Predicted mutation
evidence seq id position mutation freq annotation gene description
RA KT2440 1,584,539 A→C 20.0% G137G (GGT→GGG)  rhaS_1 ← HTH‑type transcriptional activator RhaS

Read alignment evidence...
  seq id position ref new freq score (cons/poly) reads annotation genes product
*KT24401,584,5390AC20.0% 77.9 / 6.0 52G137G (GGT→GGG) rhaS_1HTH‑type transcriptional activator RhaS
Reads supporting (aligned to +/- strand):  ref base A (28/12);  new base C (2/9);  total (31/21)
Fisher's exact test for biased strand distribution p-value = 4.06e-03
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 1.00e+00

CCCACGCAGCAGGCGGTAGAGAATCTCGCGGCGGAACAGCGGCGCCAGCATTGCGATGTCGCGAGGGGTGTCCAGCAGCCGCAGCAACCGCAGCAGGGCATCGAGTAACGCGGCATCTGTCCTTTCCACATACAAACCACGGCCGGAAGGTCGATTGGGTACCAGCATTGGCCCGCTCTCGGCGATCAGTTGGCTGATCTCCGCCGGGTCCAGGTCCATGCGCAGGCCCAGGCTTGGGTTCTCGGGGCTGGCATCCAGCCTCACGGC  >  KT2440/1584404‑1584670
                                                                                                                                       |                                                                                                                                   
cccACGCAGCAGGCGGTAGAGAATCTCGCGGCGGAACAGCGGCGCCAGCATTGCGATGTCGCGAGGGGTGTCCAGCAGCCGCAGCAACCGCAGCAGGGCATCGAGTAACGCGGCATCTGTCCTTTCCACATACaaa                                                                                                                                     >  7:422876/1‑136 (MQ=255)
     gcagcaGGCGGTAGAGAATCTCGCGGCGGAACAGCGGCGCCAGCATTGCGATGTCGCGAGGGGTGTCCAGCAGCCGCAGCAACCGCAGCAGGGCATCGAGTAACGCGGCATCTGTCCTTTCCACATACAAACCAc                                                                                                                                 >  6:266392/1‑135 (MQ=255)
      cagcagGCGGTAGAGAATCTCGCGGCGGAACAGCGGCGCCAGCATTGCGATGTCGCGAGGGGTGTCCAGCAGCCGCAGCAACCGCAGCAGGGCATCGAGTAACGCGGCATCTGTCCTTTCCACATACAAACCACgg                                                                                                                               >  8:76854/1‑136 (MQ=255)
      cagcagGCGGTAGAGAATCTCGCGGCGGAACAGCGGCGCCAGCATTGCGATGTCGCGAGGGGTGTCCAGCAGCCGCAGCAACCGCAGCAGGGCATCGAGTAACGCGGCATCTGTCCTTTCCACATACAAACCACgg                                                                                                                               >  7:177433/1‑136 (MQ=255)
      cagcagGCGGTAGAGAATCTCGCGGCGGAACAGCGGCGCCAGCATTGCGATGTCGCGAGGGGTGTCCAGCAGCCGCAGCAACCGCAGCAGGGCATCGAGTAACGCGGCATCTGTCCTTTCCACATACAAACCACg                                                                                                                                >  3:391901/1‑135 (MQ=255)
      cagcagGCGGTAGAGAATCTCGCGGCGGAACAGCGGCGCCAGCATTGCGATGTCGCGAGGGGTGTCCAGCAGCCGCAGCAACCGCAGCAGGGCATCGAGTAACGCGGCATCTGTCCTTTCCACATACAAACCACg                                                                                                                                >  4:149313/1‑135 (MQ=255)
       agctgGCGGTAGAGAATCTCGCGGCGGAACAGCGGCGCCAGCATGGCGATGGCGCGAGGGGGGTCCAGCAGCCGCAGCAACCGCAGCAGGGCATCGAGTAACGCGGCATCTGTCCTTTCCACATACAAACCACGGc                                                                                                                              <  7:293335/136‑1 (MQ=255)
       agcagGCGGTAGAGAATCTCGCGGCGGAACAGCGGCGCCAGCATTGCGATGTCGCGAGGGGTGTCCAGCAGCCGCAGCAACCGCAGCAGGGCATCGAGTAACGCGGCATCTGTCCTTTCCACATACAAACCACgg                                                                                                                               >  1:334836/1‑135 (MQ=255)
