Predicted mutation
evidence seq id position mutation freq annotation gene description
RA CP000730 2,102,803 A→G 10.0% intergenic (‑263/+53) USA300HOU_1961 ← / ← USA300HOU_1962 hypothetical bacteriophage protein/hypothetical bacteriophage protein

Read alignment evidence...
  seq id position ref new freq score (cons/poly) reads annotation genes product
*CP0007302,102,8030AG10.0% 94.8 / 3.9 40intergenic (‑263/+53)USA300HOU_1961/USA300HOU_1962hypothetical bacteriophage protein/hypothetical bacteriophage protein
Reads supporting (aligned to +/- strand):  ref base A (20/16);  new base G (2/2);  total (22/18)
Fisher's exact test for biased strand distribution p-value = 1.00e+00
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 7.01e-01

CCGCAGTGACTTGACCATCACTATTGATTGATACAATATTCGTTTGATCTGTTGTGTATTTCAATAACTTACTTTGATTAGATGGCTCTACTACAACATTTAAATCATATGTGTTGCCAACTTTTAGTGTTTTAAAACTATCTGGTATATTAACCGACTTTATCTCAGTTTCCGATGAAGCCGGTTGCGTTACAAAGTTTCGCCGTTATCCTCTGTCACGTTTCCAGTATATTCTTCGCCTAAAATTTTCTTTAAGAAAGCCTCTTCGCCTTTTT  >  CP000730/2102667‑2102941
                                                                                                                                        |                                                                                                                                          
ccGCAGTGACTTGACCATCACTATTGATTGATACAATATTCGTTTGATCTGTTGTGTATTTCAATAACTTACTTTGATTAGATGGCTCTACTACAACATTTAAATCATATGTGTTGCCAACTTTTAGTGTTTTAAAACTAt                                                                                                                                        >  1:64652/1‑141 (MQ=255)
       gACTTGACCATCACTATTGATTGATACAATATTCGGTTGATCTGTTGTGTATTTCAATAACTTACTTTGATTAGATGGCTCTACTACAACATTTAAATCATATGTGTTGCCAACTTTTAGTGTTTTAAAACTATCTGGtat                                                                                                                                 >  2:363659/1‑141 (MQ=255)
       gACTTGACCATCACTATTGATTGATACAATATTCGAATGATCTGATATGAATACCAATAACTTACTTTGATTAAATGGCTATCCTACAACATTTAAATCATATGTGTTGCCAACTTTTCGTGTTTTAAAAGTATCtcgcct                                                                                                                                 >  2:339682/1‑136 (MQ=255)
              ccATCACTATTGATTGATACAATATTCGTTTGATCTGTTGTGTATTTCAATAACTTACTTTGATTAGATGGCTCTACTACAACATTTAAATCATATGTGTTGCCAACTTTTAGTGTTTTAAAACTATCTGGTATATTAAcc                                                                                                                          <  1:87037/141‑1 (MQ=255)
                 tCACTATTGATTGATACAATATTCGTTTGATCTGTTGTGTATTTCAATAACTTACTTTGATTAGATGGCTCTACTACAACATTTAAATCATATGTGTTGCCAACTTTTAGTGTTTTAAAACTATCTGGTATATTAACCGAc                                                                                                                       <  1:84078/141‑1 (MQ=255)
                 tCACTATTGATTGATACAATATTCGTTTGATCTGTTGTGTATTTCAATAACTTACTTTGATTAGATGGCTCTACTACAACATTTAAATCATATGTGTTGCCAACTTTTAGTGTTTTAAAACTATCTGGTATATTAACCGAc                                                                                                                       <  1:67261/141‑1 (MQ=255)
                   aCTATTGATTGATACAATATTCGTTTGATCTGTTGTGTATTTCAATAACTTACTTTGATTAGATGGCTCTACTACAACATTTAAATCATATGTGTTGCCAACTTTTAGTGTTTTAAAACTATCTGGTATATTAACCGACtt                                                                                                                     >  1:391411/1‑141 (MQ=255)
