Predicted mutation
evidence seq id position mutation freq annotation gene description
RA CP009273 2,007,748 C→T 17.4% P347S (CCG→TCG)  fliF → flagellar basal‑body MS‑ring and collar protein

Read alignment evidence...
  seq id position ref new freq score (cons/poly) reads annotation genes product
*CP0092732,007,7480CT17.4% 52.6 / 2.4 29P347S (CCG→TCG) fliFflagellar basal‑body MS‑ring and collar protein
Reads supporting (aligned to +/- strand):  ref base C (12/11);  new base T (2/3);  total (15/14)
Fisher's exact test for biased strand distribution p-value = 1.00e+00
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 1.00e+00

CGGTTATCCGGGCGGCGTACCGGGGGCGTTGTCGAATCAACCGGCACCTGCGAATAACGCGCCAATCAGCACGCCTCCGGCAAATCAAAATAACCGCCAGCAGCAGGCGAGCACCACCAGCAATAGTGGGCCGCGTAGCACACAGCGGAATGAAACCAGTAACTACGAAGTCGATCGCACCATTCGTCATACCAAAATGAACGTGGGCGATGTGCAACGTCTGTCAGTCGCGGTCGTGGTGAATTACAAAACCTTGCCAGATGGCAAAC  >  CP009273/2007618‑2007886
                                                                                                                                  |                                                                                                                                          
cGGTTATCCGGGCGGCGTACCGGGGGCGTTGTCGAATCAACCGGCACCTGCGAATAACGCGCCAATCAGCACGCCTCCGGCAAATCAAAATAACCGCCAGCAGCAGGCGAGCACCACCAGCAATAGTGGGCCGCGTAGCACACAg                                                                                                                              <  2:316735/145‑1 (MQ=255)
 ggTTATCCGGGCGGCGTACCGGGGGCGTTGTCGAATCAACCGGCACCTGCGAATAACGCGCCAATCAGCACGCCTCCGGCAAATCAAAATAACCGCCAGCAGCAGGCGAGCACCACCAGCAATAGTGGGCCGCGTAGCACACAGc                                                                                                                             >  2:170000/1‑145 (MQ=255)
  gTTAACCGGGCGGCGTACCGGGGGCGTTGTCGAATCAACCGGCACCTGCGAATAACGCGCCAATCAGCACGCCTCCGGCAAATCAAAATAACCGCCAGCAGCAGGCGAGCACCACCAGCAATAGTGGGCCGCGTAGCACACAGCg                                                                                                                            <  2:109476/145‑1 (MQ=255)
        cGGGCGGCGTACCGGGGGCGTTGTCGAATCAACCGGCACCTGCGAATAACGCGCCAATCAGCACGCCTCCGGCAAATCAAAATAACCGCCAGCAGCAGGCGAGCACCACCAGCAATAGTGGGCCGCGTAGCACACAGCGGAATGa                                                                                                                      >  2:325639/1‑145 (MQ=255)
        cGGGCGGCGTACCGGGGGCGTTGTCGAATCAACCGGCACCTGCGAATAACGCGCCAATCAGCACGCCTCCGGCAAATCAAAATAACCGCCAGCAGCAGGCGAGCACCACCAGCAATAGTGGGCCACGAAGCCCACAGCGGAATGa                                                                                                                      >  1:180024/1‑145 (MQ=255)
         gggCGGCGTACCGGGGGCGTTGTCGAATCAACCGGCACCTGCGAATAACGCGCCAATCAGCACGCCTCCGGCAAATCAAAATAACCGCCAGCAGCAGGCGAGCACCACCAGCAATAGTGGGTCGCGTAGCACACAGCGGAATGaa                                                                                                                     >  2:229557/1‑145 (MQ=255)
         gggCGGCGTACCGGGGGCGTTGTCGAATCAACCGGCACCTGCGAATAACGCGCCAATCAGCACGCCTCCGGCAAATCAAAATAACCGCCAGCAGCAGGCGAGCACCACCAGCAATAGTGGGTCGCGTAGCACACAGCGGAATGaa                                                                                                                     >  2:229572/1‑145 (MQ=255)
          ggcggcGTACCGGGGGCGTTGTCGAATCAACCGGCACCTGCGAATAACGCGCCAATCAGCACGCCTCCGGCAAATCAAAATAACCGCCAGCAGCAGGCGAGCACCACCAGCAATAGTGGGCCGCGTAGCACACAGCGGAATGaaa                                                                                                                    <  2:37411/145‑1 (MQ=255)
