New junction evidence
		seq id	position	reads (cov)	reads (cov)	score	skew	freq	annotation	gene	product
*	?	USA300TCH1516_ALE	512620 =	35 (1.060)	23 (1.010) +TTATCTTGTCCATTTTATTTTTTAACCAAAATTTGATTAA	19/180	NT	48.8%	intergenic (+688/‑6075)	recR/speA_2	Recombination protein RecR/Arginine decarboxylase
	?	USA300TCH1516_ALE	1998278 =	NA (NA)					intergenic (‑6/+3329)	USA300TCH1516_01882/USA300TCH1516_01883	tRNA‑Val/tRNA‑Ala

AGTCAGTTGCTCTACCAATTGAGCTAGGCCGGCAATATGTAAGAATAAATGGTGGAGAATGACGGGTTCGAACCGCCGACCCTCTGCTTGTAAGGCAGATGCTCTCCCAGCTGAGCTAATTCTCCGATTTAAAACTGCCTGGCAACGTTCTACTCTAGCGGAACGTAAGTTCGACTACCATCGACGCTAAGGAGCTTAACTTCTGTGTTCGGCATGGGAACAGGTGTGACCTCCTTGCTATAGTCACCAGACATATGAATGTAA  >  USA300TCH1516_ALE/1998148‑1998411                                                                                                                                   |                                                                                                                                      aGTCAGTTGCTCTACCAATTGAGCTAGGCCGGCAATATGTAAGAATAAATGGTGGAGAATGACGGGTTCGAACCGCCGACCCTCTGCTTGTAAGGCAGATGCTCTCCCAGCCGAGCTAATTCTCCGATCTAAAcctgcctg                                                                                                                             >  2:118263/1‑141 (MQ=255)    cAGTTGCTCTACCAATTGAGCTAGGCCGGCAATATGTAAGAATAAATGGTGGAGAATGACGGGTTCGAACCGCCGACCCTCTGCTTGTAAGGCAGATGCTCTCCCAGCTGAGCTAATTCTCCGATTTAAAACTGCCTGGCa                                                                                                                          >  1:282176/1‑141 (MQ=255)       ttGCTCTACCAATTGAGCTAGGCCGGCAATATGTAAGAATAAATGGTGGAGAATGACGGGTTCGAACCGCCGACCCTCTGCTTGTAAGGCAGATGCTCTCCCAGCTGAGCTAATTCTCCGATTTAAAACTGCCTGGCAACg                                                                                                                       <  1:120617/141‑1 (MQ=255)       ttGCTCTACCAATTGAGCTAGGCCGGCAATATGTAAGAATAAATGGTGGAGAATGACGGGTTCGAACCGCCGACCCTCTGCTTGTAAGGCAGATGCTCTCCCAGCTGAGCTAATTCTCCGATTTAAAACTGCCTGGCAACg                                                                                                                       >  1:229920/1‑141 (MQ=255)          ctctAGCAATTGAGCTAGGCCGGCAATATGTAAGAATAAATGGTGGAGAATGACGGGTTCGAACCGCCGACCCTCTGCTTGTAAGGCAGATGCTCTCCCAGCTGAGCTAATTCTCCGATTTAAAACTGCCTGGCAACGTTc                                                                                                                    <  2:102415/141‑1 (MQ=255)          ccctACCAATTGAGCCAGGCCCGCAATATGTAAGAATAAATGGTGGAGAATGACGGGTTCGAACCGCCGACCCTCTGCTTGTAAGGCAGATGCTCTCCCAGCTGAGCTAATTCTCCGATTTAAAACTGCCTGGCAACGTTc                                                                                                                    <  1:22446/139‑1 (MQ=255)               ccaaccgAGCTAGGCCGGCAATAGGTAAGAATAAATGGTGGAGAATGACGGGTTCGAACCGCCGACACTCTGCTTGTAAGGCAGTTGCTCTCACAGCTGAGCTAATTCTCCGATTTAAAACTGCCTGGCAACGTTCTActc                                                                                                               >  1:293735/7‑141 (MQ=17)               ccAATTGAGCTAGGCCGGCAATATGTAAGAATAAATGGTGGAGAATGATGGATTAGCACCGCCGACACTCTGCTTGTAAGCAAAAAACTCTCCCAGCTGAGCTAATCCACCAAACTAAAACTGCCTGGCAACGTTCTActc                                                                                                               >  2:133670/1‑141 (MQ=17)                    tGAGCTAGGCCGGCAATATGTAAGAATAAATGGTGGAGAATGACGGGTTCGAACCGCCGACCCTCTGCTTGTAAGGCAGATGCTCTCCCAGCTGAGCTAATTCTCCGATTTAAAACTGCCTGGCAACGTTCTACTCTAGCg                                                                                                          <  1:253102/141‑1 (MQ=255)                      aGCTAGGCCGGCAATAAGTAACAATAAATGGTGGAGAATGACGGGTTCGAACCGCCGACCCTCTGCTTGTAAGGCAGATGGTCTCCCAGCTGAGCTAATTCTCCGATTTAAAACTGCCTGGCAACGTTCTACTCTAGCGGa                                                                                                        >  1:205497/1‑141 (MQ=255)                              cGGCAATATGTAAGAATAAATGGTGGAGAATGACGGGTTCGAACCGCCGACCCTCTGCTTGTCAGGCAGATGCTCTCCCAGCCGAGCTAATTCTCCGAGTTACAACTGGCTGGCCACGTGCTACTCCAGCGGGACGTAAGt                                                                                                >  2:104228/1‑141 (MQ=14)                                gCAATATGTAAGAATAAATGGGGGAGAATGACGGGTTCGAACCGCCGACCCTCTGCTTGTAAGGCAGATGCTCTCCCAGCTGAGCTAATTCTCCGATTTAAAACTGCCTGGCAACGTTCTACTCTAGCGGAACGTAAGTTc                                                                                              <  1:84490/141‑1 (MQ=255)                                gCAATAGGTAAGAATAAATGGTGGAGAATGACGGGTTCGAACCGCCGACCCTCTGCTTGTAAGGCAGATGCTCTCCCAGCTGAGCTAATTCTCCGATTTAAAACTGCCTGGCAACGTTCTACTCTAGCGGAACGTAAGTTc                                                                                              <  1:3361/141‑1 (MQ=255)                                      tGTAAGAATAAATGGTGGAGAATGACGGGTTCGAACCGCCGACCCTCTGCTTGTAAGGCAGATGCTCTCCCAGCTGAGCTAATTCTCCGATTTAAAACTGCCTGGCAACGTTCTACTCTAGCGGAACGTAAGTTCGACTAc                                                                                        <  1:83308/141‑1 (MQ=255)                                       gTAAGAATAAATGGTGGAGAATGACGGGTTCGAACCGCCGACCCTCTGCTTGTAAGGCAGATGCTCTCCCAGCTGAGCTAATTCTCCGGTTTAAAACTGCCTGGCAACGTCCTACTCTAGCGGAACGTAAGTTCGACTAcc                                                                                       >  1:111200/1‑141 (MQ=255)                                       gTAAGAATAAATGGTGGAGAATGACGGGTTCGAACCGCCGACCCTCTGCTTGTAAGGCAGATGCTCTCCCAGCTGAGCTAATTCTCCGATTTAAAACTGCCTGGCAACGTTCTACTCTAGCGGAACGTAAGTTCGACTAcc                                                                                       >  1:250897/1‑141 (MQ=255)                                       gTAAGAATAAATGGTGGAGAATGACGGGTTCGAACCGCCGACCCTCTGCTTGTAAGGCAGATGCTCTCCCAGCTGAGCTAATTCTCCGATTTAAAACTGCCTGGCAACGTTCTACTCTAGCGGAACGTAAGTTCGACTAcc                                                                                       >  1:59981/1‑141 (MQ=255)                                               aattggtggAGAATGACGGGTTCGAACCGCCGACCCTCTGCTTGTAAGGCAGATGCTCTCCCAGCTGAGCTAATTCTCCGATTTAAAACTGCCTGGCAACGTTCTACTCTAGCGGAACGTAAGTTCGACTACCATCGACGc                                                                               <  2:378238/138‑1 (MQ=255)                                                aaTGGTGGAGAATGACGGGTTCGAACCGCCGACCCTCTGCTTGTAAGGCAGATGCTCTCCCAGCTGAGCTAATTCTCCGATTTAAAACTGCCTGGCAACGTTCTACTCTAGCGGAACGTAAGTTCGACTACCATCGACGCt                                                                              >  1:150256/1‑141 (MQ=255)                                                    gtggAGAATGACGGGTTCGAACCGCCGACCCTCTGCTTGTAAGGCAGATGCTCTCCCAGCTGAGCTAATTCTCCGATTTAAAACTGCCTGGCAACGTTCTACTCTAGCGGAACGTAAGTTCGACTACCATCGACGCTAAgg                                                                          >  1:375257/1‑141 (MQ=255)                                                      ggAGAATGACGGGTTCGAACCGCCGACCCTCTGCTTGTAAGGCAGATGCTCTCCCAGCTGAGCTAATTCTCCGATTTAAAACTGCCTGGCAACGTTCTACTCTAGCGGAACGTAAGTTCGACTACCATCGACGCTAAGGAg                                                                        <  2:205497/141‑1 (MQ=255)                                                       gagaATGACGGGTCCGAACCGCCGACCCTCTGCTGGTAAGGCAGATGCTCTCCCAGCTGAGCTAATGCTCCGATTTAAAACTGCCTGGCAACGTTCTACTCTAGCGGAACGTAAGTTCGACTACCATCGACGCTAAGGAGc                                                                       <  1:91410/141‑1 (MQ=255)                                                                gggTTCGAACCGCCGACCCTCTGCTTGTAAGGCAGATGCTCTCCCAGCTGAGCTAATTCTCCGATTTAAAACTGCCTGGCAACGTTCTACTCTAGCGGAACGTAAGTTCGACTACCATCGACGCTGAGGGGCTTCACTTCt                                                              >  1:109942/1‑141 (MQ=255)                                                                     