Predicted mutation
evidence seq id position mutation freq annotation gene description
RA NC_000913 998,448 T→A 9.3% intergenic (+41/‑42) elfA → / → elfD laminin‑binding fimbrin subunit/putative periplasmic pilin chaperone

Read alignment evidence...
  seq id position ref new freq score (cons/poly) reads annotation genes product
*NC_000913998,4480TA 9.3% 135.5 / 5.5 43intergenic (+41/‑42)elfA/elfDlaminin‑binding fimbrin subunit/putative periplasmic pilin chaperone
Reads supporting (aligned to +/- strand):  ref base T (22/17);  new base A (2/2);  total (24/19)
Fisher's exact test for biased strand distribution p-value = 1.00e+00
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 7.92e-01

GATCAGACGTTGACTTTTAAAGTTGATTATATCGCTACGGGGAAAGCGACTTCAGGTAATGTGAATGCGGTAACAAATTTCCATATTAACTATTATTAATAGAACTCATTAATTGTTTTATTAATTAGTACCCCTCCAGTGTTCTGGAGGGGATATTCATATTTTTTAAGAGTGACTATTTATGAAAACTTGCATAACAAAGGGAATTGTGACCGTAAGTTTAACGGCAATATTACTCAGCTGCTCATCCGCATGGGCGGCAGGTAAAGGCGGGATTGGACTTGCA  >  NC_000913/998309‑998594
                                                                                                                                           |                                                                                                                                                  
gaTCAGACGTTGACTTTTAAAGTTGATTATATCGCTACGGGGAAAGCGACTTCAGGTAATGTGAATGCGGTAACAAATTTCCATATTAACTATTATTAATAGAACTCATTAATTGTTTTATTAATTAGTACCCCTCCAGTGTTCTGGAg                                                                                                                                           <  3:69665/149‑1 (MQ=255)
  tCAGACGTTGACTTTTAAAGTTGATTATATCGCTACGGGGAAAGCGACTTCAGGTAATGTGAATGCGGTAACAAATTTCCATATTAACTATTATTAATAGAACTCATTAATTGTTTTATTAATTAGTACCCCTCCAGAACACTGGAggg                                                                                                                                         <  2:473772/149‑1 (MQ=255)
   cAGACGTTGACTTTTAAAGTTGATTATATCGCTACGGGGAAAGCGACTTCAGGTAATGTGAATGCGGTAACAAATTTCCATATTAACTATTATTAATAGAACTCATTAATTGTTTTATTAATTAGTACCCCTCCAGAACACTGGAgggg                                                                                                                                        <  1:392954/149‑1 (MQ=255)
    aGACGTTGACTTTTAAAGTTGATTATATCGCTACGGGGAAAGCGACTTCAGGTAATGTGAATGCGGTAACAAATTTCCATATTAACTATTATTAATAGAACTCATTAATTGTTTTATTAATTAGTACCCCTCCAGTGTTCTGGAGGGGa                                                                                                                                       >  4:56973/1‑149 (MQ=255)
    aGACGTTGACTTTTAAAGTTGATTATATCGCTACGGGGAAAGCGACTTCAGGTAATGTGAATGCGGTAACAAATTTCCATATTAACTATTATTAATAGAACTCATTAATTGTTTTATTAATTAGTACCCCTCCAGTGTTCTGGAGGGGa                                                                                                                                       <  1:76427/149‑1 (MQ=255)
      aCGTTGACTTTTAAAGTTGATTATATCGCTACGGGGAAAGCGACTTCAGGTAATGTGAATGCGGTAACAAATTTCCATATTAACTATTATTAATAGAACTCATTAATTGTTTTATTAATTAGTACCCCTCCAGTGTTCTGGAGGGGata                                                                                                                                     >  3:55663/1‑149 (MQ=255)
           gACTTTTAAAGTTGATTATATCGCTACGGGGAAAGCGACTTCAGGTAATGTGAATGCGGTAACAAATTTCCATATTAACTATTATTAATAGAACTCATTAATTGTTTTATTAATTAGTACCCCTCCAGTGTTCTGGAGGGGATATTCat                                                                                                                                >  1:325623/1‑149 (MQ=255)
              ttttAAAGTTGATTATATCGCTACGGGGAAAGCGACTTCAGGTAATGTGAATGCGGTAACAAATTTCCATATTAACTATTATTAATAGAACTCATTAATTGTTTTATTAATTAGTACCCCTCCAGTGTTCTGGAGGGGATATTCATAtt                                                                                                                             >  3:365743/1‑149 (MQ=255)
