New junction evidence
		seq id	position	reads (cov)	reads (cov)	score	skew	freq	annotation	gene	product
*	?	CP000730	512620 =	25 (1.090)	19 (1.200) +TTATCTTGTCCATTTTATTTTTTAACCAAAATTTGATTAA	18/180	NT	52.4%	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

ATACTAAATAATGTTTGTAACTTATAGTTACGTTTTTTGGAATTAACGTTGACATATTGTCATTCAGTTTTCAATGTTCATTTTTCTTACCGACAAGAATTAATTATACATTTTATTAACATTTAAGTCAATAACTTTTT‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑  <  CP000730/512759‑512620 ‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑AAAACTGCCTGGCAACGTTCTACTCTAGCGGAACGTAAGTTCGACTACCATCGACGCTAAGGAGCTTAACTTCTGTGTTCGGCATGGGAACAGGTGTGACCTCCTTGCTATAGTCACCAGACATA  >  CP000730/1998278‑1998402                                                                                                                                             ||||||||||||||||||||||||||||||||||||||||                                                                                                                              ATACTAAATTATGTTTGTAACTTATAGTTACGTTTTTTTGAATTAACGTTGACATATTGTCATTCAGTTTTCAATTTTCATTTTTCTTACCGACAAGAATTAATTATACATTTTATCAACATTTAAGTCAATAACTTTTTT                                                                                                                                                                      <  1:190994/141‑1              TTTGTAACTTATAGTTACGTTTTTTGGAATTAACGTTGACATATTGTCATTCAGTTTTCAATGTTCATTTTTCTTACCGCCAAGAATTAATTATACATTTTATCAACATTTAAGTCAATACCTTTTTTTGTCTTTTCCATT                                                                                                                                                         >  1:250812/1‑141              TTTGTAACTTATAGTTACGTTTTTTGGAATTAACGTTGACATATTGTCATTCAGTTTTCAATGTTCATTTTTCTTACCGACAAGAATTAATTATACATTTTATCAACATTTAAGTCAATAACTTTTTTTATCTTGTCCATT                                                                                                                                                         >  1:230104/1‑141                TGTAACTTATAGTTACGTTTTTTGGTCTTAACGTTGAAATATTGTCATTCAGTTTTCAATGTTCATTTTTCTTACCGTCATGAGTTAATTCTATATTTTATCAACATTTACGTCAATAACTTTTTTTATCTTGTCATTTTT                                                                                                                                                       >  2:154149/1‑141                TGTAACTTATAGTTACGTTTTTTGGAATTAACGTTGACATATTGTCATTCAGTTTTCAATGTTCATTTTTCTTACCGACAAGAATTAATTATACATTTTATCAACATTTAAGTCAATAACTTTTTTTATCTTTTCCATTTT                                                                                                                                                       >  1:14307/1‑141                TGTAACTTATAGTTACGTTTTTTGGAATTAACGTTGACATATTGTCATGCAGTTTTCAATGTTCATTTTTCTTACCGACAAGAATTAATTATACATTTTATCAACATTTAAGTCAATAACTTTTTTTATCTTGTCCATTTT                                                                                                                                                       >  1:185732/1‑141                  TAACTTATAGTTACGTTTTTTGGAATTAACGTTGACATATTGTAATTCAGTTTTCAATGGTCATTTTTCTTACAGACAAGAATTACTCATACATTTTATCAACATTTTAGTCAATAACTTTTTTTATCTTATTCATTTTAT                                                                                                                                                     >  2:148805/1‑141                  TAACTTATAGTTACGTTTTATGGAATTAACGTTGACATATTGTCATTCAGTTTTCAATGTTCATTTTTCTTACCGACAAGAATTAATTATACATTTTATCAACATTTAAATCAATAACTTTTTTTATCTgtctcatttttt                                                                                                                                                     >  2:207742/1‑129                       TATAGTTACGTTTTTTGGAATTAACGTTGACATATTGTCATTCAGTTTTCAATGTTCATTTTTCTTACCGACAAGAATTAATTATACATTTTATCAACATTTAAGTCAATAACTTTTTTTATCTTGTCCATTTTATTTTTT                                                                                                                                                >  2:33779/1‑141                                  TTTTTGGAATTAACGTTGACATATTGTCATTCAGTTTTCAATGTTCATTTTTCTTAACGAAAAAAATTAATTATACATTTTATCAACATTTAAGTCAATAACTTGTTTTATCTTGTCCATTTTCTTTTTCAACCAAAATTT                                                                                                                                     <  2:193162/141‑1                                   