New junction evidence
		seq id	position	reads (cov)	reads (cov)	score	skew	freq	annotation	gene	product
*	?	USA300TCH1516_ALE	2716742 =	99 (0.790)	3 (0.030)	3/236	NT	3.5%	intergenic (+50/+100)	USA300HOU_RS13965/USA300HOU_RS13970	hypothetical protein/hypothetical protein
	?	USA300TCH1516_ALE	2716816 =	75 (0.660)					intergenic (+124/+26)	USA300HOU_RS13965/USA300HOU_RS13970	hypothetical protein/hypothetical protein
Rejected: Frequency below/above cutoff threshold.

TGTTCAAAGATCTTGATGGACACCATTTTAATTTTTTGGTCTGCTAAAATGAAATTCTCAAAAGAATAAATAAAAAGCCCATACAGAGATGAAGCGTAATGTGCACCATGGTGCGACACATTAGTGTCTTCAATCAGTATGGGCTTT‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑  <  USA300TCH1516_ALE/2716888‑2716742 ‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑gtatgggctttTTATTTATTCTTTTGAGAATTTCATTTTAGCAGACCAAAAAATTAAAATGGTGTCCATCAAGATCTTTGAACATTGCTCCATAAAACCCTTGGCTTACTGTTGGTTCTTGAACGACTGTGCCACCCGCTTCTTTCACTTT  >  USA300TCH1516_ALE/2716816‑2716955                                                                                                                                                                                                                                                                                                 TGTTCAAAGATCTTGATGGACACCATTTTAATTTTTTGGTCTGCTAAAATGAAATTCTCAAAAGAATAAATAAAAAGCCCATACAGAGATGAAGCGTAATGTGCACCATGGTGCGACACATTAGTGTCTTCAATCAGTATG                                                                                                                                                    >  2:948861/1‑141  GTTCAAAGATCTTGATGGACACCATTTTAATTTTTTGGTCTGCTAAAATGAAATTCTCAAAAGAATAAATAAAAAGCCCATACAGAGATGAAGCGTAATGTGCACCATGGTGCGACACATTAGTGTCTTCAATCAGTATGG                                                                                                                                                   >  2:705638/1‑141  GTTCAAAGATCTTGATGGACACCATTTTAATTTTTTGGTCTGCTAAAATGAAATTCTCAAAAGAATAAATAAAAAGCCCATACAGAGATGAAGCGTAATGTGCACCATGGTGCGACACATTAGTGTCTTCAATCAGTATGG                                                                                                                                                   >  2:429253/1‑141   TTCAAAGATCTTGATGGACACCATTTTAATTTTTTGGTCTGCTAAAATGAAATTCTCAAAAGAATAAATAAAAAGCCCATACAGAGATGAAGCGTAATGTGCACCATGGTGCGACACATTAGTGTCTTCAATCAGTATGGG                                                                                                                                                  >  4:266512/1‑141    TCAAAGATCTTGATGGACACCATTTTAATTTTTTGGTCTGCTAAAATGAAATTCTCAAAAGAATAAATAAAAAGCCCATACAGAGATGAAGCGTAATGTGCACCATGGTGCGACACATTAGTGTCTTCAATCAGTATGGGC                                                                                                                                                 >  2:328620/1‑141    TCAAAGATCTTGATGGACACCATTTTAATTTTTTGGTCTGCTAAAATGAAATTCTCAAAAGAATAAATAAAAAGCCCATACAGAGATGAAGCGTAATGTGCACCATGGTGCGACACATTAGTGTCTTCAATCAGTATGGGC                                                                                                                                                 <  2:195591/141‑1     CAAAGATCTTGATGGACACCATTTTAATTTTTTGGTCTGCTAAAATGAAATTCTCAAAAGAATAAATAAAAAGCCCATACAGAGATGAAGCGTAATGTGCACCATGGTGCGACACATTAGTGTCTTCAATCAGTATGGGCT                                                                                                                                                <  2:635676/141‑1     CAAAGATCTTGATGGACACCATTTTAATTTTTTGGTCTGCTAAAATGAAATTCTCAAAAGAATAAATAAAAAGCCCATACAGAGATGAAGCGTAATGTGCACCATGGTGCGACACATTAGTGTCTTCAATCAGTATGGGCT                                                                                                                                                >  1:859460/1‑141      AAAGATCTTGATGGACACCATTTTAATTTTTTGGTCTGCTAAAATGAAATTCTCAAAAGAATAAATAAAAAGCCCATACAGAGATGAAGCGTAATGTGCACCATGGTGCGACACATTAGTGTCTTCAATCAGTATGGGCTT                                                                                                                                               <  1:34857/141‑1       AAGATCTTGATGGACACCATTTTAATTTTTTGGTCTGCTAAAATGAAATTCTCAAAAGAATAAATAAAAAGCCCATACAGAGATGAAGCGTAATGTGCACCATGGTGCGACACATTAGTGTCTTCAATCAGTATGGGCTTT                                                                                                                                              <  1:15544/141‑1       AAGATCTTGATGGACACCATTTTAATTTTTTGGTCTGCTAAAATGAAATTCTCAAAAGAATAAATAAAAAGCCCATACAGAGATGAAGCGTAATGTGCACCATGGTGCGACACATTAGTGTCTTCAATCAGTATGGGCTTT                                                                                                                                              <  2:1029671/141‑1       