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

CATGTTAAATGGAGTTTGAATTGCGATATTAATAATGAAGCAGCATTAAAGTTATATAAAAAAGTAGGCTTTATATCTGATGGACAGATTGAATTATACAAGCACATGTATCATCATTTAATTGTTAAATAAAAAAACTCGACAGTTCGATGTAAGTCGATTGCCGAGTAGTATCATTTTCTATTAAATGCCTGCAAATAATGCACTAATATAAATACCTAATGCATATAATAAACCGAAAAATGTATTTGTTTTACCAGCAGCAGCCATTGCTGGC  >  CP000730/1045692‑1045968                                                                                                                                             |                                                                                                                                         caTGTTAAATGGAGTTTGAATTGCGATATTAATAATGAAGCAGCATTAAAGTTATATAAAAAAGTAGGCTTTATATCTGATGGACAGATTGAATTATACAAGCACATGTATCATCATTTAATTGTTAAATAAAAAAACTCG                                                                                                                                          >  2:121389‑M1/1‑141 (MQ=255)         aTGGAGTTTGAATTGCGATATTAATAATGAAGCAGCATTAAAGTTATATAAAAAAGTAGGCTTTATATCTGATGGACAGATTGAATTATACAAGCACATGTATCATCATTTAATTGTTAAATAAAAAAACTCGACAGTTCg                                                                                                                                  <  1:174173/141‑1 (MQ=255)                 tGAATTGCGATATTAATAATGAAGCAGCATTAAAGTTATATAAAAAAGTAGGCTTTATATCTGATGGACAGATTGAATTATACAAGCACATGTATCATCATTTAATTGTTAAATAAAAAAACTCGACAGTTCGATGTAAGt                                                                                                                          <  1:78000/141‑1 (MQ=255)                             ttAATAATGAAGCAGCATTAAAGTTATATAAAAAAGTAGGCTTTATATCTGGGGGACATATTGAATTATACAAGCACATGTATGATCATTTAATTGTTAAATAAACAAACTCGgcaatcgacttacatcgaactgtcgtgt                                                                                                              <  2:57908‑M1/141‑29 (MQ=255)                               aataatGAAGCAGCATTAAAGTTATATAAAAAAGTAGGCTTTATATCTGATGGACAGATTGAATTATACAAGCACATGTATCATCATTTAATTGTTAAATAAAAAAACTCGACAGTTCGATGTAAGTCGATTGCCGagtag                                                                                                            <  1:106797/141‑1 (MQ=255)                               aataatGAAGCAGCATTAAAGTTATATAAAAAAGTAGGCTTTATATCTGATGGACAGATTGAATTATACAAGCACATGTATCATCATTTAATTGTTAAATAAAAAAACTCGACAGTTCGATGTAAGTCGATTGCCGagtag                                                                                                            <  1:121389/141‑1 (MQ=255)                                      aaGCAGCATTAAAGTTATATAAAAAAGTAGGCTTTATATCTGATGGACAGATTGAATTATACAAGCACATGTATCATCATTTAATTGTTAAATAAAAAAACTCGACAGTTCGATGTAAGTCGATTGCCGAGTAGTATCAtt                                                                                                     <  1:228652/141‑1 (MQ=255)                                          agcaTTAAAGTTATATAAAAAAGTAGGCTTTATATCTGATGGACAGATTGAATTATACAAGCACATGTATCATCATTTAATTGTTAAATAAAAAAACTCGACAGTTCGATGTAAGTCGATTGCCGAGTAGTATCATTTTCt                                                                                                 >  2:169611/1‑141 (MQ=255)                                          agcaTTAAAGTTATATAAAAAAGTAGGCTTTATATCTGATGGACAGATTGAATTATACAAGCACATGTATCATCATTTAATTGTTAAATAAAAAAACTCGACAGTTCGATGTAAGTCGATTGCCGAGTAGTATCATTTTCt                                                                                                 <  1:127659/141‑1 (MQ=255)                                             aTTAAAGTTATATAAAAAAGTAGGCTTTATATCTGATGGACAGATTGAATTATACAAGCACATGTATCATCATTTAATTGTTAAATAAAAAAACTCGACAGTTCGATGTAAGTCGATTGCCGAGTAGTATCATTTTCTAtt                                                                                              <  1:32000/141‑1 (MQ=255)                                                         taAAAAAGTAGGCTTTATATCTGATGGACAGATTGAATTATACAAGCACATGTATCATCATTTAATTGTTAAATAAAAAAACTCGgcaatcgacttacatcgaactgtc                                                                                                                  >  2:143704‑M1/1‑85 (MQ=255)                                                         taAAAAAGTAGGCTTTATATCTGATGGACAGATTGAATTATACAAGCACATGTATCATCATTTAATTGTTAAATAAAAAAACTCGgcaatcgacttacatcgaactgtc                                                                                                                  >  2:143678‑M1/1‑85 (MQ=255)                                                         taAAAAAGTAGGCTTTATATCTGATGGACAGATTGAATTATACAAGCACATGTATCATCATTTAATTGTTAAATAAAAAAACTCGgcaatcgacttacatcgaactgtc                                                                                                                  <  1:143678‑M1/109‑25 (MQ=255)                                                         taAAAAAGTAGGCTTTATATCTGATGGACAGATTGAATTATACAAGCACATGTATCATCATTTAATTGTTAAATAAAAAAACTCGgcaatcgacttacatcgaactgtc                                                                                                                  <  1:143704‑M1/109‑25 (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                                                    <  2:92363/141‑1 (MQ=255)                                                                                       gATTGAATTATACAAGCACATGTATCATCATTTAATTGTTAAATAAAAAAACTCGACAGTTCGATGTAAGTCGATTGCCGAGTAGTATCATTTTCTATTAAATGCCTGCAAATAATGCACTAATATAAATACCTAATGCat                                                    >  1:159233/1‑141 (MQ=255)                                                                                       gATTGAATTATACAAGCACATGTATCATCATTTAATTGTTAAATAAAAAAACTCGACAGTTCGATGTAAGTCGATTGCCGAGTAGTATCATTTTCTATTAAATGCCTGCAAATAATGCACTAATATAAATACCTAATGCat                                                    <  1:50236/141‑1 (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                              >  2:143704‑M2/1‑24 (MQ=255)                                                                                                                                             gACAGTTCGATGTAAGTCGATTGCcgagtttttttatttaacaattaaatgatgatacatgtgcttgtataattcaatctgtccatcagatataaagcctactttttta                              <  1:143704‑M2/109‑86 (MQ=255)                                                                                                                                             gACAGTTCGATGTAAGTCGATTGCcgagtttttttatttaacaattaaatgatgatacatgtgcttgtataattcaatctgtccatcagatataaagcctactttttta                              <  1:143678‑M2/109‑86 (MQ=255)                                                                                                                                             |                                                                                                                                         CATGTTAAATGGAGTTTGAATTGCGATATTAATAATGAAGCAGCATTAAAGTTATATAAAAAAGTAGGCTTTATATCTGATGGACAGATTGAATTATACAAGCACATGTATCATCATTTAATTGTTAAATAAAAAAACTCGACAGTTCGATGTAAGTCGATTGCCGAGTAGTATCATTTTCTATTAAATGCCTGCAAATAATGCACTAATATAAATACCTAATGCATATAATAAACCGAAAAATGTATTTGTTTTACCAGCAGCAGCCATTGCTGGC  >  CP000730/1045692‑1045968

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