Predicted mutation
evidence seq id position mutation freq annotation gene description
RA KT2440 120,975 Δ1 bp 100% intergenic (+272/+100) polA → / ← engB DNA polymerase I/putative GTP‑binding protein EngB

Read alignment evidence...
  seq id position ref new freq score (cons/poly) reads annotation genes product
*KT2440120,9750T.91.1% 212.7 / 9.6 56intergenic (+272/+100)polA/engBDNA polymerase I/putative GTP‑binding protein EngB
Reads supporting (aligned to +/- strand):  ref base T (1/2);  new base . (36/15);  total (37/19)
Fisher's exact test for biased strand distribution p-value = 2.30e-01
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 1.00e+00
Rejected as polymorphism: Variant not supported by required number of reads on each strand.
Rejected as polymorphism: Polymorphic indel expands or contracts a homopolymer stretch.

CTCAGAGTAACTGAATGGCTGGTGAAGCCCTTCGATGCTCCTATGTTGTGTTAAGTGTTGGCAGATATCTGGACCCCGCCCTAGCGGTCCGGACTTGGACCCCGAACTTCCCCCTCCCCATACGAAGTCCGGGGTTTTTTTTTGCCCGGAATTTGCCGGGAGCGGGTTTTCTCGCGAATGCGATGTCGAATACACCGCCGCATTCGCGGGTAAACCCGGGTCAGGCGCAAACCACTAAACGACCGGCTTGTCTTCCAGTTCCATCCA  >  KT2440/120841‑121107
                                                                                                                                      |                                                                                                                                    
cTCAGAGTAACTGAATGGCTGGTGAAGCCCTTCGATGCTCCTATGTTGTGTTAAGTGTTGGCAGATATCTGGACCCCGCCCTAGCGGTCCGGACTTGGACCCCGAACTTCCCCCTCCCCATACTAAGTCCGGGGt                                                                                                                                      >  4:76655/1‑135 (MQ=255)
             aaTGGCTGGTGAAGCCCTTCGATGCTCCTATGTTGTGTTAAGTGTTGGCAGATATCTGGACCCCGCCCTAGCGGTCCGGACTTGGACCCCGAACTTCCCCCTCCCCATACGAAGTCCGGGG‑TTTTTTTTGCCCg                                                                                                                         >  1:258806/1‑134 (MQ=255)
              aTGGCTGGTGAAGCCCTTCGATGCTCCTATGTTGCGTTAAGGGTTGGCAGATATCTGGACCCCGCCCTAGCGGTCCGGACTTGGACCCCGAACTTCCCCCTCCCCATACGAAGTCCGGGG‑TTTTTTTTGCCCGGa                                                                                                                       <  8:181903/135‑1 (MQ=255)
                  cTGGTGAAGCCCTTCGATGCTCCTATGTTGTGTTAAGTGTTGGCAGATATCTGGACCCCGCCCTAGCGGTCCGGACTTGGACCCCGAACTTCCCCCGCCCCATACGAACTCCGGGG‑GTTTTTTTGCCCGGAAttt                                                                                                                   >  3:134921/1‑135 (MQ=255)
                      tGAAGCCCTTCGATGCTCCTATGTTGTGTTAAGTGTTGGCAGATATCTGGACCCCGCCCTAGCGGTCCGGACTTGGACCCCGAACTTCCCCCTCCCCATACGAAGTCCGGGG‑TTTTTTTTGCCCGGAATTTGCCg                                                                                                               >  5:121012/1‑135 (MQ=255)
                       gAAGCCCTTCGATGCTCCTATGTTGTGTTAAGTGTTGGCAGATATCTGGACCCCGCCCTAGCGGTCCGGACTTGGACCCCGAACTTCCCCCTCCCCATACGAAGTCCGGGG‑TTTTTTTTGGCCGGAATTTGCCgg                                                                                                              >  5:338944/1‑135 (MQ=255)
                              ttCGATGCTCCTATGTTGTGTTAAGTGTTGGCAGATATCTGGACCCCGCCCTAGCGGTCCGGACTTGGACCCCGAACTTCCCCCTCCCCATACGAAGTCCGGGG‑TTTTTTTTGCCCGGAATTTGCCGGGAGCggg                                                                                                       >  2:176238/1‑135 (MQ=255)
