New junction evidence
		seq id	position	reads (cov)	reads (cov)	score	skew	freq	annotation	gene	product
*	?	CP000730	2388283 =	35 (1.140)	3 (0.110)	3/224	NT	10.1%	intergenic (+18/+84)	USA300HOU_2247/USA300HOU_2248	MFS family major facilitator transporter/hypothetical protein
	?	CP000730	2388362 =	23 (0.860)					intergenic (+97/+5)	USA300HOU_2247/USA300HOU_2248	MFS family major facilitator transporter/hypothetical protein

AATTCATGGACGTCATGTAACTAGAAATGCCATGAACTAAATATTTATATTCAAAAATAAAAAGCATGCCAATCTCTATTCATCATTTGTCTGTCCCCAAGACGCAATTATGATGTACTGATTGGCATGCTTTTTAAGTTTTTAGTTTGTAACGCTTAACACTTCTATTTCTTTAGTAATTTTATCTAACAATTTCTTTTGAGAAGTACTATAGAAATAGAATACTTGTCTTTCATCCGTTTCAGAACGCAATTTAGAAA  >  CP000730/2388226‑2388485                                                                                                                                         |                                                                                                                            aaTTCATGGACGTCATGTAACTAGAAATGCCATGAACTAAATATTTATATTCAAAAATAAAAAGCATGCCAATCTCTATTCATCATTTGTCTGTCCCCAAGACGCAATTATGATGTACTGATTGGCATGCTTTTTAAGtt                                                                                                                          >  1:226702/1‑140 (MQ=255)   tgttagataaaattactaaagaaatagaagtgttaagcgttacaaactaaaaacttaaaaagcatgccaatcagtacatcataattgcgtcttggggacagacaaatgatgaatagagattggcatgctttttaAGtttt                                                                                                                        >  1:180307‑M2/135‑140 (MQ=255)   tgttagataaaattactaaagaaatagaagtgttaagcgttacaaactaaaaactTAAAAAGCATGCCAATCTCTATTCATCATTTGTCTGTCCCCAAGACGCAATTATGATGTACTGATTGGCATGCTTTTTAAGtttt                                                                                                                        <  2:180307‑M1/85‑1 (MQ=255)           cGTCATGTAACTAGAAATGCCATGAACTAAATATTTATATTCAAAAATAAAAAGGATGCCAATCTCTATTCATCATTTGTCTGTCCCCAAGACGCAATTATGATGTACTGATTGGCATGCTTTTTAAGTTTTTAGTTTGt                                                                                                                >  1:237155/1‑140 (MQ=255)            gTCATGTAACTAGAAATGCCATGAACTAAATATTTATATTCAAAAATAAAAAGCATGCCAATCTCTATTCATCATTTGTCTGTCCCCAAGACGCAATTATGATGTACTGATTGGCATGCTTTTTAAGTTTTTAGTTTGTa                                                                                                               <  1:290591/140‑1 (MQ=255)            gTCATGTAACTAGAAATGCCATGAACTAAATATTTATATTCAAAAATAAAAAGCATGCCAATCTCTATTCATCATTTGTCTGTCCCCAAGACGCAATTATGATGTACTGATTGGCATGCTTTTTAAGTTTTTAGTTTGTa                                                                                                               <  1:141211/140‑1 (MQ=255)              cATGTAACTAGAAATGCCATGAACTAAATATTTATATTCAAAAATAAAAAGCATGCCAATCTCTATTCATCATTTGTCTGTCCCCAAGACGCAATTATGATGTACTGATTGGCATGCTTTTTAAGTTTTTAGTTTGTAAc                                                                                                             >  2:107382/1‑140 (MQ=255)               aTGTAACTAGAAATGCCATGAACTAAATATTTATATTCAAAAATAAAAAGCATGCCAATCTCTATTCATCATTTGTCTGTCCCCAAGACGCAATTATGATGTACTGATTGGCATGCTTTTTAAGTTTTTAGTTTGTAACg                                                                                                            >  1:325031/1‑140 (MQ=255)                tGTAACTAGAAATGCCATGAACTAAATATTTATATTCAAAAATAAAAAGCATGCCAATCTCTATTCATCATTTGTCTGTCCCCAAGACGCAATTATGATGTACTGATTGGCATGCTTTTTAAGTTTTTAGTTTGTAACGc                                                                                                           <  2:199485/140‑1 (MQ=255)                 gTAACTAGAAATGCCATGAACTAAATATTTATATTCAAAAATAAAAAGCATGCCAATCTCTATTCATCATTTGTCTGTCCCCAAGACGCAATTATGATGTACTGATTGGCATGCTTTTTAAGTTTTTAGTTTGTAACGCt                                                                                                          >  1:125990/1‑140 (MQ=255)                      