New junction evidence
		seq id	position	reads (cov)	reads (cov)	score	skew	freq	annotation	gene	product
*	?	USA300TCH1516_ALE	= 2057387	137 (0.750)	7 (0.040)	4/232	NT	5.2%	intergenic (+144/+148)	USA300HOU_RS10370/USA300HOU_RS10375	hypothetical protein/hypothetical protein
	?	USA300TCH1516_ALE	= 2057403	132 (0.790)					intergenic (+160/+132)	USA300HOU_RS10370/USA300HOU_RS10375	hypothetical protein/hypothetical protein

GTCATAAGACTATCTAGATATGATTAAGTAAACTATTAATCTTATTAAAGGTCTCTAGGAAG‑AAAAAATTTCATGCGATGAGATTGTTTTAGAAAAAGCGACGATATATATAATCTAACAATAATTTTTAAAATATTAAGAACCCCCAGCA‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑  >  USA300TCH1516_ALE/2057237‑2057387 ‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑aacccccagca‑A‑GCTATATAAAGCATATGCTGGGGGTTCTTAATATTTTAAAAATTATTGTTAGATTATATATATCGTCGCTTTTTCTAAAACAATCTCATCGCATGAAATTTTTTCTTCCTAGAGACCTTTAATAAGATTAATAGTTTAC  <  USA300TCH1516_ALE/2057403‑2057264                                                                                                                                                                                                                                                                                                        GTCATAAGACTATCTAGATATGATTAAGTAAACTATTAATCTTATTAAAGGTCTCTAGGAAG‑AAAAAATTTCATGCGATGAGATTGTTTTAGAAAAAGCGACGATATATATAATCTAACAATAATTTTTAAAATATTAAGA                                                                                                                                                          >  1:888656/1‑141    ATAAGACTATCTAGATATGATTAAGTAAACTATTAATCTTATTAAAGGTCTCTAGGAAG‑AAAAAATTTCATGCGATGAGATTGTTTTAGAAAAAGCGACGATATATATAATCTAACAATAATTTTTAAAATATTAAGAACC                                                                                                                                                       >  1:949078/1‑141      AAGACTATCTAGATATGATTAAGTAAACTATTAATCTTATTAAAGGTCTCTAGGAAG‑AAAAAATTTCATGCGATGAGATTGTTTTAGAAAAAGCGACGATATATATAATCTAACAATAATTTTTAAAATATTAAGAACCCC                                                                                                                                                     >  1:1212422/1‑141      AAGACTATCTAGATATGATTAAGTAAACTATTAATCTTATTAAAGGTCTCTAGGAAG‑AAAAAATTTCATGCGATGAGATTGTTTTAGAAAAAGCGACGATATATATAATCTAACAATAATTTTTAAAATATTAAGAACCCC                                                                                                                                                     >  4:465567/1‑141      AAGACTATCTAGATATGATTAAGTAAACTATTAATCTTATTAAAGGTCTCTAGGAAG‑AAAAAATTTCATGCGATGAGATTGTTTTAGAAAAAGCGACGATATATATAATCTAACAATAATTTTTAAAATATTAAGAACCCC                                                                                                                                                     >  4:367651/1‑141      AAGACTATCTAGATATGATTAAGTAAACTATTAATCTTATTAAAGGTCTCTAGGAAG‑AAAAAATTTCATGCGATGAGATTGTTTTAGAAAAAGCGACGATATATATAATCTAACAATAATTTTTAAAATATTAAGAACCCC                                                                                                                                                     >  1:38371/1‑141      AAGACTATCTAGATATGATTAAGTAAACTATTAATCTTATTAAAGGTCTCTAGGAAG‑AAAAAATTTCATGCGATGAGATTGTTTTAGAAAAAGCGACGATATATATAATCTAACAATAATTTTTAAAATATTAAGAACCCC                                                                                                                                                     >  1:610944/1‑141       AGACTATCTAGATATGATTAAGTAAACTATTAATCTTATTAAAGGTCTCTAGGAAG‑AAAAAATTTCATGCGATGAGATTGTTTTAGAAAAAGCGACGATATATATAATCTAACAATAATTTTTAAAATATTAAGAACCCCC                                                                                                                                                    <  1:1186526/141‑1       AGACTATCTAGATATGATTAAGTAAACTATTAATCTTATTAAAGGTCTCTAGGAAG‑AAAAAATTTCATGCGATGAGATTGTTTTAGAAAAAGCGACGATATATATAATCTAACAATAATTTTTAAAATATTAAGAACCCCC                                                                                                                                                    >  2:843651/1‑141        GACTATCTAGATATGATTAAGTAAACTATTAATCTTATTAAAGGTCTCTAGGAAG‑AAAAAATTTCATGCGATGAGATTGTTTTAGAAAAAGCGACGATATATATAATCTAACAATAATTTTTAAAATATTAAGAACCCCCA                                                                                                                                                   <  3:331987/141‑1         ACTATCTAGATATGATTAAGTAAACTATTAATCTTATTAAAGGTCTCTAGGAAG‑AAAAAATTTCATGCGATGAGATTGTTTTAGAAAAAGCGACGATATATATAATCTAACAATAATTTTTAAAATATTAAGAACCCCCAG                                                                                                                                                  <  1:494543/141‑1         ACTATCTAGATATGATTAAGTAAACTATTAATCTTATTAAAGGTCTCTAGGAAG‑AAAAAATTTCATGCGATGAGATTGTTTTAGAAAAAGCGACGATATATATAATCTAACAATAATTTTTAAAATATTAAGAACCCCCAG                                                                                                                                                  >  3:668267/1‑141         ACTATCTAGATATGATTAAGTAAACTATTAATCTTATTAAAGGTCTCTAGGAAG‑AAAAAATTTCATGCGATGAGATTGTTTTAGAAAAAGCGACGATATATATAATCTAACAATAATTTTTAAAATATTAAGAACCCCCAG                                                                                                                                                  <  1:1287769/141‑1          CTATCTAGATATGATTAAGTAAACTATTAATCTTATTAAAGGTCTCTAGGAAG‑AAAAAATTTCATGCGATGAGATTGTTTTAGAAAAAGCGACGATATATATAATCTAACAATAATTTTTAAAATATTAAGAACCCCCAGC                                                                                                                                                 >  2:953270/1‑141           TATCTAGATATGATTAAGTAAACTATTAATCTTATTAAAGGTCTCTAGGAAG‑AAAAAATTTCATGCGATGAGATTGTTTTAGAAAAAGCGACGATATATATAATCTAACAATAATTTTTAAAATATTAAGAACCCCCAGCA                                                                                                                                                >  1:816363/1‑141           TATCTAGATATGATTAAGTAAACTATTAATCTTATTAAAGGTCTCTAGGAAG‑AAAAAATTTCATGCGATGAGATTGTTTTAGAAAAAGCGACGATATATATAATCTAACAATAATTTTTAAAATATTAAGAACCCCCAGCA                                                                                                                                                <  1:459410/141‑1           TATCTAGATATGATTAAGTAAACTATTAATCTTATTAAAGGTCTCTAGGAAG‑AAAAAATTTCATGCGATGAGATTGTTTTAGAAAAAGCGACGATATATATAATCTAACAATAATTTTTAAAATATTAAGAACCCCCAGCA                                                                                                                                                <  1:1045978/141‑1                          AAGTAAACTATTAATCTTATTAAAGGTCTCTAGGAAG‑AAAAAATTTCATGCGATGAGATTGTTTTAGAAAAAGCGACGATATATATAATCTAACAATAATTTTTAAAATATTAAGAACCCCCA                                                                                                                                                   >  1:977957/1‑123                          AAGTAAACTATTAATCTTATTAAAGGTCTCTAGGAAG‑AAAAAATTTCATGCGATGAGATTGTTTTAGAAAAAGCGACGATATATATAATCTAACAATAATTTTTAAAATATTAAGAACCCCCA                                                                                                                                                   <  2:977957/123‑1                           AGTAAACTATTAATCTTATTAAAGGTCTCTAGGAAG‑AAAAAATTTCATGCGATGAGATTGTTTTAGAAAAAGCGACGATATATATAATCTAACAATAATTTTTAAAATATTAAGAACCCCCAGCA‑A‑GCTATATAAAGCATA                                                                                                                              <  3:85971/141‑1                           AGTAAACTATTAATCTTATTAAAGGTCTCTAGGAAG‑AAAAAATTTCATGCGATGAGATTGTTTTAGAAAAAGCGACGATATATATAATCTAACAATAATTTTTAAAATATTAAGAACCCCCAGCA‑A‑GCTATATAAAGCATA                                                                                                                              <  1:866556/141‑1                           AGTAAACTAGTAATCTTATAAAAAGTCTCTAAGAAG‑AAAAAATGTCATGCGATGAGATTGTTTTAGAAAAAGCGACGATATATAGAATCTAACAATAATTTTTAAAATATTAAGAACCCCCAGCA‑A‑GCTATATAAAGCATA                                                                                                                              <  4:576190/141‑1                            GTAAACTATTAATCTTATTAAAGGTCTCTAGGAAGAAAAAAATTTCATGCGATGAGATTGTTTTAGAAAAAGCGACGATATATATAATCTAACAATAATTTTTAAAATATTAAGAACCCCCAGCA‑A‑GCTATATAAAGCATA                                                                                                                              <  2:1294669/141‑1                                                                                                   GCGACGATATATATAATCTAACAATAATTTTTAAAATATTAAGAACCCCCAGCATATGCTTTATATAGC‑T‑TGCTGGGGGTTCTTAATATTTTAAAAATTATTGTTAGATTATATATATCGTCGCTTTTTCTAAAACAATCT                                                       >  3:367651/1‑141                                                                                                                                       TATTAAGAACCCCCAGCATATGCTTTATATAGC‑T‑TGCTGGGGGTTCTTAATATTTTAAAAATTATTGTTAGATTATATATATCGTCGCTTTTTCTAAAACAATCTCATCGCATGAAATTTTTTCTTCCTAGAGACCTT                      >  