New junction evidence
		seq id	position	reads (cov)	reads (cov)	score	skew	freq	annotation	gene	product
*	?	USA300TCH1516_ALE	= 1030896	178 (0.870)	10 (0.060)	8/134	NT	5.7%	intergenic (+19/‑117)	ktrB_1/yfkN_2	Ktr system potassium uptake protein B/Trifunctional nucleotide phosphoesterase protein YfkN
	?	USA300TCH1516_ALE	= 1030919	181 (1.060)					intergenic (+42/‑94)	ktrB_1/yfkN_2	Ktr system potassium uptake protein B/Trifunctional nucleotide phosphoesterase protein YfkN

TTAATATCATTTATCATTATGATAGCAGGACGTCGAGAACCAGATAAATTCCATTATCCAAAAGAACGTATTCAAATAGGATAATATAATAGCAATCTAAGTT‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑  >  USA300TCH1516_ALE/1030794‑1030896 ‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑agcaatctaagttCCAGTTAAAATCTACATTAACTAAACTTAGATTGCTATTATATTATCCTATTTGAATACGTTCTTTTGGATAATGGAATTTATCTGGTTC  <  USA300TCH1516_ALE/1030919‑1030830                                                                                                                                                                                                   TTAATATCATTTATCATTATGATAGCAGGACGTCGAGAACCAGATAAATTCCATTATCCAAAAGAACGTATTCAAATAGGATAATATAATA                                                                                                        <  2:723090/91‑1  TAATATCATTTATCATTATGATAGCAGGACGTCGAGAACCAGATAAATTCCATTATCCAAAAGAACGTATTCAAATAGGATAATATAATAG                                                                                                       >  2:921327/1‑91  TAATATCATTTATCATTATGATAGCAGGACGTCGAGAACCAGATAAATTCCATTATCCAAAAGAACGTATTCAAATAGGATAATATAATAG                                                                                                       >  1:2455200/1‑91  TAATATCATTTATAAATATGATAGCAGGACGTCGAGAACCAGATAAATTCCATTATCTAAAAGAACGTCTTCATATAGGATAAGATAATAG                                                                                                       >  2:1199411/1‑91    ATATCATTTATCATTATGATAGCAGGACGTCGAGAACCAGATAAATTCCATTATCCAAAAGAACGTATTCAAATAGGATAATATAATAGCA                                                                                                     <  2:921383/91‑1    ATATCATTTATCATTATGATAGCAGGACGTCGAGAACCAGATAAATTCCATTATCCAAAAGAACGTATTCAAATAGGATAATATAATAGCA                                                                                                     >  1:3722921/1‑91    ATATCATTTATCATTATGATAGCAGGACGTCGAGAACCAGATAAATTCCATTATCCAAAAGAACGTATTCAAATAGGATAATATAATAGCA                                                                                                     <  2:1239579/91‑1    ATATCATTTATCATTATGATAGCAGGACGTCGAGAACCAGATAAATTCCATTATCCAAAAGAACGTATTCAAATAGGATAATATAATAGCA                                                                                                     <  2:1944743/91‑1     TATCATTTATCATTATGATAGCAGGACGTCGAGAACCAGATAAATTCCATTATCCAAAAGAACGTATTCAAATAGGATAATATAATAGCAA                                                                                                    >  1:648157/1‑91     TATCATTTATCATTATGATAGCAGGACGTCGAGAACCAGATAAATTACATTATCCAAAAGAACGTATTCAAATAGGATAATATAATAGCAA                                                                                                    >  2:318097/1‑91      ATCATTTATCATTATGATAGCAGGACGTCGAGAACCAGATAAATTCCATTATCCAAAAGAACGTATTCAAATAGGATAATATAATAGCAAT                                                                                                   >  1:3801765/1‑91      ATCATTTATCATTATGATAGCAGGACGTCGAGAACCAGATAAATTCCATTATCCAAAAGAACGTATTCAAATAGGATAATATAATAGCAAT                                                                                                   <  2:2895032/91‑1      ATCATTTATCATTATGATAGCAGGACGTCGAGAACCAGATAAATTCCATTATCCAAAAGAACGTATTCAAATAGGATAATATAATAGCAAT                                                                                                   <  2:3771124/91‑1      ATCATTTATCATTATGATAGCAGGACGTCGAGAACCAGATAAATTCCATAATCCAAAAGAACGTATTCAAATAGGATAATATAATAGCcac                                                                                                   >  2:3476817/1‑88       TCATTTATCATTATGATAGCAGGACGTCGAGAACCAGATAAATTCCATTATCCAAAAGAACGTATTCAAATAGGATAATATAATAGCAATC                                                                                                  <  1:2422547/91‑1       TCATTTATCATTATGATAGCAGGACGTCGAGAACCAGATAAATTCCATTATCCAAAAGAACGTATTCAAATAGGATAATATAATAGCAATC                                                                                                  <  2:1451063/91‑1       TCATTTATCATTATGATAGCAGGACGTCGAGAACCAGATAAATTCCATTATCCAAAAGAACGTATTCAAATAGGATAATATAATAGCAATC                                                                                                  >  1:2646722/1‑91        CATTTATCATTATGATAGCAGGACGTCGAGAACCAGATAAATTCCATTATCCAAAAGAACGTATTCAAATAGGATAATATAATAGCAATCT                                                                                                 <  1:2463026/91‑1        CATTTATCATTATGATAGCAGGACGTCGAGAACCAGATAAATTCCATTATCCAAAAGAACGTATTCAAATAGGATAATATAATAGCAATCT                                                                                                 <  1:2462307/91‑1        CATTTATCATTATGATAGCAGGACGTCGAGAACCAGATAAATTCCATTATCCAAAAGAACGTATTCAAATAGGATAATATAATAGCAATCT                                                                                                 <  1:609777/91‑1        CATTTATCATTATGATAGCAGGACGTCGAGAACCAGATAAATTCCATTATCCAAAAGAACGTATTCAAATAGGATAATATAATAGCAATCT                                                                                                 <  1:1470908/91‑1         ATTTATCATTATGATAGCAGGACGTCGAGAACCAGATAAATTCCATTATCCAAAAGAACGTATTCAAATAGGATAATATAATAGCAATCTA                                                                                                >  1:1569613/1‑91          TTTATCATTATGATAGCAGGACGTCGAGAACCAGATAAATTCCATTATCCAAAAGAACGTATTCAAATAGGATAATATAATAGCAATCTAA                                                                                               >  2:1936666/1‑91          TTTATCATTATGATAGCAGGACGTCGAGAACCAGATAAATTCCATTATCCAAAAGAACGTATTCAAAGAGGATAATATAGTAGCAATCTAA                                                                                               >  2:3015941/1‑91            TATCATTATGATAGCAGGACGTCGAGAACCAGATAAATTCCATTATCCAAAAGAACGTATTCAAATAGGATAATATAATAGCAATCTAAGT                                                                                             <  2:736178/91‑1            TATCATTATGATAGCAGGACGTCGAGAACCAGATAAATTCCATTATCCAAAAGAACGTATTCAAATAGGATAATATAATAGCAATCTAAGT                                                                                             >  1:1064932/1‑91            TATCATTATGATAGCAGGACGTCGAGAACCAGATAAATTCCATTATCCAAAAGAACGTATTCAAATAGGATAATATAATAGCAATCTAAGT                                                                                             <  1:588226/91‑1            TATCATTATGATAGCAGGACGTCGAGAACCAGATAAATTCCATTATCCAAAAGAACGTATTCAAATAGGATAATATAATAGCAATCTAAGT                                                                                             <  1:588328/91‑1             ATCATTATGATAGCAGGACGTCGAGAACCAGATAAATTCCATTATCCAAAAGAACGTATTCAAATAGGATAATATAATAGCAATCTAAGTT                                                                                            >  1:2386347/1‑91                                 TCGAGAACCAGATAAATTCCATTATCCAAAAGAACGTATTCAAATAGGATAATATAATAGCAATCTAAGTT‑TAGTTAAAATCTACATTAAC                                                                       <  2:2690924/91‑1                                 TCGAGAACCAGATAAATTCCATTATCCAAAAGAACGTATTCAAATAGGATAATATAATAGCAATCTAAGTT‑TAGTTAAAATCTACATTAAC                                                                       <  2:2325827/91‑1                                     GAACCAGATAAATTCCATTATCCAAAAGAACGTATTCAAATAGGATAATATAATAGCAATCTAAGTTCCAGTTAAAATCTACATTAACTAA                                                                    <  1:1490299/91‑1                                      AACCAGATAAATTCCATTATCCAGAAGAACGTATTCAAATAGGATAATATAATAGCAATCTAAGTTCCAGTTAAATTCTACATTAACTAAA                                                                   <  2:1750023/91‑1                                      AACCAGATAAATTCCATTATCCAAAAGGACGTATTCAAATAGGATAATATAATAGCAATCTAAGTTCCAGTTAAAATCTACATTAACTAAA                                                                   <  2:1750033/91‑1                                        CCAGATAAATTCCATTATCCAAAAGAACGTATTCAAATAGGATAATATAATAGCAATCTAAGTTCCAGTTAAAATCTACATTAACTAAACT                                                                 <  1:3401567/91‑1                                         CAGATAAATTCCATTATCCAAAAGAACGTATTCAAATAGGATAATATAATAGCAATCTAAGTTCCAGTTAAAATCTACATTAACTAAACTT                                                                <  2:598904/91‑1                                          AGATAAATTCCATTATCCAAAAGAACGTATTCAAATAGGATAATATAATAGCAATCTAAGTTCCAGTTAAAATCTACATTAACTAAACTTA                                                               <  1:1804437/91‑1                                            ATAAATTCCATTATCCAAAAGAACGTATTCAAATAGGATAATATAATAGCAATCTAAGTTCCAGTTAAAATCTACATTAACTAAACTTAGA                                                             <  2:1759935/91‑1                                               AATTCCATTATCCAAAAGAACGTATTCAAATAGGATAATATAATAGCAATCTAAGTTCCAGTTAAAATCTACATTAACTAAACTTAGATTG                                                          <  1:3280882/91‑1                                                                                           AGCAATCTAAGTTCCAGTTAAAATCTACATTAACTAAACTTAGATTGCTATTATATTATCCTATTTGAATACGTTCTTTTGGATAATGGAA              <  1:820305/91‑1                                                                                           AGCAATCTAAGTTCCAGTTAAAATCTACATTAACTAAACTTAGATTGCTATTATATTATCCTATTTGAATACGTTCTTTTGGATAATGGAA              <  1:2667036/91‑1                                                                                           AGCAATCTAAGTTCCAGTTAAAATCTACATTAACTAAACTTAGATCGCTATTATATGATCCTATTTGAATACGTTCTTTTGGATAATGGAA              >  2:252816/1‑91                                                                                            GCAATCTAAGTTCCAGTTAAAATCTACATTAACTAAACTTAGATTGCTATTATATTATCCTATTTGAATACGTTCTTTTGGATAATGGAAT             >  1:2364799/1‑91                                                                                            GCAATCTAAGTTCCAGTTAAAATCTACATTAACTAAACTTAGATTGCTATTATATTATCCTATTTGAATACGTTCTTTTGGATAATGGAAT             >  1:588017/1‑91                                                                                            GCAATCTAAGTTCCAGTTAAAATCTACATTAACTAAACTTAGATTGCTATTATATTATCCTATTTGAATACGTTCTTTTGGATAATGGAAT             >  1:3571218/1‑91                                                                                            GCAATCTAAGTTACAGTTAAAATCTACATTAACTAAACTTAGATTGCTATTATATTATCCTATTTGAATACGTTCTTTTGGATCATGGAAT             >  1:1687967/1‑91                                                                                             CAATCTAAGTTCCAGTTAAAATCTACATTAACTAAACTTAGATTGCTATTATATTATCCTATTTGAATACGTTCTTTTGGATAATGGAATT            <  1:342165/91‑1                                                                                              AATCTAAGTTCCAGTTAAAATCTACATTAACTAAACTTAGATTGCTATTATATTATCCTATTTGAATACGTTCTTTTGGATAATGGAATTT           >  1:3125509/1‑91                                                                                              AATCTAAGTTCCAGTTAAAATCTACATTAACTAAACTTAGATTGCTATTATATTATCCTATTTGAATACGTTCTTTTGGATAATGGAATTT           >  2:1359220/1‑91                                                                                               ATCTAAGTTCCAGTTAAAATCTACATTAACTAAACTTAGATTGCTATTATATTATCCTATTTGAATACGTTCTTTTGGATAATGGAATTTA          >  1:1909734/1‑91                                                                                                TCTAAGTTCCAGTTAAAATCTACATTAACTAAGCTTAGATTGCTATTATATTATCCTATTTGAATACGTTCTTTTGGATAATGGAAGTTAT         <  2:788241/91‑1                                                                                                TCTAAGTTCCAGTTAAAATCTACATTAACTAAACTTAGATTGCTATTATATTATCCTATTTGAATACGTTCTTTTGGATAATGGAATTTAT         <  2:1483149/91‑1                                                                                                TCTAAGTTCCAGTTAAAATCTACATTAACTAAACTTAGATTGCTATTATATTATCCTATTTGAATACGTTCTTTTGGATAATGGAATTTAT         <  1:1632561/91‑1                                                                                                 CTAAGTTCCAGTTAAAATCTACATTAACTAAACTTAGATTGCTATTATATTATCCTATTTGATTACGTTCTTTTGGATAATGGAATTTATC        >  2:624155/1‑91                                                                                                 CTAAGTTCCAGTTAAAATCTACATTAACTAAACTTAGATTGCTATTATATTATCCTATTTGAATACGTTCTTTTGGATAATGGAATTTATC        >  2:2576123/1‑91                                                                                                 CTAAGTTCCAGTTAAAATCTACATTAACTAAACTTAGATTGCTATTACATTATCCTATTTGAATACGTTCTTTTGGACAATGGAATTTATC        >  1:3961490/1‑91                                                                                                  TAAGTTCCAGTTAAAATCTACATTAACTAAACTTAGATTGCTATTATATTATCCTATTTGAATACGTTCTTTTGGATAATGGAATTTATCT       >  1:2407311/1‑91                                                                                                   AAGTTCCAGTTAAAATCTACATTAACTAAACTTAGATTGCTATTATATTATCCTATTTGAATACGTTCTTTTGGATAATGGAATTTATCTG      <  1:905861/91‑1                                                                                                   AAGTTCCAGTTAAAATCTACATTAACTAAACTTAGATTGCTATTATATTATCCTATTTGAATACGTTCTTTTGGATAATGGAATTTATCTG      <  1:3633820/91‑1                                                                                                   AAGTTCCAGTTAAAATCTACATTAACTAAACTTAGATTGCTATTATATTATCCTATTTGAATACGTTCTTTTGGATAATGGAATTTATCTG      <  1:9160/91‑1                                                                                                    AGTTCCAGTTAAAATCTACATTAACTAAACTTAGATTGCTATTATATTATCCTATTTGAATACGTTCTTTTGGATAATGGAATTTATCTGG     >  1:1373771/1‑91                                                                                                    AGTTCCAGTTAAAATCTACATTAACTAAACTTAGATTGCTATTATATTATCCTATTTGAATACGTTCTTTTGGATAATGGAATTTATCTGG     <  1:3102781/91‑1                                                                                                     GTTCCAGTTAAAATCTAGATTAACTAAACTTAGATTGCTATTATATTATCCTATTTGAATACGTTCTTTTGGATAATGGAATTTATCTGGT    <  1:3388655/91‑1                                                                                                      TTCCAGTTAAAATCTACATTAACTAAACTTAGATTGCTATTATATTATCCTATTTGAATACGTTCTTTTGGATAATGGAATTTATCTGGTT   <  2:2307679/91‑1                                                                                                      TTCCAGTTAAAATCTACATTAACTAAACTTAGATTGCTATTATATTATCCTATTTGAATACGTTCTTTTGGATAATGGAATTTATCTGGTT   >  1:435005/1‑91                                                                                                       TCCAGTTAAAATCTACATTAACTAAACTTAGATTGCTATTATATTATCCTATTTGAATACGTTCTTTTGGATAATGGAATTTATCTGGTTC  >  2:2317591/1‑91                                                                                                       TCCAGTTAAAATCTACATTAACTAAACTTAGATTGCTATTATATTATCCTATTTGAATACGTTCTTTTGGATAATGGAATTTATCTGGTTC  <  1:3801516/91‑1                                                                                                                                                                                                   TTAATATCATTTATCATTATGATAGCAGGACGTCGAGAACCAGATAAATTCCATTATCCAAAAGAACGTATTCAAATAGGATAATATAATAGCAATCTAAGTT‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑  >  USA300TCH1516_ALE/1030794‑1030896 ‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑agcaatctaagttCCAGTTAAAATCTACATTAACTAAACTTAGATTGCTATTATATTATCCTATTTGAATACGTTCTTTTGGATAATGGAATTTATCTGGTTC  <  USA300TCH1516_ALE/1030919‑1030830

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.