New junction evidence
		seq id	position	reads (cov)	reads (cov)	score	skew	freq	annotation	gene	product
*	?	CP000730	99262 =	41 (1.110)	2 (0.060)	4/230	NT	5.4%	intergenic (+56/+16)	tfoX/USA300HOU_0099	hypothetical protein/possible MFS family major facilitator transporter
	?	CP000730	99291 =	34 (1.030)					coding (1208/1221 nt)	USA300HOU_0099	possible MFS family major facilitator transporter

ATGATATTAATTCTAGACTTTACCGAAGCAACAAATCTCACTGATTTATTTAAGACCATAAAAAATGATTTGAAAAAGTGAAGTAGTGAAGTGTGGGTGCAGAGAGAACTAAGCCCATCGATAAATGGTCGCTTGTTAAAGAAGAGTGACGGTCACTCTTCTTTATGTGCATATTTTATTTTGCCTGTTTTGTTAACAAGCAGCAGTGTAACAAATATGAGTAAGGATAAAATGAGTATAATATAGAAACCGAATTTATCATTAATTTCATTAATCC  >  CP000730/99126‑99402                                                                                                                                         |                                                                                                                                             taattgctccatttttaggaagatggattaatgaaattaatgataaattcggtttctatattatactcattttatccttactcatatttgttacactgctgcttgttaacaaaacaggcaaaataaaatatgcacaTAaag                                                                                                                                          <  1:409325‑M1/5‑1 (MQ=255)      gctccatttttaggaagatggattaatgaaattaatgataaattcggtttctatattatactcattttatccttactcatatttgttacactgctgcttgttaacaaaacaggcaaaataaaatatgcacaTAAAGAagag                                                                                                                                     <  1:203879‑M1/10‑1 (MQ=255)       ctccatttttaggaagatggattaatgaaattaatgataaattcggtttctatattatactcattttatccttactcatatttgttacactgctgcttgttaacaaaacaggcaaaataaaatatgcacaTAAAGAAGAGt                                                                                                                                    >  2:134382‑M1/131‑141 (MQ=255)             ttttaggaagatggattaatgaaattaatgataaattcggtttctatattatactcattttatccttactcatatttgttacactgctgcttgttaacaaaacaggcaaaataaaatatgcacaTAAAGAAGAGTGACGGt                                                                                                                              >  1:40621‑M1/125‑141 (MQ=255)             ttttaggaagatggattaatgaaattaatgataaattcggtttctatattatactcattttatccttactcatatttgttacactgctgcttgttaacaaaacaggcaaaataaaatatgcacaTAAAGAAGAGTGACGGt                                                                                                                              >  1:116468‑M1/125‑141 (MQ=255)             ttttaggaagatggattaatgaaattaatgataaattcagtttctatattataatcattttatccttaataatatttgttatactgctgcttgttaacaaaacaggcaaaacaaaatatgcacaGAAAGAAGAGTGACGGt                                                                                                                              >  2:384665‑M1/125‑141 (MQ=255)               aGACTTTACCGAAGCAACAAATCTCACTGATTTATTTAAGACCATAAAAAATGATTTGAAAAAGTGAAGTAGTGAAGTGTGGGTGCAGAGAGAACTAAGCCCATCGATAAATGGTCGCTTGTTAAAGAAGAGTGACGGTCa                                                                                                                            >  1:198645/1‑141 (MQ=255)                 gcTTGACCGAAGCAACAAATCTCACTGATTTATTTAAGACCATAAAGAATGATTTGAAAAAGTGAAGTAGTGAAGTGTGGGTGCAGAGAGAACTAAGCCCATCGATAAATGGTCGCTTGTTAAAGAAGAGTGACGGTCAct                                                                                                                          <  2:91955/140‑1 (MQ=255)                 aCTTTACCGAAGCAACAAATCTCACTGATTTATTTAAGACCATAAAAAATGATTTGAAAAAGTGAAGTAGTGAAGTGTGGGTGCAGAGAGAACTAAGCCCATCGATAAATGGTCGCTTGTTAAAGAAGAGTGACGGTCAct                                                                                                                          <  2:113310/141‑1 (MQ=255)                 aCTTTACCGAAGCAACAAATCTCACTGATTTATTTAAGACCATAAAAAATGATTTGAAAAAGTGAAGTAGTGAAGTGTGGGTGCAGAGAGAACTAAGCCCATCGATAAATGGTCGCTTGTTAAAGAAGAGTGACGGTCAct                                                                                                                          <  2:66411/141‑1 (MQ=255)                     tACCGAAGCAACAAATCTCACTGATTTATTTAAGACCATAAAAAATGATTTGAAAAAGTGAAGTAGTGAAGTGTGGGTGCAGAGAGAACTAAGCCCATCGATAAATGGTCGCTTGTTAAAGAAGAGTGACGGTCACtcttc                                                                                                                      <  2:35946/141‑1 (MQ=255)                     tACCGAAGCAACAAATCTCACTGATTTATTTAAGACCATAAAAAATGATTTGAAAAAGTGAAGTAGTGAAGTGTGGGTGCAGAGAGAACTAAGCCCATCGATAAATGGTCGCTTGTTAAAGAAGAGTGACCGTCACtcttc                                                                                                                      <  1:192376/141‑1 (MQ=255)                       ccGAAGCAACAAATCTCACTGATTTATTTAAGACCATAAAAAATGATTTGAAAAAGTGAAGTAGTGAAGTGTGGGTGCAGAGAGAACTAAGCCCATCGATAAATGGTCGCTTGTTAAAGAAGAGTGACGGTCACTcttctt                                                                                                                    >  1:34898/1‑141 (MQ=255)                                   aTCTCACTGATTTATTTAAGACCATAAAAAATGATTTGAAAAAGTGAAGTAGTGAAGTGTGGGTGCAGAGAGAACTAAGCCCATCGATAAATGGTCGCTTGTTAAAGAAGAGTGACGGTCACTCTTCTTTATGTGCAtatt                                                                                                        >  2:444703/1‑141 (MQ=255)                                      tcACTGATTTATTTAAGACCATAAAAAATGATTTGAAAAAGTGAAGTAGTGAAGTGTGGGTGCAGAGAGAACTAAGCCCATCGATAAATGGTCGCTTGTTAAAGAAGAGTGACGGTCACTCTTCTTTATGTGCAtatttta                                                                                                     >  2:4753/1‑141 (MQ=255)                                       cACTGATTTATTTAAGACCATAAAAAATGATTTGAAAAAGTGAAGTAGTGAAGTGTGGGTGCAGAGAGAACTAAGCCCATCGATAAATGGTCGCTTGTTAAAGAAGAGTGACGGTCACTCTTCTTTATGTGCAtattttat                                                                                                    >  2:211648/1‑141 (MQ=255)                                         cTGATTTATTTAAGACCATAAAAAATGATTTGAAAAAGTGAAGTAGTGAAGTGTGGGTGCAGAGAGAACTAAGCCCATCGATAAATGGTCGCTTGTTAAAGAAGAGTGACGGTCACTCTTCTTTATGTGCAtattttattt                                                                                                  <  1:105824/141‑1 (MQ=255)                                         cTGATTTATTTAAGACCATAAAAAATGATTTGAAAAAGTGAAGTAGTGAAGTGTGGGTGCAGAGAGAACTAAGCCCATCGATAAATGGTCGCTTGTTAAAGAAGAGTGACGGTCACTCTTCTTTATGTGCAtattttattt                                                                                                  >  1:62157/1‑141 (MQ=255)                                           gATTTATTTAAGACCATAAAAAATGATTTGAAAAAGTGAAGTAGTGAAGTGTGGGTGCAGAGAGAACTAAGCCCATCGATAAATGGTCGCTTGTTAAAGAAGAGTGACGGTCACTCTTCTTTATGTGCATATTTTATTTTg                                                                                                <  1:448872/141‑1 (MQ=255)                                            atttatttAAGACCATAAAAAATGATTTGAAAAAGTGAAGTAGTGAAGTGTGGGTGCAGAGAGAACTAAGCCCATCGATAAATGGTCGCTTGTTAAAGAAGAGTGACGGTCACTCTTCTTTATGTGCATATTTTATTTTGc                                                                                               >  2:391915/1‑141 (MQ=255)                                              ttatttaAGACCATAAAAAATGATTTGAAACAGTGAAGTAGTGAAGTGTGGGTGCAGAGAGAACTAAGCCCATCGATAAATGGTCGCTTGTTAAAGAAGAGTGACGGTCACTCTTCTTTATGTGCATATTTTATTTTGCCt                                                                                             <  2:184742/141‑1 (MQ=255)                                              ttatttaAGACCATAAAAAATGATTTGAAAAAGTGGAGTAGTGAAGTGTGGGTGCAGAGAGAACTAAGCCCATCGATAAATGGTCGCTTGTTAAAGAAGAGTGACGGTCACTCTTCTTTATGTGCATATTTTATTTTGCCt                                                                                             <  2:315506/141‑1 (MQ=255)                                                agttaAGACCATAAAAAATGATTTGAAAAAGTGAAGTAGTGAAGTGTGGGTGCAGAGAGAACTAAGCCCATCGATAAATGGTCGCTTGTTAAAGAAGAGTGACGGTCACTCTTCTTTATGTGCATATTTTATTTTGCCTGt                                                                                           <  2:303281/139‑1 (MQ=255)                                                 tttaAGACCGGAAAAACTGATTTGCGCAAGCGAAGAAGTGACGGGTGGGGGCAGTGAGAACTAAGCCGATCGATAAATGGTCGCTTGTTAAAGAAGAGTGACGGTCACTCTTCTTTATGTGCATATTTTATTTGGCCTGtt                                                                                          >  2:281183/1‑141 (MQ=255)                                                     aGACCATAAAAAATGATTTGAAAAAGTGAAGTAGTGAAGTGTGGGTGCAGAGAGAACTAAGCCCATCGATAAATGGTCGCTTGTTAAAGAAGAGTGACGGTCACTCTTCTTTATGTGCATATTTTATTTTGCCTGTTTTGt                                                                                      >  1:257877/1‑141 (MQ=255)                                                     aGACCATAAAAAATGATTTGAAAAAGTGAAGTAGTGAAGTGTGGGTGCAGAGAGAACTAAGCCCATCGATAAATGGTCGCTTGTTAAAGAAGAGTGACGGTCACTCTTCTTTATGTGCATATTTTATTTTGCCTGTTTTGt                                                                                      >  1:69660/1‑141 (MQ=255)                                                         cATAAAAAATGATTTGAAAAAGTGAAGTAGTGAAGTGTGGGTGCAGAGAGAACTAAGCCCATCGATAAATGGTCGCTTGTTAAAGAAGAGTGACGGTCACTCTTCTTTATGTGCATATTTTATTTTGCCTGTTTTGTTAAc                                                                                  >  1:106656/1‑141 (MQ=255)                                                              aaaaTGATTTGAAAAAGTGAAGTAGTGAAGTGTGGGTGCAGAGAGAACTAAGCCCATCGATAAATGGTCGCTTGTTAAAGAAGAGTGACGGTCACTCTTCTTTATGTGCATATTTTATTTTGCCTGTTTTGTTAACAagca                                                                             <  1:211648/141‑1 (MQ=255)                                                                aaTGATTTGAAAAAGTGAAGTAGTGAAGTGTGGGTGCAGAGAGAACTAAGCCCATCGATAAATGGTCGCTTGTTAAAGAAGAGTGACGGTCACTCTTCTTTATGTGCATATTTTATTTTGCCTGTTTTGTTAACAagcagc                                                                           >  1:294863/1‑141 (MQ=255)                                                                   gATTTGAAAAAGTGAAGTAGTGAAGTGTGGGTGCAGAGAGAACTAAGCCCATCGATAAATGGTCGCTTGTTAAAGAAGAGTGACGGTCACTCTTCTTTATGTGCATATTTTATTTTGCCTGTTTTGTTAACAAGCAGCAgt                                                                        >  1:168671/1‑141 (MQ=255)                                                                     