTCGCCTTTAACTTTATCTTTAAAGTTGGCTTGTTTATCCTGAGTACAAGCCTGAACGATAGCTGGGGTTACGGTTGCAATACCCTGAACATCTAAAACCGCAtcttc                                                                                     <  2:44822/149‑1 (MQ=255)                                                        gtcgttctcaaaatcggtggagctgcatgacaaagtcatcgggcagtatctgaacataaaacactatcaataagttggagtcattaccGCCTGAACGATAGCTGGGGTTACGGTTGCAATACCCTGAACGTCTAAAACCTCATATTCTg                                                                                   >  1:440075‑M2/89‑149 (MQ=255)                                                            ttctcaaaatcggtggagctgcatgacaaagtcatcgggcattatctgaacataaaacactatcaataagttggggtcattaccGCCTGAACGATAGCTGGGGTTACGGTTGCAATACCCTGAACATCTAAAACCGCATCTTCTGGttt                                                                               >  2:650655‑M2/85‑149 (MQ=255)                                                                     tACATATCTTTCTTAATTGTGTCCCATTCGCCTTTAACTTTATCTTTAAAGTTGGCTTGTTTATCCTGAGTACAAGCCTGAACGATAGCTGGGGTTACGGTTGCAATACCCTGAACATCTAAAACCGCATCTTCTGGTTTATCTttgtt                                                                      <  2:524152/149‑1 (MQ=255)                                                                          atCTTTCTTAATTTTGTCCCATTCGCCTTTAACTTTATCTTTAAAGTTGGCTTGTTTATCCTGAGTACAAGCCTGAACGATAGCTGGGGTTACGGTTGCAATACCCTGAACATCTAAAACCGCATCTTCTGGTTTATCTTTGTTGTTCa                                                                 >  1:440874/1‑149 (MQ=255)                                                                          atCTTTCTTAATTTTGTCCCATTCGCCTTTAACTTTATCTTTAAAGTTGGCTTGTTTATCCTGAGTACAAGCCTGAACGATAGCTGGGGTTACGGTTGCAATACCCTGAACATCTAAAACCGCATCTTCTGGTTTATCTTTGTTGTTCa                                                                 <  2:670017/149‑1 (MQ=255)                                                                            ctttcttAATTTTGTCCCATTCGCCTTTAACTTTATCTTTAAAGTTGGCTTGTTTATCCTGAGTACAAGCCTGAACGATAGCTGGGGTTACGGTTGCAATACCCTGAACATCTAAAACCGCATCTTCTGGTTTATCTTTGTTGTTCAgc                                                               >  2:619884/1‑149 (MQ=255)                                                                              ctgcatgacaaagtcatcgggcattatctgaacataaaacactatcaataagttggagtcattaccGCCTGAACGATAGCTGGGGTTACGGTTGCAATACCCTGAACATCTAAAACCGCATCTTCTGGTTTATCTTTGTTGTTCAgcgc                                                             <  1:420747‑M2/83‑1 (MQ=255)                                                                                gcagggcaaggtcagcgggcattatctgaacataagacactatcaagaagttggagtcattaccGGCTGAACGATAGCTGGGGTTACGGTGGCCATACCCTGAACATCTAAAACCGCATCTTCTGGTTTATCTTTGTTGTTCAGCGCtt                                                           <  1:697835‑M2/85‑1 (MQ=255)                                                                                 ttAATTTTGTCCCATTCGCCTTTAACTTTATCTTTAAAGTTGGCTTGTTTATCCTGAGTACAAGCCTGAACGATAGCTGGGGTTACGGTTGCAATACCCTGAACATCTAAAACCGCATCTTCTGGTTTATCTTTGTTGTTCAGCGCTTc                                                          >  2:751800/1‑149 (MQ=255)                                                                                 ttAATTTTGTCCCATTCGCCTTTAACTTTATCTTTAAAGTTGGCTTGTTTATCCTGAGTACAAGCCTGAACGATAGCTGGGGTTACGGTTGCAATACCCTGAACATCTAAAACCGCATCTTCTGGTTTATCTTTGTTGTTCAGCGCTTc                                                          >  2:575492/1‑149 (MQ=255)                                                                                    aTTTTGTCCCGTTCGCCTTTAACATGATCTTTAAAGTTGGCTTGTTTATCCTGAGTACCAGCCTGAACGATAGCTGGGGTTACGGTTGCAATACCCTGAACATCTAAAACCGCATCTTCTGGTTTATCTTTGTTGTTCAGCGCTTCAGc                                                       <  1:513005/149‑1 (MQ=255)                                                                                    aTTTTGTCCCATGCGCCTTTAACTTGATCTTTAAAGGTTGCTTGTTTATCCTGAGTACCAGCCTGAACGATAGCTGGGGTTACGGTTGCAATACCCGGAACATCTAAAACCGCATCTTCTGGTTTATCTTTGTTGTTCAGCGCTTCAGc                                                       <  1:176347/149‑1 (MQ=255)                                                                                     ttttGTCCCATTCGCCTTTAACTTTATCTTTAAAGTTGGCTTGTTTATCCTGAGTACAAGCCTGAACGATAGCTGGGGTTACGGTTGCAATACCCTGAACATCTAAAACCGCATCTTCTGGTTTATCTTTGTTGTTCAGCGCTTCAGCa                                                      >  2:673168/1‑149 (MQ=255)                                                                                        tGTCCCATTCGCCTTTAACTTTATCTTTAAAGTTGGCTTGTTTATCCTGAGTACAAGCCTGAACGATAGCTGGGGTTACGGTTGCAATCCCCTGAGCAGCTAAAACCGCATCTTCTGGTTTATCTTTGTTGTTCAGCGCTTCAGCaaaa                                                   <  2:816260/149‑1 (MQ=255)                                                                                        tGTCCCATTCGCCTTTAACTTTATCTTTAAAGTTGGCTTGTTTATCCTGAGTACAAGCCTGAACGATAGCTGGGGTTACGGTTGCAATACCCTGAACATCTAAAACCGCATCTTCTGGTTTATCTTTGTTGTTCAGCGCTTCAGCaaaa                                                   <  2:136386/149‑1 (MQ=255)                                                                                           cccATTCGCCTTTAACTTTATTTTTAAAGTTGGCTGGGTTATCCTGGGTACAAGCCTGAACGATAGCTGGGGTTATGGTTGCAATACCCTGAACATTTAAAACTGCATCTTCTGGTTTATTTTTGTTGTTTTTCGCTTCAGGAAAAGCa                                                >  1:403643/1‑149 (MQ=255)                                                                                            ccATTCGCCTTTAACTTTTTCTTTAAAGTTGGCTTGTTTATCCTGAGTACAAGCCTGAACGATAGCTGGGGTTACGGTTGCAATACCCTGAACATCTAAAACCGCATCTTCTGGTTTATCTTTGTTGTTCAGCGCTTCAGCAAAACCaa                                               <  1:470454/149‑1 (MQ=255)                                                                                            ccATTCGCCTTTAACTTTATCTTTAAAGTTGGCTTGTTTATCCTGAGTACAAGCCTGAACGATAGCTGGGGTTACGGTTGCAATACCCTGAACATCTAAAACCGCATCTTCTGGTTTATCTTTGTTGTTCAGCGCTTCAGCAAAACCaa                                               >  1:271505/1‑149 (MQ=255)                                                                                                        tgtgaacgtacaacactatcaataagttggagtcattcccGGCTGAACGATAGCTGGGGTTACGGTTGCAATACCCTGAACATCTAAAACCGCATGTTCTGGTTTATCTTTGTTGTTCAGCGCTTCAGCAAAACCAACTGCAGTTGGCt                                   <  1:391472‑M2/109‑1 (MQ=255)                                                                                                        aaCTTTCTCTTTAATGTTGGCTTGTTTATCCTGAGTGCAAGCATGAACGATAGCTGGGGTTACGGTTGCAATACCCTGAACATCTACAACCGCCTCTTCTGGTTTATCTTTGTTGTTCAGCGCTTCATCAAAACCCACTGCAGTTGGCt                                   <  2:614183/149‑1 (MQ=255)                                                                                                        aaCTTGAGCTTTAAAGTTGGCTTGTTTATCCTGAGTACAAGCCTGAACGATAGCTGGGGTTACGGTTGCAATACCCTGAACATCTAAAACCGCATCTTCTGGTTTATCTTTGTTGTTCAGCGCTTCAGCAAAACCAACTGCAGTTGGCt                                   <  2:805629/149‑1 (MQ=255)                                                                                                                 tttAAAGTTGGCTTGTTTATCCTGAGTACAAGCCTGAACGATAGCTGGGGTTACGGTTGCAATACCCTGAACATCTAAAACCGCATCTTCTGGTTTATCTTTGTTGTTCAGCGCTTCAGCAAAACCAACTGCAGTTGGCTGGAAGGAtt                          >  1:755599/1‑149 (MQ=255)                                                                                                                 aaaacactatcaataagttggagtcattaccGCCTGAACGATAGCTGGGGTTACGGTTGCAATACCCTGAACATCTAAAACCGCATCTTCTGGTTTATCTTTGTTGTTCAGCGCTTCAGCAAAACCAACTGCAGTTGGCTGGAAGGAtt                          <  2:859825‑M2/118‑1 (MQ=255)                                                                                                                  ttAAAGTTGGCTTGTTTATCCTGAGTACAAGCCTGAACGATAGCTGGGGTTACGGTTGCAATACCCTGAACATCTAAAACCGCATCTTCTGGTTTATCTTTGTTGTTCAGCGCTTCAGCAAAACCAACTGCAGTTGGCTGGAGGGATTc                         >  1:417192/1‑149 (MQ=255)                                                                                                                    aaaGTTGGCTTGTTTATCCTGAGTACAAGCCTGAACGTTAGCTGGGGTTACGGTTGCAATACCCTGAACATCTAAAACCGCATCTTCTGGTTTATCTTTGTTGTTCAGCGCTTCAGCAAACCCAATTGCAGTTGGCTGGAAGGATTCGt                       <  2:567934/149‑1 (MQ=255)                                                                                                                            aataagttggagtcattaccGCCTGAACGATAGCTGGGGTTACGGTTGCAATACCCTGAACATCTAAAACCGCATCTTCTGGTTTATCTTTGTTGTTCAGCGCTTCAGCAAAACCAACTGCAGTTGGCTGGAAGGATTCGTCCACAGcc               >  1:602882‑M2/21‑149 (MQ=255)                                                                                                                             ataagttggagtcattaccGCCTGATCGATAGCTGGGGTTACGGTTGCAATACCCTGAACATCTAAAACCGCATCTTCTGGTTTATCTTTGTTGTTCAGCGCTTCAGCAAAACCAACTGCAGTTGGCTGGAAGGATTCGTCCACAGCCa              <  1:756352‑M2/130‑1 (MQ=255)                                                                                                                                      cTGAGTACAAGCCTGAACGATAGCTGGGGTTACGGTTGCAATACCCTGAACATCTAAAACCGCATCTTCTGGTTTATCTTTGTTGTTCAGCGCTTCAGCAAAACCAACTGCAGTTGGCTGGAAGGATTCGTCCACAGCCAGGAAATCtt     >  2:347384/1‑149 (MQ=255)                                                                                                                                       tGAGTACAAGCCTGAACGATAGCTGGGGTTACGGTTGCAATACCCTGAACATCTAAAACCGCATCTTATGGTTTATCTTTGTTGTTCAGCGCTTCAGCAAAACCAACTGCAGTTGGCTGGAAGGATTCGTCCACAGCCCGGGAATCTTc    >  2:121491/1‑149 (MQ=255)                                                                                                                                        gAGTACAATCCTGAACGATAGCTGGGGTTACGGTTGCAATACCCTGAACATCTAAAACCGCATCTTCTGGTTTATCTTTGTTGTTCAGCGCTTCAGCAAAACCAACTGCAGTTGGCTGGAAGGATTCGTCCACAGCCAGGAAATCTTca   <  1:311013/149‑1 (MQ=255)                                                                                                                                        gAGGACAAGCCTGAACGATAGCTGGGGTTACGGTTGCAATACCCCGAACATCTAAAACCGCATCTTCTGGTTTATCTTGGTTGTTCAGCGCTTCAGCAAAACCAACTGCAGTTGGCTGGAAGGATTCGTCCACAGCCAGGAAATCTTca   <  1:299078/149‑1 (MQ=255)                                                                                                                                         ggtccAAGCCTGAACGATAGCTGGGGTTAGGGTTGCAATACCCTGAACATCTAAAACCGCATCTTCTGGTTTATCTTTGTTGGTCAGCGCTTCAGCAAAACCAACTGCAGTTGGCTGGAAGGATTCGTCCACAGCCAGGAAATCTTcac  <  1:557834/145‑1 (MQ=255)                                                                                                                                         aggaCAAGCCTGAACGGTAGCTGGGGTTACGGTTGCAATACCCTGAACATCTAAAACCGCACCTTCTGGTTTATCTTTGTTGTTCAGCGCTTCAGCAAAACCAACTGCAGTTGGCTGGAAGGATTCGTCCACAGCCAGGAAATCTTcac  <  2:151056/146‑1 (MQ=255)                                                                                                                                         aGTACAAGCCTGAACGATAGCTGGGGTTACGGTTGCAATACCCTGAACATCTAAAACCGCATCTTCTGGTTTATCTTTGTTGTTCAGCGCTTCAGCAAAACCAACTGCAGTTGGCTGGAAGGATTCGTCCACAGCCAGGAAATCTTcac  <  2:151129/149‑1 (MQ=255)                                                                                                                                                |                                                                                                                                              TGCTTTTAAAGAAGATATTCCGGCCTGTTCAATATGCAAGGAAGTACGATGTAACGCATTCCCGGAATTACATATCTTTCTTAATTTTGTCCCATTCGCCTTTAACTTTATCTTTAAAGTTGGCTTGTTTATCCTGAGTACAAGCCTGAACGATAGCTGGGGTTACGGTTGCAATACCCTGAACATCTAAAACCGCATCTTCTGGTTTATCTTTGTTGTTCAGCGCTTCAGCAAAACCAACTGCAGTTGGCTGGAAGGATTCGTCCACAGCCAGGAAATCTTCAC  >  CP009273/3649701‑3649985

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 12 ≤ ATCG/ATCG < 22 ≤ ATCG/ATCG < 32 ≤ 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.