                                  aTGCTCCTATGTTGTGTTAAGTGTTGGCAGATATCTGGACCCCGCCCTAGCGGTCCGGACTTGGACCCCGAACTTCCCCCTCCCCATACGAAGTCCGGGG‑TTTTTTTTGCCCGGAATTTGCCGGGAGCGGGtttt                                                                                                   >  3:74867/1‑135 (MQ=255)
                                      tCCTATGTTGTGTTAAGTGTTGGCAGATATCTGGACCCCGCCCTAGCGGTCCGGACTTGGACCCCGAACCTCCCCCTCCCCATACGAAGTCCGGGG‑TTTTTTTTGCCCGGAATTTGCCGGGAGCGGGTTTTCTcg                                                                                               <  6:126569/135‑1 (MQ=255)
                                            gttgtGTTAAGTGTTGGCAGATATCTGGACCCCGCCCTAGCGGTCCGGACTTGGACCCCGAACTTCCCCCTCCCCATACGAAGTCCGGGG‑TTTTTTTTGCCCGGAATTTGCCGGGAGCGGGTTTTCTCGCGAAt                                                                                          <  8:292100/134‑1 (MQ=255)
                                            gttgtGTTAAGTGTTGGCAGATATCTGGACCCCGCCCTAGCGGTCCGGACTTGGACCCCGAACTTCCCCCTCCCCATACGAAGTCCGGGG‑TTTTTTTTGCCCGGAATTTGCCGGGAGCGGGTTTTCTCGCGAAt                                                                                          <  6:298189/134‑1 (MQ=255)
                                            gttgtGTTAAGTGTTGGCAGATATCTGGACCCCGCCCTAGCGGTCCGGACTTGGACCCCGAACTTCCCCCTCCCCATACGAAGTCCGGGG‑TTTTTTTTGCCCGGAATTTGCCGGGAGCGGGTTTTCTCGCGAAt                                                                                          <  8:103238/134‑1 (MQ=255)
                                            gttgtGTTAAGTGTTGGCAGATATCTGGACCCCGCCCTAGCGGTCCGGACTTGGACCCCGAACTTCCCCCTCCCCATACGAAGTCCGGGG‑TTTTTTTTGCCCGGAATTTGCCGGGAGCGGGTTTTCTCGCGAAt                                                                                          <  4:334156/134‑1 (MQ=255)
                                            gttgtGTTAAGTGTTGGCAGATATCTGGACCCCGCCCTAGCGGTCCGGACTTGGACCCCGAACTTCCCCCTCCCCATACGAAGGCCGGGG‑TTTTTTTTGCCCGGAATTTGCCGGGAGCGGGTTTTCTCGCGAAt                                                                                          <  6:121012/134‑1 (MQ=255)
                                              tgtgTTAAGTGTTGGCAGATATCTGGACCCCGCCCTAGCGGTCCGGACTTGGACCCCGAACTTCCCCCTCCCCATACGAAGTCCGGGG‑TTTTTTTTGCCCGGAATTTGCCGGGAGCGGGTTTTCTCGCGAATGCg                                                                                       <  4:34466/135‑1 (MQ=255)
                                                  ttAAGTGTTGGCAGATATCTGGACCCCGCCCTAGCGGTCCGGACTTGGACCCCGAACTTCCCCCTCCCCATACGAAGTCCGGGG‑TTTTTTTTGCCCGGAATTTGCCGGGAGCGGGTTTTCTCGCGAATGCGATGt                                                                                   >  8:358864/1‑135 (MQ=255)
                                                   tAAGTGTTGGCAGATATCTGGACCCCGCCCTAGCGGTCCGGACTTGGACCCCGAACTTCCCCCTCCCCATACGAAGTCCGGGG‑TTTTTTTTGCCCGGAATTTGCCGGGAGCGGGTTTTCTCGCGAAt                                                                                          >  5:9188/1‑127 (MQ=255)
                                                   tAAGTGTTGGCAGATATCTGGACCCCGCCCTAGCGGTCCGGACTTGGACCCCGAACTTCCCCCTCCCCATACGAAGTCCGGGG‑TTTTTTTTGCCCGGAATTTGCCGGGAGCGGGTTTTCTCGCGAAt                                                                                          <  7:139565/127‑1 (MQ=255)
