Predicted mutation
evidence seq id position mutation freq annotation gene description
RA CP000730 1,929,799 C→A 33.9% intergenic (‑882/‑286) USA300HOU_1794 ← / → USA300HOU_1796 hypothetical protein/hypothetical protein

Read alignment evidence...
  seq id position ref new freq score (cons/poly) reads annotation genes product
*CP0007301,929,7990CA33.9% 67.0 / 35.9 41intergenic (‑882/‑286)USA300HOU_1794/USA300HOU_1796hypothetical protein/hypothetical protein
Reads supporting (aligned to +/- strand):  ref base C (15/12);  new base A (9/5);  total (24/17)
Fisher's exact test for biased strand distribution p-value = 7.42e-01
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 1.00e+00

AATAAAATCGCCTACTTTCTTAAATTAACAATATCTATTCTCATAGAATTTGTCCAATTAAGTGTAGACGATTCAATCTATCAGCTAGAATCATATAACTTATCAGAAGCAAGTGACTGTGCTTGTATATTTGCCGATGATATAATAGTAGAGTCGCCTATCTCTCAGGCGTCAATTTAGACGCAGAGAGGAGGTGTATAAGGTGATGCTTATTTTCGTTCACATCATAGCACCAGTCATCAGTGGCTGTGCCATTGCGTTTTTTTC  >  CP000730/1929665‑1929931
                                                                                                                                      |                                                                                                                                       
aataaAATCGCCTACTTTCTTAAATTAACAATATCTATTCTCATAGAATTTGTCCAATTAAGTGTAGACGATTCAATCTATCAGCTAGAATCATATAACTTATCAGAAGCAAGTGACTGTGCTTGTATATTTGCCgatgat                                                                                                                                   <  1:214698/141‑1 (MQ=255)
        cGCCTACTTTCTTAAATTAACAATATCTATTCTCATAGAATTTGTCCAATTAAGTGTAGACGATTCAATCTATCAGCTAGAATCATATAACTTATCAGAAGCAAGTGACTGTGCTTGTATATTTGCCGATGATATAAtagt                                                                                                                           >  1:73530/1‑141 (MQ=255)
          ccTACTTTCTTAAATTAACAATATCTATTCTCATAGAATTTGTCCAATTAAGTGTAGACGATTCAATCTATCAGCTAGAATCATATAACTTATCAGAAGCAAGTGACTGTGCTTGTATATTTGCCGATGATATAAtagtag                                                                                                                         >  2:233101/1‑141 (MQ=255)
          ccTACTTTCTTAAATTAACAATATCTATTCTCATAGAATTTGTCCAATTAAGTGTAGACGATTCAATCTAGCAGCTAGAATCATATAACTTATCAGAAGCAAGTGACTGTGCTTGTATATTTGCCGATGATATAAtagtag                                                                                                                         <  2:250545/141‑1 (MQ=255)
            tACTTTCTTAAATTAACAATATCTATTCTCATAGAATTTGTCCAATTAAGTGTAGACGATTCAATCTATCAGCTAGAATCATATAACTTATCAGAAGCAAGTGACTGTGCTTGTATATTTGCCGATGATATAATAGTagag                                                                                                                       <  2:213237/141‑1 (MQ=255)
                ttCTTAAATTAACAATATCTATTCTCATAGAATTTGTCCAATTAAGTGTAGACGATTCAATCTATCAGCTAGAATCATATAACTTATCAGAAGCAAGTGACTGTGCTTGTATATTTGCCGATGATATAATAGTAGAGTCGc                                                                                                                   >  2:93403/1‑141 (MQ=255)
                 tCTTAAATTAACAATATCTATTCTCATAGAATTTGTCCAATTAAGTGTAGACGATTCAATCTATCAGCTAGAATCATATAACTTATCAGAAGCAAGTGACTGTGCTTGTATATTTGCCGATGATATAATAGTAGAGTCGcc                                                                                                                  <  1:51986/141‑1 (MQ=255)
                         tAACAATATCTATTCTCATAGAATTTGTCCAATTAAGTGTAGACGATTCAATCTATCAGCTAGAATCATATAACTTATCAGAAGCAAGTGACTGTGCTTGTATATTTGCCGATGATATAATAGTAGAGTCGCCTAtctctc                                                                                                          <  1:94069/141‑1 (MQ=255)
