Predicted mutation
evidence seq id position mutation freq annotation gene description
RA CP000730 2,102,773 A→G 11.8% intergenic (‑233/+83) 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
*CP0007302,102,7730AG11.8% 101.2 / 4.7 42intergenic (‑233/+83)USA300HOU_1961/USA300HOU_1962hypothetical bacteriophage protein/hypothetical bacteriophage protein
Reads supporting (aligned to +/- strand):  ref base A (20/17);  new base G (3/2);  total (23/19)
Fisher's exact test for biased strand distribution p-value = 1.00e+00
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 9.75e-01

CTTTAACCGTGGCAATACCTTGTGCTTCCGCAGTGACTTGACCATCACTATTGATTGATACAATATTCGTTTGATCTGTTGTGTATTTCAATAACTTACTTTGATTAGATGGCTCTACTACAACATTTAAATCATATGTGTTGCCAACTTTTAGTGTTTTAAAACTATCTGGTATATTAACCGACTTTATCTCAGTTTCCGATGAAGCCGGTTGCGTTACAAAGTTTCGCCGTTATCCTCTGTCACGTTTCCAGTATATTCTTCGCCTAAAATT  >  CP000730/2102640‑2102913
                                                                                                                                     |                                                                                                                                            
cTTTAACCGTGGCAATACCTTGTGCTTCCGCAGTGACTTGACCATCACTATTGATTGATACAATATTCGTTTGATCTGTTGTGTATTTCAATAACTTACTTTGATTAGATGGCTCTACTACAACATTTAAATCATATgtgt                                                                                                                                       >  1:409099/1‑141 (MQ=255)
cTTTAACCGTGGCAATACCTTGTGCTTCCGCAGTGACTTGACCATCACTATTGATTGATACAATATTCGTTTGATCTGTTGTGTATTTCAATAACTTACTTTGATTAGATGGCTCTACTACAACATTTAAATCATATgtgt                                                                                                                                       >  2:344863/1‑141 (MQ=255)
cTTTAACCGTGGCAATACCTTGTGCTTCCGCAGTGACTTGACCATCACTATTGATTGATACAATATTCGTTTGATCTGTTGTGTATTTCAATAACTTACTTTGATTAGATGGCTCTACTACAACATTTAAATCATATgtgt                                                                                                                                       >  2:344865/1‑141 (MQ=255)
   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                                                                                           <  1:67261/141‑1 (MQ=255)
                                            tCACTATTGATTGATACAATATTCGTTTGATCTGTTGTGTATTTCAATAACTTACTTTGATTAGATGGCTCTACTACAACATTTAAATCATATGTGTTGCCAACTTTTAGTGTTTTAAAACTATCTGGTATATTAACCGAc                                                                                           <  1:84078/141‑1 (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     <  1:344865/141‑1 (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)
                                                                                                                                     |                                                                                                                                            
CTTTAACCGTGGCAATACCTTGTGCTTCCGCAGTGACTTGACCATCACTATTGATTGATACAATATTCGTTTGATCTGTTGTGTATTTCAATAACTTACTTTGATTAGATGGCTCTACTACAACATTTAAATCATATGTGTTGCCAACTTTTAGTGTTTTAAAACTATCTGGTATATTAACCGACTTTATCTCAGTTTCCGATGAAGCCGGTTGCGTTACAAAGTTTCGCCGTTATCCTCTGTCACGTTTCCAGTATATTCTTCGCCTAAAATT  >  CP000730/2102640‑2102913

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: ‑