New junction evidence
		seq id	position	reads (cov)	reads (cov)	score	skew	freq	annotation	gene	product
*	?	CP000730	= 2777745	41 (0.650)	3 (0.050)	3/244	NT	6.9%	coding (495/705 nt)	USA300HOU_2631	transcriptional regulator
	?	CP000730	= 2777785	42 (0.710)					coding (455/705 nt)	USA300HOU_2631	transcriptional regulator

AAGTTCATGAATAATATGACCAGCTGTTTCCCGGGAAATCCCAGCCATATCACTCATGAGTTGAATAGTTAAAAACTGTTTGATTTCATAAAATTCATCTTGATCGTATCCTACTGTCTGACATAGATGGCATATCAATTTGATAATTCGATCTTTAGCAAATTTACTTGTTAATGCCATGTTATAGTTCATGTGTTGCTGCTCATTATCATTTATTAATGCAAAAAGTGTCAAAAATATATCATCATTAGCTTTGCACAAAAAGGCCATCA  >  CP000730/2777613‑2777884                                                                                                                                     |                                                                                                                                            aaGTTCATGAATAATATGACCAGCTGTTTCCCGGGAAATCCCAGCCATATCACTCATGAGTTGAATAGTTAAAAACTGTTTGATTTCATAAAATTCATCTTGATCGTATCCTACTGTCTGACATAGATGGCATATCAAtt                                                                                                                                      >  2:224268/1‑140 (MQ=255)    ttCATGAATAATATGACCAGCTGTTTCCCGGGAAATCCCAGCCATATCACTCATGAGTTGAATAGTTAAAAACTGTTTGATTTCATAAAATTCATCTTGATCGTATCCTACTGTCTGACATAGATGGCATATCAATTTGa                                                                                                                                   <  2:239548/140‑1 (MQ=255)     tCATGAATAATATGACCAGCTGTTTCCCGGGAAATCCCAGCCATATCACTCATGAGTTGAATAGTTAAAAACTGTTTGATTTCATAAAATTCATCTTGATCGTATCCTACTGTCTGACATAGATGGCATTTCAATTTGAt                                                                                                                                  >  2:560996/1‑140 (MQ=255)        tGAATAATATGACCAGCTGTTTCCCGGGAAATCCCAGCCATATCACTCATGAGTTGAATAGTTAAAAACTGTTTGATTTCATAAAATTCATCTTGATCGTATCCTACTGTCTGACATAGATGGCATATCAATTTGATAAt                                                                                                                               <  2:88364/140‑1 (MQ=255)                  gACCAGCTGTTTCCCGGGAAATCCCAGCCATATCACTCATGAGTTGAATAGTTAAAAACTGTTTGATTTCATAAAATTCATCTTGATCGTATCCTACTGTCTGACATAGATGGCATATCAATTTGATAATTCGATCTTTa                                                                                                                     <  2:388006/140‑1 (MQ=255)                   aCCAGCTGTTTCCCGGGAAATCCCAGCCATATCACTCATGAGTTGAATAGTTAAAAACTGTTTGATTTCATAAAATTCATCTTGATCGTATCCTACTGTCTGACATAGATGGCATATCAATTTGCTAATTCGATCtttgg                                                                                                                    >  2:163966/1‑138 (MQ=255)                   aCCAGCTGTTTCCCGGCAACTCCCAGCAATATCACTCACGAGTTGAATAGTTAAAAACTGTTTGATTTCATACAATTAATCTTGACATTATCCACAGGTCTGACGTAGATGGCATATCAATTTGTAAATCCGATCtgtcg                                                                                                                    >  1:406741/1‑136 (MQ=255)                          gTTTCCCGGGAAATCCCAGCCATATCACTCATGAGTTGAATAGTTAAAAACTGTTTGATTTCATAAAATTCATCTTGATCGTATCCTACTGTCTGACATAGATGGCATATCAATTTGATAATTCGATCTTTAGCAAAttt                                                                                                             >  2:58840/1‑140 (MQ=255)                           tttCCCGGGAAATCCCAGCCATATCACTCATGAGTTGAATAGTTAAAAACTGTTTGATTTCATAAAATTCATCTTGATCGTATCCTACTGTCTGACATAGATGGCATATCAATTTGATAATTCGATCTTTAGCAAATTTa                                                                                                            <  1:484550/140‑1 (MQ=255)                           