New junction evidence
		seq id	position	reads (cov)	reads (cov)	score	skew	freq	annotation	gene	product
*	?	USA300TCH1516_ALE	= 1735361	41 (0.890)	4 (0.100)	4/234	NT	9.8%	intergenic (+61/+100)	USA300TCH1516_01624/tcdA	putative AAA domain‑containing protein/tRNA threonylcarbamoyladenosine dehydratase
	?	USA300TCH1516_ALE	= 1735390	37 (0.890)					intergenic (+90/+71)	USA300TCH1516_01624/tcdA	putative AAA domain‑containing protein/tRNA threonylcarbamoyladenosine dehydratase

GAACAACAACTCAAAGAAATATATAACAACTTACTTAAACAAAGGCCGTAAAAATAAGATTAAATCGATTACCTTTGATATTTTAGCTATAATCAAATCAAAACTGACTAGTACACGAGGCATATTCTACTATGCTTGCGAACTAGTCAGTTTTAGTTTTATGGTGTGGTTACACTTGCCTTACGTTGAAAATTATCCCTTTCAAAATGAATTATTGCCCTTTGTCTTTAATGCGACGAACTGGAATATCTTTTAATACGTCATTCACCACATAACTTGC  >  USA300TCH1516_ALE/1735250‑1735529                                                                                                                                             |                                                                                                                                            gAACAACAACTCAAAGAAATATATAACAACTTACTTAAACAAAGGCCGTAAAAATAAGATTAAATCGATTACCTTTGATATTTTAGCTATAATCAAATCAAAACTGACTAGTACACGAGGCATATTCTACTATGCTTGCGa                                                                                                                                             <  1:558935/141‑1 (MQ=255)  aacaacaacTCAAAGAAATATATAACAACTTACTTAAACAAAGGCCGTAAAAATAAGATTAAATCGATTACCTTTGATATTTTAGCTATAATCAAATCAAAACTGACTAGTACACGAGGCATATTCTACTATGCTTGCGAa                                                                                                                                            <  1:759315‑M2/141‑2 (MQ=255)     aacaacTCAAAGAAATATATAACAACTTACTTAAACAAAGGCCGTAAAAATAAGATTAAATCGATTACCTTTGATATTTTAGCTATAATCAAATCAAAACTGACTAATACACGAGGCATATTCTACTATGCTTGCGAacta                                                                                                                                         <  1:729402‑M2/141‑5 (MQ=255)          cTCAAAGAAATATATAACAACTTACTTAAACAAAGGCCGTAAAAATAAGATTAAATCGATTACCTTTGATATTTTAGCTATAATCAAATCAAAACTGACTAGTACACGAGGCATATTCTACTATGCTTGCGAactagtcag                                                                                                                                    <  1:444644‑M2/141‑10 (MQ=255)                    tatataACAACTTACTTAAACAAAGGCCGTAAAAATAAGATTAAATCGATTACCTTTGATATTTTAGCTATAATCAAATCAAAACTGACTAGTACACGAGGCATATTCTACTATGCTTGCGAACTAGTCagttttagtttt                                                                                                                          >  1:758590/1‑141 (MQ=255)                            aacTTACTTAAACAAAGGCCGTAAAAATAAGATTAAATCGATTACCTTTGATATTTTAGCTATAATCAAATCAAAACTGACTAGTACACGAGGCATATTCTACTATGCTTGCGAACTAGTCAGTTTTAGTTTTATGGtgtg                                                                                                                  >  1:76801/1‑141 (MQ=255)                                  cttcAACAAAGGCCGTAAAAATAAGATTAAATCGATTACCTTTGATATTTTAGCTATAATCGAATCAAAACTGACTAGTACACGAGGCCTATTCTACTATGCTTGCGAACGAGTCAGTTTTAGTTTTATGGTGTGGTTaca                                                                                                            >  1:631765/1‑141 (MQ=255)                                  