New junction evidence
		seq id	position	reads (cov)	reads (cov)	score	skew	freq	annotation	gene	product
*	?	USA300TCH1516_ALE	2455747 =	108 (0.530)	13 (0.080)	5/132	NT	10.7%	intergenic (+5/+61)	lyrA/rpiA	Lysostaphin resistance protein A/Ribose‑5‑phosphate isomerase A
	?	USA300TCH1516_ALE	2455795 =	127 (0.760)					intergenic (+53/+13)	lyrA/rpiA	Lysostaphin resistance protein A/Ribose‑5‑phosphate isomerase A

TATTGTAGGCACTCAAGAGGGTGTTAAAATTTTAGAAAAATAATATATAGTATAGAAAAGCGCTTGCTAGCATCATCTTTTTAAGAGGTACTAGCAAGCGCTTT‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑  <  USA300TCH1516_ALE/2455850‑2455747 ‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑ctagcaagcgctttTCTATACTATATATTATTTTTCTAAAATTTTAACACCCTCTTGAGTGCCTACAATAACTTGATCTGCCATATCTAAGAAGTATCCTGTCT  >  USA300TCH1516_ALE/2455795‑2455884                                                                                                                                                                                                    TATTGTAGGCACTCAAGAGGGTGTTAAAATTTTAGAAAAATAATATATAGTATAGAAAAGCGCTTGCTAGCATCATCTTTTTAAGAGGTAC                                                                                                         >  1:693688/1‑91 TATTGTAGGCACTCAAGAGGGTGTTAAAATTTTAGAAAAATAATATATAGTATAGAAAAGCGCTTGCTAGCATCATCTTTTTAAGAGGTAC                                                                                                         >  2:1359271/1‑91  ATTGTAGGCACTCAAGAGGGTGTTAAAATTTTAGAAAAATAATATATAGTATAGAAAAGCGCTTGCTAGCATCATCTTTTTAAGAGGTACT                                                                                                        >  2:3835030/1‑91  ATTGTAGGCACTCAAGAGGGTGTTAAAATTTTAGAAAAATAATATATAGTATAGAAAAGCGCTTGCTAGCATCATCTTTTTAAGAGGTACT                                                                                                        >  1:1407081/1‑91   TTGTAGGCACTCAAGAGGGTGTTAAAATTTTAGAAAAATAATATATAGTATAGAAAAGCGCTTGCTAGCATCATCTTTTTAAGAGGTACTA                                                                                                       >  1:653521/1‑91   TTGTAGGCACTCAAGAGGGTGTTAAAATTTTAGAAAAATAATATATAGTATAGAAAAGCGCTTGCTAGCATCATCTTTTTAAGAGGTACTA                                                                                                       <  2:3146038/91‑1     GTAGGCACTCAAGAGGGTGTTAAAATTTTAGAAAAATAATATATAGTATAGAAAAGCGCTTGCTAGCATCATCTTTTTAAGAGGTACTAGC                                                                                                     >  2:1080438/1‑91     GTAGGCACTCAAGAGGGTGTTAAAATTTTAGAAAAATAATATATAGTATAGAAAAGCGCTTGCTAGCATCATCTTTTTAAGAGGTACTAGC                                                                                                     <  2:1784822/91‑1     GTAGGCACTCAAGAGGGTGTTAAAATTTTAGAAAAATAATATATAGTATAGAAAAGCGCTTGCTAGCATCATCTTTTTAAGAGGTACTAGC                                                                                                     <  2:3579134/91‑1      TAGGCACTCAAGAGGGTGTTAAAATTTTAGAAAAATAATATATAGTATAGAAAAGCGCTTGCTAGCATCATCTTTTTAAGAGGTACTAGCA                                                                                                    >  1:779619/1‑91       AGGCACTCAAGAGGGTGTTAAAATTTTAGAAAAATAATATATAGTATAGAAAAGCGCTTGCTAGCATCATCTTTTTAAGAGGTACTAGCAA                                                                                                   >  2:2555777/1‑91       AGGCACTCAAGAGGGTGTTAAAATTTTAGAAAAATAATATATAGTATAGAAAAGCGCTTGCTAGCATCATCTTTTTAAGAGGTACTAGCAA                                                                                                   >  2:1053896/1‑91       