TTTTGGAATTAACGTTGACATATTGTCATTCAGTTTTCAATGTTCATTTTTCTTACCGACAAGAATTAATTATACATTTTATCAACATTTAAGTCAATAACTTTTTTTATCTTGTCCATTTTATTTTTTAACCAAAATTTG                                                                                                                                    >  2:234347/1‑141                                          ATTAACGTTGACATATTGTCATTCAGTTGTCAATGTTCATTTTTCTTACCGACAAGAATTAATTATACATTTTATCAACATTTAAGTCAATAACTTTTTTTATCTTGTCCATTTTATTTTTTAACCAAAATTTGATTAAAA                                                                                                                             <  1:36618/141‑1                                           TTAACGTTGACATATTGTCATTCAGTTTTCAATGTTCATTTTTCTTACCGACAAGAATTAATTATACATTTTATCAACATTTAAGTCAATAACTTTTTTTATCTTGTCCATTTTATTTTTTAACCAAAATTTGATTAAAAA                                                                                                                            <  2:46556/141‑1                                                 TTGACATATTGTCATTCAGTTTTCAATGTTCATTTTTCTTACCGACAAGAATTAATTATACATTTTATCAACATTTAAGTCAATAACTTTTTTTATCTTTTTTTTTTTATTTTTTGACCAAAATTTGTTTAAATAACTGCC                                                                                                                      >  2:248256/1‑141                                                  TGACATATTGTCATTCAGTTTTCAATGTTCATTTTTCTTACCGACAAGAATTAATTATACATTTTATCAACATTTAAGTCAATAACTTTTTTTATCTTGTCCATTTTATTTTTTAACCAAAATTTGATTAAAAAAC                                                                                                                          <  1:49935/136‑1                                                  TGACATATTGTCATTCAGTTTTCAATGTTCATTTTTCTTACCGACAAGAATTAATTATACATTTTATCAACATTTAAGTCAATAACTTTTTTTATCTTGTCCATTTTATTTTTTAACCAAAATTTGATTAAAAAAC                                                                                                                          >  2:49935/1‑136                                                                   GTTTCCAATGTTCATTTTTCTTACCGACAAGAATTAATTATACATTTTATCAACATTTAAGTCAATAACTTTTTTTATCTTGTCCATTTTATTTTTTAACCAAAATTTGATTAAAAAACTGCCTGGCAACGTTCTACTCTA                                                                                                    >  2:187266/1‑141                                                                    TTTTCAATGTTCATTTTTCTTACCGACAAGAATTAATTATACATTTTATCAACATTTAAGTCAATAACTTTTTTTATCTTGTCCATTTTATTTTTTAACCAAAATTTGATTAAAAAACTGCCTGGCAACGCTCTACTCTAG                                                                                                   >  1:25376/1‑141                                                                        CAATGTTCATTTTTCTTACCGACAAGAATTAATTATACATTTTATCAACATTTAAGTCAATAACTTTTTTTATCTTGTCCATTTTATTTTTTAACCAAAATTTGATTAAAAAACTGCCTGGCAACGTTCTACTCTAGCGGA                                                                                               <  1:119641/141‑1                                                                           catttttgTTTCTTACCGACAAGAATTAATTATACATTTTATCAACATTTAAGTCAATAACTTTTTTTATCTTGTCCATTTTATTTTTTAACCAAAATTTGATTAAAAAACTGCCTGGCAACGTTCTACTCTAGCGGAACG                                                                                            <  2:133167/133‑1                                                                           TGTTCATTTTTCTTACCGACAAGAATTAATTATACATTTTATCAACATTTAAGTCAATAACTTTTTTTATCTTGTCCATTTTATTTTTTAACCAAAATTTGATTAAAAAACTGCCTGTCAACGTTCTACTCTAGCGGAcgg                                                                                            >  2:2385/1‑138                                                                             TTCATTTTTCTTACCGACAAGAATTAATTATACATTTTATCAACATTTAAGTCAATAACTTTTTTTATCTTGTCCATTTTATTTTTTAACCAAAATTTGATTAAAAAACTGCCTGGCAACGTTCTACTCTAGCGTAACGTA                                                                                          >  2:241790/1‑141                                                                                      CTTACCGACAAGAATTAATTATACATTTTATCAACATTTAAGTCAATAACTTTTTTTATCTTGTCCATTTTATTTTTTAACCAAAATTTGATTAAAAAACTGCCTGGCAACGTTCTACTCTAGCGGAACGTAAGTTCGACT                                                                                 >  1:12042/1‑141                                                                                         ACCGACAAGAATTAAATATACATTTGATCAACATTTAAGTCAATAACTTTTTTTATCTTGTCCATTTTATTTTTTAACCAAAATTTGATTAAAAAACTGCCTGGCAACGTTCTACTCTAGCGGAACGTAAGTTCGACTACC                                                                              >  1:136293/1‑141                                                                                                AGAATTAATTATACATTTTATCAACATTTAAGTCAATAACTTTTTTTATCTTATCCATTGTATTTTTTAACCAAAATTTGATTAAAAAACTGCCTGGCAACGTTCTACTCTAGCGGAACGTAAGTTCGACTACCATCGACG                                                                       >  1:90039/1‑141                                                                                                 GAATTAATTATACATTTTATCAACATTTAAGTCAATAACTTTTTTTATCTTGTCCATTTTATTTTTTAACCAAAATTTGATTAAAAAACTGCCTGGCAACGTTCTACTCTAGCGGAACGTAAGTTCGACTACCATCGACGC                                                                      >  1:169395/1‑141                                                                                                 GAATTAATTATACATTTTATCAACATTTAAGTCAATAACTTTTTTTATCTTGTCCATTTTATTTTTTAACCAAAATTTGATTAAAAAACTGCCTGGCAACGTTCTACTCTAGCGGAACGTAAGTTCGACTACAATGGACGC                                                                      >  1:169397/1‑141                                                                                                         TATACATTTTATCAACATTTAAGTCAATAACTTTTTTTATCTTGTCCATTTTATTTTTTAACCAAAATTTGATTAAAAAACTGCCTGGCAACGTTCTACTCTAGCGGAACGTAAGTTCGACTACCATCGACGCTAAGGAGC                                                              <  1:119524/141‑1                                                                                                             CATTTTATCAACATTTAAGTCAATAACTTTTTTTATCTTTTCCATTTTATTTTTTAACCAAAATTTGATTAAAAAACTGCCTGGCAACGTTCTACTCTAGCGGAACGTAAGTTCGACTACCATCGACGCTAAGGAGCTTAc                                                          >  1:225301/1‑140                                                                                                                  TATCAACATTTATGTCAATAACTTTTTTTATCTTGTCCATTTTATTTTTTAACCAAAATTTGAGTAAAAAACTGCCTGGCAACGTTCTACTCTAGCGGAACGTAAGTTCGACTACCATCGACGCTAAGGAGCTTAACTTCT                                                     <  2:243147/141‑1                                                                                                                    tcAACATTTAAGTCAATTACTTTTTTTATCTTGTCCATTTTATTTTTTAACCAAAATTTGATTAAAAATCTGCCTGGCAACGTTCTACTCTAGCGGAACGTAAGTTCGACTACCATCGACGCTAAGGAGCTTAACTTCTGT                                                   <  1:239691/139‑1                                                                                                                          TTTAAGTCAATAACTTTTTTTATCTTGTCCATTTTATTTTTTAACCAAAATTTGATTAAAAAACTGCCTGGCAACGTTCTACTCTAGCGGAACGTAAGTTCGACTACCATCGACGCTAAGGAGCTTAACTTCTGTGTTCGG                                             <  2:131416/141‑1                                                                                                                                 caaaatgttaTTTTATCTTGTCCATTTTATTTTTTAACCAAAATCTGATTAAAAAACTGCCTGGCAACGTTCTACTCTAGCGGAACGTAAGTGCGACTACCATCGACGCTAAGGAGCTTAACGTCTGTGTTCGGCATGGGA                                      <  1:94278/131‑1                                                                                                                                 aAATACCTTTTTTTATCTTGTCCATTTTATTTTTTAACCAAAATTTGATTAAAAAACTGCCTGGCAACGTTCTACTCTAGCGGAACGTAAGTTCGACTACCATCGACGCTAAGGAGCTTAACTTCTGTGTTCGGCATGGGA                                      <  2:18351/140‑1                                                                                                                                   ATAACTTTTTTTATCTTGTCCATTTTATTTTTTAACCAAAATTTGATTAAAAAACTGCCTGGCAACGTTCTACTCTAGCGGAACGTAAGTTCGACTACCATCGACGCTAAGGAGCTTAACTTCTGTGTTCGGCATGGGAAC                                    <  1:33779/141‑1                                                                                                                                         TTTTTTATCTTTTCCATTTTATTTGTTAACCAAAATTTGATTAAAAAACTGCCTGGCAACGTTCTACTCTAGCGGAACGTAAGTTCGACTACCATCGACGCTAAGGAGCTTAACTTCTGTGTTCGGCATGGGAACAGGTGT                              <  2:144460/141‑1                                                                                                                                           TTTTATCTTGTCCATTTTATTTTTTAACCAAAATTTGATTAAAAAACTGCCTGGCAACGTTCTACTCTAGCGGAACGTAAGTTCGACTACCATCGACGCTAAGGAGCTTAACTTCTGTGTTCGGCATGGGAACAGGTGTGA                            >  