             ggcgTACCGGGGGCGTTGTCGAATCAACCGGCACCTGCGAATAACGCGCCAATCAGCACGCCTCCGGCAAATCAAAATAACCGCCAGCAGCAGGCGAGCACCACCAGCAATAGTGGGCCGCGTAGCACACAGCGGAATGAAACCa                                                                                                                 <  2:334853/145‑1 (MQ=255)
                        ggCGTTGTCGAATCAACCGGCACCGGCGAATAACGCGCCAATCAGCACGCCTCCGGCAAATCAAAATAACCGCCAGCAGCAGGCGAGCACCACCAGCAATAGTGGGCCGCGTAGCACACAGCGGAATGAAACCAGTAACTACGaa                                                                                                      <  1:73408/145‑1 (MQ=255)
                                 gAATCAACCGGCACCTGCGAATAACGCGCCAATCAGCACGCCTCCGGCACCTCAAAATAACCGCCAGCAGCAGGCGAGCACCACCAGCAATAGTGGGCCGCGGAGCACACAGCGGAATGAAACCAGTAACTACGAAGGAGATCGc                                                                                             >  2:291666/1‑145 (MQ=255)
                                  aaTCAACCGGCACCTGCGAATAACGCGCCAATCAGCACGCCTCCGGCAAATCAAAATAACCGCCAGCAGCAGGCGAGCACCACCAGCAATAGTGGGCCGCGTAGCACACAGCGGAATGAAACCAGTAACTACGAAGTCGATCGCa                                                                                            >  1:121531/1‑145 (MQ=255)
                                                         cgcgCCAATCCGCACGCCTACGGCAAATCAAAATAACCGCCCGCAGCAGGCGAGCACCACCAGCAATAGTGGGTCGCGTAGCACACAGCGGAATGAAACCAGTAACTACGAAGTCGATCGCACCATTCGTCATACCAAAATGAAc                                                                     <  1:229557/145‑1 (MQ=255)
                                                         cgcgCCAATCAGCACGCCTCCGGCAAATCAAAATAACCGCCAGCAGCAGGCGAGCACCACCAGCAATAGTGGGTCGCGTAGCACACAGCGGAATGAAACCAGTAACTACGAAGTCGATCGCACCATTCGTCATACCAAAATGAAc                                                                     <  1:229572/145‑1 (MQ=255)
                                                          gcgcCAATCAGCACGCCTCCGGCAAATCAAAATAACCGCCAGCAGCAGGCGAGCACCACCAGCAATAGTGGGCCGCGTAGCACACAGCGGAATGAAACCAGTAACTACGAAGTCGATCGCACCATTCGTCATACCAAAATGAACg                                                                    >  2:359894/1‑145 (MQ=255)
                                                               agtCAGCACGCCTCGGGCAAATGAAAAGAACCGCCAGCAGCAGGCGAAGACCACCAGCAATGGTGGGGCGCGAAGCACACAGGGAGACGAACACAGTAAGTAGGAAGGCGAGAGAACCAGTCGCGAGACAAAAAtaggagggcgc                                                               >  1:123797/3‑135 (MQ=255)
                                                                  cAGCACGCCTCCGGCAAATCAAAATAACCGCCAGCAGCAGGCGAGCACCACCAGCAATAGTGGGCCGCGTAGCACACAGCGGAATGAAACCAGTAACTACGAAGTCGATCGCACCATTCGTCATACCAAAATGAACGTGGGCGAt                                                            <  2:121531/145‑1 (MQ=255)
                                                                     cACGCCTCCGGCAAATCAAAATAACCGCCAGCAGCAGGCGATCACCACAAACAATAGTGGGCCGCGTATCACACAGCGAAATGAAACCAGTAAATACGAAGTCGATAGAACCATTCAGCAAACGAAAAGGAAAGTAGGCGAtgtg                                                         >  2:387364/1‑145 (MQ=255)
                                                                               gCAAATCAAAATAACCGCCAGCAGCAGGCGAGCACCACCAGCAATAGTGGGCCGCGTAGCACACAGCGGAATGAAACCAGTAACTACGAAGTCGATCGCACCATTCGTCATACCAAAATGAACGTGGGCGATGTGCAACGTCTGt                                               >  2:188759/1‑145 (MQ=255)
                                                                                 aaaTCAAAATAACCGCCAGCAGCAGGCGAGCACCACCAGCAATAGTGGGCCGCGTAGCACACAGCGGAATGAAACCAGTAACTACGAAGTCGATCGCACCATTCGTCATACCAAAATGAACGTGGGCGATGTGCAACGTCTGTCa                                             <  2:102814/145‑1 (MQ=255)
