New junction evidence
		seq id	position	reads (cov)	reads (cov)	score	skew	freq	annotation	gene	product
*	?	USA300TCH1516_ALE	1853635 =	205 (1.080)	17 (0.100)	10/144	NT	8.9%	intergenic (+38/+60)	acuC/ccpA	Acetoin utilization protein AcuC/Catabolite control protein A
	?	USA300TCH1516_ALE	1853683 =	162 (0.950)					intergenic (+86/+12)	acuC/ccpA	Acetoin utilization protein AcuC/Catabolite control protein A

TACCTCACAGAATTGAATACCGAGGAACTACAAAATAAATTCACAAAATTAGGCATTCATCTAACGACCCAAATTATATGGGTGTTGGAAGAATGCCT‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑  <  USA300TCH1516_ALE/1853732‑1853635 ‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑gaatgcctAATTTTGTGAATTTATTTTGTAGTTCCTCGGTATTCAATTCTGTGAGGTAAAACTACATTTGGTTCTTCTATCTTTTCATCGTTCATATA  >  USA300TCH1516_ALE/1853683‑1853772                                                                                                                                                                                              TACCTCACAGAATTGAATACCGAGGAACTACAAAATAAATTCACAAAATTAGGCATTCATCTAACGACCCAAATTATATGGGTGTTGGAAG                                                                                                   <  1:3860402/91‑1  ACCTCACAGAATTGAATACCGAGGAACTACAAAATAAATTCACAAAATTAGGCATTCATCTAACGACCCAAATTATATGGGTGTTGGAAGA                                                                                                  >  2:2802900/1‑91   CCTCACAGAATTGAATACCGAGGAACTACAAAATAAATTCACAAAATTAGGCATTCATCTAACGACCCAAATTATATGGGTGTTGGAAGAA                                                                                                 >  1:3135025/1‑91   CCTCACAGAATTGAATACCGAGGAACTACAAAATAAATTCACAAAATTAGGCATTCATCTAACGACCCAAATTATAT‑GGTGTTGGAAGAAT                                                                                                >  2:3208012/1‑91    CTCACAGAATTGAATACCGGGGAACTACAAAATAAATTCACAAAATTAGGCATTCATCTAACGACCCAAATTATATGGGTGTTGGAAGAAT                                                                                                <  1:1318241/91‑1    CTCACAGAATTGAATACCGAGGAACTACAAAATAAATTCACAAAATTAGGCATTCATCTAACGACCCAAATTATATGGGTGTTGGAAGAAT                                                                                                <  2:1407277/91‑1     TCACAGAATTGAATACCGAGGAACTACAAAATAAATTCACAAAATTAGGCATTCATCTAACGACCCAAATTATATGGGTGTTGGAAGAATG                                                                                               <  2:3175389/91‑1      gACAGAATTGAATACCGAGGAACTACAAAATAAATTCACAAAATTAGGCATTCATCTAACGACCCAAATTATATGGGTGTTGGAAGAATGC                                                                                              <  2:759951/90‑1      CACAGAATTGAATACCGAGGAACTACAAAATAAATTCTCAAAATTAGGCATTCATCTAACGACCCAAATTATATGGGTGTTGGAAGAATGC                                                                                              <  2:2135590/91‑1      CACAGAATTGAATACCGAGGAACTACAAAATAAATTCACAAAATTAGGCATTCATCTAACGACCCAAATTATATGGGTGTTGGAAGAATGC                                                                                              <  2:1316712/91‑1       ACAGAATTGAATACCGAGGAACTACAAAATAAATTCACAAAATTAGGCATTCATCTAACGACCCAAATTATATGGGTGTTGGAAGAATGCC                                                                                             >  1:2648716/1‑91       ACAGAATTGAATACCGAGGAACTACAAAATAAATTCACAAAATTAGGCATTCATCTAACGACCCAAATTATATGGGTGTTGGAAGAATGCC                                                                                             >  2:2614655/1‑91        CAGAATTGAATACCGAGGAACTACAAAATAAATTCACAAAATTAGGCATTCATCTAACGACCCAAATTATATGGGTGTTGGAAGAATGCCT                                                                                            <  1:772938/91‑1        CAGAATTGAATACCGAGGAACTACAAAATAAATTCACAAAATTAGGCATTCATCTAACGACCCAAATTATATGGGTGTTGGAAGAATGCCT                                                                                            >  2:2156209/1‑91           AATTGAATACCGAGGAACTACAAAATAAATTCACAAAATTAGGCATTCATCTAACGACCCAAATTATATGGGTGTTGGAAGAATGCCT                                                                                            >  2:3827523/1‑88           AATTGAATACCGAGGAACTACAAAATAAATTCACAAAATTAGGCATTCATCTAACGACCCAAATTATATGGGTGTTGGAAGAATGCCT                                                                                            <  1:3827523/88‑1                                               AATTAGGCATTCATCTAACGACCCAAATTATATGGGTGTTGGAAGAATGCCTAATTTTGTGAATTTATTTTGTAGTTCCTCGGTATTCAAT                                                     >  1:3406495/1‑91                                                ATTAGGCATTCATCTAACGACCCAAATTATATGGGTGTTGGAAGAATGCCTAATTTTGTGAATTTATTTTGTAGTTCCTCGGTATTCAATT                                                    >  2:1217312/1‑91                                                 TTAGGCATTCATCTAACGACCCAAATTATATGGGTGTTGGAAGAATGCCTAATTTTGTGAATTTATTTTGTAGTTCCTCGGTATTCAATTC                                                   >  1:2815158/1‑91                                                 TTAGGCATTCATCTAACGACCCAAATTATATGGGTGTTGGAAGAATGCCTAATTTTGTGAATTTATTTTGTAGTTCCTCGGTATTCAATTC                                                   >  1:2815491/1‑91                                                    GGCATTCATCTAACGACCCACATTATATGGGTGTTGGAAGAATGCCTAATTTTGTGAATTTATTTTGTAGTTCCTCGGTATTCAATTCTGT                                                >  2:174731/1‑91                                                    GGCATTCATCTAACGACCCAAATTATATGGGTGTTGGAAGAATGCCTAATTTTGTGAATTTATTTTGTAGTTCCTCGGTATTCAATTCTGT                                                >  1:2270151/1‑91                                                     GCATTCATCTAACGACCCAAATTATATGGGTGTTGGAAGAATGCCTAATTTTGTGAATTTATTTTGTAGTTCCTCGGTATTCAATTCTGTG                                               >  2:2309557/1‑91                                                     GCATTCATCTAACGACCCAAATTATATGGGTGTTGGAAGAATGCCTAATTTTGTGAATTTATTTTGTAGTTCCTCGGTATTCAATTCTGTG                                               >  1:3069444/1‑91                                                     GCATTCATCTAACGACCCAAATTATATGGGTGTTGGAAGAATGCCTAATTTTGTGAATTTATTTTGTAGTTCCTCGGTATTCAATTCTGTG                                               >  2:2000612/1‑91                                                     GCATTCATCTAACGACCCAAATTATATGGGTGTTGGAAGAATGCCTAATTTTGTGAATTTATTTTGTAGTTCCTCGGTATTCAATTCTGTG                                               >  2:3875070/1‑91                                                     GCATTCATCTAACGACCCAAATTATATGGGTGTTGGAAGAATGCCTAATTTTGTGAAATTATTTTGTAGTTCCTCGGTATTCAATTCTGTG                                               >  1:3178803/1‑91                                                      CATTCATCTAACGACCCAAATTATATGGGTGTTGGAAGAATGCCTAATTTTGTGAATTTATTTTGTAGTTCCTCGGTATTCAATTCTGTGA                                              >  1:8115/1‑91                                                        TTCATCTAACGACCCAAATTATATGGGTGTTGGAAGAATGCCTAATTTTGTGAATTTATTTTGTAGTTCCTCGGTATTCAATTCTGTGAGG                                            >  1:2315999/1‑91                                                        TTCATCTAACGACCCAAATTATATGGGTGTTGGAAGAATGCCTAATTTTGTGAATTTATTTTGTAGTTCCTCGGTATTCAATTCTGTGAGG                                            >  2:862781/1‑91                                                             CTAACGACCCAAATTATATGGGTGTTGGAAGAATGCCTAATTTTGTGAATTTATTTTGTAGTTCCTCGGTATTCAATTCTGTGAGGTAAAA                                       >  2:940302/1‑91                                                              TAACGACCCAAATTATATGGGTGTTGGAAGAATGCCTAATTTTGTGAATTTATTTTGTAGTTCCTCGGTATTCAATTCTGTGAGGTAAAAC                                      >  1:3011476/1‑91                                                                           TATATGGGTGTTGGAAGAATGCCTAATTTTGTGAATTTATTTTGTAGTTCCTCGGTATTCAATTCTGTGAGGTAAAACTACATTTGGTTCT                         <  2:3011476/91‑1                                                                                           GAATGCCTAATTTTGTGAATTTATTTTGTAGTTCCTCGGTATTCAATTCTGTGAGGTAAAACTACATTTGGTT                           >  2:2594484/1‑73                                                                                           GAATGCCTAATTTTGTGAATTTATTTTGTAGTTCCTCGGTATTCAATTCTGTGAGGTAAAACTACATTTGGTT                           <  1:2594484/73‑1                                                                                             ATGCCTAATTTTGTGAATTTATTTTGTAGTTCCTCGGTATTCAATTCTGTGAGGTAAAACTACATTTGGTTCTTCTATCTTTTCATCGTTC       >  2:2499670/1‑91                                                                                              TGCCTAATTTTGTGAATTTATTTTGTAGTTCCTCGGTATTCAATTCTGTGAGGTAAAACTACATTTGGTTCTTCTATCTTTTCATCGTTCA      >  1:1551999/1‑91                                                                                              TGCCTAATTTTGTGAATTTATTTTGTAGTTCCTCGGTATTCAATTCTGTGAGGTAAAACTACATTTGGTTCTTCTATCTTTTCATCGTTCA      >  1:1889757/1‑91                                                                                              TGCCTAATTTTGTGAATTTATTTTGTAGTTCCTCGGTATTCAATTCTGTGAGGTAAAACTACATTTGGTTCTTCTATCTTTTCATCGTTCA      <  2:2624642/91‑1                                                                                               GCCTAATTTTGTGAATTTATTTTGTAGTTCCTCGGTATTCAATTCTGTGAGGTAAAACTACATTTGGTTCTTCTATCTTTTCATCGTTCAT     <  1:771713/91‑1                                                                                               GCCTAATTTTGTGAATTTATTTTGTAGTTCCTCGGTATTCAATTCTGTGAGGTAAAACTACATTTGGTTCTTCTATCTTTTCATCGTTCAT     <  1:1995101/91‑1                                                                                               GCCTAATTTTGTGAATTTATTTTGTAGTTCCTCGGTATTCAATTCTGTGAGGTAAAACTACATTTGGTTCTTCTATCTTTTCATCGTTCAT     <  1:234797/91‑1                                                                                               GCCTAATTTTGTGAATTTATTTTGTAGTTCCTCGGTATTCAATTCTGTGAGGTAAAACTACATTTGGTTCTTCTATCTTTTCATCGTTCAT     <  2:2490203/91‑1                                                                                               GCCTAATTTTGTGAATTTATTTTGTAGTTCCTCGGTATTCAATTCTGTGAGGTAAAACTACATTTGGTTCTTCTATCTTTTCATCGTTCAT     <  2:1484752/91‑1                                                                                                CCTAATTTTGTGAATTTATTTTGTAGTTCCTCGGTATTCAATTCTGTGAGGTAAAACTACATTTGGTTCTTCTATCTTTTCATCGTTCATA    >  1:2767549/1‑91                                                                                                CCTAATTTTGTGAATTTATTTTGTAGTTCCTCGGTATTCAATTCTGTGAGGTAAAACTACATTTGGTTCTTCTATCTTTTCATCGCTCATA    >  2:2644495/1‑91                                                                                                 CTAATTTTGTGAATTTATTTTGTAGTTCCTCGGTATTCAATTCTGTGAGGTAAAACTACATTTGGTTCTTCTATCTTTTCATCGTTCATAT   >  1:3530845/1‑91                                                                                                 CTAATTTTGTGAATTTATTTTGTAGTTCCTCGGTATTCAATTCTGTGAGGTAAAACTACATTTGGTTCTTCTATCTTTTCATCGTTCATAT   <  1:2081741/91‑1                                                                                                 CTAATTTTGTGAATTTATTTTGTAGTTCCTCGGTATTCAATTCTGTGAGGTAAAACTACATTTGGTTCTTCTATCTTTTCATCGTTCATAT   >  2:561327/1‑91                                                                                                 CTAATTTTGTGAATTTATTTTGTAGTTCCTCGGTATTCAATTCTGTGAGGTAAAACTACATTTGGTTCTTCTATCTTTTCATCGTTCATAT   >  1:509660/1‑91                                                                                                 CTAATTTTGTGAATTTATTTTGTAGTTCCTCGGTATTCAATTCTGTGAGGTAAAACTACATTTGGTTCTTCTATCTTTTCATCGTTCATAT   >  1:510404/1‑91                                                                                                 CTAATTTTGTGAATTTATTTTGTAGTTCCTCGGTATTCAATTCTGTGAGGTAAAACTACATTTGGTTCTTCTATCTTTTCATCGTTCATAT   >  2:1787596/1‑91                                                                                                  TAATTTTGTGAATTTATTTTGTAGTTCCTCGGTATTCAATTCTGTGAGGTAAAACTACATTTGGTTCTTCTATCTTTTCATCGTTCATATA  >  1:2389205/1‑91                                                                                                                                                                                              TACCTCACAGAATTGAATACCGAGGAACTACAAAATAAATTCACAAAATTAGGCATTCATCTAACGACCCAAATTATATGGGTGTTGGAAGAATGCCT‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑  <  USA300TCH1516_ALE/1853732‑1853635 ‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑gaatgcctAATTTTGTGAATTTATTTTGTAGTTCCTCGGTATTCAATTCTGTGAGGTAAAACTACATTTGGTTCTTCTATCTTTTCATCGTTCATATA  >  USA300TCH1516_ALE/1853683‑1853772

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.