New junction evidence
		seq id	position	reads (cov)	reads (cov)	score	skew	freq	annotation	gene	product
*	?	CP000730	= 1045832	29 (1.050)	5 (0.190)	3/248	NT	15.2%	intergenic (+9/+43)	USA300HOU_0988/menA	hypothetical protein/1,4‑dihydroxy‑2‑naphthoate octaprenyltransferase
	?	CP000730	= 1045855	28 (1.060)					intergenic (+32/+20)	USA300HOU_0988/menA	hypothetical protein/1,4‑dihydroxy‑2‑naphthoate octaprenyltransferase

AATAATGAAGCAGCATTAAAGTTATATAAAAAAGTAGGCTTTATATCTGATGGACAGATTGAATTATACAAGCACATGTATCATCATTTAATTGTTAAATAAAAAAACTCGACAGTTCGATGTAAGTCGATTGCCGAGTAGTATCATTTTCTATTAAATGCCTGCAAATAATGCACTAATATAAATACCTAATGCATATAATAAACCGAAAAATGTATTTGTTTTACCAGCAGCAGCCATTGCTGGCATCATTGTAGGCGGTGTATCATTCTTC  >  CP000730/1045722‑1045995                                                                                                                                      |                                                                                                                                             aataatGAAGCAGCATTAAAGTTATATAAAAAAGTAGGCTTTATATCTGATGGACAGATTGAATTATACAAGCACATGTATCATCATTTAATTGTTAAATAAAAAAACTCGACAGTTCGATGTAAGTCGATTGCCGagtag                                                                                                                                       <  1:106797/141‑1 (MQ=255) aataatGAAGCAGCATTAAAGTTATATAAAAAAGTAGGCTTTATATCTGATGGACAGATTGAATTATACAAGCACATGTATCATCATTTAATTGTTAAATAAAAAAACTCGACAGTTCGATGTAAGTCGATTGCCGagtag                                                                                                                                       <  1:121389/141‑1 (MQ=255)        aaGCAGCATTAAAGTTATATAAAAAAGTAGGCTTTATATCTGATGGACAGATTGAATTATACAAGCACATGTATCATCATTTAATTGTTAAATAAAAAAACTCGACAGTTCGATGTAAGTCGATTGCCGAGTAGTATCAtt                                                                                                                                <  1:228652/141‑1 (MQ=255)            agcaTTAAAGTTATATAAAAAAGTAGGCTTTATATCTGATGGACAGATTGAATTATACAAGCACATGTATCATCATTTAATTGTTAAATAAAAAAACTCGACAGTTCGATGTAAGTCGATTGCCGAGTAGTATCATTTTCt                                                                                                                            <  1:127659/141‑1 (MQ=255)            agcaTTAAAGTTATATAAAAAAGTAGGCTTTATATCTGATGGACAGATTGAATTATACAAGCACATGTATCATCATTTAATTGTTAAATAAAAAAACTCGACAGTTCGATGTAAGTCGATTGCCGAGTAGTATCATTTTCt                                                                                                                            >  2:169611/1‑141 (MQ=255)               aTTAAAGTTATATAAAAAAGTAGGCTTTATATCTGATGGACAGATTGAATTATACAAGCACATGTATCATCATTTAATTGTTAAATAAAAAAACTCGACAGTTCGATGTAAGTCGATTGCCGAGTAGTATCATTTTCTAtt                                                                                                                         <  1:32000/141‑1 (MQ=255)                           taAAAAAGTAGGCTTTATATCTGATGGACAGATTGAATTATACAAGCACATGTATCATCATTTAATTGAAAAAAAAAAAAACTCGACAGTTCGATGTAAGTCGATTGCCGAGTAGTATCATTTTCTATTAAATGCCTGCaa                                                                                                             <  2:257711/141‑1 (MQ=255)                            aaaaaaGTAGGCTTTATATCTGATGGACAGATTGAATTATACAAGCACATGTATCATCATTTAATTGTTAAATAAAAAAACTCGACAGTTCGATGTAAGTCGATTGCCGAGTAGTATCATTTTCTATTAAATGCCTGCaaa                                                                                                            <  2:252598/141‑1 (MQ=255)                                 aGTAGGCTTTATATCTGATGGACAGATTGAATTATACAAGCACATGTATCATCATTTAATTGTTAAATAAAAAAACTCGACAGTTCGATGTAAGTCGATTGCCGAGTAGTATCATTTTCTATTAAATGCCTGCAAATAATg                                                                                                       >  1:180086/1‑141 (MQ=255)                                     ggCTTTATATCTGATGGACAGATTGAATTATACAAGCACATGTATCATCATTTAATTGTTAAATAAAAAAACTCGACAGTTCAATGTAAGTCGATTGCCGAGTAGTATCATTTTCTATTAAATGCCTGCAAATAATGCACt                                                                                                   >  2:266235/1‑141 (MQ=255)                                     