New junction evidence
		seq id	position	reads (cov)	reads (cov)	score	skew	freq	annotation	gene	product
*	?	CP000730	1994322 =	NA (NA)	3 (0.040)	3/246	NT	25.9%	intergenic (‑429/‑64)	USA300HOU_1854/USA300HOU_1855	hypothetical protein/IS1181 transposase
	?	CP000730	1994387 =	9 (0.100)					coding (2/1362 nt)	USA300HOU_1855	IS1181 transposase

TTATTAGAAAAGTTGAAACAAATATATAACCCCAGATAATATAATCATTATCATTAATGTAATACCAAAAAAAGAAGTTAAACAGGTTCTTCATCTTTTATGGTGGGAAGGTAAAACTTCCTGCTTTTTTTAATACACAAAAAGCGCAATTGCCTCTATAATTTAAAGTGACCAAACCCAAACTAAAGGAGACAAGTGCGCCTATGTGTAATGATACCTTAG  >  CP000730/1994183‑1994404                                                                                                                                            |                                                                                   ttattaGAAAAGTTGAAACAAATATATAACCCCAGATAATATAATCATTATCATTAATGTAATACCAAAAAAAGAAGTTAAACAGGTTCTTCATCTTTTATGGTGGGAAGGTAAAACTTCCTGCTTTTTTTAATACACaaa                                                                                   >  1:197293/1‑141 (MQ=255)   attaGAAAAGTTGAAACAAATATATAACCCCAGATAATATAATCATTATCATTAATGTAATACCAAAAAAAGAAGTTAAACAGGTTCTTCATCTTTTATGGTGGGAAGGTAAAACTTCCTGCTTTTTTTAATACACaaaaa                                                                                 >  1:818159/1‑141 (MQ=255)    ttaGAAAAGTTGAAACAAATATATAACCCCAGATAATATAATCATTATCATTAATGTAATACCAAAAAAAGAAGTTAAACAGGTTCTTCATCTTTTATGGTGGGAAGGTAAAACTTCCTGCTTTTTTTAATACACAAAAAg                                                                                <  1:1022319/141‑1 (MQ=255)    ttaGAAAAGTTGAAACAAATATATAACCCCAGATAATATAATCATTATCATTAATGTAATACCAAAAAAAGAAGTTAAACAGGTTCTTCATCTTTTATGGTGGGAAGGTAAAACTTCCTGCTTTTTTTAATACACAAAAAg                                                                                <  2:1080286/141‑1 (MQ=255)    ttaGAAAAGTTAAAACAAATATATAACCCCAGATAATATAATCATTATCATTAATGTAATACCAAAAAAAGAAGTTAAACAGGTTCTTCATCTTTTATGGTGGGAAGGTAAAACTTCCTGCTTTTTTTAATACACAAAAAg                                                                                <  2:304038/141‑1 (MQ=255)      aaaaaaGTTAAAAAAAAAATATAACTCAAAATAATATAATTATTAACATTAAAAAAAAAAAAAAAAAAGAAGTTAAACAGGTTCTTCATCTTTTATGGTGGGAAGGTAAAACTTCCTGCTTTTTTTAATACACAAAAAgcg                                                                              <  2:843904/139‑1 (MQ=18)      aGAAAAGTTGAAACAAATATATAACCCCAGATAATATAATCATTATCATTAATGTAATACCAAAAAAAGAAGTTAAACAGGTTCTTCATCTTTTATGGTGGGAAGGTAAAACTTCCTGCTTTTTTTAATACACAAAAAgcg                                                                              <  1:453049/141‑1 (MQ=255)      aGAAAAGTTGAAACAAATATATAACCCCAGATAATATAACCCTTATCATTAATGTACTACCAAAAAAAGAAGTTAAACAGGTTCTTCATCTTTTATGGTGGGAAGGTAAAACTTCCTGCTTTTTTTAATACACAAAAAgcg                                                                              <  1:919091/141‑1 (MQ=255)        aaaaGTTGAAACAAATATATAACCCCAGATAATATAATCATTATCATTAATGTAATACCAAAAAAAGAAGTTAAACAGGTTCTTCATCTTTTATGGTGGGAAGGTAAAACTTCCTGCTTTTTTTAATACACAAAAAGCGCa                                                                            <  1:493005/141‑1 (MQ=255)        aaaaGTTGAAACAAATATATAACCCCAGATAATATAATCATTATCATTAATGTAATACCAAAAAAAGAAGTTAAACAGGTTCTTCATCTTTTATGGTGGGAAGGTAAAACTTCCTGCTTTTTTTAATACACAAAAAGCGCa                                                                            <  1:493008/141‑1 (MQ=255)         aaaGTTGAAACAAATATATAACCCCAGATAATATAATCATTATCATTAATGTAATACCAAAAAAAGAAGTTAAACAGGTTCTTCATCTTTTATGGTGGGAAGGTAAAACTTCCTGCTTTTTTTAATACACAAAAAGCGCaa                                                                           >  1:527448/1‑141 (MQ=255)         aaaGTTGAAACAAATATATAACCCCAGATAATATAATCATTATCATTAATGTAATACCAAAAAAAGAAGTTAAACAGGTTCTTCATCTTTTATGGTGGGAAGGTAAAACTTCCTGCTTTTTTTAATACACAAAAAGCGCaa                                                                           <  1:835669/141‑1 (MQ=255)           aGTTGAAACAAATATATAACCCCAGATAATATAATCATTATCATTAATGTAATACCAAAAAAAGAAGTTAAACAGGTTCTTCATCTTTTATGGTGGGAAGGTAAAACTTCCTGCTTTTATAAAAAAAAAAAAAGCGCAAtt                                                                         <  2:78733/141‑1 (MQ=37)             ttGAAACAAATATATAACCCCAGATAATATAATCATTATCATTAATGTAATACCAAAAAAAGAAGTTAAACAGGTTCTTCCTCTTTTATGGTGGGAAGGTAAAACTTCCTGCTTTTTTTAATACACAAAAAGCGCAATTGc                                                                       >  1:510984/1‑141 (MQ=255)             ttGAAACAAATATATAACCCCAGATAATATAATCATTATCATTAATGTAATACCAAAAAAAGAAGTTAAACAGGTTCTTCATTTAGAATTGTGGGAAGGTAAAACTTCCTGCTTTTTTTAATACACAAAAAGCGCAATTGc                                                                       >  1:510724/1‑141 (MQ=37)               gAAACAAATATATAACCCCAGATAATATAATCATTATCATTAATGTAATACCAAAAAAAGAAGTTAAACAGGTTCTTCATCTTTTATGGTGGGAAGGTAAAACTTCCTGCTTTTTTTAATACTCAAAAAGCGCAATTGCct                                                                     >  2:786255/1‑141 (MQ=255)                aaaCAAATATATAACCCCAGATAATATAATCATTATCATTAATGTAATACCAAAAAAAGAAGTTAAACAGGTTCTTCATCTTTTATGGTGGGAAGGTAAAACTTCCTGCTTTTTTTAATACACAAAAAGCGCAATTGCctc                                                                    >  1:994279/1‑141 (MQ=255)                  aCAAATATATAACCCCAGATAATATAATCATTATCATTAATGTAATACCAAAAAAAGAAGTTAAACAGGTTCTTCATCTTTTATGGTGGGAAGGTAAAACTTCCTGCTTTTTTTAATACACAAAAAGCGCAATTGCCTCta                                                                  <  2:919679/141‑1 (MQ=255)                       tatataACCCCAGATAATATAATCATTATCATTAATGTAATACCAAAAAAAGAAGTTAAACAGGTTCTTCATCTTTTATGGTGGGAAGGTAAAACTTCCTGCTTTTTTTAATACACAAAAAGCGCAATTGCCTCTATAAtt                                                             <  1:392970/141‑1 (MQ=255)                        atataACCCCAGATAATATAATCATTATCATTAATGTAATACCAAAAAAAGAAGTTAAACAGGTTCTTCATCTTTTATGGTGGGAAGGTAAAACTTCCTGCTTTTTTTAATACACAAAAAg                                                                                >  2:821748/1‑121 (MQ=255)                        atataACCCCAGATAATATAATCATTATCATTAATGTAATACCAAAAAAAGAAGTTAAACAGGTTCTTCATCTTTTATGGTGGGAAGGTAAAACTTCCTGCTTTTTTTAATACACAAAAAg                                                                                <  1:821748/121‑1 (MQ=255)                           taACCCCAGATAATATAATCATTATCATTAATGTAATACCAAAAAAAGAAGTTAAACAGGTTCTTCATCTTTTATGGTGGGAAGGTAAAACTTCCTGCTTTTTTTAATACACAAAAAGCGCAACTGCCTCTATAATTTaaa                                                         >  2:597965/1‑141 (MQ=255)                            