New junction evidence
		seq id	position	reads (cov)	reads (cov)	score	skew	freq	annotation	gene	product
*	?	NC_000913_3_pae_pgi	3583428 =	NA (NA)	25 (0.470)	25/270	NT	43.1%	intergenic (+10/‑55)	yrhA/insA	pseudogene, interrupted by IS1E/IS1 repressor TnpA
	?	NC_000913_3_pae_pgi	3665150 =	33 (0.620)					coding (661/825 nt)	gadX	acid resistance regulon transcriptional activator; autoactivator

CTCTCGATTCCAGAACCTTCAGTTAAAAACCTT‑TTTGCCGTAAATGAATTTTATAGAAATAATGATGATTTCATAAACCCTGATCTACAAGAACGGTTAGTGATCGGGGATTATAGCATTTCAATATTTACTTATGACATTAAAGGTGATGCTGCCAACTTACTGATTTAGTGTATGATGGTGTTTTTGAGGTGCTCCAGTGGCTTCTGTTTCTATCAGCTGTCCCTCCTGTTCAGCTACTGACGGGGTGGTGCGTAACGGCAAAAGCACCGCCGGACATCAGCGCTA  >  NC_000913_3_pae_pgi/3583284‑3583571                                                                                                                                                  |                                                                                                                                                ctctCGATTCCAGAACCTTCAGTTAAAAACCTT‑TTTGCCGTAAATGAATTTTATAGAAATAATGATGATTTCATAAACCCTGATCTACAAGAACGGTTAGTGATCGGGGATTATAGCATTTCAATATTTACTTATGACATTAAAGGTGa                                                                                                                                             >  1:170193/1‑149 (MQ=255)  tctcGATTTCAGAATCTTTAGTTAAAAACCTT‑TTTGCCGTAAATGAATTTTATAGAAATAATGATGATTTCATAAACCCTGATCTACAAGAACGGTTAGTGATCGGGGATTATAGCATTTCAATATTTACTTATGACATTAAAGGTGAt                                                                                                                                            <  1:350137/149‑1 (MQ=255)  tctcGATTCCAGAACCTTCAGTTAAAAACCTT‑TTTGCCGTAAATGAATTTTATAGAAATAATGATGAATTCATAACCTCTGATCTACAAGAACGGTTAGTGATCGGGGATTATAGCATTTCAATATTTAATTATGACATTAAATGTGAt                                                                                                                                            >  1:739510/1‑149 (MQ=255)   cgcGATTCTAGAACCTTCAGTTAAATACGTT‑TTTGTCGGAAATGAAGTTTATAGAGATAATGATGATTTCATAAAGCCTGATGTACAAGTACGGTCAGTGTTGGGGGATGATAGCATTTCAATATTTACTTATGTCATTAAAGGTGAtg                                                                                                                                           <  2:358846/147‑1 (MQ=255)          ctaGAACATCCAGTTAAAAACCTT‑TTTGCCGTAAATAAATTTTATAGAAATAATGATGATTTCATAAACCCTGATCTACAAGAACGGTTAGTGATCGGGGATTATAGCATTTCAATATTTACTTATGACATTAAAGGTGATGCTGCCaa                                                                                                                                    <  2:327885/147‑1 (MQ=255)          ccAGAACCTGAAGTTAAAAGCCTTGTGTGCCGTAAATGAATTTTATAGAAATAATGATGATTTCATAAACCCTGATCTACAAGAACGGTTAGTGATCGGGTATTATAGCATTTCAATATTTACTTATGACATTAAAGGTGATGCTGCCa                                                                                                                                     <  2:165130/149‑1 (MQ=255)                        tAAAAACCTT‑TTTGCAGTAAATGAATTTTATAGAAATAATGATGATTTCATAAACCCTGATCTACAAGAACGGTTAGTGATCGGGGATTATAGCATTTCAATATTTACTCGTGGCGTGAGAGGTGATGCTGCCAACTTACTGATTTAgt                                                                                                                      <  1:744908/149‑1 (MQ=255)                            aaCCTT‑TTTGCCGTAAATGAATTTTATAGAAATAATGATGATTTCATAAACCCTGATCTACAAGAACGGTTAGTGATCGGGGATTATAGCATTTCAATATTTACTTATGACATTAAAGGTGATGCTGCCAACTTACTGATTTAGTGTag                                                                                                                  >  1:562560/1‑148 (MQ=255)                                tt‑tttGCCGTAAATGAATTTTATAGAAATAATGATGATTTCATAAACCCTGATCTACAAGAACGGTTAGTGATCGGGGATTATAGCATTTCAATATTTACTTATGACATTAAAGGTGATGCTTCCAACTTACTGATTTAGTGTatgatg                                                                                                              >  2:200600/1‑149 (MQ=255)                                   ttggctatAAATGAGTGTTAGAAAAATAATGATGATTTAATAAACCCTTATCTACAAGAACGGTTAGTGATCGGGGATTATAGCATTTCAATATTTACTTATGACATTAAAGGTGATGCTGCCAACTTACAGATTTAGTGTATGATGgt                                                                                                            <  2:751807/142‑1 (MQ=38)                                        cGTAAATGAATTTTATAGAAATAATGATGATTTCATAAACCCTGATCTACAAGAACGGTTAGTGATCGGGGATTATAGCATTTCAATATTTACTTATGACATTAAAAGTGATGCTGCCAACTTACTGATTTACTAGATGATGGTGtttt                                                                                                       >  1:305526/1‑149 (MQ=255)                                           aaaTGAATTTTATAGAAATAATGATGATTTCATAAACCCTGATCTACAAGAACGGTTAGTGATCGGGGATTATAGCATTTCAATATTTACTTATGACATTAAAGGTGATGCTGCCAACTTACTGATTTAGTGTATGATGGTGTTTTTGa                                                                                                    <  2:27184/149‑1 (MQ=255)                                            aaagAATTTTAAAGAAATAATGATGATTTCATAAACCCTGATCTACAAGAACGGTTAGTGATCGGGGATTATAGCATTTCAATATTTACTTATGACATTAAAGGTGATGCTGCCAACTTACTGATTTAGTGTATGATGGTGTTTTTGAg                                                                                                   <  2:327074/146‑1 (MQ=255)                                            aaTGAATTTTATAGAAATAATGATGATTTCATAAACCCTGATCTACAAGAACGGTTAGTGATCGGGGATTATAGCATTTCAATATTTACTTATGACATTAAAGGTGATGCTGCCAACTTACTGATTTAGTGTATGATGGTGTTTTTGAg                                                                                                   <  1:454651/149‑1 (MQ=255)                                                  ttttATAGAAATAATGATGATTTCATAAACCCTGATCTACAAGAACGGTTAGTGATCGGGGATTATAGCATTTCAATATTTACTTATGACATTAAAGGTGATGCTGCCAACTTACTGATTTAGTGTATGATGGTGTTTTTGAGGTGCTc                                                                                             >  1:409351/1‑149 (MQ=255)                                                      ataGAAATAATGATGATTTCATAAACCCTGATCTACAAGAACGGTTAGTGATCGGGGATTATAGCATTTCAATATTTACTTATGACATTAAAGGTGATGCTGCCAACTTACTGATTTAGTGTATGATGGTGTTTTTGAGGTGCTCCAGt                                                                                         <  1:229728/149‑1 (MQ=255)                                                          aaaTAATGATGATTTCATAAACCCTGATCTACAAGAACGGTTAGTGATCGGGGATTATAGCATTTCAATATTTACTTATGACATTAAAGGTGATGCTGCCAACTTACTGATTTAGTGTATGATGGTGTTTTTGAGGTGCTCCAGTGGCt                                                                                     >  1:1001967/1‑149 (MQ=255)                                                                tgatgaTTTCATAAACTCTGATCTACAAGAACGGGTAGTGATCGGGGATTATAGCATTTCAATGTTTACTTATTACATTAAAGGTGATGCTGCCAACTTACTGCTTTAGTGTATGATGGTGTTTTTGAGGTGCTCCATTGGCTTCTGtt                                                                               >  2:239865/1‑149 (MQ=37)                                                                tgatgaTTTCATAAACCCTGATCTACAAGAACGGTTAGTGATCGGGGATTATAGCATTTCAATATTTACTTATGACATTAAAGGTGATGCTGCCAACTTACTGATTTGGTGTATGATGATGTTTTTTAGTTTCTCCAGTGGCTTCTGtt                                                                               >  2:81439/1‑149 (MQ=37)                                                                          aTAAACCCTGATCTACAAGAACGGTTAGTGATCGGGGATTATAGCATTTCAATATTTACTTATGACATTAAAGGTGATGCTGCCAACTTACTGCTTTAGTGTATGATGGTGTTTTTGAGGTGCTCCAGTGGCTTCTGTTTCTATCAGCt                                                                     >  1:343299/1‑149 (MQ=255)                                                                          aTAAACCCTGATCTACAAGAACGGTTAGTGATCGGGGATTATAGCATTTCAATATTTACTTATGACATTAAAGGTGATGCTGCCAACTTACTGATTTAGTGTATGATGGTGTTTTTGAGGTGCTCCAGTGGCTTCTGttt                                                                              >  2:436248/1‑140 (MQ=255)                                                                          aTAAACCCTGATCTACAAGAACGGTTAGTGATCGGGGATTATAGCATTTCAATATTTACTTATGACATTAAAGGTGATGCTGCCAACTTACTGATTTAGTGTATGATGGTGTTTTTGAGGTGCTCCAGTGGCTTCTGttt                                                                              <  1:436248/140‑1 (MQ=255)                                                                          aTAAACCCTGATCTACAAGAACGGTTAGTGATCGGGGATTATAGCATTTCAATATTTACTTATGACATTAAAGGTGATGCTGCCAACTTACTGATTTAGTGTATGATGGTGTTTTTGAGGTGCTCCAGTGGCTTCTGTTTCTATCAGCt                                                                     >  2:576046/1‑149 (MQ=255)                                                                          aTAAACCCTGATCTACAAGAACGGTTAGTGATCGGGGATTATAGCATTTCAATATTTACTTATGACATTAAAGGTGATGCTGCCAACTTACTGATTTAGTGTATGATGGTGTTTTTGAGGTGCTCCAGTGGCTTCTGTTTCTATCAGCt                                                                     <  2:170193/149‑1 (MQ=255)                                                                                   gagcTACAAGAACGGTTAGTGATCGGGGATTATAGCATTTCAATATTTACTTATGACATTAAAGGTGATGCTGCCAACTTACTGATTTAGTGTATGATGGTGTTTTTGAGGTGCTCCAGTGGCTTCGGTTTCTATCAGCTGTCcctcct                                                            <  2:191167/146‑1 (MQ=255)                                                                                          aaGAACAGCTAGTGATCGGGGATTATAGCATTTCAATATTTACTTATGACATTAAAGGTGATGCTGCCAACTTACTGATTTAGTGTATGATGGTGTTTTTGAGGTGCTCCAGTGGCTTCTGTTTCTATCAGCTGTCCCTCCTGTTCAGc                                                     <  1:433027/149‑1 (MQ=255)                                                                                             gaCGGGTAGTGATCGGGGATTATAGCATTTCAATATTTACTTATGACATTAAAGGTGATGCTGCCAACTTACTGATTTAGTGTATGATGGTGTTTTTGAGGTGCTCCAGTGGCTTCTGTTCCTATCAGCTGTCCCTCCTGTTCCGCTAc                                                  <  2:830345/148‑1 (MQ=255)                                                                                             aaCGGTTAGTGATCGGGGATTATAGCATTTCAATATTTACTTATGACATTAAAGGTGATGCTGCCAACTTACTGATTTAGTGTATGATGGTGTTTTTGAGGTGCTCCAGTGGCTTCTGTTTCTATCAGCTGTCCCTCCTGTTCAGCTAc                                                  <  2:977725/149‑1 (MQ=255)                                                                                                 gTTAGTGATCTGGGATTATAGAATTTCAATAATTACTTATTGCATTAAAGGTGATGCTGCCAACTTACTGATTTAGTGTATGATGGTGTTTTTGAGGTGCTCCAGTGGCTTCTGTTTCTATCAGCTGTCCCTCCTGTTCCGCGACTGAc                                              <  2:125005/149‑1 (MQ=17)                                                                                                       gATCGGGGATTATAGCATTTCAATATTTACTTATGACATTAAAGGTGATGCTGCCAACTTACTGATTTAGTGTATGATGGTGTTTTTGAGGTGCTCCAGTGGCTTCTGTTTCTATCAGCTGTCCCTCCTGTTCAGCTACTTACggagag                                        >  1:359995/1‑145 (MQ=255)                                                                                                       gATAGGGGATTATAGCTTTTCAATATTTACTTATGACATTAAAGGTGATGCTGCCAACTTACTGATTTAGTGTATGATGGTGTTTTTGAGGTGCTCCAGTGGCTTCTGTTTCTATCAGCTGTCCCTCCTGTTCAGCTACTGACGGggtg                                        <  1:542667/149‑1 (MQ=255)                                                                                                         tCGGGGATTATAGCATTTCAATATTTACTTATGACATTAAAGGTGATGCTGCCAACTTACTGATTTAGTGTATGATGGTGTTTTTGAGGTGCTCCAGTGGCTTCTGTTTCTATCAGCTGTCCCTCCTGTTCAGCTACTGACGGggtggt                                      <  1:965077/149‑1 (MQ=255)                                                                                                                   taGCATTTCAATATTTACTTATGACATTAAAGGTGATGCTGCCAACTTACTGATTTAGTGTAAGATGGTGTTTTTGAGGTGCTCCAGTGGATCGCCACAACATCAGCTGTCCCTCCTGTTCAGCTACTGACGGGGTGGTGCGTAACGGc                            >  1:281374/1‑149 (MQ=17)                                                                                                                      cATTTCAATATTTACTTATGACATTAAAGGTGATGCTGCCAACTTACTGATTTAGTGTATGATGGTGTTTTTGAGGTGCTCCAGTGGCTTCTGTTTCTATCAGCTGTCCCTCCTGTTCAGCTACTGACGGGGTGGTGCGTAACGGCaaa                         <  1:535497/149‑1 (MQ=255)                                                                                                                       aTTTCAATATTTACTTATGACATTAAAGGTGATGCTGCCAACTTACTGATTTAGTGTATGATGGTGTTTTTGAGGTGCTCCAGTGGCTTCTGTTTCTATCAGCTGTCCCTCCTGTTCAGCTACTGACGGGGTGGTGCGTAACGGCaaaa                        <  1:956967/149‑1 (MQ=255)                                                                                                                        tttCAATATTTACTTATGACATTAAAGGTGATGCTGCCAACTTACTGATTTAGTGTATGATGGTGTTTTTGAGGTGCTCCAGTGGCTTCTGTTTCTATCAGCTGTCCCTCCTGTTCAGCTACTGACGGGGTGGTGCGTAACGGCAAAAg                       <  1:727563/149‑1 (MQ=255)                                                                                                                             atttttACTTATGACATTAAAGGTGATGCTGCCAACTTACTGATTTAGTGTATGATGGTGTTTTTGAGGTGCTCCAGTGGCTTCTGTTTCTATCAGCTGTCCCTCCTGTTCAGCTACTGACGGGGTGGTGCGTAACGGCAAAAGCAccg                  <  1:783777/146‑1 (MQ=255)                                                                                                                                tttACTTATGACATTAAAGGTGATGCTGCCAACTTACTGATTTAGTGTATGATGGTGTTTTTGAGGTGCTCCAGTGGCTTCTGTTTCTATCAGCTGTCCCTCCTGTTCAGCTACTGACGGGGTGGTGCGTAACGGCAAAAGCAccgcag               >  2:827123/1‑147 (MQ=255)                                                                                                                                 ttACTTATGACATTAAAGGTGATGCTGCCAACTTACTGATTTAGTGTATGATGGTGTTTTTGAGGTGCTCCAGTGGCTTCTGTTTCTATCAGCTGTCCCTCCTGTTCAGCTACTGACGGGGTGGTGCGTAACGGCAAAAGCACCGCCgg              >  2:704662/1‑149 (MQ=255)                                                                                                                                         gACATTAAAGGTGATGCTGCCAACTTACTGATTTAGTGTATGATGGTGTTTTTGAGGTGCTCCAGTGGCTTCTGTTTCTATCAGCTGTCCCTCCTGTTCAGCTACTGACGGGGTGGTGCGTACCGGCAAAAGCCCCGCCGGACATCCgc      >  2:243902/1‑149 (MQ=255)                                                                                                                                          aCATTAAAGGTGATGCTGCCAACTTACTGATTTAGTGTATGAGGGTGTTGTTGAGGTGCTCCAGTGGCTTCTGTTTCTATCAGCTGTCCCTCCTGTTCAGCTACTGAGGGGGTGCTACGTCACGGCAAAAGCACCGCCGGACATCAgcg     >  1:636512/1‑149 (MQ=11)                                                                                                                                             ttAAAGGTGATGCTGCCAACTTACTGATTTAGTGTATGATGGTGTTTTTGAGGTGCTCCAGTGGCTTCTGTTTCTATCAGCTGTCCCTCCTGTTCAGCTCCTGACGGGGTGGTGCGTAACGCCAAAAGCCCCCCCGGACATCCGAGCtc  >  2:539319/1‑148 (MQ=11)                                                                                                                                             ttAAAGGTGATGCTGCCAACTTACTGATTTAGTGTATGATGGTGTTTTTGAGGTGCTCCAGTGGCTTCTGTTTCTATCAGCTGTCCCTCCTGTTCAGCTACTGACGGGGTGGTGCGTAACGGCAAAAGCACCGCCGGACATCAGCGCTa  >  2:33067/1‑149 (MQ=32)                                                                                                                                                  |                                                                                                                                                CTCTCGATTCCAGAACCTTCAGTTAAAAACCTT‑TTTGCCGTAAATGAATTTTATAGAAATAATGATGATTTCATAAACCCTGATCTACAAGAACGGTTAGTGATCGGGGATTATAGCATTTCAATATTTACTTATGACATTAAAGGTGATGCTGCCAACTTACTGATTTAGTGTATGATGGTGTTTTTGAGGTGCTCCAGTGGCTTCTGTTTCTATCAGCTGTCCCTCCTGTTCAGCTACTGACGGGGTGGTGCGTAACGGCAAAAGCACCGCCGGACATCAGCGCTA  >  NC_000913_3_pae_pgi/3583284‑3583571

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.