cGAACCGCCGACCCTCTGCTTGTAAGGCAGATGCTCTCCCAGCTGAGCTAATTCTCCGATTTAAAACTGCCTGGCAACGTTCTACTCTAGCGGAACGTAAGTTCGACTACCATCGACGCTAAGGAGCTTAACTTCTGTGtt                                                         <  1:317720/141‑1 (MQ=255)                                                                               aCCCTCTGCTTGTAAGGCAGATGCTCTCCCAGCTGAGCTAATTCTCCGATTTAAAACTGCCTGGCAACGTTCTACTCTAGCGGAACGTAAGTTCGACTACCATCGACGCTAAGGAGCTTAACTTCTGTGTTCGGCATGGGa                                               >  1:275176/1‑141 (MQ=255)                                                                               aCCCTATACTTGGAAGGCAAATGCTCTCCCAGCTGAGCTAGTTCTCCGAGTTAAAACTGCCTGGCAACGTTCTACTCTAGCGGAACGTAAGTTCGACTACCATCGACGCTAAGGAGCTTAACTTCTGTGTTCGGCATGGGa                                               >  2:333719/1‑141 (MQ=14)                                                                                cccTCTGCTTGTAAGGCAGAAGCTCTCCCAGCTGAGCTAATTCTCCGATTTAAAACTGCCTGGCAACGTTCTACTCTAGCGGAACGTAAGTTCCACTACCATCGACGCTAAGAACCTTCACTTCTGTGTTCGGCATCGGaa                                              >  1:241143/1‑141 (MQ=17)                                                                                  ctctGCTTGTAAGGCAGATGCTCTCCCAGCTGAGCTAATTCTCCGATTTAAAACTGCCTGGCAACGTTCTACTCTAGCGGAACGTAAGTTCGACTACCATCGACGCTAAGGAGCTTAACTTCTGTGTTCGGCATGGGAACa                                            <  2:155546/141‑1 (MQ=255)                                                                                                   aTGCTCTCCCAGCTGAGCTAATTCTCCGATTTAAAACTGCCTGGCAACGTTCTACTCTAGCGGAACGTAAGTTCGACTAGCAGCGACGCTAAGGAGCTTAACTTCTGTGTTCGGCATGGGAACAGGTGTGACCTCCTTGCt                           >  2:141818/1‑141 (MQ=255)                                                                                                        cccccAGCTGAGCTAATTCTCCGATTTAACACTGACTGTCTTCTTTCTACTCTAGCGGAACGTAAGTTCGACTACCATCGACGCTAAGGAGCTTAACTTCTGTGTTCGGCATGGGAACAGGTGTGACCTCCTTGCTATAGt                      <  1:171314/139‑1 (MQ=14)                                                                                                           ccAGCTGAGCTAATTCTCCGATTTAAAACTGCCTGGCAACGTTCTACTCTAGCGGAACGTAAGTTCGCCTACCATCGACGCTAAGGAGCTTAACTTCTGTGTTCGGCATGGGGACAGGTGTGACCTCCTTGCTATAGTCAc                   >  1:54104/1‑141 (MQ=255)                                                                                                                         tctcCGATTTAAAACTGCCTGGCAACGTTCTACTCTAGCGGAACGTAAGTTCGACTACCATCGACGCTAAGGAGCTTAACTTCTGTGTTCGGCATGGGAACAGGTGTGACCTCCTTGCTATAGTCACCAGACATATGAATg     <  1:133670/141‑1 (MQ=255)                                                                                                                            ccGATTTAAAACTGCCTGGCAACGTTCTACTCTAGCGGAACGTAAGTTCGACTACCATCGACGCTAAGGAGCTTAACTTCTGTGTTCGGCATGGGAACAGGTGTGACCTCCTTGCTATCGTCACCAGACATATGAATGTaa  <  2:283713/141‑1 (MQ=255)                                                                                                                            ccGATTTAAAACTGCCTGGCAACGTACTACTCTAGCGGAACGTAAGTTCGACTACCATCGACGCTAAGGAGCTTAACTTCTGTGTTCGGCATGGGAACAGGTGTGACCTCCTTGCTATAGTCACCAGACATATGAATGTaa  >  1:200627/1‑141 (MQ=255)                                                                                                                                   |                                                                                                                                      AGTCAGTTGCTCTACCAATTGAGCTAGGCCGGCAATATGTAAGAATAAATGGTGGAGAATGACGGGTTCGAACCGCCGACCCTCTGCTTGTAAGGCAGATGCTCTCCCAGCTGAGCTAATTCTCCGATTTAAAACTGCCTGGCAACGTTCTACTCTAGCGGAACGTAAGTTCGACTACCATCGACGCTAAGGAGCTTAACTTCTGTGTTCGGCATGGGAACAGGTGTGACCTCCTTGCTATAGTCACCAGACATATGAATGTAA  >  USA300TCH1516_ALE/1998148‑1998411

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 12 ≤ ATCG/ATCG < 13 ≤ 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.