aaCCCCAGATAATATAATCATTATCATTAATGTAATACCAAAAAAAGAAGTTAAACAGGTTCTTCATCTTTTATGGTGGGAAGGTAAAACTTCCTGCTTTTTTTAATACACAAAAAGCGCAATTGCCTCTATAATTTAAAg                                                        <  2:68586/141‑1 (MQ=255)                             aCCCCAGATAATATAATCATTATCATTAATGTAATACCAAAAAAAGAAGTTAAACAGGTTCTTCATCTTTTATGGTGGGAAGGTAAAACTTCCTGCTTTTTTTAATACACAAAAAGCGCAATTGCCTCTATAATTTAAAGt                                                       >  2:932999/1‑141 (MQ=255)                                     taatataatCATTATCATTAATGTAATACCAAAAAAAGAAGTTAAACAGGTTCTTCATCTTTTATGGTGGGAAGGTAAAACTTCCTGCTTTTTTTAATACACAAAAAGCGCAATTGCCTCTATAATTTAAAGTGAccaaac                                               <  1:364122/141‑1 (MQ=255)                                     taatataatCATTATCATTAATGTAATACCAAAAAAAGAAGTTAAACAGGTTCTTCATCTTTTATGGTGGGAAGGTAAAACTTCCTGCTTTTTTTAATACACAAAAAGCGCAATTGCCTCTATAATTTAAAGTGAccaaac                                               <  1:597690/141‑1 (MQ=255)                                      aatataatCATTATCATTAATGTAATACCAAAAAAAGAAGTTAAACAGGTTCTTCATCTTTTATGGTGGGAAGGTAAAACTTCCTGCTTTTTTTAATACACAAAAAGCGCAATTGCCTCTATAATTTAAAGTGAccgaacc                                              <  2:625073/141‑1 (MQ=255)                                      aatataatCATTATCATTAATGTAATACCAAAAAAAGAAGTTAAACAGGTTCTTCATCTTTTATGGTGGGAAGGTAAAACTTCCTGCTTTTTTTAATACACAAAAAGCGCAATTGCCTCTATAATTTAAAGTGAccaaacc                                              <  1:563736/141‑1 (MQ=255)                                      aatataatCATTAACATTAATGTAATACCAAAAAAAGAAGTTAAACAGGTTCTTCATCTTTTATGGTGGGAAGGTAAAACTTCCTGCTTTTTTTAATACACAAAAAGCGCAATTGCCTCTATAATTTAAAGTGAccaaacc                                              <  2:625071/141‑1 (MQ=255)                                       atgattatattatcattaATGTAATACCAAAAAAAGAAGTTAAACAGGTTCTTCATCTTTTATGGTGGGAAGGTAAAACTTCCTGCTTTTTTTAATACACAAAAAGCGCAATTGCCTCTATAATTTAAAGTGAccaaaccc                                             >  2:277112/9‑141 (MQ=255)                                       atataatCATTATCATTAATGTAATACCAAAAAAAGAAGTTAAACAGGTTCTTCATCTTTTATGGTGGGAAGGTAAAACTTCCTGCTTTTTTTAATACACAAAAAGCGCAATTGCCTCTATAATTTAAAGTGAccaaaccc                                             >  1:1038899/1‑141 (MQ=255)                                        tataatCATTATCATTAATGTAATACCAAAAAAAGAAGTTAAACAGGTTCTTCATCTTTTATGGTGGGAAGGTAAAACTTCCTGCTTTTTTTAATACACAAAAAGCGCAATTGCCTCTATAATTTAAAGTGAccaaaccca                                            >  1:1074262/1‑141 (MQ=255)                                         ataatCATTATCATTAATGTAATACCAAAAAAAGAAGTTAAACAGGTTCTTCATCTTTTATGGTGGGAAGGTAAAACTTCCTGCTTTTTTTAATACACAAAAAGCGCAATTGCCTCTATAATTTAAAGTGAccaaacccaa                                           <  2:423073/141‑1 (MQ=255)                                              cattatcattaATGTAATACCAAAAAAAGAAGTTAAACAGGTTCTTCATCTTTTATGGTGGGAAGGTAAAACTTCCTGCTTTTTTTAATACACAAAAAGCGCAATTGCCTCTATAATTTAAAGTGACCAAACCCAAACTaa                                      <  2:221552/141‑1 (MQ=255)                                                  atcattaATGTAATACCAAAAAAAGAAGTTAAACAGGTTCTTCATCTTTTATGGTGGGAAGGTAAAACTTCCTGCTTTTTTTAATACACAAAAAGCGCAATTGCCTCTATCATTTCAAGTCAccaaccccaaaccacccgc                                  >  