New junction evidence
		seq id	position	reads (cov)	reads (cov)	score	skew	freq	annotation	gene	product
*	?	USA300TCH1516_ALE	= 528477	99 (0.710)	5 (0.040)	5/230	NT	5.3%	intergenic (+18/‑149)	dtd3/rnmV_1	D‑aminoacyl‑tRNA deacylase/Ribonuclease M5
	?	USA300TCH1516_ALE	= 528526	92 (0.740)					intergenic (+67/‑100)	dtd3/rnmV_1	D‑aminoacyl‑tRNA deacylase/Ribonuclease M5

TAGAGGGAAGCGAAATGAACCGGCGAGAGTAACTTTAGTAGCTGAACAAATTGCTGAATTAAAAGGCTTATCTTATGAAGAAGTGTGCGAACAAACAACTAAAAATGCAGAGAAATTGTTTAATTTAAATTCATAAAGTTAAAAGTGAGAAAGA‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑  >  USA300TCH1516_ALE/528324‑528477 ‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑aaaagtgagaaagaACCATAGCATATTAAACGAATATAGCATCGTTTACATTTATGGCGGTGATCTTTCTCACTTTTAACTTTATGAATTTAAATTAAACAATTTCTCTGCATTTTTAGTTGTTTGTTCGCACACTTCTTCATAAGATAAGCC  <  USA300TCH1516_ALE/528526‑528388                                                                                                                                                                                                                                                                                                       TAGAGGGAAGCGAAATGAACCGGCGAGAGTAACTTTAGTAGCTGAACAAATTGCTGAATTAAAAGGCTTATCTTATGAAGAAGTGTGCGAACAAACAACTAAAAATGCAGAGAAATTGTTTAATTTAAATTCATAAAGTTA                                                                                                                                                          <  2:844274/141‑1 TAGAGGGAAGCGAAATGAACCGGCGAGAGTAACTTTAGTAGCTGAACAAATTGCTGAATTAAAAGGCTTATCTTATGAAGAAGTGTGCGAACAAACAACTAAAAATGCAGAGAAATTGTTTAATTTAAATTCATAAAGTTA                                                                                                                                                          <  3:502666/141‑1   GAGGGAAGCGAAATGAACCGGCGAGAGTAACTTTAGTAGCTGAACAAATTGCTGAATTAAAAGGCTTATCTTATGAAGAAGTGTGCGAACAAACAACTAAAAATGCAGAGAAATTGTTTAATTTAAATTCATAAAGTTAAA                                                                                                                                                        <  3:183874/141‑1   GAGGGAAGCGAAATGAACCGGCGAGAGTAACTTTAGTAGCTGAACAAATTGCTGAATTAAAAGGCTTATCTTATGAAGAAGTGTGCGAACAAACAACTAAAAATGCAGAGAAATTGTTTAATTTAAATTCATAAAGTTAAA                                                                                                                                                        >  4:420228/1‑141   GAGGGAAGCGAAATGAACCGGCGAGAGTAACTTTAGTAGCTGAACAAATTGCTGAATTAAAAGGCTTATCTTATGAAGAAGTGTGAAAAAAAAAAAAAAAAAATGCAGAGAAATTGTTTAATTTAAATTCATAAAGTTAAA                                                                                                                                                        <  2:566426/141‑1    AGGGAAGCGAAATGAACCGGCGAGAGTAACTTTAGTAGCTGAACAAATTGCTGAATTAAAAGGCTTATCTTATGAAGAAGTGTGCGAACAAACAACTAAAAATGCAGAGAAATTGTTTAATTTAAATTCATAAAGTTAAAA                                                                                                                                                       <  2:694141/141‑1      GGAAGCGAAATGAACCGGCGAGAGTAACTTTAGTAGCTGAACAAATTGCTGAATTAAAAGGCTTATCTTATGAAGAAGTGTGCGAACAAACAACTAAAAATGCAGAGAAATTGTTTAATTTAAATTCATAAAGTTAAAAGT                                                                                                                                                     <  1:8225/141‑1       GAAGCGAAATGAACCGGCGAGAGTAACTTTAGTAGCTGAACAAATTGCTGAATTAAAAGGCTTATCTTATGAAGAAGTGTGCGAACAAACAACTAAAAATGCAGAGAAATTGTTTAATTTAAATTCATAAAGTTAAAAGTG                                                                                                                                                    <  1:717064/141‑1        