                        tgattgatACAATATTCGTTTGATCTGTTGTGTATTTCAATAACTTACTTTGATTAGATGGCTCTACTACAACATTTAAATCGTATGTGTCGCCAACTTTAAGTGTTTTAATGCTATCTGGTATATTAACCGACTTTaccg                                                                                                                >  1:170307/1‑138 (MQ=255)
                         gattgatACAATATTCGTTTGATCTGTTGTGTATTTCAATAACTTACTTTGATTAGATGGCTCTACTACAACATTTAAATCATATGTGTTGCCAACTTTTAGTGTTTTAAAACTATCTGGTATATTAACCGACTTTAtctc                                                                                                               >  1:390841/1‑141 (MQ=255)
                                     atTCGTTCGATCTGTTGTGTATTTCAATAACTTACTTTGATTAGATGGCTCTACTACAACATTTAAATCATATGTGTTGCCAACTTTTAGTGTTTTAAAACTATCTGGTATATTAACCGACTTTATCTCAGTTTCCGATGa                                                                                                   >  1:401639/1‑141 (MQ=255)
                                      tttgTTTGAGCTGTTGTGTATTTCAATAACTTACTGTGATTAGATGGCTCTACTACAACATGTAAATCATATTTGTTACCAACTTTTAGTGTTTTAAAACTATCTCGTATATTAACCGACTTTATCTTTGTTTCCGATTaa                                                                                                  <  2:19613/138‑1 (MQ=255)
                                      ttCGTTTGATCTGTTGTGTATTTCAATAACTTACTTTGATTAGATGGCTCTACTACAACATTTAAATCATATGTGTTGCCAACTTTTAGTGTTTTAAAACTATCTGGTATATTAACCGACTTTATCTCAGTTTCCGATGaa                                                                                                  >  2:330934/1‑141 (MQ=255)
                                      ttCGTTTGATCTGTTGTGTATTTCAATAACTTACTTTGATTAGATGGCTCTACTACAACATTTAAATCATATGTGTTGCCAACTTTTAGTGTTTTAAAACTATCTGGTATATTAACCGACTTTATCTCAGTTTCCGATGaa                                                                                                  <  2:235043/141‑1 (MQ=255)
                                          tttGATCTGTTGTGTATTTCAATAACTTACTTTGATTAGATGGCTCTACTACAACATTTAAATCATATGTGTTGCCAACTTTTAGTGTTTTAAAACTATCTGGTATATTAACCGACTTTATCTCAGTTTCCGATGAAGCCg                                                                                              <  2:358940/141‑1 (MQ=255)
                                            tGATCTGTTGTGTATTTCAATAACTTACTTTGATTAGATGGCTCTACTACAACATTTAAATCATATGTGTTGCCAACTTTTAGTGTTTTAAAACTATCTGGTATATTAACCGACTTTATCTCAGTTTCCGATGAAGCCGGt                                                                                            >  2:113740/1‑141 (MQ=255)
                                               tCTGTTGTGTATTTCAATAACTTACTTTGATTAGATGGCTCTACTACAACATTTAAATCATATGTGTTGCCAACTTTTAGTGTTTTAAAACTATCTGGTATATTAACCGACTTTATCTCAGTTTCCGATGAAGCCGGTTGc                                                                                         >  1:122022/1‑141 (MQ=255)
                                                   ttgtGTATTTCAATTACTTACTTTGATTAGATGGCTCTACTACAACATTTAAATCGTATGTGTCGCCAACTTTAAGTGTTTTAATGCTATCTGGTATATTAACCGACTTTACCGCAGTTTCCGATGAAGCCGGttttgtta                                                                                     <  2:374599/141‑7 (MQ=255)
                                                    tgtgTATTTCAATAACTTACTTTGATTAGATGGCTCTACTACAACATTTAAATCATATGTGTTGCCAACTTTTAGTGTTTTAAAACTATCTGGTATATTAACCGACTTTATCTCAGTTTCCGATGAAGCCGGTTGCGTTAc                                                                                    >  2:196562/1‑141 (MQ=255)
                                                      tgtATTTCAATAACGTACTTTGATTAGATGGCTCTACTACAACATTTAAATCATATGTGTTGCCAACTTTTAGTGTTTTAAAACTATCTGGTATATTAACCGACTTTAGCTCAGTTTCCGATGAAGCCGGTTGCGTTACaa                                                                                  <  2:446909/141‑1 (MQ=255)