                                     ttCTCATAGAATTTGTCCAATTAAGTGTAGACGATTCAATCTATCAGCTAGAATCATATAACTTATCAGAAGCAAGTGACTGTGCTTGTATATTTGCCGATGATATAATAGTAGAGTCACCTATCTCTCAGGCGTCAAttt                                                                                              >  1:75154/1‑141 (MQ=255)
                                     ttCTCACAGAATTTGTCCAATTAAGTGTAGACGATTCAATCTATCAGCTAGAATCATATAACTTATCAGAAGCAAGTGACTGTGCTTGTATATTTGCCGATGATATAATAGTAGAGTCGCCTATCTCTCAGGCGTCAAttt                                                                                              >  2:218400/1‑141 (MQ=255)
                                               aTTTGTCCAATTAAGTGTAGACGATTCAATCTATCAGCTAGAATCATATAACTTATCAGAAGCAAGTGACTGTGCTTGTATATTTGCCGATGATATAATAGTAGAGTCGCCTATCTCTCAGGCGTCAATTTAGACGCagag                                                                                    >  1:145699/1‑141 (MQ=255)
                                                    tCCAATTAAGTGTAGACGATTCAATCTATCAGCTAGAATCATATAACTTATCAGAAGCAAGTGACTGTGCTTGTATATTTGCCGATGATATAATAGTAGAGTCGCCTATCTCTCAGGCGTCAATTTAGACGCAGAgaggag                                                                               <  2:14658/141‑1 (MQ=255)
                                                             gtgtAGACGATTCAATCTATCAGCTAGAATCATATAACTTATCAGAAGCAAGTGACTGTGCTTGTATATTTGCCGATGATATAATAGTAGAGTCGCCTATCTCTCAGGCGTCAATTTAGACGCAGAGAGGAGGTGTATAAg                                                                   >  2:224027/1‑141 (MQ=255)
                                                              tgtAGACGATTCAATCTATCAGCTAGAATCATATAACTTATCAGAAGCAAGTGACTGTGCTTGTATATTTGCCGATGATATAATAGTAGAGTCGCCTATCTCTCAGGCGTCAATTTAGACGCAGAGAGGAGGTGTATAAgg                                                                  <  2:170189/141‑1 (MQ=255)
                                                               gtAGACGATTCAATCTATCAGCTAGAATCATATAACTTATCAGAAGCAAGTGACTGTGCTTGTATATTTGCCGATGATATAATAGTAGAGTCGCCTATCTCTCAGGCGTCAATTTAGACGCAGAGAGGAGGTGTATAAGGt                                                                 >  1:20277/1‑141 (MQ=255)
                                                               gtAGACGATTCAATCTATCAGCTAGAATCATATAACTTATCAGAAGCAAGTGACTGTGCTTGTATATTTGCCGATGATATAATAGTAGAGTCGCCTATCTCTCAGGCGTCAATTTAGACGCAGAGAGGAGGTGTATAAGGt                                                                 >  1:202683/1‑141 (MQ=255)
                                                                       ttCAATCTATCAGCTAGAATCATATAACTTATCAGAAGCAAGTGACTGTGCTTGTATATTTGCCGATGATATAATAGTAGAGTCGCCTATCTCTCAGGCGTCAATTTAGACGCAGAGAGGAGGTGTATAAGGTGATGCTTa                                                         >  1:107334/1‑141 (MQ=255)
                                                                         cAATCTATCAGCTAGAATCATATAACTTATCAGAAGCAAGTGACTGTGCTTGTATATTTGCCGATGATATAATAGTAGAGTCGCCTATCTCTCAGGCGTCAATTTAGACGCAGAGAGGAGGTGTATAAGGTGATGCTTAtt                                                       >  2:97535/1‑141 (MQ=255)
                                                                         cAATCTATCAGCTAGAATCATATAACTTATCAGAAGCAAGTGACTGTGCTTGTATATTTGCCGATGATATAATAGTAGAGTCGCCTATCTCTCAGGCGTCAATTTAGACGCAGAGAGGAGGTGTATAAGGTGATGCTTAtt                                                       <  2:144195/141‑1 (MQ=255)
                                                                              tATCAGCTAGAATCATATAACTTATCAGAAGCAAGTGACTGTGCTTGTATATTTGCCGATGATATAATAGTAGAGTCGCCTATCTCTCAGGCGTCAATTTAGACGCAGAGAGGAGGTGTATAAGGTGATGCTTATTTTCGt                                                  >  1:168007/1‑141 (MQ=255)
