Predicted mutation
evidence seq id position mutation freq annotation gene description
RA NC_000913_3_pae_pgi 4,182,791 A→G 54.3% D516G (GAC→GGC)  rpoB → RNA polymerase, beta subunit

Read alignment evidence...
  seq id position ref new freq score (cons/poly) reads annotation genes product
*NC_000913_3_pae_pgi4,182,7910AG54.3% 11.4 / 46.6 46D516G (GAC→GGC) rpoBRNA polymerase, beta subunit
Reads supporting (aligned to +/- strand):  ref base A (15/6);  new base G (9/16);  total (24/22)
Fisher's exact test for biased strand distribution p-value = 2.10e-02
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 8.64e-01

GGTACGTGTAGAGCGTGCGGTGAAAGAGCGTCTGTCTCTGGGCGATCTGGATACCCTGATGCCACAGGATATGATCAACGCCAAGCCGATTTCCGCAGCAGTGAAAGAGTTCTTCGGTTCCAGCCAGCTGTCTCAGTTTATGGACCAGAACAACCCGCTGTCTGAGATTACGCACAAACGTCGTATCTC‑CGCACTCGGCCCAGGCGGTCTGACCCGTGAACGTGCAGGCTTCGAAGTTCGAGACGTACACCCGACTCACTACGGTCGCGTATGTCCAATCGAAACCCCTGAA  >  NC_000913_3_pae_pgi/4182648‑4182939
                                                                                                                                               |                                                                                                                                                     
ggTACGTGTAGAGCGTGGGGTGAAAGGGCGTCTGTCTCTGGGCGATCTGGATACCCTGATGCCACAGGATATGATCAACGCCAAGCCGATTTCCGCAGCAGTGAAAGAGTTCTTCGGTTCCAGCCAGCTGTCTCAGTTTATGGACCAGa                                                                                                                                                  >  2:867217/1‑149 (MQ=255)
 gTACGTGTAGAGCGTGCGGTGAAAGAGCGTCTGTCTCTGGGCGATCTGGATACCCTGATGCCACAGGATATGATCAACGCCAAGCCGATTTCCGCAGCAGTGAAAGAGTTCTTCGGTTCCGGCCAGCTGTCTCAGTTTATGGaaatgat                                                                                                                                                 >  2:905518/1‑143 (MQ=255)
       gtAGAGCGTGCGGTGAAAGAGCGTCTGTCTCTGGGCGATCTGGATACCCTGATGCCACAGGATATGATCAACGCCAAGCCGATTTCCGCAGCAGTGAAAGAGTTCTTCGGTTCCAGCAAGCTGTCTCAGATTATGGACCAGAACAAccc                                                                                                                                           >  1:532869/1‑149 (MQ=255)
              gTGCGGGTAAAGAGCGTCTGTTTCTGGGCGATCTGGATACCCTGATGCCACAGGATATGATCAACGCCAAGCCGATTTCCGCAGCATTGAGAGAGTTCTTCGGTTCCAGCCAGCTGTCTCAGTTTATGGACCAGAACAACCCGCTGTCt                                                                                                                                    <  1:191305/149‑1 (MQ=255)
                gccgTGAAAGCGCCTCTGTCTCTTGGCGAGCTGGATACCCTGATGCCACAGGATATGATCAACGCCAAGCCGATTTCCGCAGCAGTGAAAGAGTTCTTCGGTTCCAGCCAGCTGTCTCAGTTTATGGGCCAGAACAACCCGCTGTCTga                                                                                                                                  <  2:757961/146‑1 (MQ=255)
                 cGGTGAAAGAGCGTCTGTCTCTGGGCGATCTGGATACCCTGATGCCACAGGATATGATCAACGCCAAGCCGATTTCCGCAGCAGTGAAAGAGTTCTTCGGTTCCAGCCAGCTGTCTCAGTTTATGGGCCAGAACAACCCGCTGTCTgag                                                                                                                                 <  1:659778/149‑1 (MQ=255)
                  tgggAAAGGGCGTCCGTCTCTGGGCGACCTGGCTACCCTACTGCCACAGTATATGATCAACGCCAAGCCGATTTCCGCAGCAGTGAAAGAGTTCTTCGGTTCCAGCCAGCTGTCTCAGTTTATGGGCCAGAACAACCCGCTGTCTgaga                                                                                                                                <  2:178348/146‑1 (MQ=255)
