Predicted mutation
evidence	seq id	position	mutation	annotation	gene	description
RA	NC_000913	1,134,466	C→T	A222V (GCC→GTC)	flgF →	flagellar basal‑body rod protein FlgF

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NC_000913	1,134,466	0	C	T	84.6%	49.6 / 2.6	27	A222V (GCC→GTC)	flgF	flagellar basal‑body rod protein FlgF
Reads supporting (aligned to +/- strand):  ref base C (1/3);  new base T (7/15);  total (8/19)
Fisher's exact test for biased strand distribution p-value = 1.00e+00
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 6.04e-01

GGCACAATCTCGGCGCTCAATCCGGGCGATCCGGCAAATACGGTTGCGCCAGTAGGGCGTCTTAAACTGGTGAAAGCCACGGGCAGCGAAGTGCAGCGCGGTGACGACGGCATTTTTCGTTTAAGCGCAGAAACCCAGGCCACGCGTGGGCCGGTACTGCAGGCAGATCCAACCTTGCGTGTGATGTCGGGGGTTCTGGAAGGCAGTAACGTCAATGCC‑GTTGCGGCAATGAGCGACATGATTGCCAGCGCGCGGCGTTTTGAAATGCAGATGAAGGTGATCAGCAGCGTCGATGATAACGCAGGCCGTGCCAACCAACTGCTGTCGATGAGTTAATTGAAAGGATACATGACAAGTATAAGTTGCCCGATGCGCAAGTTTATCGGGTCTATGGGGGCAATCGCAATTTATCGATTTTGCGAGCACTTGTAGGCCGGATAAGGCGTTTACGCCGCATCCGGCAAGAAGACATATGCACTTTGTCA  >  NC_000913/1134222‑1134706                                                                                                                                                                                                                                                      |                                                                                                                                                                                                                                                 ggCACAATCTCGGCGCTCAATCCGGGCGATCCGGCAAATACGGTTGCGCCAGTAGGGCGTCTTAAACTGGTGAAAGCCACGGGCAGCGAAGTGCAGCGCGGTGACGACGGCATTTTTCGTTTAAGCGCAGAAACCCAGGCAACGCGTGGGCCGGTACTGCAGGCAGATCCAACCTTGCGTGTGATGTCGGGGGTTCTGGAAGGCAGTAACGTCAATGCC‑GTTGCGGCAATGAGCGACATGATTGTCAgcgc                                                                                                                                                                                                                                            >  1:58547/1‑251 (MQ=255)  gCACAATCTCGGCGCTCAATCCGGGCGATCCGGAAAATACGGTTGCGCCAGTAGGGCGTCTTAAACTGGTGAAAGCCACGGGCAGCGAAGTGCAGCGCGGTGACGACGGCATTTTTCGTTTAAGCGCAGAAACCCAGGCCACGCGTGGGCCGGTACTGCAGGCAGATCCAACCTTGCGTGTGATGTCGGGGGTTCTGGAAGGCAGTAACGTCAATGCC‑GTTGCGGCAATGAGCGACATGATTGTCAgcgcg                                                                                                                                                                                                                                           <  2:144167/251‑1 (MQ=255)           cGGCGCTCAATCCGGGCGATCCGGCAAATACGGTTGCGCCAGTAGGGCGTCTTAAACTGGTGAAAGCCACGGGCAGCGAAGTGCAGCGCGGTGACGACGGCATTTTTCGTTTAAGCGCAGAAACCCAGGCCACGCGTGGGCCGGTACTGCAGGCAGATCCAACCTTGCGTGTGATGTCGGGGGTTCTGGAAGGCAGTAACGTCAATGCC‑GTTGCGGCAATGAGCGACATGATTGTCAGCGCGCGGCGtt                                                                                                                                                                                                                                    <  1:332775/249‑1 (MQ=255)            