New junction evidence
		seq id	position	reads (cov)	reads (cov)	score	skew	freq	annotation	gene	product
*	?	USA300TCH1516_ALE	= 800928	28 (0.940)	3 (0.110)	3/246	NT	10.3%	intergenic (+62/‑289)	hisC_1/USA300HOU_RS03915	Histidinol‑phosphate aminotransferase/Putative 5'(3')‑deoxyribonucleotidase
	?	USA300TCH1516_ALE	801948 =	26 (0.920)					intergenic (+189/+435)	USA300HOU_RS03915/USA300HOU_RS03920	Putative 5'(3')‑deoxyribonucleotidase/Putative lipid kinase

TTACAATTGGTTTTAAAGAACAAAATGATAAAATGTTAGAAGTTTTATCAAACTTTAAATACGAATAGTAAGTGGGGAGTGGGACAGAAATGATACTTTCGCAAAATTTATTTCGTCGTCCCACCCCAACTTGCATTGTCTGTAGAAATTGGGAATCCA‑ATTTCTCTTTGTTGGGGCCCCGCCGGCAAGGTTGACTAGAATTGAAAAAAGCTTGTTACAAGCGCATTTTCGTTCAGTCAACTACTGCCAATATAACTTTGTAGAGCATTG  >  USA300TCH1516_ALE/800799‑801068                                                                                                                                  |                                                                                                                                              ttACAATTGGTTTTAAAGAACAAAATGATAAAATGTTAGAAGTTTTATCAAACTTCACATACGAATAGTAAGTTGGTAGTGGGACAGAAATGATACTTTCGCAAAATTTATTTCGTCGTCCCACCCCAACTTGCATTGTCt                                                                                                                                    <  2:295461/141‑1 (MQ=255)    cAATTGGTTTTAAAGAACAAAATGATAAAATGTTAGAAGTTTTATCAAACTTTAAATACGAATAGTAAGTGGGGAGTGGGACAGAAATGATACTTTCGCAAAATTTATTTCGTCGTCCCACCCCAACTTGCATTGTCTGTa                                                                                                                                 >  1:277953/1‑141 (MQ=255)                    aCAAAATGATAAAATGTGAGAAGTTTGATCAAACTTTAAATACGAATAGTAAGGGGGGAGTGGGACAGAAATGATACTTTCGCAAAATTTATTGCGTCGTCCCACTCCAACTTGCATTGTCTGTAGAAATTGGGAATCCa‑a                                                                                                                <  2:55290/141‑1 (MQ=21)                     cAAAATGATAAAATGTTAGAAGTTTTATCAAACTTTAAATACGAATAGTAAGTGGGGAGTGGGACAGAAATGATACTTTCGCAAAATTTATTTCGTCGTCCCACCCCAACTTGCATTGTCTGTAGAAATTGGGACTCCA‑At                                                                                                               >  2:57052/1‑141 (MQ=255)                        aaTGATAAAATGTTAGAAGTTTTATCAAACTTTAAATACGAATAGTAAGTGGGGAGTGGGACAGAAATGATACTTTCGCAAAATTTATTTCGTCGTCCCACCCCAACataaagaaatactttttctttagaaattagtatt                                                                                                             <  2:216013‑M1/141‑35 (MQ=255)                         aTGATAAATTGTTAGAAGTTTTATCAAACTTTAAATACGAATAGTCAGTGGAAATAATGGGAGTAATTATACGTTCGCAAAATTTATTTCGTCGTCCCACCCCAACTTGCATTGTCTGTAGAAATTGGGAATCCA‑ATTtct                                                                                                           >  2:156344/1‑141 (MQ=18)                         aTGATAAAATGTTAGAAGTTTTCTCAAACACTAAATACGAATAGTAAGTGGGGAGTGGGACAGAAATGATACTTTCGCAAAATTTATTTCGTCGTCCCACCCCAACTTGCATTGCCTGTAGAAATTGGGAATCCACATTtc                                                                                                            >  2:74411/1‑141 (MQ=21)                           gATAAAATGTTAGAAGTTTTATCAAACTTTAAATACGAATAGTAAGTGGGGAGTGGTACAGAAATGATACTTTCGCAAAATTTATTTCGTCGTCCCACCCCAACataaagaaatactttttctttagaaattagtatttct                                                                                                          <  2:205135‑M1/141‑38 (MQ=255)                               aaaTGTTAGAAGTTTTATCAAACTTTAAATACGAATAGTAAGTGGGGAGTGGGACAGAAATGATACTTTCGCAAAATTTATTTCGTCGTCCCACCCCAACTTGCATTGTCTGTAGAAATTGGGAATCCA‑ATTTCTCTttgt                                                                                                     >  1:108473/1‑141 (MQ=255)                                 