                      aaaGAGCGTCTGTCTCTGGGCGATCTGGATACCCTGATGCCACAGGATATGATCAACGCCAAGCCGATTTCCGCAGCAGTGAAAGAGTTCTTCGGTTCCAGCCAGCTGTCTCAGTTTATGGGCCAGAACAACCCGCTGTCTGAGATTAc                                                                                                                            >  1:516631/1‑149 (MQ=255)
                         gagCGTCTGTCTCTGGGCGATCTGGATACCCTGATGCCACAGGATATGATCAACGCCAAGCCGATTTCCGCAGCAGTGAAAGAGTTCTTCAGTTCCAGCCAGCTGTCTCAGTTTATGGGCCAGAACAACCCGCTGTCTGAGATTACGca                                                                                                                         >  2:648611/1‑149 (MQ=255)
                               ctgtctCTGGGCGATCTGGATACCCTGATGCCACAGGATATGATCAACGCCAAGCCGATTTCCGCAGCAGTGAAAGAGTTCTTCGGTTCCAGCCAGCTGTCTCAGTTTATGGACCAGAACAACCCGCTGTCTGAGATTACGCACAAAcg                                                                                                                   >  2:649978/1‑149 (MQ=255)
                                 gtctCTGGGCGATCTGGATACCCTGATGCCACAGGATATGATCAACGCCAAGCCGATTTCCGCAGCAGTGAAAGAGTTCTTCGGTTCCAGCCAGCTGTCTCAGTTTATGGGCCAGAACAACCCGCTGTCTGAGATTACGCACAAAcgtc                                                                                                                 <  1:685033/149‑1 (MQ=255)
                                    tctGGGCGATCTGGATACCCTGATGCCACAGGATATGATCAACGCCAAGCCGATTTCCGCAGCAGTGAAGGAGTTCTTCGGTTGCAGCCAGCTGTATCAGCCTATTGACCAGAACAAGCCGATATCTGAGATTACGCACAAACGTCGTa                                                                                                              >  1:943275/1‑149 (MQ=255)
                                      tGGGCGATCTGGATACCCTGATGCCACAGGATATGATCAACGCCAAGCCGATTTCCGCAGCAGTGAAAGAGTTCTTCGGTTCCAGCCAGCTGTCTCAGTTTATGGGCCAGAACAACCCCCTGTCTGAGATTCCGCCCAAACGTCGTAtc                                                                                                            >  2:108152/1‑149 (MQ=255)
                                          cGATCTGGATACCCTGATGCCACAGGATATGATCAACGCCAAGCCGATTTCCGCAGCAGTGAAAGAGTTCTTCGGTTCCAGCCAGCTGTCTCAGTTTATGGACCAAAACAACCCGCTGTCTGAAATTACGCACAAACTTCGTATCTC‑Cg                                                                                                       >  1:826955/1‑149 (MQ=255)
                                            aTCTGGATACCCTGATGCCACAGGATATGATCAACGCCAAGCCGATTTCCGCAGCAGTGAAAGAGTTCTTCGGTTCCCGCCCGCTGTCTCAGTTTATGGACCAGAACAACCCGCTGTCTGAGATTACGCACAAACGTCGTATCTC‑CGCa                                                                                                     <  1:642206/149‑1 (MQ=255)
                                             tCTGGATACCCTGATGCCACAGGATATGATCAACGCCAAGCCGATTTCCGCAGCAGTGAAAGAGTTCTTCGGTTCCAGCCAGCTGTCTCAATTTATGGAACAGAACAACGAGGTGTCTGAGATTACGCACAAACGTCTTATCTC‑CGCAc                                                                                                    >  1:276406/1‑149 (MQ=255)
                                                 gATACCCTGATGCCACAGGATATGATCAACGCCAAGCCGATTTCCGCATCAGTGAAAGAGTTCTTCGGTTCCAGCCAGCTGTCTCAGTTTATGGACCAGAACAACCCGCTGTCTGAGATTACGCACAAACGTCGTATCTC‑CGCACTCgg                                                                                                >  1:488841/1‑149 (MQ=255)
                                                  aTACCCTGATGCCACAGGATATGATCAACGCCAAGCCGATTTCCGCAGCAGTGAAAGAGTTCTTCGGTTCCAGCCAGCTGTCTCAGTTTATGGGCCAGAACAACCCGCTGTCTGAGATTACGCACAAACGTCGTATCTC‑CGCACTCGGc                                                                                               <  2:775453/149‑1 (MQ=255)