                  tagaATCTCGCGGCGTAACCGCGGCGCCAGCTTTGCGATGTCGCGTGGGGGGACCTCCAGCCGCAGCAACCGCAGCAGGGCATCGAGAAACGCGGCAGCTGTCCTTTCCAAATACAAACCACGGCCGGAAGGTCGa                                                                                                                   <  8:252574/135‑1 (MQ=255)
                  gataaTCGCGCGGCGGAACCGCGGCGCCAGCTTGGCTATGGCGGGTGGGGGTGCCAGCAGCCCCACCAACCGCCGCTGGGCATCTAGTACCGCGGATTCTGTCCTAACCACAAACAAACCACGGCCGGAAGGTCGa                                                                                                                   <  8:384356/133‑1 (MQ=255)
                    gaATCTCGCGGCGGAACAGCGGCGCCAGCATTGCGATGTCGCGAGGGGTGTACAGCAGCCGCAGCAACCGCCCCAGCGCATCGAGTAACGCGGCATCTGTCCTTTCCCCATACAAGCCACGCCCGGAAGGTCGAt                                                                                                                  >  5:301063/1‑135 (MQ=255)
                       gctcGCGGCGTAACTGCGGCGCCAGCTTTGCGAGGTCGGGTGGGGGGCCCAGCCCCCGATGCAACCGCTGCTGGGCATCGAGAAACGCGGCATCTGACCTTACCACATACAACCCACGGCCGGAAGGTCGATTggg                                                                                                              <  8:417598/135‑1 (MQ=255)
                        cacgcgGGGTAACAGGGGCGCCAGCTTTGCGATGTCGGTCGGTGTGTCCAGCAGCCGCAGCAACCGCAGCAGGGCATGGATTACCGGGGATTCTGTCCTTACCAAAAACAACCCACGGCCGGAAGGTCGATTggg                                                                                                              <  6:410725/133‑1 (MQ=255)
                          cgcgGCGGACCCGCGGCGCCAGCTTTGCGAGGGCGCGTGGGGTGCCCACCAGCCGCAGCAACCGCAGCAGGGCAGCGAGTCACGCGGCATCTGTCCTTACCACAAACAAACCACGGCCGGAAGGTCGATTggg                                                                                                              <  6:81801/133‑1 (MQ=255)
                             ggcggAACAGCGGCGCCAGCATTGCGATGTCGCGAGGGGTGTCCAGCAGCCGCAGCAACCGCAGCAGGGCATCGAGTAACGCGGCATCTGTCCTTTCCACATACAAACCACGGCCGGAAGGTCGATTGGGTACCa                                                                                                         >  5:90089/1‑135 (MQ=255)
                                ggAACAGCGGCGCCAGCATTGCGAGGTCGCGAGGGGTGTCCCGCAGCCGCAGCACCCGCAGCAGGGCATCGAGTAACGCGGCATCTGTCCTTGCCACATACAACCCACGGCCGGAAGGTCCATTGGGTACCAGCa                                                                                                      >  6:50095/1‑135 (MQ=255)
                                    cAGCGGCGCCAGCATTGCGATGTCGCGAGGGGTGTCCAGCAGCCGCAGCAACCGCAGCAGGGCATCGAGTAACGCGGCATCTGTCCTTTCCACATACAAACCACGGCCGGAAGGTCGATTGGGTACCAGCATTGGc                                                                                                 >  7:47202/1‑136 (MQ=255)
                                    cAGCGGCGCCAGCATTGCGATGTCGCGAGGGGTGTCCAGCAGCCGCAGCAACCGCAGCAGGGCATCGAGTAACGCGGCATCTGTCCTTTCCACATACAAACCACGGCCGGAAGGTCGATTGGGTACCAGCATTGGc                                                                                                 >  7:40150/1‑136 (MQ=255)
                                            ccAGCATTGCGATGTCGCGAGGGGTGTCCAGCAGCCGCAGCAACCGCAGCAGGGCATCGAGTAACGCGGCATCTGTCCTTTCCACATACACACAACGGCCGGAAGGGCGATTGGGTACCAGCATTGGCCCGctca                                                                                          >  1:142247/1‑134 (MQ=255)
                                                            gggtggggCGCCCCGCCGCCGCCCCAACCGCCGGCGGCCAGCGAGTACCGCGGCAGTTGTCCTTACCACAACCAACCCACGGCCGGAAGGTCGATTGGGTACCAGCATTGGCCCGCTCTCGGCGATCAGTTGGCt                                                                          <  5:367125/131‑1 (MQ=255)
