Predicted mutation
evidence	seq id	position	mutation	annotation	gene	description
JC JC	NC_000913	3,992,705	IS5 (+) +4 bp	coding (1553‑1556/2547 nt)	cyaA →	adenylate cyclase

New junction evidence
		seq id	position	reads (cov)	reads (cov)	score	skew	freq	annotation	gene	product
*	?	NC_000913	2288919 =	NA (NA)	33 (0.740)	29/282	0.6	100%	noncoding (1195/1195 nt)	IS5	repeat region
	?	NC_000913	3992705 =	0 (0.000)					coding (1553/2547 nt)	cyaA	adenylate cyclase
*	?	NC_000913	= 2290113	NA (NA)	59 (1.330)	39/282	0.1	100%	noncoding (1/1195 nt)	IS5	repeat region
	?	NC_000913	= 3992708	0 (0.000)					coding (1556/2547 nt)	cyaA	adenylate cyclase

AAGAAAATCTCTTTTCTGGTCTGACGGCGCTTACTGCTGAATTCACTGTCGGCGAAGGTAAGTTGATGACTCATGATGAACCCTGTTCTATGGCTCCAGATGACAAACATGATCTCATATCAGGGACTTGTTCGCACCTTCCATAACGCTGTAGCCACCAGAACAGATATTGCGGAACGACAAAGAGAAACAGAACCAGATTGATGCATTGAGCTTTCATCCTATGAAATTAATTGCTGTTAAAAGCATTGGGTACAGAAAATACCCATAGCTCCATACCC  >  NC_000913/2289972‑2290252                                                                                                                                              |                                                                                                                                            aaGAAAATCTCTTTTCTGGTCTGACGGCGCTTACTGCTGAATTCACTGCCGGCGAAGGTAAGTTGATGACTCCTGATGAACCCTGTTCTATGGCTGCAGATGACAAACATGATCTCATATCAGGGACTTGTTCGCACCTTCCa                                                                                                                                            <  1:768537/143‑1 (MQ=2)   gAAAATCTCTTTTCTGGTCTGACGGCGCTTACTGCTGAATTCACTGTCGGCGAAGGTAAGTTGATGACTCATGATGAACCCTGTTCTATGGCTCCAGATGACAAACATGATCTCATATCAGGGACTTGTTCGCCCCTTCCATa                                                                                                                                          >  1:261836/1‑143 (MQ=17)      aaTCTCTTTTCTGGTCTGACGGCGCTTACTGCTGAATTCACTGTCGGCGAAGGTAAGTTGATGACTCATGATGAACCCTGTTCTATGGCTCCAGATGACAAACATGATCTCATATCAGCGACTTGTTCGCACCTTCCATAACg                                                                                                                                       >  2:301384/1‑143 (MQ=18)                 ttctcggACGGCGCGTACTGCTGCCTTTACTGTCGGACAAGGTAAGTTGATGACTCATGATGAACCCTGTTCTATGGCTCCCGATGCCCAACATGATCTCATATCCCGGACTTGTTCGCACCTTCCATAACGCTGTAGccacc                                                                                                                            <  2:554685/137‑1 (MQ=14)                   gTCTGACGGCGCGTACTGCTGAATTCACTGTCGGCGAAGGTAAGTTGATGACTCATGATGAACCCTGTTCTATGGCTCCAGATGACAAACATGATCTCATATCAGGGACTTGTTCGCACCTTCCATAACGCTGTAGCCATCAg                                                                                                                          <  2:534853/143‑1 (MQ=255)                    gctatcGGCGCATACGGCTGAAGTCACTGTCGGCGAGGTTAAGTCGATGACTAATGATGATCCCTGTTCTATGGCTCCAGAAGACAAACATGATCTCGTGTCAGGGAGTTGTTCGCACCTTCCATAACGCTGTAGCCACCAGa                                                                                                                         <  2:97025/138‑1 (MQ=14)                     cTGACGGCGCTTACTGCTGAATTCACTGTCGGCGAAGGTAAGTTGATGACTCATGATGAACCCTGTTCTATGGCTCCAGATGACAAACATGATCTCATATCAGGGACTTGTTCGCACCTTCCATAACGCTGTAGCCACCAGaa                                                                                                                        <  2:280935/143‑1 (MQ=255)                      tGACGGCGCTTACTGCTGAATTCACTGTCGGCGAAGGTAAGTTGATGACTCATGATGAACCCTGTTCTATGGCTCCAGATGACAAACATGATCTCATATCAGGGACTTGTTCGCACCTTCCATAACGCTGTAGCCACCAGAAc                                                                                                                       >  1:236624/1‑143 (MQ=255)                          ggCGCTTACTGCTGAATTCACTGTCGGCGAAGGTAAGTTGATGACTCATGATGAACCCTGTTCTATGGCTCCAGATGACAAACATGATCTCATATCAGGGACTTGTTCGCACCTTCCATAACGCTGTAGGCAGCAGaagggat                                                                                                                   >  1:845/1‑138 (MQ=255)                               ttcctgcttAATTCACTGTCGGCGAAGGTAAGTTGATGACTCATGATGAACCCTGTTCTATGGCTCCAGATGACAAACATGATCTCATATCAGGGACTTGTTCGCACCTTCCATAACGCTGTAGCCACCAGAACAGATATTGc                                                                                                              <  2:649283/140‑1 (MQ=255)                                tACTGCTGAATTCACTGTCGGCGAAGGTAAGTTGATGACTCATGATGAACCCTGTTCTATGGCTCCAGATGACAAACATGATCTCATATCAGGGACTTGTTCGCACCTTACATAACGCTGTAGCCACCAGAACAGATATTGCg                                                                                                             >  2:149032/1‑143 (MQ=255)                                  ctgctgAATTCACTGGCGGCGAAGGTAAGTTGATGACTCATGATGAACCCTGTTCTATGGCTCCAGATGACAAACATGATCTCATATCAGGGACTTGTTCGCACATTCCATAACGCTGTAGCCACCAGAACAGATATTGCGGa                                                                                                           <  2:48125/143‑1 (MQ=255)                                   tgctgAATTCACTGTCGGCGAAGGTAAGTTGATGACTCATGATGAACCCTGTTCTATGGCTCCAGATGACAAACATGATCTCATATCAGGGACTTGTTCGCACCTTCCCTAACGCTGTAGCCCCCACAACAGATCTTGCGGaa                                                                                                          >  1:269635/1‑143 (MQ=255)                                   tgctgAATTCACTGTCGGCGAAGGTAAGTTGATGACTCATGATGAACCCTGTTCTATGGCTCCAGATGACAAACATGATCTCATATCAGGGACTTGTTCGCACCTTCCATAACGCTGTAGCCACCAGAACAGCTATCGCGGaa                                                                                                          >  2:370537/1‑143 (MQ=255)                                     ctgAATTCACTGTCGGCGAAGGTAAGTTGATGACTCATGATGAACCCTGTTCTATGGCTCCAGATGACAAACATGATCTCATATCAGGGACTTGTTCGCACCTTCCATAACGCTGGAGCCACAAGAACAGATATTGCGGAACg                                                                                                        >  2:72374/1‑143 (MQ=255)                                       gAATTCACTGTCGGCGAAGGTAAGTTGATGACTCATGATGAACCCTGTTCTATGGCTCCAGATGACAAACATGATCTCATATCAGGGACTTGTTCGCACCTTCCATGCCTCGTTATCCACCAGAACAGATATTGCGGAACGAc                                                                                                      >  1:333069/1‑143 (MQ=14)                                             aCTGTCGGCGAAGGTAAGTTGATGACTCATGATGAACCCTGTTCTATGGCTCCAGATGACAAACATGATCTCATATCAGGGACTTGTTCGCACCTTCCATAACGCTGTAGCCACCAGAACAGATACTGCGGCACGACAAagcg                                                                                                >  2:544846/1‑141 (MQ=255)                                             aCTGTCGGCGAAGGTAAGTTGATGACTAATGATGAACCCTGTTCTATGGCTCCAGATGACAAAAATGATCTCATATCAGAGACTTGTTTGCAACTTCCATAACGCTGTAGCCACCAGAACAGATATTGCGGAGCGACcaacaa                                                                                                >  2:777456/1‑140 (MQ=18)                                              cTGTCGGCGAAGGTAAGTTGATGACTCATGATGAACCCTGTTCTATGGCTCCAGATGACAAACATGATCTCCTATCAGGGACTTGTTCGCACCTTCCATAACGCTGTAGCCACCAGAACAGATATTGCGGAACGACACAgaga                                                                                               >  2:331580/1‑143 (MQ=255)                                              cTGTCGGAGAAAGTAAGTTGATGACTCATGATGAACCCTGTTCTATGGCTCCAGATGACAAACATGATCTCATATCAGGGACTTGTTCGCACCTTCCATAACGCTGTAGCCACCAGAACAGATATTGCGGAACGACAAAgaga                                                                                               <  1:537059/143‑1 (MQ=255)                                                 tCGGCGAAGGTAAGTTGATGACTCATGATGAACCCTGTTCTATGGCTCCAGATGACAAACATGATCTCATATCAGGGACTTGTTCGCACCTTCCATAACGCTGTAGCCACCAGAACAGATATTGCGGAACGACAAAGAGAAAc                                                                                            >  1:457834/1‑143 (MQ=255)                                                 tCGGCGAAGGTAACTTGATGACTCATGATGATCCCTGTTCTATGGCTCCAGATGACAAACATGATCTCATATCAGGGACTTGTTCGCACCTTCCATAACGCTGTAGCCACCAGAACAGATATTGCGGAACGACAAAGAGAAAc                                                                                            <  2:186026/143‑1 (MQ=255)                                                      gAAGGTAAGTTGATGACTCATGATGAACCCTGTTCTATGGCTCCAGATGACAAACATGATCTCATATCAGGGACTTGTTCGCACCTTCCATAACGCTGTAGCCACCAGAACAGATATTGCGGAACGACAAAGAGAAACAGaaa                                                                                       <  1:216677/143‑2 (MQ=255)                                                             aGTTGATGACTCATGATGAACCCTGTTCTATGGCTCCAGATGACAAACATGATCTCATATCAGGGACTTGTTCGCACCTTCCATAACGCTGTAGCCACCAGAACAGATATTGCGGAACGACAAAGAGAAACAGAACCAGATTg                                                                                >  1:452690/1‑143 (MQ=255)                                                                tgatgcCTCATGATGAACCCTGTTCTATGGCTCCAGATGACAAACATGATCTCATATCAGGGACTTGTTCGCACCTTCCATAACGCTGTAGCCACCAGAACAGATATTGCGGAACGACAAAGAGAAACAGAACCAGATTGATg                                                                             <  2:303648/143‑1 (MQ=255)                                                                    gccTCATGATGAACCCTGTTCTATGGCTCCAGATGACAAACATCATCTCATATCAGGGACTTGTTCGCACCTTCCATAACGCTGTAGCCACCAGAACAGATATTGCGGAACGACAAAGAGAAACAGAACCAGATTGATGCAtt                                                                         <  2:588151/141‑1 (MQ=255)                                                                    gaCTCATGATGAACCCTGTTCTATGGCTCCAGATGACAAACATGATCTCATATCAGGGACTTGTTCGCACCTTCCATAACGCTGTAGCCACCAGAACAGAAATTGCGGAACGACAAAGAGAAAACGAACCAGATAGATGCaat                                                                         >  2:243085/1‑141 (MQ=255)                                                                       