                                                   tAAGTGTTGGCAGATATCTGGACCCCGCCCTAGCGGTCCGGACTTGGACCCCGAACTTCCCCCTCCCCATACGAAGTCCGGGG‑TTTTTTTTGCCCGGAATTTGCCGGGAGCGGGTTTTCTCGCGAAt                                                                                          >  8:139565/1‑127 (MQ=255)
                                                   tAAGTGTTGGCAGATATCTGGACCCCGCCCTAGCGGTCCGGACTTGGACCCCGAACTTCCCCCTCCCCATACGAAGTCCGGGG‑TTTTTTTTGCCCGGAATTTGCCGGGAGCGGGTTTTCTCGCGAAt                                                                                          <  6:9188/127‑1 (MQ=255)
                                                   tAAGTGTTGGCAGATATCTGGACCCCGCCCTAGCGGTCCGGACTTGGACCCCGAACTTCCCCCTCCCCATACGAAGTCCGGGG‑TTTTTTTTGCCCGGAATTTGCCGGGAGCGGGTTTTCTCGCGAATGCGATGt                                                                                   >  4:19372/1‑134 (MQ=255)
                                                   tAAGTGTTGGCAGATATCTGGACCCCGCCCTAGCGGTCCGGACTTGGACCCCGAACTTCCCCCTCCCCATACGAAGTCCGGGG‑TTTTTTTTGCCCGGAATTTGCCGGGAGCGGGTTTTCTCGCGAATGCGATGt                                                                                   >  2:151122/1‑134 (MQ=255)
                                                   tAAGTGTTGGCAGATATCTGGACCCCGCCCTAGCGGTCCGGACTTGGACCCCGAACTTCCCCCTCCCCATACGAAGTCCGGGG‑TTTTTTTTGCCCGGAATTTGCCGGGAGCGGGTTTTCTCGCGAATGCGATGt                                                                                   >  6:119623/1‑134 (MQ=255)
                                                   tAAGTGTTGGCAGATATCTGGACCCCGCCCTAGCGGTCCGGACTTGGACCCCGAACTTCCCCCTCCCCATACGAAGTCCGGGG‑TTTTTTTTGCCCGGAATTTGCCGGGAGCGGGTTTTCTCGCGAATGCGATGt                                                                                   >  3:299808/1‑134 (MQ=255)
                                                   tAAGTGTTGGCAGATATCTGGACCCCGCCCTAGCGGTCCGGACTTGGACCCCGAACATCCCCCTCCCCATACGAAGTCCGGGG‑TTTTTTTTGCCCGTAATTTGCCGGGAGCGGGTTTTCTATCGAATGGCATGTc                                                                                  >  6:14049/1‑135 (MQ=255)
                                                     aGTGTTGGCAGATATCTGGACCCCGCCCTAGCGGTCCGGACTTGGACCCCGAACTTCCCCCTCCCCATACGAAGTCCTGGG‑TTTTTTTTGCCCGGAATTTGCCGGGAGCGGGTTTTCTCTCGAATGCGATGTCGa                                                                                >  2:317175/1‑135 (MQ=255)
                                                             cAGATATCTGGACCCCGCCCTAGCGGTCCGGACTTGGACCCCGCACTTCCCCCTCCCCATACGAAGTCCGGGG‑TTTTTTTTGCCCGGAATTTTCCGGGAGCGGGGTTTCTCGCGCATGCGCTCTCGAATACAccg                                                                        >  6:50235/1‑135 (MQ=255)
                                                             cAGATATCTGGACCCCGCCCTAGCGGTCCGGACTTGGACCCCGAACTTCCCCCTCCCCATACGAAGTCCGGGG‑TTTTTTTTGCCCGGAATTTGCCGGGAGCGGGTTTTCTCGCGAATGGGATGTCGAATACAccg                                                                        >  7:166641/1‑135 (MQ=255)
                                                             cAGATATCTGGACCCCGCCCTAGCGGTCCGGACTTGGACCCCGAACTTCCCCCTCCCCATACGAAGTCCGGGG‑TTTTTTTTGCCCGGAATTTGCCGGGAGCGGGTTTTCTCGCGAATGCGATGTCGAATACAccg                                                                        >  8:166094/1‑135 (MQ=255)