tttGAAAAAGTGAAGTAGTGAAGTGTGGGTGCAGAGAGAACTAAGCCCATCGATAAATGGTCGCTTGTTAAAGAAGAGTGACGGTCACTCTTCTTTATGTGCATATTTTATTTTGCCTGTTTTGTTAACAAGCAGCAgtgt                                                                      <  2:153838/141‑1 (MQ=255)                                                                     tttGAAAAAGTGAAGTAGTGAAGTGCGGGTGCAGAGAGAAATACGCCCAAACATCAAACCTAAACAGTTAACGAAGTGTGTCGGTCACTCTTCTTTATGTGCATATTTTATTTTGCCTGTTTTGTTAACAAGCAGCAgtgt                                                                      <  1:42342/141‑1 (MQ=255)                                                                        gAAAAAGTGAAGTAGTGAAGTGTGGGTGCAGAGAGAACTAAGCCCATCGATAACTGGTCGCTTGTTAAAGAAGATTGACGTTCACTCTTCTTTATGTGCATATTTTATTTTGCCTGTTTTGTTAACAAGCAGCAGTGTAAc                                                                   <  1:432999/141‑1 (MQ=255)                                                                              gtgaagtagtgaagtGTGGGTGCAGAGAGAACTAAGCCCATCGATAAATGGTCGCTTGTTAAAGAAGAGTGACGGTCACTCTTCTTTATGTGCATATTTTATTTTGCCTGTTTTGTTAACAAGCAGCAGTGTAACAAatat                                                             >  1:327829/1‑141 (MQ=255)                                                                              gtgaagtagtgaagtGTGGGTGCAGAGAGAACTAAGCCCATCGATAAATGGTCGCTTGTTAAAGAAGAGTGACGGTCACTCTTCTTTATGTGCATATTTTATTTTGCCTGTTTTGTTAACAAGCAGCAGTGTAACAAatat                                                             >  1:405920/1‑141 (MQ=255)                                                                                   gtagtgaagtGTGGGTGCAGAGAGAACTAAGCCCATCGATAAATGGTCGCTTGTTAAAGAAGAGTGACGGTCACTCTTCTTTATGTGCATATTTTATTTTGCCTGTTTTGTTAACAAGCAGCAGTGTAACAAATATGAGTa                                                        >  2:203879/1‑141 (MQ=255)                                                                                       tttgttacactgctgcttgttaacaaaacaggcaaaataaaatatgcacaTAAAGAAGAGTGACCGTCACTCTTCTTTATGTGCATATTTTATTTTGCCTGTTTTGTTAACAAGCAGCAGTGTAACAAATATGAGTAAGGa                                                    <  1:220552‑M1/91‑1 (MQ=255)                                                                                        gaagtGTGGGTGCAGAGAGAACTAAGCCCATCGATAAATGGTCGCTTGTTAAAGAAAAGTGACGGTCAACCTTCTTTATGTGCATATTGTATTTTGCCTGTTTTGTTAACAAGCAGCAGTGTAACGAATATGAGTAAGGAt                                                   >  2:406094/1‑141 (MQ=255)                                                                                            tgtgGGTGCAGAGAGAACTAAGCCCATCGATAAATGGTCGCTTGTTAAAGAAGAGTGACGGTCACTCTTCTTTATGTGCATATTTTATTTTGCCTGTTTTGTTAACAAGCAGCAGTGTAACAAATATGAGTAAGGATaaaa                                               <  1:107392/141‑1 (MQ=255)                                                                                             acactgctgcttgttaacaaaacaggcaaaataaaatatgcacaTAAAGAAGAGTGACCGTCACTCTTCTTTATGTGCATATTTTATTTTGCCTGTTTTGTTAACAAGCAGCAGTGTAACAAATATGAGTAAGGATAAAAt                                              <  1:199985‑M1/97‑1 (MQ=255)                                                                                                ggTGCAGAGAGAACTAAGCCCATCGATAAATGGTCGCTTGTTAAAGAAGAGTGACGGTCACTCTTCTTTATGTGCATATTTTATTTTGCCTGTTTTGTTAACAAGCAGCAGTGTAACAAATATGAGTAAGGATAAAATGAg                                           >  1:265210/1‑141 (MQ=255)                                                                                                              