                                                  aTACCCTGATGCCACAGGATATGATCAACGCCAAGCCGATTTCCGCAGCAGTGAAAGAGTTCTTCGGTTCCAGCCAGCTGTCTCAGTTTATGGGCCAGAACAACCCGCTGTCTGAGATTACGCACAAACGTCGTATCTC‑CGCACTCGGc                                                                                               <  1:746969/149‑1 (MQ=255)
                                                    aCCCTGATGCCACAGGATATGATCAACGCCAAGCCGATTTCCGCAGCAGTGAAAGAGTTCTTCGGTTCCAGCCAGCTGTCTCAGTTTATGGACCAGAACAACTCGCTGTCTGAGATTACGCACAAACGTCGTATCTC‑CGCACTCGGccc                                                                                             <  1:905518/149‑1 (MQ=255)
                                                    aCCCTGATGCCACAGGATATGATCAACGCCAAGCCGATTTCCGCAGCAGTGAAAGAGTTCTTCGATTCCAGCCAGCTGTCTCAGTTTATGGACCAGAACAACCCGCTGTCTGAGATTACGAACAAACGTCGTATATA‑CCCACTCGGccc                                                                                             >  2:536715/1‑149 (MQ=255)
                                                       cTGATGCCACAGGATATGATCAACGCCAAGCCGATTTCCGCAGCAGTGAAAGAGTTCTTCGGTTCCAGCCAGCTGTCTCAGTTTATGGACCAGAACAACCCGCTGTCTGAGATTACGCACAAACGTCGTATCTC‑CGCACTCGGCCCAgg                                                                                          >  1:924181/1‑149 (MQ=255)
                                                              cacaGGATATGATCAACGCCAAGCCGATTTCCGCAGCAGTGAAAGAGTTCTTCGGTTCCAGCCAGCTGTCTCAGTTTATGGGCCAGAACAACCCGCTGTCTGAGATTACGCACAAACGTCGTATCTC‑CGCACGCGGCCCAGGCGGTCTg                                                                                   >  2:767263/1‑149 (MQ=255)
                                                                   gATATGATCAACGCCAAGCCGATTTCCGCAGCAGTGAAAGAGTTCTTCGGTTCCAGCCAGCTGTCTCAGTTTATGGGCCAGAACAACCCGCTGTCTGAGATTACGCACaaa                                                                                                                     >  1:918398/1‑111 (MQ=255)
                                                                   gATATGATCAACGCCAAGCCGATTTCCGCAGCAGTGAAAGAGTTCTTCGGTTCCAGCCAGCTGTCTCAGTTTATGGGCCAGAACAACCCGCTGTCTGAGATTACGCACaaa                                                                                                                     <  2:918398/111‑1 (MQ=255)
                                                                       tGATCAACGCCAAGCCGATTTCCGCAGCAGTGAAAGAGTTCTTCGGTTCCAGCCAGCTGTCTCAGTTTATGGGCCAGAACAACCCGCTGTCTGAGATTACGCACAAACGTCGTATCTC‑CGCACTCGGCCCAGGCGGTCTGACCCGTGaa                                                                          <  2:266930/149‑1 (MQ=255)
                                                                         aTCAACGCCAAGCCGATTTCCGCAGCAGTGAAAGAGTTCTTCGGTTCCAGCCAGCTGTCTCAGTTTATGGGCCAGAACAACCCGCTGTCTGAGATTACGCACAAACGTCGTAt                                                                                                             <  1:854155/113‑1 (MQ=255)
                                                                         aTCAACGCCAAGCCGATTTCCGCAGCAGTGAAAGAGTTCTTCGGTTCCAGCCAGCTGTCTCAGTTTATGGGCCAGAACAACCCGCTGTCTGAGATTACGCACAAACGTCGTAt                                                                                                             >  2:854155/1‑113 (MQ=255)
                                                                          tCAACGCCAAGCCGATTTCCGCAGCAGTGAAAGAGTTCTTCGGTTCCAGCCAGCTGTCTCAGTTTATGGGCCAGAACAACCCGCTGTCTGAGATTACGCACAACCGAAG‑AGCACACGCATGCGGCCAAGGAGGGCTGACCCGGGAACGt                                                                       >  1:276078/1‑149 (MQ=255)
