New junction evidence
		seq id	position	reads (cov)	reads (cov)	score	skew	freq	annotation	gene	product
*	?	USA300TCH1516_ALE	= 425019	204 (1.070)	14 (0.080)	10/146	NT	6.7%	intergenic (+34/‑392)	USA300HOU_RS01985/gpmA_1	hypothetical protein/2,3‑bisphosphoglycerate‑dependent phosphoglycerate mutase
	?	USA300TCH1516_ALE	= 425031	207 (1.190)					intergenic (+46/‑380)	USA300HOU_RS01985/gpmA_1	hypothetical protein/2,3‑bisphosphoglycerate‑dependent phosphoglycerate mutase

TTAATTGGTTCAATTATCTTAATTGCAATCGTAACGTTAATTTTAAGAGCTATGCGTAAATAATAAAAAAATTCAATTGGAAATTGAAATAAAGATG‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑  >  USA300TCH1516_ALE/424923‑425019 ‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑aaagatgACAACTGAATGCCATCTTTATTTCAATTTCCAATTGAATTTTTTTATTATTTACGCATAGCTCTTAAAATTAACGTTACGATTGCAATTA  <  USA300TCH1516_ALE/425031‑424942                                                                                                                                                                                             TTAATTGGTTCAATTATCTTAATTGCAATCGTAACGTTAATTTTAAGAGCTATGCGTAAATAATAAAAAAATTCAATTGGAAATTGAAATA                                                                                                  <  2:3030744/91‑1 TTAATTGGTTCAATTATCTTAATTGCAATCGTAACGTTAATTTTAAGAGCTATGCGTAAATAATAAAAAAATTCAATTGGAAATTGAAATA                                                                                                  <  1:523465/91‑1  TAATTGGTTCAATTATCTTAATTGCAATCGTAACGTTAATTTTAAGAGCTATGCGTAAATAATAAAAAAATTCAATTGGAAATTGAAATAA                                                                                                 >  2:3566178/1‑91   AATTGGTTCAATTATCTTAATTGCAATCGTAACGTTAATTTTAAGAGCTATGCGTAAATAATAAAAAAATTCAATTGGAAATTGAAATAAA                                                                                                >  1:3353320/1‑91   AATTGGTTCAATTATCTTAATTGCAATCGTAACGTTAATTTTAAGAGCTATGCGTAAATAATAAAAAAATTCAATTGGAAATTGAAATAAA                                                                                                <  1:1939826/91‑1   AATTGGTTCAATTATCTTAATTGCAATCGTAACGTTAATTTTAAGAGCTATGCGTAAATAATAAAAAAATTCAATTGGAAATTGAAATAAA                                                                                                >  1:3352498/1‑91   AATTGGTTCAATTATCTTAATTACAATCGTAACGTTAATTTTAAGAGCTATGCGTAAATAATAAAAAAATTCAATTGGAAATTGAAATAAA                                                                                                <  2:3119965/91‑1   AATTGGTACAATTATCTTAATTGCAATCGTAACGTTAATTTTAAGAGCTATGCGTAAATAATAAAAAAATTCAATTGGAAATTGAAATAAA                                                                                                <  1:1939913/91‑1    ATTGGTTCAATTATCTTAATTGCAATCGTAACGTTAATTTTAAGAGCTATGCGTAAATAATAAAAAAATTCAATTGGAAATTGAAATAAAG                                                                                               <  2:84639/91‑1    ATTGGTTCAATTATCTTAATTGCAATCGTAACGTTAATTTTAAGAGCTATGCGTAAATAATAAAAAAATTCAATTGGAAATTGAAATAAAG                                                                                               <  1:1973564/91‑1    ATTGGTTCAATTATCTTAATTGCAATCGTAACGTTAATTTTAAGAGCTATGCGTAAATAATAAAAAAATTCAATTGGAAATTGAAATAAAG                                                                                               <  2:2408669/91‑1    ATTGGTTCAATTATCTTAATTGCAATCGTAACGTTAATTTTAAGAGCTATGCGTAAATAATAAAAAAATTCAATTGGAAATTGAAATAAAG                                                                                               >  1:2990407/1‑91    ATTGGTTCAATTATCTTAATTGCAATCGTAACGTTAATTTTAAGAGCTATGCGTAAATAATAAAAAAATTCAATTGGAAATTGAAATAAAG                                                                                               >  1:3445233/1‑91     TTGGTTCAATTATCTTAATTGCAATCGTAACGTTAATTTTAAGAGCTATGCGTAAATAATAAAAAAATTCAATTGGAAATTGAAATAAAGA                                                                                              >  1:3431566/1‑91       GGTTCAATTATCTTAATTGCAATCGTAACGTTAATTTTAAGAGCTATGCGTAAATAATAAAAAAATTCAATTGGAAATTGAAATAAAGATG                                                                                            >  1:2042978/1‑91       