tAAGCCCATCGATAAATGGTCGCTTGTTAAAGAAGAGTGACGGTCAGTCTTCTTTATGTGCATATTTTATTTTGCCTGTTTTGTTAACAAGCAGCAGTGTAACAAATATGAGTAAGGACAAAATGAGTATAATATAGAAAc                             >  1:378662/1‑141 (MQ=255)                                                                                                               aaGCCCATCGATAAATGGTCGCTTGTTAAAGAAGAGTGAAGGTCACACTACTTTATGTGCTTTTTAAATTTTGACTGTTTTGTTAACAAGCAGCAGTGTAACAAATATGAGTAAGGATAAAATGAGTATAATATAGAAAcc                            <  1:224128/141‑1 (MQ=255)                                                                                                                       cGATAAATGGTCGCTTGTTAAAGAAGAGTGACGGTCCCTCTGCTTTATGTGCATATTTTATTTTGCCTGTTTTGTTAACAAGCAGCAGTGTAACAAATATGAGTAAGGATAAAATGAGTATAATAAAGAAACCGAATTTAt                    >  2:381313/1‑141 (MQ=255)                                                                                                                        gATAAATGGTCGCTTGTTAAAGAAGAGTGACGGTCACTCTTCTTTATGTGCATATTTTATTTTGCCTGTTTTGTTAACAAGCAGCAGTGTAACAAATATGAGTAAGGATAAAATGAGTATAATATAGAAACCGAATTTATc                   <  2:156250/141‑1 (MQ=255)                                                                                                                         aTAAATGGTCGCTTGTTAAAGAAGAGTGACGGTCACTCTTCTTTATGTGCATATTTTATTTTGCCTGTTTTGTTAACAAGCAGCAGTGTAACAAATATGAGTAAGGATAAAATGAGTATAATATAGAAACCGAATTTATCa                  >  1:178121/1‑141 (MQ=255)                                                                                                                               ggTCGCTTGTTAAAGAAGAGTGACGGTCACTCATCTTTATGTGCATATTTTATTTTGCCTGTTTTGTTAACAAGCAGCAGTGTAACAAATATGAGTAAGGATAAAATGAGTATAATATAGAAACCGAATTTATCATTAAtt            <  1:407335/141‑1 (MQ=255)                                                                                                                                  cGCTTGTTAAAGAAGAGTGACGGTCACTCTTCTTTATGTGCATATTTTATTTTGCCTGTTTTGTTAACAAGCAGCAGTGTAACAAATATGAGTAAGGATAAAATGAGTATAATATAGAAACCGAATTTATCATTAATTTCa         <  1:444703/141‑1 (MQ=255)                                                                                                                                   gCTTGTTAAAGAAGAGTGACGGTCACTCTTCTTTATGTGCATATTTTATTTTGCCTGTTTTGTTAACAAGCAGCAGTGTAACAAATATGAGTAAGGATAAAATGAGTATAATATAGAAACCGAATTTATCATTAATTTCAt        <  1:329582/141‑1 (MQ=255)                                                                                                                                         TAAAGAAGAGTGACGGTCACTCTTCTTTATGTGCATATTTTATTTTGCCTGTTTTGTTAACAAGCAGCAGTGTAACAAATATGAGTAAGGATAAAATGAGTATAATATAGAAACCGAATTTATCATTAATTTCATTAATcc  <  2:239411‑M1/141‑1 (MQ=255)                                                                                                                                         |                                                                                                                                             ATGATATTAATTCTAGACTTTACCGAAGCAACAAATCTCACTGATTTATTTAAGACCATAAAAAATGATTTGAAAAAGTGAAGTAGTGAAGTGTGGGTGCAGAGAGAACTAAGCCCATCGATAAATGGTCGCTTGTTAAAGAAGAGTGACGGTCACTCTTCTTTATGTGCATATTTTATTTTGCCTGTTTTGTTAACAAGCAGCAGTGTAACAAATATGAGTAAGGATAAAATGAGTATAATATAGAAACCGAATTTATCATTAATTTCATTAATCC  >  CP000730/99126‑99402

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 12 ≤ ATCG/ATCG < 22 ≤ ATCG/ATCG < 37 ≤ 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.