Predicted mutation
evidence seq id position mutation freq annotation gene description
RA KT2440 4,163,919 C→T 7.7% intergenic (‑382/‑5) katG ← / → leuO_2 Catalase‑peroxidase/HTH‑type transcriptional regulator LeuO

Read alignment evidence...
  seq id position ref new freq score (cons/poly) reads annotation genes product
*KT24404,163,9190CT 7.7% 168.8 / 3.6 52intergenic (‑382/‑5)katG/leuO_2Catalase‑peroxidase/HTH‑type transcriptional regulator LeuO
Reads supporting (aligned to +/- strand):  ref base C (37/11);  new base T (2/2);  total (39/13)
Fisher's exact test for biased strand distribution p-value = 2.57e-01
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 5.82e-01

GAGGCCGGCACATCCATACAAGGCACAAGGCCCCGCGCCATGCTTCAATACACAGCCATACCCTTTGCCCAGGACGCCGAGCCCTCATGAACCGCAACGACCTGCGCCGCGTCGACATGAACCTGCTGGTGCTGTTCGAAGCCCTGATGATCGAACGCAACCTGACCCGCGTGGGTGAAAAGCTGTTTATCACCCAATCCACCGTCAGCGCCGCC  >  KT2440/4163838‑4164052
                                                                                 |                                                                                                                                     
gggcccGGCACATCCATACAAGGCACAAGGCCCCGCGCCATGCTTCAATACACAGCCATACCCTTTGCCCAGGACGCCGAGCCCTCATGAACCGCAACGACCTGCGCCGCGTCGACATGAACCTGCTGGTGCTGt                                                                                  <  8:172528/131‑1 (MQ=255)
  ccccGGCACATCCATACAAGGCACAAGGCCCCGCGCCATGCTTCAATACACAGCCATACCCTTTGCCCAGGACGCCGAGCCCTCATGAACCGCAACGACCTGCGCCGCGTCGACATGAACCTGCTGGTGCTGTTc                                                                                <  6:55319/133‑1 (MQ=255)
      ggCACATCCATACCAGGCACAAGGCCCCGCGCCATGCTTCAATACACAGCCATACCCTTTGCCCAGGACGCCGAGCCCTCATGAACCGCAACGACCTGCGCCGCGTCGACATGAACCTGCTTGTGCTGTTCGacg                                                                            >  6:241101/1‑133 (MQ=255)
                tACAAGCCACAAGGCACCGCGCCATGCTTCAATACACAGCAATACCCTTTGCCCAGTACGCCGCGCCCTCATGAACCGCAACGACCTGCGCCGCGTCGACATCAACCTGCTGCTGCTGTTCGACGCCCTgattat                                                                  >  1:211835/1‑135 (MQ=255)
                  caagccacacggcCCCGCGCCATGCTTCAATACACAGCCATACCCTTTGCCCAGGACGCCGAGCCCTCATGAACCGCAACGACCTGCGCCGCGTCGACATGAACCTGCTGGTGCTGTTCGAAGCCCTGATGATCg                                                                <  5:32543/135‑1 (MQ=255)
                        acaaggcCCCGCGCCATGCTTCAATACACAGCCATACCCTTTGCCCAGGACGCCGAGCCCTCATGAACCGCAACGACCTGCGCCGCGTCGACATGAACCTGCTGGTGCTGTTc                                                                                >  4:72897/1‑113 (MQ=255)
                        acaaggcCCCGCGCCATGCTTCAATACACAGCCATACCCTTTGCCCAGGACGCCGAGCCCTCATGAACCGCAACGACCTGCGCCGCGTCGACATGAACCTGCTGGTGCTGTTc                                                                                <  3:72897/113‑1 (MQ=255)
