New junction evidence
		seq id	position	reads (cov)	reads (cov)	score	skew	freq	annotation	gene	product
*	?	USA300TCH1516_ALE	2508438 =	233 (1.280)	11 (0.070)	8/232	NT	5.4%	intergenic (+26/+81)	USA300TCH1516_02393/narT	Acid shock protein/putative nitrate transporter NarT
	?	USA300TCH1516_ALE	2508486 =	174 (1.040)					intergenic (+74/+33)	USA300TCH1516_02393/narT	Acid shock protein/putative nitrate transporter NarT

TGGATGTATTGCATTATTTACCATGCGTCATTTATACCAAAAAGAATATGGCTCATTGAAAAACGGTTGATATGTAATACATGCCATTCATTTAGTTAAATACAAAGCCTTAATATCATGCGCAATATTCGTAGCATGACATTAAGGCTTT‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑  <  USA300TCH1516_ALE/2508588‑2508438 ‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑attaaggctttGTATTTAACTAAATGAATGGCATGTATTACATATCAACCGTTTTTCAATGAGCCATATTCTTTTTGGTATAAATGACGCATGGTAAATAATGCAATACATCCAAATACCGCTAAGAAAATAAATGCTAAATGACTTGATC  >  USA300TCH1516_ALE/2508486‑2508625                                                                                                                                                                                                                                                                                                     TGGATGTATTGCATTATTTACCATGCGTCATTTATACCAAAAAGAATATGGCTCATTGAAAAACGGTTGATATGTAATACATGCCATTCATTTAGTTAAATACAAAGCCTTAATATCATGCGCAATATTCGTAGCATGACA                                                                                                                                                        <  3:119625/141‑1 TGGATGTATTGCATTATTTACCATGCGTCATTTATACCAAAAAGAATATGGCTCATTGAAAAACGGTTGATATGTAATACATGCCATTCATTTAGTTAAATACAAAGCCTTAATATCATGCGCAATATTCGTAGCATGACA                                                                                                                                                        <  2:992925/141‑1  GGATGTATTGCATTATTTACCATGCGTCATTTATACCAAAAAGAATATGGCTCATTGAAAAACGGTTGATATGTAATACATGCCATTCATTTAGTTAAATACAAAGCCTTAATATCATGCGCAATATTCGTAGCATGACAT                                                                                                                                                       <  3:609834/141‑1  GGATGTATTGCATTATTTACCATGCGTCATTTATACCAAAAAGAATATGGCTCATTGAAAAACGGTTGATATGTAATACATGCCATTCATTTAGTTAAATACAAAGCCTTAATATCATGCGCAATATTCGTAGCATGACAT                                                                                                                                                       <  1:533128/141‑1   GATGTATTGCATTATTTACCATGCGTCATTTATACCAAAAAGAATATGGCTCATTGAAAAACGGTTGATATGTAATACATGCCATTCATTTAGTTAAATACAAAGCCTTAATATCATGCGCAATATTCGTAGCATGACATT                                                                                                                                                      >  1:1156142/1‑141    ATGTATTGCATTATTTACCATGCGTCATTTATACCAAAAAGAATATGGCTCATTGAAAAACGGTTGATATGTAATACATGCCATTCATTTAGTTAAATACAAAGCCTTAATATCATGCGCAATATTCGTAGCATGACATTA                                                                                                                                                     <  3:428826/141‑1     TGTATTGCATTATTTACCATGCGTCATTTATACCAAAAAGAATATGGCTCATTGAAAAACGGTTGATATGTAATACATGCCATTCATTTAGTTAAATACAAAGCCTTAATATCATGCGCAATATTCGTAGCATGACATTAA                                                                                                                                                    >  4:286418/1‑141     TGTATTGCATTATTTACCATGCGTCATTTATACCAAAAAGAATATGGCTCATTGAAAAACGGTTGATATGTAATACATGCCATTCATTTAGTTAAATACAAAGCCTTAATATCATGCGCAATATTCGTAGCATGACATTAA                                                                                                                                                    >  2:1218012/1‑141      GTATTGCATTATTTACCATGCGTCATTTATACCAAAAAGAATATGGCTCATTGAAAAACGGTTGATACGTAATACATGCCATTCATTTAGTTAAATACAAAGCCTTAATATCATGCGCAATATTCGTAGCATGACATTAAG                                                                                                                                                   >  1:827127/1‑141       taaTGCATTATTTACCATGCGAAATTTATACCAAAAAGAAAATGGCTGCTTGAAAAATGGATGATATGTCATACATGCCATTCATTTAGTTAAATATAAAGCCTTAATATCATGCGCAATATTCGTAGCATGACATTTAGG                                                                                                                                                  >  4:430645/4‑141        ATTGCATTATTTACCATGCGTCATTTATACCAAAAAGAATATGGCTCATTGAAAAACGGTTGATATGTAATACATGCCATTCATTTAGTTAAATACAAAGCCTTAATATCATGCGCAATATTCGTAGCATGACATTAAGGC                                                                                                                                                 >  1:1102567/1‑141        ATTGCATTATTTACCATGCGTCATTTATACCAAAAAGAATATGGCTCATTGAAAAACGGTTGATATGTAATACATGCCATTCATTTAGTTAAATACAAAGCCTTAATATCATGCGCAATATTCGTAGCATGACATTAAGGC                                                                                                                                                 <  3:339227/141‑1        ATTGCATTATTTACCATGCGTCATTTATACCAAAAAGAATATGGCTCATTGAAAAACGGTTGATATGTAATACATGCCATTCATTTAGTTAAATACAAAGCCTTAATATCATGCGCAATATTCGTAGCATGACATTAAGGC                                                                                                                                                 <  3:442522/141‑1        ATTGCATTATTTACCATGCGTCATTTATACCAAAAAGAATATGGCTCATTGAAAAACGGTTGATATGTAATACATGCCATTCATTTAGTTAAATACAAAGCCTTAATATCATGCGCAATATTCGTAGCATGACATTAAGGC                                                                                                                                                 <  2:321757/141‑1         TTGCATTATTTACCATGCGTCATTTATACCAAAAAGAATATGGCTCATTGAAAAACGGTTGATATGTAATACATGCCATTCATTTAGTTAAATACAAAGCCTTAATATCATGCGCAATGTTCGTAGCATGACATTAAGGCT                                                                                                                                                >  2:353234/1‑141           GCATTATTTACCATGCGTCATTTATACCAAAAAGAATATGGCTCATTGAAAAACGGTTGATATGTAATACATGCCATTCATTTAGTTAAATACAAAGCCTTAATATCATGCGCAATATTCGTAGCATGACATTAAGGCTTT                                                                                                                                              <  1:1218012/141‑1           GCATTATTTACCATGCGTCATTTATACCAAAAAGAATATGGCTCATTGAAAAACGGTTGATATGTAATACATGCCATTCATTTAGTTAAATACAAAGCCTTAATATCATGCGCAATATTCGTAGCATGACATTAAGGCTTT                                                                                                                                              <  3:628783/141‑1                                               TATGGCTCATTGAAAAACGGTTGATATGTAATACATGCCATTCATTTAGTTAAATACAAAGCCTTAATATCATGCGCAATATTCGTAGCATGACA                                                                                                                                                        <  1:1333/95‑1                                               TATGGCTCATTGAAAAACGGTTGATATGTAATACATGCCATTCATTTAGTTAAATACAAAGCCTTAATATCATGCGCAATATTCGTAGCATGACA                                                                                                                                                        >  2:1333/1‑95                                                                                                       CAAAGCCTTAATATCATGCGCAATATTCGTAGCATGACATTAAGGCTTTGTATTTAACTAAATGAATGGCATGTATTACATATCAACCGTTTTTCAATGAGCCATATTCTTTTTGGTATAAATGACGCATGGTAAATAATG                                                  >  2:1564831/1‑141                                                                                                       CAAAGCCTTAATATCATGCGCAATATTCGTAGCATGACATTAAGGCTTTGTATTTAACTAAATGAATGGCATGTATTACATATCAACCGTTTTTCAATGAGCCATATTCTTTTTGGTATAAATGACGCATGGTAAATAATG                                                  >  1:1657285/1‑141                                                                                                           