Predicted mutation
evidence seq id position mutation freq annotation gene description
RA CP000730 1,929,797 G→A 43.6% intergenic (‑880/‑288) USA300HOU_1794 ← / → USA300HOU_1796 hypothetical protein/hypothetical protein

Read alignment evidence...
  seq id position ref new freq score (cons/poly) reads annotation genes product
*CP0007301,929,7970GA43.6% 19.9 / 41.2 42intergenic (‑880/‑288)USA300HOU_1794/USA300HOU_1796hypothetical protein/hypothetical protein
Reads supporting (aligned to +/- strand):  ref base G (9/14);  new base A (8/10);  total (18/24)
Fisher's exact test for biased strand distribution p-value = 7.60e-01
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 1.00e+00

TTGTCATAATAAAATCGCCTACTTTCTTAAATTAACAATATCTATTCTCATAGAATTTGTCCAATTAAGTGTAGACGATTCAATCTATCAGCTAGAATCATATAACTTATCAGAAGCAAGTGACTGTGCTTGTATATTTGCCGATGATATAATAGTAGAGTCGCCTATCTCTCAGGCGTCAATTTAGACGCAGAGAGGAGGTGTATAAGGTGATGCTTATTTTCGTTCACATCATAGCACCAGTCATCAGTGGCTGTGCCATTGCGTTTTTTT  >  CP000730/1929658‑1929930
                                                                                                                                           |                                                                                                                                         
ttGTCATAATAAAATCGCCTACTTTCTTAAATTAACAATATCTATTCTCATAGAATTTGTCCAATTAAGTGTAGACGATTCAATCTATCAGCTAGAATCATATAACTTATCAGAAGCAAGTGACTGTGCTTGTATATTTGc                                                                                                                                          <  1:200802/141‑1 (MQ=255)
    cATAATAAAATCGCCTACTTTCTTAAATTAACAATATCTATTCTCATAGAATTTGTCCAATTAAGTGTAGACGATTCAATCTATCAGCTAGAATCATATAACTTATCAGAAGCAAGTGACTGTGCTTGTATATTTGCCgat                                                                                                                                      <  1:167988/141‑1 (MQ=255)
       aataaAATCGCCTACTTTCTTAAATTAACAATATCTATTCTCATAGAATTTGTCCAATTAAGTGTAGACGATTCAATCTATCAGCTAGAATCATATAACTTATCAGAAGCAAGTGACTGTGCTTGTATATTTGCCgatgat                                                                                                                                   <  1:134826/141‑1 (MQ=255)
                         tttAAATTAACAATATCTATTCTCATAGAATTTGTCCAATTAAGTGTAGACGATTCAATCTATCAGCTAGAATCATATAACTTATCAGAAGCAAGTGACTGTGCTTGTATATTTGCCGATGATATAATAGTAGAGTCGCCt                                                                                                                 <  2:79189/140‑1 (MQ=255)
                               ttAACAATATCTATTCTCATAGAATTTGTCCAATTAAGTGTAGACGATTCAATCTATCAGCTAGAATCATATAACTTATCAGAAGCAAGTGACTGTGCTTGTATATTTGCCGATGATATAATAGTAGAGTCGCCTAtctct                                                                                                           >  2:331103/1‑141 (MQ=255)
                                tAACAATATCTATTCTCATAGAATTTGTCCAATTAAGTGTAGACGATTCAATCTATCAGCTAGAATCATATAACTTATCAGAAGCAAGTGACTGTGCTTGTATATTTGCCGATGATATAATGGTAGAGTCGCCTGactctc                                                                                                          >  1:181922/1‑141 (MQ=255)
                                  aCAATCTCTATTCTCATAGAATTTGTCCAATTAAGTGTAGACGATTCAATCTATCAGCTAGAATCATATAACTTATCAGAAGCAAGTGACTGTGCTTGTATATTTGCCGATGATATAATAGTAGAGTCGCCTATCTCTCAg                                                                                                        <  2:304180/141‑1 (MQ=255)
                                   cAATATCTATTCTCATAGAATTTGTCCAATTAAGTGTAGACGATTCAATCTATCAGCTAGAATCATATAACTTATCAGAAGCAAGTGACTGTGCTTGTATATTTGCCGATGATATAATAGTAGAGTCGCCTATCTCTCAgg                                                                                                       >  1:374347/1‑141 (MQ=255)