GGTTCAATTATCTTAATTGCAATCGTAACGTTAATTTTAAGAGCTATGCGTAAATAATAAAAAAATTCAATTGGAAATTGAAATAAAGATG                                                                                            >  1:1272415/1‑91                     AATTGCAATCGTAACGTTAATTTTAAGAGCTATGCGTAAATAATAAAAAAATTCAATTGGAAATTGAAATAAAGATGACAACTGAATGCCA                                                                              <  1:338613/91‑1                       TTGCAATCGTAACGTTAATTTTAAGAGCTATGCGTAAATAATAAAAAAATTCAATTGGAAATTGAAATAAAGATGACAACTGAATGCCATC                                                                            <  2:1668458/91‑1                        TGCAATCGTAACGTTAATTTTAAGAGCTATGCGTAAATAATAAAAAAATTCAATTGGAAATTGAAATAAAGATGACAACTGAATGCCATCT                                                                           <  2:948665/91‑1                           AATCGTAACGTTAATTTTAAGAGCTATGCGTAAATAATAAAAAAATTCAATTGGAAATTGAAATAAAGATGACAACTGAATGCCATCTTTA                                                                        <  1:2153413/91‑1                            ATCGTAACGTTAATTTTAAGAGCTATGCGTAAATAATAAAAAAATTCAATTGGAAATTGAAATAAAGATGACAACTGAATGCCATCTTTAT                                                                       <  2:556479/91‑1                            ATCGTAACGTTAATTTTAAGAGCTATGCGTAAATAATAAAAAAATTCAATTGGAAATTGAAATAAAGATGACAACTGAATGCCATCTTTAT                                                                       <  1:1730522/91‑1                            ATCGTAACGTTAATTTTAAGAGCTATGCGTAAATAATAAAAAAATTCAATTGGAAATTGAAATAAAGATGACAACTGAATACCATCTTTAT                                                                       <  2:3736474/91‑1                             TCGTAACGTTAATTTTAAGAGCTATGCGTAAATAATAAAAAAATTCAATTGGAAATTGAAATAAAGATGACAACTGAATGCCATCTTTATT                                                                      <  1:2298932/91‑1                               GTAACGTTAATTTTAAGAGCTATGCGTAAATAATAAAAAAATTCAATTGGAAATTGAAATAAAGATGACAACTGAATGCCATCTTTATTTC                                                                    <  2:2462698/91‑1                               GTAACGTTAATTTTAAGAGCTATGCATAAATAATAAAAAAATTCAATTGGAAATTGAAATAAAGATGACAACTGAATGCCATCTTTATTTC                                                                    <  2:1204891/91‑1                                TAACGTTAATTTTAAGAGCTATGCGTAAATAATAAAAAAATTCAATTGGAAATTGAAATAAAGATGACAACTGAATGCCATCTTTATTTCA                                                                   <  2:1871767/91‑1                                TAACGTTAATTTTAAGAGCTATGCGTAAATAATAAAAAAATTCAATTGGAAATTGAAATAAAGATGACAACTGAATGCCATCTTTATTTCA                                                                   <  2:1871602/91‑1                                 AACGTTAATTTTAAGAGCTATGCGTAAATAATAAAAAAATTCAATTGGAAATTGAAATAAAGATGACAACTGAATGCCATCTTTATTTCAA                                                                  <  1:3394032/91‑1                                                   TATGCGTAAATAATAAAAAAATTCTATTGGAATTTGAAATAAAGATGACAACTGAATGCCATCTTTATTTCAATTTCCAATTGAATTTTTT                                                <  2:1491818/91‑1                                                                                           AAAGATGACAACTGAATGCCATCTTTATTTCAATTTCCAATTGAATTTTTTTATTATTTACGCATAGCTCTTAAAATTAACGTTACGATTG        >  1:2622685/1‑91                                                                                           AAAGATGACAACTGAATGCCATCTTTATTTCAATTTCCAATTGAATTTTTTTATTATTTACGCATAGCTCTTAAAATTAACGTTACGATTG        <  2:634620/91‑1                                                                                           AAAGATGACAACTGAATGCCATCTTTATTTCAATTTCCAATTGAATTTTTTTATTATTTACGCATAGCTATTAAAATTAACGTTACGATTG        <  2:1298569/91‑1                                                                                            AAGATGACAACTGAATGCCATCTTTATTTCAATTTCCAATTGAATTTTTTTATTATTTACGCATAGCTCTTAAAATTAACGTTACGATTGC       <  2:2274300/91‑1                                                                                            AAGATGACAACTGAATGCCATCTTTATTTCAATTTCCAATTGAATTTTTTTATTATTTACGCATAGCGCTTAAAATTAACGTTACGATTGC       >  