New junction evidence
		seq id	position	reads (cov)	reads (cov)	score	skew	freq	annotation	gene	product
*	?	USA300TCH1516_ALE	= 1199293	163 (0.800)	18 (0.100)	7/144	NT	9.7%	intergenic (+20/‑63)	USA300HOU_RS05980/USA300HOU_RS05985	hypothetical protein/hypothetical protein
	?	USA300TCH1516_ALE	= 1199312	189 (1.030)					intergenic (+39/‑44)	USA300HOU_RS05980/USA300HOU_RS05985	hypothetical protein/hypothetical protein

GCTGCAATTATCGTTTTAGTATTATTCCAAAAAGGGTTACTCCAAATCTTTAATTGGATTTTAATTCAATTACAATAAATTAAGCGACATAACGAGGC‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑  >  USA300TCH1516_ALE/1199196‑1199293 ‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑aacgaggcTAAAGTATCATGTACCCTTGCCTCGTTATGTCGCTTAATTTATTGTAATTGAATTAAAATCCAATTAAAGATTTGGAGTAACCCTTTTTG  <  USA300TCH1516_ALE/1199312‑1199223                                                                                                                                                                                              GCTGCAATTGTCGTTTTAGTATTATTCCAAAAAGGGTTACTCCAAATCTTTAATTGGATTTTAATTCAATTACAATAAATTAAGCGACATA                                                                                                   <  2:1655024/91‑1 GCTGCAATTATCGTTTTAGTATTATTCCAAAAAGGGTTACTCCAAATCTTTAATTGGATTTTAATTCAATTACAATAAATTAAGCGACATA                                                                                                   >  1:3591289/1‑91 GCTGCAATTATCGTTTTAGTATTATTCCAAAAAGGGTTACTCCAAATCTTTAATTGGATTTTAATTCAATTACAATAAATTAAGCGACATA                                                                                                   <  1:3645068/91‑1  CTGCAATTATCGTTTTAGTATTATTCCAAAAAGGGTTACTCCAAATCTTTAATTGGATTTTAATTCAATTACAATAAATTAAGCGACATAA                                                                                                  <  1:327017/91‑1  CTGCAATTATCGTTTTAGTATTATTCCAAAAAGGGTTACTCCAAATCTTTAATTGGATTTTAATTCAATTACAATAAATTAAGCGACATAA                                                                                                  <  2:3136233/91‑1  CTGCAATTATCGTTTTAGTATTATTCCAAAAAGGGTTACTCCAAATCTTTAATTGGATTTTAATTCAATTACAATAAATTAAGCGACATAA                                                                                                  <  1:233986/91‑1   TGCAATTATCGTTTTAGTATTATTCCAAAAAGGGTTACTCCAAATCTTTAATTGGATTTTAATTCAATTACAATAAATTAAGCGACATAAC                                                                                                 <  2:1597919/91‑1   TGCAATTATCGTTTTAGTATTATTCCAAAAAGGGTTACTCCAAATCTTTAATTGGATTTTAATTCAATTACAATAAATTAAGCGACATAAC                                                                                                 <  2:3496625/91‑1   TGCAATTATCGTTTTAGTATTATTCCAAAAAGGGTTACTCCAAATCTTTAATTGGATTTTAATTCAATTACAATAAATTAAGCGACATAAC                                                                                                 >  2:3336084/1‑91    GCAATTATCGTTTTAGTATTATTCCAAAAAGGGTTACTCCAAATCTTTAATTGGATTTTAATTCAATTACAATAAATTAAGCGACATAACa                                                                                                >  2:3955758/1‑90    GCAATTATCGTTTTAGTATTATTCCAAAAAGGGTTACTCCAAATCTTTAATTGGATTTTAATTCAATTACAATAAATTAAGCGACATAACG                                                                                                <  2:2319517/91‑1    GCAATTATCGTTTTAGTATTATTCCAAAAAGGGTTACTCCAAATCTTTAATTGGATTTTAATTCAATTACAATAAATTAAGCGACATAACG                                                                                                >  1:958911/1‑91    GCAATTATCGTTTTAGTATTATTCCAAAAAGGGTTACTCCAAATCTTTAATTGGATTTTAATTCAATTACAATAAATTAAGCGACATAACG                                                                                                <  2:956262/91‑1      AATTATCGTTTTAGTATTATTCCAAAAAGGGTTACTCCAAATCTTTAATTGGATTTTAATTCAATTACAATAAATTAAGCGACATAACGAG                                                                                              <  2:854170/91‑1      AATTATCGTTTTAGTATTATTCCAAAAAGGGTTACTCCAAATCTTTAATTGGATTTTAATTCAATTACAATAAATTAAGCGACATAACGAG                                                                                              >  2:2303293/1‑91       