New junction evidence
		seq id	position	reads (cov)	reads (cov)	score	skew	freq	annotation	gene	product
*	?	USA300TCH1516_ALE	895785 =	54 (1.170)	4 (0.100)	3/212	NT	9.4%	coding (806/822 nt)	metQ_2	Methionine‑binding lipoprotein MetQ
	?	USA300TCH1516_ALE	= 909740	31 (0.780)					intergenic (‑663/‑371)	USA300HOU_RS04500/csbD_1	hypothetical protein/Stress response protein CsbD

TGAGCGTATTTTTTTGTTTAAAATTCGATAATTTGCATATACTGCCCCTTTTGTGCCCTTTTTTATTTTCAATACCACAAAAATAACCCCTTAATCGTTGTTATTAAAGGGTATTTTTATTTAATTGGTATTATTTAGCAGGAATAA‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑  <  USA300TCH1516_ALE/895931‑895785 ‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑ttatttagcaggaataaTTAGCCAGATTATCAAGGAAGTTCAAGGGCAATCAAAACATTGTTATATATGCATTTATAAAATTTTCAAGATAATTTATTATTCATACCCTTGCCCTTTGTTTCAAAATTATGCCCTTTTTTTGCC  <  USA300TCH1516_ALE/909740‑909614                                                                                                                                                                                                                                                                                    TGAGCGTATTTTTTTGTTTAAAATTCGATAATTTGCATATACTGCCCCTTTTGTGCCCTTTTTTGTTTTCAATACCACAAAAATAACCCCCGAATCGTTGTTATTAACGGGTATTTTTATTTAATTGGTATTAT                                                                                                                                              >  1:573957/1‑134 TGAGCGTATTTTTTTGTTTAAAATTCGATAATTTGCATATACTGCCCCTTTTGTGCCCTTTTTTATTTTCTATACCTCAAAAATAACCCCTTAATAGTTGATATTAAAGGATATTATTATTTAATTGGTAATAT                                                                                                                                              >  1:30508/1‑134          TTTTTTGTTTAAAATTCGATAATTTGCATATACTGCCCCTTTTGTGCCCTTTTTTATTTTCAATACCACAAAAATAACCCCTTAATCGTTGTTATTAAAGGGTATTTTTATTTAATTGGTATTATTTAGCAGGA                                                                                                                                     >  2:292249/1‑134           TTTTTGTTTAAAATTCGATAATTTGCATATACTGCCCCTTTTGTGCCCTTTTTTATTTTCAATACTACAAAAATAACCCCTTAATCGTTGTTATTAAAGGGTATTTTTATTTAATTGGTATTATTTAGCAGGAA                                                                                                                                    >  1:159635/1‑134                                           TGCCCCTTTTGTGCACTTTTTTATTTTCAATACCACAAAAATATCCCCCTAATCGTTGTTGTTAAAAAGTATTTTTATTTAATGGGTATTATTTAGCAGGAATAATTAGCCAGATTATCAAGGAAGTTCAAGGG                                                                                                    <  1:226939/134‑1                                               CCTTTTGTGCCCTTTTTTATTTTCAATACCACAAAAATAACCCCTTAATCGTTGTTATTAAAGGGTATTTTTATTTAATTGGTATTATTTAGCAGGAATAATTAGCCAGATTATCAAGGAAGTTCAAGGGCAAT                                                                                                <  1:543685/134‑1                                                                                                                      TATTTATTTGGTATTATTTAGCAGGAATAATTAGCCAGATTATCAAGGAAGTTCAAGGGCAATCAAAACATTGTTATATATGCATTTATAAAATTTTCAAGATAATTTATTATTCATACCCTTGCCCTTTGTTT                         <  1:526322/134‑1                                                                                                                      TATTTAATTAGTATTATTTAGCAGGAATAATTAGCCAGATTATCAAGGAAGTTCAAGGGCAATCAAAACATTGTTATATATGCATTTATAAAATTTTCAAGATAATTTATTATTCATACCCTTGCCCTTTGTTT                         <  1:468042/134‑1                                                                                                                                        