tttCCCGGGAAATCCCAGCAATAATACTCAGTAGTTGAATAGTTAAAAACTGTTTGATTTCATAAAATTCATCTTGATCGTATCCTACTGTCTGACATAGATGGCATATCAATTTGATAATTCGATCTTTAGCAAATTTa                                                                                                            >  2:515188/1‑140 (MQ=255)                            ttCCCGGGAAATCCCATCCATATCACTCATGAGTTGAATAGTTAAAAACTGTTTGATTTCATAAAATTCATCTTGATCGTATCCTACTGTCTGACATAGATGGCATATCAATTTGATAATTCGATCTTTAGCAAATTTAc                                                                                                           <  1:40468/140‑1 (MQ=255)                             tCCCGGGAAATCCCAGCCATATCACTCATGAGTTGAATAGTTAAAAACTGTTTGATTTCATAAAATTCATCTTGATCGTATCCTACTGTCTGACATAGATGGCATATCAATTTGATAATTCGATCTTTAGCAAATTTACt                                                                                                          >  2:351652/1‑140 (MQ=255)                                 tgtaaaTCCCTGCCATATCACTCATGAGTTGAATAGTTAAAAACTGTTTGATTTCATAAAATTCATCTTGATCGTATCCTACTGTCTGACATAGATGGCATATCAATTTGATAATTCGATCTTTAGCAAATTTACTTGtt                                                                                                      <  2:18721/137‑1 (MQ=255)                                   gAAATCCCAGCCATATCACTCATGAGTTGAATAGTTAAAAACTGTTTGATTTCATAAAATTCATCTTGATCGTATCCTACTGTCTGACATAGATGGCATtaacaagtaaatttgctaaagatcgaattatcaaattgata                                                                                                    <  1:665579‑M1/140‑42 (MQ=255)                                   gAAATCCCAGCCATATCACTCATGAGTTGAATAGTTAAAAACTGTTTGATTTCATAAAATTCATCTTGATCGTATCCTACTGTCTGACATAGATGGCATATCAATTTGATAATTCGATCTTTAGCAAATTTACTTGTTAa                                                                                                    >  1:674707‑M2/1‑139 (MQ=255)                                      aTCCCAGCCATATCACTCATGAGTTGAATAGTTAAAAACTGTTTGATTTCATAAAATTAATTTTGGTCGTATCCTACTGTCTGACATAGATGGCATATCAATTTGATAATTCGATCTTTAGCAAATTTACTTGTTAttgc                                                                                                 <  2:605885‑M2/140‑5 (MQ=255)                                           aGCCATATCACTCATGAGTTGAATAGTTAAAAACTGTTTGATTTCATAAAATTCATCTTGATCGTATCCTACTGTCTGACATAGATGGCATATCAATTTGATAATTCGATCTTTAGCAAATTTACTTGTTAATGCCATGt                                                                                            <  1:575947/140‑1 (MQ=255)                                           aGCCATATCACTCATGAGTTGAATAGTTAAAAACTGTTTGATTTCATAAAATTCATCTTGATCGTATCCTACTGTCTGACATAGATGGCATATCAATTTGATAATTCGATCTTTAGCAAATTTACTTGTTAATGCCATGt                                                                                            <  1:407979/140‑1 (MQ=255)                                                tatCACTCATGAGTTGAATAGTTAAAAACTGTTTGATTTCATAAAATTCATCTTGATCGTATCCTACTGTCTGACATAGATGGCATATCAATTTGATAATTCGATCTTTAGCAAATTTACTTGTTAATGCCATGTTATAg                                                                                       <  1:515624/140‑1 (MQ=255)                                                  tCACTCATGAGTTGAATAGTTAAAAACTGTTTGATTTCATAAAATTCATCTTGATCGTATCCTACTGTCTGACATAGATGGCATtaaaaagtaaatttgctaaagatcgaattatcaaattgatatgccatctatgtcag                                                                                     >  2:596489‑M1/1‑84 (MQ=255)                                                  tCACTCATGAGTTGAATAGTTAAAAACTGTTTGATTTCATAAAATTCATCTTGATCGTATCCTACTGTCTGACATAGATGGCATATCAATTTGATAATTCGATCTTTAGCAAATTTACTTTTTAatgccatctatgtcag                                                                                     <  1:596489‑M2/140‑17 (MQ=255)                                                        