Predicted mutation
evidence seq id position mutation freq annotation gene description
RA KT2440 4,703,371 G→A 8.7% P138S (CCG→TCG)  sixA ← Phosphohistidine phosphatase SixA

Read alignment evidence...
  seq id position ref new freq score (cons/poly) reads annotation genes product
*KT24404,703,3710GA 8.7% 140.7 / 4.1 46P138S (CCG→TCG) sixAPhosphohistidine phosphatase SixA
Reads supporting (aligned to +/- strand):  ref base G (23/19);  new base A (2/2);  total (25/21)
Fisher's exact test for biased strand distribution p-value = 1.00e+00
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 9.36e-01

AAAAATGCCAGTTGCCTTATCGATCTTTACCCATGCCAGCATGCAGACGCGAGCGAAACATTGGCCTGCACAAGCCATGGGAAGTTCACGCGGGTGAGTGGATGGCCCGAAGCGTCATCAACCCGGCCAGCGGCCACTCCCCTTCCAGCTCCGCCAGGCTGGCAGTGCTCATGGCTGCCGGCTGTTGCCTGTCGCCGTGCTCCAGTGCACCGACCAAGGTACCTACCAGCGGCTGGTGGCTGACCAGCAGCACATGCTCGAGCC  >  KT2440/4703239‑4703502
                                                                                                                                    |                                                                                                                                   
aaaacTGCCAGTTGCCTTATCGATCTTTCCCCATGCCAGCATGCAGACGCGAGCGAAACATTGGCCTGCACAAGCCATGGGAAGTTCACGCGGGTGAGTGGATGGCCCGAAGCGTCATCAACCCGGCCAGCGGcc                                                                                                                                   <  6:172806/135‑1 (MQ=255)
aaaaaTGCGAGTTGGCTTATCGATCTTTACCCATGCCAGCATGCAGACGCGAGCGAAACATTGGCCTGCACAAGCCATGGGAAGTTCACGCGGGTGAGTGGATGGCCCGAAGCGTCATCAACCCGTCCAGCGGcc                                                                                                                                   <  5:60798/135‑1 (MQ=255)
          gTTGCCTTATCGATCTTTACCCATGCCAGCATGCAGACGCGAGCGAAACATTGGCCTGCACAAGCCATGGGAAGTTCACGCGGGTGAGTGGATGGCCCGAAGCGTCATCAACCCGGCCAGCGGCCACTCCCCTTc                                                                                                                         <  1:197969/135‑1 (MQ=255)
                ttATCGATCTTTACCCATGCCAGCATGCAGACGCGAGCGAAACATTGGCCTGCACAAGCCATGGGAAGTTCACGCGGGTGAGTGGATGGCCCGAAGCGTCATCAACCCGGCCAGCGGCCACTCCCCTTCCAGCTc                                                                                                                   <  1:242634/135‑1 (MQ=255)
                            aCCCCTGCCAGACTGCAGAGGCTAGCTATACTTTGGCCTGAACATGCCATGGGAAGTTCACGCGGGTGAGTGGATGGCCCGAAGCGTAATCAACCCGGCCAGCGGCCACTCCCCTTCCAGCTCCGCCAGGCTg                                                                                                         <  6:184800/133‑1 (MQ=255)
                            aCCCATGCCAGCATGCAGACGCGAGCGAAACATTGGCCTGCACCAGCCATGGGAAGGTCACGCGGGTGAGTGGATGGCCCGAAGCGTCATCACCCCGGCCAGCGGCCACTCCCATTACATCTACGCCAGGCTGGCa                                                                                                      <  7:224407/136‑1 (MQ=255)
                                    cAGCATGCAGACGCGAGCGAAACATTGGCCTGCACAAGCCATGGGAAGTTCACGCGGGTGAGTGGATGGCCCGAAGCGTCATCAACCCGGCCAGCGGCCACTCCCCTTCCAGCTCCGCCAGGCTGGCAGTGCTCa                                                                                               >  4:67914/1‑135 (MQ=255)