tAGCGAAATGAACCGGCGAGAGTAACTTTAGTAGCTGAACAAATTGCTGAATTAAAAGGCTTATCTTATGAAGAAGTGTGCGAACAAACAACTAAAAATGCAGAGAAATTGTTTAATTTAAATTCATAAAGTTAAAAGTGA                                                                                                                                                   <  3:214305/140‑1        AAGCGAAATGAACCGGCGAGAGTAACTTTAGTAGCTGAACAAATTGCTGAATTAAAAGGCTTATCTTATGAAGAAGTGTGCGAACAAACAACTAAAAATGCAGAGAAATTGTTTAATTTAAATTCATAAAGTTAAAAGTGA                                                                                                                                                   >  1:1164389/1‑141         AGCGAAATGAACCGGCGAGAGTAACTTTAGTAGCTGAACAAATTGCTGAATTAAAAGGCTTATCTTATGAAGAAGTGTGCGAACAAACAACTAAAAATGCAGAGAAATTGTTTAATTTAAATTCATAAAGTTAAAAGTGAG                                                                                                                                                  >  2:628351/1‑141          GCGAAATGAACCGGCGAGAGTAACTTTAGTAGCTGAACAAATTGCTGAATTAAAAGGCTTATCTTATGAAGAAGTGTGCGAACAAACAACTAAAAATGCAGAGAAATTGTTTAATTTAAATTCATAAAGTTAAAAGTGAGA                                                                                                                                                 >  3:452166/1‑141           CGAAATGAACCGGCGAGAGTAACTTTAGTAGCTGAACAAATTGCTGAATTAAAAGGCTTATCTTATGAAGAAGTGTGCGAACAAACAACTAAAAATGCAGAGAAATTGTTTAATTTAAATTCATAAAGTTAAAAGTGAGAA                                                                                                                                                >  4:44133/1‑141             AAATGAACCGGCGAGAGTAACTTTAGTAGCTGAACAAATTGCTGAATTAAAAGGCTTATCTTATGAAGAAGTGTGCGAACAAACAACTAAAAATGCAGAGAAATTGTTTAATTTAAATTCATAAAGTTAAAAGTGAGAAAG                                                                                                                                              >  3:148863/1‑141             AAATGAACCGGCGAGAGTAACTTTAGTAGCTGAACAAATTGCTGAATTAAAAGGCTTATCTTATGAAGAAGTGTGCGAACAAACAACTAAAAATGCAGAGAAATTGTTTAATTTAAATTCATAAAGTTAAAAGTGAGAAAG                                                                                                                                              >  2:1083690/1‑141              AATGAACCGGCGAGAGTAACTTTAGTAGCTGAACAAATTGCTGAATTAAAAGGCTTATCTTATGAAGAAGGGTGCGAACAAACAACTAAAAATGCAGAGAAATTGTTTAATTTAAATTCATAAAGTTAAAAGTGAGAAAGA                                                                                                                                             >  2:304791/1‑141                                                                           ATGAAGAAGTGTGCGAACAAACAACTAAAAATGCAGAGAAATTGTTTAATTTAAATTCATAAAGTTAAAAGTGAGAAAGAACCATAGCATATTAAACGAATATAGCATCGTTTACATTTATGGCGGTGATCTTTCTCACTT                                                                                <  1:166289/141‑1                                                                                  AGTGTGCGAACAAACAACTAAAAATGCAGAGAAATTGTTTAATTTAAATTCATAAAGTTAAAAGTGAGAAAGAACCATAGCATATTAAACGAATATAGCATCGTTTACATTTATGGCG                                                                                                <  2:59633/118‑1                                                                                  AGTGTGCGAACAAACAACTAAAAATGCAGAGAAATTGTTTAATTTAAATTCATAAAGTTAAAAGTGAGAAAGAACCATAGCATATTAAACGAATATAGCATCGTTTACATTTATGGCG                                                                                                >  1:59633/1‑118                                                                                    TGTGCGAACAAACAACTAAAAATGCAGAGAAATTGTTTAATTTAAATTCATAAAGTTAAAAGTGAGAAAGAACCATAGCATATTAAACGAATATAGCATCGTTTACATTTATGGCGGTGATCTTTCTCACTTTTAACTTTA                                                                       <  