New junction evidence
		seq id	position	reads (cov)	reads (cov)	score	skew	freq	annotation	gene	product
*	?	USA300TCH1516_ALE	895785 =	36 (1.180)	19 (0.710)	15/246	0.6	36.0%	coding (806/822 nt)	metQ_2	Methionine‑binding lipoprotein MetQ
	?	USA300TCH1516_ALE	= 909740	36 (1.350)					intergenic (‑663/‑371)	USA300HOU_RS04500/csbD_1	hypothetical protein/Stress response protein CsbD

CGCTCAAATCTGAGCGTATTTTTTTGTTTAAAATTCGATAATTTGCATATACTGCCCCTTTTGTGCCCTTTTTTATTTTCAATACCACAAAAATAACCCCTTAATCGTTGTTATTAAAGGGTATTTTTATTTAATTGGTATTATTTAGCAGGAATAA‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑  <  USA300TCH1516_ALE/895941‑895785 ‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑ttatttagcaggaataaTTAGCCAGATTATCAAGGAAGTTCAAGGGCAATCAAAACATTGTTATATATGCATTTATAAAATTTTCAAGATAATTTATTATTCATACCCTTGCCCTTTGTTTCAAAATTATGCCCTTTTTTTGCCCTTGAAAACAA  <  USA300TCH1516_ALE/909740‑909603                                                                                                                                                                                                                                                                                                         CGCTCAAATCTGAGCTTATTTTTTTGTTTAAAATTTGATAATTTGCATATACTGCACCTTTTGTGTCCTTTTTTATTTTCAATACCACAAAAATAACCTCTTAATCGTTGTTATTAAAGGGTATTTTTATTTAATTGGTAT                                                                                                                                                            <  2:20731/141‑1  cCTCAAATCTGAGCGTATTTTTTTGTTTAAAATTCGATAATTTGCATATACTGCCCCTTTTGTGCCCTTTTTTATTTTCAATACCACAAAAATAACCCCTTAATCGTTGTTATTAAAGGGTATTTTTATTTAATTGGTATT                                                                                                                                                           <  1:141772/140‑1  GCTCAAATCTGAGCGTATTTTTTTGTTTAAAATTCGATAATTTGCATATACTGCACCTTTTGTGCCCTTTTTTATTTTCAATACCACAAAAATAACCCCTTAATCGTTGTTATTAAAGGGTATTTTTATTTAATTGGTATT                                                                                                                                                           <  2:137983/141‑1   tTCAAATCTGAGCGTATTTTTTTGTTTAAAATTCGATAATTTGCATATACTGCCACTTTTGTGCCCTTTTTTATTTTCAATACCACAATAATATCCCCTTAATCGTTGTTATTAAAGGGTATTTTTATTTAATTGGTATTA                                                                                                                                                          <  2:345158/140‑1   tTCAAATCTGAGCGTATTTTTTTGTTGAAAATTCGATAATTTGCATATACTGACGCTTTTGTGCCCTTTTTTATTTTCAATACCATAAAAATAACCCTTTAATCGTTGTTATTAAAGGGTATTTTTATTTAATTGGTATTA                                                                                                                                                          <  2:353496/140‑1   aTCAAATCTGAGCGTATTTTTTTGTTTAAAATTCGATAATTTGCATATACTGCCCCTTTTGTGCCCTTTTTTATTTTCAATACCACAAAAATAACCCCTTAATCGTTGTTATTAAAGGGTATTTTTATTTAATTGGTATTA                                                                                                                                                          <  2:294912/140‑1    TCAAATCTGAGCGTATTTTTTTGTTTAAAATTCGATAATTTGCATATACTGCCCCTTTTGTGCCCTTTTTTATTTTCAATACCACAAAAATAACCCCTTAATCGTTGTTATTAAAGGGTATTTTTATTTAATTGGTATTAT                                                                                                                                                         <  2:314125/141‑1          