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

GATAGATTAGTTGTACATTACCACGATTTTGACTCGGCTCATTATTTGCCCGCTTGAGACATTGTTTCCATATGTACGCGGGCGAATAAATAGAGGAATCTGATTACTTCCTTCATGGGGATGCTGAAAAGAGTAGTAATTGCTGGTAATGACTCCAACTTATTGATAGTGTTTTATGTTCAGATAATGCCCGATGACTTTGTCATGCAGCTCCACCGATTTTGAGAACGACAGCGACTTCCGTCCCAGCCGTGCCAGGTGCTGCCTCAGATTCAGGTTATGCCGCTCAATT  >  CP009273/19652‑19943                                                                                                                                                 |                                                                                                                                                    gatcgatTAGTTGGACATTACCACGATTTTGGCTTCGCTCATTATTGGCCCGCTTGAGACAGTGTTTCCATATGGACGCGGGCGAATAAATAGAGGAATCTGTTTACTTCCTTCATGGGGATGCTGAAAAGAGTAGTAATTGCTGGTaa                                                                                                                                                 <  1:50821/149‑1 (MQ=255) gatagatTAGTTGTACATTACCACGATTTTGACTCGGCTCATTATTTGCCCGCTTGAGACATTGTTTCCATATGTACGCGGGCGAATAAATAGAGGAATCTGATTACTTCCTTCATGGGGATGCTGAAAAGAGTAGTAATTGCTGGTaa                                                                                                                                                 <  2:428950/149‑1 (MQ=255)    agatTAGTTGTACATTACCACGATTTTGACTCGGCTCATTATTTGCCCGCTTGAGACATTGTTTCCATATGTACGCGGGCGAATAAATAGAGGAATCTGATTACTTCCTTCATGGGGATGCTGAAAAGAGTAGTAATTGCTGGTAATGa                                                                                                                                              >  1:94148/1‑149 (MQ=255)       ttAGTTGTACATTACCACGATTTTGACTCGGCTCATTATTTGCCCGCTTGAGACATTGTTTCCATATGTACGCGGGCGAATAAATAGAGGAATCTGATTACTTCCTTCATGGGGATGCTGAAAAGAGTAGTAATTGCTGGTAATGACTc                                                                                                                                           <  2:81218/149‑1 (MQ=255)       ttAGTTGTACATTACCACGATTTTGACTCGGCTCATTATTTGCCCGCTTGAGACATTGTTTCCATATGTACGCGGGCGAATAAATAGAGGAATCTGATTACTTCCTTCATGGGGATGCTGAAAAGAGTAGTAATTGCTGGTAATGACTc                                                                                                                                           <  1:238861/149‑1 (MQ=255)           ttGTACATTACCAGGATTTTGACTCGGCTCATTATTTGCCCGCTTGAGACGTTGTTTTCATATGTAGGGGGGCGAATAAATAGAGGAATCTGATTACTTCCTTCATGGGGATGGTGAAAGGGGTTGTAATTGCTGGTGATgctgcctat                                                                                                                                       >  1:178456/1‑141 (MQ=255)              tACATTACCACGATTTTGACTCGGCTCATTATTTGCCCGCTTGAGACATTGTTTCCATCTGTACGCGGGCGAATAAATAGAGGAATCTGATTACTTCCTTCCTGGGGATGCTGAAAAGAACAGTAATTGCTGGAAATGAATCCAACTTa                                                                                                                                    >  1:667296/1‑149 (MQ=255)                cATTCCCTCGATTGTGACCCGGCTCATTATTTGCCCGCTTGAGACATTGTTTCCATATGTACGCGGGCGAATAAATAGAGGAATCTGATTACTTCCTTCATGTGGATGCTGAAAAGAGTAGTAATTGCTCGTAATGACGCCAACTTAtt                                                                                                                                  <  1:797517/149‑1 (MQ=255)                   tACCACGATTTTGACTCGGCTCATTATTTGCCCGCTTGAGACATTGTTTCCATATGTACGCGGGCGAATAAATAGAGGAATCTGATTACTTCCTTCATGGGGATGCTGAAAAGAGTAGTAATTGCTGGTAATGACTCCAACTTATTGAt                                                                                                                               <  1:475799/149‑1 (MQ=255)                      cACGATTTTGACTCGGCTCATTATTTGCCCGCTTGAGACATTGTTTCCATATGTACGCGGGCGAATAAATAGAGGAATCTGATTACTTCCTTCATGGGGATGCTGAAAAGAGTAGTAATTGCTGGTAATGACTCCAACTTATTGATAgt                                                                                                                            >  2:253208/1‑149 (MQ=255)                       aCGATTTTGACTCGGCTCATTATTTGCCCGCTTGAGACATTGTTTCCATATGTACGCGGGCGAATAAATAGAGGAATCTGATTACTTCCTTCATGGGGATGCTGAAAAGAGTAGTAATTGCTGGTAATGACTCCAACTTATTGATAgtg                                                                                                                           >  1:556745/1‑149 (MQ=255)                             ttGACTCGGCTCATTATTTGCCCGTTTAAGACATTGTTTCCATATGTACGCGGGCGAATAAATAGAGGAATCTGATTACTTCCTTCATGGGGATGCTGAAAAGAGTAGTAATTGCTGGTAATGACTCCAACTTATTGATAGTGTTTTAt                                                                                                                     <  1:866236/149‑1 (MQ=255)                              tGACTCGGCGTATTATTTGCCCGCTTCGGACATTGTTTCCATATGTACGCGGGCGAATAAATAGAGGAATCTGATTACTTCCTTCATGGGGATGCTGAAAAGAGTAGTAATTGCTGGTAATGACTCCAACTTATTGATAGTGTTTTATg                                                                                                                    <  1:392242/149‑1 (MQ=255)                                           tattTGCCCGCTTGAGACATTGTTTCCATATGTACCCCGGCGAATAAATAGAGGAATCTGATTACTTCCTTCATGGGGATGCTGAAAGGAGTAGTAATTGCTGGTAATGACTCCAACTTATTGATAGTGTTTTATGTTCAGATAATGcc                                                                                                       >  1:726028/1‑149 (MQ=255)                                             tttGCCCGCTTGAGACATTGTTTCCATATGTACGCGGGCGAATAAATAGAGGAATCTGATTACTTCCTTCATGGGGATGCTGAAAAGAGTAGTAATTGCTGGTAATGACTCCAACTTATTGATAGTGTTTTATGTTCAGATAATGCCCg                                                                                                     >  2:864080/1‑149 (MQ=255)                                              ttGCCCGCTTGAGACATTGTTTCCATATGGACGCGGGCGAATAAATAGAGGAATCTGATTACTTCCTTCATGGGGATGCTGAAAAGAGTAGTAATTGCTGGTAATGACTCCAACTTATTGATAATGTTTTATGTTCAGATAATGCCCGa                                                                                                    >  2:528218/1‑149 (MQ=255)                                                      tttagaCATTGGTTCCATATGTACGCGGGCGAATAAATAGAGGTATCTGATTAATTCCTTCATGGGGATGCTGAAAATAGTAGTCATTTCTGGTAATGACTCCAACTTATTGATAGTGTTTTATGTTCAGATAATGCCCGATGACTTTg                                                                                            <  1:351186/146‑1 (MQ=37)                                                      ttGAGACATTGTTTCAATATGTACGCGGGCGAATAAATAGCGGTGCCTCGTCACGCCATTAATCGTGTTGCTGAAAAGAGTAGTAATTGCTGGTAATGACTCCAACTTATTGATAGTGTTTTATGTTCAGATAATGCCCGATGACTTTg                                                                                            >  2:421557/1‑149 (MQ=21)                                                       tGAGACATTGTTTCCATATGTACGCGGGCGAATAAATAGAGGAATCTGATTACTTCCTTCATGGGGATGCTGAAAAGAGTAGTAATTGCTGGTAATGACTCCAACTTATTGATAGTGTTTTATGTTCAGATAATGCCCGATGACTTTGt                                                                                           <  1:700846/149‑1 (MQ=255)                                                           aCATTGTTTCCATATGTACGCGGGCGAATAAATAGAGGAATCTGATTACTTCCTTCATGGGGATGCTGAAAAGAGTAGTAATTGCTGGTAATGACTCCAACTTATTGATAGTGTTTTATGTTCAGATAATGCCCGATGACTTTGTCATg                                                                                       >  1:671248/1‑149 (MQ=255)                                                                gTTTCCATATGTACGCGGGCGAATAAATAGAGGAATCTGATTACTTCCTTCATGGGGATGCTGAAAAGAGTAGTAATTGCTGGTAATGACTCCAACTTATTGATAGTGTTTTATGTTCAGATAATGCCCGATGAcaaagtcatcgggca                                                                                  <  2:573609/149‑15 (MQ=255)                                                                gTTTCCATATGTACGCGGGCGAATAAATAGAGGAATCTGATTACTTCCTTCATGGGGATGCTGAAAAGAGTAGTAATTGCTGGTAATGACTCCAACTTATTGATAGTGTTTTATGTTCAGATAATGCCCGATGAcaaagtcatcgggca                                                                                  <  2:152342/149‑15 (MQ=255)                                                                    ccATATGTACGCGGGCGAATAAATAGAGGAATCTGATTACTTCCTTCATGGGGATGCTGAAAAGAGTAGTAATTGCTGGTAATGACTCCAACTTATTGATAGTGTTTTATGTTCAGATAATGCCCGATGACTTTGTCATGCAGCTCCAc                                                                              >  1:553623/1‑149 (MQ=255)                                                                          gTACGCGGGCGAATAAATAGAGGAATCTGATTACTTCCTTCATGGGGATGCTGAAAAGAGTAGTAATTGCTGGTAATGACTCCAACTTATTGATAGTGTTTTATGTTCAGATAATGCCCGATGACTTTGTCATGCAGCTCCACCGAttt                                                                        >  2:739981/1‑149 (MQ=255)                                                                              gcgGGCGAATAAATAGAGGAATCTGATTACTTCCTTCATGGGGATGCTGAAAAGAGTAGTAATTGCTGGTAATGACTCCAACTTATTGATAGTGTTTTATGTTCAGATAATGCCCGATGACTTTGTCATGCCGCTCCACCGATTTTgag                                                                    <  1:80291/149‑1 (MQ=255)                                                                                   cGAATAAATAGAGTAATCTGATTACTTCCTTCATGGGGATGCTGAAAAGAGTAGGAATTGCTGGTAATGACTCCAACTTATTGATAGTGTTTTATGTTCAGATAATGCCCGATGACGTTGTTATGCAGCTCCACCGATTTTGAGAACGa                                                               <  1:333285/149‑1 (MQ=255)                                                                                       taaataGAGGAATCTGATTACTTCCTTCATGGGGATGCTGAAAAGAGTAGTAATTGCTGGTAATGACTCCAACTTATTGATAGTGTTTTATGTTCAGATAATGCCCGATGCCTTTGTCATGCAGCTCCCCCGATTTTGGGAACGACCGc                                                           >  2:688865/1‑149 (MQ=255)                                                                                       taaataGAGGAATCTGATTACTTCCTTCATGGGGATGCTGAAAAGAGTAGTAATTGCTGGTAATGACTCCAACTTATTGATAGTGTTTTATGTTCAGATAATGCCCGATGACTTTGTCCTGCAGCCCCGCCGATTTTGGGAACGACAGc                                                           >  1:826343/1‑149 (MQ=255)                                                                                              agGAATCTGCTTACTTCCTTCATGGGGATGCTGAAAAGAGTAGTAATTGCTGGTAATGACTCCAACTTATTGATAGTGTTTTATGTTCAGATACTGCCCGATGACTTTGTCATGCAGCTCCACCGATTTTGAGTACGACAGCGACTTcc                                                    <  1:239533/149‑1 (MQ=255)                                                                                              agGAATCTGATTACTTCCTTCATGGGGATGCTGAAAAGAGTAGTAATTGCTGGTAATGACTCCAACTTATTGATAGTGTTTTATGTTCAGATAATGCCCGATGACTTTGTCATGCAGCTCCACCGATTTTGCGAACGACAGCGACTTcc                                                    >  1:628470/1‑149 (MQ=255)                                                                                                gAATCTGATTACTTCCTTCATGGGGATGCTGAAAAGAGTAGTAATTGCTGGTAATGACTCCCACTTATTGATAGTGGTTTCTGTTCAGATAATGCCCGATGACTTTGTCCTGCAGCTCCACCGATCTTGAGCACGACAGCGCCCTCCGt                                                  >  2:823441/1‑149 (MQ=21)                                                                                                gAATCTGATTACTTCCTTCATGGGGATGCTGAAAAGAGTAGTAATTGCTGGTAATGACTCCAACTTATTGATAGTGTTTTATGTTCAGATAATGCCCGATGACTTTGTCATGCAGCTCCACCGATTTTGAGAACGACAGCGACTTCCGt                                                  <  2:743261/149‑1 (MQ=255)                                                                                                  aTCTGATTACTTCCTTCATGGGGATGCTGAAAAGAGTAGTAATTGCTGGTAATGACTCCAACTTATTGATAGTGTTTTATGTTCAGATAATGCCCGATGACTTTGTCATGCAGCTCCACCGATTTTGAGAACGACAGCGACTTCCGTcc                                                <  1:512541/149‑1 (MQ=255)                                                                                                        ttACTTCCTTCATGGGGATGCTGAAAAGAGTAGTAATTGCTGGTAATGACTCCAACTTATTGATAGTGTTTTATGTTCAGATAATGCCCGATGACTTTGTCATGCAGCTCCACCGATTTTGAGAACGACGGCGACTTCCGTCCCAGCCg                                          >  2:228119/1‑149 (MQ=255)                                                                                                        ttACTTCCTTCATGGGGATGCTGAAAAGAGTAGTAATTGCTGGTAATGACTCCAACTTATTGATAGTGTTTTATGTTCAGATAATGCCCGATGACTTTGTCATGCAGCTCCACCGATTTTGAGAACGACAGCGACTTCCGTCCCAGCCg                                          >  1:804862/1‑149 (MQ=255)                                                                                                        ttACTTCCTTCATGGGGATGCTGAAAAGAGTAGTAATTGCTGGTAATGACTCCAACTTATTGATAGTGTTTTATGTTCAGATAATGCACGATGACAGTGTCATGCAGCTCGCACGCTGTTGAGCACGACAGCGCATTCCGTCACAGCCg                                          >  1:808951/1‑149 (MQ=18)                                                                                                              ccttgATGGGGATGCTGAAAAGATTAGTAAGTGCTGGTAATGACTCCAACTTATTGATAGTGTTTTATGTTCAGATAATGCCCGATGACTTTGTCATGCAGCTCCACCGATTTTGAGAACGACAGCGACTTCCGTCCCAGCCGTGCCAg                                    <  2:667296/149‑1 (MQ=255)                                                                                                              ccttcATGGGGATGCTGAAAAGAGTAGTAATTGCTGGTAATGACTCCAACTTATTGATAGTGTTTTATGTTCAGATAATGCCCGATGACTTTGTCATGCAGCTTCACCGATTTTGAGGACGACAGCGACTTCCGTCCCAGCCGTGCCAg                                    >  2:290045/1‑149 (MQ=255)                                                                                                               cttcATGGGGATGCTGAAAAGAGTAGTAATTGCTGGTAATGACTCCAACTTATTGATCGTGTTTTATGGTCAGATAATGCCCGATGACTTTGTCATGCAGCTCCACCGATTTTGAGAACGACAGCGCCTTCCGTCCCAGCCGTGCCCgg                                   >  1:698817/1‑149 (MQ=255)                                                                                                                    gggggATGCTGAAAAGAGTAGTAATTGCTGGTAATGACTCCAACTTATTGATAGTGTTTTATGTTCAGATAATGCCCGATGACTTTGTCATGCATCTCCACCGATTTTGAGAACGACAGCGACTTCCGTCCCAGCCGTGCCAGGtgctg                              <  1:652805/148‑1 (MQ=255)                                                                                                                                aaaGAGTAGTAATTGCTGGTAATGCCTCCAACTTATTGATAGTGTTTTATGTTCAGATAATGCCCGATGACTTTGTCATGCAGCTCCACCGATTTTGAGAACGACAGCGACTTCCGTCCCAGCCGTGCCAGGTGCTGCCTCAGATTCAg                  <  1:459382/149‑1 (MQ=255)                                                                                                                                aaaGAGTAGTAATTGCTGGTAATGACTCCAACTTATTGATAGTGTTTTATGTTCAGATAATGCCCGATGACTTTGTCATGCAGCTCCACCGATTTTGAGAACGACAGCGACTTCCGTCCCAGCTGTGCCAGGTGCTGCCTCAGATTCAg                  <  2:434699/149‑1 (MQ=255)                                                                                                                                  agagTAGTAATTGCTGGTAATGACTCCAACTTATTGATAGTGTTTTATGTTCAGATAATGCCCGATGACTTTGTCATGCAGCTCCACCGATTTTGAGAACGACAGCGACTTCCGTCCCAGCCGTGCCAGGTGCTGCCTCAGATTCAGGt                <  2:94148/149‑1 (MQ=255)                                                                                                                                   gaggagTAATTGCTGGTAATGACTCCAACTTATTGATAGTGTTTTATGTTCAGATAATGCCCGATGACTTTGTCATGCAGCTCCACCGATTTTGAGAACGACAGCGACTTCCGTCCCAGCCGTGCCAGGTGCTGCCTCAGATTCAGGtt               <  1:204947/149‑1 (MQ=38)                                                                                                                                     gtaggaATTGCTGGTAATGACTCCAACTTATTGATAGTGTTTTATGTTCAGATAATGCCCGATGACTTTGTCATGCAGCTCCACCGATTTTGAGAACGACAGCGACTTCCGTCCCAGCCGTGCCAGGTGCTGCCTCAGATTCAGGTTAt             <  2:788565/149‑1 (MQ=37)                                                                                                                                                tGGTAATGACTCCAACTTATTGATAGTGTTTTATGTTCAGATAATGCCCGATGACTTTGTCATGCAGCTCCACCGATTTTGAGAACGACAGCGACTTCCGTCCCAGCCGTGCCAGGTGCTGCCACAGATTCAGGTTATGCCGCTCaagt  >  1:249343/1‑147 (MQ=11)                                                                                                                                                 |                                                                                                                                                    GATAGATTAGTTGTACATTACCACGATTTTGACTCGGCTCATTATTTGCCCGCTTGAGACATTGTTTCCATATGTACGCGGGCGAATAAATAGAGGAATCTGATTACTTCCTTCATGGGGATGCTGAAAAGAGTAGTAATTGCTGGTAATGACTCCAACTTATTGATAGTGTTTTATGTTCAGATAATGCCCGATGACTTTGTCATGCAGCTCCACCGATTTTGAGAACGACAGCGACTTCCGTCCCAGCCGTGCCAGGTGCTGCCTCAGATTCAGGTTATGCCGCTCAATT  >  CP009273/19652‑19943

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.