1:3019579/1‑91                                                                                             AGATGACAACTGAATGCCATCTTTATTTCAATTTCCAATTGAATTTTTTTATTATTTACGCATAGCTCTTAAAATTAACGTTACGATTGCA      >  2:126477/1‑91                                                                                             AGATGACAACTGAATGCCATCTTTATTTCAATTTCCAATTGAATTTTTTTATTATTTACGCATAGCTCTTAAAATTAACGTTACGATTGCA      >  2:258510/1‑91                                                                                             AGATGACAACTGAATGCCATCTTTATTTCAATTTCCAATTGAATTTTTTTATTATTTACGCATAGCTCTTAAAATTAACGTTACGATTGCA      >  1:1582827/1‑91                                                                                              GATGACAACTGAATGCCATCTTTATTTCAATTTCCAATTGAATTTTTTTATTATTTACGCATAGCTCTTAAAATTAACGTTACGATTGCAA     <  1:2333134/91‑1                                                                                                TGACATCTGAATGCCATCTTTACTTCAATTTCCAATTGAATTTTTTTATTATTTACGCATAGCTCTTAAAATTAACGTTACGATTGCAATT   <  2:3136433/91‑1                                                                                                TGACAACTGAATGCCATCTTTATTTCAATTTCCAATTGAATTTTTTTATTATTTACGCATAGCTCTTAAAATTAACGTTACGATTGCAATT   >  1:1205729/1‑91                                                                                                TGACAACTGAATGCCATCTTTATTTCAATTTCCAATTGAATTTTTTTATTATTTACGCATAGCTCTTAAAATTAACGTTACGATTGCAATT   >  2:1784582/1‑91                                                                                                TGACAACTGAATGCCATCTTTATTTCAATTTCCAATTGAATTTTTTTATTATTTACGCATAGCTCTTAAAATTAACGTTACGATTGCAATT   >  1:370510/1‑91                                                                                                TGACAACTGAATGCCATCTTTATTTCAATTTCCAATTGAATTTTTTTATTATTTACGCATAGCTCTTAAAATTAACGTTACGATTGCAATT   >  2:3750675/1‑91                                                                                                TGACAACTGAATGCCATCTTTATTTCAATTTCCAATTGAATTTTTTTATTATTTACGCATAGCTCTTAAAATTAACGTTACGATTGCAATT   >  1:370864/1‑91                                                                                                TGACAACTGAATGCCATCTTTATTTCAATTTCCAATTGAATTTTTTTATTATTTACGCATAGCTCTTAAAATTAACGTTACGATTGCAATT   <  2:3551220/91‑1                                                                                                TGACAACTGAATGCCATCTTTATTTCAATTTCCAATTGAATTTTTTTATTATTTACGCATAGCTCTTAAAATTAACGTTACGATTGCAATT   <  1:93851/91‑1                                                                                                 GACAACTGAATGCCATCTTTATTTCAATTTCCAATTGAATTTTTTTATTATTTACGCATAGCTCTTAAAATTAACGTTACGATTGCAATTA  >  2:3315094/1‑91                                                                                                 GACAACTGAATGCCATCTTTATTTCAATTTCCAATTGAATTTTTTTATTATTTACGCATAGCTCTTAAAATTAACGTTACGATTGCAATTA  >  1:158285/1‑91                                                                                                 GACAACTGAATGCCATCTTTATTTCAATTTCCAATTGAATTTTTTTATTATTTACGCATAGCTCTTAAAATTAACGTTACGATTGCAATTA  >  1:234003/1‑91                                                                                                 GACAACTGAATGCCATCTTTATTTCAATTTCCAATTGAATTTTTTTATTATTTACGCATAGCTCTTAAAATTAACGTTACGATTGCAATTA  >  1:1301873/1‑91                                                                                                 GACAACTGAATGCCATCTTTATTTCAATTTCCAATTGAATTTTTTTATTATTTACGCATAGCTCTTAAAATTAACGTTACGATTGCAATTA  >  2:2276332/1‑91                                                                                                                                                                                             TTAATTGGTTCAATTATCTTAATTGCAATCGTAACGTTAATTTTAAGAGCTATGCGTAAATAATAAAAAAATTCAATTGGAAATTGAAATAAAGATG‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑  >  USA300TCH1516_ALE/424923‑425019 ‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑aaagatgACAACTGAATGCCATCTTTATTTCAATTTCCAATTGAATTTTTTTATTATTTACGCATAGCTCTTAAAATTAACGTTACGATTGCAATTA  <  USA300TCH1516_ALE/425031‑424942

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.