Predicted mutation
evidence seq id position mutation annotation gene description
RA NC_000913 249,970 G→A pseudogene (101/1713 nt) lfhA ← flagellar system protein, promoterless fragment

Read alignment evidence...
  seq id position ref new freq score (cons/poly) reads annotation genes product
*NC_000913249,9700GA98.0% 161.5 / ‑6.3 49pseudogene (101/1713 nt)lfhAflagellar system protein, promoterless fragment
Reads supporting (aligned to +/- strand):  ref base G (1/0);  new base A (23/25);  total (24/25)
Fisher's exact test for biased strand distribution p-value = 4.90e-01
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 1.00e+00

GGCGATGGCGTCCCCGCGCACAAACTTCGATGCCCCGTCCATCGCGCCGTAGAAATCGGCCTCGCTGGCAACATCTTTACGCCGGGTTTGCGCCTGCGCCTGGTTGATCAATCCGGCGTTAAGATCGGCGTCAATCGCCATCTGTTTGCCGGGCATCGCGTCTAAGGTAAAGCGGGCAGAAACCTCGGAAATACGCTCGGCCCCTTTGGTGACGACAATAAAGTTGATTGTCAACAGCGTCAGTAAATCCGAGCGTGAAAGCATTATC  >  NC_000913/249834‑250101
                                                                                                                                        |                                                                                                                                   
ggCGATGGCGTCCCCGCGCACAAACTTCGATGCCCCGTCCATCGCGCCGTAGAAATCGGCCTCGCTGGCAACATCTTTACGCCGGGTTTGCGCCTGCGCCTGGTTGATCAATCCGGCGTTAAGATCGGCGTCAATCAcc                                                                                                                                   >  1:873709/1‑139 (MQ=255)
ggCGATGGCGTCCCCGCGCACAAACTTCGATGCCCCGTCCATCGCGCCGTAGAAATCGGCCTCGCTGGCAACATCTTTACGCCGGGTTTGCGCCTGCGCCTGGTTGATCAATCCGGCGTTAAGATCGGCGTCAATCAcc                                                                                                                                   <  2:873709/139‑1 (MQ=255)
ggCGATGGCGTCCCCGCGCACAAACTTCGATGCCCCGTCCATCGCGCCGTAGAAATCGGCCTCGCTGGCAACATCTTTACGCCGGGTTTGCGCCTGCGCCTGGTTGATCAATCCGGCGTTAAGATCGGCGTCAATCACCa                                                                                                                                  >  2:406402/1‑140 (MQ=255)
 gCGATGGCGTCCCCGCGCACAAACTTCGATGCCCCGTCCATCGCGCCGTAGAAATCGGCCTCGCTGGCAACATCTTTACGCCGGGTTTGCGCCTGCGCCTGGTTGATCAATCCGGCGTTAAGATCGGCGTCAATCACCAt                                                                                                                                 >  2:166339/1‑140 (MQ=255)
   gATGGCGTCCCCGCGCACAAACTTCGATGCCCCGTCCATCGCGCCGTAGAAATCGGCCTCGCTGGCAACATCTTTACGCCGGGTTTGCGCCTGCGCCTGGTTGATCAATCCGGCGTTAAGATCGGCGTCAATCACCATCt                                                                                                                               <  1:449842/140‑1 (MQ=255)
     tGGCGTCCCCGCGCACAAACTTCGATGCCCCGTCCATCGCGCCGTAGAAATCGGCCTCGCTGGCAACATCTTTACGCCGGGTTTGCGCCTGCGCCTGGTTGATCAATCCGGCGTTAAGATCGGCGTCAATCACCATCTGt                                                                                                                             <  2:670652/140‑1 (MQ=255)
      ggCGTCCCCGCGCACAAACTTCGATGCCCCGTCCATCGCGCCGTAGAAATCGGCCTCGCTGGCAACATCTTTACGCCGGGTTTGCGCCTGCGCCTGGTTGATCAATCCGGCGTTAAGATCGGCGTCAATCACCATCTGtt                                                                                                                            >  2:618369/1‑140 (MQ=255)