tAGAAATGCGATGAACTAAATATTTATATTCAAAAATAAAAAGCATGCCAATCTCTATTCATCATTTGTCTGTCCCCAAGACGCAATTATGATGTACTGATTGGCATGCTTTTTAAGTTTTTAGTTTGTAACGCTTAaca                                                                                                     <  1:341261/140‑1 (MQ=255)                        gAAATGCCATGAACTAAATATTTATATTCAAAAATAAAAAGCATGCCAATCTCTATTCATCATTTGTCTGTCCCCCAGACGCGATTATGATGTACTGCTTGGCATGCTTTTTTAGTTTTTAGTTTGTAACGCTTAACACt                                                                                                   >  1:158473/1‑140 (MQ=255)                        gAAATGCCATGAACTAAATATTTATATTCAAAAATAAAAAGCATGCCAATCTCTATTCATCATTTGTATGTCCCCAAGACGCAATTATCATGTAGTATTTGGCATGCTTTTTAAGTTTTTAGTTTGTAACGCTTAACACt                                                                                                   >  2:37411/1‑140 (MQ=255)                                aTGAACTAAATATTTATATTCAAAAATAAAAAGCATGCCAATCTCTATTCATCATTTGTCTGTCCCCAAGACGCAATTATGATGTACTGATTGGCATGCTTTTTAAGTTTTTAGTTTGTAACGCTTAACACTTCTATTTc                                                                                           >  2:329005/1‑140 (MQ=255)                                aTGAACTAAATATTTATATTCAAAAATAAAAAGCATGCCAATCTCTATTCATCATTTGTCTGTCCCCAAGACGCAATTATGATGTACTGATTGGCATGCTTTTTAAGTTCTTCGTTTGTAACGCTTAACACTTCTATTTc                                                                                           >  2:43693/1‑140 (MQ=255)                                      tAAATATTTATATTCAAAAATAAAAAGCATGCCAATCTCTATTCATCATTTGTCTGTCCCCAAGACGCAATTATGATGTACTGATTGGCATGCTTTTTAAGTTTTTAGTTTGTAACGCTTAACACTTCTATTTCTTTAGt                                                                                     >  1:22620/1‑140 (MQ=255)                                       aaaTATTTATATTCAAAAATAAAAAGCATGCCAATCTCTATTCATCATTTGTCTGTCCCCAAGACGCAATTATGATGTACTGATTGGCATGCTTTTTAAGTTTTTAGTTTGTAACGCTTAACACTTCTATTTCTTTAGTa                                                                                    >  1:319011/1‑140 (MQ=255)                                       aaaTATTTATATTCAAAAATAAAAAGCATGCCAATCTCTATTCATCATTTGTCTGTCCCCAAGACGCAATTATGATGTACTGATTGGCATGCTTTTTAAGTTTTTAGTTTGTAACGCTTAACACTTCTATTTCTTTAGTa                                                                                    >  1:302051/1‑140 (MQ=255)                                         atatTTATATTCAAAAATAAAAAGCATGCCAATCTCTATTCATCATTTGTCTGTCCCCAAGACGCAATTATGATGTACTGATTGGCATGCTTTTTAAGTTTTTAGTTTGTAACGCTTAACACTTCTATTTCTTTAGTAAt                                                                                  <  1:247900/140‑1 (MQ=255)                                           atTTATATTCAAAAATAAAAAGCATGCCAATCTCTATTCATCATTTGTCTGTCCCCAAGACGCAATTATGATGTACTGATTGGCATGCTTTTTAAGTTTTTAGTTTGTAACGCTTAACACTTCTATTTCTTTAGTAAttt                                                                                >  2:165819/1‑140 (MQ=255)                                                  ttCAAAAATAAAAAGCATTCCAATCTCTATTCATCATTTGTCTGTCCCCAAGACGCAATTATGATGTACTGATTGGCATGCTTTTTAAGTTTTTAGTTTGTAACGCTTAACACTTCTATTTCTTTAGTAATTTTATCTaa                                                                         <  2:272557/140‑1 (MQ=255)                                                    aaaacttaaaaagcatgccaatcagtacatcataattgcgtcttggggacagacaaatgatgaatagagattggcatgctttttaAGTTTTTAGTTTGTAACGCTTAACACTTCTATTTCTTTAGTAATTTTATCTAACa                                                                       <  2:180307‑M2/55‑1 (MQ=255)                                                    aaaactTAAAAAGCATGCCAATCTCTATTCATCATTTGTCTGTCCCCAAGACGCAATTATGATGTACTGATTGGCATGCTTTTTAAGTTTTTAGTTTGTAACGCTTAACACTTCTATTTCTTTAGTAATTTTATCTAACa                                                                       >  1:180307‑M1/7‑140 (MQ=255)                                                     aaaaaTAAAAAGCATGCCAATCTCTATTCATCATTTGTCTGTCCCCAAGACGCAATTATGATGTACTGATTGGCATGCTTTTTAAGTTTTTAGTTTGTAACGCTTAACACTTCTATTTCTTTAGTAATTTTATCTAACaa                                                                      <  1:299841/140‑1 (MQ=255)                                                      