New junction evidence
		seq id	position	reads (cov)	reads (cov)	score	skew	freq	annotation	gene	product
*	?	USA300TCH1516_ALE	= 2504209	189 (0.990)	8 (0.050)	7/144	NT	4.1%	intergenic (+134/‑131)	ydaG/USA300HOU_RS12890	General stress protein 26/hypothetical protein
	?	USA300TCH1516_ALE	= 2504234	209 (1.220)					intergenic (+159/‑106)	ydaG/USA300HOU_RS12890	General stress protein 26/hypothetical protein
Rejected: Frequency below/above cutoff threshold.

TAGATATAACAATGTTAAATACTTAAAATAACTCGCTATAATTAAAGTGTTTAATATGTTTACAATTCAATTTGCAATGTATTGTTTTTTAGACACAC‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑  >  USA300TCH1516_ALE/2504112‑2504209 ‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑agacacacCCTAATCACGTTAAATGTGAATAAAGTGTGTCTAAAAAACAATACATTGCAAATTGAATTGTAAACATATTAAACACTTTAATTATAGCG  <  USA300TCH1516_ALE/2504234‑2504145                                                                                                                                                                                              TAGATATAACAATGTTAAATACTTAAAATAACTCGCTATAATTAAAGTGTTTAATATGTTTACAATTCAATTTGCAATGTATTGTTTTTTA                                                                                                   <  1:1809573/91‑1 TAGATATAACAATGTTAAATACTTAAAATAACTCGCTATAATTAAAGTGTTTAATATGTTTACAATTCAATTTGCAATGTATTGTTTTTTA                                                                                                   <  2:3832632/91‑1  AGATATAACAATGTTAAATACTTAAAATAACTCGCTATAATTAAAGTGTTTAATATGTTTACAATTCAATTTGCAATGTATTGTTTTTTAG                                                                                                  <  1:1039137/91‑1  AGATATAACAATGTTAAATACTTAAAATAACTCGCTATAATTAAAGTGTTTAATATGTTTACAATTCAATTTGCAATGTATTGTTTTTTAG                                                                                                  <  1:3173708/91‑1  AGATATAACAATGTTAAATACTTAAAATAACTCGCTATAATTAAAGTGTTTAATATGTTTACAATTCAATTTGCAATGTATTGTTTTTTAG                                                                                                  <  1:1301713/91‑1  AGATATAACAATGTTAAATACTTAAAATAACTCGCTATAATTAAAGTGTTTAATATGTTTACAATTCAATTTGCAATGTATTGTTTTTTAG                                                                                                  <  1:1275027/91‑1   GATATAACAATGTTAAATACTTAAAATAACTCGCTATAATTAAAGTGTTTAATATGTTTACAATTCAATTTGCAATGTGTTGTTTTTTAGA                                                                                                 <  1:2982155/91‑1   GATATAACAATGTTAAATACTTAAAATAACTCGCTATAATTAAAGTGTTTAATATGTTTACAATTCAATTTGCAATGTATTGTTTTTTAGA                                                                                                 >  1:1345164/1‑91   GATATAACAATGTTAAATACTTAAAATAACTCGCTATAATTAAAGTGTTTAATATGTTTACAATTCAATTTGCAATGTATTGTTTTTTAGA                                                                                                 >  1:2337002/1‑91   GATATAACAATGTTAAATACTTAAAATAACTCGCTATAATTAAAGTGTTTAATATGTTTACAATTCAATTTGCAATGTATTGTTTTTTAGA                                                                                                 <  2:1491848/91‑1    ATATAACAATGTTAAATACTTAAAATAACTCGCTATAATTAAAGTGTTTAATATGTTTACAATTCAATTTGCAATGTATTGTTTTTTAGAC                                                                                                <  2:896626/91‑1    ATATAACAATGTTAAATACTTAAAATAACTCGCTATAATTAAAGTGTTTAATATGTTTACAATTCAATTTGCAATGTATTGTTTTTTAGAC                                                                                                <  2:3720990/91‑1    ATATAACAATGTTAAATACTTAAAATAACTCGCTATAATTAAAGTGTTTAATATGTTTACAATTCAATTTGCAATGTATTGTTTTTTAGAC                                                                                                >  2:2067612/1‑91    