aTGAGTTGAATAGTTAAAAACTGTTTGATTTCATAAAATTCATCTTGATCGTATCCTACTGTCTGACATAGATGGCATATCAATTTTATAATTCTATCTTTAGCAAATTTACTTGTTAATGCCATGTTATAGTTCAtgtg                                                                               <  2:51157/140‑1 (MQ=255)                                                         tGAGTTGAATAGTTAAAAACTGTTTGATTTCATAAAATTCATCTTGATCGTATCCCACTGTCTGACATCGACCGCATATCAATTGGATAATTCGATCTTTAGCAAATTTACTTGTTAATGCCATGTTATAGTTCATgtgt                                                                              <  2:181126/140‑1 (MQ=255)                                                               gAATAGTTAAAAACTGTTTGATTTCATAAAATTCATCTTGATCGTATCCTACTGTCTGACATAGATGGCATATCAATTTGATAATTCGATCTTTAGCAAATTTACTTGTTAATGCCATGTTATAGTTCATGTGTtgctgc                                                                        >  1:475879/1‑140 (MQ=255)                                                               gAATAGTTAAAAACTGTTTGATTTCATAAAATTCATCTTGATCGTATCCTACTGTCTGACATAGATGGCATATCAATTTGATAATTCGATCTTTAGCAAATTTACTTGTTAATGCCATGTTATAGTTCATGTGTtgctgc                                                                        <  1:553930/140‑1 (MQ=255)                                                                 atcgTTAAAAACTGTTTGATTTCATAAAATGCATCTTGATCGTATCCTACTGTCTGACATAGGTGGCATATCAATTTGATAATTCGATCTTTAGCAAATTTACTTGTTAATGCCATGTTATAGTTCATGTGTTGCTGCTc                                                                      >  2:425020/4‑140 (MQ=255)                                                                 aTAGTTAAAAACTGTTTGATTTCATAAAATTCATCTTGATCGTATCCTACTGTCTGACATAGATGGCATATCAATTTGATAATTCGATCTTTAGCAAATTTACTTGTTAATGCCATGTTATAGTTCATGTGTTGCTGCTc                                                                      >  1:615579/1‑140 (MQ=255)                                                                   aGTTAAAAACTGTTTGATTTCATAAAATTCATCTTGATCGTATCCTACTGTCTGACATAGATGGCATATCAATTTGATAATTCGATCTTTAGCAAATTTACTTGTTAATGCCATGTTATAGTTCATGTGTTGCTGCTCAt                                                                    <  1:228567/140‑1 (MQ=255)                                                                      tAAAAACTGTTTGATTTCATAAAATTCATCTTGATCGTATCCTACTGTCTGACATAGATGGCATATCAATTTGATAATTCGATCTTTAGCAAATTTACTTGTTAATGCCATGTTATAGTTCATGTGTTGCTGCTCATTAt                                                                 >  2:386159/1‑140 (MQ=255)                                                                        aaaaCTGTTTGATTTCATAAAATTCTTCTTGATCGTATCCTACTGTCTGACATAGATTGCATATCAATTTGATAATTCGATCTTTAGCAAATTTACTTGTTAATGCCATGTTATAGTTCATGTGTTGCTGCTCATTATCa                                                               <  2:141207/140‑1 (MQ=255)                                                                          aaCTGTTTGATTTCATAAAATTCATCTTGATCGTATTCTACTGTCTGACATAGATGGCATATCAATTTGATAATTCTATCTTTAGCAAATTTACTTGTTATTGCCATGTTATAGTTCATGTGTTGCTGCTCATTATCAtt                                                             <  2:3773/140‑1 (MQ=255)                                                                                ttGATTTCATAAAATTCATCTTGATCGTATCCTTCTGTCTGACATAGATGGCATATCAATTTGATAATTCGATCTTTAGCAAATTTACTTGTTAATGCCATGTTATAGTTCATGTGTTGCTGCTCATTATCATTTATTaa                                                       <  1:243361/140‑1 (MQ=255)                                                                                        aTAAAATTCATCTTGATCGTATCCTACTGTCTGACATAGATGGCATATCAATTTGATAATTCGATCTTTAGCAAATTTACTTGTTAATGCCATGTTATAGTTCATGTGTTGCTGCTCATTATCATTTATTAATGCaaaaa                                               <  2:560392/140‑1 (MQ=255)                                                                                         