Predicted mutation
evidence seq id position mutation freq annotation gene description
RA CP000730 2,102,781 T→C 9.8% intergenic (‑241/+75) 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
*CP0007302,102,7810TC 9.8% 100.1 / 4.0 41intergenic (‑241/+75)USA300HOU_1961/USA300HOU_1962hypothetical bacteriophage protein/hypothetical bacteriophage protein
Reads supporting (aligned to +/- strand):  ref base T (20/17);  new base C (2/2);  total (22/19)
Fisher's exact test for biased strand distribution p-value = 1.00e+00
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 7.72e-01

TAACCGTGGCAATACCTTGTGCTTCCGCAGTGACTTGACCATCACTATTGATTGATACAATATTCGTTTGATCTGTTGTGTATTTCAATAACTTACTTTGATTAGATGGCTCTACTACAACATTTAAATCATATGTGTTGCCAACTTTTAGTGTTTTAAAACTATCTGGTATATTAACCGACTTTATCTCAGTTTCCGATGAAGCCGGTTGCGTTACAAAGTTTCGCCGTTATCCTCTGTCACGTTTCCAGTATATTCTTCGCCTAAAATTTTCTTTAA  >  CP000730/2102643‑2102921
                                                                                                                                          |                                                                                                                                            
tAACCGTGGCAATACCTTGTGCTTCCGCAGTGACTTGACCATCACTATTGAGTGATATAATATTCGTTGGATCTGTTGTGTATTTCAATAACTTACTTTGATTAGATGGCTCTACTACAACATTTAAATCATATGTGTTGc                                                                                                                                            <  1:223189/141‑1 (MQ=255)
      tGGCAATACCTTGTGCTTCCGCAGTGACTTGACCATCACTATTGATTGATACAATATTCGTTTGATCTGTTGTGTATTTCAATAACTTACTTTGATTAGATGGCTCTACTACAACATTTAAATCATATGTGTTGCCAACtt                                                                                                                                      <  2:234970/141‑1 (MQ=255)
       ggCAATACCTTGTGCTTCCGCAGTGACTTGACCATCACTATTGATTGATACAATATTCGTTTGATCTGTTGTGTATTTCAATAACTTACTTTGATTAGATGGCTCTACTACAACATTTAAATCATATGTGTTGCCAACttt                                                                                                                                     >  2:217819/1‑141 (MQ=255)
                  gtgCTTCCGCAGTGACTTGACCATCACTATTGATTGATACAATATTCGTTTGATCTGTTGTGTATTTCAATAACTTACTTTGATTAGATGGCTCTACTACAACATTTAAATCGTATGTGTTGCCAACTTTTAGTGTTTTaa                                                                                                                          >  1:403949/1‑141 (MQ=255)
                        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                                                                              <  2:235043/141‑1 (MQ=255)
                                                              ttCGTTTGATCTGTTGTGTATTTCAATAACTTACTTTGATTAGATGGCTCTACTACAACATTTAAATCATATGTGTTGCCAACTTTTAGTGTTTTAAAACTATCTGGTATATTAACCGACTTTATCTCAGTTTCCGATGaa                                                                              >  2:330934/1‑141 (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             <  1:344865/141‑1 (MQ=255)
                                                                                                                               aTCATATGTGTTGCCAACTTTTAGTGTTTTAAAACTATCTGGTATATTAACCGACTTTATCTCAGTTTCCGATGAAGCCGGTTGCGTTACAAAGTTTCGCCGTTATCCTCTGTCACGTTTCCAGTATATTCTTCGCCTaaa             <  1:344863/141‑1 (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)
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TAACCGTGGCAATACCTTGTGCTTCCGCAGTGACTTGACCATCACTATTGATTGATACAATATTCGTTTGATCTGTTGTGTATTTCAATAACTTACTTTGATTAGATGGCTCTACTACAACATTTAAATCATATGTGTTGCCAACTTTTAGTGTTTTAAAACTATCTGGTATATTAACCGACTTTATCTCAGTTTCCGATGAAGCCGGTTGCGTTACAAAGTTTCGCCGTTATCCTCTGTCACGTTTCCAGTATATTCTTCGCCTAAAATTTTCTTTAA  >  CP000730/2102643‑2102921

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: ‑