New junction evidence
		seq id	position	reads (cov)	reads (cov)	score	skew	freq	annotation	gene	product
*	?	USA300TCH1516_ALE	= 2358790	76 (1.160)	4 (0.060)	3/248	NT	5.1%	coding (128/945 nt)	rpoA_1	DNA‑directed RNA polymerase subunit alpha
	?	USA300TCH1516_ALE	= 2358806	77 (1.220)					coding (112/945 nt)	rpoA_1	DNA‑directed RNA polymerase subunit alpha

AGTAAATTTTCAATGCTAATTGTTTAATGTTCATAATAATTGTAGAAACATCTTCAACTACATTGTCTACTGCTGAGAATTCATGTAAAACTCCCTCAATTTCAATATACTTAACGGCTGCACCTGGTAATGAAGATAGTAGGA‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑  >  USA300TCH1516_ALE/2358647‑2358790 ‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑taggaAACTCCTTACGTCGTATCCTACTATCTTCATTACCAGGTGCAGCCGTTAAGTATATTGAAATTGAGGGAGTTTTACATGAATTCTCAGCAGTAGACAATGTAGTTGAAGATGTTTCTACAATTATTATGAACATT  <  USA300TCH1516_ALE/2358806‑2358672                                                                                                                                                                                                                                                                                         AGTAAATTTTCAATGCTAATTGTTTAATGTTCATAATAATTGTAGAAACATCTTCAACTACATTGTCTACTGCTGAGAATTCATGTAAAACTCCCTCAATTTCAATATACTTAACGGCTGCACCTGGTAATGAAGGTAGT                                                                                                                                             >  1:48125/1‑140    AAATTTTCAATGCTAATTGTTTAATGTTCATAATAATTGTAGAAACATCTTCAACTACATTGTCTACTGCTGAGAATTCATGTAAAACTCCCTCAATTTCAATATACTTAACGGCTGCACCTGGTAATGAAGATAGTAGG                                                                                                                                          <  1:507579/140‑1     AATTTTCAATGCTAATTGTTTAATGTTCATAATAATTGTAGAAACATCTTCAACTACATTGTCTACTGCTGAGAATTCATGTAAAACTCCCTCAATTTCAATATACTTAAAGGCTGCACCTGGTAATGAAGGTAGTAGGA                                                                                                                                         >  2:594232/1‑140                     tcTTTAATGTTCATAATAATTGTAGAAACATCTTCAACTACATTGTCTACTGCTGAGAATTCATGTAAAACTCCCTCAATTTCAATATACTTAACGGCTGCACCTGGTAATGAAGATAGTAGGAAACTCCTTACGTCGTA                                                                                                                         <  1:212226/138‑1                     TGTTTAAGGTTCATAATAATTGTAGAAACATCTTCAACTACATTGTCTACTGCTGAGAATTCATGTAAAACTCCCTCAATTTCAATATACTTAACGGCTGCACCTGGTAATGAAGATAGTAGGAAACTCCTTACGTCGTA                                                                                                                         <  2:232252/140‑1                                                                                                                  acgtcacCACCTGGTATTGAAGATAGTAGGATACGACGTAAGGAGTTTCCTACTATCTTCATTACCAGGTGCAGCCGTTAAGTATATTGAAATTGAGGGAGTTTTACATGAATTCTCAGCAGTAGACAATGTAGTTGAAG                            <  2:773765/133‑1                                                                                                                      CTGCACCTGGTAATGAAGATAGTAGGATACGACGTAAGGAGTTTCCTACTATCTTCATTACCAGGTGCAGCCGTTAAGTATATTGAAATTGAGGGAGTTTTACATGAATTCTCAGCAGTAGACAATGTAGTTGAAGATGT                        >  1:773765/1‑140                                                                                                                                            TAGGAAACGTCTTACGTCGTATCCTACTATCTTCATTACCAGGTGCAGCCGTTAAGTATATTGAAATTGAGGGAGTTTTACATGAATTCTCAGCAGTAGACAATGTAGTTGAAGATGTTTCTACAATTATTATGAACATT  <  2:369900/140‑1                                                                                                                                                                                                                                                                                         AGTAAATTTTCAATGCTAATTGTTTAATGTTCATAATAATTGTAGAAACATCTTCAACTACATTGTCTACTGCTGAGAATTCATGTAAAACTCCCTCAATTTCAATATACTTAACGGCTGCACCTGGTAATGAAGATAGTAGGA‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑  >  USA300TCH1516_ALE/2358647‑2358790 ‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑taggaAACTCCTTACGTCGTATCCTACTATCTTCATTACCAGGTGCAGCCGTTAAGTATATTGAAATTGAGGGAGTTTTACATGAATTCTCAGCAGTAGACAATGTAGTTGAAGATGTTTCTACAATTATTATGAACATT  <  USA300TCH1516_ALE/2358806‑2358672

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.