                                                             cAGATATCTGGACCCCGCCCTAGCGGTCCGGACTTGGACCCCGAACTTCCCCCTCCCCATACGAAGTCCGGGG‑TTTTTTTTGCCCGGAATTTGCCGGGAGCGGGTTTTCTCGCGAATGCGATGTCGAATACAccc                                                                        >  7:82641/1‑134 (MQ=255)
                                                             cAGATATCTGGACCCCGCCCTAGCGGTCCGGACTTGGACCCCGAACTTCCCCCTCCCCATACGAAGTCCGGGG‑TTTTTTTTGCCCGGAATTTGCAGGGAGCGGGTTTTCTCGCGATTGCGAGCTCGATGACAccg                                                                        >  2:320553/1‑135 (MQ=255)
                                                                    cTGGACCCCGCCCTAGCGGTCCGGACTTGGACCCCGAACTTCCCCCTCCCCATACGAAGTCCGGGG‑TTTTTTTTGCCCGGAATTTGCCGGGAGCGGGTTTTCTCGCGAATGCGATGTCGAATACACCGCCGCAtt                                                                 >  4:305236/1‑135 (MQ=255)
                                                                             gCCCTAGCGGTCCGGACTTGGACCCCGAACTTCCCCCTCCCCATACGAAGTCCGGGG‑TTTTTTTTGCCCGGAATTTGCCGGGGGCGGGTTTTCTCGCGAATGCGATGTCGAATACACCGCCGCATTCGCGGGTa                                                         >  2:226009/1‑134 (MQ=255)
                                                                               ccTAGCGGTCCGGACTTGGACCCCGCACTTCCCCCTCCCCATACGAAGTCCGGGGTTTTTTTTT‑CCCGGAATTTGCCGGGAGCGGGTTTTCTCGCGAATGCGATGTCGAATACACCGCCGCATTCGCGGGTAAAc                                                      >  3:274821/1‑135 (MQ=255)
                                                                               ccTAGCGGTCCGGACTTGGACCCCGAACTTCCCCCTCCCCATACGAAGTCCGGGG‑TTTTTTTTGCCCGGAATTTGCCGGGCGCGGGTTTTCTCGCGAATGCGATGTCGAATACCCCGCCGCATTCGCGGGTAAAc                                                      >  5:71226/1‑135 (MQ=255)
                                                                               ccTAGCGGTCCGGACTTGGACCCCGAACTTCCCCCTCCCCATACGAAGTCCGGGG‑TTTTTTTTGCCCGGAATTTGCCGGGAGCGGGTTTTCTCGCGAATGCGATGTCGAATACACTGCCGCATTCGCGGGTCAAc                                                      >  3:251309/1‑135 (MQ=255)
                                                                               ccTAGCGGTCCGGACTTGGACCCCGAACTTCCCCCTCCCCATACGAAGTCCGGGG‑TTTTTTTTGCCCGGAATTTGCCGGGAGCGGGTTTTCTCGCGAATGCGATGTCGAATACACCGCCGCATTCGCGGGTAAAc                                                      >  1:125676/1‑135 (MQ=255)
                                                                               ccTAGCGGTCCGGACTTGGACCCCGAACTTCCCCCTCCCCATACGAAGTCCGGGG‑TTTTTTTTGCCCGGAATTTGCCGGGAGCGGGTTTTCTCGCGAAGGCGATGTCGAATACACCGCCGCATTCCCCGGTAAAc                                                      >  5:372095/1‑135 (MQ=255)
                                                                               ccTAGCGGTCCGGACTTGGACCCCGAACTTCCCCCTCCCCATACGAAGTCCGGGG‑TTTTTTTTGCCCGGAATTTGCCGGGAGCGGGGTTTCTCGCGCATGCGATGGCGAATACCCCGCCGCATTCGCGGGTAAAc                                                      >  2:192228/1‑135 (MQ=255)
                                                                                 tAGCGGTCCGGACTTGGACCCCGAACTTCCCCCTCCCCATACGAAGTCCGGGG‑TTTTTTTTGCCCGGAATTTGCCGGGAGCGGGTTTTCTCGCGAATGCGCTGTCGAATACACCGCCGCCTTCGCGGGTAAAccc                                                    >  2:156875/1‑135 (MQ=255)