2:557900/1‑134 (MQ=18)                                                  atcattaATGTAATACCAAAAAAAGAAGTTAAACAGGTTCTTCATCTTTTATGGTGGGAAGGTAAAACTTCCTGCTTTTTTTAATACACAAAAAGCGCAATTGCCTCTATAATTTAAAGTGACCAAACCCAAACTAAAGga                                  >  2:998191/1‑141 (MQ=255)                                                  atcattaATGTAATACCAAAAAAAGAAGTTAAACAGGTTCTTCATCTTTTATGGTGGGAAGGTAAAACTTCCTGCTTTTTTTAATACACAAAAAGCGCAATTGCCTCTATAATTTAAAGTGACCAAACCCAAACTAAAGga                                  >  1:496764/1‑141 (MQ=255)                                                    cattaATGTAATACCAAAAAAAGAAGTTAAACAGGTTCTTCATCTTTTATGGTGGGAAGGTAAAACTTCCTGCTTTTTTTAATACACAAAAAGCGCAATTGCCTCTATAATTTAAAGTGACCAAACCCAAACTAAAGgaga                                >  2:886524/1‑141 (MQ=255)                                                        aaTTTAATACCAAAAAAAGAAAGTATACAGGTTCTTCATCTTTTATGGTGGGAAGGTAAAACTTCCTGCTTTTTTTAATACACAAAAAGCGCAATTGCCTCGATGATTGAATGTGACCAAACCCAATCTATAGGAGACAAg                            <  2:267496/141‑1 (MQ=14)                                                        aaTGTAATACCAAAAAAAGAAGTTAAACAGGTTCTTCATCTTTTATGGTGGGAAGGTAAAACTTCCTGCTTTTTTTTTTTTTCAAAAAGCGCAATTGCCTCTATAATTTAAAGTGACCAAACCCAAACTAAAGGAGACAAg                            >  2:463359/1‑141 (MQ=17)                                                        aaTGTAATACCAAAAAAAGAAGTTAAACAGGTTCTTCATCTTTTATGGTGGGAAGGTAAAACTTCCTGCTTTTTTTAATACACAAAAAGCGCAATTGCCTCTATAATTTAAAGTGACCAAACCCAAACTAAAGGAGACAAg                            <  1:255997/141‑1 (MQ=255)                                                         aTGTAATACCAAAAAAAGAAGTTAAACAGGTTCTTCATCTTTTATGGTGGGAAGGTAAAACTTCCTGCTTTTTTTAATATACAAAAAGCGCAATTGCCTCTATAATTTAAAGTGACCAAACCCAAACTAAAGGAGACAAGt                           >  2:770635/1‑141 (MQ=255)                                                         aTGTAATACCAAAAAAAGAAGTTAAACAGGTTCTTCATCTTTTATGGTGGGAAGGTAAAACTTCCTGCTTTTTTTAATACACAAAAAGCGCAATTGCCTCTATAATTTAAAGTGACCAAACCCAAACTAAAGGAGACAAGt                           >  1:868138/1‑141 (MQ=255)                                                          tGTAATACCAAAAAAAGAAGTTAAACAGGTTCTTCATCTTTTATGGTGGGAAGGTAAAACTTCCTGCTTTTTTTAATACACAAAAAGCGCAATTGCCTCTATAATTTAAAGTGACCAAACCCAAACTAAAGGAGACAAGTg                          >  2:680777/1‑141 (MQ=255)                                                          tGTAATACCAAAAAAAGAAGTTAAACAGGTTCTTCATCTTTTATGGTGGGAAGGTAAAACTTCCTGCTTTTTTTAATACACAAAAAGCGCAATTGCCTCTATAATTTAAAGTGACCAAACCCAAACTAAAGGAGACAAGTg                          >  1:1009169/1‑141 (MQ=255)                                                            tAATACCAAAAAAAGAAGTTAAACAGGTTCTTCATCTTTTATGGTGGGAAGGTAAAACTTCCTGCTTTTTTTTTTTCACTAAAAGCGCAATTGCCTCTATAATTTAAAGTGACCAAACTCAAAATAAAGGAGACAAGTgct                        >  2:994702/1‑140 (MQ=17)                                                              aTACCAAAAAAAGAAGTTAAACAGGTTCTTCATCTTTTATGGTGGGAAGGTAAAACTTCCTGCTTTTTTTAATACACAAAAAGCGCAATTGCCTCTATAATTTAAAGTGACCAAACCCAAACTAAAGGAGACAAGTGCGcc                      <  1:805851/141‑1 (MQ=255)                                                              aTACCAAAAAAAGAAGTTAAACAGGTTCTTCATCTTTTATGGTGGGAAGGTAAAACTTCCTGCTTTTTTTAATACACAAAAAGCGCAATTGCCTCTATAATTTAAAGTGACCAAACCCAAACTAAAGGAGACAAGTGCGcc                      <  2:794463/141‑1 (MQ=255)                                                                  cAAAAAAAGAAGTTAAACAGGTTCTTCATCTTTTATGGTGGGAAGGTAAAACTTCCTGCTTTTTTTAATACACAAAAAGCGCAATTGCCTCTATAATTTAAAGTGACCAAACCCAAACTAAAGGAGACAAGTGCGCCTAtg                  >  1:967466/1‑141 (MQ=255)                                                                      aaaaGAAGTTAAACAGGTTCTTCATCTTTTATGGTGGGAAGGTAAAACTTCCTGCTTTTTTTAATACACAAAAAGCGCAATTGCCTCTATAATTTAAAGTGACCAAACCCAAACTAAAGGAGACAAGTGCGCCTATGTGTa              >  2:41768/1‑141 (MQ=40)                                                                         agaagTTAAACAGGTTCTTCATCTTTTATGGTGGGAAGGTAAAACTTCCTGCTTTTTTTAATACACAAAAAGCGCAATTGCCTCTATAATTTAAAGTGACCAAACCCAAACTAAAGGAGACAAGTGCGCCTATGTGTAATg           >  2:961771/1‑141 (MQ=38)                                                                           aagTTAAACAGGTTCTTCATCTTTTATGGTGGGAAGGTAAAACTTCCTGCTTTTTTTAATACACAAAAAGCGCAATTGCCTCTATAATTTAAAGTGACCAAACCCAAACTAAAGGAGACAAGTGCGCCTATGTGTAATGAt         >  1:26227/1‑141 (MQ=35)                                                                            agTTAAACAGGTTCTTCATCTTTTATGGTGGGAAGGTAAAACTTCCTGCTTTTTTTAATACACAAAAAGCGCAATTGCCTCTATAATTTAAAGTGACCAAACCCAAACTAAAGGAGACAAGTGCGCCTATGTGTAATGATa        >  2:1082941/1‑141 (MQ=35)                                                                            agTTAAACAGGTTCTTCATCTTTTATGGTGGGAAGGTAAAACTTCCTGCTTTTTTTAATACACAAAAAGCGCAATTGCCTCTATAATTTAAAGTGACCAAACCCAAACTAAAGGAGACAAGTGCGCCTATGTGTAATGATa        >  2:713446/1‑141 (MQ=35)                                                                            agTTAAACAGGTTCTTCATCTTTTATGGTGGGAAGGTAAAACTTCCTGCTTTTTTTAATACACAAAAAGCGCAATTGCCTCTATAATTTAAAGTGACCAAACCCAAACTAAAGGAGACAAGTGCGCCTATGTGTAATGATa        >  2:283503/1‑141 (MQ=35)                                                                               tAAACAGGTTCTTCATCTTTTATGGTGGGAAGGTAAAACTTCCTGCTTTTTTTAATACACAAAAAGCGCAATTGCCTCTATAATTTAAAGTGACCAAACCCAAACTAAAGGAGACAAGTGCGCCTATGTGTAATGATACCt     >  2:938855/1‑141 (MQ=32)                                                                                  aCAGGTTCTTCATCTTTTATGGTGGGAAGGTAAAACTTCCTGCTTTTTTTAATACACAAAAAGCGCAATTGCCTCTATAATTTAAAGTGACCAAACCCAAACTAAAGGAGACAAGTGCGCCTATGTGTAATGATACCttca  >  2:991451/1‑139 (MQ=14)                                                                                  aCAGGTTCTTCATCTTTTATGGTGGGAAGGTAAAACTTCCTGCTTTTTTTAATACACAAAAAGCGCAATTGCCTCTATAATTTAAAGTGACCAAACCCAAACTAAAGGAGACAAGTGCGCCTATGTGTAATGATACCTTAg  <  2:707869/141‑1 (MQ=31)                                                                                                                                            |                                                                                   TTATTAGAAAAGTTGAAACAAATATATAACCCCAGATAATATAATCATTATCATTAATGTAATACCAAAAAAAGAAGTTAAACAGGTTCTTCATCTTTTATGGTGGGAAGGTAAAACTTCCTGCTTTTTTTAATACACAAAAAGCGCAATTGCCTCTATAATTTAAAGTGACCAAACCCAAACTAAAGGAGACAAGTGCGCCTATGTGTAATGATACCTTAG  >  CP000730/1994183‑1994404

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 12 ≤ ATCG/ATCG < 27 ≤ 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.