New junction evidence
		seq id	position	reads (cov)	reads (cov)	score	skew	freq	annotation	gene	product
*	?	USA300TCH1516_ALE	1392266 =	121 (1.230)	11 (0.130)	9/140	NT	10.1%	intergenic (+40/‑460)	alsT/glcT	Amino‑acid carrier protein AlsT/GlcA/glcB genes antiterminator
	?	USA300TCH1516_ALE	1392308 =	90 (1.050)					intergenic (+82/‑418)	alsT/glcT	Amino‑acid carrier protein AlsT/GlcA/glcB genes antiterminator

TAATCAAATCTTAGATTAACTAGTGTAATGATACAGATGATAATTGAGTACAAATTTAAAACCCTGAGATTTTCGCTTTAATTTGAAAACCTCAGGGTTT‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑  <  USA300TCH1516_ALE/1392365‑1392266 ‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑ctcagggtttTAAATTTGTACTCAATTATCATCTGTATCATTACACTAGTTAATCTAAGATTTGATTATATATTAATATAGTAAGGTTGAGATTTATTTC  >  USA300TCH1516_ALE/1392308‑1392397                                                                                                                                                                                                TAATCAAATCTTAGATTAACTAGTGTAATGATACAGATGATAATTGAGTACAAATTTAAAACCCTGAGATTTTCGCTTTAATTTGAAAACC                                                                                                     <  1:3947461/91‑1   ATCAAATCTTAGATTAACTAGTGTAATGATACAGATGATAATTGAGTACAAATTTAAAACCCTGAGATTTTCGCTTTAATTTGAAAACCTC                                                                                                   <  1:3210374/91‑1   ATCAAATCTTAGATTAACTAGTGTAATGATACAGATGATAATTGAGTACAAATTTAAAACCCTGAGATTTTCGCTTTAATTTGAAAACCTC                                                                                                   <  1:3208695/91‑1    TCAAATCTTAGATTAACTAGTGTAATGATACAGATGATAATTGAGTACAAATTTAAAACCCTGAGATTTTCGCTTTAATTTGAAAACCTCA                                                                                                  >  1:1067612/1‑91    TCAAATCTTAGATTAACTAGTGTAATGATACAGATGATAATTGAGTACAAATTTAAAACCCTGAGATTTTCGCTTTAATTTGAAAACCTCA                                                                                                  <  1:1047351/91‑1    TCAAATCTTAGATTAACTAGTGTAATGATACAGATGATAATTGAGTACAAATTTAAAACCCTGAGATTTTCGCTTTAATTTGAAAACCTCA                                                                                                  >  1:1917840/1‑91     CAAATCTTAGATTAACTAGTGTAATGATACAGATGATCATTGAGTACAAATTTAAAACCCTGAGATTTTCGCTTTAATTTGAAAACCTCAG                                                                                                 >  1:3505882/1‑91     CAAATCTTAGATTAACTAGTGTAATGATACAGATGATAATTGAGTACAAATTTAAAACCCTGAGATTTTCGCTTTAATTTGAAAACCTCAG                                                                                                 <  1:4001892/91‑1       AATCTTAGATTAACTAGTGTAATGATACAGATGATAATTGAGTACAAATTTAAAACCCTGAGATTTTCGCTTTAATTTGAAAACCTCAGGG                                                                                               >  1:2736835/1‑91       AATCTTAGATTAACTAGTGTAATGATACAGATGATAATTGAGTACAAATTTAAAACCCTGAGATTTTCGCTTTAATTTGAAAACCTCAGGG                                                                                               <  1:3767142/91‑1       AATCTTAGATTAACTAGTGTAATGATACAGATGATAATTGAGTACAAATTTAAAACCCTGAGATTTTCGCTTTAATTTGAAAACCTCAGGG                                                                                               >  1:3048729/1‑91       AATCTTAGATTAACTAGTGTAATGATACAGATGATAATTGAGTACAAATTTAAAACCCTGAGATTTTCGCTTTAATTTGAAAACCTCAGGG                                                                                               >  1:1802936/1‑91        ATCTTAGATTAACTAGTGTAATGATACAGATGATAATTGAGTACAAATTTAAAACCCTGAGATTTTCGCTTTAATTTGAAAACCTCAGGGT                                                                                              >  1:3391195/1‑91        ATCTTAGATTAACTAGTGTAATGATACAGATGATAATTGAGTACAAATTTAAAACCCTGAGATTTTCGCTTTAATTTGAAAACCTCAGGGT                                                                                              >  1:34718/1‑91         TCTTAGATTAACTAGTGTAATGATACAGATGATAATTGAGTACAAATTTAAAACCCTGAGATTTTCGCTTTAATTTGAAAACCTCAGGGTT                                                                                             <  1:4038517/91‑1          CTTAGATTAACTAGTGTAATGATACAGATGATAATTGAGTACAAATTTAAAACCCTGAGATTTTCGCTTTAATTTGAAAACCTCAGGGTTT                                                                                            <  1:1125527/91‑1                                                           