Predicted mutation
evidence seq id position mutation annotation gene description
RA NC_000913 4,543,047 T→G intergenic (+414/‑68) fimE → / → fimA regulator for fimA/type 1 fimbriae major subunit

Read alignment evidence...
  seq id position ref new freq score (cons/poly) reads annotation genes product
*NC_0009134,543,0470TG94.1% 42.6 / ‑5.4 17intergenic (+414/‑68)fimE/fimAregulator for fimA/type 1 fimbriae major subunit
Reads supporting (aligned to +/- strand):  ref base T (0/1);  new base G (10/6);  total (10/7)
Fisher's exact test for biased strand distribution p-value = 4.12e-01
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 6.25e-01

ATGTAAAGCTAACGTTTCTGTGGCTCGACGCATCTTCCTCATTCTTCTCTCCAAAAACCACCTCATGCAATATAAACATCTATAAATAAAGATAACAATAGAATATTAAGCCAACAAATAAACTGAAAAAGTTTGTCCGCGATGCTTTCCTCTATGAGTCAAAATGGCCCCAAATGTTTCATCTTTTGGGGGAAAACTGTGCAGTGTTGGCAGTCAAACTCGTTTACA‑AAACAAAGTGTACAGAACGACTGCCCATGTCGATTTAGAAATAGTTTTTTGAAAGGAAAGCAGCATGAAAATTAAAACTCTGGCAATCGTTGTTCTGTCGGCTCTGTCCCTCAGTTCTACAGCGGCTCTGGCCGCTGCCACGACGGTTAATGGTGGGACCGTTCACTTTAAAGGGGAAGTTGTTAACGCCGCTTGCG  >  NC_000913/4542823‑4543247
                                                                                                                                                                                                                                |                                                                                                                                                                                                         
atGTAAAGCTAACGTTTCTGTGGCTCGACGCATCTTCCTCATTCTTCTCTCCAAAAACCACCTCATGCAATATAAACATCTATAAATAAAGATAACAATAGAATATTAAGCCAACAAATAAACTGAAAAAGTTTGTCCGCGATGCTTTCCTCTATGAGTCAAAATGGCCCCAAATGTTTCATCTTTTGGGGGAAAACTGTGCAGTGTTGGCAGTCAAACTCGTTGACA‑AAACAAAGTGTACAGAACGACTg                                                                                                                                                                                >  1:149256/1‑251 (MQ=255)
               ttCTGTGGCTCGACGCATCTTCCTCATTCTTCTCTCCAAAAACCACCTCATGCAATCTAAACATCTATAAATAAAGATAACAATAGAATATTAAGCCAACAAATAAACTGAAAAAGTTTGTCCGAGATGCTTTCCTCTATGAGTCAAAATGGCCCCAAATGTTTCATCTTTTGGGGGAAAACTGTGCCGTGTTGGCAGTCAAACCCGTTGACA‑AAACAAAGTGTACAGCACGACTGCCCATGTCGAttt                                                                                                                                                                   >  1:35320/1‑249 (MQ=255)
                       cactaagCATCTTCCTCCTTTTTCTCTGCAAAAACCACCTCAAGCAATATAAACATCTATAAATAAAGTTAACAATAGAATATTAAGCCAACAAATAAACAGATAAAGTTTTTCCGCGATGCTTTCCTCTATGAGTCAAAATGGCCCCAAATGTTTCATCTTTTGGGGGAAAACTGTGCATTGTTGGCAGTCAAACTCGTTGACA‑AATCAAAGTGTACAGAACGACTTCCCATGTCGATTTAGAAATAGtt                                                                                                                                                         <  2:267057/245‑1 (MQ=255)
                                                      aaaCAACCTCATGGAATAAAAACATCTAGAAATAAAGAGAACAATAAAATATTAAGCAAACAAATAAACTGCAAAAGTTTGTCCGCGAAGCTTTCCTCTATTAGTCAAAATGGCCCCAAATGTTTCATCATTAGGAGGAAAACAGTGCAGTGTTGGCAGTCAAACTCGTTGACA‑AAACAAAGTGTAAAGAACGACGGCCCATGTCGATTGAGAAATAGTTTTTTGAAAGGAAAGCAGCATGAAAATTaaaa                                                                                                                          <  2:8556/251‑1 (MQ=255)
                                                               aaaataatataatcctatataAATAAAGATAACAATAACATATTAAGGCAACAAATAAACTCAAAATGTTTGGCCGAGATGCCATCCTCTATGAGACAAAAAGGCCCCAAATGTTTCAGCTATTGGGGGAAAACTGTGCAGTGTTGGCAGTCAAAATC‑TTTGCATAAACAAAGTGTACAGAACGACTGCCAATGTAGATTTAGAAATAGTTGTTTGAACGGACAGCATCATGAAAATTAAAACTCTTGCaa                                                                                                                 <  2:230076/234‑1 (MQ=255)
                                                                                         aGATAAAAATAGAATAATAAGCAAAAAAATATACTGAAAAATATTGTCCGCGCTGCTTGCCTCCATGAGTCAAAATGTCCCCTAATATTTCATCTTTTGGGGGAAAACTGTGCAGTGTTGGAAGTCAAACTCGTTGACA‑AATCAAAGTGTTCATAACGACTGCCCATTTAGATTTAGAAATAGTGTTTTGAAAGGACATCATCATGAAAATTAAAACTTTGGCAATCGTTGTTCTGTCGGCTCTGTCCCTc                                                                                       <  2:17612/251‑1 (MQ=255)
                                                                                               cAATAGAATATTCAGCCAACAAATAAACTGAAAAAGTTTGTCCGCGATGCTTTCCTCTATGAGTCAAAATGGCCCCAAATGTTTCATCTTTTGGGGGAAAACTGTGCAGTGTTGGAAGTCAAACTCGTTGACA‑AAACAAAGTGTACAGAACGACTGCCCATGTCGATTTAGAAATAGTTTTTTGAAAGGAAAGCAGCATGAAAATTAAAACTCTGGCAATCGTTGTTCTGTCGGCTCTGTCCCTCAGTTCt                                                                                 >  1:98479/1‑251 (MQ=255)
                                                                                                           aaGCCAACAAATAAACTGAAAAAGTTTGTCCGCGATGCTTTCCTCTATGAGTCAAAATGGCCCCAAATGTTTCATCTTTTGGGGGAAAACTGTGCAGTGTTGGCAGTCAAACTCGTTGACA‑AAACAAAGTGTACAGAACGACTGCCCATGTCGATTTAGAAATAGTTTTTTGAAAGGAAAGCAGCATGAAAATTAAAACTCTGGCAATCGTTGTTCTGTCGGCTCTGTCCCTCAGTTCTACAGCGGCTCTg                                                                     >  1:258836/1‑251 (MQ=255)
                                                                                                                             aaaaaGTTTGTCCGCGATGCTTTCCTCTATGAGTCAAAATGGCCCCAAATGTTTCATCTTTTGGGGGAAAACTGTGCAGTGTTGGCAGTCAAACTCGTTGACA‑AAACAAAGTGTACAGAACGACTGCCCATGTCGATTTAGAAATAGTTTTTTGAAAGGAAAGCAGCATGAAAATTAAAACTCTGGCAATCGTTGTTCTGTCGGCTCTGTCCCTCAGTTCTACAGCGGCTCTGGCCGCTGCCACGCCGGtt                                                   >  1:319840/1‑251 (MQ=255)
                                                                                                                                 aGTTTGTCCGCGATGCTTTCCTCTATGAGTCAAAATGGCCCCAAATGTTTCATCTTTTGGGGGAAAACTGTGCAGTGTTGGCAGTCAAACTCGTTGACA‑AAACAAAGTGTACAGAACGACTGCCCATGTCGATTTAGAAATAGTTTTTTGAAAGGAAAGCAGCATGAAAATTAAAACTCTGGCAATCGTTGTTCTGTCGGCTCTGTCCCTCAGTTCTACAGCGGCTCTGGCCGCTGCCACGACGGTTAAtg                                               >  1:1323/1‑251 (MQ=255)
                                                                                                                                                 tttCCTCTATGAGTCAAAATGGCCCCAAATGTTTCATCTTTTGGGGGAAAACTGTGCAGTGTTGGCAGTCAAACTCGTTGACA‑AAACAAAGTGTACAGAACGACTGCCCATGTCGATTTAGAAATAGTTTTTTGAAAGGAAAGCAGCATGAAAATTAAAACTCTGGCAATCGTTGTTATGTCGGCTCTGTCCCTCAGTTCTACAGCGGCTCTGGCCGCTGCCACGACGGTTAATGGTGGGACAGTTCACtt                               >  1:95488/1‑251 (MQ=255)
                                                                                                                                                         atgtgTCAAAATGGCCCCAAATGTTTCATCTTTTGGGGGAAAACTGTGCAGTGTTGGCAGTCAAACTCGTTGAAA‑AAACAAAGTGTACAGAACGACTGCCCATGTCGATTTAGAAATAGTTTTTTGAAAGGAAAGCAGCATGAAAATTAAAACTCTGGCAATCGTTGTTCTGTCGGCTCTGTCCCTCAGTTCTACAGCGGCTCTGGCCGCTGCCACGACGGTTAATGGTGGGACCGTTCACTTTAAAggg                        <  2:47452/246‑1 (MQ=255)
