New junction evidence
		seq id	position	reads (cov)	reads (cov)	score	skew	freq	annotation	gene	product
*	?	USA300TCH1516_ALE	895785 =	50 (0.660)	10 (0.150)	8/226	NT	18.3%	coding (806/822 nt)	metQ_2	Methionine‑binding lipoprotein MetQ
	?	USA300TCH1516_ALE	= 909740	46 (0.700)					intergenic (‑663/‑371)	USA300HOU_RS04500/csbD_1	hypothetical protein/Stress response protein CsbD

CGCTCAAATCTGAGCGTATTTTTTTGTTTAAAATTCGATAATTTGCATATACTGCCCCTTTTGTGCCCTTTTTTATTTTCAATACCACAAAAATAACCCCTTAATCGTTGTTATTAAAGGGTATTTTTATTTAATTGGTATTATTTAGCAGGAATAA‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑  <  USA300TCH1516_ALE/895941‑895785 ‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑ttatttagcaggaataaTTAGCCAGATTATCAAGGAAGTTCAAGGGCAATCAAAACATTGTTATATATGCATTTATAAAATTTTCAAGATAATTTATTATTCATACCCTTGCCCTTTGTTTCAAAATTATGCCCTTTTTTTGCCCTTGAAAACAACC  <  USA300TCH1516_ALE/909740‑909601                                                                                                                                                                                                                                                                                                           CGCTCAAATCTGAGCGTATTTTTTTGTTTAAAATTCGATAATTTGCATATACTGCCCCTTTTGTGCCCTTTTTTATTTTCAATACCACAAAAATAACCCCTTAATCGTTGTTATTAAAGGGTATTTTTATTTAATTGGTAT                                                                                                                                                              <  2:246983/141‑1       AATCTGAGCGTATTTTTTTGTTAAAAATGCTATAATTTGCATAGACTGCCCCTTTTGTGCCCTTTTTTATTTTCAATACCACAAAAATAACCCCTTAATCGTTGTTATTAAAGGGTATTTTTATTTAATTGGTATTATTTA                                                                                                                                                        <  2:871703/141‑1          CTGAGCGTATTTTTTTGTTTAAAATTCGATAATTTGCATATACTGCCCCTTTTGTGCCCTTTTTTATTTTCAATACCACAAAAATAACCCCTTAATCGTTGTTATTAAAGGGTATTTTTATTTAATTGGTATTATTTAGCA                                                                                                                                                     >  1:824585/1‑141             AGCGTATTTTTTTGTTTAAGATTCGATAATTTGCATATACTGCCCCTTTTGTGCCCTTTTTTATTTTCAATACCACAAAAATAACCCCTTAATCGTTGTTATTAAAGGGTATTTTTATTTAATTGGTATTATTTAGCAGGA                                                                                                                                                  >  1:543947/1‑141             AGCGTATTTTTTTGTTTAAAATTCGATAATTTGCATATACTGCCCCTTTTGTGCCCTTTTTTATTTTCAATACCACTAAATATGCCCCTTAATCGTTGTTATTAAAGGGTATTTTTATTTAATTGGTATTATTTAGCAGGA                                                                                                                                                  >  1:662530/1‑141             AGCGTATTATATGGGTAAAAATTCGATAATTTGCATATACTGCCCCTTTTGTGCCTTTTTTTATTTTCAATACCACAAAAATAACCCCTTAATCGTTGTTATTAAAGGGTATTTTTATTTAATTGGTATTATTTAGCAGGA                                                                                                                                                  >  2:421728/1‑141               CGTATTTTTTTTTTTAATTTTCGATAATTTGCATATACTGCCCCTTTTGTGCCCTTTTTTATTTTCAATACCACAAAAATAACCCCTTAATCGTTGTTATTAAAGGGTATTTTTATTTAATTGGTATTATTTAGCAGGAAT                                                                                                                                                >  2:733895/1‑141                ttctgTTTTTTTTTAAAATTCGATAGTTTGCATATACTGCCTCTTTTGTGCTCTTTTTGATTTTCAATACCACAAAAATAACCCCTTAATCGTTGTTATTAAAGTGTATTTTTATTTAATTGGTATTATTTTGCAGGAATA                                                                                                                                               <  2:585032/136‑1                tTATTTTTTTTTTTAAAATTCGATAATTTGCATATACCGCCCCTTTTGTGCCCTTTTTTATTTTCAATACCACAAAAATAACCCCTTAATCGTTGTTATTAAAGGGTATTTTTATTTAATTGGTATTATTTAGCAGGAATA                                                                                                                                               <  1:851103/140‑1                cTATTTTTTTGTTTAAGATTCGATGATTTTCATATACTGCCCCTTTTCTGCTCTTTTTTATTTTCTATACCACAAAAATAACCCCTTAATCGTTGTTATTAAAGGGTATTTTTATTTAATTGGTATTATTTAGCAGGAATA                                                                                                                                               <  2:451975/140‑1                GTATTTTTTTGTTTAAAATTCGATAATTTGCATATACTGCCCCTTTTGTGCCCTTTTTTATTTTCAATACCACAAAAATAACCCCTTAAGCGTTGTTATTAAAGGGTATTTTTATCTAAAACGTATTATTTAGCAGGAATA                                                                                                                                               <  2:647537/141‑1                 TATTTTTTTGTTTAAAATTCGATAATTTGCATATACTGCCCCTTTTGTGCCCTTTTTTATTTTCAATACCACAAAAATAACCCCTTAATCGTTGTTATTAAAGGGTATTTTTATTTAATTGGTATTATTTAGCAGGAATAA                                                                                                                                              <  1:347532/141‑1                             TAAAATTCGATAATTTGCATATACTGCCCCTTTTGTGCCCTTTTTTATTTTCAATACCACAAAAATAACCCCTTAATCGTTGTTATTAAAGGGTATTTTTATTTAATTGGTATTATTTAGCAGGAATAATTAGCCAGATTA                                                                                                                                  <  2:350327/141‑1                                                     TGCCCCTTTTGTGCCCTTTTTTATTTTCAATACCACAAAAATAACCCCTTAATCGTTGTTATTAAAGGGTATTTTTATTTAATTGGTATTATTTAGCAGGAATAATTAGCCAGATTATCAAGGAAGTTCAAGGGCAATCAA                                                                                                          <  2:787413/141‑1                                                           TTTTGTGCCCTTTTTTATTTTCAATACCCCAAAAATAACCCCTTAATCGTTGTTATTAAAGGGTATTTTTATTTAATTGGTATTATTTAGCAGGAATAATTAGCCAGATTATCAAGGAAGTTCAAGGGCAATCAAAACATT                                                                                                    >  2:382326/1‑141                                                           TTTTGTGCCCTTTTTTATTTTCAATACCACAAAAATAACCCCTTAATCGTTGTTGTTAAAGGGTATTTTTATTTAATTCGTATTATTTAGCAGGAATACTTAGCCAGATTATCAAGGAAGTTCAAGGGCAATCAAAATATT                                                                                                    >  2:759223/1‑141                                                           TTTTGTGCCCTTTTTTATTTTCAATACCACAAAAATAACCCCTTAATCGTTGTTATTAAAGGGTATTTTTATTTAATTGGTATTATTTAGCAGGAATAATTAGCCAGATTATCAAGGAAGTTCAAGGGCAATCAAAACATT                                                                                                    >  2:466642/1‑141                                                              TGTGCCCTTTTTTATTTTCAATACCACAAAAATAACCCCTTAATCGTTGTTATTAAAGGGTATTTTTATTTAATTGGTATTATTTAGCAGGAATAATTAGCCAGATTATCAAGGAAGTTCAAGGGCAATCAAAACATTGTT                                                                                                 <  2:663795/141‑1                                                                TGCTCTTTTTTTGTTTCAATACCAAAAAAATAACCCCTTAATCGTTATTATTAAAGGGTATTTTTATTTAAGTGGTATTATTTAGCAGGAATAATTAGCCAGATTATCAAGGAAGTTCAAGGGCAATCAAAACATTGTTAT                                                                                               <  1:832159/141‑1                                                                                             ATAACCCCTTAATCGTTGTTATTAAAGGGTATTTTTATTTAATTGGTATTATTTAGCAGGAATAATTAGCCAGATTATCAAGGAAGTTCAAGGGCAATCAAAACATTGTTATATATGCATTTATAAAATTTTAAAAATAAT                                                                  >  2:37825/1‑141                                                                                              TAACCCCTTAATCGTTGTTATTAAAGGGTATTTTTATTTAATTGGTATTATTTAGCAGGAATAATTAGCCAGATTATCAAGGAAGTTCAAGGGCAATCAAAACATTGTTATATATGCATTTATAAAATTTTCAAGATAATT                                                                 >  1:480600/1‑141                                                                                              TAACCCCTTAATCGGTGTTATTAAAGGGTATTTTTATTTAATCGGTATTATTTAGCAGGAATAATTAGCCAGATTATCAAGGAAGTTCAAGGGCAATCAAAACATTGTTATATATGCATTTATAAAATTTTCAAGATAATT                                                                 <  1:81497/141‑1                                                                                                                                              TATTTAGCAGGAATAATTAGCCAGATTATGAAGGAAGTTCAAGGGCAATCAAAACATTGTTATATATGCATTTATAAAATTTTCAAGATAATTTATTATTCATACCCTTGCCCTTTGTTTCAAAATTATGCCTTTTTTTTG                 >  2:837429/1‑141                                                                                                                                              TATTTAGCAGGAATAATTAGCCAGATTATCAAGGAAGTTCAAGGGCAATCAAAACATTGTTATATATGCATTTATAAAATTTTCAAGATAATTTATTATTCATACCCTTGCCCTTTGTTTCAAAATTATGCCCTTTTTTTt                 >  2:795801/1‑140                                                                                                                                               ATTTAGCAGGAATAATTAGCCAGATTATCAAGGAAGTTCAAGGGCAATCAAAACATTGTTATATATGCATTTATAAAATTTTCAAGATAATTTATTATTCATACCCTTGCCCTTTGTTTCATAATTATGCCCTTTTTTTGC                >  1:844754/1‑141                                                                                                                                               