1:955453/1‑138                                                                                                                                       TATTAAGAACCCCCAGCATATGCTTTATATAGC‑T‑TGCTGGGGGTTCTTAATATTTTAAAAATTATTGTTAGATTATATATATCGTCGCTTTTTCTAAAACAATCTCATCGCATGAAATTTTTTCTTCCTAGAGACCTT                      <  2:955453/138‑1                                                                                                                                               ACCCCCAGCA‑A‑GCTATATAAAGCATATGCTGGGGGTTCTTAATATTTTAAAAATTATTGTTAGATTATATATATCGTCGCTTTTTCTAAAACAATCTCATCGCATGAAATTTTTTCTTCCTAGAGACCTTTAATAAGATTA           >  1:967656/1‑141                                                                                                                                                CCCCCAGCA‑A‑GCTATATAAAGCATATGCTGGGGGTTCTTAATATTTTAAAAATTATTGTTAGATTATATATATCGTCGCTTTTTCTAAAACAATCTCATCGCATGAAATTTTTTCTTCCTAGAGACCTTTAATAAGATTAA          >  1:273317/1‑141                                                                                                                                                 CCCCAGCA‑A‑GCTATATAAAGCATATGCTGGGGGTTCTTAATATTTTAAAAATTATTGTTAGATTATATATATCGTCGCTTTTTCTAAAACAATCTCATCGCATGAAATTTTTTCTTCCTAGAGACCTTTAATAAGATTAAT         >  3:501721/1‑141                                                                                                                                                    CAGCA‑A‑GCTATATAAAGCATATGCTGGGGGTTCTTAATATTTTAAAAATTATTGTTAGATTATATATATCGTCGCTTTTTCTAAAACAATCTCATCGCATGAAATTTTTTCTTCCTAGAGACCTTTAATAAGATTAATAGT      <  1:747518/141‑1                                                                                                                                                    CAGCA‑A‑GCTATATAAAGCATATGCTGGGGGTTCTTAATATTTTAAAAATTATTGTTAGATTATATATATCGTCGCTTTTTCTAAAACAATCTCATCGCATGAAATTTTTTCTTCCTAGAGACCTTTAATAAGATTAATAGT      <  1:215540/141‑1                                                                                                                                                     AGCA‑A‑GCTATATAAAGCATATGCTGGGGGTTCTTAATATTTTAAAAATTATTGTTAGATTATATATATCGTCGCTTTTTCTAAAACAATCTCATCGCATGAAATTTTTTCTTCCTAGAGACCTTTAATAAGATTAATAGTT     >  2:618183/1‑141                                                                                                                                                     AGCA‑A‑GCTATATAAAGCATATGCTGGGGGTTCTTAATATTTTAAAAATTATTGTTAGATTATATATATCGTCGCTTTTTCTAAAACAATCTCATCGCATGAAATTTTTTCTTCCTAGAGACCTTTAATAAGATTAATAGTT     <  4:520106/141‑1                                                                                                                                                      GCA‑A‑GCTATATAAAGCATATGCTGGGGGTTCTTAATATTTTAAAAATTATTGTTAGATTATATATATCGTCGCTTTTTCTAAAACAATCTCATCGCATGAAATTTTTTCTTCCTAGAGACCTTTAATAAGATTAATAGTTT    >  2:1518586/1‑141                                                                                                                                                      GCA‑A‑GCTATATAAAGCATATGCTGGGGGTTCTTAATATTTTAAAAATTATTGTTAGATTATATATATCGTCGCTTTTTCTAAAACAATCTCATCGCATGAAATTTTTTCTTCCTAGAGACCTTTAATAAGATTAATAGTTT    >  2:1517799/1‑141                                                                                                                                                       CA‑A‑GCTATATAAAGCATATGCTGGGGGTTCTTAATATTTTAAAAATTATTGTTAGATTATATATATCGTCGCTTTTTCTAAAACAATCTCATCGCATGAAATTTTTTCTTCCTAGAGACCTTTAATAAGATTAATAGTTTA   >  4:191536/1‑141                                                                                                                                                        A‑A‑GCTATATAAAGCATATGCTGGGGGTTCTTAATATTTTAAAAATTATTGTTAGATTATATATATCGTCGCTTTTTCTAAAACAATCTCATCGCATGAAATTTTTTCTTCCTAGAGACCTTTAATAAGATTAATAGTTTAC  <  1:1312990/141‑1                                                                                                                                                                                                                                                                                                        GTCATAAGACTATCTAGATATGATTAAGTAAACTATTAATCTTATTAAAGGTCTCTAGGAAG‑AAAAAATTTCATGCGATGAGATTGTTTTAGAAAAAGCGACGATATATATAATCTAACAATAATTTTTAAAATATTAAGAACCCCCAGCA‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑  >  USA300TCH1516_ALE/2057237‑2057387 ‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑aacccccagca‑A‑GCTATATAAAGCATATGCTGGGGGTTCTTAATATTTTAAAAATTATTGTTAGATTATATATATCGTCGCTTTTTCTAAAACAATCTCATCGCATGAAATTTTTTCTTCCTAGAGACCTTTAATAAGATTAATAGTTTAC  <  USA300TCH1516_ALE/2057403‑2057264

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