New junction evidence
		seq id	position	reads (cov)	reads (cov)	score	skew	freq	annotation	gene	product
*	?	USA300TCH1516_ALE	895785 =	59 (0.950)	12 (0.220)	10/226	NT	18.7%	coding (806/822 nt)	metQ_2	Methionine‑binding lipoprotein MetQ
	?	USA300TCH1516_ALE	= 909740	53 (0.990)					intergenic (‑663/‑371)	USA300HOU_RS04500/csbD_1	hypothetical protein/Stress response protein CsbD

GCTCAAATCTGAGCGTATTTTTTTGTTTAAAATTCGATAATTTGCATATACTGCCCCTTTTGTGCCCTTTTTTATTTTCAATACCACAAAAATAACCCCTTAATCGTTGTTATTAAAGGGTATTTTTATTTAATTGGTATTATTTAGCAGGAATAA‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑  <  USA300TCH1516_ALE/895940‑895785 ‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑ttatttagcaggaataaTTAGCCAGATTATCAAGGAAGTTCAAGGGCAATCAAAACATTGTTATATATGCATTTATAAAATTTTCAAGATAATTTATTATTCATACCCTTGCCCTTTGTTTCAAAATTATGCCCTTTTTTTGCCCTTGAAAACAACC  <  USA300TCH1516_ALE/909740‑909601                                                                                                                                                                                                                                                                                                          GCTCAAATCTGAGCGTATTTTTTTGTTTAAAATTCGATAATTTGCATATACTGCCCCTTTTGTGCCCTTTTTTATTTTCAATACCACAAAAATAACCCCTTAATCGTTGTTATTAAAGGGTATTTTTATTTAATTGGTATT                                                                                                                                                             >  1:188525/1‑141 GCTCAAATCTGAGCGTATTTTTTTGTTTAAAATTCGATAATTTGCATATACTGCCCCTTTTGTGCCCTTTTTTATTTTCAATACCACAAAAATAACCCCTTAATCGTTGTTATTAAAGGGTATTTTTATTTAATTGGTATT                                                                                                                                                             >  1:370244/1‑141 GCTCAAATCTGAGCGTATTTTTTTGTTTAAAATTCGATAATTTGCATATACTGCCCCTTTTGTGCCCTTTTTTATTTTCAATACCACAAAAATAACCCCTTAATCGTTGTTATTAAAGGGTATTTTTATTTAATTGGTATT                                                                                                                                                             >  1:428552/1‑141 GCTCAAATCTGAGCGTATTTTTTTGTTTAAAATTCGATAATTTGCATATACTGCCCCTTTTGTGCCCTTTTTTATTTCCAATACCACAAAAATAACCCCTTAATCGTTGTTATTAAAGGGTATTTTTATTTAATTGGTATT                                                                                                                                                             <  1:107601/141‑1          TGAGCGTATTTTTTTGTTTAAAATTCGATAATTTGCATATACTGCCCCTTTTGTGCCCTTTTTTATTTTCAATACCACAAAAATAACCCCTTAATCGTTGTTATTAAAGGGTATTTTTATTTAATTTGTATTATTTAGCAG                                                                                                                                                    <  1:661886/141‑1          TGAGCGTATTTTTTTGTTTAAAATTCGATAATTTGCATATACTGCCCCTTTTGTGCCCTTTTTTATTTTCAATACCACAAAAATAACCCCTTAATCGTTGTTATTAAAGGGTATTTTTATTTAATTGGTATTATTTAGCAG                                                                                                                                                    >  1:197381/1‑141             GCGTATTTTTTTGTTTAAAATTCGATAATTTGCATATACTGCCCCTTTTGTGCCCTTTTTTATTTTCAATACCACAAAAATAACCCCTTAATCGTTGTTATTAAAGGGTATTTTTATTTAATTGGTATTATTTAGCAGGAA                                                                                                                                                 <  1:118275/141‑1             GCGTATTTTTTTGTGTAAAATTCGATAATTTGCAATTAATGCATCTTTTGTGCCCTTTTGTATTTTCAATACCACAAAAATAACCCCTTAATCGTTGTTATTAAAGAGTATTTTTATTTAATTGGTATTATTTAGCAGGAA                                                                                                                                                 <  2:304629/141‑1             GCGTATTTTTTTGCTTGAGGTTCGATGAGTTGCATATACTGCCCCTTTTGTGCCCTTTTTTATTTTCAATACCACAAAAATAACCCCTTAATCGTTGTTATTAAAGGGTATTTTTATTTAATTGGTATTATTTAGCAGGAA                                                                                                                                                 <  1:667558/141‑1                                 TTCGATAATTTGCATATACTGCCCCTTTTGTGCCCTTTTTTATTTTCAATACCACAAAAATAACCCCTTAATCGTTGTTATTAAAGGGTATTTTTATTTAATTGGTATTATTTAGCAGGAATAATTAGCCAGATTATCAAG                                                                                                                             <  1:257286/141‑1                                                  ACTGCCCCTTTTTTGCTCGTTTTTATTTTCAATACCACAAAAATAACCCCTTAATTGTTGTTATTAAAGGGTATTTTTATTTAATTGGTATTATTTAGCAGGAATAATTAGCCAGATTATCAAGGAAGTTCAAGGGCAATC                                                                                                            <  2:23572/141‑1                                                  ACTGCCCCTTTTGTGCCCTTTTTTATTTTCAAAACCAGAATTATAACCAATTCATCGTTGTTATTAAAGGGTATTTTTATTTAATTGGTATTATTTAGCAGGAATAATTAGCCAGATTATCAAGGAAGTTCAAGGGCAATC                                                                                                            <  2:369346/141‑1                                                      CCCCTTTTGTGCCCTTTTTTATTTTCAATACCACAAAAATAACCCCTTAATCGTTGTTATTAAAGGGTATTTTTATTTAATTGGTATTATTTAGCAGGAATAATTAGCCAGATTATCAAGGAAGTTCAAGGGCAATCAAAA                                                                                                        >  1:645706/1‑141                                                          TTTTGTGCCCTTTTTTATTTTCAATACCACAAAAATAACCCCTTAATCGTTGTTATTAAAGGGTATTTTTATTTAATTGGTATTATTTAGCAGGAATAATTAGCCAGATTATCAAGGAAGTTCAAGGGCAATCAAAACATT                                                                                                    >  1:490223/1‑141                                                                        TTATTTTCAATACCACAAAAATAACCCCTTAATCGTTGTTATTAAAGGGTATTTTTATTTAATTGGTATTATTTAGCAGGAATAATTAGCCAGATTATCAAGTAAGTTCAAGGGCAATCACAACATTGTTATATATGCATT                                                                                      >  2:331641/1‑141                                                                                       aAAAAATAACACCTTAATCGTTGTTAGTAAAGGGTATTATTATTTAATTGGTATTATTTAGCAGGAATAATTAGCCAGATTATCAAGGAAGTTCAAGGGCAATCAAAACATTGTTATATATGCATTTATAAAATTTTCAAG                                                                       <  2:680439/140‑1                                                                                             TAACCCCTTAATCGTTGTTATTAAAGGGTATTTTTATTTAATTGGTATTATTTAGCAGGAATAATTAGCCAGATTATCAAGGAAGTTCAAGGGCAATCAAAACATTGTTATATATGCCTCTGTAATATTGTCAAGATAATT                                                                 >  1:101228/1‑141                                                                                              AACCCCTTAATCGTTGTTATTAAAGGGTATTATTATTTAATTGGTATTATTTAGCAGGAATAATTAGCCAGATGATCAAGGAAGTTCAAGGGCAATCAAAACATTGTTATATATGCATTTATAAAATTTTCAAGATAATTT                                                                <  2:319516/141‑1                                                                                                                       GGTATTTTTATTTAATTGGTATTATTTAGCAGGAATAATTAGCCAGATTATCAAGGAAGTTCAAGGGCAATCAAAACATGGTTATATATGCAGTTATAAAATTTTCAAGATAATTTATTATTAATACCATTGACCTTTGTT                                       >  2:541401/1‑141                                                                                                                       GGTATTTTTATTTAATTGGTATTATTTAGCAGGAATAATTAGCCAGATTATAAAGGAAGTTCAAGGGCAATCAAAACATTGTTATATATGCATTTATAAAATTTTCAAGATAATTTATTATTCATACCCTTGCCCTTTGTT                                       >  2:203977/1‑141                                                                                                                                ATTTAATTGGTATTATTTAGCAGGAATAATTAGCCAGATTATCAAGGAAGTTCAAGGGCAATCAAAACATTGTTATATATGCATTTATAAAATTTTCAAGATAATTTATTATTCATACCCTTGCCCTTTTTATCAATATTA                              >  2:1848/1‑141                                                                                                                                             