CTGAGCGTATTTTTTTGTTTAAAATGCGATAATTTGCATATACTGCCCCTCTTGTGCCCTTTTTTATTTTCAATACCACAAAAATAACCCCTTAATCGTTGTTATTAAAGGGTATTTTTATTTAATTGGTATTATTTAGCA                                                                                                                                                   <  1:101796/141‑1            tatCGTCTTTTTTTGTTTAAAATTCGATAATTTGCATATACTGCCCCTTTTGTGCCCTTTTTTATTTTCAATACCACAAAAATAACCCCTTAATCGTTGTTATTAAAGGGTATTTTTATTTAATTGGTATTATTTAGCAGG                                                                                                                                                 <  1:305841/138‑1              GCGTATTTTTTTGTTTAAAATTCGATAATTTGCATATACTGCCCCTTTTGTGCCCTTTTTTATTTTCAATACCACAAAAATAACCCCTTAATCGTTGTTATTAAAGGGTATTTTTATTTAATTGGTATTATTTAGCAGGAA                                                                                                                                               <  1:63996/141‑1               tGTATTTTTTAGTTAAAAATTCAATAATTTGCATATACTGCCCATTTTGTGCGCTTTTTTATTTTCAATACCACAAAAATAACCCCTTAATTGTTGTTATTAAAGGGTATTTTTATTTAATTGGTATTATTTAGCAGGAAT                                                                                                                                              <  2:141308/140‑1               CGTATTTTTTTGTTTAAAATTCGATAATTTGCATATACTGCCCCTTTTGTGCCCTTTTTTATTTTCAATACCACAAAAATAACCCCTTAATCGTTGTTATTAAAGGGTATTTTTATTTAATTGGTATTATTTAGCAGGAAT                                                                                                                                              <  2:349547/141‑1                      TTTTGTTTAAAATTCGATAATTTGCATATACTGCCCCTTTTGTGCCCTTTTTTATTTTCAATACCACAAAAATAACCCCTTAATCGTTGTTATTAAAGGGTATTTTTATTTAATTGGTATTATTTAGCAGGAATAATTAGC                                                                                                                                       <  2:56101/141‑1                                               ATATACTGCCCCTTTTGTGCCCTTTTTTATTTTCAATACCACAAAAATAACCCCTTAATCGTTGTTATTAAAGGGTATTTTTATTTAATTGGTATTATTTAGCAGGAATAATTAGCCAGATTATCAAGGAAGTTCAAGGGC                                                                                                              <  1:203456/141‑1                                                TATACTGCCCCTTTTGTGCCCTTTTTTATTTTCAATACCACAAAAATAACCCCTTAATCGTTGTTATTAAAGGGTATTTTTATTTAATTGGTATTATTTAGCAGGAATAATTAGCCAGATTATCAAGGAAGTTCAAGGGCA                                                                                                             <  1:160021/141‑1                                                TATACTGCCCCTTTTGTGCCCTTTTTTATTTTCAATACCACAAAAATAACCCCTTAATCGTTGTTATTAAAGGGTATTTTTATTTAATTGGTATTATTTAGCAGGAATAATTAGCCAGATTATCAAGGAAGTTCAAGGGCA                                                                                                             <  1:179319/141‑1                                                TATACTGCCCCTTTTGTGCCCTTTTTTAGTTTCAATACCACAAAAATAACCCCTTAATCGTTGTTATTAAAGCGTATTTTGATTTAATGGGTATTATTTAGCAGGAATAATTAGCCAGATTATCAAGGAAGGTCAAGGGCA                                                                                                             <  1:345829/141‑1                                                            TTTGTGCCCTTTTTTATTTTCAATACCACAAAAATAACCCCTTAATCGTTGTTATTAAAGGGTATTTTTATTTAATTGGTATTATTTAGCAGGAATAATTAGCCAGATTATGAAGGTAGTTCAAGGGCAATCAAAACATTG                                                                                                 >  1:335942/1‑141                                                             