AGGCACTCAAGAGGGTGTTAAAATTTTAGAAAAATAATATATAGTATAGAAAAGCGCTTGCTAGCATCATCTTTTTAAGAGGTACTAGCAA                                                                                                   >  2:3710439/1‑91        GGCGCTCAAGAGGGTGTTAAAATTTTAGAAAAATAATATATAGTATAGAAAAGCGCTTGCTAGCATCATCTTTTTAAGAGGTACTAGCAAG                                                                                                  <  1:3555885/91‑1        GGCACTCAAGAGGGTGTTAAAATTTTAGAAAAATAATATATAGTATAGAAAAGCGCTTGCTAGCATCATCTTTTTAAGAGGTACTAGCAAG                                                                                                  >  1:423490/1‑91        GGCACTCAAGAGGGTGTTAAAATTTTAGAAAAATAATATATAGTATAGAAAAGCGCTTGCTAGCATCATCTTTTTAAGAGGTACTAGCAAG                                                                                                  >  2:303387/1‑91        GGCACTCAAGAGGGTGTTAAAATTTTAGAAAAATAATATATAGTATAGAAAAGCGCTTGCTAGCATCATCTTTTTAAGAGGTACTAGCAAG                                                                                                  >  1:768932/1‑91        GGCACGCAAGAGGGTGTTAAAATTTTAGAAAAATAATATATAGTATAGAAAAGCGCTTGCTAGCATCATCTTTTTAAGAGGTACTAGCAAG                                                                                                  <  1:602742/91‑1         GCACTCAAGAGGGTGTTAAAATTTTAGAAAAATAATATATAGTATAGAAAAGCGCTTGCTAGCATCATCTTTTTAAGAGGTACTAGCAAGC                                                                                                 >  2:2059076/1‑91         GCACTCAAGAGGGTGTTAAAATTTTAGAAAAATAATATATAGTATAGAAAAGCGCTTGCTAGCATCATCTTTTTAAGAGGTACTAGCAAGC                                                                                                 >  1:2419764/1‑91          CACTCAAGAGGGTGTTAAAATTTTAGAAAAATAATATATAGTATAGAAAAGCGCTTGCTAGCATCATCTTTTTAAGAGGTACTAGCAAGag                                                                                                <  2:2729043/91‑3          CACTCAAGAGGGTGTTAAAATTTTAGAAAAATAATATATAGTATAGAAAAGCGCTTGCTAGCATCATCTTTTTAAGAGGTACTAGCAAGCG                                                                                                <  1:2695740/91‑1          CACTCAAGAGGGTGTTAAAATTTTAGAAAAATAATATATAGTATAGAAAAGCGCTTGCTAGCATCATCTTTTTAAGAGGTACTAGCAAGCG                                                                                                <  2:3079168/91‑1          CACTCAAGAGGGTGTTAAAATTTTAGAAAAATAATATATAGTATAGAAAAGCGCTTGCTAGCATCATCTTTTTAAGAGGTACTAGCAAGCG                                                                                                <  2:3078742/91‑1          CACTCAAGAGGGTGTTAAAATTTTAGAAAAATAATATATAGTATAGAAAAGCGCTTGCTAGCATCATCTTTTTAAGAGGTACTAGCAAGCG                                                                                                <  1:2947661/91‑1          CACTCAAGAGGGTGTTAAAATTTTAGAAAAATAATATATAGTATAGAAAAGCGCTTGCTAGCATCATCTTTTTAAGAGGTACTAGCAAGCG                                                                                                >  1:3214752/1‑91          CACTCAAGAGGGTGTTAAAATTTTAGAAAAATAATATATAGTATAGAAAAGCGCTTGCTAGCATCATCTTTTTAAGAGGTACTAGCAAGCG                                                                                                >  1:3214751/1‑91           ACTCAAGAGGGTGTTAAAATTTTAGAAAAATAATATATAGTATAGAAAAGCGCTTGCTAGCATCATCTTTTTAAGAGGTACTAGCAAGCGC                                                                                               <  1:1474673/91‑1           ACTCAAGAGGGTGTTAAAATTTTAGAAAAATAATATATAGTATAGAAAAGCGCTTGCTAGCATCATCTTTTTAAGAGGTACTAGCAAGCGC                                                                                               >  1:1307396/1‑91             TCAAGAGGGTGTTAAAATTTTAGAAAAATAATATATAGTATAGAAAAGCGCTTGCTAGCATCATCTTTTTAAGAGGTACTAGCAAGCGCTT                                                                                             <  2:376967/91‑1                                                                  GCTAGCATCATCTTTTTAAGAGGTACTAGCAAGCGCTTTTCTATACTATATATTATTTTTCTAAAATTTTAACACCCTCTTGAGTGCCTAC                                        >  1:1358185/1‑91                                                                      GCATCATCTTTTTAAGAGGTACTAGCAAGCGCTTTTCTATACTATATATTATTTTTCTAAAATTTTAACACCCTCTTGAGTGCCTACAATA                                    >  1:2688042/1‑91                                                                      GCATCATCTTTTTAAGAGGTACTAGCAAGCGCTTTTCTATACTATATATTATTTTTCTAAAATTTTAACACCCTCTTGAGTGCCTACAATA                                    >  1:277117/1‑91                                                                      GCATCATCTTTTTAAGAGGTACTAGCAAGCGCTTTTCTATACTATATATTATTTTTCTAAAATTTTAACACCCTCTTGAGTGCCTACAATA                                    >  1:276545/1‑91                                                                      GCATCATCTTTTTAAGAGGTACTAGCAAGCGCTTTTCTATACTATATATTATTTTTCTAAAATTTTAACACCCTCTTGAGTGCCTACAATA                                    >  1:276523/1‑91                                                                       CATCATCTTTTTAAGAGGTACTAGCAAGCGCTTTTCTATACTATATATTATTTTTCTAAAATTTTAACACCCTCTTGAGTGCCTACAATAA                                   >  2:2665316/1‑91                                                                       CATCATCTTTTTAAGAGGTACTAGCAAGCGCTTTTCTATACTATATATTATTTTTCTAAAATTTTAACACCCTCTTGAGTGCCTACAATAA                                   >  1:2809851/1‑91                                                                       CATCATCTTTTTAAGAGGTACTAGCAAGCGCTTTTCTATACTATATATTATTTTTCTAAAATTTTAACACCCTCTTGAGTGCCTACAATAA                                   >  2:2665332/1‑91                                                                       CATCATCTTTTTAAGAGGTACTAGCAAGCGCTTTTCTATACTATATATTATTTTTCTAAAATTTTAACACCCTCTTGAGTGCCTACAATAA                                   >  1:1914579/1‑91                                                                        ATCATCTTTTTAAGAGGTACTAGCAAGCGCTTTTCTATACTATATATTATTTTTCTAAAATTTTAACACCCTCTTGAGTGCCTACAATAAC                                  >  1:405097/1‑91                                                                        ATCATCTTTTTAAGAGGTACTAGCAAGCGCTTTTCTATACTATATATTATTTTTCTAAAATTTTAACACCCTCTTGAGTGCCTACAATAAC                                  >  1:560151/1‑91                                                                        ATCATCTTTTTAAGAGGTACTAGCAAGCGCTTTTCTATACTATATATTATTTTTCTAAAATTTTAACACCCTCTTGAGTGCCTACAATAAC                                  >  1:1354387/1‑91                                                                               TTTTAAGAGGTACTAGCAAGCGCTTTTCTATACTATATATTATTTTTCTAAAATTTTAACACCCTCTTGAGTGCCTACAATCACTTGATCT                           >  2:2914166/1‑91                                                                                           CTAGCAAGCGCTTTTCTATACTATATATTATTTTTCTAAAATTTTAACACCCTCTTGAGTGCCTACAATAACTTGATCTGCCATATCTAAG               <  2:469988/91‑1                                                                                             AGCAAGCGCTTTTCTATACTATATATTATTTTTCTAAAATTTTAACACCCTCTTGAGTGCCTACAATAACTTGATCTGCCATATCTAAGAA             >  1:3065880/1‑91                                                                                             