                                                        tATTTCAATAACTTACTTTGATTAGATGGCTCTACTACAACATTTAAATCATATGTGTTGCCAACTTTTAGTGTTTTAAAACTATCTGGTATATTAACCGACNTNATCTCANTTTCCGATGAAGCCGGTTGCGTTACAAAg                                                                                <  1:183554/141‑1 (MQ=255)
                                                                  acttacttTGATTAGATGGCTCTACTACAACATTTAAATCATATGTGTTGCCAACTTTTAGTGTTTTAAAACTATCTGGTATATTAACCGACTTTATCTCAGTTTCCGATGAAGCCGGTTGCGTTACAAAGTTTCGCCGtt                                                                      <  1:69959/141‑1 (MQ=255)
                                                                   cttacttTGATTAGATGGCTCTACTACAACATTTAAATCATATGTGTTGCCAACTTTTAGTGTTTTAAAACTATCTGGTATATTAACCGACTTTATCTCAGTTTCCGATGAAGCCGGTTGCGTTACAAAGTTTCGCCGTTa                                                                     <  1:332167/141‑1 (MQ=255)
                                                                    ttacttTGATTAGATGGCTCTACTACAACATTTAAATCGTATGTGTCGCCAACTTTAAGTGTTTTAATGCTATCTGGTATATTAACCGACTTTACCGCAGTTTCCGATGAAGCCGGTTTTGTTACa                                                                                   >  2:276736/1‑126 (MQ=255)
                                                                    ttacttTGATTAGATGGCTCTACTACAACATTTAAATCGTATGTGTCGCCAACTTTAAGTGTTTTAATGCTATCTGGTATATTAACCGACTTTACCGCAGTTTCCGATGAAGCCGGTTTTGTTACa                                                                                   <  1:276736/126‑1 (MQ=255)
                                                                            aTTAGATGGCTCTACTACAACATTTAAATCATATGTGTTGCCAACTTTTAGTGTTTTAAAACTATCTGGTATATTAACCGACTTTATCTCAGTTTCCGATGAAGCCGGTTGCGTTACAAAGTTTCGCCGTTATCCTCTGTc                                                            <  2:142310/141‑1 (MQ=255)
                                                                               aGATGGCTCTACTACAACATTTAAATCATATGTGTTGCCAACTTTTAGTGTTTTAAAACTATCTGGTATATTAACCGACTTTATCTCAGTTTCCGATGAAGCCGGTTGCGTTACAAAGTTTCGCCGTTATCCTCTGTCACg                                                         >  1:426386/1‑141 (MQ=255)
                                                                                 aTGGCTCTACTACAACATTTAAATCATATGTGTTGCCAACTTTTAGTGTTTTAAAACTATCTGGTATATTAACCGACTTTATCTCAGTTTCCGATGAAGCCGGTTGCGTTACAAAGTTTCGCCGTTATCCTCTGTCACGtt                                                       >  1:100857/1‑141 (MQ=255)
                                                                                    gCTCTACTACAACATTTAAATCATATGTGTTGCCAACTTTTAGTGTTTTAAAACTATCTGGTATATTAACCGACTTTATCTCAGTTTCCGATGAAGCCGGTTGCGTTACAAAGTTTCGCCGTTATCCTCTGTCACGTTTcc                                                    <  2:314826/141‑1 (MQ=255)
                                                                                     ctctACTACAACATTTAAATCATATGTGTTGCCAACTTTTAGTGTTTTAAAACTATCTGGTATATTAACCGACTTTATCTCAGTTTCCGATGAAGCCGGTTGCGTTACAAAGTTTCGCCGTTATCCTCTGTCACGTTTCCa                                                   >  1:215600/1‑141 (MQ=255)
                                                                                      tctACTACAACATTTAAATCATATGTGTTGCCAACTTTTAGTGTTTTAAAACTATCTGGTATATTAACCGACTTTATCTCAGTTTCCGATGAAGCCGGTTGCGTTACAAAGTTTCGCCGTTATCCTCTGTCACGTTTCCAg                                                  >  2:52104/1‑141 (MQ=255)
                                                                                         acaataacaTTTAAATCATATGTGTTGCCAACTTTTAGTGTTTTAAAACTATCTGGTATATTAACCGACTTTATCTCAGTTTCCGATGAAGCCGGTTGCGTTACAAAGTTTCGCCGTTATCCTCTGTCACGTTTCCAGtat                                               >  2:216551/6‑141 (MQ=255)