AAACCCTGAGATTTTCGCTTTAATTTGAAAACCTCAGGGTTTTAAATTTGTACTCAATTATCATCTGTATCATTACACTAGTTAATCTAAG                                           >  1:2641219/1‑91                                                            AACCCTGAGATTTTCGCTTTAATTTGAAAACCTCAGGGTTTTAAATTTGTACTCAATTATCATCTGTATCATTACACTAGTTAATCTAAGA                                          >  1:3969743/1‑91                                                               CCTGAGATTTTCGCTTTAATTTGAAAACCTCAGGGTTTTAAATTTGTACTCAATTATCATCTGTATCATTACACTAGTTAATCTAAGATTT                                       >  1:2574173/1‑91                                                               CCTGAGATTTTCGCTTTAATTTGAAAACCTCAGGGTTTTAAATTTGTACTCAATTATCATCTGTATCATTACACTAGTTAATCTAAGATTT                                       >  1:1308997/1‑91                                                                CTGAGATTTTCGCTTTAATTTGAAAACCTCAGGGTTTTAAATTTGTACTCAATTATCATCTGTATCATTACACTAGTTAATCTAAGATTTG                                      >  1:1317540/1‑91                                                                  GAGATTTTCGCTTTAATTTGAAAACCTCAGGGTTTTAAATTTGTACTCAATTATCATCTGTATCATTACACTAGTTAATCTAAGATTTGAT                                    >  1:1566676/1‑91                                                                      TTTTCGCTTTAATTTGAAAACCTCAGGGTTTTAAATTTGTACTCAATTATCATCTGTATCATTACACTAGTTAATCTAAGATTTGATTATA                                >  1:1556891/1‑91                                                                       TTTCGCTTTAATTTGAAAACCTCAGGGTTTTAAATTTGTACTCAATTATCATCTGTATCATTACACTAGTTAATCTAAGATTTGATTATAT                               >  1:128389/1‑91                                                                        TTCGCTTTAATTTGAAAACCTCAGGGTTTTAAATTTGTACTCAATTATCATCTGTATCATTACACTAGTTAATCTAAGATTTGATTATATA                              >  1:830669/1‑91                                                                        TTCGCTTTAATTTGAAAACCTCAGGGTTTTAAATTTGTACTCAATTATCATCTGTATCATTACACTAGTTAATCTAAGATTTGATTATATA                              >  1:604201/1‑91                                                                                    TGAAAACCTCAGGGTTTTAAATTTGTACTCAATTATCATCTGTATCATTACACTAGTTAATCTAAGATTTGATTATATATTAATATAGTAA                  >  1:2411811/1‑91                                                                                           CTCAGGGTTTTAAATTTGTACTCAATTATCATCTGTATCATTACACTAGTTAATCTAAGATTTGATTATATATTAATATAGTAAGGTTGAG           <  1:1284727/91‑1                                                                                            TCAGGGTTTTAAATTTGTACTCAATTATCATCTGTATCATTACACTAGTTAATCTAAGATTTGATTATATATTAATATAGTAAGGTTGAGA          <  1:1967864/91‑1                                                                                             CAGGGTTTTAAATTTGTACTCAATTATCATCTGTATCATTACACTAGTTAATCTAAGATTTGATTATATATTAATATAGTAAGGTTGAGAT         <  1:1332794/91‑1                                                                                              AGGGTTTTAAATTTGTACTCAATTATCATCTGTATCATTACACTAGTTAATCTAAGATTTGATTATATATTAATATAGTAAGGTTGAGATT        <  1:3565454/91‑1                                                                                              AGGGTTTTAAATTTGTACTCAATTATCATCTGTATCATTACACTAGTTAATCTAAGATTTGATTATATATTAATATAGTAAGGTTGAGATT        <  1:1980840/91‑1                                                                                                   TTTAAATTTGTACTCAATTATCATCTGTATCATTACACTAGTTAATCTAAGATTTGATTATATATTAATATAGTAAGGTTGAGATTTATTT   >  1:3918809/1‑91                                                                                                    TTAAATTTGTACTCAATTATCATCTGTATCATTACACTAGTTAATCTAAGATTTGATTATATATTAATATAGTAAGGTTGAGATTTATTTC  <  1:699830/91‑1                                                                                                                                                                                                TAATCAAATCTTAGATTAACTAGTGTAATGATACAGATGATAATTGAGTACAAATTTAAAACCCTGAGATTTTCGCTTTAATTTGAAAACCTCAGGGTTT‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑  <  USA300TCH1516_ALE/1392365‑1392266 ‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑ctcagggtttTAAATTTGTACTCAATTATCATCTGTATCATTACACTAGTTAATCTAAGATTTGATTATATATTAATATAGTAAGGTTGAGATTTATTTC  >  USA300TCH1516_ALE/1392308‑1392397

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.