                                                                                            atatAACTTATCAGAAGCAAGTGACTGTGCTTGTATATTTGCCGATGATATAATAGTAGAGTCGCCTATCTCTCAGGCGTCAATTTAGACGCAGAGAGGAGGTGTATAAGGTGATGCTTATTTTCGTTCACATCATAGCAc                                    >  2:40339/1‑141 (MQ=255)
                                                                                                        aGAAGCAAGTGACTGTGCTTGTATATTTGCCGATGATATAATAGTAGAGTCGCCTATCTCTCAGGCGTCAATTTAGACGCAGAGAGGAGGTGTATAAGGTGATGCTTATTTTCGTTCACATCATAGCACCAGTCATCAGTg                        >  2:27677/1‑141 (MQ=255)
                                                                                                         atcggaagtagatatgCTTGTATATTCACAGATGGTATAATAATAGAGTCGCCTATCTCTCAGGCGTCAATT‑‑GACGAAGAGAGGAGGTGCATTACTTTGCTAATCATTTTCGTTCACATCATAGCACCAGTCATCAGTGGc                      >  1:36142/15‑141 (MQ=255)
                                                                                                          aaGCAAGTGACTGTGCTTGTATATTTGCCGATGATATAATAGTAGAGTCGCCTATCTCTCAGGCGTCAATTTAGACGCAGAGAGGAGGTGTATAAGGTGATGCTTATTTTCGTTCACATCATAGCACCAGTCATCAGTGGc                      <  2:145699/141‑1 (MQ=255)
                                                                                                           cggaagtagatatgCTTGTATATTCACAGATGGTATAATAATAGAGTCGCCTATCTCTCAGGCGTCAATT‑‑GACGAAGAGAGGAGGTGCATTACTTTGCTAATCATTTTCGTTCACATCATAGCACCAGTCATCAGTGGCtg                    >  1:169751/13‑141 (MQ=255)
                                                                                                            gCAAGTGACTGTGCTTGTATATTTGCCGATGATATAATAGTAGAGTCGCCTATCTCTCAGGCGTCAATTTAGACGCAGAGAGGAGGTGTATAAGGTGATGCTTATTTTCGTTCACATCATAGCACCAGTCATCAATGGcac                    <  1:93403/141‑3 (MQ=255)
                                                                                                              aagtagatatgCTTGTATATTCACAGATGGTATAATAATAGAGTCGCCTATCTCTCAGGCGTCAATT‑‑GACGAAGAGAGGAGGTGCATTACTTTGCTAATCATTTTCGTTCACATCATAGCACCAGTCATCAGTGGCTGTGc                 >  2:201856/10‑141 (MQ=255)
                                                                                                                gtagatatgCTTGTATATTCACAGATGGTATAATAATAGAGTCGCCTATCTCTCAGGCGTCAATT‑‑GACGAAGAGAGGAGGTGCATTACTTTGCTAATCATTTTCGTTCACATCATAGCACCAGTCATCAGTGGCTGTGctg               >  2:37420/8‑139 (MQ=255)
                                                                                                                gtagatatgCTTGTATATTCACAGATGGTATAATAATAGAGTCGCCTATCTCTCAGGCGTCAATT‑‑GACGAAGAGAGGAGGTGCATTACTTTGCTAATCATTTTCGTTCACATCATAGCACCAGTCATCAGTGGCTGTGctg               >  2:31933/8‑139 (MQ=255)
                                                                                                                  gACTGTGCTTGTATATTTGCCGATGATATAATAGTAGAGTCGCCTATCTCTCAGGCGTCAATTTAGACGCAGAGAGGAGGTGTATAAGGTGATGCTTATTTTCGTTCACATCATAGCACAAGTCATCAGTGGCTGTGCCAt              >  1:26346/1‑141 (MQ=255)
                                                                                                                   gatatgCTTGTATATTCACAGATGGTATAATAATAGAGTCGCCTATCTCTCAGGCGTCAATT‑‑GACGAAGAGAGGAGGTGCCTCACCGTTCTAATCATTTTCGTTCACATCATAGCACCAGTCATCAGTGGCTGTGctgttg            >  1:257066/5‑136 (MQ=255)
                                                                                                                   gatatgCTTGTATATTCACAGATGGTATAATAATAGAGTCGCCTATCTCTCAGGCGTCAATT‑‑GACGAAGAGAGGAGGTGCATTTCCTTGCTAATCATTTTCGTTCACATCATAGCACCAGTCATCAGTGGCTGTGctgttg            >  1:256963/5‑136 (MQ=255)
