Predicted mutation
evidence seq id position mutation freq annotation gene description
RA CP000730 2,102,791 T→A 10.3% intergenic (‑251/+65) 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
*CP0007302,102,7910TA10.3% 109.7 / 5.4 39intergenic (‑251/+65)USA300HOU_1961/USA300HOU_1962hypothetical bacteriophage protein/hypothetical bacteriophage protein
Reads supporting (aligned to +/- strand):  ref base T (20/15);  new base A (2/2);  total (22/17)
Fisher's exact test for biased strand distribution p-value = 1.00e+00
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 6.22e-01

GTGCTTCCGCAGTGACTTGACCATCACTATTGATTGATACAATATTCGTTTGATCTGTTGTGTATTTCAATAACTTACTTTGATTAGATGGCTCTACTACAACATTTAAATCATATGTGTTGCCAACTTTTAGTGTTTTAAAACTATCTGGTATATTAACCGACTTTATCTCAGTTTCCGATGAAGCCGGTTGCGTTACAAAGTTTCGCCGTTATCCTCTGTCACGTTTCCAGTATATTCTTCGCCTAAAATTTTCTTTAA  >  CP000730/2102661‑2102921
                                                                                                                                  |                                                                                                                                  
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)
                                                                                                                                  |                                                                                                                                  
GTGCTTCCGCAGTGACTTGACCATCACTATTGATTGATACAATATTCGTTTGATCTGTTGTGTATTTCAATAACTTACTTTGATTAGATGGCTCTACTACAACATTTAAATCATATGTGTTGCCAACTTTTAGTGTTTTAAAACTATCTGGTATATTAACCGACTTTATCTCAGTTTCCGATGAAGCCGGTTGCGTTACAAAGTTTCGCCGTTATCCTCTGTCACGTTTCCAGTATATTCTTCGCCTAAAATTTTCTTTAA  >  CP000730/2102661‑2102921

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: ‑