Predicted mutation
evidence seq id position mutation freq annotation gene description
RA CP000730 1,929,797 G→A 39.0% 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
*CP0007301,929,7970GA39.0% 25.7 / 35.8 41intergenic (‑880/‑288)USA300HOU_1794/USA300HOU_1796hypothetical protein/hypothetical protein
Reads supporting (aligned to +/- strand):  ref base G (13/12);  new base A (6/10);  total (19/22)
Fisher's exact test for biased strand distribution p-value = 5.22e-01
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 8.31e-01

GTCATAATAAAATCGCCTACTTTCTTAAATTAACAATATCTATTCTCATAGAATTTGTCCAATTAAGTGTAGACGATTCAATCTATCAGCTAGAATCATATAACTTATCAGAAGCAAGTGACTGTGCTTGTATATTTGCCGATGATATAATAGTAGAGTCGCCTATCTCTCAGGCGTCAATTTAGACGCAGAGAGGAGGTGTATAAGGTGATGCTTATTTTCGTTCACATCATAGCACCAGTCATCAGTGGCTGTGCCATTGCGTTTTTTTCTTAT  >  CP000730/1929660‑1929935
                                                                                                                                         |                                                                                                                                             
gTCATAATAAAATCGCCTACTTTCTTAAATTAACAATATCTATTCTCATAGAATTTGTCCAATTAAGTGTAGACGATTCAATCTATCAGCTAGAATCATATAACTTATCAGAAGCAAGTGACTGTGCTTGTATATTTGCCg                                                                                                                                            <  1:247755/141‑1 (MQ=255)
            tCGCCTACTTTCTTAAATTAACAATATCTATTCTCATAGAATTTGTCCAATTAAGTGTAGACGCTTCAATCTATCAGCTAGAATCATATAACTTATCAGAAGCAAGTGACTGTGCTTGTATATTTGCCGCTGATATAAtag                                                                                                                                >  1:311642/1‑141 (MQ=255)
              gCCTACTTTCTTAAATTAACAATATCTATTCTCATAGAATTTGTCCAATTAAGTGTAGACGATTCAATCTATCAGCTAGAATCATATAACTTATCAGAAGCAAGTGACTGTGCTTGTATATTTGCCGATGATATAAtagta                                                                                                                              <  2:386227/141‑1 (MQ=255)
              gCCTACTTTCTTAAAGTAACAATATCTATTCTCATAGAATTTGTCCAATTAAGTGTAGACGATTCAATCTATCAGCTAGAATCATATAACTTATCAGAAGCAAGTGACTGTGCTTGTGTATTTGCCGATGATATAAtagca                                                                                                                              >  2:295689/1‑139 (MQ=255)
                         tAAATTAACAATATCTATTCTCATAGAATTTGTCCAATTAAGTGTAGACGATTCAATCTATCAGCTAGAATCATATAACTTATCAGAAGCAAGTGACTGTGCTTGTATATTTGCCGATGATATAATAGTAGAGTCGCCTAt                                                                                                                   <  1:46149/141‑1 (MQ=255)
                                   atatCTATTCTCATAGAATTTGTCCAATTAAGTGTAGACGATTCAATCTATCAGCTAGAATCATATAACTTATCAGAAGCAAGTGACTGTGCTTGTATATTTGCCGATGATATAATAGTAGAGTCGCCTATCTCTCAGGCg                                                                                                         >  2:24325/1‑141 (MQ=255)
                                        tATTCTCATAGAATTTGTCCAATTAAGTGTAGACGATTCAATCTATCAGCTAGAATCATATAACTTATCAGAAGCAAGTGACTGTGCTTGTATATTTGCCGATGATATAATAGTAGAGTCGCCTATCTCTCAGGCGTCAAt                                                                                                    <  1:46137/141‑1 (MQ=255)
                                                tAGAATTTGTCCAATTAAGTGTAGACGATTCAATCTATCAGCTAGAATCATATAACTTATCAGAAGCAAGTGACTGTGCTTGTATATTTGCCGATGATATAATAGTAGAGTCGCCTATCTCTCAGGCGTCAATTTAGACGc                                                                                            >  2:233838/1‑141 (MQ=255)