                                                                                                                   gatatgCTTGTATATTCACAGATGGTATAATAATAGAGTCGCCTATCTCTCAGGCGTCAATT‑‑GACGAAGAGAGGAGGTGCATTACTTTGCTAATCATTTTCGTTCACATCATAGCACCAGTCATCAGTGGCTGTGctgttg            >  1:182972/5‑136 (MQ=255)
                                                                                                                   gatatgCTTGTATATTCACAGATGGTATAATAATAGAGTCGCCTATCTCTCAGGCGTCAATT‑‑GACGAAGAGAGGAGGTGCATTACTTTGCTAATCATTTTCGTTCACATCATAGCACCAGTCATCAGTGGCTGTGctgttg            <  2:175738/137‑6 (MQ=255)
                                                                                                                      atgCTTGTATATTCACAGATGGTATAATAATAGAGTCGCCTATCTCTCAGGCGTCAATT‑‑GACGAAGAGAGGAGGTGCATTACTTTGCTAATCATTTTCGTTCACATCATAGCACCAGTCATCAGTGGCTGTGCTGTTGCGt         <  1:261135/140‑1 (MQ=255)
                                                                                                                       tgCTTGTATATTCACAGATGGTATAATAATAGAGTCGCCTATCTCTCAGGCGTCAATT‑‑GACGAAGAGAGGAGGTGCATTACTTTGCTAATCATTTTCGTTCACATCATAGCACCAGTCATCAGTGGCTGTGCTGTTGCGta        <  1:84797/141‑2 (MQ=255)
                                                                                                                       tgCTTGTATATTCACAGATGGTATAATAATAGAGTCGCCTATCTCTCAGGCGTCAATT‑‑GACGAAGAGAGGAGGTGCATTACTTTGCTAATCATTTTCGTTCACATCATAGCACCAGTCATCAGTGGCTGTGCTGTTGCGta        >  1:194815/1‑140 (MQ=255)
                                                                                                                          ttGTATATTCACAGATGGTATAATAATAGAGTCGCCTATCTCTCAGGCGTCAATT‑‑GACGAAGAGAGGAGGTGCATTACTTTGCTAATCATTTTCGTTCACATCATAGCACCAGTCATCAGTGGCTGTGCTGTTGCGtatta     <  1:85715/141‑5 (MQ=255)
                                                                                                                           tGTATATTCACAGATGCCTTAATAATAGAGTCGCCTATCTCTCAGGCGTCAATT‑‑GACGAAGAGAGGAGGTGCATTACTTTGCTAATCATTTTCGTTCACATCATAGCACCAGTCATCAGTGGCTGTGCTGTTGCGtattat    <  1:201988/141‑6 (MQ=255)
                                                                                                                            gTATATTTGCCGATGATATAATAGTAGAGTCGCCTATCTCTCAGGCGTCAATTTAGACGCAGAGAGGAGGTGTATAAGGTGATGCTTATTTTCGTTCACATCATAGCACCAGTCATCAGTGGCNGTGCCATTGCGtttttt    <  1:163016/141‑1 (MQ=255)
                                                                                                                              atatTTGCCGATGATATAATAGTAGAGTCGCCTATCTCTCAGGCGTCAATTTAGACGCAGAGAGGAGGTGTATAAGGTGATGCTTATTTTCGTTCACATCATAGCACCAGTCATCAGTGGCTGTGCCATTGCGTTTTTTTc  <  2:202683/141‑1 (MQ=255)
                                                                                                                                      |                                                                                                                                       
AATAAAATCGCCTACTTTCTTAAATTAACAATATCTATTCTCATAGAATTTGTCCAATTAAGTGTAGACGATTCAATCTATCAGCTAGAATCATATAACTTATCAGAAGCAAGTGACTGTGCTTGTATATTTGCCGATGATATAATAGTAGAGTCGCCTATCTCTCAGGCGTCAATTTAGACGCAGAGAGGAGGTGTATAAGGTGATGCTTATTTTCGTTCACATCATAGCACCAGTCATCAGTGGCTGTGCCATTGCGTTTTTTTC  >  CP000730/1929665‑1929931

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 27 ≤ ATCG/ATCG < 37 ≤ ATCG/ATCG < 41 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap:     Deleted base: