New junction evidence
		seq id	position	reads (cov)	reads (cov)	score	skew	freq	annotation	gene	product
*	?	USA300TCH1516_ALE	= 1199293	128 (0.670)	14 (0.080)	9/144	NT	9.7%	intergenic (+20/‑63)	USA300HOU_RS05980/USA300HOU_RS05985	hypothetical protein/hypothetical protein
	?	USA300TCH1516_ALE	= 1199312	147 (0.860)					intergenic (+39/‑44)	USA300HOU_RS05980/USA300HOU_RS05985	hypothetical protein/hypothetical protein

GCTGCAATTATCGTTTTAGTATTATTCCAAAAAGGGTTACTCCAAATCTTTAATTGGATTTTAATTCAATTACAATAAATTAAGCGACATAACGAGGC‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑  >  USA300TCH1516_ALE/1199196‑1199293 ‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑aacgaggcTAAAGTATCATGTACCCTTGCCTCGTTATGTCGCTTAATTTATTGTAATTGAATTAAAATCCAATTAAAGATTTGGAGTAACCCTTTTTG  <  USA300TCH1516_ALE/1199312‑1199223                                                                                                                                                                                              GCTGCAATTATCGTTTTAGTATTATTCCAAAAAGGGTTACTCCAAATCTTTAATTGGATTTTAATTCAATTACAATAAATTAAGCGACATA                                                                                                   <  1:856443/91‑1  CTGCAATTATCGTTTTAGTATTATTCCAAAAAGGGTTACTCCAAATCTTTAATTGGATTTTAATTCAATTACAATAAATTAAGCGACATAA                                                                                                  >  2:3142454/1‑91   TGCAATTATCGTTTTAGTATTATTCCAAAAAGGGTTACTCCAAATCTTTAATTGGATTTTAATTCAATTACAATAAATTAAGCGACATAAC                                                                                                 >  1:2278194/1‑91   TGCAATTATCGTTTTAGTATTATTCCAAAAAGGGTTACTCCAAATCTTTAATTGGATTTTAATTCAATTACAATAAATTAAGCGACATAAC                                                                                                 <  1:430622/91‑1   TGCAATTATCGTTTTAGTATTATTCCAAAAAGGGTTACTCCAAATCTTTAATTGGATTTTAATTCAATTACAATAAATTAAGCGACATAAC                                                                                                 <  1:575435/91‑1   TGCAATTATCGTTTTAGTATTATTCCAAAAAGGGTTACTCCAAATCTTTAATTGGATTTTAATTCAATTACAATAAATTAAGCGACATAAC                                                                                                 >  2:3781112/1‑91   TGCAATTATCGTTTTAGTATTATTCCAAAAAGGGTTACTCCAAATCTTTAATTGGATTTTAATTCAATTACAATAAATTAAGCGACATAAC                                                                                                 >  2:3503716/1‑91     CAATTATCGTTTTAGTATTATTCCAAAAAGGGTTACTCCAAATCTTTAATTGGATTTTAATTCAATTACAATAAATTAAGCGACATAACGA                                                                                               <  2:197643/91‑1     CAATTATCGTTTTAGTATTATTCCAAAAAGGGTTACTCCAAATCTTTAATTGGATTTTAATTCAATTACAATAAATTAAGCGACATAACGA                                                                                               <  1:2685184/91‑1      AATTATCGTTTTAGTATTATTCCAAAAAGGGTTACTCCAAATCTTTAATTGGATTTTAATTCAATTACAATAAATTAAGCGACATAACGAG                                                                                              >  1:131962/1‑91       ATTATCGTTTTAGTATTATTCCAAAAAGGGTTACTCCAAATCTTTAATTGGATTTTAATTCAATTACAATAAATTAAGCGACATAACGAGG                                                                                             >  1:649396/1‑91        TTATCGTTTTAGTATTATTCCAAAAAGGGTTACTCCAAATCTTTAATTGGATTTTAATTCAATTACAATAAATTAAGCGACATAACGAGGC                                                                                            <  2:1815082/91‑1        TTATCGTTTTAGTATTATTCCAAAAAGGGTTACTCCAAATCTTTAATTGGATTTTAATTCAATTACAATAAATTAAGCGACATAACGAGGC                                                                                            <  1:2331792/91‑1           TCGTTTTAGTATTATTCCAAAAAGGGTTACTCCAAATCTTTAATTGGATTTTAATTCAATTACAATAAATTAAGCGACATAACGAGGCTAA                                                                                         >  2:1112442/1‑91                          TCCAAAAAGGGTTACTCCAAATCTTTAATTGGATTTTAATTCAATTACAATAAATTAAGCGACATAACGAGGCTAAAGTATCATGTACCCT                                                                          <  2:701456/91‑1                           CCAAAAAGGGTTACTCCAAATCTTTAATTGGATTTTAATTCAATTACAATAAATTAAGCGACATAACGAGGCTAAAGTATCATGTACCCTT                                                                         <  2:276976/91‑1                            CAAAAAGGGTTACTCCAAATCTTTAATTGGATTTTAATTCAATTACAATAAATTAAGCGACATAACGAGGCTAAAGTATCATGTACCCTTG                                                                        <  1:3638271/91‑1                             AAAAAGGGTTACTCCAAATCTTTAATTGGATTTTAATTCAATTACAATAAATTAAGCGACATAACGAGGCTAAAGTATCATGTACCCTTGC                                                                       <  2:2296455/91‑1                             AAAAAGGGTTACTCCAAATCTTTAATTGGATTTTAATTCAATTACAATAAATTAAGCGACATAACGAGGCTAAAGTATCATGTACCCTTGC                                                                       <  1:2883704/91‑1                              AAAAGGGTTACTCCAAATCTTTAATTGGATTTTAATTCAATTACAATAAATTAAGCGACATAACGAGGCTAAAGTATCATGTACCCTTGCC                                                                      <  1:1112442/91‑1                              AAAAGGGTTACTCCAAATCTTTAATTGGATTTTAATTCAATTACAATAAATTAAGCGACATAACGAGGCTAAAGTATCATGTACCCTTGCC                                                                      <  1:2467979/91‑1                               AAAGGGTTACTCCAAATCTTTAATTGGATTTTAATTCAATTACAATAAATTAAGCGACATAACGAGGCTAAAGTATCATGTACCCTTGCCT                                                                     <  1:546717/91‑1                               AAAGGGTTACTCCAAATCTTTAATTGGATTTTAATTCAATTACAATAAATTAAGCGACATAACGAGGCTAAAGTATCATGTACCCTTGCCT                                                                     <  1:35152/91‑1                               AAAGGGTTACTCCAAATCTTTAATTGGATTTTAATTCAATTACAATAAATTAAGCGACATAACGAGGCTAAAGTATCATGTACCCTTGCCT                                                                     <  1:2333458/91‑1                                 AGGGTTACTCCAAATCTTTAATTGGATTTTAATTCAATTACAATAAATTAAGCGACATAACGAGGCTAAAGTATCATGTACCCCTGCCTCG                                                                   <  1:2259800/91‑1                                           CAAATCTTTAATTGGATTTTAATTCAATTACAATAAATTAAGCGACATAACGAGGCTAAAGTATCATGTACCCTTGCCTCGTTATGTCGCT                                                         <  1:2057918/91‑1                                                                   CAATTACAATAAATTAAGCGACATAACGAGGCTAAAGTATCATGTACCCTTGCCTCGTTATGTCGCTTAATTTATTGTAATTGAATTAAAA                                 <  2:1374670/91‑1                                                                   CAATTACAATAAATTAAGCGACATAACGAGGCTAAAGTATCATGTACCCTTGCCTAGTTATGTCGCTTAATTTATTGTAATTGAATTAAAA                                 <  2:1374368/91‑1                                                                                           gACGAGGCTAAAGTATCATGTACCCGTGCCTCGTTATGTCGCTTAATTTATTGTAATTGAATTAAAATCCAATTAAAGATTTGGAGTAACC         <  2:3862087/90‑1                                                                                           AACGAGGCTGAAGTATCATGTACCCTTGCCTCGTTATGTCGCTTAATTTATTGTAATTGAATTAAAATCCAATTAAAGATTTGGAGTAACC         <  1:3716044/91‑1                                                                                           AACGAGGCTAAAGTATCATGTACCCTTGCCTCGTTATGTCGCTTAATTTATTGTAATTGAATTAAAATCCAATTAAAGATTTGGAGTAACC         <  2:483461/91‑1                                                                                           AACGAGGCTAAAGTATCATGTACCCTTGCCTCGTTATGTCGCTTAATTTATTGTAATTGAATTAAAATCCAATTAAAGATTTGGAGTAACC         <  2:3095520/91‑1                                                                                           AACGAGGCTAAAGTATCATGTACCCTTGCCTCGTTATGTCGCTTAATTTATTGTAATTGAATTAAAATCCAATTAAAGATTTGGAGTAACC         <  2:844701/91‑1                                                                                           AACGAGGCTAAAGTATCATGTACCCTTGCCTCGTTATGTCGCTTAATTTATTGTAATTGAATTAAAATCCAATTAAAGATTTGGAGTAACC         <  2:2038233/91‑1                                                                                           AACGAGGCTAAAGTATCATGTACCCTTGCCTCGTTATGTCGCTTAATTTATTGTAATTGAATTAAAATCCAATTAAAGATTTGGAGTAACC         <  2:732501/91‑1                                                                                           AACGAGGCTAAAGTATCATGTACCCTTGCCTCGTTATGTCGCTTAATTTATTGTAATTGAATTAAAATCCAATTAAAGATTTGGAGTAACC         >  2:442802/1‑91                                                                                           AACGAGGCTAAAGTATCATGTACCCTTGCCTCGTTATGTCGCTTAATTTATTGTAATTGAATTAAAATCCAATTAAAGATTTGGAGTAACC         >  2:442910/1‑91                                                                                           AACGAGGCTAAAGTATCATGTACCCTTGCCTCGTTATGTCGCTTAATTTATTGTAATTGAATTAAAATCCAATTAAAGATTTGGAGTAACC         <  2:483382/91‑1                                                                                            ACGAGGCTAAAGTATCATGTACCCTTGCCTCGTTATGTCGCTTAATTTATTGTAATTGAATTAAAATCCAATTAAAGATTTGGAGTAACCC        <  1:219539/91‑1                                                                                            ACGAGGCTAAAGTATCATGTACCCTTGCCTCGTTATGTCGCTTAATTTATTGTAATTGAATTAAAATCCAATTAAAGATTTGGAGTAACCC        <  2:2166790/91‑1                                                                                            ACGAGGCTAAAGTATCATGTACCCTTGCCTCGTTATGTCGCTTAATTTATTGTAATTGAATTAAAATCCAATTAAAGATTTGGAGTAACCC        >  1:2068587/1‑91                                                                                            ACGAGGCTAAAGTATCATGTACCCTTGCCTCGTTATGTCGCTTAATTTATTGTAATTGAATTAAAATCCAATTAAAGATTTGGAGTAACCC        >  2:740024/1‑91                                                                                            ACGAGGCTAAAGTATCATGTACCCTTGCCTCGTTATGTCGCTTAATTTATTGTAATTGAATTAAAATCCAATTAAAGATTTGGAGTAACCC        >  1:792417/1‑91                                                                                              GAGGCTAAAGTATCATGTACCCTTGCCTCGTTATGTCGCTTAATTTATTGTAATTGAATTAAAATCCAATTAAAGATTTGGAGTAACCCTT      >  1:1131162/1‑91                                                                                              GAGGCTAAAGTATCATGTACCCTTGCCTCGTTATGTCGCTTAATTTATTGTAATTGAATTAAAATCCAATTAAAGATTTGGAGTAACCCTT      >  1:195562/1‑91                                                                                              GAGGCTAAAGTATCATGTACCCTTGCCTCGTTATGTCGCTTAATTTATTGTAATTGAATTAAAATCCAATTAAAGATTTGGAGTAACCCTT      <  2:2528985/91‑1                                                                                               AGGCTAAAGTATCATGTACCCTTGCCTCGTTATGTCGCTTAATTTATTGTAATTGAATTAAAATCCGATTAAAGATTTGGAGTAACCCTTT     >  2:3600433/1‑91                                                                                               AGGCTAAAGTATCATGTACCCTTGCCTCGTTATGTCGCTTAATTTATTGTAATTGAATTAAAATCCAATTAAAGATTTGGAGTAACCCTTT     >  2:2515512/1‑91                                                                                               AGGCTAAAGTATCATGTACCCTTGCCTCGTTATGTCGCTTAATTTATTGTAATTGAATTAAAATCCAATTAAAGATTTGGAGTAACCCTTT     >  2:58035/1‑91                                                                                                GGCTAAAGTATCATGTACCCTTGCCTCGTTATGTCGCTTAGTTTATTGTAATTGAATTAAAATCCAATTAAAGATTTGGAGTAACCCTTTT    >  2:3181543/1‑91                                                                                                GGCTAAAGTATCATGTACCCTTGCCTCGTTATGTCGCTTAATTTATTGTAATTGAATTAAAATCCAATTAAAGATTTGGAGTAACCCTTTT    >  2:209404/1‑91                                                                                                 GCTAAAGTATCATGTACCCTTGCCTCGTTATGTCGCTTAATTTCTTGTAATTGAATTAAAATCCAATTAAAGATTTGGAGTAACCCTTTTT   >  2:143514/1‑91                                                                                                 GCTAAAGTATCATGTACCCTTGCCTCGTTATGTCGCTTAATTTATTGTAATTGAATTAAAATCCAATTAAAGATTTGGAGTAACCCTTTTT   >  1:2142857/1‑91                                                                                                 GCTAAAGTATCATGTACCCTTGCCTCGTTATGTCGCTTAATTTATTGTAATTGAATTAAAATCCAATTAAAGATTTGGAGTAACCCTTTTT   >  2:1462188/1‑91                                                                                                 GCTAAAGTATCATGTACCCTTGCCTCGTTATGTCGCTTAATTTATTGTAATTGAATTAAAATCCAATTAAAGATTTGGAGTAACCCTTTTT   >  1:3564178/1‑91                                                                                                 GCTAAAGTATCATGTACCCTTGCCTCGTTATGTCGCTTAATTTATTGTAATTGAATTAAAATCCAATTAAAGATTTGGAGTAACCCTTTTT   >  1:3355162/1‑91                                                                                                  CTAAAGTATCATGTACCCTTGCCTCGTTATGTCGCTTAATTTATTGTAATTGAATTAAAATCCAATTAAAGATTTGGAGTAACCCTTTTTG  >  2:1798357/1‑91                                                                                                  CTAAAGTATCATGTACCCTTGCCTCGTTATGTCGCTTAATTTATTGTAATTGAATTAAAATCCAATTAAAGATTTGGAGTAACCCTTTTTG  >  1:1897552/1‑91                                                                                                  CTAAAGTATCATGTACCCTTGCCTCGTTATGTCGCTTAATTTATTGTAATTGAATTAAAATCCAATTAAAGATTTGGAGTAACCCTTTTTG  >  2:3530272/1‑91                                                                                                  CTAAAGTATCATGTACCCTTGCCTCGTTATGTCGCTTAATTTATTGTAATTGAATTAAAATCCAATTAAAGATTTGGAGTAACCCTTTTTG  <  2:3396040/91‑1                                                                                                  CTAAAGTATCATGTACCCTTGCCTCGTTATGTCGCTTAATTTATTGTAATTGAATTAAAATCCAATTAAAGATTTGGAGTAACCCTTTTTG  <  2:3283108/91‑1                                                                                                                                                                                              GCTGCAATTATCGTTTTAGTATTATTCCAAAAAGGGTTACTCCAAATCTTTAATTGGATTTTAATTCAATTACAATAAATTAAGCGACATAACGAGGC‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑  >  USA300TCH1516_ALE/1199196‑1199293 ‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑aacgaggcTAAAGTATCATGTACCCTTGCCTCGTTATGTCGCTTAATTTATTGTAATTGAATTAAAATCCAATTAAAGATTTGGAGTAACCCTTTTTG  <  USA300TCH1516_ALE/1199312‑1199223

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.