New junction evidence
		seq id	position	reads (cov)	reads (cov)	score	skew	freq	annotation	gene	product
*	?	USA300TCH1516_ALE	895785 =	27 (0.830)	8 (0.280)	8/226	NT	24.8%	coding (806/822 nt)	metQ_2	Methionine‑binding lipoprotein MetQ
	?	USA300TCH1516_ALE	= 909740	25 (0.890)					intergenic (‑663/‑371)	USA300HOU_RS04500/csbD_1	hypothetical protein/Stress response protein CsbD

AGATAATCCTTATGCAAACTTAATTGCTGTTAAAGAAGGACATCAAGATGATAAGAAAATCAAAGCATTAATTGAAGTATTACAATCTAAAGATATTCAAGACTTCATTAATGAAAAATACAATGGTGCAGTTATTCCTGCTAAATAATACCAATTAAATAAAAATACCCTTTAATAACAACGATTAAGGGGTTATTTTTGTGGTATTGAAAATAAAAAAGGGCACAAAAGGGGCAGTATATGCAAATTATCGAATTTTAAACAAAAAAAT  >  USA300TCH1516_ALE/895654‑895924                                                                                                                                    |                                                                                                                                            aGATAATACTTATGCAAACTTAATTGCTGTTAAAGAAGGACATCAAGATGATAAGAAAATCAAAGCATTAATTGAAGTATTACAATCTAAAGATATTCAAGACTTCATTAATGAAAAATACAATGGTGCAGTTATTCCTGc                                                                                                                                    <  2:310166/141‑1 (MQ=255)       gaaaaaaagggcataattttgaaacaaagggcaagggtatgaataataaattatattgacaattttatgaatgcatatataacaatgttttgattgcccttgaacttccttgataatctggctaaTTATTCCTGCTAaata                                                                                                                              >  2:141271‑M1/126‑141 (MQ=255)                 aaCTTAATTGCTGTTAAAGAAGGACATCAAGATGATAAGAAAATCAAAGCATTAATTGAAGTATTACAATCTAAAGATATTCAAGACTTCATTAATGAAAAATACAATGGTGCAGTTATTCCTGCTAAATAATACCAATta                                                                                                                    >  1:80562/1‑141 (MQ=255)                    ttAAATGCTATTAAAGAAGGACATCAAGATGATAAGAAAATCAAAGCATTAATTGAAGTATTACAATCTAAAGATATTCAAGACTTCATTAATGAAAAATACAATGGTGCAGTTATTCCTGCTAAATAATACCAATtaaat                                                                                                                 <  2:299363/141‑1 (MQ=255)                    tgaaTGGCTGATAAAGAAGGACATCAAGATGATAAGAAAATCAAAGCATTAATTGAAGTATTACAATCTAAAGATATTCAAGACTTCATTAATGAAAAATACAATGGTGCAGTTATTCCTGCTAAATAATACCAATtaaat                                                                                                                 <  1:126767/139‑1 (MQ=255)                        tttgaaacaaagggcaagggtatgaataataaattatcttgaaaattttataaatgcatatataacaatgttttgattgcccttgaacttccttgataatctggctaaTTATTACTGCTAAATAATACCAattaaataaca                                                                                                             <  2:361274‑M1/33‑3 (MQ=255)                                 aagggcaagggtatgaataataaattatcttgaaaattttataaatgcatatataacaatgttttgattgcccttgtacttccttgataatctggctaaTTATTCCTGCTAAATAATACCAATTAAATAAAAATACCCttt                                                                                                    >  2:247714‑M1/100‑141 (MQ=255)                                   aaaagACATCAAGATGATAAGAAAATCAAAGCATTAATTGAAGTATTACAATCTAAAGATATTCAAGACTTCATTAATGAAAAATACAATGGTGCAGTTATTCCTGCTAAATAATACCAATAAAATATGTTTACCCTTtaa                                                                                                  <  2:145075/137‑1 (MQ=255)                                    aagGACATCAAGATGATAAGAAAATCAAAGCATTAATTGAAGTATTACAATCTAAAGATATTCAAGACTTCATTAATGAAAAACACAATGGTGCAGTTATTCCTGCTAAATAATACTAATTAAATAAAAATACCATTtaat                                                                                                 >  1:238270/1‑141 (MQ=255)                                     gcaagggtatgaataataaattatcttgaaaattttataaatgcatatataacaatgttttgattgcccttgaacctccttgataatctggctaaTTATTCCTGCTAAATAATACCAATTAAATAAAAATACCCTTtaata                                                                                                >  2:38699‑M1/96‑141 (MQ=255)                                        aCATCAAGATGATAAGAAAATCAAAGCATTAAGTGAAGTATTACAATCTAAAGATATTCAAGACTTCATTAATGAAAAATACAATGGTGCAGTTATTCCTGCTAAATAATACCAATTAAATAAAAATACCCTTTAATaaca                                                                                             <  1:163745/141‑1 (MQ=255)                                          