1:963997/141‑1                                                                                      TGCGAACAAACAACTAAAAATGCAGAGAAATTGTTTAATTTAAATTCATAAAGTTAAAAGTGAGAAAGAACCATAGCATATTAAACGAATATAGCATCGTTTACATTTATGGCGGTGATCTTTCTCACTTTTAACTTTATG                                                                     <  3:344884/141‑1                                                                                                                                             AAAAGTGAGAAAGAACCATAGCATATTAAACGAATATAGCATCGTTTACATTTATGGCGGTGATCTTTCTCACTTTTAACTTTATGAATTTAAATTAAACAATTTCTCTGCATTTTTAGTTGTTTGTTCGCACNCTTCTTC              >  2:896664/1‑141                                                                                                                                             AAAAGTGAGAAAGAACCATAGCATATTAAACGAATATAGCATCGTTTACATTTATGGCGGTGATCTTTCTCACTTTTAACTTTATGAATTTAAATTAAACAATTTCTCTGCATTTTTAGTTGTTTGTTCGCACACTTCTTC              >  3:497986/1‑141                                                                                                                                               AAGTGAGAAAGAACCATAGCATATTAAACGAATATAGCATCGTTTACATTTATGGCGGTGATCTTTCTCACTTTTAACTTTATGAATTTAAATTAAACAATTTCTCTGCATTTTTAGTTGTTTGTTCGCACACTTCTTCAT            <  1:1176295/141‑1                                                                                                                                                 GTGAGAAAGAACCATAGCATATTAAACGAATATAGCATCGTTTACATTTATGGCGGTGATCTTTCTCACTTTTAACTTTATGAATTTAAATTAAACAATTTCTCTGCATTTTTAGTTGTTTGTTCGCACACTTCTTCATAA          >  3:468075/1‑141                                                                                                                                                 GTGAGAAAGAACCATAGCATATTAAACGAATATAGCATCGTTTACATTTATGGCGGTGATCTTTCTCACTTTTAACTTTATGAATTTAAATTAAACAATTTCTCTGCATTTTTAGTTGTTTGTTCGCACACTTCTTCATAA          >  1:304791/1‑141                                                                                                                                                  TGAGAAAGAACCATAGCATATTAAACGAATATAGCATCGTTTACATTTATGGCGGTGATCTTTCTCACTTTTAACTTTATGAATTTAAATTAAACAATTTCTCTGCATTTTTAGTTGTTTGTTCGCACACTTCTTCATAAG         <  4:67862/141‑1                                                                                                                                                  TGAGAAAGAACCATAGCATATTAAACGAATATAGCATCGTTTACATTTATGGCGGTGATCTTTCTCACTTTTAACTTTATGAATTTAAATTAAACAATTTCTCTGCATTTTTAGTTGTTTGTTCGCACACTTCTTCATAAG         <  4:502202/141‑1                                                                                                                                                  TGAGAAAGAACCATAGCATATTAAACGAATATAGCATCGTTTACATTTATGGCGGTGATCTTTCTCACTTTTAACTTTATGAATTTAAATTAAACAATTTCTCTGCATTTTTAGTTGTTTGTTCGCACACTTCTTCATAAG         <  2:200472/141‑1                                                                                                                                                   GAGAAAGAACCATAGCATATTAAACGAATATAGCATCGTTTACATTTATGGCGGTGATCTTTCTCACTTTTAACTTTATGAATTTAAATTAAACAATTTCTCTGCATTTTTAGTTGTTTGTTCGCACACTTCTTCATAAGA        <  3:378405/141‑1                                                                                                                                                   GAGAAAGAACCATAGCATATTAAACGAATATAGCATCGTTTACATTTATGGCGGTGATCTTTCTCACTTTTAACTTTATGAATTTAAATTAAACAATTTCTCTGCATTTTTAGTTGTTTGTTCGCACACTTCTTCATAAGA        <  2:191805/141‑1                                                                                                                                                     GAAAGAACCATAGCATATTAAACGAATATAGCATCGTTTACATTTATGGCGGTGATCTTTCTCACTTTTAACTTTATGAATTTAAATTAAACAATTTCTCTGCATTTTTAGTTGTTTGTTCGCACACTTCTTTATACGATA      >  4:459337/1‑141                                                                                                                                                      AAAGAACCATAGCATATTAAACGAATATAGCATCGTTTACATTTATGGCGGTGATCTTTCTCACTTTTAACTTTATGAATTTAAATTAAACAATTTCTCTGCATTTTTAGTTGTTTGTTCGCACACTTCTTCATAAGATAA     <  3:371759/141‑1                                                                                                                                                      AAAGAACCATAGCATATTAAACGAATATAGCATCGTTTACATTTATGGCGGTGATCTTTCTCACTTTTAACTTTATGAATTTAAATTAAACAATTTCTCTGCATTTTTAGTTGTTTGTTCGCACACTTCTTCATAAGATAA     <  2:5822/141‑1                                                                                                                                                      AAAGAACCATAGCATATTAAACGAATATAGCATCGTTTACATTTATGGCGGTGATCTTTCTCACTTTTAACTTTATGAATTTAAATTAAACAATTTCTCTGCATTTTTAGTTGTTTGTTCGCACACTTCTTCATAAGATAA     <  2:319203/141‑1                                                                                                                                                      AAAGAACCATAGCATATTAAACGAATATAGCATCGTTTACATTTATGGCGGTGATCTTTCTCACTTTTAACTTTATGAATTTAAATTAAACAATTTCTCTGCATTTTTAGTTGTTTGTTCGCACACTTCTTCATAAGATAA     >  4:1080/1‑141                                                                                                                                                      AAAGAACCATAGCATATTAAACGAATATAGCATCGTTTACATTTATGGCGGTGATCTTTCTCACTTTTAACTTTATGAATTTAAATTAAACAATTTCTCTGCATTTTTAGTTGTTTGTTCGCACACTTCTTCATAAGATAA     <  1:1162613/141‑1                                                                                                                                                       AAGAACCATAGCATATTAAACGAATATAGCATCGTTTACATTTATGGCGGTGATCTTTCTCACTTTTAACTTTATGAATTTAAATTAAACAATTTCTCTGCATTTTTAGTTGTTTGTTCGCACACTTCTTCATAAGATAAG    <  2:201234/141‑1                                                                                                                                                        AGAACCATAGCATATTAAACGAATATAGCATCGTTTACATTTATGGCGGTGATCTTTCTCACTTTTAACTTTATGAATTTAAATTAAACAATTTCTCTGCATTTTTAGTTGTTTGTTCGCACACTTCTTCATAAGATAAGC   <  1:1014463/141‑1                                                                                                                                                         GAACCATAGCATATTAAACGAATATAGCATCGTTTACATTTATGGCGGTGATCTTTCTCACTTTTAACTTTATGAATTTAAATTAAACAATTTCTCTGCATTTTTAGTTGTTTGTTCGCACACTTCTTCATAAGATAAGCC  >  2:799471/1‑141                                                                                                                                                         GAACCATAGCATATTAAACGAATATAGCATCGTTTACATTTATGGCGGTGATCTTTCTCACTTTTAACTTTATGAATTTAAATTAAACAATTTCTCTGCATTTTTAGTTGTTTGTTCGCACACTTCTTCATAAGATAAGCC  <  2:366795/141‑1                                                                                                                                                                                                                                                                                                       TAGAGGGAAGCGAAATGAACCGGCGAGAGTAACTTTAGTAGCTGAACAAATTGCTGAATTAAAAGGCTTATCTTATGAAGAAGTGTGCGAACAAACAACTAAAAATGCAGAGAAATTGTTTAATTTAAATTCATAAAGTTAAAAGTGAGAAAGA‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑  >  USA300TCH1516_ALE/528324‑528477 ‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑aaaagtgagaaagaACCATAGCATATTAAACGAATATAGCATCGTTTACATTTATGGCGGTGATCTTTCTCACTTTTAACTTTATGAATTTAAATTAAACAATTTCTCTGCATTTTTAGTTGTTTGTTCGCACACTTCTTCATAAGATAAGCC  <  USA300TCH1516_ALE/528526‑528388

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.