New junction evidence
		seq id	position	reads (cov)	reads (cov)	score	skew	freq	annotation	gene	product
*	?	USA300TCH1516_ALE	= 1217693	54 (0.620)	3 (0.040)	3/264	7.3	5.4%	intergenic (+22/‑415)	USA300HOU_RS06060/USA300HOU_RS06065	hypothetical protein/hypothetical protein
	?	USA300TCH1516_ALE	= 1217729	56 (0.730)					intergenic (+58/‑379)	USA300HOU_RS06060/USA300HOU_RS06065	hypothetical protein/hypothetical protein
Rejected: Coverage evenness skew score above cutoff.
Rejected: Frequency below/above cutoff threshold.

GTAGTCACGATGTCGACGAAAGTTCAACGAAGCAAAAACATATAAAAAATAAAACAACTATAGATCATAATGATGATTTATTTAAACATGTAAAGGATATATTACGTAAACAAGAACAAATTTAAAAACAAAAAAGCTATAGTGTTTAATATCAGGGGCTGCTTAACCGCATCCGAATATTACAAACACTATAGCTTTTATTATATAAAAAATTTATTAGCGGATAATTAACTTTATTAAAATCCAACCAATTAAGAATACGAGTAATAGGACTAATACTGGAATCACATAATG  >  USA300TCH1516_ALE/1217547‑1217840                                                                                                                                                   |                                                                                                                                                    gtagtCACGATGTCGACGAAAGTTCAACGAAGCAAAAACATATAAAAAATAAAACAACTATAGATCATAATGATGATTTATTTAAACATGTAAAGGATATATTACGTAAACAAGAACAAATTTAAAAACAAAAAAGCTATAGTGTTTaa                                                                                                                                                   <  1:128548/149‑1 (MQ=255)  tagtCACGATGTCGACGAAAGTTCAACGAAGCAAAAACATATAAAAAATAAAACAACTATAGATCATAATGATGATTTATTTAAACATGTAAAGGATATATTACGTAAACAAGAACAAATTTAAAAACAAAAAAGCTATAGTGTTTAat                                                                                                                                                  >  1:396263/1‑149 (MQ=255)    gtCACGATGTCGACGAAAGTTCAACGAAGCAAAAACATATAAAAAATAAAACAACTATAGATCATAATGCTGATTTATTTAAACATGTAAAGGATATATTACGTAAACAAGAACAAATTTAAAAACAAAAAAGCTATAGTGTTTAatat                                                                                                                                                >  1:424265/1‑149 (MQ=255)     tCACGATGTCGACGAAAGTTCAACGAAGCAAAAACATATAAAAAATAAAACAACTATAGATCATAATGATGATTTATTTAAACATGTAAAGGATATATTACGTAAACAAGAACAAATTTAAAAACAAAAAAGCTATAGTGTTTAATATc                                                                                                                                               >  1:203484/1‑149 (MQ=255)                        tCAACGAAGCAAAAACATATAAAAAATAAAACAACTATAGATCATAATGATGATTTATTTAAACATGTAAAGGATATATTACGTAAACAAGAACAAATTTAAAAACAAAAAAGCTATAGTGTTTAATATCAGGGGCTGCTTAACCGCAt                                                                                                                            <  1:432189/149‑1 (MQ=255)                        tCAACGAAGCAAAAACATATAAAAAATAAAACAACTATAGATCATAATGATGATTTATTTAAACAAGTAAAGGATATATTACGTAAACAAGAACAAATTTAAAAACAAAAAAGCTATAGTGTTTAATATCAGGGGCTGCTTAACCGCAt                                                                                                                            <  1:215796/149‑1 (MQ=255)                          aaCGAAGCAAAAACATATAAAAAATAAAACAACTATAGATCATAATGATGATTTATTTAAACATGTAAAGGATATATTACGTAAACAAGAACAAATTTAAAAACAAAAAAGCTATAGTGTTTAATATCAGGGGCTGCTTAACCGCATcc                                                                                                                          <  1:338684/149‑1 (MQ=255)                            cGAAGCAAAAACATATAAAAAATAAAACAACTATAGATCATAATGATGATTTATTTAAACATGTAAAGGATATATTACGTAAACAAGAACAAATTTAAAAACAAAAAAGCTATAGTGTTTAATATCAGGGGCTGCTTAACCGCATCCGa                                                                                                                        <  1:891156/149‑1 (MQ=255)                                   aaaaCATATAAAAAATAAAACAACTATAGATCATAATGATGATTTATTTAAACATGTAAAGGATATATTACGTAAACAAGAACAAATTTAAAAACAAAAACGCTATAGTGTTTAATATCAGGGGCTACATAACCGCCTCCGAATAATAc                                                                                                                 >  1:720197/1‑149 (MQ=255)                                    aaaCATATAAAAAATAAAACAACTCTAGATCATAATGATGATTTATTTAAACATATAAAGGATATATTACGTAAACAAGAACAAATTTAAAAACAAAAAAGCTATAGTGTTTAATATCAGGGGCTGCTTAACCGCATCCGAATATTACa                                                                                                                >  2:335717/1‑149 (MQ=255)                                     aaCATATAAAAAATAAAACAACTATAGATCATAATGATGATTTATTTAAACATGTAAAGGATATATTACGTAAACAAGAACAAATTTAAAAACAAAAAAGCTATAGTGTTTAATATCAGGGGCTGCTTAACCGCATCCGAATATTACaa                                                                                                               <  1:740773/149‑1 (MQ=255)                                       cATATAAAAAATAAAACAACTATAGATCATAATGATGATTCAGTTAAACAAGTAAAGGATATATTACGTAAACAAGAACAAATTTAAAAACAAAAAAGCTATAGTGTTTAATATCAGGGGCTGCTTAACCGCATCCGAATATTACaacc                                                                                                             <  2:35355/149‑3 (MQ=255)                                       aaaatgaaaaaaaaaaCAACTATAGATCATAATGATGATTTATTTAAACATGTAAAGGATATATTACGTAAACAAGAACAAATTTATAAACAAAAAAGCTATAGTGTTTAATATCAGGGGCTGCTTAACCGCATCCGAATATTACAAac                                                                                                             <  2:35232/143‑1 (MQ=255)                                              aaaaTAAAACAACTATAGATCATAATGATGTTTTATTTAAACATGTAAAGGATACATTACGTAAACAAGAACAAATTTAAAAACAAAAAATCTATAGTGTTTAATATCAGGGGCTGCTTAACCGCATCCGAACATTACAAACACTATAg                                                                                                      <  2:686679/149‑1 (MQ=255)                                              aaaaTAAAACAACTATAGATCATAATGATGATTTATTTAAACATGTAAAGGATATATTACGTAAACAAGAACAAATTTAAAAACAAAAAAGCTATAGTGTTTAATATCAGGGGCTGCTTAACCGCATCCGAATATTACAAACACTATAg                                                                                                      >  1:741782/1‑149 (MQ=255)                                              aaaaTAAAACAACTAAAGATCATAATGATGATTTATATAAACCTGTAAAGGATATATTACGTAAACAAGAACAAAAAAAAAAAAAAAAAAGCTATAGTGTTTAATATCAGGGGCTGCTTAACCGCATCCGAATATTACAAACACTATAg                                                                                                      <  2:745314/149‑1 (MQ=255)                                                    aaaCAACTATAGATCATAATGATGATTTATTTAAACATGTAAAGGATATATTACGTAAACAAGAACAAATTTAAAAACAAAAAAGCTATAGTGTTTAATATCAGGGGCTGCTTAACCGCATCCGAATATTACAAACACTATAGCTTtta                                                                                                >  2:735531/1‑149 (MQ=255)                                                    aaaCAACTATAGATCATAATGATGATTTATTTAAACATGTAAAGGATATATTACGTAAACAAGAACAAATTTAAAAACAAAAAAGCTATAGTGTTTAATATCAGGGGCTGCTTAACCGCATCCGAATATTACAAACACTATAGCTTtta                                                                                                <  2:203484/149‑1 (MQ=255)                                                        aacTATAGATGATGAGGATGATTTATTTAAACATGTAATGGATATATTACGGAAACAAGAACAAATTTAAAAACAAAAAAGCTATAGTGTTTAATATCAGGGGCTGCTTAACCGCATCCGAATATTACAAACACTATAGCTTTtattat                                                                                            <  2:105364/149‑1 (MQ=255)                                                        aacTATAGATCATAATGATGATTTATTTAAACATGTAAAGGATATATTACGTAAACAAGAACAAATTTAAAAACAAAAAAGCTATAGTGTTTAATATCAGGGGCTGCTTAACCGCATCCGAATATTACAAACACTATAGCTTTtattat                                                                                            <  2:55925/149‑1 (MQ=255)                                                        aacTATAGATCATAATGATGATTTATTTAAACATGTAAAGGATATATTACGTAAACAAGAACAAATTTAAAAACAAAAAAGCTATAGTGTTTAATATCAGGGGCTGCTTAACCGCATCCGAATATTACAAACACTATAGCTTTtattat                                                                                            >  1:132546/1‑149 (MQ=255)                                                         acTATAGATCATAATGATGATTTATTTAAACATGTAAAGGATATATTACGTAAACAAGAACAAATTTACAAACAAAAAAGCTATAGTGTTTAATATCAGGGGCTGCTTAACCGCATCCGACTATTACAAACACTACAGCttttttgttt                                                                                           >  1:284785/1‑143 (MQ=255)                                                               aaTCATAATGATGATTTATTTAAACATGTAAAGGATATATTACGTAAACAAGAACAAATTTAAAAACAAAAAAGCTATAGTGTTTAATATCAGGGGCTGCTTAACCGCATCCGAATATTACAAACACTATAGCTTTTATTATATaaaaa                                                                                     <  1:205336/148‑1 (MQ=255)                                                                    tAATGATGATTTATTTAAACATGTAAAGGATATATTACGTAAACAAGAACAAATTTAAAAACAAAAAAGCTATAGTGTTTAATATCAGGGGCTGCTTAACCGCATCCGAATATTACAAACACTATAGCTTTTATTATATAAAAAATtta                                                                                >  1:804489/1‑149 (MQ=255)                                                                        gatgatTTATTTAAACACCCAATTGATATAGTACGTAAACAAGAACAAACTTAAAAACAAAAAAGCTATAGTGTTTAATATCAGGGGCTGCTTAACCGCATCCGAATATTACAAACACTATAGCTTTTATTATATAAAAAATTTATTAg                                                                            <  1:250197/149‑1 (MQ=255)                                                                        gatgatCTATTTAAACATTTAAAGGATATATTACGTAAACATGAACAAATTTAAAAACAAAAAAGCTATAGTGTTTAATATCAGGGGCTGCTTAACCGCATCCGAATATTACAAACACTATAGCTTTTATTATATAAAAAATTTATTAg                                                                            <  2:133173/149‑1 (MQ=255)                                                                            atttatttAAACATGTAAAGGATATATTACGTAAACAAGAACAAATTTAAAAACAAAAAAGCTATAGTGTTTAATATCAGGGGCTGCTTAACCGCATCCGAATATTACAAACACTATAGCTTTTATTATATAAAAAATTTATTAGCGGa                                                                        <  1:830173/149‑1 (MQ=255)                                                                             tttatttaAACATGAAAAGGATATATTACGTAAACAAGAACAAATTAAAAAACAAAAAAGCTATAGTGTTTAATATCAGGGGCTGCTTAACCGCATCCGAATATTACAAACACTATAGCTTTTATTATATAAAAAATTTATTAGCGGAt                                                                       <  1:713572/149‑1 (MQ=255)                                                                               tatttaAACATGTAAAGGATATATTACGTAAACAAGAACAAATTTAAAAACAAAAAAGCTATAGTGTTTAATATCAGGGGCTGCTTAACCGCATCCGAATATTACAAACACTATAGCTTTTATTATATAAAAAATTTATTAGCGGATaa                                                                     <  1:671222/149‑1 (MQ=255)                                                                                    aaaCATGTAAAGGATATATTACGTAAACAAGAACAAATTTAAAAACAAAAAAGCTAAGGCGATTAATATCAGGGGCTGCTTAACCGCATCCGAATATTACAAACACTATAGCTTTTATTATATAAAAAATTTATTAGCGGATAATTAAc                                                                <  1:440944/149‑1 (MQ=255)                                                                                     aaCATGTAAAGGATATATTACGTAAACAAGAACAAATTTAAAAACAAAAAAGCTATAGTGTTTAATATCAGGGGCTGCTTAACCGCATCCGAATATTACAAACACTATAGCTTTTATTATATAAAAAATTTATTAGCGGATAATTAACt                                                               <  2:805689/149‑1 (MQ=255)                                                                                         tGTAAAGGATATATTACGTAAACAAGAACAAATTTAAAAACAAAAAAGCTATAGTGTTTAATATCAGGGGCTGCTTAACCGCATCCGAATATTACAAACACTATAGCTTTTATTATATAAAAAATTTATTAGCGGATAATTAACTttat                                                           >  2:785425/1‑149 (MQ=255)                                                                                            aaaGGATATATTACGTAAACAAGAACAAATTTAAAAACAAAAAAGCTATAGTGTTTAATATCAGGGGCTGCTTAACCGCATCCGAATATTACAAACACTATAGCTTTTATTATATAAAAAATTTATTAGCGGATAATTAACTTTATTaa                                                        >  1:831736/1‑149 (MQ=255)                                                                                               ggATATATTACGTAAACAAGAACAAATTTAAAAACAAAAAAGCTATAGTGTTTAATATCAGGGGCTGCTTAACCGCATCCGAATATTACAAACACTATAGCTTTTATTATATAAAAAATTTATTAGCGGATAATTAACTTTATTAAAAt                                                     >  2:460983/1‑149 (MQ=255)                                                                                                aatatatTACGTAAAAAAAAAAAAAAAAAAAAAAAAAAAAGCTATAGTGTTTAATATCAGGGGCTGCTTAACCGCATCCGAATATTACAAACACTATAGCTTTTATTATATAAAAAATTTATTAGCGGATAATTAACTTTATTAAAATc                                                    <  2:111681/148‑1 (MQ=255)                                                                                                 atatatTACGTAAACAAGAACAAATTTAAAAACAAAAAAGCTATAGTGTTTAATATCAGGGGCTGCTTAACCGCATCCGAATATTACAAACACTATAGCTTTTATTATATAAAAAATTTATTAGCGGATAATTAACTTTATTAAAATcc                                                   <  1:76309/149‑1 (MQ=255)                                                                                                 atatatTACGTAAACAAGAACAAATTTAAAAACAAAAAAGCTATAGTGTTTAATATCAGGGGCTGCTTAACCGCATCCGAATATTACAAACACTATAGCTTTTATTATATAAAAAATTTATTAGCGGATAATTAACTTTATTAAAATcc                                                   <  1:728311/149‑1 (MQ=255)                                                                                                  tatatTACGTAAACAAGAACAAATTTAAAAACAAAAAAGCTATAGTGTTTAATATCAGGGGCTGCTTAACCGCATCCGAATATTACAAACACTATAGCTTTTATTATATAAAAAATTTATTAGCGGATAATTAACTTTATTAAAATcca                                                  <  1:426500/149‑1 (MQ=255)                                                                                                    tatTACCTAAACAAGAACAAATTTAAAAACAAAAAAGCTATAGTGTTTAATATCAGGTGCTGCTTAACCGCATCCGAATATTACAAACACTATAGCTTTTATTATATAAAAAATTTATTAGCGGATAATTAACTTTATTAAAATccaac                                                <  1:123967/149‑1 (MQ=255)                                                                                                      ttACGTAAACAAGAACAAATTTAAAAACAAAAAAGCTATAGTGTTTAATATCAGGGGCTGCTTAACCGCATCCGAATATTACAAACACTATAGCTTTTGTTATATAAAAAATTTATTAGCGGATAATTAACTTTATTAAAATacaacca                                              >  2:634808/1‑149 (MQ=255)                                                                                                      ttACGTAAACAAGAACAAATTTAAAAACAAAAAAGCTATAGTGTTTAATATCAGGGGCTGCTTAACCGCATCCGAATATTACAAACACTATAGCTTTTATTATATAAAAAATTTATTAGCGGATAATTAACTTTATTAAAATcaaacca                                              >  2:903650/1‑149 (MQ=255)                                                                                                       tACGTAAACAAGAACAAATTTAAAAACAAAAAAGCTATAGTGTTTAATATCAGGGGCTGCTTAACCGCATCCGAATATTACAAACACTATAGCTTTTATTATATAAAAAATTTATTAGCGGATAATTAACTTTATTAAAATccaaccaa                                             >  1:652235/1‑149 (MQ=255)                                                                                                        aCGTAAACAAGAACAAATTTAAAAACAAAAAAGCTATAGTGTTTAATATCAGGGGCTGCTTAACCGCATCCGAATATTACAAACACTATAGCTTTTATTATATAAAAAATTTATTAGCGGATAATTAACTTTATTAAAATCCAACCAAt                                            >  2:874558/1‑149 (MQ=255)                                                                                                        aCGTAAACAAGAACAAAAAAAAAAAAAAAAAAGCTATAGTGTTTAATATCAGGGGCTGCTTAACCGCATCCGAATATTACAAACACTATAGCTTTTATTATATAAAAAATTTATTAGCGGATAATTAACTTTATTAAAATCCAACCAAt                                            <  2:462953/149‑1 (MQ=255)                                                                                                          gTAAACAACAACAAATATAAAAACAAAAAAACTATAGTGTTTAATATCAGGGGCTGCTTAACCGCATCCGAATATTACAAACACTATAGCTTTTATTATATAAAAAATTTATTAGCGGATAATTAACTTTATTAAAATCCAACCAATTa                                          <  2:589741/149‑1 (MQ=255)                                                                                                              