cttaAACAAAGGCCGTAAAAATAAGATTAAATCGATTACCTTTGATATTTTAGCTATAATCAAATCAAAACTGACTAGTACACGAGGCATATTCTACTATGCTTGCGAACTAGTCAGTTTTAGTTTTATGGTGTGGTTaca                                                                                                            >  2:334041/1‑141 (MQ=255)                                    taAACAAAGGCCGTAAAAATAAGATTAAATCGATTACCTTTGATATTTTAGCTATAATCAAACAAAAACTGACTACTACACGAGGCATATTCTACTATGCTTGCGAACTAGTCAGTTTTAGTTTTATGGTGTGGTTACACt                                                                                                          <  2:165216/141‑1 (MQ=255)                                       aCAAAGGCCGTAAAAATAAGATTAAATCGATTACCTTTGATATTTTAGCTATAATCAAATCAAAACTGACTAGTACACGAGGCATATTCTACTATGCTTGCGAACTAGTCAGTTTTAGTTTTATGGTGTGGTTACACTTGc                                                                                                       >  1:187129/1‑141 (MQ=255)                                        cAAAGGCCGTAAAAATAAGATTAAATCGATTACCTTTGATATTTTAGCTATAATCAAATCAAAACTGACTAGTACACGAGGCATATTCTACTATTCTTGCGAacgagtcagttttgatttgattatagcaaaaatatcaga                                                                                                      <  1:398453‑M2/141‑40 (MQ=255)                                              ccGTAAAAATAAGATTAAATCGATTACCTTTGATATTTTAGCTATAATCAAATCAAAACTGACTAGTACACGAGGCATATTCTACTATGCTTGCGAACTAGTCAGTTTTAGTTTTATGGTGTGGTTACACTTGCCTTACGt                                                                                                >  1:287959/1‑141 (MQ=255)                                              ccGTAAAAATAAGATTAAATCGATTACCTTTGATATTTTAGCTATAATCAAATCAAAACTGACTAGTACACGAGGCATATTCTACTATGCTTGCGAACTAGTCAGTTTTAGTTTTATGGTGTGGTTACACTTGCCTTACGt                                                                                                <  2:320503/141‑1 (MQ=255)                                                  aaaaaTAAGATTAAATCGATTACCTTTGATATTTTAGCTATAATCAAATCAAAACTGACTAGTACACGAGGCATATTCTACTATGCTTGCGAACTAGTCAGTTTTAGTTTTATGGTGTGGTTACACTTGCCTTACGTTGaa                                                                                            >  1:186952/1‑141 (MQ=255)                                                        aaGATTAAATCGATTACCTTTGATATTTTAGCTATAATCAAATCAAAACTGACTAGTACACGAGGCATATTCTACTATGCTTGCGAACTAGTCAGTTTTAGTTTTATGGTGTGGTTACACTTGCCTTACGTTGAAAATTAt                                                                                      <  1:318739/141‑1 (MQ=255)                                                          gATTAAATCGATTACCTTTGATATTTTAGCTATAATCAAATCAAAACTGACTAGTACACGAGGCATATTCTACTATGCTTGCGAACTAGTCAGTTTTAGTTTTATGGTGTGGTTACACTTGCCTTACGTTGAAAATTATcc                                                                                    <  1:364749/141‑1 (MQ=255)                                                           aTTAAATCGATTACCTTTGATATTTTAGCTATAATCAAATCAAAACTGACTAGTACACGAGGCATATTCTACTATGCTTGCGAACTAGTCAGTTTTAGTTTTATGGTGTGGTTACACTTGCCTTACGTTGAAAATTATccc                                                                                   <  2:301787/141‑1 (MQ=255)                                                              aaaTCGATTACCTTTGATATTTTAGCTATAATCAAATCAAAACTGACTAGTACACGAGGCATATTCTACTATGCTTGCGAACTAGTCAGTTTTAGTTTTATGGTGTGGTTACACTTGCCTTACGTTGAAAATTATCCCttt                                                                                <  1:215528/141‑1 (MQ=255)                                                                 