                                                                                                                                                                       ccccAAATGTTTCATCTTTTGGGGGAAAACTGGGCAGTGTTGGCAGTCAAATTTGTTGACA‑TAACAAAGTGGAAAGAACGACTGCCCTTGTCGATTTAGAAATAGTTTTTTGAAAGGAAAGCAGCATGAAAATTAATACTCTGGCAATCGTGGTTCTGTCGGCACCGTCACTCAGTTCTACAGCGGCACAGGCCGATGCCACGACGGTTAATGGAGGGACCGTTCACTTTAACGGGGAAGTTGTTAAcgtg         >  2:282146/1‑249 (MQ=255)
                                                                                                                                                                        cccAAATGTTTCATCTTTTGGGGGAAAACTGTGCAGTGTTGGCAGTCAAGCTCGTTGACA‑AATCAAAGTGTACAGAACGACTGCCCATGTCGATTTAGAAATAGTTTTTTGAAAGGAAAGAAGCATGAAAATTAACACTCTGGCAATCGTTGTTCTGTCGGCTCTGTCCCGCAGTTCTACAGCGGCACTTGCCGCTGACACGACGGTAAGTGGGGGGACCGTTTACTTTatagtgtcagatgttaaggccg        >  2:276375/1‑230 (MQ=255)
                                                                                                                                                                               gTTTCATCTTTTGGGGGAAAACTGTGCAGTGTTGGCAGTCAAACTCGTTGACA‑AAACAAAGTGTACAGAACGACTGCCCATGTCGATTTAGAAATAGTTTTTTGAAAGGAAAGCAGCATGAAAATTAAAACTCTGGCAATCGTTGTTCTGTCGGCTCTGTCCCTCAGTTCTACAGCGGCTCTGGCCGCTGCCACGACGGTTAATGGTGGGACCGTTCACTTTAAAGGGGAAGTTGTTAACGCCGCTTgcg  <  1:288672/250‑1 (MQ=255)
                                                                                                                                                                                                 aaaCTGTGCAGTGTTGGCAGTCAAACTCGTTGACA‑AAACAAAGTGTACAGAACGACTGCCCATGTCGATTTAGAAATAGTTTTTTGAAAGGAAAGCAGCATGAAAATTAAAACTCTGGCAATCGTTGTTCTGTCGGCTCTGTCCCTCAGTTCTACAGCGGCTCTGGCCGCTGCCACGACGGTTAATGGTGGGACCGTTCACTTTAAAGGGGAAGTTGTTAACGCCGCt      >  1:336902/1‑228 (MQ=255)
                                                                                                                                                                                                 aaaCTGTGCAGTGTTGGCAGGCAAACTCGTTGAAA‑AAACAAAGTGTACAGAACGACTGCCCATGTCGATTTAGAAATAGTTTTTTGAAAGGAAAGCAGCATGAAAATTAAAACTCTGGCAAGCGTTGTTCTGTCGGCTCTGTCCCTCAGTTCTACAGCGGCTCTGGCCTCTGCCACGACGGTTAATGGTGGGACCGTTCACTTTAAAGGGGAAGTTGTTAACGCCGCt      <  2:336902/228‑1 (MQ=255)
                                                                                                                                                                                                                                |                                                                                                                                                                                                         
ATGTAAAGCTAACGTTTCTGTGGCTCGACGCATCTTCCTCATTCTTCTCTCCAAAAACCACCTCATGCAATATAAACATCTATAAATAAAGATAACAATAGAATATTAAGCCAACAAATAAACTGAAAAAGTTTGTCCGCGATGCTTTCCTCTATGAGTCAAAATGGCCCCAAATGTTTCATCTTTTGGGGGAAAACTGTGCAGTGTTGGCAGTCAAACTCGTTTACA‑AAACAAAGTGTACAGAACGACTGCCCATGTCGATTTAGAAATAGTTTTTTGAAAGGAAAGCAGCATGAAAATTAAAACTCTGGCAATCGTTGTTCTGTCGGCTCTGTCCCTCAGTTCTACAGCGGCTCTGGCCGCTGCCACGACGGTTAATGGTGGGACCGTTCACTTTAAAGGGGAAGTTGTTAACGCCGCTTGCG  >  NC_000913/4542823‑4543247

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 13 ≤ ATCG/ATCG < 15 ≤ ATCG/ATCG < 27 ≤ ATCG/ATCG < 39 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