ATTATCGTTTTAGTATTATTCCAAAAAGGGTTACTCCAAATCTTTAATTGGATTTTAATTCAATTACAATAAATTAAGCGACATAACGAGG                                                                                             >  1:3394346/1‑91       ATTATCGTTTTAGTATTATTCCAAAAAGGGTTACTCCAAATCTTTAATTGGATTTTAATTCAATTACAATAAATTAAGCGACATAACGAGG                                                                                             >  1:820259/1‑91       ATTATCGTTTTAGTATTATTCCAAAAAGGGTTACTCCAAATCTTTAATTGGATTTTAATTCAATTACAATAAATTAAGCGACATAACGAGG                                                                                             >  2:3414256/1‑91       ATTATCGTTTTAGTATTATTCCAAAAAGGGTTACTCCAAATCTTTAATTGGATTTTAATTCAATTACAATAAATTAAGCGACATAACGAGG                                                                                             <  1:2861698/91‑1       ATTATCGTTTTAGTATTATTCCAAAAAGGGTTACTCCAAATCTTTAATTGGATTTTAATTCAATTACAATAAATTAAGCGACATAACGAGG                                                                                             <  2:3104129/91‑1        TTATCGTTTTAGTATTATTCCAAAAAGGGTTACTCCAAATCTTTAATTGGATTTTAATTCAATTACAATAAATTAAGCGACATAACGAGGC                                                                                            <  2:2390811/91‑1        TTATCGTTTTAGTATTATTCCAAAAAGGGTTACTCCAAATCTTTAATTGGATTTTAATTCAATTACAATAAATTAAGCGACATAACGAGGC                                                                                            <  2:2391630/91‑1        TTATCGTTTTAGTATTATTCCAAAAAGGGTTACTCCAAATCTTTAATTGGATTTTAATTCAATTACAATAAATTAAGCGACATAACGAGGC                                                                                            <  1:3087779/91‑1        TTATCGTTTTAGTATTATTCCAAAAAGGGTTACTCCAAATCTTTAATTGGATTTTAATTCAATTACAATAAATTAAGCGACATAACGAGGC                                                                                            <  2:2390633/91‑1                        ATTCCAAAAAGGGTTACTCCAAATCTTTAATTGGATTTTAATTCAATTACAATAAATTAAGCGACATAACGAGGCTAAAGTATCATGTACC                                                                            <  2:2009727/91‑1                          TCCAAAAAGGGTTACTCCAAATCTTTAATTGGATTTTAATTCAATTACAATAAATTAAGCGACATAACGAGGCTAAAGTATCATGTACCCT                                                                          <  1:2539040/91‑1                          TCCAAAAAGGGTTACTCCAAATCTTTAATTGGATTTTAATTCAATTACAATAAATTAAGCGACATAACGAGGCTAAAGTATCATGTACCCT                                                                          <  1:3702320/91‑1                          TCCAAAAAGGGTTACTCCAAATCTTTAATTGGATTTTAATTCAATTACAATAAATTAAGCGACATAACGAGGCTAAAGTATCATGTACCCT                                                                          <  1:135537/91‑1                           CCAAAAAGGGTTACTCCAAATCTTTAATTGGATTTTAATTCAATTACAATAAATTAAGCGACATAACGAGGCTAAAGTATCATGTACCCTT                                                                         <  2:1376029/91‑1                           CCAAAAAGGGTTACTCCAAATCTTTAATTGGATTTTAATTCAATTACAATAAATTAAGCGACATAACGAGGCTAAAGTATCATGTACCCTT                                                                         <  2:1042964/91‑1                           CCAAAAAGGGTTACTCCAAATCTTTAATTGGATTTTAATTCAAGTACAATAAATTAAGCGACATAACGAGGCTAAAGTATCATGTACCCTT                                                                         <  1:3957506/91‑1                            CAAAAAGGGTTACTCCAAATCTTTAATTGGATTTTAATTCAATTACAATAAATTAAGCGACATAACGAGGCTAAAGTATCATGTACCCTTG                                                                        <  2:62214/91‑1                            CAAAAAGGGTTACTCCAAATCTTTAATTGGATTTTAATTCAATTACAATAAATTAAGCGACATAACGAGGCTAAAGTATCATGTACCCTTG                                                                        <  2:62380/91‑1                            CAAAAAGGGTTACTCCAAATCTTTAATTGGATTTTAATTCAATTACAATAAATTAAGCGACATAACGAGGCTAAAGTATCATGTACCCTTG                                                                        <  1:1233747/91‑1                             AAATAGGGTTACTCCAAATCTTTAATTGGATTTTAATTCAATTACAATAAATTAAGCGACATAACGAGGCTAAAGTATGATGTACCCTTGC                                                                       <  1:3056911/91‑1                             AAATAGGGTTACTCCAAATCTTTAATTGGATTTTAATTCAATTACAATAAATTAAGCGACATAACGAGGCTAAAGTATGATGTACCCTTGC                                                                       <  1:3056860/91‑1                             AAAAATGGTTACTTAAAATATTTAATTGGATTTTAATTCAATTACAATAAATTAAGCGACGTAACGGGGCTAAAGTATCATGTACCCTTGC                                                                       <  2:483296/91‑1                             AAAAAGGGTTACTCCAAATCTTTAATTGGATTTTAATTCAATTACAATAAATTAAGCGACATAACGAGGCTAAAGTATCATGTACCCTTGC                                                                       <  1:1524096/91‑1                             AAAAAGGGTTACTCCAAATCTTTAATTGGATTTTAATTCAATTACAATAAATTAAGCGACATAACGAGGCTAAAGTATCATGTACCCTTGC                                                                       <  1:2360701/91‑1                             AAAAAGGGTTACGCCAAATCTTTAATTGGATTTTAATTCAATTACAATAAATTAAGCGACATAACGAGGCTAAAGTATCATGTACCCTTGC                                                                       <  2:483269/91‑1                              AAAAGGGTTACTCCAAATCTTTAATTGGATTTTAATTCAATTACAATAAATTAAGCGACATAACGAGGCTAAAGTATCATGTACCCTTGCC                                                                      <  1:2932865/91‑1                                AAGGGTTACTCCAAATCTTTAATTGGATTTTAATTCAATTACAATAAATTAAGCGACATAACGAGGCTAAAGTATCATGTACCCTTGCCTC                                                                    <  1:1580908/91‑1                                                                                         aatACGAGGCTAAAGTATCATGTACCCTTGCCTCGTTATGTCGCTTAATTTATTGTAATTGAATTAAAATCCAATTAAAGATTTGGAGTAA           <  1:2869589/88‑1                                                                                           AACGAGGCTAAAGTATCATGTACCCTTGCCTCGTTATGTCGCTTAATTTATTGTAATTGAATTAAAATCCAATTAAAGATTTGGAGTAACC         >  2:228231/1‑91                                                                                           AACGAGGCTAAAGTATCATGTACCCTTGCCTCGTTATGTCGCTTAAGTTATTGTAATTGAATTAAAATCCAATTAAAGATTTGGAGTAACC         <  2:492908/91‑1                                                                                            ACGAGGCTAAAGTATCATGTACCCTTGCCTCGTTATGTCGCTTAATTTATTGTAATTGAATTAAAATCCAATTAAAGATTTGGAGTAACCC        <  1:640901/91‑1                                                                                            ACGAGGCTAAAGTATCATGTACCCTTGCCTCGTTATGTCGCTTAATTTATTGTAATTGAATTAAAATCCAATTAAAGATTTGGAGTAACCC        <  2:983465/91‑1                                                                                            ACGAGGCTAAAGTATCATGTACCCTTGCCTCGTTATGTCGCTTAATTTATTGTAATTGAATTAAAATCCAATTAAAGATTTGGAGTAACCC        <  1:2829399/91‑1                                                                                            ACGAGGCTAAAGTATCATGTACCCTTGCCTCGTTATGTCGCTTAATTTATTGTAATTGAATTAAAATCCAATTAAAGATTTGGAGTAACCC        <  1:639160/91‑1                                                                                            ACGAGGCTAAAGTATCATGTACCCTTGCCTCGTTATGTCGCTTAATTTATTGTAATTGAATTAAAATCCAATTAAAGATTTGGAGTAACCC        <  2:1571236/91‑1                                                                                            ACGAGGCTAAAGTATCATGTACCCTTGCCTCGTTATGTCGCTTAATTTATTGTAATTGAATTAAAATCCAATTAAAGACTTGGAGTAACCC        <  1:3032682/91‑1                                                                                             CGAGGCTAAAGTATCATGTACCCTTACCTCGTTATGTCGCTTAATTTATTGTAATTGAATTAAAATCCAATTAAAGATTTGGAGTAACCCT       <  1:3667782/91‑1                                                                                              GAGGCTAAAGTATCATGTACCCTTGCCTCGTTATGTCGCTTAATTTATTGTAATTGAATTAAAATCCAATTAAAGATTTGGAGTAACCCTT      <  2:884238/91‑1                                                                                              GAGGCTAAAGTATCATGTACCCTTGCCTCGTTATGTCGCTTAATTTATTGTAATTGAATTAAAATCCAATTAAAGATTTGGAGTAACCCTT      >  1:532611/1‑91                                                                                              GAGGCTAAAGTATCATGTACCCTTGCCTCGTTATGTCGCTTAATTTATTGTAATTGAATTAAAATCCAATTAAAGATTTGGAGTAACCCTT      <  1:2166169/91‑1                                                                                               AGGCTAAAGTATCATGTACCCTTGCCTCGTTATGTCGCTTAATTTATTGTAATTGAATTAAAATCCAATTCAAGATTTGGAGTAACCCTTT     >  2:3711112/1‑91                                                                                               AGGCTAAAGTATCATGTACCCTTGCCTCGTTATGTCGCTTAATTTATTGTAATTGAATTAAAATCCAATTAAAGATTTGGAGTAACCCTTT     <  2:2853542/91‑1                                                                                               AGGCTAAAGTATCATGTACCCTTGCCTCGTTATGTCGCTTAATTTATTGTAATTGAATTAAAATCCAATTAAAGATTTGGAGTAACCCTTT     >  2:403505/1‑91                                                                                               AGGCTAAAGTATCATGTACCCTTGCCTCGTTATGTCGCTTAATTTATTGTAATTGAATTAAAATCCAATTAAAGATTTGGAGTAACCCTTT     <  2:3370080/91‑1                                                                                               AGGCTAAAGTATCATGTACCCTTGCCTCGTTATGTCGCATAATTTATTGTAATTGAATTAAAATCCCATTAAAGATTTGGAGTAACCCTTT     >  2:2304795/1‑91                                                                                                GGCTACAGTATCATGTACCCTAGCCTCGTTATGTCGCTTAATTTATTGTAATTGAAGTAAAATCCAGTTAAAGATTTGGAGTAACACTTTT    <  2:775685/91‑1                                                                                                GGCTAAAGTATCATGTACCCTTGCCTCGTTATGTCGCTTAATTTATTGTAATTGAATTAAAATCCAATTAAAGATTTGGAGTAACCCTTTT    >  1:1726117/1‑91                                                                                                GGCTAAAGTATCATGTACCCTTGCCTCGTTATGTCGCTTAATTTATTGTAATTGAATTAAAATCCAATTAAAGATTTGGAGTAACCCTTTT    <  1:166502/91‑1                                                                                                GGCTAAAGTATCATGTACCCTTGCCTCGTTATGTCGCTTAATTTATTGTAATTGAATTAAAATCCAATTAAAGATTTGGAGTAACCCTTTT    <  2:1728803/91‑1                                                                                                GGCTAAAGTATCATGTACCCTTGCCTCGTTATGTCGCTTAATTTATTGTAATTGAATTAAAATCCAATTAAAGATTTGGAGTAACCCTTTT    >  1:3605709/1‑91                                                                                                GGCTAAAGTATCATGTACCCTTGCCTCGTTATGTCGCTTAATTTATTGTAATTGAATTAAAATCCAATTAAAGATTTGGAGTAACCCTTTT    >  2:2474533/1‑91                                                                                                GGCTAAAGTATCATGTACCCTTGCCTCGTTATGTCGCTTAATTTATTGTAATTGAATTAAAATCCAATTAAAGATTTGGAGTAACCCTTTT    >  1:1573986/1‑91                                                                                                 GCTAAAGTATCATGTACCCTTGCCTCGTTATGTCGCTTAATTTATTGTAATTGAATTAAAATCCAATTAAAGATTTGGAGTAACCCTTTTT   >  1:1906350/1‑91                                                                                                 GCTAAAGTATCATGTACCCTTGCCTCGTTATGTCGCTTAATTTATTGTAATTGAATTAAAATCCAATTAAAGATTTGGAGTAACCCTTTTT   >  1:2375780/1‑91                                                                                                 GCTAAAGTATCATGTACCCTTGCCTCGTTATGTCGCTTAATTTATTGTAATTGAATTAAAATCCAATTAAAGATTTGGAGTAACCCTTTTT   >  2:2816208/1‑91                                                                                                 GCTAAAGTATCATGTACCCTTGCCTCGTTATGTCGCTTAATTTATTGTAATTGAATTAAAATCCAATTAAAGATTTGGAGTAACCCTTTTT   <  1:1195942/91‑1                                                                                                 GCTAAAGTATCATGTACCCTTGCCTCGTTATGTCGCTTAATTTATTGTAATTGAATTAAAATCCAATTAAAGATTTGGAGTAACCCTTTTT   <  1:708187/91‑1                                                                                                  CTAAAGTATCATGTACCCTTGCCTCGTTATGTCGCTTAATTTATTGTAATTGAATTAAAATCCAATTAAAGATTTGGAGTAACCCTTTTTG  >  2:2123552/1‑91                                                                                                  CTAAAGTATCATGTACCCTTGCCTCGTTATGTCGCTTAATTTATTGTAATTGAATTAAAATCCAATTAAAGATTTGGAGTAACCCTTTTTG  >  2:2277084/1‑91                                                                                                                                                                                              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 < 12 ≤ ATCG/ATCG < 32 ≤ 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.