GCCTTAATATCATGCGCAATATTCGTAGCATGACATTAAGGCTTTGTATTTAACTAAATGAATGGCATGTATTACATATCAACCGTTTTTCAATGAGCCATATTCTTTTTGGTATAAATGACGCATGGTAAATAATGCAAT                                              >  1:1414759/1‑141                                                                                                            CCTTAATATCATGCGCAATATTCGTAGCATGACATTAAGGCTTTGTATTTAACTAAATGAATGGCATGTATTACATATCAACCGTTTTTCAATGAGCCATATTCTTTTTGGTATAAATGACGCATGGTAAATAATGCAATA                                             >  1:161329/1‑141                                                                                                                AATATCATGCGCAATATTCGTAGCATGACATTAAGGCTTTGTATTTAACTAAATGAATGGCATGTATTACATATCAACCGTTTTTCAATGAGCCATATTCTTTTTGGTATAAATGACGCATGGTAAATAATGCAATACATC                                         >  1:1582200/1‑141                                                                                                                AATATCATGCGCAATATTCGTAGCATGACATTAAGGCTTTGTATTTAACTAAATGAATGGCATGTATTACATATCAACCG                                                                                                      >  2:1240802/1‑80                                                                                                                AATATCATGCGCAATATTCGTAGCATGACATTAAGGCTTTGTATTTAACTAAATGAATGGCATGTATTACATATCAACCG                                                                                                      <  1:1240802/80‑1                                                                                                                 ATATCATGCGCAATATTCGTAGCATGACATTAAGGCTTTGTATTTAACTAAATGAATGGCATGTATTACATATCAACCGTTTTTCAATGAGCCATATTCTTTTTGGTATAAATGACGCATGGTAAATAATGCAATACATCC                                        >  3:576866/1‑141                                                                                                                 ATATCATGCGCAATATTCGTAGCATGACATTAAGGCTTTGTACTTAACTAAATGAATGGCATGTATTACATATCAACCGTTTTTCAATGAGCCATATTCTTTTTGGTATAAATGACGCATGGTAAATAATGCAATACATCC                                        <  2:1582200/141‑1                                                                                                                    TCATGCGCAATATTCGTAGCATGACATTAAGGCTTTGTATTTAACTAAATGAATGGCATGTATTACATATCAACCGTTTTTCAATGAGCCATATTCTTTTTGGTATAAATGACGCATGGTAAATAATGCAATACATCCAAA                                     >  3:460143/1‑141                                                                                                                    TCATGCGCAATATTCGTAGCATGACATTAAGGCTTTGTATTTAACTAAATGAATGGCATGTATTACATATCAACCGTTTTTCAATGAGCCATATTCTTTTTGGTATAAATGACGCATGGTAAATAATGCAATACATCCAAA                                     >  1:511829/1‑141                                                                                                                                           atcTTAATGCTTTGTATATAACTAAACGAATGTCACGTATTCTCTATCAACCGTTTTTCAATGATCCATATTCTTTTTGGTATAAATGACGCAGGGTAAATAATGCAATACATCCAAATACCGCTAAGAAAATAAATGCTA              <  1:1306627/138‑1                                                                                                                                             ATTAAGGCTTTGTATTTAACTAAATGAATGGCATGTATTACATATCAACCGTTTTTCAATGAGCCATATTCTTTTTGGTATAAATGACGCATGGTAAATAATGCAATACATCCAAATACCGCTAAGAAAATAAATGCTAAA            >  2:110645/1‑141                                                                                                                                              TTAAGGCTTTGTATTTAACTAAATGAATGGCATGTATTACATATCAACCGTTTTTCAATGAGCCATATTCTTTTTGGTATAAATGACGCATGGTAAATAATGCAATACATCCAAATACCGCTAAGAAAATAAATGCTAAAT           <  3:31972/141‑1                                                                                                                                              TTAAGGCTTTGTATTTAACTAAATGAATGGCATGTATTACATATCAACCGTTTTTCAATGAGCCATATTCTTTTTGGTATAAATGACGCATGGTAAATAATGCAATACATCCAAATACCGCTAAGAAAATAAATGCTAAAT           <  