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

ATTACGAACCAAAAACGACATCTAAAAGTGAACAACAACTCAAAGAAATATATAACAACTTACTTAAACAAAGGCCGTAAAAATAAGATTAAATCGATTACCTTTGATATTTTAGCTATAATCAAATCAAAACTGACTAGTACACGAGGCATATTCTACTATGCTTGCGAACTAGTCAGTTTTAGTTTTATGGTGTGGTTACACTTGCCTTACGTTGAAAATTATCCCTTTCAAAATGAATTATTGCCCTTTGTCTTTAATGCGACGAACTGGAATATCTT  >  USA300TCH1516_ALE/1735221‑1735501                                                                                                                                             |                                                                                                                                             attaCGAACCAAAAACGACATCTAAAAGTGAACAACAACTCAAAGAAATATATAACAACTTACTTAAACAAAGGCCGTAAAAATAAGATTAAATCGATTACCTTTGATATTTTAGCTATAATCAAATCAAAACTGACTAGT                                                                                                                                              >  1:740065‑M1/1‑141 (MQ=255)     cGAACCAAAAACGACATCTAAAAGTGAACAACAACTCAAAGAAATATATAACAACTTACTTAAACAAAGGCCGTAAAAATAAGATTAAATCGATTACCTTTGATATTTTAGCTATAATCAAATCAAAACTGACTAGTacac                                                                                                                                          <  2:127447/141‑1 (MQ=255)           aaaaaCGACATCTAAAAATAAACAACAACTCAAAGAAATATATAACAACTTACTTAAACAAAGGCCGTAAAAATAAGATTAAATCGATTACCTTTGATATTTTAGCTATAATCAAATCAAAACTGACTAGTACCCGAGGCa                                                                                                                                    <  1:148662/141‑1 (MQ=255)              aaCGACATCTAAAAGTGAACAACAACTCAAAGAAATATATAACAACTTACTTAAACAAAGGCCGTAAAAATAAGATTAAATCGATTACCTTTGATATTTTAGCTATAATCAAATCAAAACTGACTAGTACACGAGGCatat                                                                                                                                 >  1:228685/1‑141 (MQ=255)               aCGACATCTAAAAGTGAACAACAACTCAAAGAAATATATAACAACTTACTTAAACAAAGGCCGTAAAAATAAGATTAAATCGATTACCTTTGATATTTTAGCTATAATCAAATCAAAACTGACTAGTACACGAGGCATAtt                                                                                                                                <  2:251088/141‑1 (MQ=255)                cGACATCTAAAAGTGAACAACAACTCAAAGAAATATATAACAACTTACTTAAACAAAGGCCGTAAAAATAAGATTAAATCGATTACCTTTGATATTTTAGCTATAATCAAATCAAAACTGACTAGTACACGAGGCATATTc                                                                                                                               >  1:597774/1‑141 (MQ=255)                cGACATCTAAAAGTGAACAACAACTCAAAGAAATATATAACAACTTACTTAAACAAAGGCCGTAAAAATAAGATTAAATCGATTACCTTTGATATTTTAGCTATAATCAAATCAAAACTGACTAGTACACGAGGCATATTc                                                                                                                               <  1:341253/141‑1 (MQ=255)                     tCTAAAAGTGAACAACAACTCAAAGAAATATATAACAACTTACTTAAACAAAGGCCGTAAAAATAAGATTAAATCGATTACCTTTGATATTTTAGCTATAATCAAATCAAAACTGACTAGTACACGAGGCATATTctacta                                                                                                                          >  1:502588/1‑141 (MQ=255)                       tAAAAGTGAACAACAACTCAAAGAAATATATAACAACTTACTTAAACAAAGGCCGTAAAAATAAGATTAAATCGATTACCTTTGATATTTTAGCTATAATCAAATCAAAACTGACTAGTACACGAGGCATATTCTACTATg                                                                                                                        <  1:96038/141‑1 (MQ=255)                         aaaGTGAACAACAACTCAAAGAAATATATAACAACTTACTTAAACAAAGGCCGTAAAAATAAGATTAAATCGATTACCTTTGATATTTTAGCTATAATCAAATCAAAACTGACTAGTACACGAGGCATATTCTACTATGCt                                                                                                                      <  1:362915/141‑1 (MQ=255)                         aaaGTGAACAACAACACAAAGAAATATACAACAACTTACTTAAACAAAGGCCGTAAAAATAAGATTAAATCGATTACCTTTGATATTTTAGCTATAATCAAATCAAAACTGACTAGTACACGAGGCATATTCTACTATGCt                                                                                                                      <  1:162411/141‑1 (MQ=255)                            gTGAACAACAACTCAAAGAAATATATAACAACTTACTTAAACAAAGGCCGTAAAAATAAGATTAAATCGATTACCTTTGATATTTTAGCTATAATCAAATCAAAACTGACTAGTACACGAGGCATATTCTACTATGCTTGc                                                                                                                   >  1:684366/1‑141 (MQ=255)                             tGAACAACAACTCAAAGAAATATATAACAACTTACTTAAACAAAGGCCGTAAAAATAAGATTAAATCGATTACCTTTGATATTTTAGCTATAATCAAATCAAAACTGACTAGTtcgcaagcatagtagaatatgcctcgtg                                                                                                                  <  2:308251‑M1/141‑29 (MQ=255)                              gAACAACAACTCAAAGAAATATATAACAACTTACTTAAACAAAGGCCGTAAAAATAAGATTAAATCGATTACCTTTGATATTTTAGCTATAATCAAATCAAAACTGACTAGTtcgcaagcatagtagaatatgcctcgtgt                                                                                                                 <  