ggCGCTCAATCCGGGCGATCCGGCAAATACGGTTGCGCCAGTAGGGCGTCTTAAACTGGTGAAAGCCACGGGCAGCGAAGTGCAGCGCGGTGACGACGGCATTTTTCGTTTAAGCGCAGAAACCCAGGCCACGCGTGGGCCGGTACTGCAGGCAGATCCAACCTTGCGTGTGATGTCGGGGGTTCTGGAAGGCAGTAACGTCAATGCC‑GTTGCGGCAATGAGCGACATGATTGTCAGCGCGCGGCGTTTTg                                                                                                                                                                                                                                 >  1:304354/1‑251 (MQ=255)                      ccGGGCGATCCGGCAAATACGGTTGCGCCAGTAGGGCGTCTTAAACTGGTGAAAGCCACGGGCAGCGAAGTGCAGCGCGGTGACGACGGCATTTTTCGTTTAAGCTCAGAAACCCAGGCCACGCGTGGGCCGGTACTGCAGGCAGATCCAACCTTGCGTGTGATGTCGGGGGTTCTGGAAGGCAGTAACGTCAATGCC‑GTTGCGGCAATGAGCGACATGATTGCCAGCGCGCGGCGTTTTGAAATGCAGAt                                                                                                                                                                                                                       <  2:68851/251‑1 (MQ=255)                         ggCGAGCCGGCAAATACGGTTGCGCCAGTAGGGCGTCTTAAACTGGTGAAAGCCACGGGCAGCGAAGTGCAGCGCGGTGACGACGGCATTTTTCGTTTAAGCGCAGAAACCCAGGCCACGCGTGGGCCGGTACTGCAGGCAGATCCAACCTTGCGTGTGATGTCGGGGGTTCTGGAAGGCAGTAACGTCAATGCC‑GTTGCGGCAATGAGCGACATGATTGTCAGCGCGCGGCGTTTTGAAATGCAGATGaa                                                                                                                                                                                                                    <  1:13193/251‑1 (MQ=255)                            gATCCGGCAAATACGGTTGCGCCAGTAGGGCGTCTTAAACTGGTGAAAGCCACGGGCAGCGAAGTGCAGCGCGGTGACGACGGCATTTTTCGTTTAAGCTCAGAAACCCAGGCCACTCGTGGGCCTGTACTGCAGGCAGATCCAACCTTGCGTGTGATGTCGGGGGTTCTGGAAGGCAGTAACGTCAATGCC‑GTTGCGGCAATGAGCGACATTATTGTCAGCGCGCGGCGTTTTGAAATGCAGATGAAGGt                                                                                                                                                                                                                 <  1:210635/251‑1 (MQ=255)                             gtCCGGCAAATTCGGTTGCGCCAGTAGGGCGTCTTAAACTGGTGAAAGCCACGGTCAGCTAAGTGCAGCGCGGTGACGACGGCATTTTTCGTTTAAGCGCAGAAACCCAGGCCACGCGTGGGCCGGTACTGCAGGCAGATCCAACCTTGCGTGTGATGTCGGGGGTTCTGGAAGGCAGTAACGTCAATGCC‑GTTGCGGCAATGAGCGACATGATTGTCAGCGCGCGGCGTTTTGAAATGCAGATGAAGGTg                                                                                                                                                                                                                <  1:31846/250‑1 (MQ=255)                                                      aGGGCGTCTTAAACTGGTGAAAGCCACGGGCAGCGAAGTGCAGCGCGGTGACGACGGCATTTTTCGTTTAAGCGCAGAAACCCAGGCCACGCGTGGGCCGGTACTGCAGGCAGATCCAACCTTGCGTGTGATGTCGGGGGTTCTGGAAGGCAGTAACGTCAATGCC‑GTTGCGGCAATGAGCGACATGATTGTCAGCGCGCGGCGTTTTGAAATGCAGATGAAGGTGATCAGCAGCGTCGATGATAACGCAg                                                                                                                                                                                       <  1:186694/251‑1 (MQ=255)                                                       gggCGTCTTAAACTGGTGAAAGCCACGGGCAGCGAAGTGCAGCGCGGTGACGACGGCATTTTTCGTTTAAGCGCAGAAACCCAGGCCACGCGTGGGCCGGTACTGCAGGCAGATCCAACCTTGCGTGTGATGTCGGGGGTTCTGGAAGGCAGTAACGTCAATGCC‑GTTGCGGCAATGAGCGACATGATTGTCAGCGCGCGGCGTTTTGAAATGCAGATGAAGGTGATCAGCAGCGTCGATGATAACGCAgg                                                                                                                                                                                      <  1:157746/251‑1 (MQ=255)                                                       gggCGGCTTAAACTGGTGAAAGCCACGGGCAGCGAAGTGCAGCGCGGTGACGACGGCATTTTTCGTTTAAGCGCAGAAACCCAGGCCACGCGTGGGCCGGTACTGCAGGCAGATCCAACCTTGCGTGTGATGTCGGGGGTTCTGGAAGGCAGTAACGTCAATGCC‑GTTGCGGCAATGAGCGACATGATTGTCAGCGCGCGGCGTTTTGAAATGCAGATGAAGGTGATCAGCAGCGTCGATGATAACGCAgg                                                                                                                                                                                      <  1:103218/251‑1 (MQ=255)                                                                   cTGGTGAAAGCCACGGGCAGCGAAGTGCAGCGCGGTGACGACGGCATTTTTCGTTTAAGCGCAGAAACCCAGGCCACGCGAGGGCCGGTACTGCAGGCAGATCCAACCTTGCGTGTGATGTCGGGGGTTCTGGACGGCAGTAACGTCAATGCC‑GTTGCGGCAATGAGCGACATGATTGTCAGCGCGCGGCGTTTTGAAATGCAGATGAAGGTGATCAGCAGCGTCGATGATAACGCAGGCAGTGccaacc                                                                                                                                                                           >  1:240037/1‑250 (MQ=255)                                                                      gTGAAAGCCACGGGCAGCGAAGTGCAGCGCGGTGACGACTGCATTTTTCGTTTAAGCGCAGAAACCCAGGCCACGCGTGGGCCGGTACTGCAGGCAGATCCAACCTTGCGTGTGATGTCGGGGGTTCTGGAAGGCAGTAACGTCAATGCC‑GTTGCGGCAATGAGCGACATGATTGTCAGCGCGCGGCGTTTTGAAATGCAGATTAAGGTGATCAGCAGCGTCGATGATAACGCAGGCCGTGCCAACCAAct                                                                                                                                                                       <  1:243230/251‑1 (MQ=255)                                                                                         aaGTGCAGCGCGGTGACGACGGCATTTTTCGTTTAAGCGCAGAAACCCAGGCCACGCGTGGGCCGGTACTGCAGGCAGATCCCACCTTGCGTGTGATGTCGGGGGTTCTGGAAGGCAGTAACGTCAATGCC‑GTTGCGACAATGAGCGACATGATTGCCAGCGCGCGGCGTTTTGACATGCAGATGAAGGTGATCAGCAGCGTCGATGTTAACGCAGGCCGTGCCAACCAACTGCTGTCGATGAGTTAATTg                                                                                                                                                    >  1:349467/1‑251 (MQ=255)                                                                                                                            agtacaggaaCCCCGGCCATGAGTGGGCAGGTACGGCAGGCAGATCCAACCGTGCTGGGGATGGTGGGGGTTCTGGAAAGCAGTAACGTCAATGGC‑GTTGCGTCAATGAGCGACATTATTGTCAGGGAGCGGCGTTTTGAAATGCAGATGAAGGTGATCAGCAGCGTCGATGATAACGCAGGCCGTGCCAAACAACTGCTGTCGATGATTTAATTTAAAGGATACTGGAAAAGTAGAAGTTGCTCGATgc                                                                                                                  <  2:265865/242‑1 (MQ=255)                                                                                                                                             cACGCGTGGGCCGGTACTGCAGGCAGATCCAACCTTGCGTGTGATGTCGGGGGTTCTGGAAGGCAGTAACGTCAATGCC‑GTTGCGGCAATGAGCGACATGATTGTCAGCGCGAGGCGTTTTGCAATGCAGATGAAGGTGATCAGCCGCGTCGATGATAACGCAGGCCGTGCCAACCAACTGCTGTCGCTGAGTTAATTGAAAGGATACATGACAAGTATAAGTTGCCCGATGCGCTAGTTTATCGGGTCt                                                                                                 >  2:308401/1‑250 (MQ=255)                                                                                                                                                            