New junction evidence
		seq id	position	reads (cov)	reads (cov)	score	skew	freq	annotation	gene	product
*	?	USA300TCH1516_ALE	2207748 =	59 (1.280)	3 (0.070)	3/238	NT	5.6%	intergenic (+109/+155)	rodA/USA300HOU_RS11255	Peptidoglycan glycosyltransferase RodA/hypothetical protein
	?	USA300TCH1516_ALE	2207798 =	47 (1.110)					intergenic (+159/+105)	rodA/USA300HOU_RS11255	Peptidoglycan glycosyltransferase RodA/hypothetical protein

GATTGTGAATCACACACCGTTAAAGCTATCGTCGGACTATTCGATGATAGCTTTTTTGACTGGATTTACTAAAATGAAAGCAAGTACTATATAACAAAATCCCTCTTTAGAGTGTACATTTTACAATGTGTACTTCAAAGAGGGATT‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑  <  USA300TCH1516_ALE/2207894‑2207748 ‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑aaagagggattTTGTTATATAGTACTTGCTTTCATTTTAGTAAATCCAGTCAAAAAAGCTATCATCGAATAGTCCGACGATAGCTTTAACGGTGTGTGATTCACAATCACAGTCAATTATTTTAATTCGTGACTTACTTTATTAGATGCTG  >  USA300TCH1516_ALE/2207798‑2207937                                                                                                                                                                                                                                                                                                 GATTGTGAATCACACACCGTTAAAGCTATCGTCGGACTATTCGATGATAGCTTTTTTGACTGGATTTACTAAAATGAAAGCAAGTACTATATAACAAAATCCCTCTTTAGAGTGTACATTTTACAATGTGTACTTCAAAGA                                                                                                                                                    <  1:289266/141‑1      TGAATCACACACCGTTAAAGCTATCGTCGGACTATTCGATGATAGCTTTTTTGACTGGATTTACTAAAATGAAAGCAAGTACTATATAACAAAATCCCTCTTTAGAGTGTACATTTTACAATGTGTACTTCAAAGAGGGAT                                                                                                                                               <  2:46852/141‑1       GAATCACACACCGTTAAAGCTATCGTCGGACTATTCGATGATAGCTTTTTTGACTGGATTTACTAAAATGAAAGCAAGTACTATATAACAAAATCCCTCTTTAGAGTGTACATTTTACAATGTGTACTTCAAAGAGGGATT                                                                                                                                              <  1:670527/141‑1                                                                                             AACAAAATCCCTCTTTAGAGTGTACATTTTACAATGTGTACTTCAAAGAGGGA‑‑TTGTTATATAGTACTTGCTTTCATTTTAGTAAATCCAGTCAAAAAAGCTATCATCGAATAGTCCGACGATAGCTTTAACGGTGTGTGA                                                      >  2:268478/1‑141                                                                                                       CTCTTTAGAGTGTACATTTTACAATGTGTACTTCAAAGAGGGATTTTGTTATATAGTACTTGCTTTCATTTTAGTAAATCCAGTCAAAAAAGCTATCATCGAATAGTCCGACGATAGCTTTAACGGTGTGTGATTCACAAT                                              >  1:125560/1‑141                                                                                                        TCTTTAGAGTGTACATTTTACAATGTGTACTTCAAAGAGGGATTTTGTTATATAGTACTTGCTTTCATTTTAGTAAATCCAGTCAAAAAAGCTATCATCGAATAGTCCGACGATAGCTTTAACGGTGTGTGATTCACAATC                                             >  1:72093/1‑141                                                                                                                                           AGAGGGATTTTGTTATATAGTACTTGCTTTCATTTTAGTTAATCCAGTCAAAAAAGCTATCATCGAATAGTCCGACGATAGCTTTAACGGTGTGTGATTCACAATCACAGTCAATTATTTTAATTCGTGACTTACTTTATT          <  1:605959/141‑1                                                                                                                                                  TTTTGTTATATAGTACTTGCTTTCATTTTAGTAAATCCAGTCAAAAAAGCTATCATCGAATAGTCCGACGATAGCTTTAACGGTGTGTGATTCACAATCACAGTCAATTATTTTAATTCGTGACTTACTTTATTAGATGCT   >  1:712698/1‑141                                                                                                                                                   TTTGTTATATAGTACTTGCTTTCATTTTAGTAAATCCAGTCAAAAAAGCTATCATCGAATAGTCCGACGATAGCTTTAACGGTGTGTGATTCACAATCACAGTCAATTATTTTAATTCGTGACTTACTTTATTAGATGCTG  <  1:183663/141‑1                                                                                                                                                                                                                                                                                                 GATTGTGAATCACACACCGTTAAAGCTATCGTCGGACTATTCGATGATAGCTTTTTTGACTGGATTTACTAAAATGAAAGCAAGTACTATATAACAAAATCCCTCTTTAGAGTGTACATTTTACAATGTGTACTTCAAAGAGGGATT‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑  <  USA300TCH1516_ALE/2207894‑2207748 ‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑aaagagggattTTGTTATATAGTACTTGCTTTCATTTTAGTAAATCCAGTCAAAAAAGCTATCATCGAATAGTCCGACGATAGCTTTAACGGTGTGTGATTCACAATCACAGTCAATTATTTTAATTCGTGACTTACTTTATTAGATGCTG  >  USA300TCH1516_ALE/2207798‑2207937

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