New junction evidence
		seq id	position	reads (cov)	reads (cov)	score	skew	freq	annotation	gene	product
*	?	USA300TCH1516_ALE	512620 =	16 (1.240)	8 (0.970) +TTATCTTGTCCATTTTATTTTTTAACCAAAATTTGATTAAAAAAC	8/160	NT	39.8%	intergenic (+688/‑6075)	recR/speA_2	Recombination protein RecR/Arginine decarboxylase
	?	USA300TCH1516_ALE	= 517814	22 (1.700)					intergenic (+5882/‑881)	recR/speA_2	Recombination protein RecR/Arginine decarboxylase

TTCAGTACAGATGACAAAGGTGTAATTTTTACTGTTGTTAAGCAGTTTGAAAGCCTGTATAGTATTTATTTGTTGAGGCAAACAAAACAACTCAACTTAAGAAATAACTTGAATTACTAACGAAAATTAATTTTAAAAAGTTATTGACTTAAATGTTAATAAAATGTATAATTAATTCTTGTCGGTAAGAAAAATGAACATTGAAAACTGAATGACAATATGTCAACGTTAATTCCAAAAAACGTAACTATAAGTTACAAACATTAT  >  USA300TCH1516_ALE/512486‑512752                                                                                                                                       |                                                                                                                                     ttCAGTACAGATGACAAAGGTGTAATTTTTACTGTTGTTAAGCAGTTTGAAAGCCTGTATAGTATTTATTTGTTGAGGCAAACAAAACAACTCAACTTAAGAAATAACTTGAATTACTAACGAAAATTAATTTTaa                                                                                                                                     >  2:77227/1‑136 (MQ=255) cctgttcccatgccgaaaacaaaagttaagctacttagcgtcgaaggtagtcgaacttacgttccgctagagtagaacgttgccaggcagttttttaatcaaattttggttaaaaaataaaatggacaagataaaa                                                                                                                                     <  1:136286‑M1/2‑1 (MQ=255)  ctgttcccatgccgaacacagaagttaagctccttagcgtcgatggtagtcgaacttacgttccgctagagtagaacgttgccaggcagttttttaatcaaattttggttaaaaaataaaatggacaagataaaaa                                                                                                                                    <  2:17805‑M1/3‑1 (MQ=255)    aGTACAGTTGACAAAGGTGTAATTTTTACTGTTGTTAAACAGTTTGAAAACATATATAGTATTTATTTGTTGAGGCAAACAAAACAACTCAACTTAAGAAATAACTTGAATTACTACCGAAAATTAATTTTaaaaa                                                                                                                                  >  1:49699/1‑136 (MQ=255)     gTACAGATGACAAAGGTGTAATTTTTACTGTTGTTAAGCAGTTTGAAAGCCTGTATAGTATTTATTTGTTGAGGCAAACAAAACAACTCAACTTAAGAAATAACTTGAATTACTAACGAAAATTAATTTTAAAAAg                                                                                                                                 >  1:19781/1‑136 (MQ=255)         catgccgaacacagaagttaagctccttagcgtcgatggtagtcgaacttacgttccgctagagtagaacgttgccaggcagttttttaatcaaattttggttaaaaaataaaatggacaagataaAAAAAGTTAt                                                                                                                             <  2:31053‑M1/10‑1 (MQ=255)           aTGACAAAGGTGTAAGTTTTACTGGTGTTAAGGAGTTTTAAAGTCTGTATAGTATTTATTTGTTGAGGCATACAAAACAACTCAAATTAAGAAATAACTTGAATTACTAACGAAAATTAATTTTAAAAAGTTATTg                                                                                                                           <  2:86301/136‑1 (MQ=255)               cAAAGGTGTAATTTTTACTGTTGTTAAGCAGATTGAAAGCCTGTATAGTATTTATTTGTTGAGGCAAACAAAACAACTCCACTTCAGAAAAAAAATCCATTACTAACGCAAATGAATTTTAACAAGTTATTGACtt                                                                                                                       >  2:145700/1‑136 (MQ=255)                  aGGTGTAATTTTTACTGTTGTTAAGCAGTTTGAAAGCCTGTATAGTATTTATTTGTTGAGGCAAACAAAACAACTCAACTTAAGAAATAACTTGAATTACTAACGAAAATTAATTTTAAAAAGTTATTGACTTaaa                                                                                                                    >  1:162985/1‑136 (MQ=255)                  