aCTGCAGGCAGATCCAACCTTGCGTGTGATGTCGGGGGTTCTGGAAGGCAGTAACGTCAATGCC‑GTTGCGGCAATGAGCGACATGATTGTCAGCGCGCGGCGTTTTGAAATGCAGATGAAGGTGATCAGCAGCGTCGATGATAACGCAGGCCGTGCCAACCAACTGCTGTCGATGAGTTAATTGAAAGGATACATGACAAGTATAAGTTGCCCGATGCGCAAGTTTATCGGGTCTATGGGGGCAATCGCa                                                                                  <  1:64804/250‑1 (MQ=255)                                                                                                                                                                           aaCCTTGCGTGTGATGTCGGGGGTTCTGGAAGGCAGTAACGTCAATGCC‑GTTGCGGCAATGAGCGACATGATTGTCAGCGCGCGGCGTTTTGAAATGAAGATGAAGGTGATCAGCAGCGTCGATGATAACGCAGGCCGTGCCAACCAACTGCTGTCGATGAGTTAATTGAAAGGATACATGACAAGTATAAGTTGCCCGATGCGCAAGTTTATCGGGTCTATGGGGGCAATCGCAATTTATCGATTTTGCg                                                                  >  1:44495/1‑251 (MQ=255)                                                                                                                                                                                  cGTGTGATGTCGGGGGTTCTGGAAGGCAGTAACGTCAATGCC‑GTTGCGGCAATGAGCGACATGATTGTCAGCGCGCGGCGTTTTGAAATGCAGATGAAGGTGATCAGCAGCGTCGATGATAACGCAGGCCGTGCCAACCAACTGCTGTCGATGAGTTAATTGAAAGGATACATGACAAGTATAAGTTGCCCGATGCGCAAGTTTATCGGGTCTATGGGGGCAATCGCAATTTATCGATTTTGCGAGCACtt                                                           <  1:287134/251‑1 (MQ=255)                                                                                                                                                                                           tCGGGGGTTCTGGAAGGCAGTAACGTCAATGCC‑GTTGCGGCAATGAGCGACATGATTGTCAGCGCGCGGCGTTTTGAAATGCAGATGAAGGTGATCAGCAGCGTCGATGATAACGCAGGCCGTGCCAACCAACTGCTGTCGATGAGTTAATTGAAAGGATACATGACAAGTATAAGTTGCCCGATGCGCAAGTTTATCGGGTCTATGGGGGCAATCGCAATTTATCGATTTTGCGAGCACTTGTAGGCCgg                                                  >  1:69587/1‑251 (MQ=255)                                                                                                                                                                                             ggggtTTCTGGAAGGCAGTAACGTCAATGCCTGTT‑CGGCAATGAGCGACATGATTGCCAGCGCGCGGCGTTTTGAAATTCAGATTAAGGTGATCAGCAGCGTCGATGATAACGCAGGCCGTGCCAACCAACTGCTGTCGATGAGTTAATTGAAAGGATACATGACAAGTATAAGTTGCCCGATGCGCAAGTTTATCAGGTCTATGGGGGCAATCGCAATTTATCGATTTTGCGAGCACTTGTAGGCCGGAt                                                <  2:198016/251‑1 (MQ=255)                                                                                                                                                                                                ggTTCTGGAAGGCAGTAACGTCAATGCC‑GATGAGGCAATGAGCGACATGATTGTCAGCGCGCGGCGTTTTGAAATGCAGATGAAGGTGATCAGCAGCGTCGATGATAACGCAGGCCGTGCCAACCAACTGCTGTCGATGAGTTAATTGAAAGGATACATGACAAGTATAAGTTGCCCGATGCGCAAGTTTATCGGGTCTATGGGGGCAATCGCAATTTATCGATTTTGCGAGCACTTGTAAGCCGGATa                                               >  1:289334/1‑249 (MQ=255)                                                                                                                                                                                                           gcattAACTTCAATGCC‑GTTTCGGCATTGTGCGACATTATTGCCAGCGCGCTGCGTTTTGAAATGCAGATGAAGGTGATCAGCAGCGTCGATGAGAACGCATGCCGTGCCAACCATCTGCTGTCGATGAGTTAATTGAGAGGATACATGACGCGTATAAGTTGCCCGATGCGCAAGTTTATCGTGTCTATTGGGGCATTCGCAATTTATCGATTTTGCTCGCACTTGTAGGCCGGATAGGACGTTTAcgcc                                  <  2:99181/247‑1 (MQ=255)                                                                                                                                                                                                                 aCGTCAATGCC‑GTTGCGGCAATGAGCGACATGATTGTCAGCGCGCGGCGTTTTGAAATGCAGATGAAGGTGATCAGCAGCGTCGATGATAACGCAGGCCGTGCCAACCAACTGCTGTCGATGAGTTAATTGAAAGGATACATGACAAGTATAAGTTGCCCGATGCGCAAGTTTATCGGGTCTATGGGGGCAATCGCAATTTATCGATTTTGCGAGCACTTGTAGGCCGGATAAGGCGTTTACGCCGCATcc                            <  1:308401/251‑1 (MQ=255)                                                                                                                                                                                                                                      aggAGCGACATGATTGTCAGCGCGCGGCGTTTTGAAATGCAGATGAAGGTGATCAGCAGCGTCGATGATAACGCAGGCCGTGCCAACCAACTGCTGTCGATGAGTTAATTGAAAGGATACATGACAAGTATAAGTTGCCCGATGCGCAAGTTTATCGGGTCTATGGGGGCAATCGCAATTTATCGATTTTGCGAGCACTTGTAGGCCGGATAAGGCGTTTACGCCGCATCCGGCAAGAAGACATATGCACt        <  2:182511/249‑1 (MQ=255)                                                                                                                                                                                                                                      aTGAGCGACATGATTGTCAGCGCGCGGCGTTTTGAAATGCAGATGAAGGTGATCAGCAGCGTCGATGATAACGCAGGCCGTGCCAACCAACTGCTGTCTATGAGTTAATTGAAAGGATACATGACAAGTATAAGTTGCCCGATGCGCAAGTTTATCGGGTCTATGGGGGCAATCGCAATTTATCGATTTTGCGAGCACTTGTAGGCCGGATAAGGCGTTTACGCCGCATCCGGCAAGAAGACATATGCACt        <  1:363938/251‑1 (MQ=255)                                                                                                                                                                                                                                            gACATGATTGGCAGCGCGCGTCGTTTTGAAATGCAGATGAAGGTGATCAGCAGCGTCGATGATAACGCAGGCCGTGCCAACCAACTTCTGTCGATGAGTTAATTGAAAGGATACATGACAAGTATAAGTTGCCCGATGCGCAAGTTTATCGGGTCTATGGGGGCAATCGCAATTTATCGATTTTGCGAGCACTTGTAGGCCGGATAAGGCGTTTACGCCGCATCCGGCAAGAAGACATATGCACTTTGTCa  <  2:69587/251‑1 (MQ=255)                                                                                                                                                                                                                                                      |                                                                                                                                                                                                                                                 GGCACAATCTCGGCGCTCAATCCGGGCGATCCGGCAAATACGGTTGCGCCAGTAGGGCGTCTTAAACTGGTGAAAGCCACGGGCAGCGAAGTGCAGCGCGGTGACGACGGCATTTTTCGTTTAAGCGCAGAAACCCAGGCCACGCGTGGGCCGGTACTGCAGGCAGATCCAACCTTGCGTGTGATGTCGGGGGTTCTGGAAGGCAGTAACGTCAATGCC‑GTTGCGGCAATGAGCGACATGATTGCCAGCGCGCGGCGTTTTGAAATGCAGATGAAGGTGATCAGCAGCGTCGATGATAACGCAGGCCGTGCCAACCAACTGCTGTCGATGAGTTAATTGAAAGGATACATGACAAGTATAAGTTGCCCGATGCGCAAGTTTATCGGGTCTATGGGGGCAATCGCAATTTATCGATTTTGCGAGCACTTGTAGGCCGGATAAGGCGTTTACGCCGCATCCGGCAAGAAGACATATGCACTTTGTCA  >  NC_000913/1134222‑1134706

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 12 ≤ ATCG/ATCG < 14 ≤ ATCG/ATCG < 32 ≤ ATCG/ATCG < 39 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