              ttttAAAGTTGATTATATCGCTACGGGGAAAGCGACTTCAGGTAATGTGAATGCGGTAACAAATTTCCATATTAACTATTATTAATAGAACTCATTAATTGTTTTATTAATTAGTACCCCTCCAGTGTTCTGGAGGGGATATTCATAtt                                                                                                                             >  4:345142/1‑149 (MQ=255)
                 tAAAGTTGATTATATCGCTACGGGGAAAGCGACTTCAGGTAATGTGAATGCGGTAACAAATTTCCATATTAACTATTATTAATAGAACTCATTAATTGTTTTATTAATTAGTACCCCTCCAGTGTTCTGGAGGGGATATTCATAttttt                                                                                                                          <  4:365743/149‑1 (MQ=255)
                   aaGTTGATTATATCGCTACGGGGAAAGCGACTTCAGGTAATGTGAATGCGGTAACAAATTTCCATATTAACTATTATTAATAGAACTCATTAATTGTTTTATTAATTAGTACCCCTCCAGTGTTCTGGAGGGGATATTCATATTTTTTa                                                                                                                        >  3:75744/1‑149 (MQ=255)
                     gTTGATTATATCGCTACGGGGAAAGCGACTTCAGGTAATGTGAATGCGGTAACAAATTTCCATATTAACTATTATTAATAGAACTCATTAATTGTTTTATTAATTAGTACCCCTCCAGTGTTCTGGAGGGGATATTCATATTTTTTAag                                                                                                                      >  4:330310/1‑149 (MQ=255)
                        gATTATATCGCTACGGGGAAAGCGACTTCAGGTAATGTGAATGCGGTAACAAATTTCCATATTAACTATTATTAATAGAACTCATTAATTGTTTTATTAATTAGTACCCCTCCAGTGTTCTGGAGGGGATATTCATATTTTTTAAGAGt                                                                                                                   <  1:186914/149‑1 (MQ=255)
                         aTTATATCGCTACGGGGAAAGCGACTTCAGGTAATGTGAATGCGGTAACAAATTTCCATATTAACTATTATTAATAGAACTCATTAATTGTTTTATTAATTAGTACCCCTCCAGTGTTCTGGAGGGGATATTCATATTTTTTAAGAGTg                                                                                                                  >  1:336215/1‑149 (MQ=255)
                             tatCGCTACGGGGAAAGCGACTTCAGGTAATGTGAATGCGGTAACAAATTTCCATATTAACTATTATTAATAGAACTCATTAATTGTTTTATTAATTAGTACCCCTCCAGTGTTCTGGAGGGGATATTCATATTTTTTAAGAGTGACTa                                                                                                              <  3:56973/149‑1 (MQ=255)
                                                    cAGGTAATGTGAATGCGGTAACAAATTTCCATATTAACTATTATTAATAGAACTCATTAATTGTTTTATTAATTAGTACCCCTCCAGTGTTCTGGAGGGGATATTCATATTTTTTAAGAGTGACTATTTATGAAAACTTGCATAACaaa                                                                                       <  4:75744/149‑1 (MQ=255)
                                                           tgtgAATGCGGTAACAAATTTCCATATTAACTATTATTAATAGAACTCATTAATTGTTTTATTAATTAGTACCCCTCCAGTGTTCTGGAGGGGATATTCATATTTTTTAAGAGTGACTATTTATGAAAACTTGCATAACAAAGGGAAtt                                                                                >  4:46370/1‑149 (MQ=255)
                                                              gAATGCGGTAACAAATTTCCATATTAACTATTATTAATAGAACTCATTAATTGTTTTATTAATTAGTACCCCTCCAGTGTTCTGGAGGGGATATTCATATTTTTTAAGAGTGACTATTTATGAAAACTTGCATAACAAAGGGAATtgtg                                                                             <  4:164533/149‑1 (MQ=255)
                                                                           aaTTTCCATATTAACTATTATTAATAGAACTCATTAATTGTTTTATTAATTAGTACCCCTCCAGTGTTCTGGAGGGGATATTCATATTTTTTAAGAGTGACTATTTATGAAAACTTGCATAACAAAGGGAATTGTGACCGTAAGTTTaa                                                                <  3:330310/149‑1 (MQ=255)
                                                                             tttCCATATTAACTATTATTAATAGAACTCATTAATTGTTTTATTAATTAGTACCCCTCCAGTGTTCTGGAGGGGATATTCATATTTTTTAAGAGTGACTATTTATGAAAACTTGCATAACAAAGGGAATTGTGACCGTAAGTTTAACg                                                              >  1:74464/1‑149 (MQ=255)
                                                                                     ttAACTATTATTAATAGAACTCATTAATTGTTTTATTAATTAGTACCCCTCCAGTGTTCTGGAGGGGATATTCATATTTTTTAAGAGTGACTATTTATGAAAACTTGCATAACAAAGGGAATTGTGACCGTAAGTTTAACGGCAATAtt                                                      >  4:236698/1‑149 (MQ=255)