AGCAAGCGCTTTTCTATACTATATATTATTTTTCTAAAATTTTAACACCCTCTTGAGTGCCTACAATAACTTGATCTGCCATATCTAAGAA             >  1:3065463/1‑91                                                                                              GCAAGCGCTTTTCTATACTATATATTATTTTTCTAAAATTTTAACACCCTCTTGAGTGCCTACAATAACTTGATCTGCCATATCTAAGAAG            >  1:2219635/1‑91                                                                                               CAAGCGCTTTTCTATACTATATATTATTTTTCTAAAATTTTAACACCCTCTTGAGTGCCTACAATAACTTGATCTGCCATATCTAAGAAGT           >  2:2683595/1‑91                                                                                               CAAGCGCTTTTCTATACTATATATTATTTTTCTAAAATTTTAACACCCTCTTGAGTGCCTACAATAACTTGATCTGCCATATCTAAGAAGT           <  2:3415586/91‑1                                                                                                AAGCGCTTTTCTATACTATATATTATTTTTCTAAAATTTTAACACCCTCTTGAGTGCCTACAATAACTTGATCTGCCATATCTAAGAAGTA          <  2:3071184/91‑1                                                                                                AAGCGCTTTTCTATACTATATATTATTTTTCTAAAATTTTAACACCCTCTTGAGTGCCTACAATAACTTGATCTGCCATATCTAAGAAGTA          <  2:3659126/91‑1                                                                                                AAGCGCTTTTCTATACTATATATTATTTTTCTAAAATTTTAACACCCTCTTGAGTGCCTACAATAACTTGATCTGCCATATCTAAGAAGTA          <  2:766349/91‑1                                                                                                AAGCGCTTTTCTATACTATATATTATTTTTCTAAAATTTTAACACCCTCTTGAGTGCCTACAATAACTTGATCTGCCATATCTAAGAAGTA          >  1:1656907/1‑91                                                                                                 AGCGCTTTTCTATACTATATATTATTTTTCTAAAATTTTAACACCCTCTTGAGTGCCTACAATAACTTGATCTGCCATATCTAAGAAGTAT         >  1:1457550/1‑91                                                                                                  GCGCTTTTCTATACTATATATTATTTTTCTAAAATTTTAACACCCTCTTGAGTGCCTACAATAACTTGATCTGCCATATCTAAGAAGTATC        >  1:1168362/1‑91                                                                                                   CGCTTTTCTATACTATATATTATTTTTCTAAAATTTTAACACCCTCTTGAGTGCCTACAATAACTTTATCTGCCATCTCTAAGAAGTATCC       >  2:2478115/1‑91                                                                                                   CGCTTTTCTATACTATATATTATTTTTCTAAAATTTTAACACCCTCTTGAGTGCCTACAATAACTTGATCTGCCATATCTAAGAAGTATCC       <  2:1967795/91‑1                                                                                                   CGCTTTTCTATACTATATATTATTTTTCTAAAATTTTAACACCCTCTTGAGTGCCTACAATAACTTGATCTGCCATATCTAAGAAGTATCC       <  1:1723469/91‑1                                                                                                   CGCTTTTCTATACTATATATTATTTTTCTAAAATTTTAACACCCTCTTGAGTGCCTACAATAACTTGATCTGCCATATCTAAGAAGTATCC       <  2:323356/91‑1                                                                                                    GCTTTTCTATACTATATATTATTTTTCTAAAATTTTAACACCCTCTTGAGTGCCTACAATAACTTGATCTTCCATATCTAAGAAGTCTCCT      >  2:3435182/1‑91                                                                                                    GCTTTTCTATACTATATATTATTTTTCTAAAATTTTAACACCCTCTTGAGTGCCTACAATAACTTGATCTGCCATATCTAAGAAGTATCCT      <  1:1254019/91‑1                                                                                                    GCTTTTCTATACTATATATTATTTTTCTAAAATTTTAACACCCTCTTGAGTGCCTACAATAACTTGATCTGCCATATCTAAGAAGTATCCT      <  1:555515/91‑1                                                                                                    