                                                                                       aaaTAACCGCCAGCAGCAGGCGAGCACCACCAGCAATAGTGGGCCGCGTAGCACACAGCGGAATGAAACCAGTAACTACGAAGTCGATCGCACCATTCGTCATACCAAAATGAACGTGGGCGATGTGCAACGTCTGTCAGTcgcg                                       <  1:325639/145‑1 (MQ=255)
                                                                                             ccGCCAGCAGCAGGCGTGCATCTCCTGGTATAGTGGGCCGCGTAGCACACAGCGGAATGAAACCAGTAACTCCGAAGTCGATCGCACCCTTCGTCATACCAAAATGAACGTGGGCGATGTGCAACGTCTGTCAGTCGCGGTCgcg                                 <  2:228097/145‑3 (MQ=255)
                                                                                               gCCAGCAGCAGGCGAGCACCACCAGCAATAGTGGGCCGCGTAGCACACAGCGGAATGAAACCAGTAACTACGAAGTCGATCGCACCATTCGTCATACCAAAATGAACGTGGGCGATGTGCAACGTCTGTCAGTCGCGGTCgtggt                               >  1:161047/1‑145 (MQ=255)
                                                                                               gCCAGCAGCAGGCGAGCACCACCACCAATAGTGGGTCGCGTAGCACACAGCGGAATGAAAACAGTAACCACGAAGTCGATCGCACCACTCGACATACCAACATGAACGTGGGCTATCTGCAACGTCTGTCAGCCGCGGTCgtggt                               <  1:319724/145‑1 (MQ=255)
                                                                                                         ggCGAGCACCACCAGCAATAGTGGGCCGCGTAGCACACAGCGGAATGAAACCAGTAACTACGAAGTCGATCGCACCATTCGTCATACCAAAATGAACGTGGGCGATGTGCAACGTCTGTCAGTCGCGGTCGTGGTGAATTACaaa                     <  2:361253/145‑1 (MQ=255)
                                                                                                          gCGAGCACCACCAGGAATAGTGGGCCGCGTAGCACACAGCGGAATGAAACCAGTAACTACGAAGTCGATCGCACCATTCGTCATACCAAAATGAACGTGGGCGATGTGCAACGTCAGACAGTCGCGGTCCTGGTAAATTACaaaa                    >  2:62757/1‑145 (MQ=255)
                                                                                                            gAGCACCACCAGCAATAGTGGGCCGCGTAGCACACAGCGGAATGAAACCAGTAACTACGAAGTCGATCGCACCATTCGTCATACCAAAATGAACGTGGGCGATGTGCAACGTCTGTCAGTCGCGGTCGTGGTGAATTACAAAAcc                  <  1:188759/145‑1 (MQ=255)
                                                                                                                        cAATAGTGGGCCGCGTAGCACACAGCGGAATGAAACCAGTAACTACGAAGACGATCGCACCATTCGTCATACGAAAATGAACGTGGGCGATGTGCACCGTCTGTCAGTCGCGGTCGTGGGGAATTGCAAAACCTTGCCACTTGGc      >  1:358442/1‑145 (MQ=255)
                                                                                                                            actGGGCCGCGTAGCACACAGCGGAATGAAACCAGTTACTACGAAGTCGATCGCACCATTCGTCATACCAAAATGAACGTGGGCGATGTGCAACGCCTGTCATTCGCGGTCGTGGTGAATTACAAAACATTGCCAGATGGCAAAc  >  1:51832/3‑145 (MQ=255)
                                                                                                                                  |                                                                                                                                          
CGGTTATCCGGGCGGCGTACCGGGGGCGTTGTCGAATCAACCGGCACCTGCGAATAACGCGCCAATCAGCACGCCTCCGGCAAATCAAAATAACCGCCAGCAGCAGGCGAGCACCACCAGCAATAGTGGGCCGCGTAGCACACAGCGGAATGAAACCAGTAACTACGAAGTCGATCGCACCATTCGTCATACCAAAATGAACGTGGGCGATGTGCAACGTCTGTCAGTCGCGGTCGTGGTGAATTACAAAACCTTGCCAGATGGCAAAC  >  CP009273/2007618‑2007886

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 8 ≤ ATCG/ATCG < 12 ≤ ATCG/ATCG < 27 ≤ ATCG/ATCG < 41 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