4:31616/141‑1                                                                                                                                              TTAAGGCTTTGTATTTAACTAAATGAATGGCATGTATTACATATCAACCGTTTTTCAATGAGCCATATTCTTTTTGGTATAAATGACGCATGGTAAATAATGCAATACATCCAAATACCGCTAAGAAAATAAATGCTAAAT           <  1:272443/141‑1                                                                                                                                                AAGGCTTTGTATTTAACTAAATGAATGGCATGTATTACATATCAACCGTTTTTCAATGAGCCATATTCTTTTTGGTATAAATGACGCATGGTAAATAATGCAATACATCCAAATACCGCTAAGAAAATAAATGCTAAATGA         <  2:1017448/141‑1                                                                                                                                                 AGGCTTTGTATTTAACTAAATGAATGGCATGTATTACATATCAACCGTTTTTCAATGAGCCATATTCTTTTTGGTATAAATGACGCATGGTAAATAATGCAATACATCCAAATACCTCTAAGAAAATAAATGCTAAATGAC        >  4:347515/1‑141                                                                                                                                                 AGGCTTTGTATTTAACTAAATGAATGGCATGTATTACATATCAACCGTTTTTCAATGAGCCATATTCTTTTTGGTATAAATGACGCATGGTAAATAATGCAATACATCCAAATACCGCTAAGAAAATAAATGCTAAATGAC        >  2:1492667/1‑141                                                                                                                                                   GCTTTGTATTTAACTAAATGAATGGCATGTATTACATATCAACCGTTTTTCAATGAGCCATATTCTTTTTGGTATAAATGACGCATGGTAAATAATGCAATACATCCAAATACCGCTAAGAAAATAAATGCTAAATGACTT      <  2:828762/141‑1                                                                                                                                                   GCTTTGTATTTAACTAAATGAATGGCATGTATTACATATCAACCGTTTTTCAATGAGCCATATTCTTTTTGGTATAAATGACGCATGGTAAATAATGCAATACATCCAAATACCGCTAAGAAAATAAATGCTAAATGACTT      <  2:828368/141‑1                                                                                                                                                   GCTTTGTATTTAACTAAATGAATGGCATGTATTACATATCAACCGTTTTTCAATGAGCCATATTCTTTTTGGTATAAATGACGCATGGTAAATAATGCAATACATCCAAATACCGCTAAGAAAATAAATGCTAAATGACTT      <  2:828362/141‑1                                                                                                                                                      TTGTATTTAACTAAATGAATGGCATGTATTACATATCAACCGTTTTTCAATGAGCCATATTCTTTTTTGTATATATTACTCATGGTAAATAATGCAATACATCCAAATACCGCTAAGAAAATAAATGCTAAATGACTTGAT   >  4:231383/1‑141                                                                                                                                                      TTGTATTTAACTAAATGAATGGCATGTATTACATATCAACCGTTTTTCAATGAGCCATATTCTTTTTGGTATAAATGACGCATGGTAAATAATGCAATACATCCAAATACCGCTAAGAAAATAAATGCTAAATGACTTGAT   >  3:3118/1‑141                                                                                                                                                       TGTATTTAACTAAATGAATGGCATGTATTACATATCAACCGTTTTTCAATGAGCCATATTCTTTTTGGTATAAATGACGCATGGTAAATAATGCAATACATCCAAATACCGCTAAGAAAATAAATGCTAAATGACTTGATC  <  1:690191/141‑1                                                                                                                                                                                                                                                                                                     TGGATGTATTGCATTATTTACCATGCGTCATTTATACCAAAAAGAATATGGCTCATTGAAAAACGGTTGATATGTAATACATGCCATTCATTTAGTTAAATACAAAGCCTTAATATCATGCGCAATATTCGTAGCATGACATTAAGGCTTT‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑  <  USA300TCH1516_ALE/2508588‑2508438 ‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑attaaggctttGTATTTAACTAAATGAATGGCATGTATTACATATCAACCGTTTTTCAATGAGCCATATTCTTTTTGGTATAAATGACGCATGGTAAATAATGCAATACATCCAAATACCGCTAAGAAAATAAATGCTAAATGACTTGATC  >  USA300TCH1516_ALE/2508486‑2508625

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