aCAAGAACAAATTTAAAAACAAAAAAGCTATAGTGTTTAATATCAGGGGCTGCTTAACCGCATCCGAATATTACAAACACTATAGCTTTTATTATATAAAAAATTTATTAGCGGATAAGTAACTTTATTAAAATCCAACCAATTAAGaa                                      >  2:583917/1‑149 (MQ=255)                                                                                                                aaaaaCAAATTTAAAAACAAAAAAGCTATAGTGTTTAATATCAGGGGCTGCTTAACCGCATCCGAATATTACAAACACTATAGCTTTTATTATATAAAAAATTTATTAGCGGATAATTAACTTTATTAAAATCCAACCAATTAAGAATa                                    <  2:804489/146‑1 (MQ=255)                                                                                                                   aaCAAATTTAAAAACAAAAAAGCTATAGTGTTTAATATCAGGGGCTGCTTAACCGCATCCGAATATTACAAACACTATAGCTTTTATTATATGAAAAATTGATTAGCGGATAATTAACTTTATTAAAATCCAACCAATTAAGAATACGa                                 >  1:687958/1‑149 (MQ=255)                                                                                                                            aaaaaCAAAAAAGCTATAGTGTTTAATATCAGGGGCTGCTTAACCGCACCCGAATATTACAAACACTATAGCTTTTATTATATAAAAAATTTATTAGCGGATAATTAACTTTATTAAAATCCAACCAATTAAGAATACGAGTAATAGGa                        <  1:351161/149‑1 (MQ=255)                                                                                                                               aaCAAAAAATCTCTTGTGTTGAATATCCGCGGCTGCTTAACCGCATCCTAATATTACAAACACTATAGCTTTAATTATATAAAAAATTTATTAGCGGATAATTAACTTTATTAAAATCCAACCAATTAAGAATACGAGTAATAGGACTa                     <  2:855850/149‑1 (MQ=255)                                                                                                                                           agaGTGTTTAATATCAGGGGCTGCTTAACCGCATCCGAATATTACAAACACTATAGCTTTTATTATATAAAAAATTTATTAGCGGATAATTAACTTTATTAAAATCCAACCAATTAAGAATACGAGTAATAGGACTAATACTGGAATca         <  1:266631/147‑1 (MQ=255)                                                                                                                                            taGTGTTTAATATCAGGGGCTGCTTAACCGCATCCGAATATTACAAACACTATAGCTTTTATTATATAAAAAATTTATTAGCGGATAATTAACTTTATTAAAATCCAACCAATTAAGAATACGAGTAATAGGACTAATACTGGAATcac        <  1:903745/149‑1 (MQ=255)                                                                                                                                                  ttAATATCAGGGGCTGCTTAACCGCATCCGAATATTACAAACACTATAGCTTTTATTATATAAAAAATTTATTAGCGGATAATTAACTTTATTAAAATCCAACCAATTAAGAATACGAGTAATAGGACTAATACTGGAATaaccacatt  >  1:802618/1‑143 (MQ=255)                                                                                                                                                  ttAATATCAGGGGCTGCTTAACCGCATCCGAATATTACAAACACTATAGCTTTTATTATATAAAAAATTTATTAGCGGATAATTAACTTTATTAAAATCCAACCAATTAAGAATACGAGTAATAGGACTAATACTGGAATCACATAATg  >  2:442003/1‑149 (MQ=255)                                                                                                                                                  ttAATATCAGGGGCTGCTTAACCGCATCCGAATATTACAAACACTATAGCTTTTATTATATAAAAAATTTATTAGCGGATAATTAACTTTATTAAAATCCAACCAATTAAGAATACGAGTAATAGGACTAATACTGGAATCACATAATg  >  2:441766/1‑149 (MQ=255)                                                                                                                                                   |                                                                                                                                                    GTAGTCACGATGTCGACGAAAGTTCAACGAAGCAAAAACATATAAAAAATAAAACAACTATAGATCATAATGATGATTTATTTAAACATGTAAAGGATATATTACGTAAACAAGAACAAATTTAAAAACAAAAAAGCTATAGTGTTTAATATCAGGGGCTGCTTAACCGCATCCGAATATTACAAACACTATAGCTTTTATTATATAAAAAATTTATTAGCGGATAATTAACTTTATTAAAATCCAACCAATTAAGAATACGAGTAATAGGACTAATACTGGAATCACATAATG  >  USA300TCH1516_ALE/1217547‑1217840

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 12 ≤ ATCG/ATCG < 22 ≤ 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.