                                    aaTATCTATTCTCATAGAATTTGTCCAATTAAGTGTAGACGATTCAATCTATCAGCTAGAATCATATAACTTATCAGAAGCAAGTGACTGTGCTTGTATATTTGCCGATGATATAATAGTAGAGTCGCCTATCTCTCAGGc                                                                                                      <  1:323341/141‑1 (MQ=255)
                                                cctataaTTTGTCCAATTAAGTGTAGACGATTCAATCTATCAGCTAGAATCATATAACTTATCAGAAGCAAGTGACTGTGCTTGTATATTTGCCGATGATATAATAGTAGAGTCGCCTATCTCTCAGGCGTctaaattgac                                                                                          <  2:333373/136‑10 (MQ=255)
                                                    gactttGTACAATTAAGTGTAGAGGACTCAATCTATAAGCTAGAATCATATAAGTTATCAGAAGCAAGTGACTGTGCTTGTATATTTTACGATGAGCAAAAATNAGAGTCGACGATCTCTTAGTCTTCAAGTTAAACGCag                                                                                      >  2:626/4‑141 (MQ=255)
                                                    gAATTTGTCCAATTAAGTGTAGACGATTCAATCTATCAGCTAGAATCATATAACTTATCAGAAGCAAGTGACTGAGCTTGTATATTTGCCGATGATATAATAGTAGAGTCGCCTATCTCTCAGGCGTCAATTTAGACGCag                                                                                      >  1:372521/1‑141 (MQ=255)
                                                       tttGTCCAATTAAGTGTAGACGATTCAATCTATCAGCTAGAATCATATAACTTATCAGAAGCAAGTGACTGTGCTTGTATATTTGCCGATGATATAATAGTAGAGTCGCCTATCTCTCAGGCGTCAATTTAGACGCagaga                                                                                   <  1:82290/141‑1 (MQ=255)
                                                                                 aaTCTATCAGCTAGAATCATATAACTTATCCGAAGCAAGTGACTGTGCTTGTATATTTGCCGATGATATAATAGTAGAGTCGCCTATCTCTCAGGCGTCAATTTAGACGCAGAGAGGAGGTGTATAAGGTGATGCTTAttt                                                     <  1:45392/141‑1 (MQ=255)
                                                                                                 tCATATAACTTATCAGAAGCAAGTGACTGTGCTTGTATATTTGCCGATGATATAATAGTAGAGTCGCCTATCTCTCAGGCGTCAATTTAGACGCAGAGAGGAGGTGTATAAGGTGATGCTTATTTTCGTTCACATCATAGc                                     <  1:148237/141‑1 (MQ=255)
                                                                                                 tCATATAACTTATCAGAAGCAAGTGACTGTGCTTGTATATTTGCCGATGATATAATAGTAGAGTCGCCTATCTCTCAGGCGTCAATTTAGACGCAGAGAGGAGGTGTATAAGGTGATGCTTATTTTCGTTCACATCATAGc                                     <  2:119294/141‑1 (MQ=255)
                                                                                                    aataACCTATCAGAAGCAACTGACTGTGCTTGTATATTTGCCGATGATATAATAGTAGAGTCGCCTATCTCTCAGGCGTCAATTTAGACGCAGAGAGGAGGTGTATAAGGTGATGCTTATTTTCGTTCACATCATAGCAcc                                  <  2:371816/140‑1 (MQ=255)
                                                                                                             tCAGAAGCAAGTGACTGTGCTTGTATATTTGCCGATGATATAATAGTAGAGTCGCCTATCTCTCAGGCGTCAATTTAGACGCAGAGAGGAGGTGTATAAGGTGATGCTTATTTTCGTTCACATCATAGCACCAGTCATCAg                         <  1:331103/141‑1 (MQ=255)
                                                                                                             tCAGAAGCAAGTGACTGTGCTTGTATATTTGCCGATGATATAATAGTAGAGGCGCCTATCTCTCAGGCGTCAATTTAGACGCAGAGAGGAGGTGTATAAGGTGATGCTTATTTTCGTTCACATCATAGCACCAGTCATCAg                         >  1:352187/1‑141 (MQ=255)
                                                                                                                gAAGCAAGTGACTGTGCTTGTATATTTGCCGATGATATAATAGTAGAGTCGCCTATCTCTCAGGCGTCAATTTAGACGCAGAGAGGAGGTGTATAAGGTGATGCTTATTTTCGTTCACATCATAGCACCAGTCATCCGTgg                      >  2:228990/1‑141 (MQ=255)