tCGATTACCTTTGATATTTTAGCTATAATCAAATCAAAACTGACTAGTACACGAGGCATATTCTACTATGCTTGCGAACTAGTCAGTTTTAGTTTTATGGTGTGGTTACACTTGCCTTACGTTGAAAATTATCCCTTTCaa                                                                             <  2:201602/141‑1 (MQ=255)                                                                      tACCTTTGATATTTTAGCTATAATCAAATCAAAACTGACTAGTACACGAGGCATATTCTACTATGCTTGCGAACTAGTCAGTTTTAGTTTTATGGTGTGGTTACACTTGCCTTACGTTGAAAATTATCCCTTTCAAAATGa                                                                        <  1:344970/141‑1 (MQ=255)                                                                          tttGATATTTTAGCTATAATCAAATCAAAACTGACTAGTACACGAGGCATATTCTACTATGCTTGCGAACTAGTCAGTTTTAGTTTTATGGTGTGGTTACACTTGCCTTACGTTGAAAATTATCCCTTTCAAAATGAatta                                                                    <  1:745190/141‑1 (MQ=255)                                                                            tGATATTTTAGCTATAATCAAATCAAAACTGACTAGTACACGAGGCATATTCTACTATGCTTGCGAACTAGTCAGTTTTAGTTTTATGGTGTGGTTACACTTGCCTTACGTTGAAAATTATCCCTTTCAAAATGAattatt                                                                  <  1:643644/141‑1 (MQ=255)                                                                               tatTTTAGCTATAATCAAATCAAAACTGACTAGTACACGAGGCATATTCTACTATGCTTGCGAACTAGTCAGTTTTAGTTTTATGGTGTGGTTACACTTGCCTTACGTTGAAAATTATCCCTTTCAAAATGAATTATTGcc                                                               <  1:768648/141‑1 (MQ=255)                                                                                  tttAGCTATAATCAAATCAAAACTGACTAGTACACGAGGCATATTCTACTATGCTTGCGAACTAGTCAGTTTTAGTTTTATGGTGTGGTTACACTTGCCTTACGTTGAAAATAATCCCTTTCAAAATGAATTATTGCCCtt                                                            >  1:287376/1‑141 (MQ=255)                                                                                   ttAGCTATAATCAAATCAAAACTGACTAGTACACGAGGCATATTCTACTATGCTTGCGAACTAGTCAGTTTTAGTTTTATGGTGTGGTTACACTTGCCTTACGTTGAAAATTATCCCTTTCAAAATGAATTATTGCCCttt                                                           >  1:308717/1‑141 (MQ=255)                                                                                     aGCTATAATCAAATCAAAACTGACTAGTACACGAGGCATATTCTACTATGCTTGCGAACTAGTCAGTTTTAGTTTTATGGTGTGGTTACACTTGCCTTACGTTGAAAATTATCCCTTTCAAAATGAATTATTGCCCTTTGt                                                         <  1:270565/141‑1 (MQ=255)                                                                                        tataATCAAATCAAAACTGACTAGTACACGAGGCATATTCTACTATGCTTGCGAACTAGTCAGTTTTAGTTTTATGGTGTGGTTACACTTGCCTTACGTTGAAAATTATCCCTTTCAAAATGAATTATTGCCCTTTGTCtt                                                      <  1:120480/141‑1 (MQ=255)                                                                                          taATCAAATCAAAACTGACTAGTACACGAGGCATATTCTACTATGCTTGCGAACTAGTCAGTTTTAGTTTTATGGTGTGGTTACACTTGCCTTACGTTGAAAATTATCCCTTTCAAAATGAATTATTGCCCTTTGTCTTTa                                                    >  1:435875/1‑141 (MQ=255)                                                                                                  tcaaaACTGACTAGTACACGAGGCATATTCTACTATGCTTGCGAACTAGTCAGTTTTAGTTTTATGGTGTGGTTACACTTGCCTTACGTTGAAAATTATCCCTTTCAAAATGAATTATTGCCCTTTGTCTTTAATGcgacg                                            >  2:137733/1‑141 (MQ=255)                                                                                                   