GCTTTTCTATACTATATATTATTTTTCTAAAATTTTAACACCCTCTTGAGTGCCTACAATAACTTGATCTGCCATATCTAAGAAGTATCCT      <  1:3835816/91‑1                                                                                                     CTTTTCTATACTATATATTATTTTTCTAAAATTTTAACACCCTCTTGAGTGCCTACAATAACTTGATCTGCCATATCTAAGAAGTATCCTG     <  1:1520351/91‑1                                                                                                      TTTTCTATACTATATATTATTTTTCTAAAATTTTAACACCCTCTTGAGTGCCTACAATAACTTGATCTGCCATATCTAAGAAGTATCCTGT    >  1:1784061/1‑91                                                                                                       TTTCTATACTATATATTATTTTTCTAAAATTTTAACACCCTCTTGAGTGCCTACAATAACTTGATCTGCCATATCTAAGAAGTATCCTGTC   <  1:1134144/91‑1                                                                                                       TTTCTATACTATATATTATTTTTCTAAAATTTTAACACCCTCTTGAGTGCCTACAATAACTTGATCTGCCATATCTAAGAAGTATCCTGTC   >  2:340211/1‑91                                                                                                       TTTCTATACTATATATTATTTTTCTAAAATTTTAACACCCTCTTGAGTGCCTACAATAACTTGATCTGCCATATCTAAGAAGTATCCTGTC   <  1:1872376/91‑1                                                                                                       TTTCTATACTATATATTATTTTTCTAAAATTTTAACACCCTCTTGAGTGCCTACAATAACTTGATCTGCCATATCTAAGAAGTATCCTGTC   >  1:3236949/1‑91                                                                                                       TTTCTATACTATATATTATTTTTCTAAAATTTTAACACCCTCTTGAGTGCCTACAATAACTTGATCTGCCATATCTAAGAAGTATCCTGTC   >  1:657308/1‑91                                                                                                       TTTCTATACTATATATTATCTTTCTAAAATTTTAACACCCTCTTGAGTGCCTACACTAACTTCATCTGCCATTTCTAAGAAGCATCCTGTC   >  2:2364651/1‑91                                                                                                        TTCTATACTATATATTATTTTTCTAAAATTTTAACACCCTCTTGAGTGCCTACAATAACTTGATCTGCCATATCTAAGAAGTATCCTGTCT  <  1:1843078/91‑1                                                                                                        TTCTATACTATATATTATTTTTCTAAAATTTTAACACCCTCTTGAGTGCCTACAATAACTTGATCTGCCATATCTAAGAAGTATCCTGTCT  <  1:1843079/91‑1                                                                                                        TTCTATACTATATATTATTTTTCTAAAATTTTAACACCCTCTTGAGTGCCTACAATAACTTGATCTGCCATATCTAAGAAGTATCCTGTCT  >  1:3720225/1‑91                                                                                                        TTCTATACTATATATTATTTTTCTAAAATTTTAACACCCTCTTGAGTGCCTACAATAACTTGATCTGCCATATCTAAGAAGTATCCTGTCT  <  2:2449200/91‑1                                                                                                        TTCTATACTATATATTATTTTTCTAAAATTTTAACACCCTCTTGAGTGCCTACAATAACTTGATCTGCCATATCTAAGAAGTATCCTGTCT  <  2:2449546/91‑1                                                                                                                                                                                                    TATTGTAGGCACTCAAGAGGGTGTTAAAATTTTAGAAAAATAATATATAGTATAGAAAAGCGCTTGCTAGCATCATCTTTTTAAGAGGTACTAGCAAGCGCTTT‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑  <  USA300TCH1516_ALE/2455850‑2455747 ‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑ctagcaagcgctttTCTATACTATATATTATTTTTCTAAAATTTTAACACCCTCTTGAGTGCCTACAATAACTTGATCTGCCATATCTAAGAAGTATCCTGTCT  >  USA300TCH1516_ALE/2455795‑2455884

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.