                                                                                                                atcggaagtagatatgCTTGTATATTCACAGATGGTATAATAATAGAGTCGCCTATCTCTCAGGCGTCAATT‑‑GACGAAGAGAGGAGGTGCATTACTTTGCTAATCATTTTCGTTCACATCATAGCACCAGTCATCAGTGGc                     <  1:258370/127‑1 (MQ=255)
                                                                                                                atcggaagtagatatgCTTGTATATTCACAGATGGTATAATAATAGAGTCGCCTATCTCTCAGGCGTCAATT‑‑GACGAAGAGAGGAGGGGCATTACTTTGCTAATCATTTTCGTTCACATCATAGCACCAGTCATCAGTGGc                     >  1:309528/15‑141 (MQ=255)
                                                                                                                 tcggaagtagatatgCTTGTATATTCACAGATGGTATAATAATAGAGTCGCCTATCTCTCAGGCGTCAATT‑‑GACGAAGAGAGGAGGTGCATTACTTTGCTAATCATTTTCGTTCACATCATAGCACCAGTCATCAGTGGCt                    <  2:159485/128‑1 (MQ=255)
                                                                                                                 tcggaagaagatatgCTTGTATATTCACAGATGGTATAATAATATAGTCGCCTATCTCTCAGGCGTGAATT‑‑GATGACGAGAGGAGGGGCAGTACGGTGCTAATCATTTTCGTTCACATCATAGCACCAGTCATCAGTTGcg                    >  2:262988/14‑140 (MQ=255)
                                                                                                                 aaGCAAGTGACTGTGCTTGTATATTTGCCGATGATATAATAGTAGAGTCGCCTATCTCTCAGGCGTCAATTTAGACGCAGAGAGGAGGTGTATAAGGTGATGCTTATTTTCGTTCCCATCATAGCACCAGTCATCAGTGGc                     >  1:286233/1‑141 (MQ=255)
                                                                                                                  agccagcgtcggtgCTTGTCTATTTGCTGATGATATAATAGTAGAGTCGCCTATCTCTCAGGCGGCTATTTAGCCGCAGAGAGGAGGTGTATAATGTGATGCTTATTTTCGTTCACATCATAGCACCAGTCATCAGTGGCt                    <  1:240800/130‑1 (MQ=255)
                                                                                                                    gaagtagttatgCTTGGATATTCACAGATGGTATAATAATAGAGTCGCCTATCTCTCAGGCGCCAATT‑‑GACGAAGAGAGGAGGTGCATTACTTTGCTAATCATTTTCGTTCACATCATAGCACCAGTCATCAGTGGCtgtg                 <  1:4203/131‑1 (MQ=255)
                                                                                                                    gaagtagatatgCTTGTATATTCACAGATGGTATAATAATAGAGTCGCCTATCTCTCAGGCGTCAATT‑‑GACGAAGAGAGGAGGTGCATTACTTTGCTAATCATTTTCGTTCACATCATAGCACCAGTCATCAGTGGCtgtg                 >  2:75261/11‑141 (MQ=255)
                                                                                                                    gaagtagatatgCTTGTATATTCACAGATGGTATAATAATAGAGTCGCCTATCTCTCAGGCGTCAATT‑‑GACGAAGAGAGGAGGTGCATTACTTTGCTAATCATTTTCGTTCACATCATAGCACCAGTCATCAGTGGCtgtg                 <  1:4168/131‑1 (MQ=255)
                                                                                                                    gaagtagatatgCTTGTATATTCACAGATGGTATAATAATAGAGTCGCCAATCTCTCAGGCGTCAATT‑‑GACGAAGAGAGGAGGTGCATTACTTTGCTAATCATTTTCGTTCACATCATAGCACCAGTCATCAGTGGCtgtg                 <  1:161606/131‑1 (MQ=255)
                                                                                                                      agtagatatgCTTGTATATTCACAGATGGTATAATAATAGAGTCGCCTATCTTTCAGGCGTCAATT‑‑GACGAAGAGAGGAGGTGCATTACTTTGCTAATCATTTTCGTTCACATCATAGCACCAGTCATCAGTGGCTGTGct               <  2:320757/133‑2 (MQ=255)
                                                                                                                      agtagatatgCTTGTATATTCACAGATGGTATAATAATAGAGTCGCCTATCTCTCAGGCGTCAATT‑‑GACGAAGAGAGGAGGTGCATTACTTTGCTAATCATTTTCGTTCACATCATAGCACCAGTCATCAGTGGCTGTGct               <  1:36955/133‑2 (MQ=255)