          tCCCCGCGCACAAACTTCGATGCCCCGTCCATCGCGCCGTAGAAATCGGCCTCGCTGGCAACATCTTTACGCCGGGTTTGCGCCTGCGCCTGGTTGATCAATCCGGCGTTAAGATCGGCGTCAATCACCATCTGTTTGcc                                                                                                                        <  1:618369/140‑1 (MQ=255)
           ccccGCGCACAAACTTCGATGCCCCGTCCATCGCGCCGTAGAAATCGGCCTCGCTGGCAACATCTTTACGCCGGGTTTGCGCCTGCGCCTGGTTGATCAATCCGGCGTTAAGATCGGCGTCAATCACCATCTGTTTGCCg                                                                                                                       <  1:153977/140‑1 (MQ=255)
            cccGCGCACAAACTTCGATGCCCCGTCCATCGCGCCGTAGAAATCGGCCTCGCTGGCAACATCTTTACGCCGGGTTTGCGCCTGCGCCTGGTTGATCAATCCGGCGTTAAGATCGGCGTCAATCACCATCTGTTTGCCgg                                                                                                                      >  1:153009/1‑140 (MQ=255)
                cgcACAAACTTCGATGCCCCGTCCATCGCGCCGTAGAAATCGGCCTCGCTGGCAACATCTTTACGCCGGGTTTGCGCCTGCGCCTGGTTGATCAATCCGGCGTTAAGATCGGCGTCAATCACCATCTGTTTGCCGGGCAt                                                                                                                  >  1:410016/1‑140 (MQ=255)
                cgcACAAACTTCGATGCCCCGTCCATCGCGCCGTAGAAATCGGCCTCGCTGGCAACATCTTTACGCCGGGTTTGCGCCTGCGCCTGGTTGATCAATCCGGCGTTAAGATCGGCGTCAATCACCATCTGTTTGCCGGGCAt                                                                                                                  >  1:267546/1‑140 (MQ=255)
                cgcACAAACTTCGATGCCCCGTCCATCGCGCCGTAGAAATCGGCCTCGCTGGCAACATCTTTACGCCGGGTTTGCGCCTGCGCCTGGTTGATCAATCCGGCGTTAAGATCGGCGTCAATCACCATCTGTTTGCCGGGCAt                                                                                                                  <  1:214554/140‑1 (MQ=255)
                cgcACAAACTTCGATGCCCCGTCCATCGCGCCGTAGAAATCGGCCTCGCTGGCAACATCTTTACGCCGGGTTTGCGCCTGCGCCTGGTTGATCAATCCGGCGTTAAGATCGGCGTCAATCACCATCTGTTTGCCGGGCAt                                                                                                                  <  2:410016/140‑1 (MQ=255)
                 gcACAAACTTCGATGCCCCGTCCATCGCGCCGTAGAAATCGGCCTCGCTGGCAACATCTTTACGCCGGGTTTGCGCCTGCGCCTGGTTGATCAATCCGGCGTTAAGATCGGCGTCAATCACCATCTGTTTGCCGGGCATc                                                                                                                 >  2:561341/1‑140 (MQ=255)
                 gcACAAACTTCGATGCCCCGTCCATCGCGCCGTAGAAATCGGCCTCGCTGGCAACATCTTTACGCCGGGTTTGCGCCTGCGCCTGGTTGATCAATCCGGCGTTAAGATCGGCGTCAATCACCATCTGTTTGCCGGGCATc                                                                                                                 <  1:560368/140‑1 (MQ=255)
                 gcACAAACTTCGATGCCCCGTCCATCGCGCCGTAGAAATCGGCCTCGCTGGCAACATCTTTACGCCGGGTTTGCGCCTGCGCCTGGTTGATCAATCCGGCGTTAAGATCGGCGTCAATCACCATCTGTTTGCCGGGCATc                                                                                                                 <  1:561341/140‑1 (MQ=255)
                  cacaAACTTCGATGCCCCGTCCATCGCGCCGTAGAAATCGGCCTCGCTGGCAACATCTTTACGCCGGGTTTGCGCCTGCGCCTGGTTGATCAATCCGGCGTTAAGATCGGCGTCAATCACCATCTGTTTGCCGGGCATcg                                                                                                                >  2:423800/1‑140 (MQ=255)
