Predicted mutation
evidence seq id position mutation annotation gene description
RA NC_000913 3,440,194 C→A G279V (GGT→GTT)  rpoA ← RNA polymerase, alpha subunit

Read alignment evidence...
  seq id position ref new freq score (cons/poly) reads annotation genes product
*NC_0009133,440,1940CA97.7% 164.4 / ‑3.0 44G279V (GGT→GTT) rpoARNA polymerase, alpha subunit
Reads supporting (aligned to +/- strand):  ref base C (0/1);  new base A (20/23);  total (20/24)
Fisher's exact test for biased strand distribution p-value = 1.00e+00
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 9.00e-01

GCTTGCCGGTGGCCAGTTTTCCAGGCGCATGCCCAGAGACAGTCCACGGGAAGCCAGCACGTCTTTAATCTCAGTAAGAGATTTTTTACCAAGGTTAGGCGTTTTAAGGAGCTCAACCTCGGTACGCTGTACCAGATCACCGATATAGTGGATAGCTTCTGCTTTAAGGCAGTTAGCAGAGCGGACAGTCAATTCCAGATCGTCAACAGGGCGCAGCAGGATCGGATCGAACTCTGGTTTCTCTTCTTTCACTTCAGGCTGACGTACATCACGTAAGTCAAC  >  NC_000913/3440055‑3440336
                                                                                                                                           |                                                                                                                                              
gCTTGCCGGTGGCCAGTTTTCCAGGCGCATACCCAGAGACAGTCCACGGGAAGCCAGCACGTCTTTAATCTCAGTAAGAGATTTTTTACCAAGGTTAGGCGTTTTAAGGAGCTCAACCTCGGTACGCTGTACCAGATCAACGATATAGTg                                                                                                                                      <  1:1132776/150‑1 (MQ=255)
   tGCCGGTGGCCAGTTTTCCAGGCGCATGCCCAGAGACAGTCCACGGGAAGCCAGCACGTCTTTAATCTCAGTAAGAGATTTTTTACCAAGGTTAGGCGTTTTAAGGAGCTCAACCTCGGTACGCTGTACCAGATCAACGATATAGTGGAt                                                                                                                                   <  1:2897370/150‑1 (MQ=255)
   tGCCGGTGGCCAGTTTTCCAGGCGCATGCCCAGAGACAGTCCACGGGAAGCCAGCACGTCTTTAATCTCAGTAAGAGATTTTTTACCAAGGTTAGGCGTTTTAAGGAGCTCAACCTCGCTACGCTGTACCAGATCACCGATATAGTggt                                                                                                                                    <  1:612999/149‑2 (MQ=255)
    gCCGGTGGCCAGTTTTCCAGGCGCATGCCCAGAGACAGTCCACGGGAAGCCAGCACGTCTTTAATCTCAGTAAGAGATTTTTTACCAAGGTTAGGCGTTTTAAGGAGCTCAACCTCGGTACGCTGTACCAGATCAACGATATAGTGGATa                                                                                                                                  <  1:3980827/150‑1 (MQ=255)
    gCCGGTGGCCAGTTTTCCAGGCGCATGCCCAGAGACAGTCCACGGGAAGCCAGCACGTCTTTAATCTCAGTAAGAGATTTTTTACCAAGGTTAGGCGTTTTAAGGAGCTCAACCTCGGTACGCTGTACCAGATCAACGATATAGTGGATAg                                                                                                                                 <  1:3070760/151‑1 (MQ=255)
          ggCCAGTTTTCCAGGCGCATGCCCAGAGACAGTCCACGGGAAGCCAGCACGTCTTTAATCTCAGTAAGAGATTTTTTACCAAGGTTAGGCGTTTTAAGGAGCTCAACCTCGGTACGCTGTACCAGATCAACGATATAGTGGATAGCTTCTg                                                                                                                           <  1:3291936/151‑1 (MQ=255)
            ccAGTTTTCCAGGCGCATGCCCAGAGACAGTCCACGGGAAGCCAGCACGTCTTTAATCTCAGTAAGAGATTTTTTACCAAGGTTAGGCGTTTTAAGGAGCTCAACCTCGGTACGCTGTACCAGATCAACGATATAGTGGATAGCTTCTGCt                                                                                                                         >  2:1643456/1‑151 (MQ=255)
             cAGTTTTCCAGGCGCATGCCCAGAGACAGTCCACGGGAAGCCAGCACGTCTTTAATCTCAGTAAGAGATTTTTTACCAAGGTTAGGCGTTTTAAGGAGCTCAACCTCGGTACGCTGTACCAGATCAACGATATAGTGGATAGCTTCTGCtt                                                                                                                        <  2:2620271/151‑1 (MQ=255)
                                ccAGAGACAGTCCACGGGAAGCCAGCACGTCTTTAATCTCAGTAAGAGATTTTTTACCAAGGTTAGGCGTTTTAAGGAGCTCAACCTCGGTACGCTGTACCAGATCAACGATATAGTGGATAGCTTCTGCTTTAAGGCAGTTAGCAGAGCg                                                                                                     <  1:123624/151‑1 (MQ=255)
                                      aCAGTCCACGGGAAGCCAGCACGTCTTTAATCTCAGTAAGAGATTTTTTACCAAGGTTAGGCGTTTTAAGGAGCTCAACCTCGGTACGCTGTACCAGATCAACGATATAGTGGATAGCTTCTGCTTTAAGGCAGTTAGCAGAGCGGACAGt                                                                                               <  2:2623896/151‑1 (MQ=255)
                                       cAGTCCACGGGAAGCCAGCACGTCTTTAATCTCAGTAAGAGATTTTTTACCAAGGTTAGGCGTTTTAAGGAGCTCAACCTCGGTACGCTGTACCAGATCAACGATATAGTGGATAGCTTCTGCTTTAAGGCAGTTAGCAGAGCGGACAGTc                                                                                              <  1:1034996/151‑1 (MQ=255)
                                        aGTCCACGGGAAGCCAGCACGTCTTTAATCTCAGTAAGAGATTTTTTACCAAGGTTAGGCGTTTTAAGGAGCTCAACCTCGGTACGCTGTACCAGATCAACGATATAGTGGATAGCTTCTGCTTTAAGGCAGTTAGCAGAGCGGACAGTCa                                                                                             <  2:28862/151‑1 (MQ=255)
                                                  aaGCCAGCACGTCTTTAATCTCAGTAAGAGATTTTTTACCAAGGTTAGGCGTTTTAAGGAGCTCAACCTCGGTACGCTGTACCAGATCAACGATATAGTGGATAGCTTCTGCTTTAAGGCAGTTAGCAGAGCGGACAGTCAATTcc                                                                                        >  1:3065463/1‑146 (MQ=255)
                                                           cGTCTTTAATCTCAGTAAGAGATTTTTTACCAAGGTTAGGCGTTTTAAGGAGCTCAACCTCGGTACGCTGTACCAGATCAACGATATAGTGGATAGCTTCTGCTTTAAGGCAGTTAGCAGAGCGGACAGTCAATTCCAGATCGTCAACAgg                                                                          <  2:2296735/151‑1 (MQ=255)
                                                            gTCTTTAATCTCAGTAAGAGATTTTTTACCAAGGTTAGGCGTTTTAAGGAGCTCAACCTCGGTACGCTGTACCAGATCAACGATATAGTGGATAGCTTCTGCTTTAAGGCAGTTAGCAGAGCGGACAGTCAATTCCAGATCGTCAACAggg                                                                         >  1:767706/1‑151 (MQ=255)
                                                                ttAATCTCAGTAAGAGATTTTTTACCAAGGTTAGGCGTTTTAAGGAGCTCAACCTCGGTACGCTGTACCAGATCAACGATATAGTGGATAGCTTCTGCTTTAAGGCAGTTAGCAGAGCGGACAGTCAATTCCAGATCGTCAACAGGgcgc                                                                      >  1:3779125/1‑150 (MQ=255)
                                                                    tctcAGTAAGAGATTTTTTACCAAGGTTAGGCGTTTTAAGGAGCTCAACCTCGGTACGCTGTACCAGATCAACGATATAGTGGATAGCTTCTGCTTTAAGGCAGTTAGCAGCGCGGACAGTCAATTCCAGATCGTCAACAGGGCgcagc                                                                   >  2:1711223/1‑149 (MQ=255)
                                                                     gtcAGGAAGAGAGTTGTTAACGGGGATAGGGGGTTCCAGGAGTTCAACCTCGGTGGGCGGTACCAGATTAAAAAAATAAAAGATAGCTTCTGCTTTAAGGCAGTTAGCAGAGCGGACAGTCAATTCCAGATCGTCAACAGGGCGCAGCAgg                                                                >  1:351255/2‑151 (MQ=255)
                                                                           aaGAGATTTTTTACCAAGGTTAGGCGTTTTAAGGAGCTCAACCTCGGTACGCTGTACCAGATCAACGATATAGTGGATAGCTTCTGCTTTAAGGCAGTTAGCAGAGCGGACAGTCAATTCCAGATCGTCAACAGGGCGCAGCAggatcgg                                                           >  2:470594/1‑150 (MQ=255)
                                                                            agagATTTTTTACCAAGGTTAGGCGTTTTAAGGAGCTCAACCTCGGTACGCTGTACCAGATCAACGATATAGTGGATAGCTTCTGCTTTAAGGCAGTTAGCAGAGCGGACAGTCAATTCCAGATCGTCAACAGGGCGCAGCAggatcggat                                                         <  1:942392/151‑1 (MQ=255)
                                                                               gaTTTTTTACCAAGGTTAGGCGTTTTAAGGAGCTCAACCTCGGTACGCTGTACCAGATCAACGATATAGTGGATAGCTTCTGCTTTAAGGCAGTTAGCAGAGCGGACAGTCAATTCCAGATCGTCAACAGGGCGCAGCAGGATCGGATCGa                                                      <  2:2218230/151‑1 (MQ=255)
                                                                                   ttttACCAAGGTTAGGCGTTTTAAGGAGCTCAACCTCGGTACGCTGTACCAGATCAACGATATAGTGGATAGCTTCTGCTTTAAGGCAGTTAGCAGAGCGGACAGTCAATTCCAGATCGTCAACAGGGCGCAGCAGGATCGGATCGAActc                                                  >  2:2944508/1‑151 (MQ=255)
                                                                                               tAGGCGTTTTAAGGAGCTCAACCTCGGTACGCTGTACCAGATCAACGATATAGTGGATAGCTTCTGCTTTAAGGCAGTTAGCAGAGCGGACAGTCAATTCCAGATCGTCAACAGGGCGCAGCAGGATCGGATCGAACTCTGGTTTCtcttc                                      >  1:3873096/1‑151 (MQ=255)
                                                                                                       ttAAGGAGCTCAACCTCGGTACGCTGTACCAGATCAACGATATAGTGGATAGCTTCTGCTTTAAGGCAGTTAGCAGAGCGGACAGTCAATTCCAGATCGTCAACAGGGCGCAGCAGGATCGGATCGAACTCTGGTTTCTC‑TCCTTCACtt                              <  2:796671/150‑1 (MQ=255)
                                                                                                           ggAGCTCAACCTCGGTACGCTGTACCAGATCAACGATATAGTGGATAGCTTCTGCTTTAAGGCAGTTAGCAGAGCGGACAGTCAATTCCAGATCGTCAACAGGGCGCAGCAGGATCGGATCGAACTCTGGTTTCTCTTCTTTCACTTCAgg                          >  2:2352198/1‑151 (MQ=255)
                                                                                                             aGCTCAACCTCGGTACGCTGTACCAGATCAACGATATAGTGGATAGCTTCTGCTTTACGGCAGTTAGCAGAGCGGACAGTCAATTCCAGATCGTCAACAGGGCGCAGCAGGATCGGATCGAACTCTGGCTTCTCTTCTTTCACTTCAGGc                         >  1:4065694/1‑150 (MQ=255)
                                                                                                             aGCTCAACCTCGGTACGCTGTACCAGATCAACGATATAGTGGATAGCTTCTGCTTTAAGGCAGTTAGCAGAGCGGACAGTCAATTCCAGATCGTCAACAGGGCGCAGCAGGATCGGATCGAACTCTGGTTTCTCTTCTTTCACTTCAGGCt                        <  2:2321723/151‑1 (MQ=255)
                                                                                                                 cAACCTCGGTACGCTGTACCAGATCAACGATATAGTGGATAGCTTCTGCTTTAAGGCAGTTAGCAGAGCGGACAGTCAATTCCAGATCGTCAACAGGGCGCAGCAGGATCGGATCGAACTCTGGTTTCTCTTCTTTCACTTCAGGCTGAc                     <  1:2854921/150‑1 (MQ=255)
                                                                                                                 cAACCTCGGTACGCTGTACCAGATCAACGATATAGTGGATAGCTTCTGCTTTAAGGCAGTTAGCAGAGCGGACAGTCAATTCCAGATCGTCAACAGGGCGCAGCAGGATCGGATCGAACTCTGGTTTCTCTTCTTTCACTTCAGGCTGACg                    >  2:2392580/1‑151 (MQ=255)
                                                                                                                   aCCTCGGTACGCTGTACCAGATCAACGATATAGTGGATAGCTTCTGCTTTAAGGCAGTTAGCAGAGCGGACAGTCAATTCCAGATCGTCAACAGGGCGCAGCAGGATCGGATCGAACTCTGGTTTCTCTTCTTTCACTTCAGGCTGACGt                   >  2:2148488/1‑150 (MQ=255)
                                                                                                                    ccTCGGTACGCTGTACCAGATCAACGATATAGTGGATAGCTTCTGCTTTAAGGCAGTTAGCAGAGCGGACAGTCAATTCCAGATCGTCAACAGGGCGCAGCAGGATCGGATCGAACTCTGGTTTCTCTTCTTTCACTTCAGGCTGACGTAc                 >  2:3925362/1‑151 (MQ=255)
                                                                                                                       cGGTACGCTGTACCAGATCAACGATATAGTGGATAGCTTCTGCTTTAAGGCAGTTAGCAGAGCGGACAGTCAATTCCAGATCGTCAACAGGGCGCAGCAGGATCGGATCGAACTCTGGTTTCTCTTCTTTCACTTCAGGCTGACGTACa                <  2:1128312/149‑1 (MQ=255)
                                                                                                                       cGGTACGCTGTACCAGATCAACGATATAGTGGATAGCTTCTGCTTTAAGGCAGTTAGCAGAGCGGACAGTCAATTCCAGATCGTCAACAGGGCGCAGCAGGATCGGATCGAACTCTGGTTTCTCTTCTTTCACTTCAGGCTGACGTACAt               <  1:695013/150‑1 (MQ=255)
                                                                                                                       cGGTACGCTGTACCAGATCAACGATATAGTGGATAGCTTCTGCTTTAAGGCAGTTAGCAGAGCGGACAGTCAATTCCAGATCGTCAACAGGGCGCAGCAGGATCGGATCGAACTCTGGTTTCTCTTCTTTCACTTCAGGCTGACGTACATc              <  2:3052416/151‑1 (MQ=255)
                                                                                                                        ggTACGCTGTACCAGATCAACGATATAGTGGATAGCTTCTGCTTTAAGGCAGTTAGCAGAGCGGACAGTCAATTCCAGATCGTCAACAGGGCGCAGCAGGATCGGATCGAACTCTGGTTTCTCTTCTTTCACTTCAGGCTGACGTACATc              >  1:3135509/1‑150 (MQ=255)
                                                                                                                         gTACGCTGTACCAGATCAACGATATAGTGGATAGCTTCTGCTTTAAGGCAGTTAGCAGAGCGGACAGTCAATTCCAGATCGTCAACAGGGCGCAGCAGGATCGGATCGAACTCTGGTTTCTCTTCTTTCACTTCAGGCTGACGTACATCAc            <  2:145006/151‑1 (MQ=255)
                                                                                                                          tACGCTGTACCAGATCAACGATATAGTGGATAGCTTCTGCTTTAAGGCAGTTAGCAGAGCGGACAGTCAATTCCAGATCGTCAACAGGGCGCAGCAGGATCGGATCGAACTCTGGTTTCTCTTCTTTCACTTCAGGCTGACGTACATCACg           >  2:462633/1‑151 (MQ=255)
                                                                                                                           aCGCTGTACCAGATCAACGATATAGTGGATAGCTTCTGCTTTAAGGCAGTTAGCAGAGCGGACAGTCAATTCCAGATCGTCAACAGGGCGCAGCAGGATCGGATCGAACTCTGGTTTCTCTTCTTTCACTTCAGGCTGACGTACATCACGt          >  2:841359/1‑151 (MQ=255)
                                                                                                                            cGCTGTACCAGATCAACGATATAGTGGATAGCTTCTGCTTTAAGGCAGTTAGCAGAGCGGACAGTCAATTCCAGATCGTCAACAGGGCGCAGCAGGATCGGATCGAACTCTGGTTTCTCTTCTTTCACTTCAGGCTGACGTACATCACGt          >  1:559210/1‑150 (MQ=255)
                                                                                                                               tGTACCAGATCAACGATATAGTGGATAGCTTCTGCTTTAAGGCAGTTAGCAGAGCGGACAGTCAATTCCAGATCGTCAACAGGGCGCAGCAGGATCGGATCGAACTCTGGTTTCTCTTCTTTCACTTCAGGCTGACGTACATCACGTAAGt      >  1:3719381/1‑151 (MQ=255)
                                                                                                                                gTACCAGATCAACGATATAGTGGATAGCTTCTGCTTTAAGGCAGTTAGCAGAGCGGACAGTCAATTCCAGATCGTCAACAGGGCGCAGCAGGATCGGATCGAACTCTGGTTTCTCTTCTTTCACTTCAGGCTGACGTACATCACGTAAGt      <  2:1294186/150‑1 (MQ=255)
                                                                                                                                  aCCAGATCAACGATATAGTGGATAGCTTCTGCTTTAAGGCAGTTAGCAGAGCGGACAGTCAATTCCAGATCGTCAACAGGGCGCAGCAGGATCGGATCGAACTCTGGTTTCTCTTCTTTCACTTCAGGCTGACGTACATCACGTAAGTCa    <  1:113948/150‑1 (MQ=255)
                                                                                                                                   ccAGATCAACGATATAGTGGATAGCTTCTGCTTTAAGGCAGTTAGCAGAGCGGACAGTCAATTCCAGATCGTCAACAGGGCGCAGCAGGATCGGATCGAACTCTGGTTTCTCTTCTTTCACTTCAGGCTGACGTACATCACGTAAGTCAAc  <  2:1405729/151‑1 (MQ=255)
                                                                                                                                   ccAGATCAACGATATAGTGGATAGCTTCTGCTTTAAGGCAGTTAGCAGAGCGGACAGTCAATTCCAGATCGTCAACAGGGCGCAGCAGGATCGGATCGAACTCTGGTTTCTCTTCTTTCACTTCAGGCTGACGTACATCACGTAAGTCAAc  >  2:4056109/1‑151 (MQ=255)
                                                                                                                                           |                                                                                                                                              
GCTTGCCGGTGGCCAGTTTTCCAGGCGCATGCCCAGAGACAGTCCACGGGAAGCCAGCACGTCTTTAATCTCAGTAAGAGATTTTTTACCAAGGTTAGGCGTTTTAAGGAGCTCAACCTCGGTACGCTGTACCAGATCACCGATATAGTGGATAGCTTCTGCTTTAAGGCAGTTAGCAGAGCGGACAGTCAATTCCAGATCGTCAACAGGGCGCAGCAGGATCGGATCGAACTCTGGTTTCTCTTCTTTCACTTCAGGCTGACGTACATCACGTAAGTCAAC  >  NC_000913/3440055‑3440336

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 16 ≤ ATCG/ATCG < 33 ≤ ATCG/ATCG < 38 ≤ ATCG/ATCG < 39 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