                                                                                    cGGTCCGTACTTGGACCCCGAACTTCCCCCTCCCCATACGAAGTCCGGGG‑TTTTTTTTGCCCGGAATTTGCCGGGAGCGGGTTTTCTCGCGAATGCGATGTCGAATACACCGCCGCATTCGCGGGTAAACCCg                                                   <  2:213006/133‑1 (MQ=255)
                                                                                    cGGTCCGGACTTGGACCCCGAACTTCCCCCTCCCCATACGAAGCCCGGGG‑TTTTTTTTGCCCGGAATTTGCCGGGAGCGGGTTTTCTCGCGAATGCGATGTCGAATACACCGCCGCATTCGCGGGTAAACCCg                                                   <  3:342379/133‑1 (MQ=255)
                                                                                            aCTTGGACCCCGAACTTCCCCCTCCCCATAAGAAGTCCGGGG‑TTTTTTTTGCCCGGAATTTGCCGGGAGCGGGTTTTCTCGCGAATGCGATGTAGAATACAAAGCCGAATTCGCGGGTAAAACCGGGTCATgcg                                          >  8:155784/1‑134 (MQ=255)
                                                                                                    cccTAACTTCCCCCTCCCAATACGAAGT‑CGGGGGTTTTTTTTGCCGGTATTTTGCGGGGAGGGGGTTTTCGCGCTAATGCTATGGCTAATACACCGCCGCATTCGGGGTTAAACCCGGGTCAGGCGCAAACCACt                                 <  4:299808/135‑1 (MQ=255)
                                                                                                    cccGAACTTCCCCCTCCCCATACGAAGTCCGGGG‑TTTTTTTTGCCCGGAATTTGCCGGGAGCGGGTTTTCTCGCGAATGCGATGTCGAATACACCGCCGCATTCGCGGGTAAACCCGGGTCAGGCGCAAACCAc                                  >  5:199398/1‑134 (MQ=255)
                                                                                                         aCTTCCCCCTCCCCATACGAAGTCCGGGG‑TTTTTTTTGCCCGGAATTTGCCGGGAGCGGGTTTTCTAGCGAATGCGGTGTCGATTACACCGCCGCATTCGCGGGTAAACCCGGGTCAGGCGCCAACCACTAAACg                            >  2:311057/1‑135 (MQ=255)
                                                                                                           ttCCCCCTCCCCATACGAAGTCCGGGG‑TTTTTTTTGCCCGGAATTTGCCGGGAGCGGGTTTTCTCGCGAATGCGATGTCGAATACACCGCCGCATTCGCGGGTAAACCCGGGTCAGGCGCAAACCACTAAACGAc                          >  4:298891/1‑135 (MQ=255)
                                                                                                               cccTCCCATTACGATGT‑CGGGGGTTTTTTTTGCCCGTAATTTGCGGGGTGGGGGTTTTCTCGCTATTGCTTTGTCTAATACACCGCCGCATTCGCGGTAAAACCGGGGTCAGGCACAAACCAAAAAACGACCGGc                      <  4:74867/135‑1 (MQ=255)
                                                                                                                    cccATACGACG‑GCGGGGTTTTTTTTTGCCCGTAATTTGCCGGGTGGGGTTTTTCGCGCTAATGCGATGTCTAAACCCCCGCCGCATGCGCGGGTAAACCGGGGTCCGGCGCAAACCACTAAACGACCGGCTTGTc                 <  2:125676/135‑1 (MQ=255)
                                                                                                                    cccATACGAAGTCCGGGG‑TTTTTTTGGCCCGTATTTTGCCGGGAGGGGGTTTGCGCGCGAAGGCGATGTCCAAAACACCGCCGCATTCGCGGTTAAACCCGGGTCAGGCGCAAACCACAACACGACCGGCTTGTc                 <  3:274837/135‑1 (MQ=255)
                                                                                                                      cATACGAAGTCCGGGG‑TTTTTTTTGCCCGGAATTTGCCGGGAGCGGGTTTTCTCGCGAATGCGATGTCGAATACACCGCCGCATTCGCGGGTAAACCCGGGTCAGGCGCAAACCACTAAACGACCGGCTTGTCtt               >  7:237090/1‑135 (MQ=255)
                                                                                                                      cATACGAAGTCCGGGG‑TTTTTTTTGCCCGGAATTTGCCGGGAGCGGGGTTTCTCGCGAATGCGCTGTCGAAGACACCGCCGCATTCGCGTGTAAACCCGGGGCAGGCGCACCCCCCTAAACGACCGGCTTGtggt               >  6:53137/1‑132 (MQ=255)
