Predicted mutation
evidence seq id position mutation annotation gene description
RA NC_000913_3_KO_pgi 3,440,135 A→C S299A (TCT→GCT)  rpoA ← RNA polymerase, alpha subunit

Read alignment evidence...
  seq id position ref new freq score (cons/poly) reads annotation genes product
*NC_000913_3_KO_pgi3,440,1350AC97.7% 142.9 / ‑5.2 44S299A (TCT→GCT) rpoARNA polymerase, alpha subunit
Reads supporting (aligned to +/- strand):  ref base A (1/0);  new base C (22/21);  total (23/21)
Fisher's exact test for biased strand distribution p-value = 1.00e+00
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 9.50e-01

GATGGCGCATGACCTTATCCTTCTCAGTAAAACCTTAACCTGTGATCCGGTTACTCGTCAGCGATGCTTGCCGGTGGCCAGTTTTCCAGGCGCATGCCCAGAGACAGTCCACGGGAAGCCAGCACGTCTTTAATCTCAGTAAGAGATTTTTTACCAAGGTTAGGCGTTTTAAGGAGCTCAACCTCGGTACGCTGTACCAGATCACCGATATAGTGGATAGCTTCTGCTTTAAGGCAGTTAGCAGAGCGGACAGTCAATTCCAGATCGTCAACAGGGCGCAGCAGGATC  >  NC_000913_3_KO_pgi/3439990‑3440277
                                                                                                                                                 |                                                                                                                                              
gATGGCGCATGACCTTATCCTTCTCAGTAAAACCTTAACCTGTGATCCGGTTACTCGTCAGCGATGCTTGCCGGTGGCCAGTTTTCCAGGCGCATGCCCAGAGACAGTCCACGGGAAGCCAGCACGTCTTTAATCTCAGTGAGAGCttt                                                                                                                                             >  1:221974/1‑149 (MQ=255)
    gcgaaggACCTTTTCCTTCTCAGTAAAACCTTAACCTGTGATCCGGTTACTCGTCAGCGATGCTTGCCGGTGGCCAGTTTTCCAGGCGCATGCCCAGAGACAGTCCACGGGAAGCCAGCACGTCTTTAATCTCAGTAAGAGCTGTTTTa                                                                                                                                         <  2:182760/143‑1 (MQ=255)
       cATGACCTTATCCTTCTCAGTAAAACCTTAACCTGTGATCCGGTTACTCGTCAGCGATGCTTGCCGGTGGCCAGTTTTCCAGGCGCATGCCCAGAGACAGTCCACGGGAAGCCAGCACGTCTTTAATCTCAGTAAGAGCTTTTTTACCa                                                                                                                                      >  1:482914/1‑149 (MQ=255)
          gACCTTATCCTTCTCAGTAAAACCTTAACCTGTGATCCGGTTACTCGTCACCGATGCTTGCCGGTGGCCGGTTTTCCAGGCGCATGCCCAGAGACAGTCAACGGGCAGCCCGCGCGTCTTTAATCTCAGTCATAGCTTTTTTATCacag                                                                                                                                   >  2:100980/1‑146 (MQ=255)
            ccTTATCCTTCTCAGTAAAACCTTAACCTGTGATCCGGTTACTCGTCAGCGATGCTTGCCGGTGGCCAGTTTTCCAGGCGCATGCCCAGAGACAGTCCACGGGAAGCCAGCACGTCTTTAATCTCAGTAAGAGCTTTTTTACCAAGGtt                                                                                                                                 <  1:79476/149‑1 (MQ=255)
             cTTATCCTTCTCAGTAAAACCTTAACCTGTGATCCGGTTACTCGTCAGCGATGCTTGCCGGTGGCCAGTTTTCCAGGCGCATGCCCAGAGACAGTCCACGGGAAGCCAGCACGTCTTTAATCTCAGTAAGAGCTTTTTTACCAAGGTTa                                                                                                                                >  1:4550/1‑149 (MQ=255)