tCATGATGAACCCTGTTCTATGGCTCCAGATGACAAACATGATCTCATATCAGGGACTTGTTCGCACCTTCCATAACGCTGTAGCCACCAGAACAGATATTGCGGAACGACAAAGAGAAACAGAACCAGATTGATGCATTGAg                                                                      >  2:151234/1‑143 (MQ=255)                                                                       tCATGATGAACCCTGTTCTATGGCTCCAGATGACAAACATGATCTCATATCAGGGACTTGTTCGCACCTTCCATAACGCTGTAGCCACCAGAACAGATATTGCGGAACGACAAAGAGAAACAGAACCAGATTGATGCATTGAg                                                                      >  2:452736/1‑143 (MQ=255)                                                                       tCATGATGAACCCTGTTCTATGGCTCAAGAAGACAGACATGATCTCATATCAGGGACTTGTTCGCACCCACCATCATTGCGGAGCCTGCAGAATAGGGATTGCGGAACGACAAAGAGAAACGGAACCAGATTGATGCATTGAg                                                                      >  2:435643/1‑143 (MQ=18)                                                                         atgatgAACCCTGTTCTATGGCTCCAGATGACAAACATGATCTCATATCAGGGACTTGTTCGCACCTTCCATAACGCTGTAGCCACCAGAACAGATATTGCGGAACGACAAAGAGAAACAGAACCAGATTGATGCATTGAGCt                                                                    >  1:530376/1‑143 (MQ=255)                                                                         atgatgAACCCTGTTCTATGGCTCCAGATGAAAAACATTATCTCATATCAGGGACTTGTTCGCACCTTCCATAACGCTGTAGCCACCAGAACGGATGTTACGGAACGACTACGAGAAACATAATCGGATTGATGCATGGAggt                                                                    >  1:67037/1‑141 (MQ=21)                                                                          tgatgaACCCTGTTCTATGGCTCCAGATGACAAACATGATCTCATATCAGGGACTTGTTCGCACCTTCCAGAACGCTGTAGCCACCAGAACAGATATTGCGGAACGACAAAGAGAAACAGAACCAGATTGATGCATTGAGCtt                                                                   <  1:233705/143‑1 (MQ=255)                                                                             tgaACCCTGTTCTATGGCTCCAGATGACAAACATGATCTCATATCAGGGACTTGTTCGCACCTTCCATAACGCTGTAGCCACCAGAACAGATATTGCGGAACGACAAAGAGAAACAGAACCAGATTGATGCATTGAGCTTTCa                                                                >  1:107975/1‑143 (MQ=255)                                                                                  ccTGTTCTATGGCTCCAGATGACAAACATGATCTCATATCAGGGACTTGTTCGCACCTTCCATAACGCTGTAGCCACCAGAACAGATATTGCGGAACGACAAAGAGAAACAGAACCAGATTGGTGCATTGAGCTTTCATGCTa                                                           >  1:604058/1‑143 (MQ=255)                                                                                  ccTGTTCTATGGCTCCAGATGACAAACATGATCTCATATCAGGGACTTGTTCGCACCTTCCATAACGCTGTAGCCACCAGAACAGATATTGCGGAACGACAAAGAGAAACAGAACCAGATTGATGCATTGAGCTTTCATCCTa                                                           >  1:535825/1‑143 (MQ=255)                                                                                   cTGTTCTAGGGCTCCAGATGCCAAACATGCTCTCATATCAGGGACTTGTTCGCACCTTCCATAACGCTGTAGCCACCAGAACAGATATTGCGGAACGACAAAGAGAAACAGAACCAGATTGATGCATTGAGCTTTCATCCTAt                                                          <  2:826/143‑1 (MQ=255)                                                                                    tGTTCTATGGCTCCAGATGACAAACATGATCTCATATCAGGGACTTGTTCGCACCTTCCATAACGCTGTAGCCACCAGAACAGATATTGCGGAACGACAAAGAGAAACAGAACCAGATTGATGCATTGAGCTTTCATCCTATg                                                         >  1:693117/1‑143 (MQ=255)                                                                                       tCTATGGCTCCAGATGACAAACGTGATCTCATATCAGGGACTTGTTCGCACCTTCCATAACGCTGTAGCCACCAGAACAGATATTGCGGAACGACAAAGAGAAACAGAACCAGATTGATGCATTGAGCTTTCATCGTATGaaa                                                      >  1:196197/1‑143 (MQ=255)                                                                                              cTCCAGACGACAAACATGAGCTCATATCAGGGACTTGTTCACACCTTCCATAACGCTGTAGCCACCATAACAGATATTGCGGAACGACAAAGATAAACAGAACCAGATTGATGCATTGAGCTTTCATCCTATGAAATTAATTg                                               <  2:345485/143‑1 (MQ=255)                                                                                                gccgATGACCAACATGATGTCATAGCAGGGACGTGTTCGCACCGGCCGTAGAGCTGTAGCCACCAGAACAGATAATGCGGAACGACAAAGAGAAACAGAACCAGATTGATGCATTGAGCTTTCATCCTATGAAATTAATTGCt                                             <  2:40228/140‑1 (MQ=255)                                                                                                              tGATTTCATATCACGGTCTTGTTCGGATTTTTCATAACGTTGTAGCCATCAGAACAGATATTGCGGAACGACAAAGAGAAACAGAACCAGATTGATGCATTGAGCTTTCATCCTATGAAATTAATTGCTGTTAAAAGCATTgg                               <  1:10219/143‑1 (MQ=255)                                                                                                              tGATCTCATATCAGGGACTTGTTCGCACCTTCCATAACGCTGTAGCCACCAGAACAGATATTGCGGAACGACAAAGAGAAACAGAACCAGATTGATGCATTGAGCTTTCATCCTATGAAATTAATTGCTGTTAAAAGCATTgg                               >  2:553135/1‑143 (MQ=255)                                                                                                               gATCCCATATCAGGGACTTGTTCGCACCGTACATACCGCTGTAGCCACCAGAACAGATATTGCGGAACGACAAAGATAAACCGAACCAGTTTGATGCATTGAGCTTTCATCCTATGAAATTAATTGCTGTTAAAAGCATTggg                              <  1:116327/143‑1 (MQ=255)                                                                                                                 tctcATATCAGGGACTTGTTCGCACCTTCCATAACGCTGTAGCCACCAGAACAGATATTGCGGAACGACAAAGCGAAACAGAACCAGAATGATGCATTGAGCGTGAAGCCTATGAAATTAATTGCTGAGAAAAGCATAGGGTa                            >  1:310327/1‑143 (MQ=255)                                                                                                                 nctcATATCAGGGACTTGTTCGCACCTTCCATAACGCTGTAGCCACCAGCACAGATATTGCGGAACGCCACAGCGAAACAGAACCAGATTGCTGCATTNAGCTTTCATCCTATGCCATTAATTGCTGTTATAACCAtgtgata                            >  2:309290/2‑137 (MQ=255)                                                                                                                   tcATATCAGGGACTTGTACGCACCTTCCATAACGCTATAGCGACCAGAACAGATATTGCGGAACGACAAAGAGAAACAGAACCAGATTGATGCATTGAGCTTTCATCCAATGAAATTAATTGCTGTTAAAAGCATTGGATACa                          >  2:486026/1‑143 (MQ=255)                                                                                                                       atCAGGGACTTGTTCGCACCTTCCATAACGCTGTAGCCACCAGAACAGATATTGCGGAACGACAAAGAGAAACAGAACCAGATTGATGCATTGAGCTTTCATCCTATGAAATTAATTGCTGTTAAAAGCATTGGGTACAGaaa                      >  1:311011/1‑143 (MQ=255)                                                                                                                       