                        acaaggcCCCGCGCCATGCTTCAATACACAGCCATACCCTTTGCCCAGGACGCCGAGCCCTCATGAACCGCAACGACCTGCGCCGCGTCGACATGAACCTGCTGGTGCTGTTCGAAGCCCTGATGATCGAACGCa                                                          >  1:188942/1‑135 (MQ=255)
                        acaaggcCCCGCGCCATGCTTCAATACACAGCCATACCCTTTGCCCAGGACGCCGAGCCCTCATGAACCGCAACGACCTGCGCCGCGTCGACATGAACCTGCTGGTGCTGTTCGAAGCCCTGATGATCGAACGCa                                                          >  6:13460/1‑135 (MQ=255)
                        acaaggcCCCGCGCCATGCTTCAATACACAGCCATACCCTTTGCCCAGGACGCCGAGCCCTCATGAACCGCAACGACCTGCGCCGCGTCGACATGAACCTGCTGGTGCTGTTCGAAGCCCTGATGATCGAACGCa                                                          >  1:59517/1‑135 (MQ=255)
                        acaaggcCCCGCGCCATGCTTCAATACACAGCCATACCCTTTGCCCAGGACGCCGAGCCCTCATGAACCGCAACGACCTGCGCCGCGTCGACATGAACCTGCTGGTGCTGTTCGAAGCCCTGATGATCGAACGCa                                                          >  5:336426/1‑135 (MQ=255)
                        acaaggcCCCGCGCCATGCTTCAATACACAGCCATACCCTTTGCCCAGGACGCCGAGCCCTCATGAACCGCAACGACCTGCGCCGCGTCGACATGAACCTGCTGGTGCTGTTCGAAGCCCTGATGATCGAACGCa                                                          >  6:62168/1‑135 (MQ=255)
                        acaaggcCACGCGCCATGCTTCAATACACAGCCATACCCTTAGCACAGGACTCCGAGCCCTCATGAACCGCAACGACCTGCGCCGCGTCGACATGAACCTGCTGGTGCTGTTCGAAGCCCTGATGATCGAACGCa                                                          >  7:146719/1‑135 (MQ=255)
                             gcCCCGCGCCATGCTTCAATACACAGCCATACCCTTTGCCCAGGACGCCGAGCCCTCATGAACCGCAACGACCTGCGCCGCGTCGACATGAACctgctg                                                                                         <  8:93956/99‑1 (MQ=255)
                             gcCCCGCGCCATGCTTCAATACACAGCCATACCCTTTGCCCAGGACGCCGAGCCCTCATGAACCGCAACGACCTGCGCCGCGTCGACATGAACctgctg                                                                                         >  7:93956/1‑99 (MQ=255)
                                    gcCATGCTTCAATACACAGCCATACCCTTTGCCCAGGACGCCGAGCCCTCATGAACCGCAACGCCCTGCGCCGCGTCGACATGAACCTGCTGGTGCTGTGCGAAGCCCTGATGATCGAACGCAACCTGACCcgcg                                              >  5:195219/1‑135 (MQ=255)
                                           ttCAATACACAGCCATCCCCTTAGCCCAGGACGCCGAGCCCGCATGAACCGCACCCCCCAGCGCCCCGTCGACATGATCAGGCTGGAGCGCTTCGAAGACCTCAGGATCCAACGCCCCCGGACCCGCGTGGGTGa                                       >  3:176137/1‑135 (MQ=255)
                                           ttCAATACACAGCCATACCCTTTGCCCAGGACGCCGAGCCCTCATGAACCGCAACGACCTGCGCCGCGTCGACATGAACCTGCTGGTGCTGTTCGAAGCCCTGATGATCGAACGCAACCTGACCCGCGTGGGTg                                        >  3:158924/1‑134 (MQ=255)
                                              aaTACACAGCCATACCCTTTGCCCAGGACGCCGAGCCCTCATGAACCGCAACGAGCTGCGCCGCGTCGACATGAACCTGCTGGTGCTGTTCGAAGCCCTGATGATCGAACGCAACCTGACCCGCGTGGGTGaaa                                     <  5:101672/134‑1 (MQ=255)
