New junction evidence
		seq id	position	reads (cov)	reads (cov)	score	skew	freq	annotation	gene	product
*	?	USA300TCH1516_ALE	458102 =	NA (NA)	3 (0.030)	3/280	2.5	NA	coding (712/1557 nt)	hsdM_1	Type I restriction enzyme EcoKI M protein
	?	USA300TCH1516_ALE	458161 =	NA (NA)					coding (771/1557 nt)	hsdM_1	Type I restriction enzyme EcoKI M protein

AAAGGCTGGGTTTTCCAATGTGTCATCATTACGGATATCGAAGTTCTCATAACGCACATCATGTAATAACATATTCATGCGTGCTAAGTTGTATGTAGTATTGTTACGTTCTTGACCGAAATAACGATACACTTGTGTTTCTTTACCAACACGTAACAA‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑  <  USA300TCH1516_ALE/458260‑458102 ‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑acgtaacaaTACTACATACAACTTAGCACGCATGAATATGTTATTACATGATGTGCGTTATGAGAACTTCGATATCCGTAATGATGACACATTGGAAAACCCAGCCTTTTTAGGCAATACATTTGATGCGGTTATTGCGAACCCACCGTATAGTGCGAA  >  USA300TCH1516_ALE/458161‑458310                                                                                                                                                                                                                                                                                                                       AAAGGCTGGGTTTTCCAATGTGTCATCATTACGGATATCGAAGTTCTCATAACGCACATCATGTAATAACATATTCATGCGTGCTAAGTTGTATGTAGTATTGTTACGTTCTTGACCGAAATAACGATACACTTGTGTTTCTTTACCAACA                                                                                                                                                                <  2:11555/151‑1 AAAGGCTGGGTTTTCCAATGTGTCATCATTACGGATATCGAAGTTCTCATAACGCACATCATGTAATAACATATTCATGCGTGCTAAGTTGTATGTAGTATTGTTACGTTCTTGACCGAAATAACGATACACTTGTGTTTCTTTACCAACA                                                                                                                                                                <  4:336361/151‑1  AAGGCTGGGTTTTCCAATGTGTCATCATTACGGATATCGAAGTTCTCATAACGCACATCATGTAATAACATATTCATGCGTGCTAAGTTGTATGTAGTATTGTTACGTTCTTGACCGAAATAACGATACACTTGTGTTTCTTTACCAACAC                                                                                                                                                               <  3:63279/151‑1  AAGGCTGGGTTTTCCAATGTGTCATCATTACGGATATCGAAGTTCTCATAACGCACATCATGTAATAACATATTCATGCGTGCTAAGTTGTATGTAGTATTGTTACGTTCTTGACCGAAATAACGATACACTTGTGTTTCTTTACCAACAC                                                                                                                                                               <  2:1039073/151‑1   AGGCTGGGTTTTCCAATGTGTTATCATTACGGTTATCCAAGTTCTCATAACGCACATCATGTAATAACATATTTATGCGTGCTAAGTTGTATGTAATATTGTTTCGTTCTTGACCGTAATAACGTTACACTTCTGTTTCTTTAGCAACACG                                                                                                                                                              <  4:60416/151‑1   AGGCTGGGTTTTCCAATGTGTCATCATTACGGATATCGAAGTTCTCATAACGCACATCATGTAATAACATATTCATGCGTGCTAAGTTGTATGTAGTATTGTTACGTTCTTGACCGAAATAACGATACACTTGTGTTTCTTTACCAACACG                                                                                                                                                              <  2:382650/151‑1    GGCTGGGTTTTCCAATGTGTCATCATTACGGATATCGAAGTTCTCATAACGCACATCATGTAATAACATATTCATGCGTGCTAAGTTGTATGTAGTATTGTTACGTTCTTGACCGAAATAACGATACACTTGTGTTTCTTTACCAACACGT                                                                                                                                                             <  2:60778/151‑1    GGCTGGGTTTTCCAATGTGTCATCATTACGGATATCGAAGTTCTCATAACGCACATCATGTAATAACATATTCATGCGTGCTAAGTTGTATGTAGTATTGTTACGTTCTTGACCGAAATAACGATACACTTGTGTTTCTTTACCAACACGT                                                                                                                                                             >  2:802023/1‑151     