tAAAATTCATCTTGATCGTATCCTACTGTCTGACATAGATGGCATATCAATTTGATAATTCGATCTTTAGCAAATTTACTTGTTAATGCCATGTTATAGTTCATGTGTTGCTGCTCATTATCATTTATTAATGCAAAAAg                                              <  1:224268/140‑1 (MQ=255)                                                                                         tAAAATTCATCTTGATCGTATCCTACTGTCTGACATAGATGGCATATCAATTTGATAATTCGATCTTTAGCAAATTTACTTGTTAATGCCATGTTATAGTTCATGTGTTGCTGCTCATTATCATTTATTAATGCAAAAAg                                              <  1:409933/140‑1 (MQ=255)                                                                                         tAAAATTCATCTTGATCGTATCCTACTGTCTGACATAGATGGCATATCAATTTGATAATTCGATCTTTAGCAAATTTACTTGTTAATGCCATGTTATAGTTCATGTGTTGCTGCTCATTATCATTTATTAATGCAAAAAg                                              <  1:288706/140‑1 (MQ=255)                                                                                           aaaTTCATCTTGATCGTATCCTACTGTCTGACATAGATGGCATCTCAATTTGATAATTCGATCTTTAGCAAATTTACTTGTTAATGCCATGTTATAGTTCATGTTTTGCTGCTAATTATCATTTATTAATGCAAAAAgtg                                            >  1:209784/1‑140 (MQ=255)                                                                                           aaaTTCATCTTGATCGTATCCTACTGTCTGACATAGATGGCATATCAATGTGATAATTCGATCTTTAGCAAATTTACTTGTTAATGCCATGTTATAGTTCATGTGTTGCTGCTCATTATCATTTATTAATGCAAAAAgtt                                            >  2:67901/1‑139 (MQ=255)                                                                                                      gcttgTATCCTACTGTCTTATATTGATGGCATATCAATTTGATAATTCGATCTTTAGCAAGTTTCCTTGTTAATGCCATGTTATAGTTCATTTGTTGCTGCTCATTATCATTTATTAATGCAAAAAGTGTCAAAAatata                                 <  1:581313/136‑1 (MQ=255)                                                                                                      gATCGTATCCTACTGTCTGACATAGATGGCATATCAATTTGATAATTCGATCTTTAGCAAATTTACTTGTTAATGCCATGTTATAGTTCATGTGTTGCTGCTCATTATCATTTATTAATGCAAAAAGTGTCAAAAatata                                 >  2:343573/1‑140 (MQ=255)                                                                                                           tATCCTACTGTCTGACATAGATGGCATATCAATTTGATAATTCGATCTTTAGCAAATTTACTTGTTAATGCCATGTTATAGTTCATGTGTTGCTGCTCATTATCATTTATTAATGCAAAAAGTGTCAAAAATATatcatc                            <  1:214905/140‑1 (MQ=255)                                                                                                                      cTGACATAGATGGCATtaaaaagtaaatttgctaaagatcgaattatcaaattgatatgccatctatgtcagacagtaggatacgatcaagatgaattttatgaaatcaaacagtttttaactattcaactcatgagtga                 <  1:596489‑M1/140‑125 (MQ=255)                                                                                                                      cTGACATAGATGGCATATCAATTTGATAATTCGATCTTTAGCAAATTTACTTTTTAatgccatctatgtcagacagtaggatacgatcaagatgaattttatgaaatcaaacagtttttaactattcaactcatgagtga                 >  2:596489‑M2/1‑56 (MQ=255)                                                                                                                       tGACATAGTTCGCATATCAATTTGATAATTCGATATCTACCAAAGTGACTTGTGCCTGGCATGGTATCGTTCATGTGTTGCTGCTAATTATACTTTATTAATGCAAAAACAGACAAACATGAATAATCATTAGCGTGGca                >  2:49068/1‑140 (MQ=255)                                                                                                                       tGACATAGATGGCATATCAATTTGATAATTCGATCTTTAGCAAATTTACTTGTTAATGCCATGTTATAGTTCATGTGTTGCTGCTCATTATCATTTATCCATGAAAGAAGTGTCAAACATATATCATCATTATCTTTGcg                >  1:676587/1‑139 (MQ=255)                                                                                                                          cATAGATGGCATATCAATTTGATAATTCGATCTTTAGCAAATTTACTTGTTAATGCCATGTTATAGTTCATGTGTTGCTGCTCATTATCATTTATTAATGCAAAAAGTGTCAAAAATATATCATCATTAGCTTTGCACaa             >  1:126774/1‑140 (MQ=255)                                                                                                                          cATAGATGGCATATCAATTTGATAATTCGATCTCTAGAAAAGTGACTTGGTAATGCCATGTTATAGTTCATGTGTTGCTGCTCATTATCATTTATTAATGCAAAAAGTGTCAAAAATATATCATCATTAGCTTTGCACaa             <  1:677308/140‑1 (MQ=255)                                                                                                                              gATGGCATATCAATTTGATAATTCGATCTTTAGCAAATTTACTTGTTAATGCCATGTTATAGTTCATGTGTTGCTGCTCATTATCATTTATTAATGCAAAAAGTGTCAAAAATATATCATCATTAGCTTTGCACAAAAAg         >  1:355552/1‑140 (MQ=255)                                                                                                                                 ggCATATCAATTTGATAATTCGATCTTTAGCAAATTTACTTGTTAATGCCATGTTATAGTTCATGTGTTGCTGCTCATTATCATTTATTAATGCAAAAAGTGTCAAAAATATATCATCATTAGCTTTGCACAAAAAGGcc      >  2:18866/1‑140 (MQ=255)                                                                                                                                 ggCATATCAATTTGATAATTCGATCTTTAGCAAATTTACTTGTTAATGCCATGTTATAGTTCATGTGTTGCTGCTCATTATCATTTATTAATGCAAAAAGTGTCAAAAATATATCATCATTAGCTTTGCACAAAAAGGcc      >  2:379179/1‑140 (MQ=255)                                                                                                                                  gCATATCAATTTGATAATTCGATCTTTAGCAAATTTACTTGTTAATGCCATGTTATAGTTCATGTGTTGCTGCTCATTATCATTTATTAATGCAAAAAGTGTCAAAAATATATCATCATTAGCTTTGCACAAAAAGGCCa     <  1:75937/140‑1 (MQ=255)                                                                                                                                  gCATATCAATTTGATAATTCCATCTTTAGCAAATTTACTTGTTAATGCCATGTTATAGTTCATGTGTTGCTGCTCATTATCATTTATTAATGCAAAAAGTGTCAAAAATATATCATCATTAGCTTTGCACAAAAAGGCCa     <  2:71858/140‑1 (MQ=255)                                                                                                                                  gCAAtaacaagtaaatttgctaaagatcgaattatcaaattgatatgccatctatgtcagacagtaggatacgaccaaaattaattttatgaaatcaaacagtttttaactattcaactcatgagtgatatggctgggat     <  2:605885‑M1/140‑137 (MQ=255)                                                                                                                                     ttaacaagtaaatttgctaaagatcgaattatcaaattgatatgccatctatgtcagacagtaggatacgatcaagatgaattttatgaaatcaaacagtttttaactattcaactcatgagtgatatggctgggatttc  >  1:674707‑M1/1‑1 (MQ=255)                                                                                                                                     tatCAATTTGATAATTCGATCTTTAGCAAATTTACTTGTTAatgccatctatgtcagacagtaggatacgatcaagatgaattttatgaaatcaaacagtttttaactattcaactcatgagtgatatggctgggatttc  <  1:665579‑M2/140‑100 (MQ=255)                                                                                                                                     |                                                                                                                                            AAGTTCATGAATAATATGACCAGCTGTTTCCCGGGAAATCCCAGCCATATCACTCATGAGTTGAATAGTTAAAAACTGTTTGATTTCATAAAATTCATCTTGATCGTATCCTACTGTCTGACATAGATGGCATATCAATTTGATAATTCGATCTTTAGCAAATTTACTTGTTAATGCCATGTTATAGTTCATGTGTTGCTGCTCATTATCATTTATTAATGCAAAAAGTGTCAAAAATATATCATCATTAGCTTTGCACAAAAAGGCCATCA  >  CP000730/2777613‑2777884

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 12 ≤ ATCG/ATCG < 13 ≤ 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.