AAGATCTTGATGGACACCATTTTAATTTTTTGGTCTGCTAAAATGAAATTCTCAAAAGAATAAATAAAAAGCCCATACAGAGATGAAGCGTAATGTGCACCATGGTGCGACACATTAGTGTCTTCAATCAGTATGGGCTTT                                                                                                                                              <  1:5576/141‑1                                                        TCTCAAAAGAATAAATAAAAAGCCCATACAGAGATGAAGCGTAATGTGCACCATGGTGCGACACATTAGTGTCTTCAATCAGTATGGGCTTTTTATTTATTCTTTTGAGAATTTCATTTTAGCAGACCAAAAAATTAAAAT                                                                                             >  1:225638/1‑141                                                                               CCATACAGAGATGAAGCGTAATGTGCACCATCGGGTTACACATTAGGGTCTTCAATCAGTATGGGCTTTTTATTTATTCTTTTGAGAATTTCATTTTAGCAGACCAAAAAATTAAAATGGTGTCCATCAAGATCTTTGAAC                                                                      >  2:49212/1‑141                                                                                    CAGAGATGAAGCGTAATGTGCACCATGGTGCGACACATTAGTGTCTTCAATCAGTATGGGCTTTTTATTTATTCTTTTGAGAATTTCATTTTAGCAGACCAAAAAATTAAAATGGTGTCCATCAAGATCTTTGAACATTGC                                                                 >  3:125975/1‑141                                                                                                                                         GTATGGGCTTTTTATTTATTCTTTTGAGAATTTCATTTTAGCAGACCAAAAAATTAAAATGGTGTCCATCAAGATCTTTGAACATTGCTCCATAAAACCCTTGGCTTACTGTTGGTTCTTGAACGACTGTGCCACCCGCTT            >  1:976723/1‑141                                                                                                                                           ATGGGCTTTTTATTTATTCTTTTGAGAATTTCATTTTAGCAGACCAAAAAATTAAAATGGTGTCCATCAAGATCTTTGAACATTGCTCCATAAAACCCTTGGCTTACTGTTGGTTCTTGAACGACTGTGCCACCCGCTTCT          <  1:939824/141‑1                                                                                                                                             GGGCTTTTTATTTATTCTTTTGAGAATTTCATTTTAGCAGACCAAAAAATTAAAATGGTGTCCATCAAGATCTTTGAACATTGCTCCATAAAACCCTTGGCTTACTGTTGGTTCTTGAACGACTGTGCCACCCGCTTCTTT        <  3:280986/141‑1                                                                                                                                             GGGCTTTTTATTTATTCTTTTGAGAATTTCATTTTAGCAGACCAAAAAATTAAAATGGTGTCCATCAAGATCTTTGAACATTGCTCCATAAAACCCTTGGCTTACTGTTGGTTCTTGAACGACTGTGCCACCCGCTTCTTT        <  3:281017/141‑1                                                                                                                                              GGCTTTTTATTTATTCTTTTGAGAATTTCATTTTAGCAGACCAAAAAATTAAAATGGTGTCCATCAAGATCTTTGAACATTGCTCCATAAAACCCTTGGCTTACTGTTGGTTCTTGAACGACTGTGCCACCCGCTTCTTTC       <  1:761625/141‑1                                                                                                                                                CTTTTTATTTATTCTTTTGAGAATTTCATTTTAGCAGACCAAAAAATTAAAATGGTGTCCATCAAGATCTTTGAACATTGCTCCATAAAACCCTTGGCTTACTGTTGGTTCTTGAACGACTGTGCCACCCGCTTCTTTCAC     >  1:1015772/1‑141                                                                                                                                                CTTTTTATTTATTCTTTTGAGAATTTCATTTTAGCAGACCAAAAAATTAAAATGGTGTCCATCAAGATCTTTGAACATTGCTCCATAAAACCCTTGGCTTACTGTTGGTTCTTGAACGACTGTGCCACCCGCTTCTTTCAC     <  1:864792/141‑1                                                                                                                                                  TTTTATTTATTCTTTTGAGAATTTCATTTTAGCAGACCAAAAAATTAAAATGGTGTCCATCAAGATCTTTGAACATTGCTCCATAAAACCCTTGGCTTACTGTTGGTTCTTGAACGACTGTGCCACCCGCTTCTTTCACTT   >  2:439298/1‑141                                                                                                                                                   TTTTTTTTTTTTTTTGAGAATTTAATTTTAGCAGACCAAAAAATTAAAATGGTGTCCATCAAGATCTTTGAACCTTGCTCCATAAAACCCTTGGCTTATTGTTGGTTCTTGAACGACTGTGCCACCCGCTTCTTTCACTTT  >  4:146106/1‑141                                                                                                                                                                                                                                                                                                 TGTTCAAAGATCTTGATGGACACCATTTTAATTTTTTGGTCTGCTAAAATGAAATTCTCAAAAGAATAAATAAAAAGCCCATACAGAGATGAAGCGTAATGTGCACCATGGTGCGACACATTAGTGTCTTCAATCAGTATGGGCTTT‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑  <  USA300TCH1516_ALE/2716888‑2716742 ‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑gtatgggctttTTATTTATTCTTTTGAGAATTTCATTTTAGCAGACCAAAAAATTAAAATGGTGTCCATCAAGATCTTTGAACATTGCTCCATAAAACCCTTGGCTTACTGTTGGTTCTTGAACGACTGTGCCACCCGCTTCTTTCACTTT  >  USA300TCH1516_ALE/2716816‑2716955

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.