                     aaaCTTCGATGCCCCGTCCATCGCGCCGTAGAAATCGGCCTCGCTGGCAACATCTTTACGCCGGGTTTGCGCCTGCGCCTGGTTGATCAATCCGGCGTTAAGATCGGCGTCAATCACCATCTGTTTGCCGGGCATCGCGt                                                                                                             <  1:406402/140‑1 (MQ=255)
                     aaaCTTCGATGCCCCGTCCATCGCGCCGTAGAAATCGGCCTCGCTGGCAACATCTTTACGCCGGGTTTGCGCCTGCGCCTGGTTGATCAATCCGGCGTTAAGATCGGCGTCAATCACCATCTGTTTGCCGGGCATCGCGt                                                                                                             <  1:426743/140‑1 (MQ=255)
                           cGATGCCCCGTCCATCGCGCCGTAGAAATCGGCCTCGCTGGCAACATCTTTACGCCGGGTTTGCGCCTGCGCCTGGTTGATCAATCCGGCGTTAAGATCGGCGTCAATCACCATCTGTTTGCCGGGCATc                                                                                                                 <  2:464875/130‑1 (MQ=255)
                           cGATGCCCCGTCCATCGCGCCGTAGAAATCGGCCTCGCTGGCAACATCTTTACGCCGGGTTTGCGCCTGCGCCTGGTTGATCAATCCGGCGTTAAGATCGGCGTCAATCACCATCTGTTTGCCGGGCATc                                                                                                                 >  1:464875/1‑130 (MQ=255)
                                 cccGTCCATCGCGCCGTAGAAATCGGCCTCGCTGGCAACATCTTTACGCCGGGTTTGCGCCTGCGCCTGGTTGATCAATCCGGCGTTAAGATCGGCGTCAATCACCATCTGTTTGCCGGGCATCGCGTCTAAGGTAAAGc                                                                                                 >  1:180743/1‑140 (MQ=255)
                                     tCCATCGCGCCGTAGAAATCGGCCTCGCTGGCAACATCTTTACGCCGGGTTTGCGCCTGCGCCTGGTTGATCAATCCGGCGTTAAGATCGGCGTCAATCACCATCTGTTTGCCGGGCATCGCGTCTAAGGTAAAGCGGGc                                                                                             >  1:884907/1‑140 (MQ=255)
                                              ccGTAGAAATCGGCCTCGCTGGCAACATCTTTACGCCGGGTTTGCGCCTGCGCCTGGTTGATCAATCCGGCGTTAAGATCGGCGTCAATCACCATCTGTTTGCCGGGCATCGCGTCTAAGGTAAAGCGGGCAGAAACCTc                                                                                    <  1:166339/140‑1 (MQ=255)
                                               cGTAGAAATCGGCCTCGCTGGCAACATCTTTACGCCGGGTTTGCGCCTGCGCCTGGTTGATCAATCCGGCGTTAAGATCGGCGTCAATCACCATCTGTTTGCCGGGCATCGCGTCTAAGGTAAAGCGGGCAGAAACCTCg                                                                                   >  1:415835/1‑140 (MQ=255)
                                                    aaaTCGGCCTCGCTGGCAACATCTTTACGCCGGGTTTGCGCCTGCGCCTGGTTGATCAATCCGGCGTTAAGATCGGCGTCAATCACCATCTGTTTGCCGGGCATCGCGTCTAAGGTAAAGCGGGCAGAAACCTCGGAAAt                                                                              <  2:180743/140‑1 (MQ=255)
                                                           ccTCGCTGGCAACATCTTTACGCCGGGTTTGCGCCTGCGCCTGGTTGATCAATCCGGCGTTAAGATCGGCGTCAATCACCATCTGTTTGCCGGGCATCGCGTCTAAGGTAAAGCGGGCAGAAACCTCGGAAATACGCTCg                                                                       >  1:810839/1‑140 (MQ=255)
                                                           ccTCGCTGGCAACATCTTTACGCCGGGTTTGCGCCTGCGCCTGGTTGATCAATCCGGCGTTAAGATCGGCGTCAATCACCATCTGTTTGCCGGGCATCGCGTCTAAGGTAAAGCGGGCAGAAACCTCGGAAATACGCTCg                                                                       >  2:162372/1‑140 (MQ=255)
                                                           ccTCGCTGGCAACATCTTTACGCCGGGTTTGCGCCTGCGCCTGGTTGATCAATCCGGCGTTAAGATCGGCGTCAATCACCATCTGTTTGCCGGGCATCGCGTCTAAGGTAAAGCGGGCAGAAACCTCGGAAATACGCTCg                                                                       >  1:885916/1‑140 (MQ=255)
                                                           ccTCGCTGGCAACATCTTTACGCCGGGTTTGCGCCTGCGCCTGGTTGATCAATCCGGCGTTAAGATCGGCGTCAATCACCATCTGTTTGCCGGGCATCGCGTCTAAGGTAAAGCGGGCAGAAACCTCGGAAATACGCTCg                                                                       <  1:423800/140‑1 (MQ=255)
                                                             tCGCTGGCAACATCTTTACGCCGGGTTTGCGCCTGCGCCTGGTTGATCAATCCGGCGTTAAGATCGGCGTCAATCACCATCTGTTTGCCGGGCATCGCGTCTAAGGTAAAGCGGGCAGAAACCTCGGAAATACGCTCGGc                                                                     <  2:810839/140‑1 (MQ=255)
                                                              cGCTGGCAACATCTTTACGCCGGGTTTGCGCCTGCGCCTGGTTGATCAATCCGGCGTTAAGATCGGCGTCAATCACCATCTGTTTGCCGGGCATCGCGTCTAAGGTAAAGCGGGCAGAAACCTCGGAAATACGCTCGGcc                                                                    <  2:267546/140‑1 (MQ=255)
                                                               gCTGGCAACATCTTTACGCCGGGTTTGCGCCTGCGCCTGGTTGATCAATCCGGCGTTAAGATCGGCGTCAATCACCATCTGTTTGCCGGGCATCGCGTCTAAGGTAAAGCGGGCAGAAACCTCGGAAATACGCTCGGccc                                                                   <  2:153009/140‑1 (MQ=255)
                                                                     aaCATCTTTACGCCGGGTTTGCGCCTGCGCCTGGTTGATCAATCCGGCGTTAAGATCGGCGTCAATCACCATCTGTTTGCCGGGCATCGCGTCTAAGGTAAAGCGGGCAGAAACCTCGGAAATACGCTc                                                                        <  1:593471/129‑1 (MQ=255)
                                                                     aaCATCTTTACGCCGGGTTTGCGCCTGCGCCTGGTTGATCAATCCGGCGTTAAGATCGGCGTCAATCACCATCTGTTTGCCGGGCATCGCGTCTAAGGTAAAGCGGGCAGAAACCTCGGAAATACGCTc                                                                        >  2:593471/1‑129 (MQ=255)
                                                                                  cGGGTTTGCTCCTGCGCCTGGTTGATCAATCCGGCGTTAAGATCGGCGTCAATCGCCATCTGTTTGCCGTGCATCGCGTCTAAGGTAAAGCGGGCAGAAACCTCGGAAATACGCTCGGCCCCTTTGGTGACGACAATaaa                                                >  2:646739/1‑140 (MQ=255)
                                                                                  cGGGTTTGCGCCTGCGCCTGGTTGATCAATCCGGCGTTAAGATCGGCGTCAATCACCATCTGTTTGCCGGGCATCGCGTCTAAGGTAAAGCGGGCAGAAACCTCGGAAATACGCTCGGCCCCTTTGGTGACGACAATaaa                                                >  2:93860/1‑140 (MQ=255)
                                                                                                  cctgGTTGATCAATCCGGCGTTAAGATCGGCGTCAATCACCATCTGTTTGCCGGGCATCGCGTCTAAGGTAAAGCGGGCAGAAACCTCGGAAATACGCTCGGCCCCTTTGGTGACGACAATAAAGTTGATTGTCAACAGc                                <  1:510271/140‑1 (MQ=255)
                                                                                                          aTCAATCCGGCGTTAAGATCGGCGTCAATCACCATCTGTTTGCCGGGCATCGCGTCTAAGGTAAAGCGGGCAGAAACCTCGGAAATACGCTCGGCCCCTTTGGTGACGACAATAAAGTTGATTGTCaa                                    >  1:232869/1‑128 (MQ=255)