caaaACTAACTAGTACACGAGGCATATTCTACTATGCTTGCGAACTAGTCAGTTTTAGTTTTATGGTGTGGTTACACTTGCCTTACGTTGAAAATTATCCCTTTCAAAATGAATTATTGCCCTTTGTCTTTAATGcgacga                                           >  1:622723/1‑141 (MQ=255)                                                                                                    aaaaCTGACTAGTACACGAGGCATATTCTACTATGCTTGCGAACTAGTCAGTTTTAGTTTTATGGTGTGGTTACACTTGCCTTACGTTGAAAATTATCCCTTTCAAAATGAATTATTGCCCTTTGTCTTTAATGCGACGaa                                          <  2:189646/141‑1 (MQ=255)                                                                                                      aaCTGACTAGTACACGAGGCATATTCTACTATGCTTGCGAACTAGTCAGTTTTAGTTTTATGGTGTGGTTACACTTGCCTTACGTTGAAAATTATCCCTTTCAAAATGAATTATTGCCCTTTGTCTTTAATGCGACGAACt                                        >  2:280510/1‑141 (MQ=255)                                                                                                        cTGACTAGTACACGAGGCATATTCTACTATGCTTGCGAACTAGTCAGTTTTAGTTTTATGGTGTGGTTACACTTGCCTTACGTTGAAAATTATCCCTTTCAAAATGAATTATTGCCCTTTGTCTTTAATGCGACGAACTgg                                      <  2:210177/141‑1 (MQ=255)                                                                                                        cTGACTAGTACACGAGGCATATTCTACTATGCTTGCGAACTAGTAAGTTTTAGTTTTATGGTGTGGTTACACCTGCATTACGTTGAAAATTCTCCCTTTCAAAATGAATTATTGCCCTTTGTCTTTAATGCGACGAACTgg                                      <  1:785466/141‑1 (MQ=255)                                                                                                           aCTAGTACACGAGGCATATTCTACTATGCTTGCGAACTAGTCAGTTTTAGTTTTATGGTGTGGTTACACTTGCCTTACGTTGAAAATTATCCCTTTCAAAATGAATTATTGCCCTTTGTCTTTAATGCGACGAACTGGAat                                   <  1:184972/141‑1 (MQ=255)                                                                                                              aGTACACGAGGCATATTCTACTATGCTTGCGAACTAGTCAGTTTTAGTTTTATGGTGTGGTTACACTTGCCTTACGTTGAAAATTATCCCTTTCAAAATGAATTATTGCCCTTTGTCTTTAATGCGACGAACTGGAATATc                                <  2:261801/141‑1 (MQ=255)                                                                                                               gTACACGAGGCATATTCTACTATGCTTGCGAactagtcagttttgatttgattatagctaaaatatcaaaggtaatcgatttaatcttatttttacggcctttgtttaagtaagttgttatatatttctttgagttgttgt                               <  1:456317‑M2/141‑111 (MQ=255)                                                                                                                 acacGAGGCATATTCTACTATGCTTGCGAactagtcagttttgatttgattatagctaaaatatcaaaggtaatcgatttaatcttatttttacggcctttgtttaagtaagttgttatatatttctttgagttgttgttc                             <  1:182276‑M2/141‑113 (MQ=255)                                                                                                                  cacGAGGCATATTCTACTATGCTTGCGAactagtcagttttgatttgattatagctaaaatatcaaaggtaatcgatttaatcttatttttacggcctttgtttaagtaagttgttatatatttctttgagttgttgttca                            <  2:308251‑M2/141‑114 (MQ=255)                                                                                                                  cacGAGGCATATTCTACTATGCTTGCGAACTAGTCAGTTTTAGTTTTATGGTGTGGTTACACTTGCCTTACGTTGAAAATTATCCCTTTCAAAATGAATTATTGCCCTTTGTCTTTAATGCGACGAACTGGAATATCtttt                            <  2:91547/141‑1 (MQ=255)                                                                                                                    cGAGGCATATTCTACTATGCTTGCGAACTAGTCAGTTTTAGTTTTATGGTGTGGTTACACTTGCCTTACGTTGAAAATTATCCCTTTCAAAATGAATTATTGCCCTTTGTCTTTAATGCGACGAACTGGAATATCTTTTaa                          >  2:232576/1‑141 (MQ=255)                                                                                                                      aGGCATATTCTACTATGCTTGCGAACTAGTCAGTTTTAGTTTTATGGTGTGGTTACACTTGCCTTACGTTGAAAATTATCCCTTTCAAAATGAATTATTGCCCTTTGTCTTTAATGCGACGAACTGGAATATCTTTTAATa                        >  1:73144/1‑141 (MQ=255)                                                                                                                        gCATATTCTACTATGCTTGCGAACTAGTCAGTTTTAGTTTTATGGTGTGGTTACACTTGCCTTACGTTGAAAATTATCCCTTTCAAAATGAATTATTGCCCTTTGTCTTTAATGCGACGAACTGGAATATCTTTTAATACg                      <  1:123181/141‑1 (MQ=255)                                                                                                                            atTCTACTATGCTTGCTAACTAGTCAGTTTTAGTTTTATGGTGTGGTTACACTTGCCTTACGTTGAAAATTATCCCTTTCAAAATGAATTATTGCCCTTTGTCTTTAATGCGACGATCTGGAATATCTTTTAATACGTCAt                  <  2:100400/141‑1 (MQ=255)                                                                                                                                     tGCTTGCGAACTAGTCAGTTTTAGTTTTATGGTGTGGTTACACTTGCCTTACGTTGAAAATTATCCCTTTCAAAATGAATTATTGCCCTTTGTCTTTAATGCGACGAACTGGAATATCTTTTAATACGTCATTCACCACAt         >  1:31037/1‑141 (MQ=255)                                                                                                                                         tGCGAACTAGTCAGTTTTAGTTTTATGGTGTGGTTACACTTGCCTTACGTTGAAAATTATCCCTTTCAAAATGAATTATTGCCCTTTGTCTTTAATGCGACGAACTGGAATATCTTTTAATACGTCATTCACCACATAACt     <  2:30414/141‑1 (MQ=255)                                                                                                                                         tGCGAACTAGTCAGTTTTAGTTTTATGGTGTGGTTACACTTGCCTTACGTTGAAAATTATCCCTTTCAAAATGAATTATTGCCCTTTGTCTTTAATGCGACGAACTGGAATATCTTTTAATACGTCATTCACCACATAACt     <  1:388198/141‑1 (MQ=255)                                                                                                                                          gCGAACTAGTCAGTTTTAGTTTTATGGTGTGGTTACACTTGCCTTACGTTGAAAATTATCCCTTTCAAAATGAATTATTTCCCTTTGTCTTTAATGCGACGAACTGGAATATCTTTTAATACGTCATTCACCACATAACtt    >  1:710926/1‑141 (MQ=255)                                                                                                                                            gAACTAGTCAGTTTTAGTTTTATGGTGTGGTTGCACTTGCCTTTCGTTGAAAATTATCCCGTTCAAAATTAATTATTGCCCTTTGTCTTTAATGCGACGAACTGGAATATCTTTTAATACGTCATTCACCACATAACTTGc  <  1:468091/141‑1 (MQ=255)                                                                                                                                             |                                                                                                                                            GAACAACAACTCAAAGAAATATATAACAACTTACTTAAACAAAGGCCGTAAAAATAAGATTAAATCGATTACCTTTGATATTTTAGCTATAATCAAATCAAAACTGACTAGTACACGAGGCATATTCTACTATGCTTGCGAACTAGTCAGTTTTAGTTTTATGGTGTGGTTACACTTGCCTTACGTTGAAAATTATCCCTTTCAAAATGAATTATTGCCCTTTGTCTTTAATGCGACGAACTGGAATATCTTTTAATACGTCATTCACCACATAACTTGC  >  USA300TCH1516_ALE/1735250‑1735529

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.