taaCAGGAATAATTAGCCAGTTTATTAAGGAAGTTCAAGGGCAATAAAAAAATTGTTATATATGCATTTATAAAATTTTCAAGATAATTTATTATTCATACCCTTGCCCTTTGTTTCAAAATTATGCCCTTTTT       <  1:311121/131‑1                                                                                                                                        TAGCACGAATAATCAGCCAGATTACCAAGGAAGTTCAAGGGCAATCAACACATTGTTATATATGCATTTATAAAATTTTCAAGATAATTTATTATTCATACCCTTGCCCTTTGTTTCAAAATTATGCCCTTTTT       <  2:143978/134‑1                                                                                                                                         AGCAGGAATAATTAGCCAGATTATCAAGGAAGTTCAAGGGCAATCAAAACATTGTTATATATGCATTTATAAAATTTTCAAGATAATTTATTATTCATACCCTTTCCCTTTGTTTCAAAATTATGCTCTTTTTT      >  1:205344/1‑134                                                                                                                                          GCAGGAATAATTAGGCAGATTATCAAGGAAGTTCAAGGGCAATCAAAACATTGTTATATATGCATTTATAAAATTTTCAAGATAATTTATTATTCATACCATTGCCCTTAGTTTCAAAATTATGCCCTTTTTTT     >  2:371615/1‑134                                                                                                                                           aAGGAATAATTATCTATATTATTAAGTAAGTTCAAGGGCAATTAAAACATTTTTATATATGCATTTATAAAATTTTCAAGATAATTTATTATTCATACCCTTGCCCTTTGTTTCAAAATTATGCCCTTTTTTTG    <  1:393885/133‑1                                                                                                                                           CAGGAATAATTAGCCAGATTATCAAGGAAGTTCAAGGGCAATCAAAACATTGTTATATATGCATTTATAAAATTTTCAAGATAATTTATTATTCATACCCTTGCCCTTTGTTTCAAAATTATGCCCTTTTTTTG    <  2:143885/134‑1                                                                                                                                           CAGGAATAATTAGCCAGATTATCAAGGAAGTTCAAGGGCAATCAAAACATTGTTATATATGCATTTATAAAATTTTCAAGATAATTTATTATTCATACCCTTGCCCTTTGTTTCAAAATTATGCCCTTTTTTTG    <  1:511825/134‑1                                                                                                                                            AGGAATAATTAGCCAGATTATCAAGGAAGTTCAAGGCCAATCAAAACATTGATATATATGCATGTATAAAATTTTCAAGATAATTTATTATTCATACCCTTGCCCTTTGTTCTGAAATACTGCCTTTTTTGTGC   >  2:144088/1‑134                                                                                                                                             GGAATAATTAGCAAGAATATCAAGGAAGTGCAAGGGAAAGCAAAACATTGTTATATATGCATTTATAAAATTTTCAAGATAATTTATTATTCATACCCTTGCCCTTTGTTTCAAAATTATGCCCTTTTTTTGCC  <  1:195424/134‑1                                                                                                                                             GGAATAATTAGACAGATTATCAAGGAAGTTCAAGGGCAATCAAAACATTGTTATATATGCATTTATAAAATTTTCAAGATAATTTATTATTCATACCCTTGCCCTTTGTTTCAAAATTATGTCCTTTTTTTGCC  <  2:410973/134‑1                                                                                                                                                                                                                                                                                    TGAGCGTATTTTTTTGTTTAAAATTCGATAATTTGCATATACTGCCCCTTTTGTGCCCTTTTTTATTTTCAATACCACAAAAATAACCCCTTAATCGTTGTTATTAAAGGGTATTTTTATTTAATTGGTATTATTTAGCAGGAATAA‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑  <  USA300TCH1516_ALE/895931‑895785 ‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑ttatttagcaggaataaTTAGCCAGATTATCAAGGAAGTTCAAGGGCAATCAAAACATTGTTATATATGCATTTATAAAATTTTCAAGATAATTTATTATTCATACCCTTGCCCTTTGTTTCAAAATTATGCCCTTTTTTTGCC  <  USA300TCH1516_ALE/909740‑909614

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 12 ≤ ATCG/ATCG < 13 ≤ ATCG/ATCG < 22 ≤ 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.