                                                 acacAGCCATACCCTTTGCCCAGGACGCCGAGCCCTCATGAACCGCAACGACCTGCGCCGCGTCGACATGAACCTGCTGGTGCTGTTCGAAGCCCTGATGATCGAACGCAACCTGACCCGCGTGGGTGAAAAGCt                                 >  7:70611/1‑135 (MQ=255)
                                                   acaGCCATACCCTTTGCCCAGGACGCCGAGCCCTCATGAACCGCAACGACCTGCGCCGCGTCGACATGAACCTGCTGGTGCTGTTCGAAGCCCTGATGATCGAACGCAACCTGACCCGCGTGGGTGAAAAGCTGt                               <  5:278259/135‑1 (MQ=255)
                                                        cATACCCTTTGCCCAGGACGCCGAGCCCTCATGAACCGCAACGACCTGCGCCGCGTCGACATGAACCTGCTGGTGCTGt                                                                                  >  3:5997/1‑79 (MQ=255)
                                                        cATACCCTTTGCCCAGGACGCCGAGCCCTCATGAACCGCAACGACCTGCGCCGCGTCGACATGAACCTGCTGGTGCTGt                                                                                  <  4:5997/79‑1 (MQ=255)
                                                        cATACCCTTTGCCCAGGACGCCGAGCCCTCATGAACCGCAACGACCTGCGCCGCGTCGACATGAACCTGCTGGTGCTGTTCGAAGCCCTGATGATCGATCGCAACCTGACCCGCGTGGGTGAAAAGCTGTTTATc                          >  1:232120/1‑135 (MQ=255)
                                                        cATACCCTTTGCCCAGGACGCCGAGCCCTCATGAACCGCAACGACCTGCGCCGCGTCGACATGAACCTGCTGGTGCTGTTCGAAGCCCTGATGATCGAACGCAACCTGACCCGCGTGGGTGAAAAGCTGTTTATc                          >  6:166759/1‑135 (MQ=255)
                                                        cATACCCTTTGCCCAGGACGCCGAGCCCTCATGAACCGCAACGACCTGCGCCGCGTCGACATGAACCTGCTGGTGCTGTTCGAAGCCCTGATGATCGAACGCAACCTGACATGCGTGGGAGAAAAGCTGTTTATc                          >  7:49987/1‑135 (MQ=255)
                                                        cATACCCTTTGCCCAGGACGCCGAGCCCTCATGAACCGCAACGACCTGCGCCGCGTCGACATGAACCTGCTGGTGCTGTTCGAAGCCCTGATGATCGAAAGCAACCTGACCCGCGTGGGTGAAAAGCTGTTTAta                          >  3:69735/1‑134 (MQ=255)
                                                        cATACCCTTTGCCCAGGACGCCGAGCCCTCATGAAACGCAACGACCTGCGCCGCGTCGACATGAACCTGCTGGTGCTGTTCGAAGCCCTGATGATCGAACGCAACCTGACCCGCGTGGGTGAAAAGCTGTTTATc                          >  5:314690/1‑135 (MQ=255)
                                                          tACCCTTTGCCCAGGACGCCGAGTCCTCATGAACCGCAACGACCTGCGCCGCGTCGACATGAACCTGCTGGTGCTGTTCGAAGCCCTGATGATCGAACGCAACCTGACCCGCGTGGGTGaaaa                                    >  4:137966/1‑123 (MQ=255)
                                                          tACCCTTTGCCCAGGACGCCGAGTCCTCATGAACCGCAACGACCTGCGCCGCGTCGACATGAACCTGCTGGTGCTGTTCGAAGCCCTGATGATCGAACGCAACCTGACCCGCGTGGGTGaaaa                                    >  4:132638/1‑123 (MQ=255)
                                                          tACCCTTTGCCCAGGACGCCGAGTCCTCATGAACCGCAACGACCTGCGCCGCGTCGACATGAACCTGCTGGTGCTGTTCGAAGCCCTGATGATCGAACGCAACCTGACCCGCGTGGGTGaaaa                                    <  3:137966/123‑1 (MQ=255)