TTGTGCCCTTTTTTATTTTCAATACCACAAAAATAACCCCTTAATCGTTGTTATTAAAGGGTATTTTTATTTAATTGGTATTATTTAGCAGGAATAATTAGCCAGATTATCACGGAAGTTCAAGGGCAATCAAAACATTGT                                                                                                >  1:149549/1‑141                                                               ggacgCTTTTTGATTATCAATAGCACAAAAATATCCGCTTAATCGTTGTTATTAAAGGGTATTTTTATTTAATTGGTATTATTTAGCAGGAATAATTAGCCAGATTATCAAGGAAGTTCAAGGGCAATCAAAACATTGTTA                                                                                              <  2:313345/136‑1                                                               GTGCCGTTTTTTATTTTCAATAGCACAAAAATAACCCCTTAATCGTTGTTATTAAAGGGTATTTTTATTTGAGTGGTATTATTTAGCAGGAATAATTAGCCAGATTATCAAGGAAGTTCAAGGGCAATCAAAACATTGTTA                                                                                              <  2:41683/141‑1                                                                   CCTTTTTTATTTTAAATAACACATCAACAATGCCTTAATCGTTGTTATTAAAGGGTATTTTTATTTAATTGGAATTATTTAGCAGGACTAATTATCCAGATTATCAATCAAGTTCAAATGCAATCAAAACATTGTTATATA                                                                                          >  2:198632/1‑141                                                                    CTTTTTTATTTTCAATACCACAAAAATAACCCCTTAATCGTTGTTATTAAAGGGTATTTTTATTTAATTGGTATTATTTAGCAGGAATAATTAGCCAGATTATCAAGGAAGTTCAAGGGCAATCAAAACATTGTTATATAT                                                                                         >  2:279454/1‑141                                                                            TTTTCAATACCACAAAAATAACCCCTTAATCGTTGTTATTAAAGGGTATTTTTATTTAATTGGTATTATTTAGTAGGAATAATTAGCCAGATTATTAAGGAAGTTCAAGGGCAATCAAAACATTGTTATATATGCTTTTtt                                                                                 >  2:208808/1‑139                                                                            TTTTCAATACCACAAAAATAACCCCTTAATCGTTGTTATTAAAGGGTATTATTATTTAATTGGTATTATTTAGCAGGAATAATTATCAAGATTATTAAGAAATTTCAAGGACAATCAAAACATTGTTATATCTGaacttct                                                                                 >  2:134949/1‑134                                                                                     CCACAAAAATAACCCCTTAATCGTTGTTATTAAAGGGTATTTTTATTTAATTGGTATTATTTAGCAGGAATAATTAGCCAGATTATCAAGGAAGTTCAAGGGCAATCAAAACATTGTTATATATGCATTTATAAAATTTTC                                                                        >  1:181763/1‑141                                                                                                                     AAGGGTATTTTTATTTAATTGGTATTATTTAGCAGGAATAATTAGCCAGATTATCAAGGAAGTTCAAGGGCAATCACAACATTGTTATATATGCATTTATAAAATTTTCAAGATAATTTATTATTCATACTCTTGCACTTT                                        >  2:143907/1‑141                                                                                                                              TTTATTTAATTGGTATTATTTAGCAGGAATAATTAGCCAGATTATCAAGGAAGTTCAAGGGCAATCAAAACATTGTTATATATGCATTTATAAAATTTTCAAGATAATTTATTATTCATACCCTTGCCCTTTGTTTCAAAA                               >  1:38116/1‑141                                                                                                                               TTATTTAATTGGTATTATTTAGCAGGAATAATTAGCCAGATTATCAAGGAAGTTCGAGGGCAATCAAAACATTGTTATATATGCATTTATAAGATTTCAAAGAAAATTTATTATTCATACCCTTGACATTTGTTTCAAAAT                              >  2:342763/1‑141                                                                                                                                      