                                                                                          tattatTAATAGAACTCATTAATTGTTTTATTAATTAGTACCCCTCCAGTGTTCTGGAGGGGATATTCATATTTTTTAAGAGTGACTATTTATGAAAACTTGCATAACAAAGGGAATTGTGACCGTAAGTTTAACGGCAATATTACTCa                                                 >  1:115468/1‑149 (MQ=255)
                                                                                            ttattaATAGAACTCATTAATTGTTTTATTAATTAGTACCCCTCCAGTGTTCTGGAGGGGATATTCATATTTTTTAAGAGTGACTATTTATGAAAACTTGCATAACAAAGGGAATTGTGACCGTAAGTTTAACGGCAATATTACTCAgc                                               <  3:46370/149‑1 (MQ=255)
                                                                                              attaATAGAACTCATTAATTGTTTTATTAATTAGTACCCCTCCAGTGTTCTGGAGGGGATATTCATATTTTTTAAGAGTGACTATTTATGAAAAc                                                                                                   <  2:187911/95‑1 (MQ=255)
                                                                                              attaATAGAACTCATTAATTGTTTTATTAATTAGTACCCCTCCAGTGTTCTGGAGGGGATATTCATATTTTTTAAGAGTGACTATTTATGAAAAc                                                                                                   >  1:187911/1‑95 (MQ=255)
                                                                                               ttaATAGAACTCATTAATTGTTTTATTAATTAGTACCCCTCCAGTGTTCTGGAGGGGATATTCATATTTTTTAAGAGTGACTATTTATGAAAACTTGCATAACAAAGGGAATTGTGACCGTAAGTTTAACGGCAATATTACTCAgctgc                                            <  2:336215/149‑1 (MQ=255)
                                                                                               ttaATAGAACTCATTAATTGTTTTATTAATTAGTACCCCTCCAGTGTTCTGGAGGGGATATTCATATTTTTTAAGAGTGACTATTTATGAAAACTTGCATAACAAAGGGAATTGTGACCGTAAGTTTAACGGCAATATTACTCAg                                                <  2:42588/145‑1 (MQ=255)
                                                                                               ttaATAGAACTCATTAATTGTTTTATTAATTAGTACCCCTCCAGTGTTCTGGAGGGGATATTCATATTTTTTAAGAGTGACTATTTATGAAAACTTGCATAACAAAGGGAATTGTGACCGTAAGTTTAACGGCAATATTACTCAg                                                >  1:42588/1‑145 (MQ=255)
                                                                                                            ttAATTGTTTTATTAATTAGTACCCCTCCAGTGTTCTGGAGGGGATATTCATATTTTTTAAGAGTGACTATTTATGAAAACTTGCATAACAAAGGGAATTGTGACCGTAAGTTTAACGGCAATATTACTCAGCTGCTCATCCGCATggg                               >  2:225246/1‑149 (MQ=255)
                                                                                                               aTTGTTTTATTAATTAGTACCCCTCCAGTGTTCTGGAGGGGATATTCATATTTTTTAAGAGTGACTATTTATGAAAACTTGCATAACAAAGGGAATTGTGACCGTAAGTTTAACGGCAATATTACTCAGCTGCTCATCCGCATGggcgg                            >  2:462049/1‑149 (MQ=255)
                                                                                                                   ttttATTAATTAGTACCCCTCCAGTGTTCTGGAGGGGATATTCATATTTTTTAAGAGTGACTATTTATGAAAACTTGCATAACAAAGGGAATTGTGACCGTAAGTTTAACGGCAATATTACTCAGCTGCTCATCCGCATGGGCGGCAgg                        >  2:387947/1‑149 (MQ=255)
                                                                                                                     ttattaATTAGTACCCCTCCAGTGTTCTGGAGGGGATATTCATATTTTTTAAGAGTGACTATTTATGAAAACTTGCATAACAAAGGGAATTGTGACCGTaa                                                                      >  2:133288/1‑101 (MQ=255)
                                                                                                                     ttattaATTAGTACCCCTCCAGTGTTCTGGAGGGGATATTCATATTTTTTAAGAGTGACTATTTATGAAAACTTGCATAACAAAGGGAATTGTGACCGTaa                                                                      <  1:133288/101‑1 (MQ=255)