ATATAACAATGTTAAATACTTAAAATAACTCGCTATAATTAAAGTGTTTAATATGTTTACAATTCAATTTGCAATGTATTGTTTTTTAGAC                                                                                                <  1:2576206/91‑1    ATATAACAATGTTAAATACTTAAAATAACTCGCTATAATTAAAGTGTTTAATATGTTTACAATTCAATTTGCAATGTATTGTTTTTTAGAC                                                                                                <  1:2576246/91‑1     TATAACAATGTTAAATACTTAAAATAACTCGCTATAATTAAAGTGTTTAATATGTTTACAATTCAATTTGCAATGTATTGTTTTTTAGACA                                                                                               >  2:374395/1‑91     TATAACAATGTTAAATACTTAAAATAACTCGCTATAATTAAAGTGTTTAATATGTTTACAATTCAATTTGCAATGTATTGTTTTTTAGACA                                                                                               <  2:231000/91‑1      ATAACAATGTTAAATACTTAAAATAACTCGCTATAATTAAAGTGTTTAATATGTTTACAATTCAATTTGCAATGTATTGTTTTTTAGACAC                                                                                              <  1:3141343/91‑1      ATAACAATGTTAAATACTTAAAATAACTCGCTATAATTAAAGTGTTTAATATGTTTACAATTCAATTTGCAATGTATTGTTTTTTAGACAC                                                                                              <  2:3498749/91‑1      ATAACAATGTTAAATACTTAAAATAACTCGCTATAATTAAAGTGTTTAATATGTTTACAATTCAATTTGCAATGTATTGTTTTTTAGACAC                                                                                              <  2:3498700/91‑1       TAACAATGTTAAATACTTAAAATAACTCGCTATAATTAAAGTGTTTAATATGTTTACAATTCAATTTGCAATGTATTGTTTTTTAGACACA                                                                                             >  1:1193759/1‑91        AACAATGTTAAATACTTAAAATAACTCGCTATAATTAAAGTGTTTAATATGTTTACAATTCAATTTGCAATGTATTGTTTTTTAGACACAC                                                                                            <  1:1117680/91‑1        AACAATGTTAAATACTTAAAATAACTCGCTATAATTAAAGTGTTTAATATGTTTACAATTCAATTTGCAATGTATTGTTTTTTAGACACAC                                                                                            <  2:1391120/91‑1        AACAATGTTAAATACTTAAAATAACTCGCTATAATTAAAGTGTTTAATATGTTTACAATTCAATTTGCAATGTATTGTTTTTTAGACACAC                                                                                            >  1:2348785/1‑91        AACAATGTTAAATACTTAAAATAACTCGCTATAATTAAAGTGTTTAATATGTTTACAATTCAATTTGCAATGTATTGTTTTTTAGACACAC                                                                                            <  2:446956/91‑1                            ATAACTCGCTATAATTAAAGTGTTTAATATGTTTACAATTCAATTTGCAATGTATTGTTTTTTAGACACACCCTAATCACGTTAAATGTGA                                                                        <  2:1960893/91‑1                                    CTATAATTAAAGTGTTTAATATGTTTACAATTCAATTTGCAATGTATTGTTTTTTAGACACACCCTAATCACGTTAAATGTGAATAAAGTG                                                                <  1:3867456/91‑1                                      ATAATTAAAGTGTTTAATATGTTTACAATTCAATTTGCAATGTATTGTTTTTTAGACACACCCTAATCACGTTAAATGTGAATAAAGTGTG                                                              <  1:764153/91‑1                                       TAATTAAAGTGTTTAATATGTTTACAATTCAATTTGCAATGTATTGTTTTTTAGACACACCCTAATCACGTTAAATGTGAATAAAGTGTGT                                                             <  1:3294727/91‑1                                         ATTAAAGTGTTTAATATGTTTACAATTCAATTTGCAATGTATTGTTTTTTAGACACACCCTAATCACGTTAAATGTGAATAAAGTGTGTCT                                                           <  1:601592/91‑1                                         ATTAAAGTGTTTAATATGTTTACAATTCAATTTGCAATGTATTGTTTTTTAGACACACCCTAATCACGTTAAATGTGAATAAAGTGTGTCT                                                           <  1:601471/91‑1                                          TTAAAGTGTTTAATAAGTTTACAATTCAATTTGCAATGTATTGTTTTTTAGACACACCCTAATCACGTTAAATGTGAATAAAGTGTGTCTA                                                          <  2:432035/91‑1                                             AAGTGTTTAATATGTTTACAATTCAATTTGCAATGTATTGTTTTTTAGACACACCCTAATCACGTTAAATGTGAATAAAGTGTGTCTAAAA                                                       <  1:1773202/91‑1                                                                                      TTTTTAGACACACCCTAATCACGTTAAATGTGAATAAAGTGTGTCTAAAAAACAATACATTGCAAATTGAATTGTAAACATATTAAACACT              <  2:3758654/91‑1                                                                                           AGACACACCCTAATCACGTTAAATGTGAATAAAGTGTGTCTAAAAAACAATACATTGCAAATTGAATTGTAAACATATTAAACACTTTAAT         <  1:3816263/91‑1                                                                                           AGACACACCCTAATCACGTTAAATGTGAATAAAGTGTGTCTAAAAAACAATACATTGCAAATTGAATTGTAAACATATTAAACACTTTAAT         <  1:3816134/91‑1                                                                                           AGACACACCCTAATCACGTTAAATGTGAATAAAGTGTGTCTAAAAAACAATACATTGCAAATTGAATTGTAAACATATTAAACACTTTAAT         <  1:2608334/91‑1                                                                                           AGACACACCCTAATCACGTTAAATGTGAATAAAGTGTGTCTAAAAAACAATACATTGCAAATTGAATTGTAAACATATTAAACACTTTAAT         <  1:2610791/91‑1                                                                                           AGACACACCCTAATCACGTTAAATGTGAATAAAGTGTGTCTAAAAAACAATACATTGCAAATTGAATTGTAAACATATTAAACACTTTAAT         <  1:2995208/91‑1                                                                                            GACACACCCTAATCACGTTAAATGTGAATAAAGTGTGTCTAAAAAACAATACATTGCAAATTGAATTGTAAACATATTAAACACTTTAATT        >  1:2590835/1‑91                                                                                             ACACACCCTAATCACGTTAAATGTGAATAAAGTGTGTCTAAAAAACAATACATTGCAAATTGAATTGTAAACATATTAAACACTTTAATTA       >  2:926682/1‑91                                                                                             ACACACCCTAATCACGTTAAATGTGAATAAAGTGTGTCTAAAAAACAATACATTGCAAATTGAATTGTAAACATATTAAACACTTTAATTA       <  1:1431629/91‑1                                                                                             ACACACCCTAATCACGTTAAATGTGAATAAAGTGTGTCTAAAAAACAATACATTGCAAATTGAATTGTAAACATATTAAACACTTTAATTA       <  1:1126998/91‑1                                                                                              CACACCCTAATCACGTTAAATGTGAATAAAGTGTGTCTAAAAAACAATACATTGCAAATTGAATTGTAAACATATTAAACACTTTAATTAT      >  1:319004/1‑91                                                                                              CACACCCTAATCACGTTAAATGTGAATAAAGTGTGTCTAAAAAACAATACATTGCAAATTGAATTGTAAACATATTAAACACTTTAATTAT      >  1:338460/1‑91                                                                                               ACACCCTAATCACGTTAAATGTGAATAAAGTGTGTCTAAAAAACAATACATTGCAAATTGAATTGTAAACATATTAAACACTTTAATTATA     <  2:2316202/91‑1                                                                                                CACCCTAATCACGTTAAATGTGAATAAAGTGTGTCTAAAAAACAATACATTGCAAATTGAATTGTAAACATATTAAACACTTTAATTATAG    <  2:387656/91‑1                                                                                                CACCCTAATCACGTTAAATGTGAATAAAGTGTGTCTAAAAAACAATACATTGCAAATTGAATTGTAAACATATTAAACACTTTAATTATAG    <  2:387612/91‑1                                                                                                 ACCCTAATCACGTTAAATGTGAATAAAGTGTGTCTAAAAAACAATACATTGCAAATTGAATTGTAAACATATTAAACACTTTAATTATAGC   <  2:1901027/91‑1                                                                                                 