New junction evidence
  seq id position reads (cov) reads (cov) score skew freq annotation gene product
* ? CP000730 1966974 =32 (0.840)5 (0.140) 5/252 4.3 12.8% coding (29/111 nt) USA300HOU_1826 hypothetical protein
?CP000730 1966998 = 38 (1.070)coding (5/111 nt) USA300HOU_1826 hypothetical protein
Rejected: Coverage evenness skew score above cutoff.
Rejected: Frequency below/above cutoff threshold.

TGATCATTTTTAAAATTGTATTGTTTTTATTATGCACCATAAAGGCCTCCTAAATTAAAATCATTCTTATCTATATTATCATATCGCTCATTCGTTCGTATTTTCAATAAATAAATGTCATAAAACTGACATTTAATCATAGAACTATTTATTGTAAATTTAAATTCTAAAGTCCATTATTTTGTATCATTACTTCTAAATATCTCGCAAGATTCATTATAGTAATTTTAATCAATTATTAATAGTGGTAATGACTAGTTTATCATCGTATAATA  >  CP000730/1966863‑1967137
                                                                                                                                       |                                                                                                                                           
tGATCATTTTTAAAATTGTATTGTTTTTATTATGCACCATAAAGGCCTCCTAAATTAAAATCATTCTTATCTATATTATCATATCGCTCATTCGTTCGTATTTTCAATAAATAAATGTCATAAAACTGACATTTAATCATa                                                                                                                                        <  2:298071/141‑1 (MQ=255)
 gATCATTTTTAAAATTGTATTGTTTTTATTATGCACCATAAAGGCCTCCTAAATTAAAATCATTCTTATCTATATTATCATATCGCTCATTCGTTCGTATTTTCAATAAATAAATGTCATAAAACTGACATTTAATCATAg                                                                                                                                       <  1:98659/141‑1 (MQ=255)
       ttttAAAATTGTATTGTTTTTATTATGCACCATAAAGGCCTCCTAAATTAAAATCATTCTTATCTATATTATCATATCGCTCATTCGTTCGTATTTTCAATAAATAAATGTCATAAAACTGACATTTAATCATAGAACtat                                                                                                                                 <  1:353260/141‑1 (MQ=255)
       ttttAAAATTGTATTGTTTTTATTATGCACCATAAAGGCCTCCTAAATTAAAATCATTCTTATCTATATTATCATATCGCTCATTCGTTCGTATTTTCAATAAATAAATGTCATAAAACTGACATTTAATCATAGAACtat                                                                                                                                 <  1:353255/141‑1 (MQ=255)
               ttgtattgtTTTTATTATGCACCATAAAGGCCTCCTAAATTAAAATCATTCTTATCTATATTATCATATCGCTCATTCGTTCGTATTTTCAATAAATAAATGTCATAAAACTGACATTTAATCATAGAACTATTTATTGta                                                                                                                         >  2:256855/1‑141 (MQ=255)
                  tattgtTTTTATTATGCACCATAAAGGCCTCCTAAATTAAAATCATTCTTATCTATATTATCATATCGCTCATTCGTTCGTATTTTCAATAAATAAATGTCATAAAACTGACATTTAATCATAGAACTATTTATTGtaaat                                                                                                                      <  2:432365/141‑1 (MQ=255)
                         tttATTATGCACCATAAAGGCCTCCTAAATTAAAATCATTCTTATCTATATTATCATATCGGTCATTCGTTCGTATTTTCAATAAATAAATGTCATAAAACTGACATTTAAACATAGAACTATTTATTGtaaatttaaatt                                                                                                               >  2:413405/1‑141 (MQ=255)
                                 gCACCATAAAGGCCTCCTACATTAAAATCATTCTTATCTATATAATCATATCGCTCATTCGTTCGTATTTTCAATAAATAAATGTCATAAAACTGACATTTAATCATAGAACTATTTATTGTAAATTTAAATTCTAAAGTc                                                                                                       <  2:265068/141‑1 (MQ=255)
                                   aCCATAAATGCCTCCTAAATTAAAATCATTCTTATCTATATTATCATATCGCTCATTCGTTCGTATTTTCAATAAATAAATGTCATAAAACTGACATTTAATCATAGAACTATTTATTGTAAATTTAAATTCTAAAGTCCa                                                                                                     <  2:357706/141‑1 (MQ=255)
                                               tcctAAATTAAAATCATTCTTATCTATATTATCATATCGCTCATTCGTTCGTATTTTCAATAAATAAATGTCATAAAACTGACATTTAATCATAGAACTATTTATTGTAAATTTAAATTCTAAAGTCCATTATTTTGTATc                                                                                         <  1:433964/141‑1 (MQ=255)
                                               tcctAAATTAAAATCATTCTTATCTATATTATCATATCGCTCATTCGTTCGTATTTTCAATAAATAAATGTCATAAAACTGACATTTAATCATAGAACTATTTATTGTAAATTTAAATTCTAAAGTCCATTATTTTGTATc                                                                                         >  2:253673/1‑141 (MQ=255)
                                                    aaTTAAAATCATTCTTATCTATATTATCATATCGCTCATTCGTTCGTATTTTCAATAAATAAATGTCATAAAACTGACATTTAATCATAGAACTATTTATTGTAAATTTAAATTCTAAAGTCCATTATTTTGTATCATTAc                                                                                    >  2:206955/1‑141 (MQ=255)
                                                        aaaaTCATTCTTATCTATATTATCATATCGCTCATTCGTTCGTATTTTCAATAAATAAATGTCATAAAACTGACATTTAATCATAGAACTATTTATTGTAAATTTAAATTCTAAAGTCCATTATTTTGTATCATTACTTCt                                                                                >  1:200607/1‑141 (MQ=255)
                                                        aaaaTCATTCTTATCTATATTATCATATCGCTCATTCGTTCGTATTTTCAATAAATAAATGTCATAAAACTGACATTTAATCATAGAACTATTTATTGTAAATTTAAATTCTAAAGTCCATTATTTTGTATCATTACTTCt                                                                                >  1:400095/1‑141 (MQ=255)
                                                        aaaaTCATTCTTATCTATATCATCATATCGCTCATACGTTCGTATTTTCAATAAATAAATGTCATAAAACTGACATTTAATCATAGAACTATTTATTGTAAATTTAAATTCTAACGTCCATTATTTTGTATCATTACTTCt                                                                                <  2:220512/141‑1 (MQ=255)
                                                         aaaTCATTCTTATCTATATTATCATATCGCTCATTCGTTCGTATTTTCAATAAATAAATGTCATAAAACTGACATTTAATCATAGAACTATTTATTGTAAATTTAAATTCTAAAGTCCATTATTTTGTATCATTACTTCTa                                                                               >  1:380969/1‑141 (MQ=255)
                                                            tCATTCTTATCTATATTATCATATCGCTCATTCGTTCGTATTTTCAATAAATAAATGTCATAAAACTGACATTTAATCATAGAACTATTTATTGTAAATTTAAATTCTAAAGTCCATTATTTTGTATCATTACTTCTAAat                                                                            >  2:361468/1‑141 (MQ=255)
                                                              aTTCTTATCTATATTATCATATCGCTCATTCGTTCGTATTTTCAATAAATAAATGTCATAAAACTGACATTTAATCATAGAACTATTTATTGTAAATTTAAATTCTAAAGTCCATTATTTTGTATCATTACTTCTAAatat                                                                          <  1:224527/141‑1 (MQ=255)
                                                               ttCTTATCTATATTATCATATCGCTCATTCGTTCGTATTTTCAATAAATAAATGTCATAAAACTGACATTTAATCATAGAACTATTTATTGTAAATTTAAATTCTAAAGTCCATTATTTTGTATCATTACTTCTAAATAtc                                                                         <  1:62538/141‑1 (MQ=255)
                                                               ttCTTATCTATATTATCATATCGCTCATTCGTTCGTATTTTCAATAAATAAATGTCATAAAACTGACATTTAATCATAGAACTATTTATTGTAAATTTAAATTCTAAAGTCCATTATTTTGTATCATTACTTCTAAATAtc                                                                         >  1:233681/1‑141 (MQ=255)
                                                                  ttATCTATATTATCATATCGCTCATTCGTTCGTATTTTCAATAAATAAATGTCATAAAACTGACATTTAATCATAGAACTATTTATTGTAAATTTAAATTCTAAAGTCCATTATTTTGTATCATTACTTCTAAATATCTCg                                                                      <  1:233506/141‑1 (MQ=255)