                                                                                                                     ttattaATTAGTACCCCTCCAGTGTTCTGGAGGGGATATTCATATTTTTTAAGAGTGACTATTTATGAAAACTTGCATAACAAAGGGAATTGTGACCGTAAGTTTAACGGCAATATTACTCAGCTGCTCATCCGCATGGGCGGCAGGTa                      >  4:5832/1‑149 (MQ=255)
                                                                                                                       attaattaGTACCCCTCCAGTGTTCTGGAGGGGATATTCATATTTTTTAAGAGTGACTATTTATGAAAACTTGCATAACAAAGGGAATTGTGACCGTAAGTTTAACGGCAATATTACTCAGCTGCTCATCCGCATGGGCGGCAGGTaaa                    >  1:17845/1‑149 (MQ=255)
                                                                                                                            ttaGTACCCCTCCAGTGTTCTGGAGGGGATATTCATATTTTTTAAGAGTGACTATTTATGAAAACTTGCATAACAAAGGGAATTGTGACCGTAAGTTTAACGGCAATATTACTCAGCTGCTCATCCGCATGGGCGGCAGGTAAAGGCgg               <  4:55663/149‑1 (MQ=255)
                                                                                                                               gTACCCCTCCAGTGTTCTGGAGGGGATATTCATATTTTTTAAGAGTGACTATTTATGAAAACTTGCATAACAAAGGGAATTGTGACCGTAAGTTTAACGGCAATATTACTCAGCTGCTCATCCGCATGGGCGGCAGGTAAAGGCGGGAt            >  3:141049/1‑149 (MQ=255)
                                                                                                                                tACCCCTCCAGTGTTCTGGAGGGGATATTCATATTTTTTAAGAGTGACTATTTATGAAAACTTGCATAACAAAGGGAATTGTGACCGTAAGTTTAACGGCAATATTACTCAGCTGCTCATCCGCATGGGCGGCAGGTAAAGGCGGGAtt           >  3:348218/1‑149 (MQ=255)
                                                                                                                                 tccccTCCAGAGCACTGGAGGGGATATTCATATTTTTTAAGAGTGACTATTTATGAAAACTTGCATAACAAAGGGAATTGTGACCGTAAGTTTAACGGCAATATTACTCAGCTGCTCATCCGCATGGGCGGCAGGTAAAGGCGGGATTg          >  1:250079/2‑149 (MQ=255)
                                                                                                                                 tccccTCCAGAACACTGGAGGGGATATTCATATTTTTTAAGAGTGACTATTTATGAAAACTTGCATAACAAAGGGAATTGTGACCGTAAGTTTAACGGCAATATTACTCAGCTGCTCATCCGCATGGGCGGCAGGTAAAGGCGGGATTg          >  2:10281/2‑149 (MQ=255)
                                                                                                                                   cccTCCAGTGTTCTGGAGGGGATATTCATATTTTTTAAGAGTGACTATTTATGAAAACTTGCATAACAAAGGGAATTGTGACCGTAAGTTTAACGGCAATATTACTCAGCTGCTCATCCGCATGGGCGGCAGGTAAAGGCGGGATTGGa        <  2:325623/149‑1 (MQ=255)
                                                                                                                                     cTCCAGTGTTCTGGAGGGGATATTCATATTTTTTAAGAGTGACTATTTATGAAAACTTGCATAACAAAGGGAATTGTGACCGTAAGTTTAACGGCAATATTACTCAGCTGCTCATCCGCATGGGCGGCAGGTAAAGGCGGGATTGGACt      <  3:345142/149‑1 (MQ=255)
                                                                                                                                         aGTGTTCTGGAGGGGATATTCATATTTTTTAAGAGTGACTATTTATGAAAACTTGCATAACAAAGGGAATTGTGACCGTAAGTTTAACGGCAATATTACTCAGCTGCTCATCCGCATGGGCGGCAGGTAAAGGCGGGATTGGACTTgca  <  2:115468/149‑1 (MQ=255)
                                                                                                                                           |                                                                                                                                                  
GATCAGACGTTGACTTTTAAAGTTGATTATATCGCTACGGGGAAAGCGACTTCAGGTAATGTGAATGCGGTAACAAATTTCCATATTAACTATTATTAATAGAACTCATTAATTGTTTTATTAATTAGTACCCCTCCAGTGTTCTGGAGGGGATATTCATATTTTTTAAGAGTGACTATTTATGAAAACTTGCATAACAAAGGGAATTGTGACCGTAAGTTTAACGGCAATATTACTCAGCTGCTCATCCGCATGGGCGGCAGGTAAAGGCGGGATTGGACTTGCA  >  NC_000913/998309‑998594

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 30 ≤ ATCG/ATCG < 35 ≤ ATCG/ATCG < 39 ≤ ATCG/ATCG < 40 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