ggCTTTATATCTGATGGACAGATTGAATTATACAAGCACATGTATCATCATTTAATTGTTAAATAAAAAAACTCGACAGTTCAATGTAAGTCGATTGCCGAGTAGTATCATTTTCTATTAAATGCCTGCAAATAATGCACt                                                                                                   >  2:266250/1‑141 (MQ=255)                                           atatCTGATGGACAGATTGAATTATACAAGCACATGTATCATCATTTAATTGTTAAATAAAAAAACTCGACAGTTCGATGTAAGTCGATTGCCGAGTAGTATCATTTTCTATTAAATGCCTGCAAATAATGCACTAAtata                                                                                             <  2:262999/141‑1 (MQ=255)                                                 gctGGACAGATTGAATTATACAATGAAATTTATCCTCCTTTAATTTTTAAATAAATAACCTCTACAGTTCGATGTAAGTCGATTGCCGAGTAGTATCATGTTCTATTAACTGCCTGCAAATAATTCACTAATATAAATAcc                                                                                       <  1:130450/139‑1 (MQ=255)                                                 gATGGACAGATTGAATTATACAAGCACATGTATCATCATTTAATTGTTAAATAAAAAAACTCGACAGTTCGATGTAAGTCGATTGCCGAGTAGTATCATTTTCTATTAAATGCCTGCAAATAATGCACTAATATAAATAcc                                                                                       >  2:62273/1‑141 (MQ=255)                                                 gATGGACAGATTGAATTATACAAGCACATGTATCATCATTTAATTGTTAAATAAAAAAACTCGACAGTTCGATGTAAGTCGATTGCCGAGTAGTATCATTTTCTATTAAATGCCTGCAAATAATGCACTAATATAAATAcc                                                                                       >  1:15239/1‑141 (MQ=255)                                                         gATTGAATTATACAAGCACATGTATCATCATTTAATTGTTAAATAAAAAAACTCGACAGTTCGATGTAAGTCGATTGCCGAGTAGTATCATTTTCTATTAAATGCCTGCAAATAATGCACTAATATAAATACCTAATGCat                                                                               <  1:50236/141‑1 (MQ=255)                                                         gATTGAATTATACAAGCACATGTATCATCATTTAATTGTTAAATAAAAAAACTCGACAGTTCGATGTAAGTCGATTGCCGAGTAGTATCATTTTCTATTAAATGCCTGCAAATAATGCACTAATATAAATACCTAATGCat                                                                               <  2:92363/141‑1 (MQ=255)                                                         gATTGAATTATACAAGCACATGTATCATCATTTAATTGTTAAATAAAAAAACTCGACAGTTCGATGTAAGTCGATTGCCGAGTAGTATCATTTTCTATTAAATGCCTGCAAATAATGCACTAATATAAATACCTAATGCat                                                                               >  1:159233/1‑141 (MQ=255)                                                               aTTATACAAGCACATGTATCATCATTTAATTGTTAAATAAAAAAACTCGACAGTTCGATGTAAGTCGATTGCCGAGTAGTATCATTTTCTATTAAATGCCTGCAAATAATGCACTAATATAAATACCTAATGCATataata                                                                         >  2:22522/1‑141 (MQ=255)                                                                     cAAGCACATGTATCATCATTTAATTGTTAAATAAAAAAACTCGACAGTTCGATGTAAGTCGATTGCCGAGTAGTATCATTTTCTATTAAATGCCTGCAAATAATGCACTAATATAAATACCTAATGCATATAATAAACCGa                                                                   >  2:176517/1‑141 (MQ=255)                                                                      aaGCACATGTATCATCATTTAATTGTTAAATAAAAAAACTCGACAGTTCGATGTAAGTCGATTGCCGAGTAGTATCATTTTCTATTAAATGCCTGCAAATAATGCACTAATATAAATACCTAATGCATATAATAAACCGaa                                                                  >  1:222290/1‑141 (MQ=255)                                                                        gCACATGTATCATCATTTAATTGTTAAATAAAAAAACTCGACAGTTCGATGTAAGTCGATTGCCGAGTAGTATCATTTTCTATTAAATGCCTGCAAATAATGCACTAATATAAATACCTAATGCATATAATAAACCGaaaa                                                                >  2:276381/1‑141 (MQ=255)                                                                          acaTGTATCATCATTTAATTGTTAAATAAAAAAACTCGACAGTTCGATGTAAGTCGATTGCCGAGTAGTATCATTTTCTATTAAATGCCTGCAAATAATGCACTAATATAAATACCTAATGCATATAATAAACCGAAAAAt                                                              <  1:189696/141‑1 (MQ=255)                                                                               tATCATCATTTAATTGTTAAATAAAAAAACTCGACAGTTCGATGTAAGTCGATTGCCGAGTAGTATCATTTTCTATTAAATGCCTGCAAATAATGCACTAATATAAATACCTAATGCATATAATAAACCGAAAAATGTAtt                                                         >  2:126150/1‑141 (MQ=255)                                                                                 