ACCCTAATCACGTTAAATGTGAATAAAGTGTGTCTAAAAAACAATACATTGCAAATTGAATTGTAAACATATTAAACACTTTAATTATAGC   <  1:3580068/91‑1                                                                                                 ACCCTAATCACGTTAAATGTGAATAAAGTGTGTCTAAAAAACAATACATTGCAAATTGAATTGTAAACATATTAAACACTTTAATTATAGC   <  1:1640497/91‑1                                                                                                 ACCCTAATCACGTTAAATGTGAATAAAGTATGTCTAAAAAACAATACATTGCAAATTGAATTGTAAACATATTAAACACTTTCATTATAGC   >  2:3381513/1‑91                                                                                                  CCCTAATCACGTTAAATGTGAATAAAGTGTGTCTAAAAAACAATGCATTGCAACTTGAATTGTAAACATATTAAACACTTTAATTATAGCG  <  1:3098055/91‑1                                                                                                  CCCTAATCACGTTAAATGTGAATAAAGTGTGTCTAAAAAACAATACATTGCAAATTGAATTGTAAACATATTAAACACTTTAATTATAGCG  <  2:92361/91‑1                                                                                                  CCCTAATCACGTTAAATGTGAATAAAGTGTGTCTAAAAAACAATACATTGCAAATTGAATTGTAAACATATTAAACACTTTAATTATAGCG  >  1:1624853/1‑91                                                                                                  CCCTAATCACGTTAAATGTGAATAAAGTGTGTCTAAAAAACAATACATTGCAAATTGAATTGTAAACATATTAAACACTTTAATTATAGCG  <  2:2910234/91‑1                                                                                                  CCCTAATCACGTTAAATGTGAATAAAGTGTGTCTAAAAAACAATACATTGCAAATTGAATTGTAAACATATTAAACACTTTAATTATAGCG  <  1:2091069/91‑1                                                                                                  CCCTAATCACGTTAAATGTGAATAAAGTGTGTCTAAAAAACAATACATTGCAAATTGAATTGTAAACATATTAAACACTTTAATTATAGCG  <  1:2091517/91‑1                                                                                                  CCCTAATCACGTTAAATGTGAATAAAGTGTGTCTAAAAAACAATACATTGCAAATTGAATTGTAAACATATTAAACACTTTAATTATAGCG  <  1:2224164/91‑1                                                                                                  CCCTAATCACGTTAAATGTGAATAAAGTGTGTCTAAAAAACAATACATTGCAAATTGAATTGTAAACATATTAAACACTTTAATTATAGCG  >  1:471801/1‑91                                                                                                  CCCTAATCACGTTAAATGTGAATAAAGTGTGTCTAAAAAACAATACATTGCAAATTGAATTGTAAACATATTAAACACTTTAATTATAGCG  <  2:2909841/91‑1                                                                                                  CCCTAATCACGTTAAATGTGAATAAAGTGTGTCTAAAAAACAATACATTGCAAATTGAATTGTAAACATATTAAACACTTTAATTATAGCG  <  2:2657559/91‑1                                                                                                  CCCTAATCACGTTAAATGTGAATAAAGTGTGTCTAAAAAACAATACATTGCAAATTGAATTGTAAACATATTAAACACTTTAATTATAGCG  >  2:1269025/1‑91                                                                                                  CCCTAATCACGTTAAATGTGAATAAAGTGTGTCTAAAAAACAATACATTGCAAATTGAATTGTAAACATATTAAACACTTTAATTATAGCG  >  1:470781/1‑91                                                                                                                                                                                              TAGATATAACAATGTTAAATACTTAAAATAACTCGCTATAATTAAAGTGTTTAATATGTTTACAATTCAATTTGCAATGTATTGTTTTTTAGACACAC‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑  >  USA300TCH1516_ALE/2504112‑2504209 ‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑agacacacCCTAATCACGTTAAATGTGAATAAAGTGTGTCTAAAAAACAATACATTGCAAATTGAATTGTAAACATATTAAACACTTTAATTATAGCG  <  USA300TCH1516_ALE/2504234‑2504145

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 32 ≤ 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.