                                                             cgAGGGGTGTCCAGCAGCCGCAGCAACCGCAGCAGGGCATCGCGTAACGCGGCATCTGTCCTTTCCACATACAACCCACGGCCGGAAGGTCGATTGGGTACCAGCATTGGCCCGCTCTCGGCGATCAGTTGGCTg                                                                         >  2:265678/1‑135 (MQ=255)
                                                             cgAGGGGTGTCCAGCAGCCGCAGCAACCGCAGCAGGGCATCGAGTAACGCGGCATCTGTCCTTTCCACATACAAACCACGGCCGGAAGGTCGATTGGGTACCAGCATTGGCCCGCTCTCGGCGATCAGTTGGCTg                                                                         >  1:52782/1‑135 (MQ=255)
                                                                ggggTGTCCAGCAGCCGCAGCAACCGCAGCAGGGCATCGAGTAACGCGGCATCTGTCCTTTCCACATACAAACCACGGCCGGAAGGTCGATTGGGTACCAGCATTGGCCCGCTCTCGGCGATCAGTTGGCTGAtct                                                                     >  7:435312/1‑136 (MQ=255)
                                                                  ggTGTCCCCCCGCCGCCCCAACCGCCGCAGGGCATCGAGAAACGCGGAAGCTGGCCTTACCACAAACAACCCACGGCCGGAAGGTCGATTGGGTACCAGCATTGGCCCGCTCTCGGCGATCAGTTGGCTGATCTcc                                                                   <  8:222925/136‑1 (MQ=255)
                                                                  ggTGTCCAGCAGCCGCAGCAACCGCAGCAGGGCATCGAGTAACGCGGCATCTGTCCTTTCCACATACAAACCACGGCCGGAAGGTCGATTGGGTACCAGCATTGGCCCGCTCTCGGCGATCAGTTGGCTGATCTcc                                                                   >  7:205330/1‑136 (MQ=255)
                                                                   gtgcCCCGCCGCCGCAGCAACCGCGGCGGGGCATCGCGTACGGCGGAAACTGTCCTAACCACAAACCACCCACGGCCGGAAGGTCGATTGGGTACCAGCATTGGCCCGCTCTCGGCGATCAGTTGGCTGATCTcc                                                                   <  2:445330/135‑1 (MQ=255)
                                                                   gggtCCAGCTGCCGCAGCAACCGCAGCAGGGAATCGAGTAACGCGGCATGTGTCCTTTCAACATACAAACCACGGCCGGAAGGTCGATTGGGTACCAGCATTGGCCCGCTCTCGGCGATCAGTTGGCTGATCTcc                                                                   <  4:391901/133‑1 (MQ=255)
                                                                        cagcacCCCCAGCAACCGCAGCAGGGCATCGAGTAACGCGGCATGTGGCCTTTCCACATACAACCCACGGCCGGAAGGTCGATTGGGTACCAGCATTGGCCCGCTCTCGGCGATCAGTTGGCTGATCTCCGCCgg                                                              <  6:90089/135‑1 (MQ=255)
                                                                         agcagcCGCCGCAACCGCAGCAGGGCATCGAGTAACGCGGCATCTGTCCTTTCCACATACAAACCACGGCCGGAAGGTCGATTGGGTACCAGCATTGGCCCGCTCTCGGCGATCAGTTGGCTGATCTCCGCCggg                                                             >  3:343867/1‑135 (MQ=255)
                                                                         agcagcCGCAGCAACCGCAGCAGGGCATCGAGTAACGCGGCATCTGTCCTTTCCACATACAAACCACGGCCGGAAGGTCGATTGGGTACCAGCATTGGCCCGCTCTCGGCGATCAGTTGGCTGATCTCCGCCggg                                                             >  2:417183/1‑135 (MQ=255)
                                                                         agcagcCGCAGCAACCGCAGCAGGGCATCGAGTAACGCGGCATCTGTCCTTTCCACATACAAACCACGGCCGGAAGGTCGATTGGGTACCAGCATTGGCCCGCTCTCGGCGATCAGTTGGCTGATCTCCGCCGggt                                                            >  8:367751/1‑136 (MQ=255)
                                                                             cccGCAGCAACGTCTGCTGGGCATCGATAAACGGGGCATGTGTCCTTTCCCCATACAAACCACGGCCGGAAGGTCGATTGGGTACCAGCATTGGCCCGCTCTCGGCGATCAGTTGGCTGATCTCCGCCGggtcca                                                         <  6:323980/134‑1 (MQ=255)
