Predicted mutation
evidence seq id position mutation annotation gene description
RA NC_000913 4,542,683 Δ1 bp intergenic (+50/‑432) 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_0009134,542,6830T.88.2% 52.9 / 1.4 17intergenic (+50/‑432)fimE/fimAregulator for fimA/type 1 fimbriae major subunit
Reads supporting (aligned to +/- strand):  ref base T (0/0);  major base . (7/8);  minor base G (2/0);  total (9/8)
Fisher's exact test for biased strand distribution p-value = 4.71e-01
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 9.84e-01

TCCTCATATGTTAAGGCATGCTTGCGGTTATGAATTGGCGGAGCGTGGTGCAGATACTCGTTTAATTCAGGATTATCTCGGGCATCGAAATATTCGCCATACTGTGCGTTATACCGCCAGTAATGCTGCTCGTTTTGCCGGATTATGGGAAAGAAATAATCTCATAAACGAAAAATTAAAAAGAGAAGAGGTTTGATTTAACTTATTGATAATAAAGTTAAAAAAACAAATAAATACAAGACAATTGGGGCCAAA‑CTGTCCATATCATAAATAAGTTACGTATTTTTTCTCAAGCATAAAAATATTAAAAAACGACAAAAAGCATCTAACTGTTTGATATGTAAATTATTTCTATTGTAAATTAATTTCACATCACCTCCGCTATATGTAAAGCTAACGTTTCTGTGGCTCGACGCATCTTCCTCATTCTTCTCTCCAAAAACCACCTCATGCAATATAAACATCTATAAATA  >  NC_000913/4542438‑4542910
                                                                                                                                                                                                                                                     |                                                                                                                                                                                                                                    
cccTCATATTTTAAGGCATGCTTGCGGTTATGAATGGGCGGAGCGTGGTGCAAATACTCGTTTAATTCAGGATTATCTCGGGCATCGAAATATTCGCCATACTGTGCGTTATACCGCCAGTAATGCTGCTCGTTTTGCCGGATTATGGGAAAGAAATAATCTCATAAACGAAAAATTAAAAAGAGAAGAGGTTTGATTTAACTTATTGATAATAAAGTTAAAAAAACAAATAAATACAAGACAAT‑GGGGcc                                                                                                                                                                                                                                <  1:438882/250‑1 (MQ=255)
       atGTTAAGGTATTCTTGCGGTTATGAATTGGCGGAGCGTGTTGCAGATACTCGTTTAATTCAGGATTATCCCGGGCATCGAAATATTCGCGATACTGTTCGTTATACCGCCAGTAATGCTGCTCGTTTTGCCGGATTATGGGAAAGAAATAATCTCATAAACGAAAAATTAAAAAGAGAAGAGGTTTGATTTAACTTATTGATAATAAAGTTAAAAAAACAAATAAATACAAGACAAT‑GGGGCCaaaact                                                                                                                                                                                                                          <  1:35874/250‑4 (MQ=255)
                cATGCTTGGGGTTATGAATGGGCGGAGCGTGGTGCAGATACCCGTTTAATTCAGGATTATCCCGGGCATCGAAATATTCGCCATACTGTGCGTTATACCGCCAGTAATGCTGCTCGTTTTGCCGGATTATGGGAAAGAAATAATCTCATAAACGAAAAATTAAAAAGAGAAGAGGTTTGATTTAACTTATTGATAATAAAGTTAAAAAAACAAATAAATACAAGACAAT‑GGGGCCAAAACTGTCCATATCa                                                                                                                                                                                                                <  1:524853/251‑1 (MQ=255)
                              tGAATTGGCGGAGCGAGATGCAGAAAATCGGTTAATACAGGCTTATCTCGGGCATCGACATTTTCGCCATACTGTGCGTTATAACGCCAGTAATGCTGCTAGTTTTGCCGGATTATGGGAAAGAAATAATCTCTTAAACGAAAAATTAACCAGAGAAGAGGTTTGATTTCACTTATTGATAATAAAGTTAAAAAAAAGAATAAATCCCAGACACTGGGTACAAAA‑CTGTCcataacataattacgttccat                                                                                                                                                                                                  >  2:569078/1‑240 (MQ=255)