                                                                                                          aTCAATCCGGCGTTAAGATCGGCGTCAATCACCATCTGTTTGCCGGGCATCGCGTCTAAGGTAAAGCGGGCAGAAACCTCGGAAATACGCTCGGCCCCTTTGGTGACGACAATAAAGTTGATTGTCaa                                    <  2:232869/128‑1 (MQ=255)
                                                                                                          aTCAATCCGGCGTTAAGATCGGCGTCAATCACCATCTGTTTGCCGGGCATCGCGTCTAAGGTAAAGCGGGCAGAAACCTCGGAAATACGCTCGGCCCCTTTGGTGACGACAATAAAGTTGATTGTCAACAGCGTCAGTaa                        >  2:485208/1‑140 (MQ=255)
                                                                                                             aaTCCGGCGTTAAGATCGGCGTCAATCACCATCTGTTTGCCGGGCATCGCGTCTAAGGTAAAGCGGGCAGAAACCTCGGAAATACGCTCGGCCCCTTTGGTGACGACAATAAAGTTGATTGTCAACAGCGTCAGTAAATc                     <  1:162372/140‑1 (MQ=255)
                                                                                                             aaTCCGGCGTTAAGATCGGCGTCAATCACCATCTGTTTGCCGGGCATCGCGTCTAAGGTAAAGCGGGCAGAAACCTCGGAAATACGCTCGGCCCCTTTGGTGACGACAATAAAGTTGATTGTCAACAGCGTCAGTAAATc                     <  2:884907/140‑1 (MQ=255)
                                                                                                                ccGGCGTTAAGATCGGCGTCAATCACCATCTGTTTGCCGGGCATCGCGTCTAAGGTAAAGCGGGCAGAAACCTCGGAAATACGCTCGGCCCCTTTGGTGACGACAATAAAGTTGATTGTCAACAGCGTCAGTAAATCCGa                  >  1:31701/1‑140 (MQ=255)
                                                                                                                ccGGCGTTAAGATCGGCGTCAATCACCATCTGTTTGCCGGGCATCGCGTCTAAGGTAAAGCGGGCAGAAACCTCGGAAATACGCTCGGCCCCTTTGGTGACGACAATAAAGTTGATTGTCAACAGCGTCAGTAAATCCGa                  <  1:316544/140‑1 (MQ=255)
                                                                                                                   gCGTTAAGATCGGCGTCAATCACCATCTGTTTGCCGGGCATCGCGTCTAAGGTAAAGC‑GGCAGAAACCTCGGAAATACGCTCGGCCCCTTTGGTGACGACAATAAAGTTGATTGTCAACAGCGTCAGTAAATCCGAGCGt              <  2:442902/140‑1 (MQ=255)
                                                                                                                    cGTTAAGATCGGCGTCAATCACCATCTGTTTGCCGGGCATCGCGTCTAAGGTAAAGCGGGCAGAAACCTCGGAAATACGCTCGGCCCCTTTGGTGACGACAATAAAGTTGATTGTCAACAGCGTCAGTAAATCCGAGCGt              >  1:150730/1‑140 (MQ=255)
                                                                                                                                cGTCAATCACCATCTGTTTGCCGGGCATCGCGTCTAAGGTAAAGCGGGCAGAAACCTCGGAAATACGCTCGGCCCCTTTGGTGACGACAATAAAGTTGATTGTCAACAGCGTCAGTAAATCCGAGCGTGAAAGCATTATc  >  1:355168/1‑140 (MQ=255)
                                                                                                                                        |                                                                                                                                   
GGCGATGGCGTCCCCGCGCACAAACTTCGATGCCCCGTCCATCGCGCCGTAGAAATCGGCCTCGCTGGCAACATCTTTACGCCGGGTTTGCGCCTGCGCCTGGTTGATCAATCCGGCGTTAAGATCGGCGTCAATCGCCATCTGTTTGCCGGGCATCGCGTCTAAGGTAAAGCGGGCAGAAACCTCGGAAATACGCTCGGCCCCTTTGGTGACGACAATAAAGTTGATTGTCAACAGCGTCAGTAAATCCGAGCGTGAAAGCATTATC  >  NC_000913/249834‑250101

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 22 ≤ ATCG/ATCG < 33 ≤ ATCG/ATCG < 37 ≤ ATCG/ATCG < 40 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