                                                                  ttATCTATATTATCATATCGCTCATTCGTTCGTATTTTCAATAAATAAATGTCATAAAACTGACATTTAATCATAGAACTATTTATTGTAAATTTAAATTCTAAAGTCCATTATTTTGTATCATTACTTCTAAATATCTCg                                                                      >  1:85271/1‑141 (MQ=255)
                                                                  ttATCTATATTATCATATCGCTCATTCGTTCGTATTTTCAATAAATAAATGTCATAAAACTGACATTTAATCATAGAACTATTTATTGTAAATTTAAATTCTAAAGTCCATTATTTTGGATCATTACTTCTAAATATCTCg                                                                      <  1:233519/141‑1 (MQ=255)
                                                                     tCTATATTATCATATCGCTCATTCGTTCGTATTTTCAATAAATAAATGTCATAAAACTGACATTTAATCATAGAACTATTTATTGTAAATTTAAATTCTAAAGTCCATTATTTTGTATCATTACTTCTAAATATCTCGCaa                                                                   <  1:348250/141‑1 (MQ=255)
                                                                                  atCGCTCATTCGTTCGTATTTTCAATAAATAAATGTCATAAAACTGACATTTAATCATAGAACTATTTATTGTAAATTTAAATTCTAAAGTCCATTATTTTGTATCATTACTTCTAAATATCTCGCAAGATTCATTATAGt                                                      <  2:129015/141‑1 (MQ=255)
                                                                                                      ttCAATAAATAAATGTCATAAAACTGACATTTAATCATAGAACTATTTATTGTAAATTTAAATTCTAAAGTCCATTATTTTGTATCATTACTTCTAAATATCTCGCAAGATTCATTATAGTAATTTTAATCAATTATTAAt                                  <  2:144925/141‑1 (MQ=255)
                                                                                                            aaataaatGTCATAAAACTGACATTTAATCATAGAACTATTTATTGTAAATTTAAATTCTAAAGTCCATTATTTTGTATCATTACTTCTAAATATCTCGCAAGATTCATTATAGTAATTTTAATCAATTATTAATAGTGGt                            <  1:346856/141‑1 (MQ=255)
                                                                                                              ataaatGTCATAAAACTGACATTTAATCATAGAACTATTTATTGTAAATTTAAATTCTAAAGTCCATTATTTTGTATCATTACTTCTAAATATCTCGCAAGATTCATTATAGTAATTTTAATCAATTATTAATAGTGGTaa                          >  1:272807/1‑141 (MQ=255)
                                                                                                                  atGGCATAAAACTGACATTTAATCATAGAACTATTTTTTGTAAAGTTAAATTCTAAAGTCCATTATTTTGGATCATTACTACTAAATATCTCGCAAAACTCATTATTGTAAATTTAATCAATTATTAAAATTGGTAATAAc                      >  2:128103/1‑141 (MQ=255)
                                                                                                                   tgtcagttttatGACATTTAATCATAGAACTATTTATTGTAAATTTAAATTCTAAAGTCCATTATTTTGTATCATTACTTCTAAATATCTCGCAAGATTCATTATAGTAATTTTAATCAATTATTAATAGTGGTAATGACt                     <  1:81943/130‑1 (MQ=255)
                                                                                                                   tGTCATAAAACTGACATTTAATCATAGAACTATTTATTGTAAATTTAAATTCTAAAGTCCATTATTTTGTATCATTACTTCTAAATATCTCGCAAGATTCATTATAGTAATTTTAATCAATTATTAATAGTGGTAATGACt                     >  1:152073/1‑141 (MQ=255)
                                                                                                                     tCATAAAACTGACATTTAATCATAGAACTATTTATTGTAAATTTAAATTCTAAAGTCCATTATTTTGTATCATTACTTCTAAATATCTCGCaa                                                                   <  1:263330/93‑1 (MQ=255)
                                                                                                                     tCATAAAACTGACATTTAATCATAGAACTATTTATTGTAAATTTAAATTCTAAAGTCCATTATTTTGTATCATTACTTCTAAATATCTCGCaa                                                                   >  2:263330/1‑93 (MQ=255)