                                                                aTTCAGGATTATCTCGGGCATCGAAATATTCGCCATACTGTGCGTTATACCGCCAGTAATGCTGCTCGTTTTGCCGGATTATGGGAAAGAAATAATCTCATAAACGAAAAATTAAAAAGAGAAGAGGTTTGATTTAACTTATTGATAATAAAGTTAAAAAAACAAATAAATACAAGACAAT‑GGGGCCAAAACTGTCCATATCATAAATAAGTTACGTATTTTTTCTCAAGCATAAAAATATTAAAAAACg                                                                                                                                                                 >  1:184016/1‑250 (MQ=255)
                                                                   cAGGATTATCTCGGGCATCGAAATATTCGCCATACTGTGCGTTATAAAGCAAGTAATGCTGCTCGTTTTGCCGGATTATGGGAAAGAAATAATCTCATAAACGAACAATTAAAAAGAGAAGAGGTTTGATTTAACTTATTGATAATAAAGTTAAAAAAACAAATAAATACAAGACAAT‑GGGGCCAAAACTGTCCATATCATAAATAAGTTAAGTATTTTTTCTCAAGCATACAAATATTAAAAAAcaacc                                                                                                                                                              >  2:229075/1‑246 (MQ=255)
                                                                                                                       gTAATGCTGCTCGTTTTGCCGGATTATGGGAAAGAAATAATCTCATAAACGAAAAATTAAAAAGAGAAGAGGTTTGATTTAACTTATTGATAATAAAGTTAAAAAAACAAATAAATACAAGACAAT‑GGGGCCAAAACTGTCCATATCATAAATAAGTTACGTATTTTTTCTCAAGCATAAAAATATTAAAAAACGACAAAAAGCATCTAACTGTTTGATATGTAAATTATTTCTATTGTAAATTAATTTc                                                                                                          >  1:245098/1‑250 (MQ=255)
                                                                                                                                             aTTATGGGAAAGAAATAATCTCATAAACGAAAAATTAAAAAGAGAAGAGGTTTGATTTAACTTATTGATAATAAAGTTAAAAAAACAAATAAATACAAGACAAT‑GGGGCCAAAACTGTCCATATCATAAATAAGTTACGTATTTTTTCTCAAGCATAAAAATATTAAAAAACGACAAAAAGCATCTAACTGTTTGATATGTAAATTATTTCTATTGTAAATTAATTTCACATCACCTCCGCTATATGTaa                                                                                    >  1:470547/1‑250 (MQ=255)
                                                                                                                                                       agaaaTAATCTCATAAACGAAAAATTAAAAAGAGAAGAGGTTTGATTTAACTTATTGATAATAAAGTTAAAAAAACAAATAAATACAAGACAAT‑GGGGCCAAAACTGTCCATATCATAAATAAGTTACGTATTTTTTCTCAAGCATAAAAATATTAAAAAACGACAAAAAGCATCTAACTGTTTGATATGTAAATTATTTCTATTGTAAATTAATTTCACATCACCTCCGCTATATGTAAAGCTAACGttt                                                                         <  1:94391/251‑1 (MQ=255)
                                                                                                                                                        aaaaTAATCTCATAAACGAAAAATTAAAAAGAGAAGAGGTTTGATTTAACTTATTGATAATAAAGTTAAAAAAACAAATAAATACAAGACAAT‑GGGGCCAAAACTGTCCATATCATAAATAAGTTACGTATTTTTTCTCAAGCATAAAAATATTAAAAAACGACAAAAAGCATCTAACTGTTTGATATGTAAATTATTTCTATTGTAAATTAATTTCACATCACCTCCGCTATATGTAAAGCTAACGTTTc                                                                        <  1:297022/250‑1 (MQ=255)
                                                                                                                                                                ctcATCAACGTAAAATTACAAATAGAAGAGGTTTGATTTAACTTATTGATAATAAAGTTAAAAAAACAAATAAATACAAGACAAT‑GGGGCCAAAACTGTCCATATCATAAATAAGTTACGTATTTTTTCTCAAGCATAAAAATATTAAAAAACGACAAAAAGCATCTAACTGTTTGATATGTAAATTATTTCTATTGt                                                                                                                     >  2:616566/1‑198 (MQ=255)
                                                                                                                                                                ctcATAAACGAAAAATTAAAAAGAGAAGAGGTTTGATTTAACTTATGGATAATAAAGTTAAAAAAACAAATAAATACAAGACAAT‑GGGGCCAAAACTGTCCATATCATAAATAAGTTACGTATTTTTTCTCAAGCATAAAAATATTAAAAAACGACAAAAAGCATCTAACTGTTTGATATGTAAATTATTTCTATTGt                                                                                                                     <  1:616566/198‑1 (MQ=255)