                                          gCAGACGCGAGCGAAACATTGGCCTGCACAAGCCATGGGAAGTTCACGCGGGTGAGTGGATGGCCCGAAGCGTCATCAACCCGGCCAGCGGCCACTCCCCTTCCAGCTCCGCCAGGCTGGCAGTGCTCATGGCTg                                                                                         >  6:59012/1‑135 (MQ=255)
                                               cgcgAGCGAAACATTGGCCTGCACAAGCCATGGGAAGTTCCCGCGGGTGAGGGGATGGCCCGCAGCGTCATCAACCCGGCCAGCGGCCACTCCCCTTCCAGCTCCGCCAGGCTGGCAGTGCTCATGGCTGCCGGc                                                                                    >  6:152441/1‑135 (MQ=255)
                                                      gaAACATTGGCCTGCACAAGCCATGGGAAGTTCACGCGGGTGAGTGGATGGCCCGAAGCGTCATCAACCCGGCCAGCGGCCACTCCCCTTCCAGCTCCGCCAGGCTGGCAGTGCTCATGGCTGCCGGCTGTTGcc                                                                             >  3:34281/1‑135 (MQ=255)
                                                      gaAACATTGGCCTGCACAAGCCATGGGAAGTTCACGCGGGTGAGTGGATGGCCCGAAGCGTCATCAACCCGGCCAGCGGCCACTCCCCTTCCAGCTCCGCCAGGCTGGCAGTGCTCATGGCTGCCGGCTGTTGCCt                                                                            >  7:94618/1‑136 (MQ=255)
                                                             tGGCCTGCACAAGCCATGGGAAGTTCACGCGGTTGAGTGGATGGCCCGAAGCGTCATCAACCCGGCCAGCGGCCACTCCCCTTCCAGCTCCGCCAGGCTGGCAGTGCTCATGGCTGCCGGCTGTTGCCTGTCGcc                                                                      <  3:63335/135‑1 (MQ=255)
                                                             tGGCCTGCACAAGCCATGGGAAGTTCACGCGGGTGAGTGGATGGCCCGAAGCGTCATCAACCCGGCCAGCGGCCACTCCCCTTCCAGCTCCGCCAGGCTGGCAGTGCTCATGGCTGCCGGCTGTTGCCTGTCGcc                                                                      <  3:127836/135‑1 (MQ=255)
                                                                       aaGCCATGGGAAGTTCACGCGGGTGAGTGGATGGCCCGAAGCGTCATCAACCCGGCCAGCGGCCACTCCCCTTCCAGCTCCGCCAGGCTGGCAGTGCTCATGGCTGCCGGCTGTTGCCTGTCGCCGTGCTCCAGt                                                            <  3:67914/135‑1 (MQ=255)
                                                                       aaGCCATGGGAAGTTCACGCGGGTGAGTGGATGGCCCGAAGCGTCATCAACCCGGCCAGCGGCCACTCCCCTTCCAGCTCCGCCAGGCTGGCAGTGCTCATGGCTGCCGGCTGTTGCCTGTCGCCGTGCTCCAGTg                                                           >  7:172465/1‑136 (MQ=255)
                                                                         gCCATGGGAAGTTCACGCGGGTGAGTGGATGGCCCGAAGCGTCATCAACCCGGCCAGCGGCCACTCCCCTTCCAGCTCCGCCAGGCTGGCAGTGCTCATGGCTGCCGGCTGTTGCCTGTCGCCGTGCTCCAGTGc                                                          <  6:70920/135‑1 (MQ=255)
                                                                           cATGGGAAGTTCACGCGGGTGAGTGGATGGCCCGAAGCGTCATCAACCCGGCCAGCGGCCACTCCCCTTCCAGCTCCGCCAGGCTGGCAGTGCTCATGGCTGCCGGCTGTTGCCTGTCGCCGTGCTCCAGTGCAc                                                        <  5:81091/135‑1 (MQ=255)