aaaaTAAAAAGCATGCCAATCTCTATTCATCATTTGTCTGTCCCCAAGACGCAATTATGATGTACTGATTGGCATGCTTTTTAAGTTTTTAGTTTGTAACGCTTAACACTTCTATTTCTTTAGTAATTTTATCTAACAAt                                                                     <  2:311151/140‑1 (MQ=255)                                                                GCATGCCAATCTCTATTCATCATTTGTCTGTCCCCAAGACGCAATTATGATGTACTGATTGGCATGCTTTTTAAGTTTTTAGTTTGTAACGCTTAACACTTCTATTTCTTTAGTAATTTTATCTAACAATTTCTTTTgag                                                           <  1:144313‑M1/140‑1 (MQ=255)                                                                     CCAATCTCTATTCATTATTTGTCTGTCCCCAAGACGCAATTATGATGTACTGATTGGCATGCTTTTTAAGTTTTTAGTTTGTAACGCTTAACACTTCTATTTCTTTAGTAATTTTATCTAACAATTTCTTTTGAGAAGTa                                                      >  1:37517‑M1/1‑140 (MQ=255)                                                                           agtacatcataattgcgtcttggggacagacaaatgatgaatagagattggcatgctttttaAGTTTTTAGTTTGTAACGCTTAACACTTCTATTTCTTTAGTAATTTTATCTAACAATTTCTTTTGAGAAGTACTatag                                                >  1:149714‑M2/63‑140 (MQ=255)                                                                               ttCATCATTTGTCTGTCCCCAAGACGCAATTATGATGTACTGATTGGCATGCTTTTTAAGTTTTTAGTTTGTAACGCTTAACACTTCTATTTCTTTAGTAATTTTATCTAACAATTTCTTTTGAGAAGTACTatagaaat                                            <  1:179353/140‑1 (MQ=255)                                                                                                           aTTATGATGTACTGATTTGCATGCTTTTTAAGTTTTTACTTTGTAACTCTTAACACTTCTATTTCTTTATTAATTTTATCTAACAATTTCTTTTGAGAAGTACTATAGAAATAGAATACTTGTCTTTCATCCGTTTCAGa                <  2:80567/140‑1 (MQ=255)                                                                                                              atgatgTACTGATTGGCATGCTTTTTAAGTTTTTAGTTTGTAACGCTTAACACTTCTATTTCTTTAGTAATTTTATCTAACAATTTCTTTTGAGAAGTACTATAGAAATAGAATACTTGTCTTTCATCCGTTTCAGAACg             <  1:6486/140‑1 (MQ=255)                                                                                                                   gTACTGATTGGCATGCTTTTTAAGTTTTTAGTTTGTAACGCTTAACACTTCTATTTCTTTAGTAATTTTATCTAACAATTTCTTTTGAGAAGTACTATAGAAATAGAATACTTGTCTTTCATCCGTTTCAGAACGCAAtt        <  2:144313/140‑1 (MQ=255)                                                                                                                    tACTGATTGGCATGCTTTTTAAGTTTTTATTTTGTAACGCTTAACACTTCTATTTCTTTAGTAATTTTATCTAACAATTTCTTTTGAGAAGTACTATAGAAATAGAATACTTGTCTTTCATCCGTTTCAGAACGCAAttt       <  2:226702/140‑1 (MQ=255)                                                                                                                      cTGATTGGCATGCTTTTTAAGTTTTTAGTTTGTAACGCTTAACACTTCTATTTCTTTAGTAATTTTATCTAACAATTTCTTTTGAGAAGTACTATAGAAATAGAATACTTGTCTTTCATCCGTTTCAGAACGCACTTTAg     >  2:243446/1‑140 (MQ=255)                                                                                                                        gattggcatgctttttaAGTTTTTAGTTTGTAACGCTTAACACTTCTATTTCTTTAGTCATTTTTTGTAACATTTTCTTTTGAGAAGTACTATAGAAATAGAATACTTGTCTTTCATCCGTTTCAGAACGCAATTTAGaa   >  1:48903‑M2/18‑140 (MQ=255)                                                                                                                         attggaatgctttttaAGTTTTTAGTTTGTAACGCTTAACACTTCTATTTCTTTAGTAATTTTATCTAACAATTTCTTTTGAGAAGTACTATAGAAATAGAATACTTGTCTTTCATCCGTTTCAGAACGCAATTTAGaaa  <  2:312065‑M2/124‑1 (MQ=255)                                                                                                                                         |                                                                                                                            AATTCATGGACGTCATGTAACTAGAAATGCCATGAACTAAATATTTATATTCAAAAATAAAAAGCATGCCAATCTCTATTCATCATTTGTCTGTCCCCAAGACGCAATTATGATGTACTGATTGGCATGCTTTTTAAGTTTTTAGTTTGTAACGCTTAACACTTCTATTTCTTTAGTAATTTTATCTAACAATTTCTTTTGAGAAGTACTATAGAAATAGAATACTTGTCTTTCATCCGTTTCAGAACGCAATTTAGAAA  >  CP000730/2388226‑2388485

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.