TATTTAGCAGGAATAATTAGCCAGATTATCAAGGAAGTTCAAGGGCAATCAAAACATTGTTATATATGCATTTATAAAATTTTCAAGATAATTTATTATTCATACCCTTGCCCTTTGTTTCAAAATTATGCCCTTTTTTTt                 >  2:504969/1‑140                                                                                                                                                TTAGCAGGAATAATTAGCCAGATTATCAAGGAAGTTCAAGGGCAATCAAAACATTGTTATATATGCATTTATAAAATTTTCAAGATAATTTATTATTCATACCCTTGCCCTTTGTTTCAAAATTATGCCCTTTTTTTGCCC              >  1:231557/1‑141                                                                                                                                                 TAGCAGGAATAATTAGCCAGATTATCAAGGAAGTTCAAGAGCAATCAAAACATTCTTATATATGCATTTATAAAATTTTCAAGATAATTTATTATTCATATCCTAGCCCTTTTTTTCACAATTATTCCCTTTTTTTttcct             >  2:462048/1‑136                                                                                                                                                  AGCAGGAATAATTAGCCAGATTATCAAGGAAGTTCAAGGGCAATCAAAACATTGTTATATATGCATTTATAAAATTTTCAAGATAATTTATTATTCATAATAATGCCCTTTGTTTCAAAATTATGCCCTTTTTTTGCACTT            >  1:709892/1‑141                                                                                                                                                   GCAGGAATAATTAGCCAGATTATCAAGGAAGTTCAAGGGCAATCAAAACATTGTTATATATGCATTTATAAAATTTTCAAGATAATTTATTATTCATACCCTTGCCCTTTGTTTCAAAATTATGCCCTTTTTTTttttttt           >  2:280618/1‑134                                                                                                                                                          aAATTAGCAAGATTATCAAGGAAGTTCAAGGGCAATCAAAACATTGTTATATATGCATTTATAAAATTTTCAAGATAATTTATTATTCATACCCTTGCCCTTTGTTTCAAAATTATGCCCTTTTTTTGCCCTTGAAAACAA    <  2:360612/140‑1                                                                                                                                                          TAATTATCCAGATTATCAAGGAAGTTCAAGGGAAATCCATGCATTGTTATTTATGCATTTATAAAATTTTCAAGATAATTTATTATTCATACCCTTGCCCTTTGTTTCAAAATTATGCCCTTTTTTTGCCCTTGAAAACAA    <  2:369452/141‑1                                                                                                                                                          TAATTAGCCAAATTATCAAGGAAGTTCAAGGGCAATCAAAACATTGTTATATATGCATTTATAAAATTTTCAAGATAATTTATTATTCATACCCTTGCCCTTTGTTTCAAAATTATGCCCTTTTTTTGCCCTTGAAAACAA    <  2:29869/141‑1                                                                                                                                                            ATTAGCCAGATTATCAAGGAAGTTCAAGGGCAATCAAAACATTGTTATATATGCATTTATAAAATTTTCAAGATAATTTATTATTCATACCCTTGCCCTTTGTTTCAAAATTATGCCCTTTTTTTGCCCTTGAAAACAACC  >  1:753244/1‑141                                                                                                                                                            ATTAGCCAGATTATCAAGGAAGTTCAAGGGCAATCAAAACATTGTTATATATGCATTTATAAAATTTTCAAGATAATTTATTATTCATACCCTTGCCCTTTGTTTCAAAATTATGCCCTTTTTTTGCCCTTGAAAACAACC  >  1:650517/1‑141                                                                                                                                                                                                                                                                                                          GCTCAAATCTGAGCGTATTTTTTTGTTTAAAATTCGATAATTTGCATATACTGCCCCTTTTGTGCCCTTTTTTATTTTCAATACCACAAAAATAACCCCTTAATCGTTGTTATTAAAGGGTATTTTTATTTAATTGGTATTATTTAGCAGGAATAA‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑  <  USA300TCH1516_ALE/895940‑895785 ‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑ttatttagcaggaataaTTAGCCAGATTATCAAGGAAGTTCAAGGGCAATCAAAACATTGTTATATATGCATTTATAAAATTTTCAAGATAATTTATTATTCATACCCTTGCCCTTTGTTTCAAAATTATGCCCTTTTTTTGCCCTTGAAAACAACC  <  USA300TCH1516_ALE/909740‑909601

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.