                                                                            aTGGGAAGTTCACGCGGGTGAGTGGATGGCCCGAAGCGTCATCAACCCGGCCAGCGGCCACTCCCCTTCCAGCTCCGCCAGGCTGGCAGTGCTCATGGCTGCCGGCTGTTGCCTGTCGCCGTGCTCCAGTGcccc                                                       >  4:263269/1‑135 (MQ=255)
                                                                            aTGGGAAGTTCACGCGGGTGAGTGGATGGCCCGAAGCGTCATCAACCCGGCCAGCGGCCACTCCCCTTCCAGCTCCGCCAGGCTGGCAGTGCTCATGGCTGCCGGCTGTTGCCTGTCGCCGTGCTCCAGTGCAcc                                                       >  4:201680/1‑135 (MQ=255)
                                                                            aTGGGAAGTTCACGCGGGTGAGTGGATGGCCCGAAGCGTCATCAACCCGGCCAGCGGCCACTCCCCTTCCAGCTCCGCCAGGCTGGCAGTGCTCATGGCTGCCGGCTGTTGCCTGTCGCCGTGCTCCAGTGCAcc                                                       >  2:106357/1‑135 (MQ=255)
                                                                                gAAGTTCACGCGGGGGAGTGGATGGCCCGAAGCGTCATCAACCCGGCCAGCGGCCACTCCCCTTCCAGCTCCGCCAGGCTGGCAGTGCTCATGGCTGCCGGCTGTTGCCTGTCGCCGTGCTCCAGTGCACCGAcc                                                   <  3:201680/135‑1 (MQ=255)
                                                                                 aaGTTCACGCGGGTGAGTGGATGGCCCGAAGCGTCATCAACCCGGCCAGCGGCCACTCCCCTTCCAGCTCCGCCAGGCTGGCAGTGCTCATGGCTGCCGGCTGTTGCCTGTCGCCGTGCTCCAGTGCACCGAc                                                    >  3:136759/1‑133 (MQ=255)
                                                                                 aaGTTCACGCGGGTGAGTGGATGGCCCGAAGCGTCATCAACCCGGCCAGCGACCACTCCCCTTCCAGCTCCGCCAGGCTGGCAGTGCTCATGGCTGCCGGCTGTTGCCTGTCGcc                                                                      >  4:2613/1‑115 (MQ=255)
                                                                                 aaGTTCACGCGGGTGAGTGGATGGCCCGAAGCGTCATCAACCCGGCCAGCGACCACTCCCCTTCCAGCTCCGCCAGGCTGGCAGTGCTCATGGCTGCCGGCTGTTGCCTGTCGcc                                                                      <  3:5912/115‑1 (MQ=255)
                                                                                 aaGTTCACGCGGGTGAGTGGATGGCCCGAAGCGTCATCAACCCGGCCAGCGACCACTCCCCTTCCAGCTCCGCCAGGCTGGCAGTGCTCATGGCTGCCGGCTGTTGCCTGTCGcc                                                                      >  4:5912/1‑115 (MQ=255)
                                                                                 aaGTTCACGCGGGTGAGTGGATGGCCCGAAGCGTCATCAACCCGGCCAGCGACCACTCCCCTTCCAGCTCCGCCAGGCTGGCAGTGCTCATGGCTGCCGGCTGTTGCCTGTCGcc                                                                      <  3:2613/115‑1 (MQ=255)
                                                                                    ttCACGCGGGTGAGTGGATGGCCCGAAGCGTCATCAACCCGGCCAGCGGCCACTCCCCTTCCAGCTCCGCCAGGCTGGCAGTGCTCATGGCTGCCGGCTGTTGCCTGTCGCCGTGCTCCAGTGCACCGACCAAgg                                               <  4:158361/135‑1 (MQ=255)
