New junction evidence
		seq id	position	reads (cov)	reads (cov)	score	skew	freq	annotation	gene	product
*	?	USA300TCH1516_ALE	895785 =	14 (0.760)	11 (0.690)	10/222	0.5	46.7%	coding (806/822 nt)	metQ_2	Methionine‑binding lipoprotein MetQ
	?	USA300TCH1516_ALE	= 909740	13 (0.810)					intergenic (‑663/‑371)	USA300HOU_RS04500/csbD_1	hypothetical protein/Stress response protein CsbD

ATTTTTTTGTTTAAAATTCGATAATTTGCATATACTGCCCCTTTTGTGCCCTTTTTTATTTTCAATACCACAAAAATAACCCCTTAATCGTTGTTATTAAAGGGTATTTTTATTTAATTGGTATTATTTAGCAGGAATAA‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑  <  USA300TCH1516_ALE/895924‑895785 ‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑ttatttagcaggaataaTTAGCCAGATTATCAAGGAAGTTCAAGGGCAATCAAAACATTGTTATATATGCATTTATAAAATTTTCAAGATAATTTATTATTCATACCCTTGCCCTTTGTTTCAAAATTATGCCCTTTTTTTGCCC  <  USA300TCH1516_ALE/909740‑909613                                                                                                                                                                                                                                                                              ATTTTTTTTTTTAAAATTCGATAATTTGCATATCATGCCACGTTTTTTTTTTTTTTTATTTTCAATACTACAAAAATAACCCCTTAATCGTTGTTATTAAAGGGTATTTTTATTTAATTGGTATTATTT                                                                                                                                             <  1:43026/129‑1       TTGTTTAAAATTCGATAATTTGCATATACTGCCCCTTTTGTGCCCTTTTTTATTTTCAATACCACAAAAATAACCCCTTAATCGTTGTTATTAAAGGGTATTTTTATTTAATTGGTATTATTTAGCAGG                                                                                                                                       <  1:164578/129‑1              AAATTCGATAATTTGCATATACTGCCCCTTTTGTGCCCTTTTTTATTTTCAATACCACAAAAATAACCCCTTAATCGTTGTTATTAAAGGGTATTTTTATTTAATTGGTATTATTTAGCAGGAATAATT                                                                                                                                >  1:219758/1‑129              AAATTCGATAATTTGCATATACTGCCCCTTTTGTGCCCTTTTTTATTTTCAATACCAAAAAAATAACACCTTAATCGTTGTTATTAAAGGGTATTTTTATTTAATTGGTATTATTTAGCAGGAATAATT                                                                                                                                >  1:206324/1‑129                                     GCCCCTTTTGTGCCCTTTTTTATTTTCAATACCACAAAAATAACCCCTTAATCGTTGTTATTAAAGTGTATTTTTATTTAATTTGTATTATTTAGCAGGAATAATTAGCCAGATTATCAAGGAAGTTCA                                                                                                         <  1:101082/129‑1                                      CCCCTATCGTTCCCTTTTTTATTTTCAATACCACAAAAATAACCCCTTAATCGTTGTTATTAAAGGGTATTTTTATTTAATTGGTATTATTTAGCAGGAATAATTAGCCAGATTATCAAGGAAGTTCAA                                                                                                        <  2:56142/129‑1                                          TTTTGTGACCCTTTTTATTTTCAATACCACAAAAATAACCCCTTAATCGTTGTTATTAAAGGGTATTTTTATTTAATTGGTATTATTTAGCAGGAATAATTAGCCAGATTATCAAGGAAGTTCAAGGGC                                                                                                    <  2:132135/129‑1                                              GTGCCCTTTTTTATTTTCAATACCACAAAAATAACCTCTTAATCGTTGTTATTAAAGGGTATTTTTATTTAATTGGTATTATTTAGCAGGAATAATTAGCCAGATTATCAAGGAAGTTCAAGGGAAATC                                                                                                >  1:47101/1‑129                                                  CCTTTTTTATTTTAAATACCACAAAAATAAACCCTTAATCGTTGTTATTAAAGGGTATTTTTATTTAATTGGTCTTATTTAGCAGTAATAATTAACCAGATTATCAAGGAAAATGAACGTCAATCAAAA                                                                                            >  2:127773/1‑129                                                     TTTTTATTTTCAATACAACAAAAATAACCCCTTAATCGTTGTTATTAAAGGGTATTTTTATTTAATTGGTATTATTTAGCAGGAATAATTAGCCAGATTATCAAGGAAATTAAAGAGAAAAAAAAACAT                                                                                         >  2:151584/1‑129                                                            TTTCAATACCACAAAAATAACCCCTTAATCGTTGTTATTAAAGGGTATTTTTATTTAATTGGTATTATTTAGCTGTAATAATTAGCCAGATTATCAAGGAAGATCAAGGGCAATCAAAACATTGTTATA                                                                                  <  1:181113/129‑1                                                                  TACCACAAAAATAACCCCTTAATCGTTGTTATTAAAGGGTATTTTTATTTAATTTGTATTATTTAGCAGGAATAATTAGCCAGATTATCAAGGAAGTTCAAGGGCAATCAAAACATTGTTATATATGCA                                                                            <  1:55505/129‑1                                                                             TAACCCCTTAATCGTTGTTATTAAAGGGTATTTTTATTTAATTGGTATTATTTAGCAGGAATAATTAGCCAGATTATCAAGGAAGTTCAAGGGCGATCAAAACATTGTTATATATGCATTTATAAAATT                                                                 >  2:131945/1‑129                                                                                                                              ATTTAGCAGGAATAATTAGCCAGATTATCAAGGAAGTTCAAGGGCGATCAAAACATTGTTATATATGCATTTATAAAATTTTCAAGATAATTTATTATTCATACCCTTGCCCTTTGTTTCAAAATTATG                <  1:131945/129‑1                                                                                                                                 TAGCAGGAATAATTAGCCAGATTATCAAGGAAGTTCAAGGGCAATCAAAACATTGTTATATATGCATTTATAAAATTTTCAAGATAATTTATTATTCATACCCTTGCCCTTTGTTTCAAAATTATGCCC             <  2:137261/129‑1                                                                                                                                  AGCAGGAATAATTAGCCAGATTATTAAGGAAGTTCAAGTGCAATCAAAACATTGTTATATATGCATTTATAAAATTTTCAAGATAATTTATTATTCATACCCTTGCCCTTTGTTTCAAAATTATGCCCT            <  2:111484/129‑1                                                                                                                                            ATTAGCCAGATTATCAAGGAAGTTTAAGGGCAATCAAAACATTGTTATATATGCATTTATAAAATTTCCAAGATAATTTATTATTCATACCCTTGCCCTTTGTTTCAAAATTATGCCCTTTTTTTGCCC  <  2:154818/129‑1                                                                                                                                                                                                                                                                              ATTTTTTTGTTTAAAATTCGATAATTTGCATATACTGCCCCTTTTGTGCCCTTTTTTATTTTCAATACCACAAAAATAACCCCTTAATCGTTGTTATTAAAGGGTATTTTTATTTAATTGGTATTATTTAGCAGGAATAA‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑  <  USA300TCH1516_ALE/895924‑895785 ‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑ttatttagcaggaataaTTAGCCAGATTATCAAGGAAGTTCAAGGGCAATCAAAACATTGTTATATATGCATTTATAAAATTTTCAAGATAATTTATTATTCATACCCTTGCCCTTTGTTTCAAAATTATGCCCTTTTTTTGCCC  <  USA300TCH1516_ALE/909740‑909613

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.