aTGTTAGAAGTTTTATCAAACTTTAAATACGAATAGTAAGTGGGGAGTGGGACAGAAATGATACTTTCGCAAAATTTATTTCGTCGTCCCACCCCAACTTGCATTGTCTGTAGAAATTGGGAATCCA‑ATTTCTCTttgttg                                                                                                   <  1:320013/141‑1 (MQ=255)                                             ttATCAAACTTTAAATACGAATAGTAAGTGGGGAGTGGGACAGAAATGATACTTTCGCAAAATTTATTTCGTCGTCCCACCCCAACataaagaaatactttttctttagaaattagtatttcttatgcatgagtgtaactc                                                                                        <  2:292847‑M1/141‑56 (MQ=255)                                                tCAAACTTTAAATACGAATAGTAAGTGGGGAGTGGGACAGAAATGATACTTTCGCAAAATTTATTTCGTCGTCCCACCCCAACTTGCATTGTCTGTAGAAATTGGGAATCCG‑CTTTCTCTTTGTTGGGGCACCGCCGGCaa                                                                                    >  2:135549/1‑141 (MQ=255)                                                tCAAACTTTAAATACGAATAGTAAGTGGGGAGTGGGACAGAAATGATACTTTCGCAAAATTTATTTCGTCGTCCCACCCCAACTTGCATTGTCTGTAGAAATTGGGAATCCA‑ATTTCTCTTTGTTGGGGCCCCGCCGGCaa                                                                                    <  1:81682/141‑1 (MQ=255)                                                tCAAACTTTAAATACGAATAGTAAGTGGGGAGTGGGACAGAAATGATACTTTCGCAAAATTTATTTCGTCGTCCCACCCCAACTTGCATTGTCTGTAGAAATTGGGAATCCA‑ATTTCTCTTTGTTGGGGCCCCGCCGGCaa                                                                                    <  1:271619/141‑1 (MQ=255)                                                           aTACGAATAGTAAGTGGGGAGTGGGACAGAAATGATACTTTCGCAAAATTTATTTCGTCGTCCCACCCCAACTTGCATTGTCTGTAGAAATTGGGAATCCA‑ATTTCTCTTTGTTGGGGCCCCGCCGGCAAGGATGAATAGa                                                                         >  1:72309/1‑141 (MQ=255)                                                                taatggaaGTGGTGAGCGCGAGACAAATGATACTTTCGCTACGTTTATATCGCCGTCCCACCCCTACTTGCAGTGTCTGTAGAAATTGGGAATCCA‑ATTGCCCTTTGCTGGGGCCCCGCCTTCAATGTTGTCTAGAATTGa                                                                    <  2:39135/135‑1 (MQ=9)                                                                      aaGTGGGGAGTGGGACAGAAATGATACTTTCGCAAAATTTATTTCGTCGTCCCACCCCAACTTGCATTGTCTGTAGAAATTGGGAATCCA‑ATTTCTCTTTGTTGGGGCCCCGCCGGCAAGGTTGACTAGAATTGAAAAAAg                                                              >  2:222408/1‑141 (MQ=255)                                                                      aaGTGGGGAGTGGGACAGAAATGATACTTTCGCAAAATTTATTTCGTCGTCCCACCCCAACTTGCATTGTCTGTAGAAATTGGGAATCCA‑ATTTCTCTTTGTTGGGGCCCCGCCGGCAAGGTTGACTAGAATTGAAAAAAg                                                              >  1:271588/1‑141 (MQ=255)                                                                              aGTGGGACAGAAATGATACTTTCGCAAAATTTATTTCGTCGTCCCACCCCAACTTGCATTGTCTGTAGAAATTGGGAATCCA‑ATTTCTCTTTGTTGGGGCCCCGCCGGCAAGGTTGACTAGAATTGAAAAAAGCTTGTTaa                                                      >  2:83687/1‑140 (MQ=38)                                                                               gTGGGACAGAAATGATACTTTCGCAAAATTTATTTCGTCGTCCCACCCCAACTTGCATTGTCTGTAGAAATTGGGAATCCA‑ATTTCTCTTTGTTGGGGCCCCGCCGGCAAGGTTGACTAGAATTGAAAAAAGCTTGTTACa                                                     >  1:319260/1‑141 (MQ=39)                                                                                tGGGCCCGAAATGATACTTTAGCAAAATTTATTTCGTCGTCCCAACACAACTTGCATTGTCTGTAGAAACTGGGCATCCA‑CTTTACCTTTGTTCGGGACACACCGGCAAGGTTGACTAGCATTGAAAAACGCTTGTTACaa                                                    >  2:37065/1‑141 (MQ=14)                                                                                 gggACAGAAATGATACTTTCGCAAAATTTATTTCGTCGTCCCACCCCAACTTGCATTGTCTGTAGAAATTGGGAATCCA‑ATTTCTCTTTGTTGGGGCCCCGCCGGCAAGGTTGACTAGAATTGAAAAAAGCTTGTTCCAAg                                                   >  1:96909/1‑141 (MQ=255)                                                                                           