                                                                                       aCGCGGGTGAGTGGATGGCCCGAAGCGTCATCAACCCGGCCAGCGGCCACTCCCCTTCCAGCTCCGCCAGGCTGGCAGTGCTCATGGCTGCCGGCTGTTGCCTGTCGCCGAGCTCCAGTGCACCGACCAAGGta                                             >  6:141382/1‑134 (MQ=255)
                                                                                           ggggGAGTGGAGGGCCCGAAGCGTCATCAACCCGGCCAGCGGCCACTCCCCTTCCAGCTCCGCCAGGCTGGCAGTGCTCATGGCTGCCGGCTGTTGCCTGTCGCCGTGCTCCAGTGCACCGACCAAGGtacctac                                        <  3:181023/135‑1 (MQ=255)
                                                                                               gAGTGGATGGCCCGAAGCGTCATCAACCCGGCCAGCGGCCACTCCCCTTCCAGCTCCGCCAGGCTGGCAGTGCTCATGGCTGCCGGCTGTTGCCTGTCGCCGTGCTCCAGTGCACCGACCAAGGTACCTACCAGCg                                   >  8:26547/1‑136 (MQ=255)
                                                                                                   ggATGGCCCGAAGCGTCATCAACCCGGCCAGCGGCCACTCCCCTTCCAGCTCCGCCAGGCTGGCAGTGCTCATGGCTGCCGGCTGTTGCCTGTCGCCGTGCTCCAGTGCACCGACCAAGGTACCTACCAGCGGCt                                >  4:197873/1‑135 (MQ=255)
                                                                                                     aTGGCCCGAAGCGTCATCAACCCGGCCAGCGGCCACTCCCCTTCCAGCTCCGCCAGGCTGGCAGTGCTCATGGCTGCCGGCTGTTGCCTGTCGCCGTGCTCCAGTGCACCGACCAAGGTACCTACCAGCGGCtgg                              <  4:44687/135‑1 (MQ=255)
                                                                                                          ccGAAGCGTCATCAACCCGGCCAGCGGCCACTCCCCTTCCAGCTCCGCCAGGCTGGCAGTGCTCATGGCTGCCGGCTGTTGCCTGTCGCCGTGCTCCAGt                                                            <  2:78476/100‑1 (MQ=255)
                                                                                                          ccGAAGCGTCATCAACCCGGCCAGCGGCCACTCCCCTTCCAGCTCCGCCAGGCTGGCAGTGCTCATGGCTGCCGGCTGTTGCCTGTCGCCGTGCTCCAGt                                                            >  1:78476/1‑100 (MQ=255)
                                                                                                          ccGAAGCGTCATCAACCCGGCCAGCGGCCACTCCCCTTCCAGCT‑CGCCAGGCTGGCAGTGCTCATGGCTGCCGGCTGTTGCCTGTCGCCGTGCTCCAGTGCACCGACCAAGGTACCTACCAGCGGCTGGTGGCTg                        >  1:186055/1‑135 (MQ=255)
                                                                                                             aaGCGTCATCAACCCGGCCAGCGGCCACTCCCCTTCCAGCTCCGCCAGGCTGGCAGTGCTCATGGCTGCCGGCTGTTGCCTGTCGCCGTGCTCCAGTGCACCGACCAAGGTACCTACCAGCGGCTGGTGGCTGAc                      <  4:136759/135‑1 (MQ=255)
                                                                                                                      caACCCGGCCAGCGGCCACTCCCCTTCCAGCTCCGCCAGGCTGGCAGTGCTCATGGCTGCCGGCTGTTGCCTGTCGCCGTGCTCCAGTGCACCGa                                                     <  3:181841/95‑1 (MQ=255)
                                                                                                                      caACCCGGCCAGCGGCCACTCCCCTTCCAGCTCCGCCAGGCTGGCAGTGCTCATGGCTGCCGGCTGTTGCCTGTCGCCGTGCTCCAGTGCACCGa                                                     >  4:181841/1‑95 (MQ=255)
