New junction evidence
		seq id	position	reads (cov)	reads (cov)	score	skew	freq	annotation	gene	product
*	?	USA300TCH1516_ALE	298069 =	115 (1.280)	4 (0.050)	4/252	14.4	3.6%	intergenic (+208/‑220)	tarK/tarF_1	Teichoic acid ribitol‑phosphate polymerase TarK/Teichoic acid glycerol‑phosphate transferase
	?	USA300TCH1516_ALE	298125 =	110 (1.320)					intergenic (+264/‑164)	tarK/tarF_1	Teichoic acid ribitol‑phosphate polymerase TarK/Teichoic acid glycerol‑phosphate transferase
Rejected: Coverage evenness skew score above cutoff.
Rejected: Frequency below/above cutoff threshold.

ATAGCATTTCATCATAAAATACATTTAACCATTACACTTGTCGTTAATTATCATACGAAATACATGATTAATGTACCACTTTAACATAACAAAAAATCGTTATCCATTCATAACGTATGTGTTTACACATTTATGAATTAGATAACGATT‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑  <  USA300TCH1516_ALE/298218‑298069 ‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑gataacgattTTTTGTTATGTTAAAGTGGTACATTAATCATGTATTTCGTATGATAATTAACGACAAGTGTAATGGTTAAATGTATTTTATGATGAAATGCTATAATAGGCATGGTTACAATGAGCTTGCTCATACATATTAATATAATT  >  USA300TCH1516_ALE/298125‑298264                                                                                                                                                                                                                                                                                                    ATAGCATTTCATCATAAAATACATTTAACCATTACACTTGTCGTTAATTATCATACGAAATACATGATTAATGTACCACTTTAACATAACAAAAAATCGTTATCCATTCATAACGTATGTGTTTACACATTTATGAATTAG                                                                                                                                                       >  1:313867/1‑141    GCATTTCATCATAAAATACATTTAACCATTACACTTGTCGTTAATTATCATACGAAATACATGATTAATGTACCACTTTAACATAACAAAAAATCGTTATCCATTCATAACGTATGTGTTTACACATTTATGAATTAGATA                                                                                                                                                    >  1:114567/1‑141    GCATTTCATCATAAAATACATTTAACCATTACACTTGTCGTTAATTATCATACGAAATACATGATTAATGTACCACTTTAACATAACAAAAAATCGTTATCCATTCATAACGTATGTGTTTACACATTTATGAATTAGATA                                                                                                                                                    >  4:104124/1‑141      ATTTCATCATAAAATACATTTAACCATTACACTTGTCGTTAATTATCATACGAAATACATGATTAATGTACCACTTTAACATAACAAAAAATCGTTATCCATTCATAACGTATGTGTTTACACATTTATGAATTAGATAAC                                                                                                                                                  <  1:318548/141‑1        TTCATCATAAAATACATTTAACCATTACTCTTGTCGTTAATTATCATACGAAATACATGATTAATGTACCACTTTAACATAACAAAAAATCGTTATCCATTCATAACGTATGTGTTTACACATTTATGAATTAGATAACGA                                                                                                                                                <  3:152609/141‑1         TCATCATAAAATACATTTAACCATTACACTTGTCGTTAATTATCATACGAAATACATGATTAATGTACCACTTTAACATAACAAAAAATCGTTATCCATTCATAACGTATGTGTTTACACATTTATGAATTAGATAACGAT                                                                                                                                               <  2:543102/141‑1                       ATTTAACCATTACACTTGTCGTTAATTATCATACGAAATACATGATTAATGTACCACTTTAACATAACAAAAAATCGTTATCCATTCATAACGTATGTGTTTACACATTTATGAATTAGATAAC                                                                                                                                                  >  1:486934/1‑124                       ATTTAACCATTACACTTGTCGTTAATTATCATACGAAATACATGATTAATGTACCACTTTAACATAACAAAAAATCGTTATCCATTCATAACGTATGTGTTTACACATTTATGAATTAGATAAC                                                                                                                                                  <  2:486934/124‑1                         TTAACCATTACACTTGTCGTTAATTATCATACGAAATACATGATTAATGTACCACTTTAACATAATAAAAAATCGTTATCCATTCATAACGTATTTGTTTATACATTTATGAATTATTTAACGATTTTTTGTTATTTTAAA                                                                                                                               >  3:10932/1‑141                                                                                ttaaaaATAACAAAAAATCGTTAACAATTCATAACGTATGTGTTTACACATTTATGAATTAGATAACGATTTTTTGTTATGTTAAAGTGGTACATTAATCATGTATTTCGTATGATAATTAACGACAAGTGTAATGGTTAA                                                                        <  4:10932/135‑1                                                                                               AATCGTTATCCATTCATAACGTATGTGTTTACACATTTATGAATTAGATAACGATTTTTTGTTATGTTAAAGTGGTACATTAATCATGTATTTCGTATGATAATTAACGACAAGTGTAATGGTTAAATGTATTTTATGATG                                                         >  2:467441/1‑141                                                                                                ATCGTTATCCATTCATAACGTATGTGTTTACACATTTATGAATTAGATAACGATTTTTTGTTATGTTAAAGTGGTACATTAATCATGTATTTCGTATGATAATTAACGACAAGTGTAATGGTTAAATGTATTTTATGATGA                                                        >  4:236445/1‑141                                                                                                                                              ATAACGATTTTTTGTTATGTTAAAGTGGTACATTAATCATGTATTTCGTATGATAATTAACGACAAGTGTAATGGTTAAATGTATTTTATGATGAAATGCTATAATAGGCATGGTTACAATGAGCTTGCTCATACATATTA          <  2:15996/141‑1                                                                                                                                                  CGATTTTTTGTTATGTTAAAGTGGTACATTAATCATGTATTTCGTATGATAATTAACGACAAGTGTAATGGTTAAATGTATTTTATGATGAAATGCTATAATAGGCATGGTTACAATGAGCTTGCTCATACATATTAATAT      <  2:378862/141‑1                                                                                                                                                      TTTTTGTTATGTTAAAGTTGTACATTAATCATGTATTTCGTATGATAATTAACGACAAGTGTAATGGTTAAATGTATTTTATGATGAAATGCTATAATAGGCATGGTTACAATGAGCTTGCTCATACATATTAATATAATT  <  2:97982/141‑1                                                                                                                                                                                                                                                                                                    ATAGCATTTCATCATAAAATACATTTAACCATTACACTTGTCGTTAATTATCATACGAAATACATGATTAATGTACCACTTTAACATAACAAAAAATCGTTATCCATTCATAACGTATGTGTTTACACATTTATGAATTAGATAACGATT‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑  <  USA300TCH1516_ALE/298218‑298069 ‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑gataacgattTTTTGTTATGTTAAAGTGGTACATTAATCATGTATTTCGTATGATAATTAACGACAAGTGTAATGGTTAAATGTATTTTATGATGAAATGCTATAATAGGCATGGTTACAATGAGCTTGCTCATACATATTAATATAATT  >  USA300TCH1516_ALE/298125‑298264

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 12 ≤ 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.