1:154821/1‑141                                                                                                                                            TTTATCTTGTCCATTTTATTTTTTAACCAAAATTTGATTAAAAAACTGCCTGGCAACGTTCTACTCTAGCGGAACGTAAGTTCGACTACCATCGACGCTAAGGAGCTTAACTTCTGTGTTCGGCATGGGAACAGGTGTGAC                           <  2:14307/141‑1                                                                                                                                            TTTATCTTGTCCATTTTATTTTTTAACCAAAATTTGATTAAAAAACTGCCTGGCAACGTTCTACTCTAGCGGAACGTAAGTTCGACTACCATCGACGCTAAGGAGCTTAACTTCTGTGTTCGGCATGGGAACAGGTGTGAC                           <  1:55473/141‑1                                                                                                                                            TTTATCTTGTCCATTTTATTTTTTAACCAAAATTTGATTAAAAAACTGCCTGGCAACGTTCTACTCTAGCGGAACGTAAGTTCGACTACCATCGACGCTAAGGAGCTTAACTTCTGTGTTCGGCATGGGAACAGGTATGAC                           <  1:184065/141‑1                                                                                                                                             TTATCTGGTCCATTTTATTTTTTAACCAAAATTTGATTAAAAAACTGCCTGGCAACGTTCTACTCTAGCGGAACGTAAGTTCGACTACCATCGACGCTAAGGAGCTTAACTTCTGTGTTCGGCATGGGAACAGGTGTGACC                          <  1:236836/141‑1                                                                                                                                                TCTTTTTCATTTTATTTTTTAACCAAAATTTGATTAAAAAACTGCCTGGCTACGTTCTACTCTAGCGCAACGTAAGTTCGACTTCCTTCGACGCTAAGGAGCTTAACTTCTGTGTTCGGCATGTGTACAGGTGTGACCTCC                       >  2:64057/1‑141                                                                                                                                                TCTTGTCCATTTTATTTTTTAACCAAAATTTGATTAAAAAACTGCCTGGCAACGTTCTACTCTAGCGGAACGTAAGTTCGACTACCATCGACGCTAAGGAGCTTAACTTCTGTGTTAGGCATGGGAACAGtgggcaccgcc                       >  2:161606/1‑130                                                                                                                                                TCTTGTCCATTTTATTTTTTAACCAAAATTTGATTAAAAAACTGCCTGGCAACGTTCTACTCTAGCGGAACGTAAGTTCGACTACCATCGACGCTAAGGAGCTTAAATCCTGTGTTCGGCATGGGAACAGGTGTGACCTCC                       >  2:227061/1‑141                                                                                                                                                    tTCCATTTTATTTTTTAACCAAAATGTGATTAAAAAACTGCCTGGCAACGTTCTACTCTAGCGGAACGTAAGTTCGACTACCACCGACGCTAAGGAGCTTAACTTCTGTGTTCCGCCTGGGAATAGGCGCGACCTCCTTGt                   <  2:24486/140‑2                                                                                                                                                             ATTTTTTAACCAAAATTTGATTAAAAAACTGCCTGGCAACGTTCTACTCTAGCGGAACGTAAGTTCGACTACCATCGACGCTAAGGAGCTTAACTTCTGTGTTCGGCATGGGAACAGGTGTGACCTCCTTGCTATAGTCAC          >  1:154737/1‑141                                                                                                                                                             ATTTTTTAACCAAAATTTGATTAAAAAACTGACTGGCAACGTTCTACTCTAGCGGAACGTAAGTTCGACTACCATCGACGCTAAGGAGCTTAACTTCTGTGTTCGGCCTGGGACCAGGTGTGACTTCATTGCTAAAGTacc          >  2:77785/1‑138                                                                                                                                                                     ACCAAAATTTGATTAAAAAACTGACTGGCAAGGTTCTACTCTAGCGGAACGTAAGTTCGACTACCATCGACGCTAAGGAGCTTAACTTCTGTGTGCGGCATGGGAAAAGGGGTGACCTCATTGATATAGTCACCAGGCATA  >  1:25973/1‑141                                                                                                                                             ||||||||||||||||||||||||||||||||||||||||                                                                                                                              ATACTAAATAATGTTTGTAACTTATAGTTACGTTTTTTGGAATTAACGTTGACATATTGTCATTCAGTTTTCAATGTTCATTTTTCTTACCGACAAGAATTAATTATACATTTTATTAACATTTAAGTCAATAACTTTTT‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑  <  CP000730/512759‑512620 ‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑AAAACTGCCTGGCAACGTTCTACTCTAGCGGAACGTAAGTTCGACTACCATCGACGCTAAGGAGCTTAACTTCTGTGTTCGGCATGGGAACAGGTGTGACCTCCTTGCTATAGTCACCAGACATA  >  CP000730/1998278‑1998402

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.