aTCAAGATGATAAGAAAATCAAAGCATTAATTGAAGTATTACAATCTAAAGATATTCAAGACTTCATTAATGAAAAATACAATGGTGCAGTTATTCCTGCTAAATAATACCAATTAAATAAAAATACCCTTTAATaacaac                                                                                           >  2:128720/1‑141 (MQ=255)                                           tCAAGATGATAAGAAAATCAAAGCATTAATTGAAGTATTACAATCTAAAGATATTCAAGACTTCATTAATGAAAAATACAATGGTGCAGTTATTCCTGCTAAATAATACCAATTAAATAAAAATACCCTTTAATAACAACg                                                                                          >  1:377977/1‑141 (MQ=255)                                               gatgatAAGAAAATCAAAGCATTAATTGAAGTATTACAATCTAAAGATATTCAAGACTTCATTAATGAAAAATACAATGGTGCAGTTATTCCTGCTAAATAATACCAATTAAATAAAAATACCCTTTAATAACAACGATTa                                                                                      >  1:357216/1‑141 (MQ=255)                                                   atAAGAAAATCAAAGCATTAATTGAAGTATTACAATCTAAAGATATTCAAGACTTCATTAATGAAAAATACAATGGTGCAGTTATTCCTGCTACATAATACCAATTAAATAAAAATACCCTTTAATAACAACGATTAAggg                                                                                  >  1:145566/1‑141 (MQ=255)                                                     aaGAAAATCAAAGCATTAATTGAAGTATTACAATCTAAACATATTCAAGACTTCATTAATGAAAAATACAATGGTGCAGTTATTCCTGCTAAATAATACCAATTAAATAAAAATACCCTTTAATAACAACGATTAAGGGGt                                                                                <  2:109144/141‑1 (MQ=255)                                                         aaaTCAAAGCATTAATTGAAGTATTACAATCTAAAGATATTCAAGACTTCATTAATGAAAAATACAATGGTGCAGTTATTCCTGCTAAATAATACCAATTAAATAAAAATACCCTTTAATAACAACGATTAAGGGGTAAtt                                                                            >  2:20129/1‑141 (MQ=255)                                                           aTCAAAGCATTAATTGAAGTATTACAATCTAAAGATATTCAAGACTTCATTAATGAAAAATACAATGGTGCAGTTATTCCTGCTAAATAATACCAATTAAATAAAAATACCCTTTAATAACAACGATTAAGGGGTTAtttt                                                                          <  1:177208/141‑1 (MQ=255)                                                                       ttataaatggatatataacaatgttttgattgcccttgaacttccttgataatctggctaaTTATTCCTGATAAATAATAACAATTAAATAAAAATACCCTTTAATAACAACGATTAAGGGGTTATTTTTGTGTTATTGaa                                                              >  2:244417‑M1/62‑141 (MQ=255)                                                                                    aaTCTAAAGATATTCAAGACTTCATTAATGAAAAATACAATGGTGCAGTTATGCCTGCTAAATAATACCAATTAAATAAAAATACCCTTTAATAACAACGATTAAGGGGTTATTTTTGTGGTATTGAAAATAAAAAAGGGc                                                 <  1:128720/141‑1 (MQ=255)                                                                                     aTCTAAAGATATTCAAGACTACATTCATGCAAAATACCATGGTGCAGTTATTCCTGCTAAATAATACCAATTAAATAAACATACCCTTTAATAACAACGATTAAGGGGTTATTTTTGTGGTATTGAAAATAAAAAAGGGca                                                <  1:379015/141‑1 (MQ=255)                                                                                          tatgttttgattgcctttgaacttccttgataatcgggctaaTTATTCCTGCTAAATAATACCAATTAAATAAAAATACCCTTTAATAACAACGATTAAGGGGTTATTTTTGTGGTATTGAAAATAAAAAAGGGCACaaaa                                           >  1:5272‑M1/43‑141 (MQ=255)                                                                                          aatatatGCAAGACTTAATTAATGAAAAATACAATTGTGCAGTTATTCCTGCGAAATAATACCAATTAAATAAAAATACCCTTTAATAACAACGATTAAGGGGTTATTTTTGTGGTATTGAAAATAAAAAAGGGCACaaaa                                           <  2:56199/138‑1 (MQ=255)                                                                                               atTCAAGACTTCATTAATGAAAAATACAATGGTGCAGTTATTCCTGCTAAATAATACCAATTAAATAAAAATACCCTTTAATAACAACGATTAAGGGGTTATTTTTGTGGTATTGAAAATAAAAAAGGGCACAAAAGGGGc                                      <  1:11941/141‑1 (MQ=255)                                                                                                 tgattgcccttgaacttccttgataatctggctaaTTATTCCTGCTAAATAATACCAATTAAATAAAAATACCCTTTAATAACAACGATTAAGGGGTTATTTTTGTGGTATTGAAAATAAAAAAGGGCACAAAAGGGGCAg                                    <  1:52401‑M1/106‑1 (MQ=255)                                                                                                  gattgcccttgaacttccttgataatctggctaaTTATTCCTGCTAAATAATACCAATTAAATAAAAATACCCTTTAATAACAACGATTAAGAGGTTATTTTTGTGGTATTGAAAATAAAAAAGGGCACAAAAGGCGCAGt                                   <  2:395503‑M1/107‑1 (MQ=255)                                                                                                   aaGACTTCATTAATGAAAAATACAATGGTGCAGTTATTCCTGCTAAATAATACCAATTAAATAAAAATACCCTTTAATAACAACGATTAAGGGGTTATTTTTGTGGTATTGAAAATACAAAAGGGCACAAAAGGGGCAGta                                  >  2:3140/1‑141 (MQ=255)                                                                                                   aaGACTTCATTAATGAAAAATACAATGGTGCAGTTATTCCTGCTAAATAATACCAATTAAATAAAAATACCCTTTAATAACAACGATTAAGGGGTTATTTTTGTGGTATTGAAAATAAAAAAGGGCACAAAAGGGGCAGta                                  >  1:356183/1‑141 (MQ=255)                                                                                                         tCATTAATGAAAAATACAATGGTGCAGTTATTCCTGCTAAATAATACCAATTAAATAAAAATACCCTTTAATAACAACGATTAAGGGGTTATTTTTGTGGTATTGAAAATAAAAAAGGGCACAAAAGGGGCAGTATATGCa                            >  2:316507/1‑141 (MQ=255)                                                                                                           ataaagaaaaaaTACAATGGTGCAGTTATTCCTGCTAAATAATACCAATTAAATAAAAATACCCTTTAATAACAACGATTAAGGGGTTATTTTTGTGGTATTGAAAATAAAAAAGGGCACAAAAGGGGCAGTATATGCaaa                          <  2:145566/134‑1 (MQ=255)                                                                                                           aTTAATGAAAAATACAATGGTGCAGTTATTACTGCTAAATAATACCAATTAAATAAAAATACCCTTTAATAACAACGATTAAGAGGTTATTTTTGTGGTATTGAAAATAAAAAAGGGCACAAAAGGGGCAGTATATGaaaa                          >  2:102495/1‑141 (MQ=255)                                                                                                             tAATGAAAAATACAATGGTGCAGTTATTCCTGCTAAATAATACCAATTAAATAAAAATACCCTTTAATAACAACGATTAAGGGGTTATTTTTGTGGTATTGAAAATAAAAAAGGGCACAAAAGGGGCAGTATATGCAAAtt                        >  1:275954/1‑141 (MQ=255)                                                                                                                 tcattgataatctggctaaTTATTCCTGCTAAATAATACCAATTAAATAAAAATACCCTTTAATAACAACGATTAAGGGGTTATTTTTGTGGTATTGAAAATAAAAAAGGGCACAAAAGGGGCAGTATATGCAAATTATCg                    >  1:379576‑M1/20‑141 (MQ=255)                                                                                                                    aaaTACAATGGTGCAGTTATTCCTGCTAAATAATACCAATTAAATAAAAATACCCTTTAATAACAACGATTACGGGGTTATTTTTGTGGTATTGAAAATAAAAAAGGGCACAAAAGGGGCAGTATATGTAAATTGTCGAAt                 >  1:317992/1‑141 (MQ=255)                                                                                                                        aCAATGGTGCAGTTATTCCTGCTAAATAATACCAATTAAATAAAAATACCCTTTAATAACAACGATTAAGGGGTTATTTTTGTGGTATTGAAAATAAAAAAGGACAAAACAGCCGCACAAGAAGCAAATAATAGAAtttga             >  1:10931/1‑139 (MQ=255)                                                                                                                        aCAATGGTGCAGTTATTCCTGCTAAATAATACCAATTAAATAAAAATACCCTTTAATAACAACGATTAAGGGGATATTTTTATGGTATAGAAAATAAAAAAGAGCAAAAACGGGGAAGTATATGCAAATGATAGAATTTTa             >  2:338060/1‑141 (MQ=255)                                                                                                                                gCAGTTATTCCTGCTAAATAATACCAATTAAATAAAAATACCCTTTAATAACAACGATTAAGGGGTTATTTTTGTGGTATTGAAAATAAAAAAGGGCACAAAAGGGGCAGTAGATGCAAATTCTGGACTTTTCAACaaaaa     >  1:82023/1‑141 (MQ=255)                                                                                                                                   gTTATGCCTGCTAAATAATACCAATTAAATAAAAATACCCTTTAATAACAACGATTAAGGGGGTATTTTTGTGGTATTGAAAATAAAACAGGGCACAAAAGGGGCCGGATATGGAAAGTATCGAATTTTAAACGAAAAAAt  >  1:176468/1‑141 (MQ=255)                                                                                                                                    |                                                                                                                                            AGATAATCCTTATGCAAACTTAATTGCTGTTAAAGAAGGACATCAAGATGATAAGAAAATCAAAGCATTAATTGAAGTATTACAATCTAAAGATATTCAAGACTTCATTAATGAAAAATACAATGGTGCAGTTATTCCTGCTAAATAATACCAATTAAATAAAAATACCCTTTAATAACAACGATTAAGGGGTTATTTTTGTGGTATTGAAAATAAAAAAGGGCACAAAAGGGGCAGTATATGCAAATTATCGAATTTTAAACAAAAAAAT  >  USA300TCH1516_ALE/895654‑895924

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.