atgGGTATTATTTAGCAAGAATAATTAGACAGATTATTAAGTAATTTCAAGGGCAATCAAAACATTGTTATATATGCATTTATAAAATTTTCAAGATAATTTATTATTCATACCCTTGCCCTTTGTTTCAAAATTATGCCC                       <  2:282723/138‑1                                                                                                                                       aTGGTATTATGTAGCAGGAATAATTAGCCAGATTATCAAGGAAGTTCAAGGGCAATCAAAACATTGTTATATATGCATTTATAAAATTTTCAAGATAATTTATTATTCATACCCTTGCCCTTTGTTTCAAAATTATGCCCT                      <  1:283978/140‑1                                                                                                                                               ATTTAGCAGGAATAATTAGCCAGATTATCAAGGAAGTTCAAGGGCAATCAAAACATTGTTATATATGCATTTATAAAATTTTCAAGATAATTTATTATTCATACCCTTGCCCTTTGTTTCAAAATTATGCCCTTTTTTTGC              >  1:347070/1‑141                                                                                                                                               ATTTAGCAGGAATAATTAGCCAGATTATCAAGGAAGTTCAAGGGCAATCAAAACATTGTTATATATGCATTTATAAAATTTTCAAGATAATTTATTATTCATACCCTTGCCCTTTGTTTCAAAATTATGCCCTTTTTTTGC              >  1:346059/1‑141                                                                                                                                                  TAGCAGGAATAATTAGCCAGATTATCAAGGAAGTTCAAGGGCAATCAAAACATTGTTATATATGCATTTATAAAATTTTCAAGATAATTTATTATTCATACCCTTGCCCTTTGTTTCAAAATTATGCCCTTTGTTTCCCCg           <  1:280235/141‑2                                                                                                                                                   AGCAGGAATAATTAGCCAGATTATCAAGGAAGTTCAAGGGCAATCAAAACATTGTTATATATGCATTTATAAAATTTTCAAGCTACTTTATTATTCATACCCTTGCCCTTTGTTTCAAAATTATGCCCTTTTTTTGCCCTT          <  2:176145/141‑1                                                                                                                                                           aAATTAGCAAGATTAGCAAGGAAGTTCAAGGGAAATCAAAACATTGTTATATATGCATTTATAAAATTTTCAAGATAATTTATTATTCATACACTTGCCCATTAATTCAAAATTATGCCCTTTTTTTGCCCTTGAAAACAA  <  2:162538/140‑1                                                                                                                                                           TAATTAGCCAGATTATGAAGGAAGTTCAAGGGCAATCAAAATATTGTTATATATGCATTTATAAAATTTTCAAGATAATTTATTATTCATACCCCAGGTCGTTGTGTCAAAATTATGCCCTTTTTTTGCCCGTGAAAACAA  <  2:161784/141‑1                                                                                                                                                           TAATTAGCCAGATTATCAAGGAAGTTCAAGGGCAATCAAAACATTGTTATATATGCATTTATAAAATTTTCAAGATAATTTATTATTCATACCCTTGCCCTTTGTTTCAAAATTATGCCCTTTTTTTGCCCTTGAAAACAA  <  2:243052/141‑1                                                                                                                                                                                                                                                                                                         CGCTCAAATCTGAGCGTATTTTTTTGTTTAAAATTCGATAATTTGCATATACTGCCCCTTTTGTGCCCTTTTTTATTTTCAATACCACAAAAATAACCCCTTAATCGTTGTTATTAAAGGGTATTTTTATTTAATTGGTATTATTTAGCAGGAATAA‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑  <  USA300TCH1516_ALE/895941‑895785 ‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑ttatttagcaggaataaTTAGCCAGATTATCAAGGAAGTTCAAGGGCAATCAAAACATTGTTATATATGCATTTATAAAATTTTCAAGATAATTTATTATTCATACCCTTGCCCTTTGTTTCAAAATTATGCCCTTTTTTTGCCCTTGAAAACAA  <  USA300TCH1516_ALE/909740‑909603

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.