New junction evidence
		seq id	position	reads (cov)	reads (cov)	score	skew	freq	annotation	gene	product
*	?	USA300TCH1516_ALE	= 2292528	46 (1.710)	4 (0.160)	3/264	3.2	8.6%	noncoding (66/76 nt)	USA300TCH1516_02174	tRNA‑Val
	?	USA300TCH1516_ALE	= 2292586	42 (1.660)					noncoding (8/76 nt)	USA300TCH1516_02174	tRNA‑Val
Rejected: Coverage evenness skew score above cutoff.
Rejected: Frequency below/above cutoff threshold.

ATATATAGATGGTGGAGGGGGGCAGATTCGAACTGCCGAACCCGAAGGAGCGGATTTACAGTCCGCCGCGTTTAGCCACTTCGCTACCCCTCCAGCTTATTCATATAATTTAATAATCAAAATGGTGGAGAATGACGGGTTCGAACCGCCGACCCTCTGCTTGTAAGGCAGATGCTCTCCCAGCTGAGCTAATTCTCCAAAATAATGACTCCTACGGGACTCGAACCCGTGTTACCGCCGTGAAAGGGCGGTGTCTTAACCGCTTGACCAAGG  >  USA300TCH1516_ALE/2292396‑2292668                                                                                                                                     |                                                                                                                                             atatatAGATGGTGGAGGGGGGCAGATTCGAACTGCCGAACCCGAAGGAGCGGATTTACAGTCCGCCGCGTTTAGCCACTTCGCTACCCCTCCAGCTTATTCATATAATTTAATAATCAAAATGGTGGAGAATGACGGGtt                                                                                                                                      >  2:245354/1‑141 (MQ=255)      taGATGGTGGAGGGGGGCAGATTCGAACTGCCGAACCCGAAGGAGCGGATTTACAGTCCGCCGCGTTTAGCCACTTCGCTACCCCTCCAGCTTATTCATATAATTTAATAATCAAAATGGTGGAGAATGACGGGTTCGAAc                                                                                                                                 >  1:239130/1‑141 (MQ=255)              ggAGGGGGGCAGATTCGAACTGCCGAACCCGAAGGAGCGGATTTACAGTCCGCCGCGTTTAGCCACTTCGCTACCCCTCCAGCTTATTCATATAATTTAATAATCAAAATGGTGGAGAATGACGGGTTCGAACCGCCGAcc                                                                                                                         >  1:258410/1‑141 (MQ=255)               gAGGGGGGCAGATTCGAACTGCCGAACCCGAAGGAGCGGATTTACAGTCCGCCGCGTTTAGCCACTTCGCTACCCCTCCAGCTTATTCATATAATTTAATAATCAAAATGGTGGAGAATGACGGGTTCGAACCGCCGAccc                                                                                                                        >  2:183252/1‑141 (MQ=255)               gAGGGGGGCAGATTCGAACTGCCGAACCCGAAGGAGCGGATTTACAGTCCGCCGCGTTTAGCCACTTCGCTACCCCTCCAGCTTATTCATATAATTTAATAATCAAAATGGTGGAGAATGACGGGTTCGAACCGCCGAccc                                                                                                                        >  1:174270/1‑141 (MQ=255)               gAGGGGGGCAGATTCGAACTGCCGAACCCGAAGGAGCGGATTTACAGTCCGCCGCGTTTAGCCACTTCGCTACCCCTCCAGCTTATTCATATAATTTAATAATCAAAATGGTGGAGAATGACGGGTTCGAACCGCCGAccc                                                                                                                        >  1:94354/1‑141 (MQ=255)               gAGGGGGGCAGATTCGAACTGCCGAACCCGAAGAAGCGGATTTACAGTCCGCCGCGTTTAGCCACTTCGCTACCCCTCCAGCTTATTCATATAATTTAATAATCAAAATGGTGGAGAATGACGGGTTCGAACCGCCGAccc                                                                                                                        >  1:149976/1‑141 (MQ=255)                  gggggCAGATTCGAACTGCCGAACCCGAAGGAGCGGATTTACAGTCCGCCGCGTTTAGCCACTTCGCTACCCCTCCAGCTTATTCATATAATTTAATAATCAAAATGGTGGAGAATGACGGGTTCGAACCGCCGACCctct                                                                                                                     >  1:175912/1‑141 (MQ=255)                    gggCAGATTCGAACTGCCGAACCCGAAGGAGCGGATTTACAGTCCGCCGCGTTTAGCCACTTCGCTACCCCTCCAGCTTATTCATATAATTTAATAATCAAAATGGTGGAGAATGACGGGTTCGAACCGCCGACCCTCTGc                                                                                                                   <  2:42339/141‑1 (MQ=255)                     ggCAGATTCGAACTGCCGAACCCGAAGGAGCGGATTTACAGTCCGCCGCGTTTAGCCACTTCGCTACCCCTCCAGCTTATTCATATAATTTAATAATCAAAATGGTGGAGAATGACGGGTTCGAACCGCCGACCCTCTGCt                                                                                                                  >  2:243926/1‑141 (MQ=255)                         gATCCGAACTGCCGAACCCTAAGGAGCCGATTTACAGTCCGCCGCGTGCCGCCACTTCGCTACCCCTACAGCTTATTCATATATTTTAATAATCCAAATGGTGAAGAATTACGGGTTCGAACCGCCGACCCTCTGCTTGTa                                                                                                              <  2:67219/141‑1 (MQ=37)                           ttCGAACTGCCGAACCCGAAGGAGCGGATTTACAGTCCGCCGCGTTTAGCCACTTCGCTACCCCTCCAGCTTATTCATATAATTTAATAATCAAAATGGTGGAGAATGACGGGTTCGAACCGCCGACCCTCTGCTTGTAAg                                                                                                            <  2:255726/141‑1 (MQ=255)                                 cTGCCGAACCCGAAGGAGCGGATTTACAGTCCGCCGCGTTTAGCCACTTCGCTACCCCTCCAGCTTATTCATATAATTTAATAATCAAAATGGTGGAGAATGACGGGTTCGAACCGCCGACCCTCTGCTTGTAAGGCAGAt                                                                                                      <  2:118567/141‑1 (MQ=255)                                 cTGCCGAACCCGAAGGAGCGGATTTACAGTCCGCCGCGTTTAGCCACTTCGCTACCCCTCCAGCTTATTCATATAATTTAATAATCAAAATGGTGGAGAATGACGGGTTCGAACCGCCGACCCTCTGCTTGTAAGGCAGAt                                                                                                      <  2:143090/141‑1 (MQ=255)                                  tGCCGAACCCGAAGGAGCGGATTTACAGTCCGCCGCGTTTAGCCACTTCGCTACCCCTCCAGCTTATTCATATAATTTAATAATCAAAATGGTGGAGAATGACGGGTTCGAACCGCCGACCCTCTGCTTGTAAGGCAGATg                                                                                                     <  1:6384/141‑1 (MQ=255)                                   gCCGAACCCGAAGGAGCGGATTTACAGTCCGCCGCGTTTAGCCACTTCGCTACCCCTCCAGCTTATTCATATAATTTAATAATCAAAATGGTGGAGAATGACGGGTTCGAACCGCCGACCCTCTGCTTGTAAGGCAGATGc                                                                                                    >  1:238476/1‑141 (MQ=255)                                       aaCCCGAAGGAGCGGATTTACAGTCCGCCGCGTTTAGCCACTTCGCTACCCCTCCAGCTTATTCATATAATTTAATAATCAAAATGGTGGAGAATGACGGGTTCGAACCGCCGACCCTCTGCTTGTAAGGCAGATGCtctc                                                                                                >  1:238893/1‑141 (MQ=255)                                         cccGAAGGAGCGGATTTACAGTCCGCCGCGTTTAGCCACTTCGCTACCCCTCCAGCTTATTCATATAATTTAATAATCAAAATGGTGGAGAATGACGGGTTCGAACCGCCGACCCTCTGCTTGTAAGGCAGATGCTCTccc                                                                                              <  1:174257/141‑1 (MQ=255)                                         cccGAAGGAGCGGATTTACAGTCCGCCGCGTTTAGCCACTTCGCTACCCCTCCAGCTTATTCATATAATTTAATAATCAAAATGGTGGAGAATGACGGGTTCGAACCGCCGACCCTCTGCTTGTAAGGCAGATGCTCTccc                                                                                              <  2:148020/141‑1 (MQ=255)                                            gAAGGAGCGGATTTACAGTCCGCCGCGTTTAGCCACTTCGCTACCCCTCCAGCTTATTCATATAATTTAATAATCAAAATGGTGGAGAATGACGGGTTCGAACCGCCGACCCTCTGCTTGTAAGGCAGATGCTCTCCCAGc                                                                                           >  2:229724/1‑141 (MQ=255)                                              aGGAGCGGATTTACAGTCCGCCGCGTTTAGCCACTTCGCTACCCCTCCAGCTTATTCATATAATTTAATAATCAAAATGGTGGAGAATGACGGGTTCGAACCGCCGACCCTCTGCTTGTAAGGCAGATGCTCTCCCAGCTg                                                                                         <  1:274133/141‑1 (MQ=255)                                                 aGCGGATTTACAGTCCGCCTCGTTTAGCCACTTCGCTACCCCTCCAGCTTATTCATATAATTTAATAATCAAAATGGTGGAGAATGACGGGTTCGAACCGCCGACCCTCTGCTTGTAAGGCAGATGCTCTCCCAGCTGAGc                                                                                      <  2:29308/141‑1 (MQ=255)                                                           cAGTCCGCCGCGTTTAGCCACTTCGCTACCCCTCCAGCTTATTCATATAATTTAATAATCAAAATGGTGGAGAATGACGGGTTCGAACCGCCGACCCTCTGCTTGTAAGGCAGATGCTCTCCCAGCTGAGCTAATTCTCCa                                                                            >  2:225008/1‑141 (MQ=255)                                                           cAGTCCGCCGCGTTTAGCCACTTCGCTACCCCTCCAGCTTATTCATATAATTTAATAATCAAAATGGTGGAGAATGACGGGTTCGAACCGCCGACCCTCTGCTTGTAAGGCAGATGCTCTCCCAGCTGAGCTAATTCTCCa                                                                            >  1:66554/1‑141 (MQ=255)                                                              tCCGCCGCGTTTAGCCACTTCGCTACCCCTCCAGCTTATTCATATAATTTAATAATCAAAATGGTGGAGAATGACGGGTTCGAACCGCCGACCCTCTGCTTGTAAGGCAGATGCTCTCCCAGCTGAGCTAATTCTCCaaaa                                                                         >  1:201683/1‑141 (MQ=255)                                                                   cgcgTTTAGCCACTTCGCTACCCCTCCAGCTTATTCATATAATTTAATAATCAAAATGGTGGAGAATGACGGGTTCGAACCGCCGACCCTCTGCTTGTAAGGCAGATGCTCTCCCAGCTGAGCTAATTCTCCAAAATAATg                                                                    >  1:81051/1‑141 (MQ=255)                                                                                 tCGCTTCCCCTCCAGCTTATTCATATAATTTAATAATCAAAATGGTGGAGAATGACGGGTTCGAACCGCCGACCCTCTGCTTGTAAGGCAGATGCTCTCCCAGCTGAGCTAATTCTCCAAAATAATGACTCCTACGGGACt                                                      <  2:179710/141‑1 (MQ=255)                                                                                 tCGCTACCCCTCCAGCTTATTCATATAATTTAATAATCAAAATGGTGGAGAATGACGGGTTCGAACCGCCGACCCTCTGCTTGTAAGGCAGATGCTCTCCCAGCTGAGCTAATTCTCCAAAATAATGACTCCTACGGGACt                                                      <  2:50845/141‑1 (MQ=255)                                                                                     tACCCCTCCAGCTTATTCATATAATTTAATAATCAAAATGGTGGAGAATGACGGGTTCGAACCGCCGACCCTCTGCTTGTAAGGCAGATGCTCTCCCAGCTGAGCTAATTCTCCAAAATAATGACTCCTACGGGACTCGaa                                                  >  2:11357/1‑141 (MQ=255)                                                                                     tACCCCTCCAGCTTATTCATATAATTTAATAATCAAAATGGTGGAGAATGACGGGTTCGAACCGCCGACCCTCTGCTTGTAAGGCAGATGCTCTCCCAGCTGAGCTAATTCTCCAAAATAATGACTCCTACGGGACTCGaa                                                  >  2:203832/1‑141 (MQ=255)                                                                                       ccccTCCAGTCTCTTCATATAATTTACTACTCCAAATGGTGGAGAATGACGGGTTCGAACCGCCGACCCTCTGCTTGCAAGGCAGACGCCCTCCCAGCTGAGCTAATCCCCCAACATTATGACTCCTACGTGACTCGAAcc                                                <  2:242869/141‑1 (MQ=18)                                                                                       ccccTCCAGCTTATTCATATAATTTAATAATCAAAATGGTGGAGAATGACGGGTTCGAACCGCCGACCCTCTGCTTGTAAGGCAGATGCTCTCCCAGCTGAGCTAATTCTCCAAAATAATGACTCCTACGGGACTCGAAcc                                                <  2:286449/141‑1 (MQ=255)                                                                                                cTTATTCATATAATTTAATAATCAAAATGGTGGAGAATGACGGGTTCGAACCGCCGACCCTCTGCTTGTAAGGCAGATGCTCTCCCAGCTGAGCTAATTCTCCAAAATAATGACTCCTACGGGACTCGAACCCGTGTTAcc                                       >  2:27039/1‑141 (MQ=255)                                                                                                cTTATTCATATAATTTAATAATCAAAATGGTGGAGAATGACGGGTTCGAACCGCCGACCCTCTGCTTGTAAGGCAGATGCTCTCCCAGCTGAGCTAATTCTCCAAAATAATGACTCCTACGGGACTCGAACCCGTGTTAcc                                       >  2:196368/1‑141 (MQ=255)                                                                                                  tATTCATATAATTTAATAATCAAAATGGTGGAGAATGACGGGTTCGAACCGCCGACCCTCTGCTTGTAAGGCAGATGCTCTCCCAGCTGAGCTAATTCTCCAAAATAATGACTCCTACGGGACTCGAACCCGTGTTAccgc                                     <  2:94354/141‑1 (MQ=255)                                                                                                      cATATAATTTAATAATCAAAATGGTGGAGAATGACGGGTTCGAACCGCCGACCCTCTGCTTGTAAGGCAGATGCTCTCCCAGCTGAGCTAATTCTCCAAAATAATGACTCCTACGGGACTCGAACCCGTGTTACCGCCGTg                                 >  2:179129/1‑141 (MQ=255)                                                                                                      cATATAATTTAATAATCAAAATGGTGGAGAATGACGGGTTCGAACCGCCGACCCTCTGCTTGTAAGGCAGATGCTCTCCCAGCTGAGCTAATTCTCCAAAATAATGACTCCTACGGGACTCGAACCCGTGTTACCGCCGTg                                 >  1:51253/1‑141 (MQ=255)                                                                                                          taATTTAATAATCAAAATGGTGGAGAATGACGGGTTCGAACCGCCGACCCTCTGCTTGTAAGGCAGATGCTCTCCCAGCTGAGCTAATTCTCCAAAATAATGACTCCTACGGGACTCGAACCCGTGTTAccgccctttcac                             <  1:72779/141‑8 (MQ=255)                                                                                                          taATTTAATAATCAAAATGGTGGAGAATGACGGGTTCGAACCGCCGACCCTCTGCTTGTAAGGCAGATGCTCTCCCAGCTGAGCTAATTCTCCAAAATAATGACTCCTACGGGACTCGAACCCGTGTTACCGCCGTGAAAg                             <  2:174270/141‑1 (MQ=255)                                                                                                          taATTTAATAATCAAAATGGTGGAGAATGACGGGTTCGAACCGCCGACCCTCTGCTTGTAAGGCAGATGCTCTCCCAGCTGAGCTAATTCTCCAAAATAATGACTCCTACGGGACTCGAACCCGTGTTACCGCCGTGAAAg                             <  2:149976/141‑1 (MQ=255)                                                                                                            aTTTAATAATCAAAATGGTGGAGAATGACGGGTTCGAACCGCCGACCCTCTGCTTGTAAGGCAGATGCTCTCCCAGCTGTGCTAATTCGCCAAAATAATGACTCCTACGGGACTCGAACCCGTGTTACCGCCGTGAAAggg                           >  1:84668/1‑141 (MQ=255)                                                                                                                aataatCAAAATGGTGGAGAATGACGGGTTCGAACCGCCGACCCTCTGCTTGTAAGGCAGATGCTCTCCCAGCTGAGCTAATTCTCCAAAATAATGACTCCTACGGGACTCGAACCCGTGTTACCGCCGTGAAAGGGCGgt                       >  2:250340/1‑141 (MQ=255)                                                                                                                   aatCAAAATGGTGGAGAATGACGGGTTCGAACCGCCGACCCTCTGCTTGTAAGGCAGATGCTCTCCCAGCTGAGCTAATTCTCCAAAATAATGACTCCTACGGGACTCGAACCCGTGTTACCGCCGTGAAAGGGCGGTGTc                    >  2:149744/1‑141 (MQ=255)                                                                                                                         aaTGGTGGAGAATGACGGGTTCGAACCGCCGACCCTCTGCTTGTAAGGCAGATGCTCTCCCAGCTGAGCTAATTCTCCAAAATAATGACTCCTACGGGACTCGAACCCGTGTTACCGCCGTGAAAGGGCGGTGTCTTAAcc              >  1:281273/1‑141 (MQ=255)                                                                                                                              tggAGAATGACGGGTTCGAACCGCCGACCCTCTGCTTGTAAGGCAGATGCTCTCCCAGCTGAGCTAATTCTCCAAAATAATGACTCCTACGGGACTCGAACCCGTGTTACCGCCGTGAAAGGGCGGTGTCTTAACCGCTTg         >  2:34817/1‑141 (MQ=255)                                                                                                                                     tGACGGGTTCGAACCGCCGACCCTCTGCTTGTAAGGCAGATGCTCTCCCAGCTGAGCTAATTCTCCAAAATAATGACTCCTACGGGACTCGAACCCGTGTTACCGCCGTGAAAGGGCGGTGTCTTAACCGCTTGACCAAgg  >  2:167302/1‑141 (MQ=255)                                                                                                                                     |                                                                                                                                             ATATATAGATGGTGGAGGGGGGCAGATTCGAACTGCCGAACCCGAAGGAGCGGATTTACAGTCCGCCGCGTTTAGCCACTTCGCTACCCCTCCAGCTTATTCATATAATTTAATAATCAAAATGGTGGAGAATGACGGGTTCGAACCGCCGACCCTCTGCTTGTAAGGCAGATGCTCTCCCAGCTGAGCTAATTCTCCAAAATAATGACTCCTACGGGACTCGAACCCGTGTTACCGCCGTGAAAGGGCGGTGTCTTAACCGCTTGACCAAGG  >  USA300TCH1516_ALE/2292396‑2292668

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 12 ≤ ATCG/ATCG < 27 ≤ ATCG/ATCG < 37 ≤ 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.