                                                                                          ctacAACATTTAAATCATATGTGTTGCCAACTTTTAGTGTTTTAAAACTATCTGGTATATTAACCGACTTTATCTCAGTTTCCGATGAAGCCGGTTGCGTTACAAAGTTTCGCCGTTATCCTCTGTCACGTTTCCAGtata                                              >  1:47036/1‑141 (MQ=255)
                                                                                                       aTCATATGTGTTGCCAACTTTTAGTGTTTTAAAACTATCTGGTATATTAACCGACTTTATCTCAGTTTCCGATGAAGCCGGTTGCGTTACAAAGTTTCGCCGTTATCCTCTGTCACGTTTCCAGTATATTCTTCGCCTaaa                                 <  1:344863/141‑1 (MQ=255)
                                                                                                       aTCATATGTGTTGCCAACTTTTAGTGTTTTAAAACTATCTGGTATATTAACCGACTTTATCTCAGTTTCCGATGAAGCCGGTTGCGTTACAAAGTTTCGCCGTTATCCTCTGTCACGTTTCCAGTATATTCTTCGCCTaaa                                 <  1:344865/141‑1 (MQ=255)
                                                                                                         cATATGTGTTGCCAACTTTTAGTGTTTTAAAACTATCTGGTATATTAACCGACTTTATCTCAGTTTCCGATGAAGCCGGTTGCGTTACAAAGTTTCGCCGTTATCCTCTGTCACGTTTCCAGTATATTCTTCGCCTAAAAt                               <  2:262033/141‑1 (MQ=255)
                                                                                                          atatGTGTTGCCAACTTTTAGTGTTTTAAAACTATCTGGTATATTAACCGACTTTATCTCAGTTTCCGATGAAGCCGGTTGCGTTACAAAGTTTCGCCGTTATCCTCTGTCACGTTTCCAGTATATTCTTCGCCTAAAAtt                              >  1:398261/1‑141 (MQ=255)
                                                                                                          atatGTGTTGCCAACTCTTAGTGTTTTAAAACTATCTGGTATATTAACCGCCTTTATCTCAGTTTCCGATGAAGCCGGTTGCGTTACAAAGTTTCGCCGTTATCCTCTGTCACGTTTCCAGTATATTCTTCGCCTAAAAtt                              >  2:155956/1‑141 (MQ=255)
                                                                                                                  tGCCAACTTTTAGTGTTTTAAAACTATCTGGTATATTAACCGACTTTATCTCAGTTTCCGATGAAGCCGGTTGCGTTACAAAGTTTCGCCGTTATCCTCTGTCACGTTTCCAGTATATTCTTCGCCTAAAATTTTCTTTaa                      >  2:237561/1‑141 (MQ=255)
                                                                                                                             aGTGTTTTAAAACTATCTGGTATATTAACCGACTTTATCTCAGTTTCCGATGAAGCCGGTTGCGTTACAAAGTTTCGCCGTTATCCTCTGTCACGTTTCCAGTATATTCTTCGCCTAAAATTTTCTTTAAGAAAGCCTCtt           >  1:249639/1‑141 (MQ=255)
                                                                                                                             aGTGTTTTAAAACTATCTGGTATATTAACCGACTTTATCTCAGTTTCCGATGAAGCCGGTTGCGTTACAAAGTTTCGCCGTTATCCTCTGTCACGTTTCCAGTATATTCTTCGCCTAAAATTTTCTTTAAGAAAGCCTCtt           <  1:160472/141‑1 (MQ=255)
                                                                                                                                      aaaCTATCTGGTATATTAACCGACTTTATCTCAGTTTCCGATGAAGCCGGTTGCGTTACAAAGTTTCGCCGTTATCCTCTGTCACGTTTCCAGTATATTCTTCGCCTAAAATTTTCTTTAAGCAAGCCTCTTCGCCttttt  >  2:222981/1‑141 (MQ=255)
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CCGCAGTGACTTGACCATCACTATTGATTGATACAATATTCGTTTGATCTGTTGTGTATTTCAATAACTTACTTTGATTAGATGGCTCTACTACAACATTTAAATCATATGTGTTGCCAACTTTTAGTGTTTTAAAACTATCTGGTATATTAACCGACTTTATCTCAGTTTCCGATGAAGCCGGTTGCGTTACAAAGTTTCGCCGTTATCCTCTGTCACGTTTCCAGTATATTCTTCGCCTAAAATTTTCTTTAAGAAAGCCTCTTCGCCTTTTT  >  CP000730/2102667‑2102941

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: ‑