atCAGGGACTTGTTCGCACCTCCCATAACGCTGTAGCCACCAGAACAGATATTGCGGAACGACAAAGAGAAACAGAACCAGATTGATGCATTGAGCTTTCATCCTATGAAATTAATTGCTGTTAAAAGCATTGGGTACAGaaa                      >  2:674567/1‑143 (MQ=255)                                                                                                                        tCAGGGACTTGTTCGCACCTTCCATAACGCTGTAGCCACCAGAACAGATATTGCGGAACGACAAAGAGAAACAGAACCAGATTGATGCATTGAGCTTTCATCCTATGAAATTAATTGCTGTTAAAAGCATTGGGTGCAGaaaa                     >  2:332401/1‑143 (MQ=255)                                                                                                                        tCAGGGACTTGTTCGCACCTTCCATAACGCTGTAGCCACCAGAACAGATATTGCGGAACGACAAAGAGAAACAGAACCAGATTGATGCATTGAGCTTTCATCCTATGAAATTAATTGCTGTTAAAAGCATTGGGTACAGaaaa                     <  1:149032/143‑1 (MQ=255)                                                                                                                              aCTTGTTCGCACCTTCCATAACGCTGTAGCCACCAGAACAGATATTGCGGAACGACAAAGAGAAACAGAACCAGATTGATGCATTGAGCTTTCATCCTATGAAATTAATTGCTGTTAAAAGCATTGGGTACAGAAAATACCCa               <  1:326423/143‑1 (MQ=255)                                                                                                                                ttGTTCGCACCTTCCATAACGCTGTAGCCACCAGAACAGATATTGCGGAACGACAAAGAGAAACAGCACCAGATTGATGCATTGAGCTTTCATCCTATGAAATTAATTGCTGTTAAAAGCATTGGGTACAGAAAATACCCATa             >  1:220003/1‑143 (MQ=255)                                                                                                                                   ttCGCACCTTCCATAACGCTGTAGCCACCAGAACAGATATTGCGGAACGACAAAGAGAAACAGAACCAGATTGATGCATTGAGCTTTCATCCTATGAAATTAATTGCTGTTAAAAGCATTGGGTACAGAAAATAACCATAGCt          >  1:419476/1‑143 (MQ=255)                                                                                                                                   ttCGCACCTTCCATAACGCTGTAGCCACCAGAACAGATATTGCGGAACGACAAAGAGAAACAGAACCAGATTGATGCATTGAGCTTTCATCCTATGAAATTAATTGCTGTCAAAAGCATTGGGTACAGAAAATACCCATAGCt          >  2:683254/1‑143 (MQ=255)                                                                                                                                          cTTCCATAACGCTGTAGCCACCAGAACAGATATTGCGGAACGACAAAGAGAAACAGAACCAGATTGATGAATTGAGCTTTCATCCTATGAAATTAATTGCTGTTAAAAGCATTGGGTACAGAAAATACCCATAGCTCCATAcc   >  2:255637/1‑143 (MQ=255)                                                                                                                                           ttCCATAACGCTGTAGCCACCAGAACAGCTATTGCGGAACGACAAAGCGAAACAGAACCAGATTGATGCATTGAGCTTTCATCCTATGAAATTAATTGCTGTTAAAAGCATTTGGTACCGAAAATACCCCTAGCTCCATAccc  >  2:771950/1‑143 (MQ=255)                                                                                                                                              |                                                                                                                                            AAGAAAATCTCTTTTCTGGTCTGACGGCGCTTACTGCTGAATTCACTGTCGGCGAAGGTAAGTTGATGACTCATGATGAACCCTGTTCTATGGCTCCAGATGACAAACATGATCTCATATCAGGGACTTGTTCGCACCTTCCATAACGCTGTAGCCACCAGAACAGATATTGCGGAACGACAAAGAGAAACAGAACCAGATTGATGCATTGAGCTTTCATCCTATGAAATTAATTGCTGTTAAAAGCATTGGGTACAGAAAATACCCATAGCTCCATACCC  >  NC_000913/2289972‑2290252

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.