aGGTGTAATGTGTACTGTTGTTAAGCAGTTTGAAAGCCTGTATAGTATTTATTTGTTGAGGCAAACAAAACAACTCAACTTAAGAAATAACTTGAATTACTAACGAAAATTAATTTTAAAAATTTATTGACTTaaa                                                                                                                    <  2:55101/136‑1 (MQ=255)                           ttttACTGTTGTTAAGCAGTTTGAAAGCCTGTATAGTATTTATTTGTTGAGGCAAACAAAACAACTCAACTTAAGAAATAACTTGAATTACTAACGAAAATTAATTTTAAAAAGTTATTGACTTAAATGTtaataa                                                                                                           >  1:65545/1‑136 (MQ=255)                           taagctccttagcgtcgatggtagtcgaacttacgttccgctagagtagaacgttgccaggcagttttttaatcaaattttggttaaaaaataaaatgaacaagataaAAACAGTTATTGACTTCAATGTtgataa                                                                                                           <  2:107935‑M1/28‑1 (MQ=255)                                 ccttagcgtcgatagtagtcgaacttacgttccgctagagtagaacgttgccaggcagttttttaatcaaataataaataaaaaataaaatggacaagataaAAAAAGTTATTGACTTAAATGTTGATAAAATGta                                                                                                     >  2:80215‑M1/103‑136 (MQ=255)                                       cgtcgatggtagtcgaacttacgttccgctagagtagaacgttgccaggcagttttttaatcaaattttggttaaaaaataaattggacaagataaATAATGTTTTTGACTTAAATGTTGATAAAATGTAgaatta                                                                                               >  1:57276‑M1/97‑136 (MQ=255)                                              tttGAAAGCCTGTATAGTATTTATTTGTTGAGGCAAACAAAACAACTCAACTTAAGAAATAACTTGAATTACTAACGAAAATTAATTTTAAAAAGTTATTGACTTAAATGTTAATAAAATGTATAATTAATTCTTg                                                                                        >  2:67031/1‑136 (MQ=255)                                              ttggAAAGTCTGTATAGTATTTATTTGTTGAGTCAAACAAAACAACTCAACTTAAGAAATAACTTGAATTACTAACGAAAATTAATTTTAAAAAGTTATTGACTTAAATGTTAATAAAATGTATAATTAATTCTTg                                                                                        <  2:68651/133‑1 (MQ=255)                                                tagtcgaacttacgttccgctagagtagaacgttgccaggcagttttttaatcaaattttggttaaaaaataaaatggacaagataaAAAAAGTTATTGATTTAAATGTTTATAAAATGTATAATTAATTCTTGTc                                                                                      >  1:17805‑M1/88‑136 (MQ=255)                                                 agtcgaacttacgttccgctagagtagaacgttgccaggcagttttttaatcaaattttggttaaaaaataaaatggacaagataaAAAAAGTTATTGACTTAAATGTTGATAAAATGTATAATTAATTCTTGTCg                                                                                     >  1:71703‑M1/87‑136 (MQ=255)                                                      ccTGTATAGTATTTATTTGTTGAGGCAAACAAAACAACTCAACTTAAGAAATAACTTGAATTACTAACGAAAATTAATTTTAAAAAGTTATTGACTTAAATGTTAATAAAATGTATAATTAATTCTTGTCGGTAAg                                                                                >  2:48449/1‑136 (MQ=255)                                                       acttacgttccgctagagtagaacgttgccaggcagttttttaatcaaattttggttaaaaaataaaatggacaagataaAAAAAGTTATTGACTTAAATGTTGATAAAATGTATAATTAATTATTGTCGGTAAGa                                                                               <  2:55822‑M1/56‑1 (MQ=255)                                                                                    caggcagttttttaatcaaattgtgagtaaaaaataaaatggacaagataaAAAAAGTTATTGACTTAAATGTTGATAAAATGTATAATTAATTCTTGTCGGTAAGAAAAATGAACATTGAAAACTAGATGACAat                                                  <  2:50987‑M1/85‑1 (MQ=255)                                                                                      aacaacTCAACTTAAGAAATAACTTGAATTACTAACGAAAATTAATTTTAAAAAGTTATTGACTTAAATGTTAATAAAATGTATAATTAATTCTTGTCGGTAAGAAAAATGAACATTGAAAACTGAATGACAatat                                                >  2:98869/1‑136 (MQ=255)                                                                                          actcaactTAAGAAATAACTTGAATTACTAACGAAAATTAATCTTAAAAAGTTCTTGACTTAAATGTTAATAAAATCTCTAATTAATTATTGTACGTAACAAACATAACCATTGAAAACTGAATAACAATATGTCa                                            >  2:35283/1‑136 (MQ=255)                                                                                            tcaactTAAGAAATAACTTGAATTACTAACGAAAATTAATTTTAAAAAGTTATTGACTTAAATGTTAATAAAATGTATAATTAATTCTTGTCGGTACGAAAAATGAACATTGAAAACTGAATGACAATATGTCaaa                                          >  2:113277/1‑135 (MQ=255)                                                                                              tttaatcaaattttggttaaaaaataaaatggacaagataaAAAAAGTTATTGACTTAAATGTTGATAAAATGTATTATTAATTCTTGTCGGTAAGAAAAATTAACATTGAAAACTGAATGACAATATGTCAACGt                                        >  1:110461‑M1/42‑136 (MQ=255)                                                                                                               gAATTACTAACGAAAATTAATTTTAAAAAGTTATTGACTTAAATGTTAATAAAATGTATAATTAATTCTTGTCGGTAAGAAAAATGAACATTGAAAACTGAATGACAATATGTCAACGTTAATTCCAAAAAACGTa                       >  2:113104/1‑136 (MQ=255)                                                                                                                aaTTACTAACGAAAATTAATTTTAAAAAGTTATTGACTTAAATGTTAATAAAATGTATAATTAATTCTTGTCGGTAAGAAAAATGAACATTGAAAACTGAATGACAATATGTCAACGTTAATTCCAAAAAACGTaa                      <  2:65545/136‑1 (MQ=255)                                                                                                                    aCTAACGAACATTAATTTTAAAAAAATATTGACTAAAAAAATAATAAAATGTATAATTAATTCTTGTCGGTAAGAAAAATGAACATTGAAAACTGAATGACAATATGTCAACGTTAATTCCAAAAAACGTAACtat                  >  1:43732/1‑136 (MQ=25)                                                                                                                     cTAACGAAAATTAATTTTAAAAAGTTATTGACTTAAATGTTAATAAAATGTATAATTAATTCTTGTCGGTAAGAAAAATGAACAATGAAAACTGAATGACAATATGTCAACGTTAATTCCAAAAAACGTAACtata                 <  1:67031/136‑1 (MQ=255)                                                                                                                          atggacaagataaAAAAAGTTATTGACTTAAATGTTGATAAAATGTATAATTAATTCTTGTCGGTAAGAAAAATGAACATTGAAAACTGAATGACAATATGTCAACGTTAATTCCAAAAAACGTAACTATAAGTTa            <  2:86140‑M1/123‑1 (MQ=255)                                                                                                                                    taaAAAAAGTTATTGACTTAAATGTTGATAAAATGTATAATTAATTCTTGTCGGTAAGAAAAATGAACATTGAAAACTGAATGACAATATGTCAACGTTAATTCCAAAAAACGTAACTATAAGTTACAAACattat  <  2:131952‑M1/133‑1 (MQ=255)                                                                                                                                    taaAAAAAGTTATTGACTTAAATGTTGATAAAATGTATAATTAATTCTTGTCGGTAAGAAAAATGAACATTGAAAACTGAATGACAATATGTCAAAGTTAATTACAAAAAACGTAAATATAAGTTACAAACattat  <  2:127874‑M1/133‑1 (MQ=255)                                                                                                                                       |                                                                                                                                     TTCAGTACAGATGACAAAGGTGTAATTTTTACTGTTGTTAAGCAGTTTGAAAGCCTGTATAGTATTTATTTGTTGAGGCAAACAAAACAACTCAACTTAAGAAATAACTTGAATTACTAACGAAAATTAATTTTAAAAAGTTATTGACTTAAATGTTAATAAAATGTATAATTAATTCTTGTCGGTAAGAAAAATGAACATTGAAAACTGAATGACAATATGTCAACGTTAATTCCAAAAAACGTAACTATAAGTTACAAACATTAT  >  USA300TCH1516_ALE/512486‑512752

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 12 ≤ ATCG/ATCG < 13 ≤ ATCG/ATCG < 27 ≤ 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.