ATTTAGCAGGAATAATTAGCCAGATTATCAAGGAAGTTCAAGGGCAATCAAAACATTGTTATATATGCATTTATAAAATTTTCAAGATAATTTATTATTCATACCCTTGCCCTTTGTTTCAAAATTATGCCCTTTTTTTGC                <  1:54300/141‑1                                                                                                                                                  TAGCAGGAATAATTAGCCAGATTATCAAGGAAGTTCAAGGGCAATCAAAACATTGTTATATATGCATTTATAAAATTTTCAAGATAATTTATTATTCATACCCTTGCCCTTTGTTTCAAGATTATGCCCTTTTTTTGCCCT             <  1:466642/141‑1                                                                                                                                                   AGCAGGAATAATTAGCCAGATTATCAAGGAAGTTCAAGGGCAATCAAAACATTGTTATATATGCATTTATAAAATTTTCAAGATAATTTATTATTCCTACCCTTGCCCTTTGTTTCAAAATTATGCCCTTTTTTTGCCCTT            <  1:515630/141‑1                                                                                                                                                      AGGAATAATTAGCCAGATTATCAAGGAAGTTCAAGGGCAATGAAAACATTGTTATATATGCATTTATAAAATTTTCAAGCTAATCTATTATTTATACCCTTGCCCTTTGTTTCATAATTTTGCCCTTTTTTTGCCCTTGAA         >  1:117228/1‑141                                                                                                                                                       GGAATAATTAGCCAGATTATCAAGGAAGTTCAAGGGCAATCAAAACATTGTTATATATGCATTTATAAAATTTTCAAGATAATTTATTATTCATACCCTTCCCCTTTGTCTCACAATTATGCCCTTTTTTTGCCCTTGAAA        >  2:570787/1‑141                                                                                                                                                         AATAATTAGCCAGATTATCAAGGAAGTTCAAGGGCAATCAAAACATTGTTATATATGCATTTATAAAATTTTCAAGATAATTTATTATTCATACCCTTGCCCTTTGTTTCAAAATTATGCCCTTTTTTTGCCCTTGAAAAa      >  1:636640/1‑140                                                                                                                                                          atcATTAGCCAGACTATCAAGGAAGTTCAAGGGCAATTAAAACATTGTTATATATGCATTTATAAAATTTTCAAGATAATCTACTATTCATACCCTTGCCCTTTGTTTCAAAATTATGCCCTTTTTTTGCCCTTGAAAACA     <  1:759223/138‑1                                                                                                                                                          ATAATTAGCCAGATTATCAAGGAAGTTCAAGGGCAATCAAAACATTGTTATATATGCATTTATAAAATTTTCAAGATAATTTATTATTCATACCCTTGCCCTTTGTTTCAAAATTATGCCCTTTTTTTGCCCTTGAAAACA     <  1:382326/141‑1                                                                                                                                                           TAATTAGCCAGATTATCAAGGAAGTTCACGGGCAATCAAAACATTGTTATATATGCATTTATAAAATTTTCAAGATAATTTATTATTCATACCCTTGCCCTTTGTTTCAAAATTATGCCCTTTTTTTGCACTTGAAAACAA    <  1:816473/141‑1                                                                                                                                                           TAATTAGCCAGATTATCAAGGAAGTTCAAGGGCAATCAAAACATTGTTATATATGCATTTATAAAATTTTCAAGATAATTTATTATTCATACCCTTGCCCTTTGTTTCAAAATTATGCCCTTTTTTTGCCCTTGAAAACAg    >  2:860351/1‑140                                                                                                                                                            AATTAGCCAGATTATCAAGGAAGTTCAAGGGCAATCAAAACATTGTTATATATGCATTTATAAAATTTTCAAGATAATTTATTATTCATACCCTTGCCCCTTGTTTCAAAATTATGCCCTTTTTTTGCCCTTGAAAACAAC   <  2:216657/141‑1                                                                                                                                                             ATTAGCCAGATTATCAAGGAAGTTCAAGGGCAATCAAAACATTGTTATATATGCATTTATAAAATTTTCAAGATAATTTATTATTCATACCCTTGCCCTTTGTTTCAAAATTATGCCCTTTTTTTGCCCTTGAAAACAACC  >  1:46440/1‑141                                                                                                                                                             ATTAGCCAGATTATCAAGGAAGTTCAAGGGCAATCAAAACATTGTTATATATGCATTTATAAAATTTTCAAGATAATTTATTATCCAGACCCTTGCCCTTTGTTTCAAAATTATGCCCTTTTTTTGCCCTTGAAAACAACC  >  1:673269/1‑141                                                                                                                                                                                                                                                                                                           CGCTCAAATCTGAGCGTATTTTTTTGTTTAAAATTCGATAATTTGCATATACTGCCCCTTTTGTGCCCTTTTTTATTTTCAATACCACAAAAATAACCCCTTAATCGTTGTTATTAAAGGGTATTTTTATTTAATTGGTATTATTTAGCAGGAATAA‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑  <  USA300TCH1516_ALE/895941‑895785 ‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑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.