                                                                                                                     tCATAAAACTGACATTTAATCATAGAACTATTTATTGTAAATTTAAATTCTAAAGTCCATTATTTTGTATCATTACTTCTAAATATCTCGCAAGATTGATGATAGTAATTTTAATCAATTATTAATAGTGGTAATGACTAg                   >  2:192090/1‑141 (MQ=255)
                                                                                                                     tCATAAAACTGACATTTAATCATAGAACTATTTATTGTAAATTTAAATTCTAAAGTCCATTATTTTGTATCATTACTTCTAAATATCTCGCAAGATTCATTATAGTAATTTTAATCAATTATTAATAGTGGTAATGACTAg                   <  2:140572/141‑1 (MQ=255)
                                                                                                                     tCATAAAACTGACATTTAATCATAGAACTATTTATTGTAAATTTAAATTCTAAAGTCCATTATTTTGTATCATTACTTCTAAATATCTCGCAAGATTCATTATAGTAATTTTAATCAATTATTAATAGTGGTAATGACTAg                   <  1:334203/141‑1 (MQ=255)
                                                                                                                       agttttatGACATTTAATCATAGAACTATTTATTGTAAATTTAAATTCTAAAGTCCATTATTTTGTATCATTACTTCTAAATATCTCGCAAGATTCATTATAGTAATTTTAATCAATTATTAATAGTGGTAATGACTAGtt                 >  2:63722/8‑141 (MQ=255)
                                                                                                                         gaaaCTGACATTTAATAATAGAACTATTTATTGTAAATTTAAATTCTAAAGTCCATTATTTTGTATAATTACTTCTAAATATATCACAAGATTCATTATAGTAATTTTAATCAATTATTAATAGAAGTCATGACTAGTTTa               >  2:23247/2‑141 (MQ=255)
                                                                                                                           aaCTGACATTTAATCATAGAACTATTTATTGTAAATTTAAATTCTAAAGTCCATTATTTTGTATCATTACTTCTAAATATCTCGCAAGATTCATTATAGTAATTTTAATCAATTATTAATAGTGGTAATGACTAGTTTatc             >  1:27136/1‑141 (MQ=255)
                                                                                                                            aCTGACATTTAATCATAGAACTATTTATTGTAAATTTAAATTCTAAAGTCCATTATTTTGTATCATTACTTCTAAATATCTCGCAAGATTCATTATAGTAATTTTAATCAATTATTAATAGTGGTAATGACTAGTTTatca            <  1:14305/141‑1 (MQ=255)
                                                                                                                                  aTTTAATCATAGAACTATTTATTGTAAATTTAAATTCTAAAGTCCATTATTTTGTATCATTACTTCTAAATATCTCGCAAGATTCATTATAGTAATTTTAATCAATTATTAATAGTGGTAATGACTAGTTTATCATCGtat      <  1:63722/141‑1 (MQ=255)
                                                                                                                                    ttAATCATAGAACTATTTATTGTAAATTTAAATTCTAAAGTCCATTATTTTGTATCATTACTTCTAAATATCTCGCAAGATTCATTATAGTAATTTTAATCAATTATTAATAGTGGTAATGACTAGTTTATCATCGTataa    <  1:361468/141‑1 (MQ=255)
                                                                                                                                      aaTCATAGAACTATTTATTGTAAATTTAAATTCTAAAGTCCATTATTTTGTATCATTACTTCTAAATATCTCGCAAGATTCATTATAGTAATTTTAATCAATTATTAATAGTGGTAATGACTAGTTTATCATCGTataata  >  2:311903/1‑141 (MQ=255)
                                                                                                                                       |                                                                                                                                           
TGATCATTTTTAAAATTGTATTGTTTTTATTATGCACCATAAAGGCCTCCTAAATTAAAATCATTCTTATCTATATTATCATATCGCTCATTCGTTCGTATTTTCAATAAATAAATGTCATAAAACTGACATTTAATCATAGAACTATTTATTGTAAATTTAAATTCTAAAGTCCATTATTTTGTATCATTACTTCTAAATATCTCGCAAGATTCATTATAGTAATTTTAATCAATTATTAATAGTGGTAATGACTAGTTTATCATCGTATAATA  >  CP000730/1966863‑1967137

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