tGATACTTTCGCAAAATTTATTTCGTCGTCCCACCCCGACTTGCATTGTCTGTAGAAATTGGGAATCCA‑ATTTCTCTTTGTTGGGGCCCCGCCGGCAAGGTTGACTAGAATTGAAAAAAGCTTGTTACAAGCGCATTTTCg                                         >  1:326562/1‑141 (MQ=255)                                                                                               aCTTTCGCAAAATTTATTTCGTCGTCCCACCCCAACTTGCATTGTCTGTAGAAATTGGGAATCCA‑ATTTCTCTTTGTTGGGGCCCCGCCGGCAAGGTTGACTAGAATTGAAAAAAGCTTGTTCCAAGCGCATTTTCGTTCa                                     >  2:232461/1‑141 (MQ=38)                                                                                                  ttCGCAAAATTTATTTCGTCGTCCCACCCCAACTTGCATTGTCTGTAGAAATTGGGAATCCA‑ATTTCTCTTTGTTGGGGCCCCGCCGGCAAGGTTGACTAGAATTGAAAAAAGCTTGTTACAAGCGCATTTTCGTTCAGTc                                  <  1:31037/141‑1 (MQ=35)                                                                                                              atttCGTCGTCCCACCCCAACTTGCATTGTCTGTAGAAATTGGGAATCCA‑ATTTCTCTTTGTTGGGGCCCCGCCGGCAAGGTTGACTAGAATTGAAAAAAGCTTGTTACAAGCGCATTTTCGTTCAGTCAACTACTGCCaa                      <  1:83687/141‑1 (MQ=32)                                                                                                                ttCGTCGTCCCACCCCAACTTGCATTGTCTGTAGAAATTGGGAATCCA‑ATTTCTCTTTGTTGGGGCCCCGCCGGCAAGGTTGACTAGAATTGAAAAAAGCTTGTTACAAGCGCATTTTCGTTCAGTCAACTACTGCCAata                    <  1:185844/141‑1 (MQ=35)                                                                                                                 tcgtcgTCCCACCCTAACTTGCATTGTCTGTAGAAATTGGGAATCCA‑ATTTCTCTTTGTTGGGGCCCCGCCGGCAAGGTTGACTAGAATTGAAAAAAGCTTGTTACAAGCGCATTTTCGTTCAGTCAACTACTGCCAatat                   <  2:183207/141‑1 (MQ=21)                                                                                                                          cACCCCAACTTGCATTGTCTGTAGAAATTGGGAATCCA‑ATTTCTCTTTGTTGGGGCCCCGCCGGCAAGGTTGACTAGAATTGAAAAAAGCTTGTTACAAGCGCATTTTCGTTCAGTCAACTACTGCCAATATAACTTTGTa          <  1:228822/141‑1 (MQ=35)                                                                                                                           aCCCCAACTTGCATTGTCTGTAGAAATTGGGAATCCA‑ATTTCTCTTTGTTGGGGCCCCGCCGGCAAGGTTGACTAGAATTGAAAAAAGCTTGTTACAAGCGCATTTTCGTTCAGTCAACTACTGCCAATATAACTTTGTag         <  2:108506/141‑1 (MQ=35)                                                                                                                            ccccAACTTGCATTGTCTGTAGAAATTGGGAATCCA‑ATTTCTCTTTGTTGGGGCCCCGCCGGCAAGGTTGACTAGAATTGAAAAAAGCTTGTTACAAGCGCATTTTCGTTCAGTCAACTACTGCCAATATAACTTTGTaga        >  1:222855/1‑141 (MQ=35)                                                                                                                                aaCataaagaaatactttttctttagaaattagtatttcttatgcatgagtgtaactcatgcattcatatttttaagtacacattagctgtgactaatgataaagaatcgctacataatcaatcgttagtcgttgtttatc     >  1:308805‑M1/1‑3 (MQ=255)                                                                                                                                  cTTGCATTGTCTGTAGAAATTGGGAATCCA‑ATTTCTCTTTGTTGGGGCCCCGCCGGCAAGGTTGACTAGAATTGAAAAAAGCTTGTTACAAGCGCATTTTCGTTCAGTCAACTACTGCCAATATAACTTTGTAGAGCATTg  <  2:319260/141‑1 (MQ=37)                                                                                                                                  |                                                                                                                                              TTACAATTGGTTTTAAAGAACAAAATGATAAAATGTTAGAAGTTTTATCAAACTTTAAATACGAATAGTAAGTGGGGAGTGGGACAGAAATGATACTTTCGCAAAATTTATTTCGTCGTCCCACCCCAACTTGCATTGTCTGTAGAAATTGGGAATCCA‑ATTTCTCTTTGTTGGGGCCCCGCCGGCAAGGTTGACTAGAATTGAAAAAAGCTTGTTACAAGCGCATTTTCGTTCAGTCAACTACTGCCAATATAACTTTGTAGAGCATTG  >  USA300TCH1516_ALE/800799‑801068

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.