                                                                                                                        tACTAAGTCCGGGG‑TTTTTTTTCCCCGTAATTTGCGGGTAGGGTGTTTTCTCGCTAATGCGATGTCGAATACCCCGCCGCATTCGGGTTTAAACCGGGTTCAGGCGCAAACCACTAAACGACCGGCTTGTCTTcc             <  2:258806/135‑1 (MQ=255)
                                                                                                                        tACGAAGTCCGGGG‑TTTTTTTTGCCCGGAATTTGCCGGGAGCGGGTTTTCTCGCGAAt                                                                                          <  7:87092/58‑1 (MQ=255)
                                                                                                                        tACGAAGTCCGGGG‑TTTTTTTTGCCCGGAATTTGCCGGGAGCGGGTTTTCTCGCGAAt                                                                                          >  8:87092/1‑58 (MQ=255)
                                                                                                                           gAAGTCCGGGG‑TTTTTTTTGCCCGGAATTTGCCGGGAGCGGGTTTTCTCGCGAATGCGATGTCGAATACACCGCCGCATTCGCGGGTTAACCCGGGTCAGGCGCAAACCACTAAACGACCGGCTTGTCTTCCAGt          >  6:286693/1‑135 (MQ=255)
                                                                                                                                  cggggTTTTTTTTGCCCGGAATTTGCCGGGAGCGGGTTTTCTCGCGAATGCGATGTCGAATACACCGCCGCAt                                                                  <  7:196083/72‑1 (MQ=255)
                                                                                                                                  cggggTTTTTTTTGCCCGGAATTTGCCGGGAGCGGGTTTTCTCGCGAATGCGATGTCGAATACACCGCCGCAt                                                                  >  8:196083/2‑73 (MQ=255)
                                                                                                                                  cggggTTTTTTTTGCCCGGAATTTGCCGGGAGCGGGTTTTCTCGCGAATGCGATGTCGAATACACCGCCGCATTCGCGGGTAAACCCGGGTCAGGCGCAAACCACTAACCTACCGGCTTGTCTTCCAGTtccat     >  4:236534/2‑134 (MQ=255)
                                                                                                                                  cggggTTTTTTTTGCCCGGAATTTGCCGGGAGCGGGTTTTCTCGCGAATGCGATGTCGAATACACCGCCGCATTCGCGGGTAAACCCGGGTCAGGCGCAAACCACTAAACGACCGGCTTGTCTTCCAGTtccat     >  7:304039/2‑134 (MQ=255)
                                                                                                                                    ggTTTTTTTTGGCCCGTAATTTGCGGGGTGGGGGTTTTGTCGCTATTGCGATGCCTATAACACCGCCGCATTCGGGGGTAAACCGGGGTCAGGCGCAAACCACTAAACGACCGGCTTGTCTTCCAGTtccatcca  <  7:358864/135‑1 (MQ=255)
                                                                                                                                      |                                                                                                                                    
CTCAGAGTAACTGAATGGCTGGTGAAGCCCTTCGATGCTCCTATGTTGTGTTAAGTGTTGGCAGATATCTGGACCCCGCCCTAGCGGTCCGGACTTGGACCCCGAACTTCCCCCTCCCCATACGAAGTCCGGGGTTTTTTTTTGCCCGGAATTTGCCGGGAGCGGGTTTTCTCGCGAATGCGATGTCGAATACACCGCCGCATTCGCGGGTAAACCCGGGTCAGGCGCAAACCACTAAACGACCGGCTTGTCTTCCAGTTCCATCCA  >  KT2440/120841‑121107

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: ‑