              ttATCCTTCTCAGTAAAACCTTAACCTGTGATCCGGTTACTCGTCAGCGATGCTTGCCGGTGGCCAGTTTTCCAGGCGCATGCCCAGAGACAGTCCACGGGAAGCCAGCACGTCTTTAATCTCAGTAAGAGCTTTTTTACCAAGGTTAg                                                                                                                               <  1:203699/149‑1 (MQ=255)
                aTCCTTCTCAGTAAAACCTTAACCTGTGATCCGGTTACTCGTCAGCGATGCTTGCCGGTGGCCAGTTTTCCAGGCGCATGCCCAGAGACAGTCCACGGGAAGCCAGCACGTCTTTAATCTCAGTAAGAGCTTTTTTACCAAGGTTAGGc                                                                                                                             >  2:299953/1‑149 (MQ=255)
                    ttCTCAGTAAAACCTTAACCTGTGATCCGGTTACTCGTCAGCGATGCTTGCCGGTGGCCAGTTTTCCAGGCGCATGCCCAGAGACAGTCCACGGGAAGCCAGCACGTCTTTAATCTCAGTACGAGCTTTTTTACCAAGGTTAGGCGttt                                                                                                                         >  1:8999/1‑149 (MQ=255)
                     tctcAGTAAAACCTTAACCTGTGATCCGGTTACTCGTCAGCGATGCTTGCCGGTGGCCAGTTTTCCAGGCGCATGCCCAGAGACAGTCCACGGGAAGCCAGCACGTCTTTAATCTCAGTAAGAGCTTTTTTACCAAGGTTAGGCGtttt                                                                                                                        <  1:299953/149‑1 (MQ=255)
                       ccAGTAAAACCTTAACCGGTTACCTGGTTACTCGTCAGCGATGCTTGCCGGTGGCCTGTTTTCCAGGCGCATGCCCAGAGACAGTCCACGGGAAGCCAGCACGTCTTTAATCTCAGTAAGAGCTTTTTTACCAAGGTTAGGCGTTTTaa                                                                                                                      <  2:81180/148‑1 (MQ=255)
                         aGTAAAACCTTAACCTGTGATCCGGTTACTCGTCAGCGATGCTTGCCGGGGTCCAGTTTTCCAGACGCCTACCAAGAGACAGTCCACGGGAAGCCAGCACGTCTTTAATCTCAGGAAGAGCTTTTTTACCACGGTTAGGAGGTTTAAga                                                                                                                    >  2:8139/1‑148 (MQ=255)
                         aGTAAAACCTTAACCTGTGATCCGGTTACTCGTCAGCGATGCTTGCCGGGGGCCAGTTTTCCAGGCGCATGACAAGAGACAGTCCACGGGAAGCCAGCACGTCTTTACACTGAGTCACAGCTTTTTTCCCAAGATTAGGCGTGTTAAgc                                                                                                                    >  2:8149/1‑148 (MQ=255)
                            aaaaCCTTAACCTGTGATCCGGTTACTCGTCAGCGATGCTTGCCGGTGGCCAGTTTTCCAGGCGCATGCCCAGAGACAGTCCACGGGAAGCCAGCACGTCTTTAATCTCAGTAAGAGCTTTTTTACCAAGGTTAGGCGTTTTAAGGAGc                                                                                                                 <  2:311876/149‑1 (MQ=255)
                                ccTTAACCTGTGATCCGGTTACTCGTCAGCGATGCTTGCCGGTGGCCAGTTTTCCAGGCGCATGCCCAGAGACAGTCCACGGGAAGCCAGCACGTCTTTAATCTCAGTAAGAGCTTTTTTACCAAGGTTAGGCGTTTTAAGGAGCTCaa                                                                                                             >  1:443699/1‑149 (MQ=255)
                                 cTTAACCTGTGATCCGGTTACTCGTCAGCGATGCTTGCCGGTGGCCAGTTTTCCAGGCGCATGCCCAGAGACAGTCCACGGGAAGCCAGCACGTCTTTAATCTCAGTAAGAGCTTTTTTACCAAGGTTAGGCGTTTTAAGGAGCTCAAc                                                                                                            >  1:76614/1‑149 (MQ=255)
                                             tCCGGTTACTCGTCAGCGATGCTTGCCGGTGGCCAGTTTTCCAGGCGCATGCCCAGAGACAGTCCACGGGAAGCCAGCACGTCTTTAATCTCAGTAAGAGCTTTTTTACCAAGGTTAGGCGTTTTAAGGAGCTCAACCTCGGTACGCTg                                                                                                >  1:215006/1‑149 (MQ=255)
                                               cgtttACTCGTCAGCGATGCTTGCCGGTGGCCAGTTTTCCAGGCGCATGCCCAGAGACAGTCCACGGGAAGCCAGCACGTCTTTAATCTCAGTAAGAGCTTTTTTACCAAGGTTAGGCGTTTTAAGGAGCTCAACCTCGGTACGCTGTa                                                                                              <  2:336453/146‑1 (MQ=255)
                                                ggTTACTCGTCAGCGATGCTTGCCGGTGGCCAGTTTTCCAGGCGCATGCCCAGAGACAGTCCACGGGAAGCCAGCACGTCTTTAATCTCAGTAAGAGCTTTTTTACCAAGGTTAGGCGTTTTAAGGAGCTCAACCTCGGTACGCTGTAc                                                                                             <  2:518952/149‑1 (MQ=255)
                                                 gTTACTCGTCAGCGATGCTTGCCGGTGGCCAGTTTTCCAGGCGCATGCCCAGAGACAGTGCACGGGAAGCCAGCACGTCTTTAATCTCAGTAAGAGCTTTTTTACCAAGGTTAGGCGTTTTAAGGAGCACAACCTCCGTACACTGTAcc                                                                                            >  2:290525/1‑149 (MQ=255)
                                                      tCGTCAGCGATGCTTGCCGGTGGCCAGTTTTCCAGGCGCATGCCCAGAGACAGTCCACGGGAAGCCAGCACGTCTTTAATCTCAGTAAGAGCTTTTTTACCAAGGTTAGGCGTTTTAAGGAGCTCAACCTCGGTACGCTGTACCAGATc                                                                                       >  1:550615/1‑149 (MQ=255)
                                                       cGTCAGCGAAGCTTGCCGGTGGCCAGTTTTCCAGGCGCATGCCCAGAGACAGTCCACGGGAAGCCAGCACGTCTTTAATCTCAGTAAGAGCTTTTTTACCAAGGTTAGGCGTTTTAAGGAGCTCAACCTCGGTACGCTGTACCAGAtta                                                                                      <  2:64617/149‑3 (MQ=255)
                                                         tCAGCGATGCTTGCCGGTGGCCAGTTTTCCAGGCGCATGCCCAGAGACAGTCCACGGGAAGCCAGCACGTCTTTAATCTCAGTAAGAGCTTTTTTACCAAGGTTAGGCGTTTTAAGGAGCTCAACCTCGGTACGCTGTACCAGATCAcc                                                                                    <  2:665868/149‑1 (MQ=255)
                                                                ggcgtggcGGTGGCCAGTTTTCCAGGCGCATGCCCAGAGACAGTCCACGGGAAGCCAGCACGTCTTTAATCTCAGTAAGAGCTTTTTTACCAAGGTTAGGCGTTTTAAGGAGCTCAACCTCGGTACGCTGTACCAGATCACCGATATAg                                                                             <  2:443699/142‑1 (MQ=255)
                                                                    tGCCGGTGGCCAGTTTTCCAGGCGCATGCCCAGAGACAGTCCACGGGAAGCCAGCACGTCTTTAATCTCAGTAAGAGCTTTTTTACCAAGGTTAGGCGTTTTAAGGAGCTCAACCTCGGTACGCTGTACCAGATCACCGATATAGTGGa                                                                         <  2:76614/149‑1 (MQ=255)
                                                                             ccAGGTGTCAAGGTGCATGCCCAGAGATAGTCCACGGGAAGCCAGCACGTCTTTAATCTCAGTAAGAGCTTTTTTACCAAGGTTAGGCGTCTTAGGGGGCGCAACCTCGGTACGCTGTACCAGATCACCGATATAGTGGATAGCTTCTg                                                                <  2:352506/149‑1 (MQ=255)
                                                                              cAGTTTTCCAGGCGCATGCCCAGAGACAGTCCACGGGAAGCCAGCACGTCTTTAATCTCAGTAAGAGCTTTTTTACCAAGGTTAGGCGTTTTAAGGAGCTCAACCTCGGTACGCTGTACCAGATCACCGATATAGTGGATAGCTTCTGc                                                               >  2:220200/1‑149 (MQ=255)
                                                                               aGTTTTCCAGGCGCATGCCCAGAGACAGTCCACGGGAAGCCAGCACGTCTTTAATCTCAGTAAGAGCTTTTTTACCAAGGTTAGGCGTTTTAAGGAGCTCAACCTCGGTACGCTGTACCAGATCACCGATATAGTGGATAGCTTCTGCt                                                              >  1:336887/1‑149 (MQ=255)
                                                                                gTTTTCCAGGCGCATGACCAGAGACAGTCCACGGGAAGCCAGCACGTCTTTAATCTCAGTAAGAGATTTTTTACCAAGGTTAGGCGTTTTAAGGAGCTCAACCTCGGTACGCTGTACCAGATCACCGATATAGTGGATAGCTTCTGCtt                                                             >  1:131365/1‑149 (MQ=255)
                                                                                  tttCCAGGCGCATGCCCAGAGACAGTCCACGGGAAGCCAGCACGGCTTTAATCTCAGTAAGAGCTTTTTTACCAAGGTTAGGCGTTTTAAGGAGCTCAACCTCGGTACGCTGTACCAGATCACCGATATAGTGGATAGCTTCTGCTTTa                                                           <  1:377700/149‑1 (MQ=255)
                                                                                   ttCCAGGCGCATGCCCAGAGACAGTCCACGGGAAGCCAGCACGTCTTTAATCTCAGTAAGAGCTTTTTTACCAAGGTTAGGCGTTTTAAGGAGCTCAACCTCGGTACGCTGTACCAGATCACCGATATAGTGGATAGCTTCTGCTTTaa                                                          <  2:550615/149‑1 (MQ=255)
                                                                                       aGGCTCATGCCCAGAGACAGTCCACGGGAAGCCAGCACGTCTTTAATCTCAGTAAGAGCTTTTTTACCAAGGTTAGGCGTTTTAAGGAGCTCAACCTCGGTACGCTGTACCAGATCACGTAAATCGGCGATAGCTTATGCTTTAACGCa                                                      >  2:26142/1‑149 (MQ=255)
                                                                                                           tCCACGGGAAGACAGCGCGTCTTTAATCTGAGTAAGAGCTTTTTTGCCAAGGTTAGGCGTTTCAAGGAGCTCAACCTCGGTAGGCAGTACCAGATCACCGGTATAGTGGATAGCTTCTGCTTTAAGGCAGTTAGCAGAGCGGACCGTCa                                  >  2:622612/1‑149 (MQ=255)
                                                                                                                   aaGCCAGCACGTCTTTAATCTCAGTAAGAGCTTTTTTACCAAGGTTAGGCGTTTTAAGGAGCTCAACCTCGGTACGCTGTACCAGATCACCGATATAGTGGATAGCTTCTGCTTTAAGGCAGTTAGCAGAGCGGACAGTCAATTCCAGa                          >  1:499933/1‑149 (MQ=255)
                                                                                                                     gCCAGCGCGTCTTTAATCTCAGTAATAGCTTTTTTACCAAGGTTAGGCGTTTTAAGGAGCTCAATCTCGGTACGCTGTACCTCATCACCGATATAGTGGATATCTTCTGCTTTAAGGCAGTTAGCAGAGCGGACAGTCAATTCCAGATc                        <  1:622612/149‑1 (MQ=255)
                                                                                                                       cAGCACGTCTTTAATCTCAGTAAGAGCTTTTTTACCAAGGTTAGGCGTTTTAAGGAGCTCAACCTCGGTACGCTGTACCAGATCACCGATATGGTGGGTATCTTCTGCTTTAAGGCAGTTAGCAGAGCGAACAGTCAATTCCCGATCGt                      >  1:160696/1‑149 (MQ=255)
                                                                                                                        aGCACGTCTTTAATCTCAGTAAGAGCTTTTTTACCAAGGTTAGGCGTTTTAAGGAGCTCAACCTCGGTACGCTGTACCAGATCACCGATATAGTGGATAGCTTCTGCTTTAAGGCAGTTAGCAGAGCGGACAGTCAATTCCAGATCGTc                     <  2:336887/149‑1 (MQ=255)
                                                                                                                            cGTCTTTAATCTCAGTAAGAGCTTTTTTACCAAGCTTAGGCGTTTTAAGGAGCTCAACCTCGGTACGCTGTACCAGATCACCGATATAGTGGATAGCTTCTGCTTTAAGGCAGTTATCAGAGCTGACAGTCAATTCCAGATCGTCAACa                 <  2:482914/149‑1 (MQ=255)
                                                                                                                             gTCTTTAATCTCAGTAAGAGCTTTTTTACCAAGGTTAGGCGTTTTAAGGAGCTCAACCTCGGTACGCTGTACCAGATCACCGATATAGAGGATAGCTTCTGCTTTAAGGCAGTTGGCAGAGCGGACATTCAATGCCGGATCGTCAACAg                >  1:319948/1‑149 (MQ=255)
                                                                                                                                tttAATCTCAGTAAGAGCTTTTTTACCAAGGTTAGGCGTTTTAAGGAGCTCAACCTCGGTACGCTGTACCAGATCACCGATATAGTGGATCGATTATGCTTTAAGGCAGTTAGCAGAGCGGACAGTCAATTCCAGATCGTCAACAGGgc             >  1:160829/1‑149 (MQ=255)
                                                                                                                                tttAATCTCAGTAAGAGCTTTTTTACCAAGGTTAGGCGTTTTAAGGAGCTCAACCTCGGTACGCTGTACCAGATCACCGATATAGTGGATAGCTTCTGCTTTAAGGCAGTTAGCAGAGCGGACAGTCAATTCCAGATCGTCAACAGGgc             <  1:380980/149‑1 (MQ=255)
                                                                                                                                           tAAGAGCTTTTTTACCAAGGTTACGCGTTTTAAGGAGCTCAACCTCGGTACGCTGTACCAGATCACCGATATAGTGGATAGCTTCTGCTTTAAGGCAGTTAGCAGAGCGGACAGTCAATTCCAGATCGTCAACAGGGCGCAGCAggatc  <  1:54790/149‑1 (MQ=255)
                                                                                                                                             agagCTTTTTTACCAAGGTTAGGCGTTTTAAGGAGCTCAACCTCGGTACGCTGTACCAGATCAcc                                                                                    >  2:143084/1‑65 (MQ=255)
                                                                                                                                             agagCTTTTTTACCAAGGTTAGGCGTTTTAAGGAGCTCAACCTCGGTACGCTGTACCAGATCAcc                                                                                    <  1:143084/65‑1 (MQ=255)
                                                                                                                                                 |                                                                                                                                              
GATGGCGCATGACCTTATCCTTCTCAGTAAAACCTTAACCTGTGATCCGGTTACTCGTCAGCGATGCTTGCCGGTGGCCAGTTTTCCAGGCGCATGCCCAGAGACAGTCCACGGGAAGCCAGCACGTCTTTAATCTCAGTAAGAGATTTTTTACCAAGGTTAGGCGTTTTAAGGAGCTCAACCTCGGTACGCTGTACCAGATCACCGATATAGTGGATAGCTTCTGCTTTAAGGCAGTTAGCAGAGCGGACAGTCAATTCCAGATCGTCAACAGGGCGCAGCAGGATC  >  NC_000913_3_KO_pgi/3439990‑3440277

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: ‑