New junction evidence
		seq id	position	reads (cov)	reads (cov)	score	skew	freq	annotation	gene	product
*	?	USA300TCH1516_ALE	= 1365739	186 (0.980)	25 (0.140)	10/148	NT	12.5%	intergenic (+38/‑416)	rpmG2_1/rpsN2	50S ribosomal protein L33 2/Alternate 30S ribosomal protein S14
	?	USA300TCH1516_ALE	= 1365764	177 (1.010)					intergenic (+63/‑391)	rpmG2_1/rpsN2	50S ribosomal protein L33 2/Alternate 30S ribosomal protein S14

AATGAAAAAATATTGCCCAAGATTAAACAAATATACGTTACATCGTGAAACTAAGTAATTCTTATCATTCAAATACGACGATTTGAAAATAAAGCG‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑  >  USA300TCH1516_ALE/1365644‑1365739 ‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑aaagcgAGCTCCCCAATATAATAGGTAAGCCCGCTTTATTTTCAAATCGTCGTATTTGAATGATAAGAATTACTTAGTTTCACGATGTAACGTATA  <  USA300TCH1516_ALE/1365764‑1365675                                                                                                                                                                                            AATGAAAAAATATTGCCCAAGATTAAACAAATATACGTTACATCGTGAAACTAAGTAATTCTTATCATTCAAATACGACGATTTGAAAATA                                                                                                 >  1:1208095/1‑91 AATGAAAAAATATTGCCCAAGATTAAACAAATATACGTTACATCGTGAAACTAAGTAATTCTTATCATTCAAATACGACGATTTGAAAATA                                                                                                 >  2:2608276/1‑91  ATGAAAAAATATTGCCCAAGATTAAACAAATATACGTTACATCGTGAAACTAAGTAATTCTTATCATTCAAATACGACGATTTGAAAATAA                                                                                                <  1:3396489/91‑1  ATGAAAAAATATTGCCCAAGATTAAACAAATATACGTTACATCGTGAAACTAAGTAATTCTTATCATTCAAATACGACGATTTGAAAATAA                                                                                                >  1:658093/1‑91   TGAAAAAATATTGCCCAAGATTAAACAAATATACGTTACATCGTGAAACTAAGTAATTCTTATCATTCAAATACGACGATTTGAAAATAAA                                                                                               <  1:2128585/91‑1    GAAAAAATATTGCCCAAGATTAAACAAATATACGTTACATCGTGAAACTAAGTAATTCTTATCATTCAAATACGACGATTTGAAAATAAAG                                                                                              <  2:938039/91‑1    GAAAAAATATTGCCCAAGATTAAACAAATATACGTTACATCGTGAAACTAAGTAATTCTTATCATTCAAATACGACGATTTGAAAATAAAG                                                                                              <  1:3356282/91‑1    GAAAAAATATTGCCCAAGATTAAACAAATATACGTTACATCGTGAAACTAAGTAATTCTTATCATTCAAATACGACGATTTGAAAATAAAG                                                                                              <  1:619358/91‑1    GAAAAAATATTGCCCAAGATTAAACAAATATACGTTACATCGTGAAACTAAGTAATTCTTATCATTCAAATACGACGATTTGAAAATAAAG                                                                                              <  2:2154191/91‑1    GAAAAAATATTGCCCAAGATTAAACAAATATACGTTACATCGTGAAACTAAGTAATTCTTATCATTCAAATACGACGATTTGAAAATAAAG                                                                                              <  2:2154193/91‑1    GAAAAAATATTGCCCAAGATTAAACAAATATACGTTACATCGTGAAACTAAGTAATTCTTATCATTCAAATACGACGATTTGAAAATAAAG                                                                                              >  1:1599380/1‑91    GAAAAAATATTGCCCAAGATTAAACAAATATACGTTACATCGTGAAACTAAGTAATTCTTATCATTCAAATACGACGATTTGAAAATAAAG                                                                                              <  2:2879329/91‑1    GAAAAAATATTGCCCAAGATTAAACAAATATACGTTACATCGTGAAACTAAGTAATTCTTATCATTCAAATACGACGATTTGAAAATAAAG                                                                                              <  2:3470826/91‑1    GAAAAAATATTGCCCAAGATTAAACAAATATACGTTACATCGTGAAACTAAGTAATTCTTATCATTCAAATACGACGATTTGAAAATAAAG                                                                                              <  2:633839/91‑1    GAAAAAATATTGCCAAAGATTAAACAAATATACGTTACATCGTGAAACTAAGTAATTCTTATCATTCAAATACGACGATTTGAAAATAAAG                                                                                              <  2:136887/91‑1     AAAAAATATTGCCCAAGATTAAACAAATATACGTTACATCGTGAAACTAAGTAATTCTTATCATTCAAATACGACGATTTGAAAATAAAGC                                                                                             <  2:2216823/91‑1     AAAAAATATTGCCCAAGATTAAACAAATATACGTTACATCGTGAAACTAAGTAATTCTTATCATTCAAATACGACGATTTGAAAATAAAGC                                                                                             >  1:1205007/1‑91      AAAAATATTGCCCAAGATTAAACAAATATACGTTACATCGTGAAACTAAGTAATTCTTATCATTCAAATACGACGATTTGAAAATAAAGCG                                                                                            >  2:828105/1‑91      AAAAATATTGCCCAAGATTAAACAAATATACGTTACATCGTGAAACTAAGTAATTCTTATCATTCAAATACGACGATTTGAAAATAAAGCG                                                                                            >  1:2014893/1‑91      AAAAATATTGCCCAAGATTAAACAAATATACGTTACATCGTGAAACTAAGTAATTCTTATCATTCAAATACGACGATTTGAAAATAAAGCG                                                                                            >  1:2014821/1‑91                      ATTAAACAAATATACGTTACATCGTGAAACTAAGTAATTCTTATCATTCAAATACGACGATTTGAAAATAAAGCGAGCTCCCCAATATAAT                                                                            <  1:287006/91‑1                      ATTAAACAAATATACGTTACATCGTGAAACTAAGTAATTCTTATCATTCAAATACGACGATTTGAAAATAAAGCGAGCTCCCCAATATAAT                                                                            <  2:1923935/91‑1                          AACAAATATACGTTACATCGTGAAACTAAGTAATTCTTATCATTCAAATACGACGATTTGAAAATAAAGCGAGCTCCCCAATATAATAGGT                                                                        <  2:3238954/91‑1                          AACAAATATACGTTACATCGTGAAACTAAGTAATTCTTATCATTCAAATACGACGATTTGAAAATAAAGCGAGCTCCCCAATATAATAGGT                                                                        <  2:3156347/91‑1                          AACAAATATACGTTACATCGTGAAACTAAGTAATTCTTATCATTCAAATACGACGATTTGAAAATAAAGCGAGCTCCCCAATATAATAGGT                                                                        <  2:3156334/91‑1                               ATATACGTTACATCGTGAAACTGAGTAATTCTTATCATTCAAATACGACTATTTGAAAATAAAGCGAGCTCCCCAATATAATAGGTAAGCC                                                                   <  2:2942102/91‑1                               ATATACGTTACATCGTGAAACTAAGTAATTCTTATCATTCAAATACGACGATTTGAAAATAAAGCGAGCTCCCCAATATAATAGGTAAGCC                                                                   <  2:2937655/91‑1                                 ATACGTTACATCGTGAAACTAAGTAATTCTTATCATTCAAATACGACGATTTGAAAATAAAGCGAGCTCCCCAATATAATAGGTAAGCCCG                                                                 <  2:1622765/91‑1                                 ATACGTTACATCGTGAAACTAAGTAATTCTTATCATTCAAATACGACGATTTGAAAATAAAGCGAGCTCCCCAATATAATAGGTAAGCCCG                                                                 <  2:1600549/91‑1                                 