                                                                                                                       gtagatatggttGTATATTCACAGATGGTATAATAATAGAGTCGCCTATCTCTCAGGCGTCAATT‑‑GACGAAGAGAGGAGGTGCATTACTTTGCTAATCATTTTCGTTCACATCATAGCACCAGTCATCAGTGGCTGTGctg              <  2:157222/131‑3 (MQ=255)
                                                                                                                       gtagatatgCTTGTATATTCACAGATGGTATAATAATAGAGTCGCCTATCTCTCAGGCGTCAATT‑‑GACGAAGAGAGGAGGTGGATTACTTGGCTAATCATTTTCGTTCACATTATAGTACCAGTCATCCGTGGCTGTGctg              >  2:325281/8‑139 (MQ=255)
                                                                                                                       gtagatatgCTTGTATATTCACAGATGGTATAATAATAGAGTCGCCTATCTCTCAGGCGTCAATT‑‑GACGAAGAGAGGAGGTGCATTACTTTGCTAATCATTTTCGTTCACATCATAGCACCAGTCATCAGTGGCTGTGctg              >  1:356263/8‑139 (MQ=255)
                                                                                                                       gtagatatgCTTGTATATTCACAGATGGTATAATAATAGAGTCGCCTATCTATCAGGCGTTAATT‑‑GACGAAGAGAGGAGGTGCATTACTTTGCTAATCATTTTCGTTCACATCATAGCACCAGTCATCAGTGGCTGTGctg              >  1:254871/8‑139 (MQ=255)
                                                                                                                        tagagatgCTTGTATATTCACAGATGGTATAATAATAGAGTCGCCTATCTCTCAGGCGTCAATT‑‑GACGAAGAGAGGAGGTGCATTACTTTGCTAATCATTTTCGTTCACATCATAGCACCAGTCATCAGTGGCTGTGctgt             <  1:327937/135‑4 (MQ=255)
                                                                                                                        tGACTGTGCTTGTATATTTGCCGATGATATAATAGTAGAGTCGCCTATCTCTCAGGCGTCAATTTAGACGCAGAGAGGAGGTGTATAAGGTGATGCTTATTTTCGTTCACATCATAGCACCAGTCATCAGTGGCTGTGccc              >  2:113043/1‑140 (MQ=255)
                                                                                                                          gatatgCTTGTATATTCACAGATGGTATAATAATAGAGTCGCCTATCTCTCAGGCGCCCATT‑‑GACGAAGAGAGGAGGTGCATTACTTTGCTAATCATTTTCGTTCACATCATAGCACCAGTCATCAGTGGCGGTGctgttg           >  2:133121/5‑136 (MQ=255)
                                                                                                                               gCTTGTATATTTGCCGATGATATAATAGTAGAGTCGCCTATCTCTCAGGCGTCAATTTAGACGCAGAGAGGAGGTGTATAAGGTGATGCTTATTTTCGTTCACATCATAGCACCAGTAATAAGTGGCTGTGCCATTGCGtt       >  2:170420/1‑141 (MQ=255)
                                                                                                                                   gTATATTCACAGATGGTATAATAATAGCGTCGACTATCTCTCAGGCGTCAATT‑‑GACGAAGAGAGGCGGTGCATTACTTTGCTCATCATTTTCGTTCACATCATAGCACCAGTCATCAGTGGCTGTGCTGTTGCGtattata  <  2:19705/141‑7 (MQ=255)
                                                                                                                                   gTATATTCACAGATGGTATAATAATAGAGTCGCCTATCTCTCAGGCGTCAATT‑‑GACGAAGAGAGGAGGTGCATTACTTTGCTAATCATTTTCGTTCACATCATAGCACCAGTCATCAGTGGCTGTGCTGTTGCGtattatc  >  2:148393/1‑138 (MQ=255)
                                                                                                                                           |                                                                                                                                         
TTGTCATAATAAAATCGCCTACTTTCTTAAATTAACAATATCTATTCTCATAGAATTTGTCCAATTAAGTGTAGACGATTCAATCTATCAGCTAGAATCATATAACTTATCAGAAGCAAGTGACTGTGCTTGTATATTTGCCGATGATATAATAGTAGAGTCGCCTATCTCTCAGGCGTCAATTTAGACGCAGAGAGGAGGTGTATAAGGTGATGCTTATTTTCGTTCACATCATAGCACCAGTCATCAGTGGCTGTGCCATTGCGTTTTTTT  >  CP000730/1929658‑1929930

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 12 ≤ ATCG/ATCG < 13 ≤ ATCG/ATCG < 32 ≤ ATCG/ATCG < 41 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap:     Deleted base: