Predicted mutation
evidence seq id position mutation freq annotation gene description
RA CP009273 3,208,019 A→G 27.7% E538E (GAA→GAG)  rpoD → RNA polymerase, sigma 70 (sigma D) factor

Read alignment evidence...
  seq id position ref new freq score (cons/poly) reads annotation genes product
*CP0092733,208,0190AG27.7% 38.1 / 12.1 32E538E (GAA→GAG) rpoDRNA polymerase, sigma 70 (sigma D) factor
Reads supporting (aligned to +/- strand):  ref base A (10/11);  new base G (2/7);  total (12/20)
Fisher's exact test for biased strand distribution p-value = 2.49e-01
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 1.00e+00

AAGACAAGATCCGCAAAGTGCTGAAGATCGCCAAAGAGCCAATCTCCATGGAAACGCCGATCGGTGATGATGAAGATTCGCATCTGGGGGATTTCATCGAGGATACCACCCTCGAGCTGCCGCTGGATTCTGCGACCACCGAAAGCCTGCGTGCGGCAACGCACGACGTGCTGGCTGGCCTGACCGCGCGTGAAGCAAAAGTTCTGCGTATGCGTTTCGGTATCGATATGAACACCGACTACACGCTGGAAGAAGTGGGTAAACAGTTCGACGTTACCCGCGAACG  >  CP009273/3207877‑3208162
                                                                                                                                              |                                                                                                                                               
aaGACAAGATCCGCAAAGTGCTGAAGATCGCCAAAGAGCCAATCTCCATGGAAACGCCGATCGGTGATGATGAAGATTCGCATCTGGGGGATTTCATCGAGGATACCACCCTCGAGCTGCCGCTGGATTCTGCGACCACCGAGAGCCtg                                                                                                                                           >  2:234426/1‑149 (MQ=255)
  gACAAGATCCGCAAAGTGCTGAAGATCGCCAAAGAGCCAATCTCCATGGAAACGCCGATCGGTGATGATGAAGATTCGCATCTGGGGGATTTCATCGAGGATACCACCCTCGAGCTGCCGCTGGATTCTGCGACCACCGAAAGCCtgcg                                                                                                                                         >  1:336006/1‑149 (MQ=255)
               aaGTGCTGAAGATCGCCAAAGAGCCAATCTCCATGGAAACGCCGATCGGTGATGATGAAGATTCGCATCTGGGGGATTTCATCGAGGATACCACCCTCGAGCTGCCGCTGGATTCTGCGACCACCGAAAGCCTGCGTGCGGCAACGCac                                                                                                                            <  2:296871/149‑1 (MQ=255)
                  tGCTGAAGATCGCCAAAGAGCCAATCTCCATGGACACGCCGATCGGTGCTGATGACGCTTCGCGCCGCGTTGATGTCATCGCGGAGCCAATGCCCTAATCCCCTCTGCACCCTGCGACCACCGAAAGCCTGCGTGCGGCAACGCacgac                                                                                                                         >  1:76422/1‑149 (MQ=255)
                    cTGAAGATCGCCAAAGAGCCAATCTCCATGGAAACGCCGATCGGTGATGATGAAGATTCGCATCTGGGGGATTTCATCGAGGATACCACCCTCGAGCTGCCGCTGGATTCTGCGACCACCGAGAGCCTGCGTGCGGCGAGGCacgcagt                                                                                                                       >  1:240455/1‑145 (MQ=255)
                    cTGAAGATCGCCAAAGAGCCAATCTCCATGGAAACGCCGATCGGTGATGATGAAGATTCGCATCTGGGGGATTTCATCGAGGATACCACCCTCGAGCTGCCGCTGGATTCTGCGACCACCGAAAGCCtgcgtgcgttgccgcacgcagg                                                                                                                       <  2:347225/149‑15 (MQ=255)
                      gAAGATCGCCAAAGAGCCAATGTCCCTGGAAACGCCGCTCGGGGCTGATGTAGATTCGCATCTGGGGGCTTTCATCGAGGATATCACCCTTGTTTTTTTTAATGATACGGCGACCACCGAGAGCCTGCGTGCGGCAACGCACGACGTgc                                                                                                                     <  1:278048/149‑1 (MQ=255)
                          aTCGCCAAAGAGCCAATCTCCATGGAAACGCCGATCGGTGATGATGAAGATTCGCATCTGGGGGATTTCATCGAGGATACCACCCTCGAGCTGCCGCTGGATTCTGCGACCACCGAAAGCCTGCGTGCGGCAACGCACGCCGTgctggc                                                                                                                 >  2:207547/1‑149 (MQ=255)
                          aTCGCCAAAGAGCCAATCTCCATGGAAACGCCGATCGGTGATGATGAAGATTCGCATCTGGGGGATTTCATCGAGGATACCACCCTCGAGCTGCCGCTGGATTCTGCGACCACCGAAAGCCTGCGTGCGGCAACGCACGACGTgctggc                                                                                                                 >  2:37623/1‑149 (MQ=255)
                              ccAAAGAGCCAATCTCCATGGAAACGCCGATCGGTGATGATGAAGATTCGCATCTGGGGGATTTCATCGAGGATACCACCCTCGAGCTGCCGCTGGATTCTGCGACCACCGAAAGCCTGCGTGCGGCAACGCACGACGTGCtggctggc                                                                                                             <  2:336006/149‑1 (MQ=255)
                               cAAAGAGCCAATCTCCATGGAAACGCCGATCGGTGATGATGAAGATTCGCATCTGGGGGATTTCATCGAGGATACCACCCTCGAGCTGCCGCTGGATTCTGCGACCACCGAAAGCCTGCGTGCGGCAACGCACGACGTGCTGGCTGGcc                                                                                                            >  1:294490/1‑149 (MQ=255)
                                          tcccctgggcaaCGCCGATGGGTGATGTTGGAGATTCGCATCTGGGGGATTTCATCGAGGATACCACCCTTTTGTTTTTGATGGATTCGGCGACCACCGAGAGCCTGCGTGCGGCAACGCACGACGTGCTGGCTGGCCTGACCGCGCGt                                                                                                 <  1:304599/139‑1 (MQ=255)
                                           gtcCGTGGAAACGCGGATCGGGTATGATGAAGAGTCGCTCCTGGGGGAGTTCATCGAGGCTCCCGCCCGTTTTTTTTTGAATGATACGGCGACCACCGAGAGCCTGCGTGCGGCAACGCACGACGTGCTGGCTGGCCTGACCGCGCGTg                                                                                                <  1:60737/148‑1 (MQ=255)
                                                       gCCGACCGGTGATGATGAAGATTCGCATCTGGGGGAATTCAACGAGGACACCACCCTCGAGCTGCCGCTGGATACTGCGACCACCGAAAGCCTGCGTGCGGCAACGCACGACGTGCTGGCTGGCCTGACCGCGCGTGAAGCAAAAGTTc                                                                                    >  2:54608/1‑149 (MQ=255)
                                                                    gatgaGGAGTCGCATCGGGGGGATTTCATCGAGTATCGCACCCTTGTGCTGCTGAAGGATACGGCGACCACCGAGAGCCTGCGTGCGGCAACGCACGACGTGCTGGCTGGCCTGACCGCGCGTGAAGCAAAAGTTCTGCGTATGCGttt                                                                       <  1:285657/149‑1 (MQ=255)
                                                                     atgaAGATTCGCATCTGGGGGATTTCATCGAGGATACCACCCTCGAGCTGCCGCTGGATTCTGCGACCACCGAAAGCCTGCGTGCGGCAACGCACGACGTGCTGGCTGGCCTGACCGCGCGTGAAGCAAAAGTTCTGCGTATGCGTTTc                                                                      >  2:2556/1‑149 (MQ=255)
                                                                           aTTCGCATCTGGGGGATTTCATCGAGGATACCACCCTCGAGCTGCCGCTGGATTCTGCGACCACCGAAAGCCTGCGTGCGGCAACGCACGACGTGCTGGCTGGCCTGACCGCGCGTGAAGCAAAAGTTCTGCGTATGCGTTTCGGTATc                                                                >  2:17658/1‑149 (MQ=255)
                                                                             ttgcagttGGGGGCTTTCAGCGAGGATCCCACCCTCTTGTTTTTGCATGATTCGGCGACCACCGAGAGCCTGCGTGCGGCAACGCACGACGTGCTGGCTGGCCTGACCGCGCGTGAAGCAAAAGTTCTGCGTATGCGTTTCGGTATCGa                                                              <  1:115154/142‑1 (MQ=255)
                                                                                         tacgtCATCCAGCAAACCACCCCCGAGCTGCCTAATGATACGGCGACCACCGAAAGCCTGCGTGCGGCAACGCACGACGTGCTGGCTGGCCTGACCGCGCGTGAAGCAAAAGTTCTGCGTATGCGTTTCGGTATCGATATGAACACCGa                                                  <  1:89085/145‑1 (MQ=255)
                                                                                         gATTTCATCGAGGATACCCCCCTCGAGCTGCCGCTGGATTCTGTGACCACCGAAAGCCTGCGTGCGGCAACGCACGACGTGCTGGCTGGCCTGACCGCGCGTGAAGCAAAAGTTCTGCGTATGCGTTTCGGTATCGATATGAACACCGa                                                  <  1:103450/149‑1 (MQ=255)
                                                                                            ttCATCGAGGATACCACCCTCGAGCTGCCGCTGGATTCTGCGACCACCGACAGCCTGCGTGCGGCAACGCACGACGTGCTGGCTGGCCTGACCGCGCGTGAAGCAAAAGTTCTGCGTATGCGTTTCGGTATCGATATGAACACCGACTa                                               <  2:260232/149‑1 (MQ=255)
                                                                                              cATCGAGGATACCACCCTCGAGCTGCCGCTGGATTCTGCGACAAACGAAAGCCTGCGTGCGGCAACGCACGACGTGCTGGCTGGCCTGACCGCGCGTGAAGCAAAAGTTCTGCGTATGCGTTTCGGTATCGATATGAACACCGACTaca                                             <  2:294490/149‑1 (MQ=255)
                                                                                                      aTACCACCCTCGAGCTGCCGCTGGATTCTGCGACCACCGAAAGCCTGCGTGCGGCAACGCACGACGTGCTGGCTGGCCTGACCGCGCGTGAAGCAAAAGTTCTGCGTATGCGTTTCGGTATCGATATGAACACCGACTACACGCTGgaa                                     <  2:240455/149‑1 (MQ=255)
                                                                                                       tACCCCCCGCGAGCTGCCGCTGGATTCGGCGACCACCGAAAGCCTGCGTGCGGCAACGCACGACGTGCTGGCTGGCCTGACCGCGCGTGAAGCAAAAGTCCTGCGTATGCGTTTCGGTATCGATATGAACACCGACTACACGCTGgaag                                    <  2:287180/149‑1 (MQ=255)
                                                                                                             cctggtgCTGCCGCTGGATTCTGCGACCACCGAGAGCCTGCGTGCGGCAACGCACGACGTGCTGGCTGGCCTGACCGCGCGTGAAGCAAAAGTTCTGCGTATGCGTTTCGGTATCGATATGAACACCGACTACACGCTGGAAGAAGTgg                              <  1:207547/143‑1 (MQ=255)
                                                                                                                cGAGCTTCCGCTGGATTCTGCGACCACCGAAAGCCTGCGTGCGGCAACGCACGACGTGCTGGCTGGCCTGACCGCGCGTGAAGCAAAAGTTCTGCGTATGCGTTTCGGTATCGATATGAACACCGACTACACGCTGGAAGAAGTGGGTa                           <  2:241447/149‑1 (MQ=255)
                                                                                                                  tgtttctgCTGGATTCGGCGACCACCGAGAGCCTGCGTGCGGCAACGCACGACGTGCTGGCTGGCCTGACCGCGCGTGAAGCAAAAGTTCTGCGTATGCGTTTCGGTATCGATATGAACACCGACTACACGCTGGAAGAAGTGGGTaaa                         <  1:234426/142‑1 (MQ=255)
                                                                                                                        gccgggATTCGGCGACCACCGACGGCCTGCGGGCGGCAACGTACGACGTGCTGGCTGGCCTGACCGCGCGTGAAGCAAAAGTTCTGCGTATGCGTTTCGGTATCGATATGAACACCGACTACACGCTGGAAGAAGTGGGTAAACAGTTc                   <  1:85423/145‑1 (MQ=255)
                                                                                                                        cGCTGGATTCGGCGACCACCGAAAGCCTGCGTGCGGCAACGCACGACGTGCTGGCTGGCCTGACCGCGCGTGAAGCAAAAGTTCTGCGTATGCGTTTCGGTATCGATATGAACACCGACTACACGCTGGAAGAAGTGGGTAAACAGTTc                   <  1:37623/149‑1 (MQ=255)
                                                                                                                                tCTGCGACCACCGAAAGCCTGCGTGCGGCAACGCACGACGTGCTGGCTGGCCTGACCGCGCGTGAAGCAAAAGTTCTGCGTATGCGTTTCGGTATCGATATGAACACCGACTACACGCTGGAAGAAGTGGGTAAACAGTTCGACGTTAc           >  2:230728/1‑149 (MQ=255)
                                                                                                                                     gACCACCGAAAGCCTGCGTGCGGCAACGCACGACGTGCTGGCTGGCCTGACCGCGCGTGAAGCAAAAGTTCTGCGTCTGCGTTTCGGTATCGATATGAACACCGACTCCACGCTGGAAGAAGTGGGTAAACAGTTCGACGTTACCcgcg      <  2:76422/149‑1 (MQ=255)
                                                                                                                                         accGAAAGCCTGCGTGCGGCAACGCACGACGTGCTGGCTGGCCTGACCGCGCGTGAAGCAAAAGTTCTGCGTATGCGTTTCGGTATCGATATGAACACCGACTACACGCTGGAAGAAGTGGGTAAACAGTTCGACGTTACCCGCGAACg  >  2:112685/1‑149 (MQ=255)
                                                                                                                                              |                                                                                                                                               
AAGACAAGATCCGCAAAGTGCTGAAGATCGCCAAAGAGCCAATCTCCATGGAAACGCCGATCGGTGATGATGAAGATTCGCATCTGGGGGATTTCATCGAGGATACCACCCTCGAGCTGCCGCTGGATTCTGCGACCACCGAAAGCCTGCGTGCGGCAACGCACGACGTGCTGGCTGGCCTGACCGCGCGTGAAGCAAAAGTTCTGCGTATGCGTTTCGGTATCGATATGAACACCGACTACACGCTGGAAGAAGTGGGTAAACAGTTCGACGTTACCCGCGAACG  >  CP009273/3207877‑3208162

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 8 ≤ ATCG/ATCG < 12 ≤ ATCG/ATCG < 32 ≤ ATCG/ATCG < 41 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