ATACGTGACATCGTGAAACTAAGTAATTCTTATCATTCAAATACGACGATTTGAAAATAAAGCGAGCTCCCCAATATAATAGGTAAGCCCG                                                                 <  2:2542323/91‑1                                  TACGTTACATCGTGAAACTAAGTAATTCTTATCATTCAAATACGACGATTTGAAAATAAAGCGAGCTCCCCAATATAATAGGTAAGCCCGC                                                                <  2:2147829/91‑1                                  TACGTTACATCGTGAAACTAAGTAATTCTTATCATTCAAATACGACGATTTGAAAATAAAGCGAGCTCCCCAATATAATAGGTAAGCCCGC                                                                <  2:2147693/91‑1                                  TACGTTACATCGTGAAACTAAGTAATTCTTATCATTCAAATACGACGATTTGAAAATAAAGCGAGCTCCCCAATATAATAGGTAAGCCCGC                                                                <  2:1458129/91‑1                                  TACGTTACATCGTGAAACTAAGTAATTCTTATCATTCAAATACGACGATTTGAAAATAAAGCGAGCTCCCCAATATAATAGGTAAGCCCGC                                                                <  2:1087605/91‑1                                  TACGTTACATCGTGAAACTAAGTAATTCTTATCATTCAAATACGACGATTTGAAAATAAAGCGAGCTCCCCAATATAATAGGTAAGCCCGC                                                                <  1:854845/91‑1                                  TACGTTACATCGTGAAACTAAGTAATTCTTATCATTCAAATACGACGATTTGAAAATAAAGCGAGCTCCCCAATATAATAGGTAAGCCCGC                                                                <  1:2301826/91‑1                                  TACGTTACATCGTGAAACTAAGTAATTCTTATCATTCAAATACGACGATTTGAAAATAAAGCGAGCTCCCCAATATAATAGGTAAGCCCGC                                                                <  2:3152426/91‑1                                   ACGTTACATCGTGAAACTAAGTAATTCTTATCATTCAAATACGACGATTTGAAAATAAAGCGAGCTCCCCAATATAATAGGTAAGCCCGCT                                                               <  1:2269411/91‑1                                     GTTACATCGTGAAACTAAGTAATTCTTATCATTCAAATACGACGATTTGAAAATAAAGCGAGCTCCCCAATATAATAGGTAAGCCCGCTTT                                                             <  1:1226165/91‑1                                     GTTACATCGTGAAACTAAGTAATTCTTATCATTCAAATACGACGATTTGAAAATAAAGCGAGCTCCCCAATATAATAGGTAAGCCCGCTTT                                                             <  1:1132162/91‑1                                     GTTACATCGTGAAACTAAGTAATTCTTATCATTCAAATACGACGATTTGAAAATAAAGCGAGCTCCCCAATATAATAGGTAAGCCCGCTTT                                                             <  1:3833943/91‑1                                      TTACATCGTGAAACTAAGTAATTCTTATCATTCAAATACGACGATTTGAAAATAAAGCGAGCTCCCCAATATAATAGGTAAGCCCGCTTTA                                                            <  2:2086943/91‑1                                      TTACATCGTGAAACTAAGTAATTCTTATCATTCAAATACGACGATTTGAAAATAAAGCGAGCTCCCCAATATAATAGGTAAGCCCGCTTTA                                                            <  1:1451260/91‑1                                       TACATCGTGAAACTAAGTAATTCTTATCATTCAAATACGACGATTTGAAAATAAAGCGAGCTCCCCAATATAATAGGTAAGCCCGCTTTAT                                                           <  1:1297532/91‑1                                          ATCGTGAAACTAAGTAATTCTTATCATTCAAATACGACGATTTGAAAATAAAGCGAGCTCCCCAATATAATAGGTAAGCCCGCTTTATTTT                                                        <  2:3738194/91‑1                                                                                           AAAGCGAGCTCCCCAATATAATAGGTAAGCCCGCTTTATTTTCAAATCGTCGTATTTGAATGATAAGAATTACTTAGTTTCACGATGTAAC       >  2:255469/1‑91                                                                                            AAGCGAGCTCCCCAATATAATAGGTAAGCCCGCTTTATTTTCAAATCGTCGTATTTGAATGATAAGAATTACTTAGTTTCACGATGTAACG      <  1:289642/91‑1                                                                                            AAGCGAGCTCCCCAATATAATAGGTAAGCCCGCTTTATTTTCAAATCGTCGTATTTGAATGATAAGAATTACTTAGTTTCACGATGTAACG      <  1:1741458/91‑1                                                                                            AAGCGAGCTCCCCAATATAATAGGTAAGCCCGCTTTATTTTCAAATCGTCGTATTTGAATGATAAGAATTACTTAGTTTCACGATGTAACG      <  1:2798054/91‑1                                                                                            AAGCGAGCTCCCCAATATAATAGGTAAGCCCGCTTTATTTTCAAATCGTCGTATTTGAATGATAAGAATTACTTAGTTTCACGATGTAACG      <  1:2408397/91‑1                                                                                            AAGCGAGCTCCCCAATAGAATAGGTAAGCCCGCTTTATTTTCAAATCGTCGTATTTGAATGATAAGAATTACTTAGTTTCACGATGTAACG      <  1:289603/91‑1                                                                                            AAGCGAGCGCCCCAATATAATAGGTAAGCCCGCTTTATTTTCAAATCGTCGTATTTGAATGATAAGAATTACTTAGTTTCACGATGTAACG      <  1:715061/91‑1                                                                                             AGCGAGCTCCCCAATATAATAGGTAAGCCCGCTTTATTTTCAAATCGTCGTATTTGAATGATAAGAATTACTTAGTTTCACGATGTAACGT     <  2:1715126/91‑1                                                                                             AGCGAGCTCCCCAATATAATAGGTAAGCCCGCTTTATTTTCAAATCGTCGTATTTGAATGATAAGAATTACTTAGTTTCACGATGTAACGT     <  2:490150/91‑1                                                                                             AGCGAGCTCCCCAATATAATAGGTAAGCCCGCTTTATTTTCAAATCGTCGTATTTGAATGATAAGAATTACTTAGTTTCACGATGTAACGT     <  1:1742900/91‑1                                                                                              GCGAGCTCCCCAATATAATAGGTAAGCCCGCTTTATTTTCAAATCGTCGTATTTGAATGATAAGAATTACTTAGTTTCACGATGTAACGTA    <  1:3418152/91‑1                                                                                              GCGAGCTCCCCAATATAATAGGTAAGCCCGCTTTATTTTCAAATCGTCGTATTTGAATGATAAGAATTACTTAGTTTCACGATGTAACGTA    <  1:447825/91‑1                                                                                              GCGAGCTCCCCAATATAATAGGTAAGCCCGCTTTATTTTCAAATCGTCGTATTTGAATGATAAGAATTACTTAGTTTCACGATGTAACGTA    >  2:1319571/1‑91                                                                                               CGAGCTCCCCAATATAATAGGTAAGCCCGCTTTATTTTCAACTCGTCGTATTTGAATGATAAGAATTACTTAGTTTCACGATGTAACGTAT   <  1:608461/91‑1                                                                                                GAGCTCCCCAATATAATAGGTAAGCCCGCTTTATTTTCAAATCGTCGTATTTGAATGATAAGAATTACTTAGTTTCACGATGTAACGTATA  >  2:2724779/1‑91                                                                                                                                                                                            AATGAAAAAATATTGCCCAAGATTAAACAAATATACGTTACATCGTGAAACTAAGTAATTCTTATCATTCAAATACGACGATTTGAAAATAAAGCG‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑  >  USA300TCH1516_ALE/1365644‑1365739 ‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑aaagcgAGCTCCCCAATATAATAGGTAAGCCCGCTTTATTTTCAAATCGTCGTATTTGAATGATAAGAATTACTTAGTTTCACGATGTAACGTATA  <  USA300TCH1516_ALE/1365764‑1365675

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