GCTGGGTTTTCCAATGTGTCATCATTNCGGATATCGAAGNTCTCATAACGCACATCATGTAATAACATATTCATGCGTGCTAAGTTGTATGTAGTATTGTTACGTTCTTGACCGAAATAACGATACACTTGTGTTTCTTTACCAACACGTA                                                                                                                                                            >  1:685918/1‑151     GCTGGGTTTTCCAATGTGTCATCATTACGGATATCGAAGTTCTCATAACGCACATCATGTAATAACATATTCATGCGTGCTAAGTTGTATGTAGTATTGTTACGTTCTTGACCGAAATAACGATACACTTGTGTTTCTTTACCAACACGTA                                                                                                                                                            <  1:931234/151‑1     GCTGGGTTTTCCAATGTGTCATCATTACGGATATCGAAGTTCTCATAACGCACATCATGTAATAACATATTCATGCGTGCTAAGTTGTATGTAGTATTGTTACGTTCTTGACCGAAATAACGATACACTTGTGTTTCTTTACCAACACGTA                                                                                                                                                            <  4:331629/151‑1     GCTGGGTTTTCCAATGTGTCATCATTACGGATATCGAAGTTCTCATAACGCACATCATGTAATAACATATTCATGCGTGCTAAGTTGTATGTAGTATTGTTACGTTCTTGACCGAAATAACGATACACTTGTGTTTCTTTACCAACACGTA                                                                                                                                                            >  1:719137/1‑151     GCTGGGTTTTCCAATGTGTCATCATTACGGATATCGAAGTTCTCATAACGCACATCATGTAATAACATATTCATGCGTGCTAAGTTGTATGTAGTATTGTTACGTTCTTGACCGAAATAACGATACACTTGTGTTTCTTTACCAACACGTA                                                                                                                                                            <  4:379397/151‑1     GCTGGGTTTTCCAATGTGTCATCATTACGGATATCGAAGTTCTCATAACGCACATCATGTAATAACATATTCATGCGTGCTAAGTTGTATGTAGTATTGTTACGTTCTTGACCGAAATAACGATACACTTGTGTTTCTTTACCAACACGTA                                                                                                                                                            >  4:9886/1‑151     GCTGGGTTTTCCAATGTGTCATCATTACGGATATCGAAGTTCTCATAACGCACATCATGTAATAACATATTCATGCGTGCTAAGTTGTATGTAGTATTGTTACGTTCTTGACCGAAATAACGATACACTTGGGTTTCTTTACCAACACGTA                                                                                                                                                            <  1:933571/151‑1     GCTGGGTTTTCCAATGTGTCATCATTACGGATATAGAAGTGCTCATAACGCTCATCATGTAATAACATATTCATGCGTGCTAAGTTGTATGTAGTATTGTTACGTTCTTGACCGAAATAACGATACACTTGTGTTTCTTTACCAACACGTA                                                                                                                                                            <  4:375046/151‑1      CTGGGTTTTCCAATGTGTCATCATTACGGATATCGAAGTTCTCATAACGCACATCATGTAATAACATATTCATGCGTGCTAAGTTGTATGTAGTATTGTTACGTTCTTGACCGAAATAACGATACACTTGTGTTTCTTTACCAACACGTAA                                                                                                                                                           >  1:501500/1‑151      CTGGGTTTTCCAATGTGTCATCATTACGGATATCGAAGTTCTCATAACGCACATCATGTAATAACATATTCATGCGTGCTAAGTTGTATGTAGTATTGTTACGTTCTTGACCGAAATAACGATACACTTGTGTTTCTTTACCAACACGTAA                                                                                                                                                           >  1:335892/1‑151       TGGGTTTTCCAATGTGTCATCATTACGGATATCGAAGTTCTCATAACGCGCATCATGTAATAACATATTCATGCGTGCTAAGTTGTATGTAGTATTGTTACGTTCTTGACCGAAATAACGATACACTTGTGTTGCTTTACCAACACGTAAC                                                                                                                                                          <  4:249894/151‑1       TGGGTTTTCCAATGTGTCATCATTACGGATATCGAAGTTCTCATAACGCACATCATGTAATAACCTATTCATGCGTGCTAAGTTGTATGTAGTATTGTTACGTTCTTGACCGAAATAACGATACACTTGTGTTTCTTTACCAACACGTAAC                                                                                                                                                          <  4:437134/151‑1       TGGGTTTTCCAATGTGTCATCATTACGGATATCGAAGTTCTCATAACGCACATCATGTAATAACATATTCATGCGTGCTAAGTTGTATGTAGTATTGTTACGTTCTTGACCGAAATAACGATACACTTGTGTTTCTTTACCAACACGTAAC                                                                                                                                                          <  2:54506/151‑1       TGGGTTTTCCAATGTGTCATCATTACGGATATCGAAGTTCTCATAACGCACATCATGTAATAACATATTCATGCGTGCTAAGTTGTATGTAGTATTGTTACGTTCTTGACCGAAATAACGATACACTTGTGTTTCTTTACCAACACGTAAC                                                                                                                                                          <  1:187061/151‑1       TGGGTTTTCCAATGTGTCATCATTACGGATATCGAAGTTCTCATAACGCACATCATGTAATAACATATTCATGCGTGCTAAGTTGTATGTAGTATTGTTACGTTCTTGACCGAAATAACGATACACTTGTGTTTCTTTACCAACACGTAAC                                                                                                                                                          <  1:578196/151‑1        GGGTTTTCCAATGTGTCATCATTACGGATATCGAAGTTCTCATAACGCACATCATGTAATAACATATTCATGCGTGATAAGTTGTATGTAGTATTGTTACGTTCTTGACCGAAATAACGATACACTTGTGTTTCTTTACCAACACGTAACA                                                                                                                                                         >  2:118484/1‑151        GGGTTTTCCAATGTGTCATCATTACGGATATCGAAGTTATCATAACGCACATCATGTAATAACATATTCATGCGTGCTAAGTTGTATGTAGTATTGTTACGTTCTTGACCGAAATAACGATACACTTGTGTTTCTTTACCAACACGTAACA                                                                                                                                                         >  3:355216/1‑151                                                                                        GTTGTATGTAGTATTGTTACGTTCTTGACCGAAATAACGATACACTTGTGTTTCTTTACCAACACGTAACAATACTACATACAACTTAGCACGCATGAATATGTTATTACATGATGTGCGTTATGAGAACTTCGATATCCGTAATGATGAC                                                                         >  1:1004864/1‑151                                                                                         TTGTATGTAGTATTGTTACGTTCTTGACCGAAATAACGATACACTTGTGTTTCTTTACCAACACGTAACAATACTACATACAACTTAGCACGCATGAATATGTTATTACATGATGTACGTTCTGAGAACTTCGCTATCCGTAATGATGACA                                                                        >  4:380332/1‑151                                                                                                                  GACCGAAATAACGATACACTTGTGTTTCTTTACCAACACGTAACAATACTACATACAACTTAGCACGCATGAATATGTTATTACATGATGTGCGTTATGAGAACTTCGATATCCGTAATGATGACACA‑TGGAAAACCCAGCCTTTTTAGGC                                              <  2:1004864/151‑1                                                                                                                                                    ataaccTAACAAGACCACATACAACTTAGCACGCATGAATATGTTATTACATGATGTGCGTTATGAGAACTTCGATATCCGTAATGATGACACATTGGAAAACCCAGCCTTTTTAGGCAATACTTTTTTTGCGATTATTGCGAACCCACCG             <  2:874538/145‑1                                                                                                                                                     aaaccTAACAATACTACTTACAGCTTAGCTCGCATGAATCTGTTATTACATCCTGTGCGTTATGAGAACTTCGATATCCGTAATGATGTCACATTGGAAAACCCAGCCTTTTTAGGCAATACATTTTATTCGGTTATTGCGAACCCACCGT            <  4:323273/146‑1                                                                                                                                                       ACGTAACAATACTACATACAACTTAGCACGCATGAATATGTTATTACATGATGTGCGTTATGAGAACTTCGATATCCGTAATGATGACACATTGGAAAACCCAGCCTTTTTAGGCAATACATTTGATGCGGTTATTGCGAACCCACCGTAT          >  2:408311/1‑151                                                                                                                                                       ACGTAACAATACTACATACAACTTAGCACGCATGAATATGTTATTACATGATGTGCGTTATGAGAACTTCGATATCCGTAATGATGACACATTGGAAAACCCAGCCTTTTTAGGCAATACATTTGATGCGGTTATTGCGAACCCACCGTAT          >  4:402715/1‑151                                                                                                                                                       ACGTAACAATACTACATACAACTTAGCACGCATGAATATGTTATTACATGATGTGCGTTATGAGAACTTCGATATCCGTAATGATGACACATTGGAAAACCCAGCCTATTTAGGCAATACATTTGATGCGGTTATTGCGAACCCACCGTAT          >  2:349499/1‑151                                                                                                                                                        CGTAACAATACTACATACAACTTAGCACGCATGAATATGTTATTACATGATGTGCGTTATGAGAACTTCGATATCCGTAATGATGACACATTGGAAAACCCAGCCTTTTTAGGCAATACATTTGATGCGGTTATTGCGCACCCACCGTATA         <  4:244213/151‑1                                                                                                                                                         tTAACAATACTACATACAACATAGCACGCATGAATATGTTATTACATGATGTGCGTTATGAGAACTTCGATATCCGTAATGATGACACATTGGAAAACCCAGCCTTTTTAGGCAATACATTTGATGCGGTTATTGCGAACCCACCGTATAG        >  4:68492/2‑151                                                                                                                                                         GTAACAATACTACATACAACTTAGCACGCATGAATATGTTATTACATGATGTGCGTTATGAGAACTTCGATATCCGTAATGATGACACATTGGAAAACCCAGCCTTTTTAGGCAATACATTTGCTGCGGTTATTGCGAACCCACCGTATAG        >  1:1049028/1‑151                                                                                                                                                         GTAACAATACTACATACAACTTAGCACGCATGAATATGTTATTACATGATGTGCGTTATGAGAACTTCGATATCCGTAATGATGACACATTGGAAAACCCAGCCTTTTTAGGCAATACATTTGATGCGGTTATTGCGAACCCACCGTATAG        >  2:544979/1‑151                                                                                                                                                         GTAACAATACTACATACAACTTAGCACGCATGAATATGTTATTACATGATGTGCGTTATGAGAACTTCGATATCCGTAATGATGACACATTGGAAAACCCAGCCTTTTTAGGCAATACATTTGATGCGGTTATTGCGAACCCACCGTATAG        <  2:212394/151‑1                                                                                                                                                          TAACAATACTACATACAACTTAGCACGCCTGAATATGTTATTACATGATGTGCGTTATGAGAACGTCGATATCCGTAATGATGACACATTGGAACGCCCAGCCTTTTTAGGCAATACATTTGATGCGGTTATTGCGATCCCACCGTATAGn       <  2:404545/151‑2                                                                                                                                                          TAACAATACTACATACAACTTAGCACGCATGAATATGTTATTACATGATGTGCGTTATGAGAACTTCGATATCCGTAATGATGACACATTGGAAAACCCAGCCTTTTTAGGCAATACATTTGATGCGGTTATTGCGAACCCACCGTATAGT       >  2:592979/1‑151                                                                                                                                                          TAACAATACTACATACAACTTAGCACGCATGAATATGTTATTACATGATGTGCGTTATGAGAACTTCGATATCCGTAATGATGACACATTGGAAAACCCAGCCTTTTTAGGCAATACATTTGATGCGGTTATTGCGAACCCACCGTATAGT       >  2:82953/1‑151                                                                                                                                                          TAACAATACTACATACAACTTAGCACGCATGAATATGTTATTACATGATGTGCGTTATGAGAACTTCGATATCCGTAATGATGACACATTGGAAAACCCAGCCTTTTTAGGCAATACATTTGATGCGGTTATTGCGAACCCACCGTATAGT       >  3:158380/1‑151                                                                                                                                                           AACAATACTACATTCATCATCCCACACATGACGATATTACTGCATTATGGTCTTTATGAGAACTTCGATATCCGTAATGATGACACATTGGAAAACCCAGCCTTTTTAGGCAATACATTTGATGCGGTTATTGCGAACCCACCGTATAGTG      <  1:573894/151‑1                                                                                                                                                           AACAATACTACATACAACTTAGCACGCATGAATATGTTATTACATGATGTGCGTTATGAGAACTTCGATATCCGTAATGATGACACATTGGAAAACCCAGCCTTTTTAGGCAATACATTTGATGCGGTTATTGCGAACCCACCGTATAGTG      <  2:469426/151‑1                                                                                                                                                           AACAATACTACATACAACTTAGCACGCATGAATATGTTATTACATGATGTGCGTTATGAGAACTTCGATATCCGTAATGATGACACATTGGAAAACCCAGCCTTTTTAGGCAATACATTTGATGCGGTTATTGCGAACCCACCGTATAGTG      <  4:446557/151‑1                                                                                                                                                            ACAATACTACATACAACTTAGCACGCGTGAATATGTTATTACATGATGTGCGTTATGAGAACTTCGATATCCGTAATGATGACACATTGGAAAACCCAGCCTTTTTAGGCAATACATTTGATGCGGTTATTGCGAACCCACCGTATAGTGC     <  1:977128/151‑1                                                                                                                                                            ACAATACTACATACAACTTAGCACGCATGAATATGTTATTACATGATGTGCGTTATGAGAACTTCGATATCCGTAATGATGACACATTGGAAAACCCAGCCTTTTTAGGCAATACATTTGATGCGGTTATTGCGAACCCACCGTATAGTGC     >  2:1057060/1‑151                                                                                                                                                             CAATACTACATACAACTTAGCACGCATGAATATGTTATTACATGATGTGCGTTATGAGACCTTCGATATCCGTAATGATGACACATTGGAAAACCCAGCCTTTTTAGGCAATACATTTGATGCGGTTATTGCGAACCCACCGTATAGTGCG    >  2:426088/1‑151                                                                                                                                                             CAATACTACATACAACTTAGCACGCATGAATATGTTATTACATGATGTGCGTTATGAGAACTTCGATATCCGTAATGATGACACATTGGAAAACCCAGCCTTTTTAGGCAATACATTTGATGCGGTTATTGCGAACCCACCGTATAGTGag    >  2:839402/1‑149                                                                                                                                                             CAATACTACATACAACTTAGCACGCATGAATATGTTATTACATGATGTGCGTTATGAGAACTTCGATATCCGTAATGATGACACATTGGAAAACCCAGCCTTTTTAGGCAATACATTTGATGCGGTTATTGCGAACCCACCGTATAGTGCG    >  3:327550/1‑151                                                                                                                                                             CAATACTACATACAACTTAGCACGCATGAATATGTTATTACATGATGTGCGTTATGAGAACTTCGATATCCGTAATGATGACACATTGGAAAACCCAGCCTTTTTAGGCAATACATTTGATGCGGTTATTGCGAACCCACCGTATAGTGCG    >  1:280336/1‑151                                                                                                                                                             CAATACTACATACAACTTAGCACGCATGAATATGTTATTACATGATGTGCGTTATGAGAACTTCGATATCCGTAATGATGACACATTGGAAAACCCAGCCTTTTTAGGCAATACATTTGATGCGGTTATTGCGAACCCACCGTATAGTGCG    >  2:996473/1‑151                                                                                                                                                               ATACTACATACAACTTAGCACGCATGAATATGTTATTACATGATGTGCGTTATGAGAACTTCGATATCCGTAATGATGACACATTGGAAAACCCAGCCTTTTTAGGCAATACATTTGATGCGGTTATTGCGAACCCACCGTATAGTGCGAA  <  3:202383/151‑1                                                                                                                                                                                                                                                                                                                       AAAGGCTGGGTTTTCCAATGTGTCATCATTACGGATATCGAAGTTCTCATAACGCACATCATGTAATAACATATTCATGCGTGCTAAGTTGTATGTAGTATTGTTACGTTCTTGACCGAAATAACGATACACTTGTGTTTCTTTACCAACACGTAACAA‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑  <  USA300TCH1516_ALE/458260‑458102 ‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑acgtaacaaTACTACATACAACTTAGCACGCATGAATATGTTATTACATGATGTGCGTTATGAGAACTTCGATATCCGTAATGATGACACATTGGAAAACCCAGCCTTTTTAGGCAATACATTTGATGCGGTTATTGCGAACCCACCGTATAGTGCGAA  >  USA300TCH1516_ALE/458161‑458310

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