                                                   aaTTTGTCCAATTAAGTGTAGACGATTCAATCTATCAGCTAGAATCATATAACTTATCAGAAGCAAGTGACTGTGCTTGTATATTTGCCGATGATATAATAGTAGAGTCGCCTATCTCTCAGGCGTCAATTTAGACGCaga                                                                                         <  2:55197/141‑1 (MQ=255)
                                                     tttGTCCAATTAAGTGTAGACGATTCAATCTATCAGCTAGAATCATATAACTTATCAGAAGCAAGTGACTGTGCTTGTATATTTGCCGATGATATAATAGTAGAGTCGCCTATCTCTCAGGCGTCAATTTAGACGCagaga                                                                                       <  1:297053/141‑1 (MQ=255)
                                                     tttGTCCAATTAAGTGTAGACGATTCAATCTATCAGCTAGAATCATATAACTTATCAGAAGCAAGTGACTGTGCTTGTATATTTGCCGATGATATAATAGTAGAGTCGCCTATCTCTCAGGCGTCAATTTAGACGCagaga                                                                                       <  2:372714/141‑1 (MQ=255)
                                                        gTCCAATTAAGTGTAGACGATTCAATCTATCAGCTAGAATCATATAACTTATCAGAAGCAAGTGACTGTGCTTGTATATTTGCCGATGATATAATAGTAGAGTCGCCTATCTCTCAAGCGTCAATTTAGACGCAGGgaggg                                                                                    >  1:44754/1‑140 (MQ=255)
                                                         tCCAATTAAGTGTAGACGATTCAATCTATCAGCTAGAATCATATAACTTATCAGAAGCAAGTGACTGTGCTTGTATATTTGCCGATGATATAATAGTAGAGTCGCCTATCTCTCAGGCGTCAATTTAGACGCAGAgaggag                                                                                   >  2:289397/1‑141 (MQ=255)
                                                                           aTTCAATCTATCAGCTAGAATCATATAACTTATCAGAAGCAAGTGACTGTGCTTGTATATTTGCCGATGATATAATAGTAGAGTCGCCTATCTCTCAGGCGTCAATTTAGACGCAGAGAGGAGGTGTATAAGGTGATGCtt                                                              <  2:201988/141‑1 (MQ=255)
                                                                              cAATCTATCAGCTAGAATCATATAACTTATCAGAAGCAAGTGACTGTGCTTGTATATTTGCCGATGATATAATAGTAGAGTCGCCTATCTCTCAGGCGTCAATTTAGACGCAGAGAGGAGGTGTATAAGGTGATGCTTAtt                                                           >  2:93331/1‑141 (MQ=255)
                                                                                aTCTATCAGCTAGAATCACATAACTTATCAGAAGCAAGTGACTGTGCTTGTATATTTGCCGATGATATAATAGTAGAGTCGCCTATCTCTCAGGCGTCAATTTAGACCCAGAGAGGAGGTGTATAAGGGGATGCTTAtttt                                                         >  1:177470/1‑141 (MQ=255)
                                                                                     tCAGCTAGAATCATATGAATTCTGATTATCAAGTGACTGCGCTTGTATATTTGCCGCTGATATAAAAGTAGAGTCGCCTATCTCTCAGGCGTCAATTTAGACGAAGAGAGGAGGTGTATAAGGTGAGGCTTATTTTAGTTc                                                    >  2:85934/1‑141 (MQ=255)
                                                                                     tCAGCTAGAATCATATAACTTATCAGAAGCAAGTGACTGTGCTTGTATATTTGCCGATGATATAATAGTAGAGTCGGCTATCTCTCAGGCGTCAATTTAGACGCAGAGAGGAGGTGTATAAGGTGATGCTTATTTTCGTTc                                                    >  2:288682/1‑141 (MQ=255)
                                                                                            gAATCATATAACTTATCAGAAGCAAGTGACTGTGCTTGTATATTTGCCGATGATATAATAGTAGAGTCGCCTATCTCTCAGGCGTCAATTTAGACGCAGAGAGGAGGTGTATAAGGTGATGCTTATTTTCGTTTAcatcat                                             >  2:323653/1‑141 (MQ=255)
                                                                                                          aTCAGAAGCAAGTGACTGTGCTTGTATATTTGCCGATGATATAATAGTAGAGTCGCCTATCTCTCAGGCGTCAATTTAGACGCAGAGAGGAGGTGTATAAGGTGATGCTTATTTTCGTTCACATCATAGCACCAGtcatca                               >  2:51878/1‑141 (MQ=255)
                                                                                                           tcggaaggagggggcTGTGCTTGGATATTTGCCGATGATATAATAGTAGAGTCGCCTATCTCTCAGGCGTCAATTGAGACGCAGAGAGGAGGTGTATAAGGTGATGCTTATTTTCGTTCACATCATAGCACCAGTCATCAg                              <  2:382244/127‑1 (MQ=255)
                                                                                                           tCAGAAGCAAGTGACTGTGCTTGTATATTTGCCGATGATATAATAGTAGAGTCGCCTATCTCTCAGGCGTCAATTTAGACGCAGAGAGGAGGTGTATAAGGTGATGCTTATTTTCGTTCACATCATAGCACCAGTCATCAg                              <  2:330569/141‑1 (MQ=255)
                                                                                                              atcggaagtagatatgCTTGTATATTCACAGATGGTATAATAATAGAGTCGCCTATCTCTCAGGCGTCAATT‑‑GACGAAGAGAGGAGGTGCATTACTTTGCTAATCATTTTCGTTCACATCATAGCACCAGTCATCAGTGGc                          <  2:61360/127‑1 (MQ=255)
                                                                                                               tcggaagtagatatgCTTGTATATTCACAGATGGTATAATAATAGAGTCGCCTATCTCTCAGGCGTCAATT‑‑GACGAAGAGAGGAGGTGCATTACTTTGCTAATCATTTTCGTTAAAATCATAGACCCAGTCATCAGTGGCt                         >  1:365510/14‑141 (MQ=255)
                                                                                                                cggaagtagatatgCTTGTATATTCACAGATGGTATAATAATAGAGTCGCCTATCTCTCAGGCGTCAATT‑‑GACGAAGAGAGGAGGTGCATTACTTTGCTAATCATTTTCGTTCACATCATAGCACCAGTCATCAGTGGCtg                        <  1:261897/129‑1 (MQ=255)
                                                                                                                  gaagtagatatgCCTGTATATTCACAGATGCTACCATAACAGCGTCGCCTATCTCTCAGGCGTCAATT‑‑GACGAAGAGAGGAGGTGCATTACTTTGCTAATCATTTTCGTTCACATCATAGCACCAGTCATCAGTGGCtgtg                      <  1:9700/131‑1 (MQ=255)
                                                                                                                    agtagatatgCTTGTATATTCACAGATGGTATAATAATAGAGTCGCCTATCTCTCAGGCGTCAATT‑‑GACGAAGAGAGGAGGTGCATTACTTTGCTAATCATTTTCGTTCACATCATAGCACCAGTCATCAGTGGCTGTGct                    >  1:300757/9‑140 (MQ=255)
                                                                                                                     gtagatatgCTTGTATATTCACAGATGGTATAATAATAGAGTCGCCTATCTCTCAGGCGTCAATT‑‑GACGAAGAGAGGAGGTGCATTACTTTGCTAATCATTTTCGTTCACATCATAGCACCAGTCATCAGTGGCTGTGctg                   <  1:341053/134‑3 (MQ=255)
                                                                                                                     gtagatatgCTTGTATATTCACAGATGGTATAATAATAGAGTCGCCGATCTCTCAGGCGTCAATTAACGAAGAGAGGAGCTTCATTACTTTGCTAATCATTTTCGTTCCCCTCATCGCACCAGTCATCAGTGGCTGTGctg                   >  2:76933/8‑139 (MQ=255)
                                                                                                                     gTGACTGTGCTTGTATATTTGCCGATGATATAATAGTAGAGTCGCCTATCTCTCAGGCGTCAATTTAGACGCAGAGAGGAGGTGTATAAGGTGATGCTTATTTTCGTTCACATCATAGCACCAGTCATCAGTGGCTGTGcc                    >  2:211986/1‑141 (MQ=255)
                                                                                                                      tagatatgCTTGTATATTCACAGATGGTATAATAATAGAGTCGCCTATCTCTCAGGCGTCAATT‑‑GACGAAGAGAGGAGGTGCATTACTTTGCTAATCATTTTCGTTCACATCATAGCACCAGTCATCAGTGGCTGTGctgt                  <  1:264032/135‑4 (MQ=255)
                                                                                                                       agatatgCTTGTATATTCACAGATGGTATAATAATAGAGGCGCCTATCTCTCAGGCGTCAATT‑‑GACGAAGAGAGGAGGTGCATTACTTTGCTAATCATTTTAGTTCACATAATAGCACCAGTCATCAGTGCATGTGctgtt                 >  2:248424/6‑137 (MQ=255)
                                                                                                                        gatatgCTTGTATATTCACAGATGGTATAATAATAGAGTCGCCTATCTCTCAGGCGTCAATT‑‑GACGAAGAGAGGAGGTGCATTACTTTGCTAATCATTTTCGTTCACATCATAGCACCAGTCATCAGTGGCTGTGctgttg                <  1:124587/137‑6 (MQ=255)
                                                                                                                        gatatgCTTGTATATTCACAGATGGTATAATAATAGAGTCGCCTATCTCTCAGGCGTCAATT‑‑GACGAAGAGAGGAGGTGCATTACTTTGCTAATCATTTTCGTTCACATCATAGCACCAGTCATCAGTGGCTGTGctgttg                <  1:307878/137‑6 (MQ=255)
                                                                                                                          tatgCTTGTATATTCACAGATGGTATAATAATAGAGTCGCCTATCTCTCAGGCGTCAATT‑‑GACGAAGAGAGGAGGTGCATTACTTTGCTAATCATTTTCGTTCACATCATAGCACCAGTCATCAGTGGCTGTGctgttgcg              <  2:73250/139‑8 (MQ=255)
                                                                                                                          tatgCTTGTATATTCACAGATGGTATAATAATAGAGTCGCCTATCTCTCAGGCGTCAATT‑‑GACGAAGAGAGGAGGTGCATTACTTTGCTAATCATTTTCGTTCACATCATAGCACCAGTCATCAGTGGCTGTGCTGTTGCg              >  2:339333/3‑141 (MQ=255)
                                                                                                                           atgCTTGTATATTCACAGATGGTATAATAATAGAGTCGCCTATCTCTCAGGCGTCAATT‑‑GACGAAGAGAGGAGGTGCATTACTTTGCTAATCATTTTCGTTCACATCATAGCACCAGTCATCAGTGGCTGTGCTGTTGCGt             >  1:23854/2‑141 (MQ=255)
                                                                                                                                tGTATATTCACAGATGGTATAATAATAGAGTCGCCTATCTCTCAGGCGTCAATT‑‑GACGAAGAGAGGAGGTGCATTACTTTGCTAATCATTTTCGTTCACATCATAGCACCAGTCATCAGTGGCTGTGCTGTTGCGtattat        <  1:303477/141‑6 (MQ=255)
                                                                                                                                  tataTTCACAGATGGTATAATAATAGAGTCGCCTATCTCTCAGGCGTCAATT‑‑GACGAAGAGAGGAGGTGCATTACTTTGCTAATCATTTTCGTTCACATCATAGCACCAGTCGTCAGTGGCTGTGCTGTTGCGtattatac      <  2:67438/141‑8 (MQ=255)
                                                                                                                                     atTTGCCGATGATATAATAGTAGAGTCGCCTATCTCTCAGGCGTCAATTTAGACGCAGAGAGGAGGTGTATAAGGTGATGCTTATTTTCGTTCACATCATAGCACCAGTCATCAGTGGCTGTGCCATTGCTTTTTTTTCtt    <  1:288682/141‑1 (MQ=255)
                                                                                                                                       ttGCCGATGATATAATAGTAGAGTCGCCTATCTCTCAGGCGTCAATTTAGACGCAGAGAGGAGGTGTATAAGGTGATGCTTATTTTCGTTCACATCATAGCACCAGTCATCAGTGGCTGTGCCATTGCGTTTTTTTCTTAt  <  2:18332/141‑1 (MQ=255)
                                                                                                                                         |                                                                                                                                             
GTCATAATAAAATCGCCTACTTTCTTAAATTAACAATATCTATTCTCATAGAATTTGTCCAATTAAGTGTAGACGATTCAATCTATCAGCTAGAATCATATAACTTATCAGAAGCAAGTGACTGTGCTTGTATATTTGCCGATGATATAATAGTAGAGTCGCCTATCTCTCAGGCGTCAATTTAGACGCAGAGAGGAGGTGTATAAGGTGATGCTTATTTTCGTTCACATCATAGCACCAGTCATCAGTGGCTGTGCCATTGCGTTTTTTTCTTAT  >  CP000730/1929660‑1929935

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 12 ≤ ATCG/ATCG < 22 ≤ ATCG/ATCG < 37 ≤ ATCG/ATCG < 41 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap:     Deleted base: