New junction evidence
		seq id	position	reads (cov)	reads (cov)	score	skew	freq	annotation	gene	product
*	?	CP000730	512620 =	32 (1.040)	28 (1.320) +TTATCTTGTCCATTTTATTTTTTAACCAAAATTTGATTAA	22/178	NT	56.0%	intergenic (+688/‑173)	recR/rrs1	recombination protein RecR/16S ribosomal RNA
	?	CP000730	1998278 =	NA (NA)					intergenic (‑6/+5)	USA300HOU_t0050/rrf4	tRNA‑Val/5S ribosomal RNA

CTGATTACAAGTCAGTTGCTCTACCAATTGAGCTAGGCCGGCAATATGTAAGAATAAATGGTGGAGAATGACGGGTTCGAACCG‑CCGACCCTCTGCTTGTAAGGCAGATGCTCTCCCAGCTGAGCTAATTCTCCGATTTAAAACTGCCTGGCAACGTTCTACTCTAGCGGAACGTAAGTTCGACTACCATCGACGCTAAGGAGCTTAACTTCTGTGTTCGGCATGGGAACAGGTGTGACCTCCTTGCTATAGTCACCAGACATATGAATGTAATTTATA  >  CP000730/1998139‑1998417                                                                                                                                             |                                                                                                                                            cTGATTACAAGTCATTGTCTCTAACAATTGAGCTAGGCCGGCAATATGTAAGAATAAATGGTGGAGAATGACGGGTTCGAACGG‑CCGACCCTCTGCTTGTAAGGCAGGTGCTCGCCCAGCTGAGCTAATTCTCCGATTTa                                                                                                                                             >  2:92516/1‑140 (MQ=11)   gATTACAAGTCAGTTGCTCTACCAATTGAGCTAGGCCGGCAATATGTAAGAATAAATGGTGGAGAATGACGGGTTCGAACCG‑CCGACCCTCTGCTTGTAAGGCAGATGCTCTCCCAGCTGAGCTAATTCTCCGATTTaaa                                                                                                                                           <  1:28799/140‑1 (MQ=37)      tACCAGTCAGTTGCTCTACCAATTGAGCTAGGCCGGCAATATGTAAGAATAAATGGTGGAGAATGACGGGTTCGAACCG‑CCGACCCTCTGCTTGTAAGGCAGATGCTCTCCCAGCTAAGCTACTTGTCCGACTTAAAACt                                                                                                                                        >  2:42308/1‑140 (MQ=14)                ttGCTCTTCCCATTGAGCCAGGCCGGCAATATGTAAGAATAAATGGTGGAGAATGACGGGTTCGAACCG‑CCGACCCTCTGCTTGTAAGGCAGATGCTCTCCCAGCTGAGCTAATTCTCCGATTTAAAACTGCCTGGCAAc                                                                                                                              <  1:331283/140‑1 (MQ=255)                     ctACCAATTGAGCTAGGCCGGCAATATGTAAGAATAAATGGTGGAGAATGACGGGTTCGAACCG‑CCGACCCTCTGCTTGTAAGGCAGATGCTCTCCCAGCTGAGCTAATACTCCGATATAAAACTGCCTGGCAACggact                                                                                                                         >  1:206807/1‑136 (MQ=255)                        cagaTTTAGCTAGTCCGTCAATATGTAAGAATAAATGGTGGAGAATGACGGGTTCGAACCG‑CCGACCCTCTGCTTGTAAGGCAGATGCTCTCCCAGCTGAGCTAATTCTCCGATTTAAAACTGCCTGGCAACGTTCTAct                                                                                                                      <  1:344127/137‑1 (MQ=255)                               aGCTAGGCCGGCAATATGTAAGAATAAATTGTGGAGAATGACGGGTTCGAACCG‑CCGACCCTCTGCTTGTAAGGCAGATGCTCTCCCAGCTGAGCTAATTCTCCGATTTAAAACTGCCTGGCAACGTTCTTCTCTAGCgg                                                                                                               <  2:32604/140‑1 (MQ=255)                               aGCTAGGCCGGCAATATGTAAGAATAAATGGTGGAGAATGACGGGTTCGAACCG‑CCGACCCTCTGCTTGTAAGGCAGATGCTCTCCCAGCTGAGCTAATTCTCCGATTTAAAACTGCCTGGCAACGTTCTACTCTAGCgg                                                                                                               <  1:268605/140‑1 (MQ=255)                                        tgaaaTATGTCAGAATAAATTGTCGAGAATAACGGGTTCTAACCG‑CCGACCCTCTGCTTGTAAGGCAGATGCTCTCCCAGCTGAGCTAATTCTCCGATTTAAAACTGCCTGGCAACGTTCTACTCTAGCGGAACGTAAGt                                                                                                      <  2:9936/137‑1 (MQ=17)                                            atatGTAACGATCAATGGTTGAGAATGGCGGGTTCTAACGGCCCGACTC‑CTTGTTGTAGGTCGGTTGCTTTCCCATCTGGGCTAATTCTCCGATTTAAAACTGCCTGGCTACGTTCTACTCTGGCGGAACGTAAGTTCGa                                                                                                  <  2:139478/140‑1 (MQ=9)                                              atGTAAGAATAAATGGGGGAGAATGACGGGTTCGAACCG‑CCGACCCTCTGCTTGGAAGGCAGATGCTCTCCCAGCTGAGCTAATTCTCCGATTTAAAACTGCCTGGCAACGTTCTACTCTAGCGGAACGTAAGTTCGACt                                                                                                <  1:130515/140‑1 (MQ=255)                                                    gAATTACTGGTGGAGAAGCGCGGGTTCGAACCG‑CCGACCCTCTGCTTGTAAGGCAGATGCTCTCCCAGCTGAGCTAATTCTCCGATTTAAAACTGCCTGGCAACGTTCTACTCTAGCGGAACGTAAGTTCGACTACCATc                                                                                          <  2:72718/140‑1 (MQ=17)                                                       gaaaTGGTGGAGAATGACGGGTTCGAACCG‑CCGACCCTCTGCTTGTAAGGCAGATGCTCTCCCAGCTGAGCTAATTCTCCGATTTAAAACTGCCTGGCAACGTTCTACTCTAGCGGAACGTAAGTTCGACTACCATCGAc                                                                                       <  2:345449/139‑1 (MQ=255)                                                        aaaTGGTGGAGAATGACGGGTTCGAACCG‑CCGACCCACTGCTTCTAAGGCAGATCCTCTCCAAGCTGAGCTAATTCCCCGATTTAAAGCGGCCTGTCATGGTGCTTCTGTAGCGGAACGTAAGTTCGACTACCCTAGACg                                                                                      >  2:84061/1‑140 (MQ=14)                                                           tggtggAGAATGACGGGTTCGAACCG‑CCGACCCTCTGCTTGTAAGGCAGATGCTCTCCCAGCTGAGCTAATTCTCCGATTTAAAACTGGCGGGCAACGTTCTACTCTAGCGGAACGTAAGCGCGACTACCGTCGACGCtc                                                                                   >  2:23690/1‑139 (MQ=14)                                                           tggtggAGAATGACGGGTTCGAACCG‑CCGACCCTCTGCTTGTAAGGCAGATGCTCTCCCAGCTGAGCTAATTCTCCGATTTAAAACTGCCTGGCAACGTTCTACTCTAGCGGAACGTAAGTTCGACTACCATCGACGCTa                                                                                   >  2:337402/1‑140 (MQ=255)                                                            ggtggAGAATGACGGGTTCGAACCG‑CCGACCCTCTGCTTGTAAGGCAGATGCTCTCTCAGCTGAGCTAATTCTCCGATTTAAAACTGCCTGGCAACGTACTACTCTCGCGGCACGTAAGTTCGACTACCAACGAGGCTaa                                                                                  >  1:125/1‑140 (MQ=14)                                                                     tGACGGGTTCGAACCG‑CCGACCCTCTGCTTGTAAGGCAGATGCTCTCCCTGTATAACGAAGTCTACGACAGAATACTGCCTGGCAACGTTCTACTCTAGCGGAACGTAAGTTCGACTACCATCGACGCTAAGGAGCTTaa                                                                         >  1:352200/1‑140 (MQ=14)                                                                      gACGGGTTCGAACCG‑CCGACCCTCTTCTTGTAAGGCAGATGCTCTCCCAGCTGAGCTAATTCTCCGATTTAAAACTGCCTGGCAACGTTCTACTCTAGCGGAACGTAAGTTCGACTACCATCGACGCTAAGGAGCTTAAc                                                                        <  1:101322/140‑1 (MQ=255)                                                                            ttCGAACCG‑CCGACCCTCGGCTTGTAAGGCAGATGCTCTCCCAGCTGAGCTAATTCTCCGATTTAAAACTGCCTGGCAACGTTCTACTCTAGCGGAACGTAAGTTCGACTACCATCGACGCTAAGGAGCTTAACTTCtgt                                                                  >  1:190883/1‑140 (MQ=255)                                                                              cGAACCG‑CCGACCCTCTGCTTGTAAGGCAGTTGCTCTCCCAGCTGAGCTAATTCTCCGATTTAAAACTGCCTGGCAACGTTCTACTCTAGCGGAACGTAAGTTCGACTACCATCGACGCTAAGGAGCTTAACTTCTgtgt                                                                <  1:19512/140‑1 (MQ=255)                                                                              cGAACCG‑CCGACCCTCTGCTTGGAAGGCAGATGCTCTCCCAGCTGAGCTAATCCTCCGATTTAAAACTGCCTGGCAACGTTCTACTCTAGCGGAACGTAAGTTCGACTACCATCGACGCTAAGGAGCTTAACTTCTgtgt                                                                <  1:81677/140‑1 (MQ=255)                                                                               gAACCG‑CCGCTCCTCTGCTTGTAAGGTAGATTCTCTTCCAGCTGAGCTAATTCTCCGATTTAAAACTGCCTGGCAACGTTCTACTCTAGCGGAACGTAAGTTCGACTACCATCGACGCTAAGGAGCTTAACTTCTGTGtt                                                               <  2:6139/140‑1 (MQ=14)                                                                                      tcggcccGCTGCGTGTAAGGCGGGTGCTCTCGCAGCTGGGTTAGTTCTCGGATTTAAAACTGCCTGGCAACGTTCTGCTGTAGCGGAACGTAAGTTCGACTACGATCGAGGGTAAGGAGCTTAGCTTCTGTGTTCGGCAt                                                         <  2:82123/136‑1 (MQ=14)                                                                                       cgACCCTCTGCTTGTAAGGCAGATGCTCTCCCAGCTGAGCTAATTCTCCGATTTAAAACTGCCTGGCAACGTTCTACTCTAGCGGAACGTAAGTTCGACTACCATCGACGCTAAGGAGCTTAACTTCTGTGTTCGGCATg                                                        <  1:226604/140‑1 (MQ=255)                                                                                               tGCTTGGAAGGCAGATGCTCTCCCAGCTGATCTAATTCTCCGATTTAAAACTGCCTGGCAACGATCTACTCTAGCGGAACGTAAGTTCGACTACCATCGACGCTAAGGAGCTTAACTTCTGTGTTCGGCATGGGAACAgg                                                <  2:258374/140‑1 (MQ=255)                                                                                                    gTAAGGCAGATGCTCGCCCAGCTGAGCTAATTCTCCGATTTAAAACTGCCTGGCAACGTTCTACTCTTGCGGAACGGAAGTTCGACTACCATCGACGCTAAGGAGCTTAACTTCTGTGTTCGGCATGGCACCATGTGTGa                                           <  2:218246/140‑1 (MQ=14)                                                                                                      aaGGCAGATGCTCTCCCAGCTGAGCTAATTCTCCGATTTAAAACTGCCTGGCAACGTTCTACTCTAGCGGAACGTAAGTTCGACTACCATCGACGCTAAGGAGCTTAACTTCTGTGTTCGGCATGGGAACAGGTGTGAcc                                         >  2:330180/1‑140 (MQ=255)                                                                                                          cAGATGCTCTCCCAGCTGAGCTAATTCTCCGATTTAAAACTGCCTGGCAACGTTCTACTCTAGCGGAACGTAAGTTCGACTACCATCGACGCTAAGGAGCTTAACTTCTGTGTTCGGCATGGGAACAGGTGTGAcctcct                                     >  2:175513/1‑140 (MQ=255)                                                                                                          cAGATGCTCTCCCAGCTGAGCTAATTCTCCGATTTAAAACTGCCTGGCAACGTTCTACTCTAGCGGAACGTAAGTTCGACTACCATCGACGCTAAGGAGCTTAACTTCTGTGTTCGGCATGGGAACAGGTGTGAcctcct                                     <  2:253990/140‑1 (MQ=255)                                                                                                          cAGATGCTCTCCCAGCTGAGCTAATTCTCCGATTTAAAACTGCCTAGCGATGTAAGTCCCTAGCGGAACGTAAGTTCGACTACCATCGACGCTAAGGAGCTTAACTTCTGTGTTCGGCATGGGAACAGGTGTGAcctcct                                     <  1:276535/140‑1 (MQ=14)                                                                                                               gCTCTCCCAGCTGAGCTAATTCTCCGATTTAAAACTGCCTGGCAACGTTCTACTCTAGCGGAACGTAAGTTCGACTACCATCGACGCTAAGGAGCTTAACTTCTGTGTTCGGCATGGGAACAGGAGTGACCTCCTTGCta                                >  1:181564/1‑140 (MQ=255)                                                                                                                         cTGAGCTAATTCTCCGATTTAAAACTGCCTGGCAACGTTCTACTCTAGCGGAACGTAAGTTCGACTACCATCGACGCTAAGGAGCTTAACTTCTGTGTTCGGCATGGGAACAGGTGTGACCTCCTTGCTATAGTCACCAg                      >  1:265996/1‑140 (MQ=255)                                                                                                                            aGCTAATTCTCCGATTTAAAACTGCCTGGCAACGTTCTACTCTAGCGGAACGTAAGTTCGACTACCATCGACGCTAAGGAGCTTAACTTCTGTGTTCGGCATGGGAACAGGTGTGACCTCCTTGCTATAGTCACCAAACa                   >  1:31969/1‑140 (MQ=255)                                                                                                                                aaTTCTCCGATTTAAAACTGCCTGGCAACGTTCTACTCTAGCGGAACGTAAGTTCGACTACCATCGACGCTAAGGAGCTTAACTTCTGTGTGCGGCATGGGAACAGGTGTGACCTCCTTGCTATAGTCACCAGACATATg               <  1:84723/140‑1 (MQ=255)                                                                                                                                     tcCGATTTAAAACTGCCTGGCAACGTTCTACTCTAGCGGAACGTAAGTTCGACTACCATCGACGCTAAGGAGCTTAACTTCTGTGTGTGGTTTCACAACATAAGACACCTACTTACTATACTCACCAGACATATGAATGt          >  1:167612/1‑140 (MQ=14)                                                                                                                                             aaaaCTGCCTGGCAACGTTCTACTCTAGCGGAACGTAAGTTCGACTACCATCGACGCTAAGGAGCTTAACTTCTGTGTTCGGCATGGGAACAGGTGTGACCTCCTTGCTATAGTCACCAGACATATGAATGTAATTtata  <  2:299971/140‑1 (MQ=33)                                                                                                                                             |                                                                                                                                            CTGATTACAAGTCAGTTGCTCTACCAATTGAGCTAGGCCGGCAATATGTAAGAATAAATGGTGGAGAATGACGGGTTCGAACCG‑CCGACCCTCTGCTTGTAAGGCAGATGCTCTCCCAGCTGAGCTAATTCTCCGATTTAAAACTGCCTGGCAACGTTCTACTCTAGCGGAACGTAAGTTCGACTACCATCGACGCTAAGGAGCTTAACTTCTGTGTTCGGCATGGGAACAGGTGTGACCTCCTTGCTATAGTCACCAGACATATGAATGTAATTTATA  >  CP000730/1998139‑1998417

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 8 ≤ ATCG/ATCG < 12 ≤ ATCG/ATCG < 22 ≤ 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.