                                                                                                                      caACCCGGCCAGCGGCCACTCCCCTTCCAGCTCCGCCAGGCTGGCAGTGCTCATGGCTGCCGGCTGTTGCCTGTCGCCGTGCTCCAGTGCACCGACCAAGGTACCTACCAGCGGCTGGTGGCTGACCAGCAGcaca            >  7:77698/1‑136 (MQ=255)
                                                                                                                      caACCCGGCCAGCGGCCACTCCCCTTCCAGCTCCGCCAGGCTGGCAGTGCTCATGGCTGCCGGCTGTTGCCTGTCGCCGTGCTCCAGTGCACCGACCAAGGTACCTACCAGCGGCTGGTGGCTGACCAGCAGcac             >  3:255882/1‑135 (MQ=255)
                                                                                                                        aCCCGGCCAGCGGCCACTCCCCTTCCAGCTCCGCCAGGCTGGCAGTGCTCATGGCTGCCGGCTGTTGCCTGTCGCCGTGCTCCAGTGCCCCGACCAAGGTACCTACCAGCGGCTGGTGGCTGACCAGCAGCACAt           <  5:152441/135‑1 (MQ=255)
                                                                                                                                aGCGGCCACTCCCCTTCCAGCTCCGCCAGGCTGGCAGTGCTCATGGCTGCCGGCTGTTGCCTGTCGCCGTGCTCCAGTGCACCGACCAAGGTACCTACCAGCGGCTGGTGGCTGACCAGCAGCACATGCTCGCGcc  >  7:167599/1‑136 (MQ=255)
                                                                                                                                aGCGGCCACTCCCCTTCCAGCTCCGCCAGGCTGGCAGTGCTCATGGCTGCCGGCTGTTGCCTGTCGCCGTGCTCCAGTGCACCGACCAAGGTACCTACCAGCGGCTGGTGGCTGACCAGCAGCACATGCTCGAGc   >  5:3387/1‑135 (MQ=255)
                                                                                                                                aGCGGCCACTCCCCTTCCAGCTCCGCCAGGCTGGCAGTGCTCATGGCTGCCGGCTGTTGCCTGTCGCCGTGCTCCAGTGCACCGACCAAGGTACCTACCAGCGGCTGGTGGCTGACCAGCAGCACATGCTCGAGc   >  5:104378/1‑135 (MQ=255)
                                                                                                                                aGCGGCCACTCCCCTTCCAGCTCCGCCAGGCTGGCAGTGCTCATGGCTGCCGGCTGTTGCCTGTCGCCGTGCTCCAGTGCACCGACCAAGGTACCTACCAGCGGCTGGTGGCTGACCAGCAGCACATGCTCGAGc   >  2:60934/1‑135 (MQ=255)
                                                                                                                                aGCGGCCACTCCCCTTCCAGCTCCGCCAGGCTGGCAGTGCTCATGGCTGCCGGCTGTTGCCTGTCGCCGTGCTCCAGTGCACCGACCAAGGTACCTACCAGCGGCTGGTGGCTGACCAGCAGCACATGCTCGAGc   >  2:44426/1‑135 (MQ=255)
                                                                                                                                    |                                                                                                                                   
AAAAATGCCAGTTGCCTTATCGATCTTTACCCATGCCAGCATGCAGACGCGAGCGAAACATTGGCCTGCACAAGCCATGGGAAGTTCACGCGGGTGAGTGGATGGCCCGAAGCGTCATCAACCCGGCCAGCGGCCACTCCCCTTCCAGCTCCGCCAGGCTGGCAGTGCTCATGGCTGCCGGCTGTTGCCTGTCGCCGTGCTCCAGTGCACCGACCAAGGTACCTACCAGCGGCTGGTGGCTGACCAGCAGCACATGCTCGAGCC  >  KT2440/4703239‑4703502

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 14 ≤ ATCG/ATCG < 21 ≤ ATCG/ATCG < 32 ≤ ATCG/ATCG < 36 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