                                                                               cGCAGCAACCGCAGCAGGGCATCGAGTAACGCGGCATCTGTCCTTTCCACATACAAACCACGGCCGGAAGGTCGATTGGGTACCAGCATTGGCCCGCTCTCGGCGATCAGTTGGCTGATCTCCGCCGggtccagg                                                       >  6:334533/1‑135 (MQ=255)
                                                                                gcaccaACCGCAGCTGGGCATCTAGAAACGCGGCATCTGTCCTTTCCAAATAAAAACCACGGCCGGAAGGTCGATTGGGTACCAGCATTGGCCCGCTCTCGGCGATCAGTTGGCTGATCTCCGCCGggtccaggt                                                      <  6:227370/135‑1 (MQ=255)
                                                                                 cagcaACCGCAGCAGGGCATCGAGTAACGCGGCATCTGTCCTTTCCACATACAAACCACGGCCGGAAGGTCGATTGGGTACCAGCATTGGCCCGCTCTCGGCGATCAGTTGGCTGATCTCCGCCGggtccaggt                                                      >  3:145448/1‑134 (MQ=255)
                                                                                   gcaCCCGCAGCAGGCCATCCCGAACCGCGGCAGCTGTCCTTCCCACATACACCCCACGGCCGGAAGGTCGATTGGGTACCAGCATTGGCCCGCTCTCGGCGATCAGTTGGCTGATCTCCGCCGGGTCCAGGTCCAt                                                  <  8:177433/136‑1 (MQ=255)
                                                                                   gcaACCGCAGCAGGGCATCGAGTAACGCGGCATCTGTCCTTTCCACATACAAACCACGGCCGGAAGGTCGATTGGGTACCAGCATTGGCCCGCTCTCGGCGATCAGTTGGCTGATCTCCGCCGGGTCCAGGTCCAt                                                  >  8:217218/1‑136 (MQ=255)
                                                                                   gcaACCGCAGCAGGGCATCGAGTAACGCGGCATCTGTCCTTTCCACATACAAACCACCGCCGGAAGGTCGATTGGGTACCAGCATTGGCCCGCTCTCGGCGATCAGTTGGCTGATCTCCGCCGGGTCCAGGTCCAt                                                  >  8:398825/1‑136 (MQ=255)
                                                                                     acccgccgCTGGGCAGCGTTTCAGGCGGCATCGGGCCTTTCCACATACACACCACGGCCGGAAGGTCGATTGGGTACCAGCATTGGCCCGCTCTCGGCGATCAGTTGGCTGATCTCCGCCGGGTCCAGGTCCATg                                                 <  4:310230/133‑1 (MQ=255)
                                                                                         gcagcaGGGCATCGAGTAACGCGGCATCTGTCCTTTCCACATACAAACCACGGCCGGAAGGTCGATTGGGTACCAGCATTGGCCCGCTCTCGGCGATCAGTTGGCTGATCTCCGCCGGGTCCAGGTCCATGCGCAg                                            <  7:217218/136‑1 (MQ=255)
                                                                                         gcagcaGGGCAGCGAGTAACGCGGCATCTGTCCTTTCCACATACAAACCACGGCCGGAAGGTCGATTGGGTACCAGCATTGGCCCGCTCTCGGCGATCAGTTGGCTGATCTCCGCCGGGTCCAGGTCCATGCGCAg                                            <  8:39508/136‑1 (MQ=255)
                                                                                          cagccgGCCATCGCCTAACGCGGCCTCTGGCCTTACCAAAAACAACCCACGGCCCGTAGGTCGTATGGGTACCAGCATTGGCCCGCTCTCGGCGATCAGTTGGCTGATCTCCGCCGGGTCCAGGTCCATGCGCAg                                            <  4:12204/135‑1 (MQ=255)
                                                                                          cagcagGGCATCGAGTAACGCGGCATCTGGCCTTACCACAAACACACCACGGCCGGAAGGTCGATTGGGTACCAGCATTGGCCCGCTCTCGGCGATCAGTTGGCTGATCTCCGCCGGGTCCAGGTCCATGCGCAg                                            <  4:434580/135‑1 (MQ=255)
                                                                                               gggCATCGAGTAACGCGGCATCTGTCCTTTCCACATACAAACCACGGCCGGAAGGTCGATTGGGTACCAGCATTGGCCCGCTCTCGGCGATCAGTTGGCTGATCTCCGCCGGGTCCAGGTCCATGCGCAGGCCCa                                       >  1:135245/1‑135 (MQ=255)
                                                                                                    tCGAGTAACGCGGCATCTGTCCTTTCCACATACAAACCACGGCCGGAAGGTCGATTGGGTACCAGCATTGGCCCGCTCTCGGCGATCAGTTGGCTGATCTCCGCCGGGTCCAGGTCCATGCGCAGGCCCAGGCtt                                  >  4:108403/1‑135 (MQ=255)
                                                                                                        gTAACGCGGCATCTGTCCTTTCCACATACAAACCACGGCCGGAAGGTCGATTGGGTACCAGCATTGGCCCGCTCTCGGCGATCAGTTGGCTGATCTCCGCCGGGTCCAGGTCCATGCGCAGGCCCAGGCTTGGGtt                             >  7:50371/1‑136 (MQ=255)
                                                                                                          aaCGCGGCATCTGTCCTTTCCACATACAAACCACGGCCGGAAGGTCGATTGGGTACCAGCATTGGCCCGCTCTCGGCGATCAGTTGGCTGATCTCCGCCGGGTCCAGGTCCATGCGCAGGCCCAGGCTTGGGTtct                           >  7:94882/1‑136 (MQ=255)
                                                                                                               ggCATCTGTCCTTTCCACATACAAACCACGGCCGGAAGGTCGATTGGGTACCAGCATTGGCCCGCTCTCGGCGATCAGTTGGCTGATCTCCGCCGGGTCCAGGTCCATGCGCAGGCCCAGGCTTGGGTTCTCggg                       >  4:319848/1‑135 (MQ=255)
                                                                                                               ggCAACTGTCCTTTCCACATACAAACCACCGCCGGAAGGGCGATTTGGAACCAGAATTGGCCCGCTCACGTCGATCAGTTGGATCATCTCCGCCGGGTCCAGGTCCAAGCGCAGGCCCACCCTTCGGTTCTCgggg                      >  8:339969/1‑136 (MQ=255)
                                                                                                                          tttCCACATACAAACCACGGCCGGAAGGTCGATTGGGTACCAGCATTGGCCAGCTCTCGGCGATCAGTTGGCTGATCTCCGCCGGGTCCAGGTCCATGCGCAGGCCCAGGCTGGGGTTCTCGGGGCTGGCGTCCa            >  3:274780/1‑135 (MQ=255)
                                                                                                                                    cAACCCACGGCCGGACGGTCGATTGGGTACCAGCATTGGCCCGCTCTCGGCGATCAGTTGGCGGAGCTCCGCCGGGTCCAGGTCCATGCGCAGGCCCAGGCTGGGGGTCTCGGGGCTGGCATCCAGCCTCACGgc  <  1:101233/135‑1 (MQ=255)
                                                                                                                                    cAAACCACGGCCGGAAGGTCGATTGGGTACCAGCATTGGCCCGCTCTCGACGATCAGTTGGCTGATCTCCGCCGGGTCCAGGTCCATGCGCAGGCCCAGGCTTGGGt                              >  8:300819/1‑107 (MQ=255)
                                                                                                                                    cAAACCACGGCCGGAAGGTCGATTGGGTACCAGCATTGGCCCGCTCTCGACGATCAGTTGGCTGATCTCCGCCGGGTCCAGGTCCATGCGCAGGCCCAGGCTTGGGt                              <  7:300819/107‑1 (MQ=255)
                                                                                                                                       |                                                                                                                                   
CCCACGCAGCAGGCGGTAGAGAATCTCGCGGCGGAACAGCGGCGCCAGCATTGCGATGTCGCGAGGGGTGTCCAGCAGCCGCAGCAACCGCAGCAGGGCATCGAGTAACGCGGCATCTGTCCTTTCCACATACAAACCACGGCCGGAAGGTCGATTGGGTACCAGCATTGGCCCGCTCTCGGCGATCAGTTGGCTGATCTCCGCCGGGTCCAGGTCCATGCGCAGGCCCAGGCTTGGGTTCTCGGGGCTGGCATCCAGCCTCACGGC  >  KT2440/1584404‑1584670

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 14 ≤ ATCG/ATCG < 15 ≤ ATCG/ATCG < 27 ≤ ATCG/ATCG < 36 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