New junction evidence
		seq id	position	reads (cov)	reads (cov)	score	skew	freq	annotation	gene	product
*	?	USA300TCH1516_ALE	349720 =	193 (1.010)	12 (0.070)	8/142	NT	7.5%	intergenic (+272/‑314)	USA300HOU_RS01580/yezG_6	hypothetical protein/putative antitoxin YezG
	?	USA300TCH1516_ALE	349754 =	125 (0.740)					intergenic (+306/‑280)	USA300HOU_RS01580/yezG_6	hypothetical protein/putative antitoxin YezG

ATAATAGCCCTAAAACTCCTACTCATTATTTTGTCTTTCTATTTATTTAACTATTTATAATTATAGCAAAAAAGATATTAATAGTATATACTTTTTTGC‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑  <  USA300TCH1516_ALE/349818‑349720 ‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑cttttttgcTATAATTATAAATAGTTAAATAAATAGAAAGACAAAATAATGAGTAGGAGTTTTAGGGCTATTATTTACAAATAATATAATACTGCAAAG  >  USA300TCH1516_ALE/349754‑349843                                                                                                                                                                                               aaAATAGCCCTAAAACTCCAACTCATTATTTTGTCTTTCTATTTATTTAACTATTTATAATTATAGAAAAAAAGATATTAATAGTATATAC                                                                                                    <  2:3400870/89‑1  TAATAGCCCTAGAACTCCTACTGCTTATTTTGTCTTTCTATTTATTTAAGTATTTATAAGTATAGCAAAAAAGATATTAATAGTATATACT                                                                                                   <  2:2954708/91‑1   AATAGCCCTAAAACTCCTACTCATTATTTTGTCTTTCTATTTATTTAACTATTTATAATTATAGCAAAAAAGATATTAATAGTATATACTT                                                                                                  >  1:854168/1‑91   AATAGCCCTAAAACTCCTACTCATTATTTTGTCTTTCTATTTATTTAACTATTTATAATTATAGCAAAAAAGATATTAATAGTATATACTT                                                                                                  >  1:2444563/1‑91   AATAGCCCTAAAACTCCTACTCATTATTTTGTCTTTCTATTTATTTAACTATTTATAATTATAGCAAAAAAGATATTAATAGTATATACTT                                                                                                  >  1:2444547/1‑91    ATAGCCCTAAAACTCCTACTCATTATTTTGTCTTTCTATTTATTTAACTATTTATAATTATAGCAAAAAAGATATTAATAGTATATACTTT                                                                                                 <  2:24126/91‑1    ATAGCCCTAAAACTCCTACTCATTATTTTGTCTTTCTATTTATTTAACTATTTATAATTATAGCAAAAAAGATATTAATAGTATATACTTT                                                                                                 <  2:1031601/91‑1    ATAGCCCTAAAACTCCTACTCATTATTTTGTCTTTCTATTTATTTAACTATTTATAATTATAGCAAAAAAGATATTAATAGTATATACTTT                                                                                                 <  2:1898997/91‑1    ATAGCCCTAAAACTCCTACCCATTATTTTGTCTTTCTATTTATTTAACTATTTATAATTATAGCAAAAAAGATATTAATAGTATATACTTT                                                                                                 >  2:3465940/1‑91    ATAGCCCTAAAACTCCTACCCATTATTTTGTCTTTCTATTTATTTAACTATTTATAATTATAGCAAAAAAGATATTAATAGTATATACTTT                                                                                                 >  2:3465818/1‑91     TAGCCCTAAAACTCCTACTCATTATTTTGTCTTTCTATTTATTTAACTATTTATAATTATAGCAAAAAAGATGTTAATAGTATATACTTTT                                                                                                >  2:3164822/1‑91     TAGCCCTAAAACTCCTACTCATTATTTTGTCTTTCTATTTATTTAACTATTTATAATTATAGCAAAAAAGATATTAATAGTATATACTTTT                                                                                                <  1:3737775/91‑1     TAGCCCTAAAACTCCTACTCATTATTTTGTCTTTCTATTTATTTAACTATTTATAATTATAGCAAAAAAGATATTAATAGTATATACTTTT                                                                                                >  1:1849479/1‑91     TAGCCCTAAAACTCCTACTCATTATTTTGTCTTTCTATTTATTTAACTATTTATAATTATAGCAAAAAAGATATTAATAGTATATACTTTT                                                                                                >  1:1407381/1‑91     TAGCCCTAAAACTCCTACTCATTATTTTGTCTTTCTATTTATTTAACTATTTATAATTATAGCAAAAAAGATATTAATAGTATATACTTTT                                                                                                <  2:383969/91‑1      AGCCCTAAAACTCCTACTCATTATTTTGTCTTTCTATTTATTTAACTATTTATAATTATAGCAAAAAAGATATTAATAGTATATACTTTTT                                                                                               >  2:2180872/1‑91      AGCCCTAAAACTCCTACTCATTATTTTGTCTTTCTATTTATTTAACTATTTATAATTATAGCAAAAAAGATATTAATAGTATATACTTTTT                                                                                               <  2:863193/91‑1       GCCCTAAAACTCCTACTCATTATTTTGTCTTTCTATTTATTTAACTATTTATAATTATAGCAAAAAAGATATTAATAGTATATACTTTTTT                                                                                              >  2:2082534/1‑91       GCCCTAAAACTCCTACTCATTATTTTGTCTTTCTATTTATTTAACTATTTATAATTATAGCAAAAAAGATATTAATAGTATATACTTTTTT                                                                                              >  2:1555356/1‑91       GCCCTAAAACTCCTACTCATTATTTTGTCTTTCTATTTATTTAACTATTTATAATTATAGCAAAAAAGATATTAATAGTATATACTTTTTT                                                                                              >  1:355400/1‑91       GCCCTAAAACTCCTACTCATTATTTTGTCTTTCTATTTATTTAACTATTTATAATTATAGCAAAAAAGATATTAATAGTATATACTTTTTT                                                                                              >  1:1787400/1‑91        CCCTAAAACTCCTACTCATTATTTTGTCTTTCTATTTATTTAACTATTTATAATTATAGCAAAAAAGATATTAATAGTATATACTTTTTTt                                                                                             >  2:533814/1‑90        CCCTAAAACTCCTACTCATTATTTTGTCTTTCTATTTATTTAACTATTTATAATTATAGCAAAAAAGATATTAATAGTATATACTTTTTTt                                                                                             >  2:533723/1‑90        CCCTAAAACTCCTACTCATTATTTTGTCTTTCTATTTATTTAACTATTTATAATTATAGCAAAAAAGATATTAATAGTATATACTTTTTTG                                                                                             <  1:3392737/91‑1        CCCTAAAACTCCTACTCATTATTTTGTCTTTCTATTTATTTAACTATTTATAATTATAGCAAAAAAGATATTAATAGTATATACTTTTTTG                                                                                             <  2:2936423/91‑1        CCCTAAAACTCCTACTCATTATTTTGTCTTTCTATTTATTTAACTATTTATAATTATAGCAAAAAAGATATTAATAGTATATACTTTTTTG                                                                                             <  2:834795/91‑1        CCCTAAAACTCCTACTCATTATTTTGTCTTTCTATTTATTTAACTATTTATAATTATAGCAAAAAAGATATTAATAGTATATACTTTTTTG                                                                                             <  2:1946071/91‑1         CCTAAAACTCCTACTCATTATTTTGTCTTTCTATTTATTTAACTATTTATAATTATAGCAAAAAAGATATTAATAGTATATACTTTTTTGC                                                                                            >  1:229220/1‑91         CCTAAAACTCCTACTCATTATTTTGTCTTTCTATTTATTTAACTATTTATAATTATAGCAAAAAAGATATTAATAGTATATACTTTTTTGC                                                                                            >  2:1325280/1‑91         CCTAAAACTCCTACTCATTATTTTGTCTTTCTATTTATTTAACTATTTATAATTATAGCAAAAAAGATATTAATAGTATATACTTTTTTGC                                                                                            >  2:3030093/1‑91                                                       TTATAATTATAGCAAAAAAGATATTAATAGTATATACTTTTTTGCTATAATTATAAATAGTTAAATAAATAGAAAGACAAAATAATGAGTA                                              >  1:39777/1‑91                                                       TTATAATTATAGCAAAAAAGATATTAATAGTATATACTTTTTTGCTATAATTATAAATAGTTAAATAAATAGAAAGACAAAATAATGAGTA                                              >  1:38998/1‑91                                                       TTATAATTATAGCAAAAAAGATATTAATAGTATATACTTTTTTGCTATAATTATAAATAGTTAAATAAATAGAAAGACAAAATAATGAGTA                                              >  1:38417/1‑91                                                        TATAATTATAGCAAAAAAGATATTAATAGTATATACTTTTTTGCTATAATTATAAATAGTTAAATAAATAGAAAGACAAAATAATGAGTAG                                             >  1:2056404/1‑91                                                          TAATTATAGTAAAAAAGATATTAATAGTATATACTTTTTTACTATAATTATAAATAGTTAAATAAATTGAAAGACAAAATAATGAGTAGGA                                           >  1:2695919/1‑91                                                          TAATTATAGTAAAAAAGATATTAATAGTATATACTTTTTTACTATAATTATAAATAGTTAAATAAATTGAAAGACAAAATAATGAGTAGGA                                           >  1:124252/1‑91                                                                  GCAAAAAAGATATTAATAGTATATACTTTTTTGCTATAATTATAAATAGTTAAATAAATAGAAAGACAAAATAATGAGTAGGAGTTTTAGG                                   >  2:1207401/1‑91                                                                   CAAAAAAGATATTAATAGTATATACTTTTTTGCTATAATTATAAATAGTTAAATAAATAGAAAGACAAAATAATGAGTAGGAGTTTTAGGG                                  >  1:1755506/1‑91                                                                         AGATATTAATAGTATATACTTTTTTGCTATAATTATAAATAGTTAAATAAATAGAAAGACAAAATAATGAGTAGGAGTTTTAGGGCTATTA                            >  2:3467108/1‑91                                                                            TATTAATAGTATATACTTTTTTGCTATAATTATAAATAGTTAAATAAATAGAAAGACAAAATAATGAGTAGGAGTTTTAGGGCTATTATTT                         >  1:2238467/1‑91                                                                                  TAGTATATACTTTTTTTTTTTAATTATAAATAGTTAAATAAATAGAAAGACAAAATAATGAGTAGGAGTTTTAGGGCTATTATTTACAAAT                   >  2:3205619/1‑91                                                                                  TAGTATATACTTTTTTGCTATAATTATAAATAGTTAAATAAATAGAAAGACAAAATAATGAGTAGGAGTTTTAGGGCTATTATTTACAAAT                   >  2:3205566/1‑91                                                                                           CTTTTTTGCTATAATTATAAATAGTTAAATAAATAGAAAGACAAAATAATGAGTAGGGGTTTTAGGGCTATTATTTACAAATAATATAATA          <  2:1620910/91‑1                                                                                           CTTTTTTGCTATAATTATAAATAGTTAAATAAATAGAAAGACAAAATAATGAGTAGGAGTTTTAGGGCTATTATTTACAAATAATATAATA          >  1:1848017/1‑91                                                                                           CTTTTTTGCTATAATTATAAATAGTTAAATAAATAGAAAGACAAAATAATGAGTAGGAGTTTTAGGGCTATTATTTACAAATAATATAATA          >  1:1847657/1‑91                                                                                           CTTTTTTGCTATAATTATAAATAGTTAAATAAATAGAAAGACAAAATAATGAGTAGGAGTTTTAGGGCTATTATTTACAAATAATATAATA          >  2:1263066/1‑91                                                                                           CTTTTTTGCTATAATTATAAATAGTTAAATAAATAGAAAGACAAAATAATGAGTAGGAGTTTTAGGGCTATTATTTACAAATAATATAATA          >  1:974230/1‑91                                                                                           CTTTTTTGCTATAATTATAAATAATTAAATAAATAGAAAGACAAAATAATGAGTAGGAGTTTTAGGGCTATTATTTACAAATAATATAATA          <  2:2967476/91‑1                                                                                            TTTTTTGCTATAATTATAAATAGTTAAATAAATAGAAAGACAAAATAATGAGTAGGAGTTTTAGGGCTATTATTTACAAATAATATAATAC         <  2:1499517/91‑1                                                                                             TTTTTGCTATAATTATAAATAGTTAAATAAATAGAAAGACAAAATAATGAGTAGGAGTTTTAGGGCTATTATTTACAAATAATATAATACT        <  2:435296/91‑1                                                                                             TTTTTGCTATAATTATAAATAGTTAAATAAATAGAAAGACAAAATAATGAGTAGGAGTTTTAGGGCTATTATTTACAAATAATATAATACT        <  1:1223807/91‑1                                                                                              TTTTGCTATAATTATAAATAGTTAAATAAATAGAAAGACAAGATAATGAGTAGGAGTTTTAGGGCTATTATTTACAAATAATATAATACTG       <  2:3417492/91‑1                                                                                              TTTTGCTATAATTATAAATAGTTAAATAAATAGAAAGACAAAATAATGAGTAGGAGTTTTAGGGCTATTATTTACAAATAATATAATACTG       <  1:1027328/91‑1                                                                                               TTTGCTATAATTATAAATAGTTAAATAAATAGAAAGACAAAATAATGAGTAGGAGTTTTAGGGCTATTATTTACAAATAATATAATACTGC      <  1:367466/91‑1                                                                                               TTTGCTATAATTATAAATAGTTAAATAAATAGAAAGACAAAATAATGAGTAGGAGTTTTAGGGCTATTATTTACAAATAATATAATACTGC      <  2:2423737/91‑1                                                                                                TTGCTATAATTATAAATAGTTAAATAAATAGAAAGACAAAATAATGAGTAGGAGTTTTAGGGCTATTATTTACAAATAATATAATACTGCA     >  2:3417865/1‑91                                                                                                TTGCTATAATTATAAATAGTTAAATAAATAGAAAGACAAAATAATGAGTAGGAGTTTTAGGGCTATTATTTACAAATAATATAATACTGCA     >  2:760937/1‑91                                                                                                 TGCTATAATTATAAATAGTTAAATAAATAGAAAGACAAAATAATGAGTAGGAGTTTTAGGGCTATTATTTACAAATAATATAATACTGCAA    <  1:1515917/91‑1                                                                                                 TGCTATAATTATAAATAGTTAAATAAATAGAAAGACAAAATAATGAGTAGGAGTTTTAGGGCTATTATTTACAAATAATATAATACTGCAA    <  1:1515799/91‑1                                                                                                 TGCTATAATTATAAATAGTTAAATAAATAGAAAGACAAAATAATGAGTAGGAGTTTTAGGGCTATTATTTACAAATAATATAATACTGCAA    >  1:2242263/1‑91                                                                                                 TGCTATAATTATAAATAGTTAAATAAATAGAAAGACAAAATAATGAGTAGGAGTTTTAGGGCTATTATTTACAAATAATATAATACTGCAA    >  2:744419/1‑91                                                                                                  GCTATAATTATAAATAGTTAAATAAATAGAAAGACAAAATAATGAGTAGGAGTTTTAGGGCTATTATTTACAAATAATATAATACTGCAAA   <  2:2659948/91‑1                                                                                                   CTATAATTATAAATAGTTAAATAAATAGAAAGACAAAATAATGAGTAGGAGTTTTAGGGCTATTATTTACAAATAATATAATACTGCAAAG  >  2:1876767/1‑91                                                                                                   CTATAATTATAAATAGTTAAATAAATAGAAAGACAAAATAATGAGTAGGAGTTTTAGGGCTATTATTTACAAATAATATAATACTGCAAAG  >  2:1876435/1‑91                                                                                                   CTAGAATTATAAATAGTTAAATAAATAGAAAGACAAAATAATGAGTAGGAGTTTTAGGGCTATTATTTACAAATAATATAATAGTGCAAAG  >  2:3437345/1‑91                                                                                                                                                                                               ATAATAGCCCTAAAACTCCTACTCATTATTTTGTCTTTCTATTTATTTAACTATTTATAATTATAGCAAAAAAGATATTAATAGTATATACTTTTTTGC‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑  <  USA300TCH1516_ALE/349818‑349720 ‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑cttttttgcTATAATTATAAATAGTTAAATAAATAGAAAGACAAAATAATGAGTAGGAGTTTTAGGGCTATTATTTACAAATAATATAATACTGCAAAG  >  USA300TCH1516_ALE/349754‑349843

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.