1:182276‑M1/141‑30 (MQ=255)                              gAACAACAACTCAAAGAAATATATAACAACTTACTTAAACAAAGGCCGTAAAAATAAGATTAAATCGATTACCTTTGATATTTTAGCTATAATCAAATCAAAACTGACTAGTACACGAGGCATATTCTACTATGCTTGCGa                                                                                                                 <  1:558935/141‑1 (MQ=255)                               aacaacaacTCAAAGAAATATATAACAACTTACTTAAACAAAGGCCGTAAAAATAAGATTAAATCGATTACCTTTGATATTTTAGCTATAATCAAATCAAAACTGACTAGTACACGAGGCATATTCTACTATGCTTGCGAa                                                                                                                <  1:759315‑M2/141‑2 (MQ=255)                                acaacaacTCAAAGAAATATATAACAACTTACTTAAACAAAGGCCGTAAAAATAAGATTAAATCGATTACCTTTGATATTTTAGCTATAATCAAATCAAAACTGACTAGTtcgcaagcatagtagaatatgcctcgtgtac                                                                                                               <  1:456317‑M1/141‑32 (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                                                                    <  2:320503/141‑1 (MQ=255)                                                                           ccGTAAAAATAAGATTAAATCGATTACCTTTGATATTTTAGCTATAATCAAATCAAAACTGACTAGTACACGAGGCATATTCTACTATGCTTGCGAACTAGTCAGTTTTAGTTTTATGGTGTGGTTACACTTGCCTTACGt                                                                    >  1:287959/1‑141 (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)                                                                                                       tctgaTATTTTTGCTATAATCAAATCAAAACTGACTCGTtcgcaagaatagtagaatatgcctcgtgtactagtcagttttgatttgattatagctaaaatatcaaaggtaatcgatttaatcttatttttacggcctttg                                        <  1:398453‑M1/139‑103 (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)                                                                                                                                     cTGACTAGTtcgcaagcatagtagaatatgcctcgtgtactagtcagttttgatttgattatagctaaaatatcaaaggtaatcgatttaatcttatttttacggcctttgtttaagtaagttgttatatatttctttgag          <  1:444644‑M1/141‑133 (MQ=255)                                                                                                                                     cTGACTAGTACACGAGGCATATTCTACTATGCTTGCGAACTAGTCAGTTTTAGTTTTATGGTGTGGTTACACTTGCCTTACGTTGAAAATTATCCCTTTCAAAATGAATTATTGCCCTTTGTCTTTAATGCGACGAACTgg          <  2:210177/141‑1 (MQ=255)                                                                                                                                     cTGACTAGTACACGAGGCATATTCTACTATGCTTGCGAACTAGTAAGTTTTAGTTTTATGGTGTGGTTACACCTGCATTACGTTGAAAATTCTCCCTTTCAAAATGAATTATTGCCCTTTGTCTTTAATGCGACGAACTgg          <  1:785466/141‑1 (MQ=255)                                                                                                                                        aCTAGTACACGAGGCATATTCTACTATGCTTGCGAACTAGTCAGTTTTAGTTTTATGGTGTGGTTACACTTGCCTTACGTTGAAAATTATCCCTTTCAAAATGAATTATTGCCCTTTGTCTTTAATGCGACGAACTGGAat       <  1:184972/141‑1 (MQ=255)                                                                                                                                          tAGTtcgcaagcatagtagaatatgcctcgtgtattagtcagttttgatttgattatagctaaaatatcaaaggtaatcgatttaatcttatttttacggcctttgtttaagtaagttgttatatatttctttgagttgtt     <  1:729402‑M1/141‑138 (MQ=255)                                                                                                                                           aGTACACGAGGCATATTCTACTATGCTTGCGAACTAGTCAGTTTTAGTTTTATGGTGTGGTTACACTTGCCTTACGTTGAAAATTATCCCTTTCAAAATGAATTATTGCCCTTTGTCTTTAATGCGACGAACTGGAATATc    <  2:261801/141‑1 (MQ=255)                                                                                                                                            gTACACGAGGCATATTCTACTATGCTTGCGAactagtcagttttgatttgattatagctaaaatatcaaaggtaatcgatttaatcttatttttacggcctttgtttaagtaagttgttatatatttctttgagttgttgt   <  1:456317‑M2/141‑111 (MQ=255)                                                                                                                                             ttcgcaagcatagtagaatatgcctcgtgtactagtcagttttgatttgattatagctaaaatatcaaaggtaatcgatttaatcttatttttacggcctttgtttaagtaagttgttatatatttctttgagttgttgtt  <  1:759315‑M1/141‑141 (MQ=255)                                                                                                                                             |                                                                                                                                             ATTACGAACCAAAAACGACATCTAAAAGTGAACAACAACTCAAAGAAATATATAACAACTTACTTAAACAAAGGCCGTAAAAATAAGATTAAATCGATTACCTTTGATATTTTAGCTATAATCAAATCAAAACTGACTAGTACACGAGGCATATTCTACTATGCTTGCGAACTAGTCAGTTTTAGTTTTATGGTGTGGTTACACTTGCCTTACGTTGAAAATTATCCCTTTCAAAATGAATTATTGCCCTTTGTCTTTAATGCGACGAACTGGAATATCTT  >  USA300TCH1516_ALE/1735221‑1735501

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.