tcatcaTTTAATTGTTAAATAAAAAAACTCGACAGTTCGATGTAAGTCGATTGCCGAGTAGTATCATTTTCTATTAAATGCCTGCAAATAATGCACTAATATAAATACCTAATGCATATAATAAACCGAAAAATGTATTTg                                                       <  1:87795/141‑1 (MQ=255)                                                                                                     aaaaaaaCTCGACAGTTCGATGTAAGTCGATTGCCGAGTAGTATCATTTTCTATTAAATGCCTGCAAATAATGCACTAATATAAATACCTAATGCATATAATAAACCGAAAAATGTATTTGTTTTACCAGCAGCAGCCAtt                                   >  2:234631/1‑141 (MQ=255)                                                                                                      aaaaaaCTCGACAGTTCGATGTAAGTCGATTGCCGAGTAGTATCATTTTCTATTAAATGCCTGCAAATAATGCACTAATATAAATACCTAATGCATATAATAAACCGAAAAATGTATTTGTTTTACCAGCAGCAGCCATTg                                  <  1:207940/141‑1 (MQ=255)                                                                                                           acacGACAGTTCGATGTAAGTCGATTGCcgagtttgtttatttaacaattaaatgatcatacatgtgcttgtataattcaatatgtcccccagatataaagcctacttttttatataactttaatgctgcttcattattaa                             <  2:57908‑M2/141‑114 (MQ=255)                                                                                                               gACAGTTCGATGTAAGTCGATTGCcgagtttttttatttaacaattaaatgatgatacatgtgcttgtataattcaatctgtccatcagatataaagcctactttttta                                                         >  2:143678‑M2/1‑24 (MQ=255)                                                                                                               gACAGTTCGATGTAAGTCGATTGCcgagtttttttatttaacaattaaatgatgatacatgtgcttgtataattcaatctgtccatcagatataaagcctactttttta                                                         <  1:143704‑M2/109‑86 (MQ=255)                                                                                                               gACAGTTCGATGTAAGTCGATTGCcgagtttttttatttaacaattaaatgatgatacatgtgcttgtataattcaatctgtccatcagatataaagcctactttttta                                                         <  1:143678‑M2/109‑86 (MQ=255)                                                                                                               gACAGTTCGATGTAAGTCGATTGCcgagtttttttatttaacaattaaatgatgatacatgtgcttgtataattcaatctgtccatcagatataaagcctactttttta                                                         >  2:143704‑M2/1‑24 (MQ=255)                                                                                                                   gTTCGATGCAAGTCGATTGCCGAGTAGTATCATTTTCTATTAAATGCCTGCAAATAATGCACTAATATAAATACCTAATGCATAAAAAAAAAAAAAAAATGTATTTGTTTTACCAGCAGCAGCCATTGCTGGCATCATTGt                     <  2:178246/141‑1 (MQ=255)                                                                                                                       gATGTAAGTCGATTGCCGAGTAGTATCATTTTCTATTAAATGCCTGCAAATAATGCACTAATATAAATACCTAATGCATATAATAAACCGAAAAATGTATTTGTTTTACCAGCAGCAGCCATTGCTGGCATCATTGTAGGc                 <  2:288318/141‑1 (MQ=255)                                                                                                                                cGATTGCCGAGTAGTATCATGTTCTATTAAATGCCCACAAATAATGCACTAATATTAACACCTAATGCATACATTTAACCTAAAAATGTACTAGATTTACCACCAGCAGTCATTTATGACATCATTCTATTCTGTGTATCa        >  2:107919/1‑141 (MQ=255)                                                                                                                                      ccGAGTAGTATCATTTTCTATTAAATGCCTGCAAATAATGCACTAATATAAATACCTAATGCATATAATAAACCGAAAAATGTATTTGTTTTACCAGCAGCAGCCATTGCTGGCATCATTGTAGGCGGTGTATCAttcttc  >  1:132260/1‑141 (MQ=255)                                                                                                                                      |                                                                                                                                             AATAATGAAGCAGCATTAAAGTTATATAAAAAAGTAGGCTTTATATCTGATGGACAGATTGAATTATACAAGCACATGTATCATCATTTAATTGTTAAATAAAAAAACTCGACAGTTCGATGTAAGTCGATTGCCGAGTAGTATCATTTTCTATTAAATGCCTGCAAATAATGCACTAATATAAATACCTAATGCATATAATAAACCGAAAAATGTATTTGTTTTACCAGCAGCAGCCATTGCTGGCATCATTGTAGGCGGTGTATCATTCTTC  >  CP000730/1045722‑1045995

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