                                                                           cAACGCCAAGCCGATTTCCGCAGCAGTGAAAGAGTTCTTCGGTTCCAGCCAGCTGTCTCAGTTTATGGGCCAGAACAACCCGCTGTCTGAGATTACGCACAAACGTCGTATCTC‑CGCACTCGGCCCAGGCGGTCTGACCCGTGAACGTg                                                                      <  1:899659/149‑1 (MQ=255)
                                                                                  aaGCCGATTTCCGCAGCAGTGAAAGAGTTCTTCGGTTCGAGCCAGCTGTCTCAGTGTAGGGGCCAGGACAACCCTCTGTCTGAGATTACGCACAAACGTCGTATCTC‑CGCACGCGGCCCGGGGGTGGTGGCCCGTGAACGTGCAAGcgt                                                               >  2:690079/1‑147 (MQ=255)
                                                                                            ccGCAGCAGTGAAAGAGTTCTTCGGTTCCAGCCAGCTGTCTCAGTTTATGGGCCAGAACAACCCGCTGTCTGAGATTACGCACAAACGGCGTATCTC‑CGCACTCGGCCCAGGCGGTCTGACCCGTGAACGTGCAGGCTTCGAAGTTCga                                                     <  1:130465/149‑1 (MQ=255)
                                                                                                  cagTGAAAGATTTCTTCCGTTCCACCCAGCTGTCTCAGTTTATGTGCCAGAACAACCCGCTGTCTGAGATTACGCACAAACGTCGTATCTC‑CGCACTCGGCCCAGGCGGTCTGACCCGTGAACGTGCAGGCTTCGAAGTTCGAGACGTa                                               <  1:802401/149‑1 (MQ=255)
                                                                                                  cagTGAAAGAGTTCTTCGGTTCCAGCCAGCTGTCTCAGTTTATGGACCAGAACAACCCGCTGTCTGAGATTCCGCACAAACGTCGTATCTC‑CGCACTCGCCCCAGGCGGTCTAACCCGTAAACGTGCAGGCTTCGAAGTTCGAGATGTa                                               >  1:51724/1‑149 (MQ=255)
                                                                                                       aaaGAGTTCTTCGGTTCCAGCCAGCTGTCTCAGTTTATGGACCAGAACAACCCGCTGTCTGAGATTACGCACAAACGTCGTATCTC‑CGCACTCGGCCCAGGCGGTCTGACCCGTGAACGTGCAGGCTTCGAAGTTCGAGACGTAAAccc                                          >  1:844794/1‑149 (MQ=255)
                                                                                                         agagTTCTTCGGTTCCAGCCAGCTGTCTCAGTTTATGGACCAGAACAACCCGCTGTCTGAGATTACGCACAAACGTCGTATCTC‑CGCACTCGGCCCAGGCGGTCTGACCCGTGAACGTGCAGCCATCCAAATTCGACACCTGCACCCGa                                        >  2:299139/1‑149 (MQ=255)
                                                                                                                  cGGTTCCAGCCAGCTGTCTCAGTTTATGGACCAGAACAACCCGCTGTCTGAGATTACGCACAAACGTCGTATCTC‑CGCACTCGGCCCAGGCGGTCTGACCCGTGAACGTGCAGGCTTCGAAGTTCGAGACGTACACTCCACTCACTACg                               >  2:275074/1‑149 (MQ=255)
                                                                                                                        cagccagcTGTCTCAGTTTATGGGCCAGAACAACCTGCTGTCTGAGATTACGCACAAACGTCGTATCTC‑CGCACTCGGCCCAGGCGGTCTGACCCGTGAACGTGCAGGCTTCGAAGTTCGAGACGTACACCCGACTCACTACGGTcgcg                         >  2:879423/1‑149 (MQ=255)
                                                                                                                        cagccagcGGTCTCAGTTTATGGGCCAGAACAACCCGCTGTCTGAGATTACGCACAAACGGCGTATCTC‑CGCACTCGGCCCAGGCGGTCAGATCCGGCAACGTGTAGGCTTCGAAGTTCGAGACGTACACCCGACTCACTACGGTcgcg                         <  1:195899/149‑1 (MQ=255)
                                                                                                                              gcggTCCCAGTTTATGGACCAGAACAACCCGCTGTCTGAGATTACGCACAAACGTCGTATCTC‑CGCACTCGGCCCAGGCGGTCTGACCCGTGAACGTGCAGGCTTCGAAGTTCGAGACGTACACCCGACTCACTACGGTCGCGTATGTc                   <  1:921236/146‑1 (MQ=255)
                                                                                                                                   ttcAGTTTATGGGCCAGAACAACCCGCTGTCTGAGATTACGCACAAACGTCGTATCTC‑CGCACTCGGCCCAGGCGGTCTGACCCGTGAACGTGCAGGCTTCGAAGTTCGAGACGTACACCCGACTCACTACGGTCGCGTATGTCCAATc              <  1:979042/148‑1 (MQ=255)
                                                                                                                                   cttaGTTTATGTACCAGAACAACCCGCTGTCTGAGATTACGCACAAACGTCGTATCTC‑CGCACTCGGCCCAGGCGGTCTGACCCGTGAACGTGCAGGCTTCGAAGTTCTAGACGTACACCCGACTCACTTCGGTCGCGTATGTCCAATc              <  2:651930/146‑1 (MQ=255)
                                                                                                                                   ctcAGTTTATGGGCCAGAACAACCCGCTGTCTGAGATTACGCACAAACGTCGTATCTC‑CGCACTCGGCCCAGGCGGTCTGACCCGTGAACGTGCAGGCTTCGAAGTTCGAGACGTACACCCGACTCACTACGGTCGCGTATGTCCAATc              <  1:946353/149‑1 (MQ=255)
                                                                                                                                    tcAGTTTATGGACCAGAACAACCCGCTGTCTGAGATTACGCACAAACGTCGTATCTC‑CGCACTCGGCCCAGGCGGTCTGACCCGTGAACGTGCAGGCTTCGAAGTTCGAGACGTACACCCTACTCACTACCGTCGCGTATGTCCAATCg             >  2:53709/1‑149 (MQ=255)
                                                                                                                                       gTTTATGGACCAGAACAACCCGCTGTCTGAGATTACGCACAAACGTCGTATCTC‑CGCACTCGGCCCAGGCGGTCTGACCCGTGAACGTGCAGGCTTCGAAGTTCGAGACGTACACCCGACTCACTACGGTCGCGTATGTCCAATCGaaa          <  1:649978/149‑1 (MQ=255)
                                                                                                                                       atttATGGGCCAGAACAACCCGCGGTCTGAGATTACGCACAAACGTCGTATCTC‑CGCACTCGGCCCAGGCGGTCTGACCCGTGAACGTGCAGGCTTCGAAGTTCGAGACGTACACCCGACTCACTACGGTCGCGTATGTCCAATCGaaa          <  2:948242/148‑1 (MQ=255)
                                                                                                                                          tATGGACCAGAACAACCCGCTGTCTGAGATTACGCACAAACGTCGTATCTC‑CGCACTCGGCCCAGGCGGTCTGACCCGTGAACGTGCAGGCTTCGAACTTCGAGACGTACACCCGACTCACTACGGTCGCGTATGTCCAAACGAAAccc       >  2:709652/1‑149 (MQ=255)
                                                                                                                                               aCCAGAACAACCCGCTGTCTGAGATTACGCACAAACGTCGTATCTC‑CGCACTCGGCCCACGGGATCCGTGCCGTGACCGTCCGAGCTTCGAAGTACGAGTCATACATCCCACTCACTACGGACGCAAATGTCCAATCGAAACCCCCGaa  >  1:487155/1‑149 (MQ=255)
                                                                                                                                               |                                                                                                                                                     
GGTACGTGTAGAGCGTGCGGTGAAAGAGCGTCTGTCTCTGGGCGATCTGGATACCCTGATGCCACAGGATATGATCAACGCCAAGCCGATTTCCGCAGCAGTGAAAGAGTTCTTCGGTTCCAGCCAGCTGTCTCAGTTTATGGACCAGAACAACCCGCTGTCTGAGATTACGCACAAACGTCGTATCTC‑CGCACTCGGCCCAGGCGGTCTGACCCGTGAACGTGCAGGCTTCGAAGTTCGAGACGTACACCCGACTCACTACGGTCGCGTATGTCCAATCGAAACCCCTGAA  >  NC_000913_3_pae_pgi/4182648‑4182939

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 8 ≤ ATCG/ATCG < 12 ≤ ATCG/ATCG < 27 ≤ ATCG/ATCG < 41 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