                                                          tACCCTTTGCCCAGGACGCCGAGTCCTCATGAACCGCAACGACCTGCGCCGCGTCGACATGAACCTGCTGGTGCTGTTCGAAGCCCTGATGATCGAACGCAACCTGACCCGCGTGGGTGaaaa                                    <  3:132638/123‑1 (MQ=255)
                                                             ccTTTGCCCAGGACGCCGAGCCCTCATGAACCGCAACGACCTGCGCCGCGTCGACAt                                                                                                   >  7:330605/1‑57 (MQ=255)
                                                             ccTTTGCCCAGGACGCCGAGCCCTCATGAACCGCAACGACCTGCGCCGCGTCGACAt                                                                                                   <  8:330605/57‑1 (MQ=255)
                                                             ccTTTGCCCAGGACGCCGAGCCCTCATGAACCGCAACGACCTGCGCCGCGTCGACATGAACCTGCTGGTGCTGTTAGAAGCCCTGATGATCGAACGCAACCTGACCCGCGTGGGTGAAAAGCTGTTTATCACCCa                     >  8:171454/1‑135 (MQ=255)
                                                             ccTTTGCCCAGGACGCCGAGCCATCATGATCCCCAACAACCTGCGCCGCGGCGACATGAACCTGCTGGTGCTGTTCGAAGCCATGATGATCGAACGCAACCTGACCCGCGTGGGTGAAAAGATCTTAATcacaca                     >  2:122797/1‑135 (MQ=255)
                                                                  gCCCAGGACGCCGAGCCCTCATGAACCGCAACGACCTGCGCCGCGTCGACATGAACctgctg                                                                                         >  1:156615/1‑62 (MQ=255)
                                                                  gCCCAGGACGCCGAGCCCTCATGAACCGCAACGACCTGCGCCGCGTCGACATGAACctgctg                                                                                         <  2:156615/62‑1 (MQ=255)
                                                                  gCCCAGGACGCCGAGCCCTCATGAACCGCAACGACCTGCGCCGCGTCGACATGAACCTGCTGGTGCTGTTCGAAGCCCTGATGATCGAACGCAACCTGACCCTCGTGGGTGAAAAGCTGTTTATCACCCAATccc                >  2:259044/1‑134 (MQ=255)
                                                                    ccAGGACGCCGAGCCCTCATGAACCGCAACGTCCTGCGCCGCGTCGACATGAACCTGCTGGTGCTGTTCGAAGCCCTGATGATCGAACGCAACCTGACCCGCGTGGGTGAAAAGCTGttt                             <  1:136325/120‑1 (MQ=255)
                                                                    ccAGGACGCCGAGCCCTCATGAACCGCAACGACCTGCGCCGCGTCGACATGAACCTGCTGGTGCTGTTCGAAGCCCTGATGATCGAACGCAACCTGACCCGCGTGGGTGAAAAGCTGttt                             >  2:136325/1‑120 (MQ=255)
                                                                    ccAGGACGCCGAGCCCTCATGAACCGCAACGACCTGCGCCGCGTCGACATGAACCTGCTGGTGCTGTTCGAAGCCCTGATGATCGAACGCAACCTGACCCGCGTGGGTGAAAAGCTGTTTATCACCCAATCCAcc              >  5:88665/1‑135 (MQ=255)
                                                                    ccAGGACGCCGAGCCCTCATGAACCGCAACGACCTGCGCCGCGTCGACATGAACCTGCTGGTGCTGTTCGAAGCCCTGATGATCGAACGCAACCTGACCCGCGTGGGTGAAAAGCTGTTTATCACCCAATCCAcc              >  5:205495/1‑135 (MQ=255)
                                                                    ccAGGACGCCGAGCCCTCATGAACCGCAACGACCTGCGCCGCGTCGACATGAACCTGCTGGTGCTGTTCGAAGCCCTGATGATCGAACGCAACCTGACCCGCGTGGGTGAAAAGCTGTTTATCACCCAATCCAcc              >  7:11288/1‑135 (MQ=255)
                                                                    ccAGGACGCCGAGCCCTCATGAACCGCAACGACCTGCGCCGCGTCGACATGAACCTGCTGGTGCTGTTCGAAGCCCTGATGATCGAACGCAACCTGACCCGCGTGGGTGAAAAGCTGTTTATCACCCAATCCAcc              >  5:161057/1‑135 (MQ=255)
                                                                    ccAGGACGCCGAGCCCTCATGAACCGCAACGACCTGCGCCGCGTCGACATGAACCTGCTGGTGCTGTTCGAAGCCCTGATGATCGAACGCAACCTGACCCGCGTGGGTGAAAAGCTGTTTATCACCCAATCCAcc              >  3:60427/1‑135 (MQ=255)
                                                                    ccAGGACGCCGAGCCCTCATGAACCGCAACGACCTGCGCCGCGTCGACATGAACCTGCTGGTGCTGTTCGAAGCCCTGATGATCGAACGCAACCTGACCCGCGTGGGTGAAAAGCTGTTTATCACCCAATCCAcc              >  3:287090/1‑135 (MQ=255)
                                                                          cGCCGAGCCCTCATGAACCGCAACGACCTGCGCCGCGTCGACATGAACCTGCTGGTGCTGTTCGAAGCCCTGATGATCGAACGCAACCTGACCCGCGTGGGTGAAAAGCTGTTTATCACCCAATCCACCGTCAgc        >  1:59218/1‑135 (MQ=255)
                                                                                gCCCTCATGAACCGCAACGACCTGCGCCGCGTCGACATGAACCTGCTGGTGCTGTTCGAAGCCCTGCTGATCGAACGCAACCTGACCCGCGTGGGTGACAAGCTGTTTATCACCCAATCCCCCGTCAGCgccgcc  >  4:163829/1‑135 (MQ=255)
                                                                                gCCCTCATGAACCGCAACGACCTGCGCCGCGTCGACATGAACCTGCTGGTGCTGTTCGAAGCCCTGATGATCGAACGCAACCTGCCCCGCGTGGGTGAAAAGCTGTTTATCACCCAATCCCCCGTCAGCgccgcc  >  5:25841/1‑135 (MQ=255)
                                                                                gCCCTCATGAACCGCAACGACCTGCGCCGCGTCGACATGAACCTGCTGGTGCTGTTCGAAGCCCTGATGATCGAACGCAACCTGACCCGCGTGGGTGAAAAGCTGTTTATCACCCAATCCACCGTCAGcgccgc   >  6:317432/1‑134 (MQ=255)
                                                                                gCCCTCATGAACCGCAACGACCTGCGCCGCGTCGACATGAACCTGCTGGTGCTGTTCGAAGACCTGATGATCGAACGCAACCTGAACCGCGTCGGTGAAAAGCTGTTTATCACACAATCCACCGTCAGcgccgc   >  6:292252/1‑134 (MQ=255)
                                                                                 |                                                                                                                                     
GAGGCCGGCACATCCATACAAGGCACAAGGCCCCGCGCCATGCTTCAATACACAGCCATACCCTTTGCCCAGGACGCCGAGCCCTCATGAACCGCAACGACCTGCGCCGCGTCGACATGAACCTGCTGGTGCTGTTCGAAGCCCTGATGATCGAACGCAACCTGACCCGCGTGGGTGAAAAGCTGTTTATCACCCAATCCACCGTCAGCGCCGCC  >  KT2440/4163838‑4164052

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 14 ≤ ATCG/ATCG < 15 ≤ ATCG/ATCG < 32 ≤ ATCG/ATCG < 36 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