                                                                                                                                                                             aaTTAAAAAGAGAAGAGGTTTGATTTAACTTATTGATAATAAAGTTATAAAAAAAAAGAAATACACGACAATGGGGACAAAA‑CTGTCCATATCATAAATAAGTTACGACTTTTTTCTCAAGAATACAACTATTAAACAACGACAAAAAGCATCTAACTGTTTGATATGTAAATTATTTCTATTGTAAATTAATTTCCCATCACCTCCGCTATATGTACAGCTAACGTTTCTGTGGCTCGACGCCTCTTcac                                                   >  2:351175/1‑249 (MQ=255)
                                                                                                                                                                                       agaagagGTTTGATTTAACTTATTGATAATAAAGTTAAAAAAACAAATAAATACAAGACAAT‑GGGGCCAAAACTGTCCATATCATAAATAAGTTACGTATTTTTTCTCAAGCATAAAAATATTAAAAAACGACAAAAAGCATCTAACTGTTTGATATGTAAATTATTTCTATTGTAAATTAATTTCACATCACCTCCGCTATATGTAAAGCTAACGTTTCTGTGGCTCGACGCATCTTCCTCATTCTtctc                                         <  1:211909/251‑1 (MQ=255)
                                                                                                                                                                                                     ttAACTTATTTATAATAAAGTTAAAAAAACAAATAAATATAAGATAAT‑GGGGCCAAAACTGTCCATATCAAAAATAAATTACGTATTTTTTCGCAAGCATAAAAATATTAAAAAACGACAAAAAGCATCTAACTGTTTGATATGTAAATTATTTCTATTGTAAATTAATTTCACATCACCTCCGCTATAAGTAAAGCTAACGTTTCTGTGGCTCGACGCATCTTCCTCATTCTTCTCTCCAAATaccacc                            <  2:380444/250‑1 (MQ=255)
                                                                                                                                                                                                                            aacaaaCAAATAAATACAAGACAAT‑GGGGCCAAAACTGTCCATATCATCAATAAGTTACGTATTTTTTCTCAAGCATAAAAATATTAAAAAAAGACAAAAAGCATCTAACTGTTTGATATGTAAATTATTTCTATTGTAAATTAATTTCACATCACCTCCGCTATATGTAAAGCTAACGTTTCTGTGGCTCGACGCATCTTCCTCATTATTATCTCCAAAAACCACCCAATGCAATATAACCATTTataa     >  2:517833/4‑250 (MQ=255)
                                                                                                                                                                                                                               aaaCAAATAAATACAAGACAAT‑GGGGCCAAAACTGTCCATATCATAAATAAGTTACGTATTTTTTCTCAAGCATAAAAATATTAAAAAACGACAAAAAGCATCTAACTGTTTGATATGTAAATTATTTCTATTGTAAATTAATTTCACATCACCTCCGCTATATGTAAAGCTAACGTTTCTGTGGCTCGACGCATCTTCCTCATTCTTCTCTCCAAAAACCACCTCATGCAATATAAACATCTataaata  >  1:90777/1‑250 (MQ=255)
                                                                                                                                                                                                                                                     |                                                                                                                                                                                                                                    
TCCTCATATGTTAAGGCATGCTTGCGGTTATGAATTGGCGGAGCGTGGTGCAGATACTCGTTTAATTCAGGATTATCTCGGGCATCGAAATATTCGCCATACTGTGCGTTATACCGCCAGTAATGCTGCTCGTTTTGCCGGATTATGGGAAAGAAATAATCTCATAAACGAAAAATTAAAAAGAGAAGAGGTTTGATTTAACTTATTGATAATAAAGTTAAAAAAACAAATAAATACAAGACAATTGGGGCCAAA‑CTGTCCATATCATAAATAAGTTACGTATTTTTTCTCAAGCATAAAAATATTAAAAAACGACAAAAAGCATCTAACTGTTTGATATGTAAATTATTTCTATTGTAAATTAATTTCACATCACCTCCGCTATATGTAAAGCTAACGTTTCTGTGGCTCGACGCATCTTCCTCATTCTTCTCTCCAAAAACCACCTCATGCAATATAAACATCTATAAATA  >  NC_000913/4542438‑4542910

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 13 ≤ ATCG/ATCG < 15 ≤ ATCG/ATCG < 32 ≤ ATCG/ATCG < 39 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