Predicted mutation
evidence	seq id	position	mutation	freq	annotation	gene	description
RA	NC_002947	4,964,217	C→A	23.5%	V416V (GTG→GTT)	fliF ←	flagellar M‑ring protein

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NC_002947	4,964,217	0	C	A	23.5%	37.7 / 3.0	17	V416V (GTG→GTT)	fliF	flagellar M‑ring protein
Reads supporting (aligned to +/- strand):  ref base C (4/9);  new base A (2/2);  total (6/11)
Fisher's exact test for biased strand distribution p-value = 5.84e-01
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 8.65e-01

TGTCGCCACGGCTGGCATCGAAGCCGACTGCGTCCTGCACCAGGCGGGTAAAGCGCGCCAGGTCCTCGGCACCCCACGGTGCCCGCGTGGTATCGCCTGTGGCCGGGTCGATCTTGACCTGGTCGTCCACCACCACCGCTACCGACAGGCGGGCCATGCGCCCCTGCTGCTGGCGGGTGTGGCTGATGGAACGGTCCAGCTCGAAATTCTTGGTGCTTTGCTGACGTTTGTCTGACGGGTACGGCGCGAGCATCGGCTGACCGG  >  NC_002947/4964087‑4964350                                                                                                                                   |                                                                                                                                      tGTCGCCACGGCTGGCATCGAAGCCGACTGCGTCCTGCACCAGGCGGGTAAAGCGCGCCAGGTCCTCGGCACCCCACGGTGCCCGCGTGGTATCGCCTGTGGCCGGGTCGATCTTGACCTGGTCGTCcaccaccac                                                                                                                                  >  2:444871/1‑136 (MQ=255)     gCCACGGCTGGCATCGAAGCCGACTGCGTCCTGCACCAGGCGGGTAAAGCGCGCCAGGTCCTCGGCACCCCACGGTGCCCGCGTGGTATCGCCTGTGGCCGGGTCGATCTTGACCTGGTCGTCCACCACCACCGCt                                                                                                                              <  2:259115/136‑1 (MQ=255)      ccACGGCTGGCATCGAAGCCGACTGCGTCCTGCACCAGGCGGGTAAAGCGCGCCAGGTCCTCGGCACCCCACGGTGCCCGCGTGGTATCGCCTGTGGCCGGGTCGATCTTGACCTGGTCGTccaccac                                                                                                                                     <  2:411184/128‑1 (MQ=255)      ccACGGCTGGCATCGAAGCCGACTGCGTCCTGCACCAGGCGGGTAAAGCGCGCCAGGTCCTCGGCACCCCACGGTGCCCGCGTGGTATCGCCTGTGGCCGGGTCGATCTTGACCTGGTCGTccaccac                                                                                                                                     >  1:411184/1‑128 (MQ=255)      ccACGGCTGGCATCGAAGCCGACTGCGTCCTGCACCAGGCGGGTAAAGCGCGCCAGGTCCTCGGCACCCCACGGTGCCCGCGTGGTATCGCCTGTGGCCGGGTCGATCTTGACCTGGTCGTCCACCACCACCGCTa                                                                                                                             >  1:410608/1‑136 (MQ=255)                cATCGAAGCCGACTGCGTCCTGCACCAGGCGGGTAAAGCGCGCCAGGTCCTCGGCACCCCACGGTGCCCGCGTGGTATCGCCTGTGGCCGGGTCGATCTTGACCTGGTCGTCCACCACCACCGCTACCGACAGGCg                                                                                                                   >  1:36757/1‑136 (MQ=255)                    gAAGCCGACTGCGTCCTGCACCAGGCGGGTAAAGCGCGCCAGGTCCTCGGCACCCCACGGTGCCCGCGTGGTATCGCCTGTGGCCGGGTCGATCTTGACCTGGTCGTCCACCACCACCGCTACCGACAGGCGGGcc                                                                                                               <  1:499577/136‑1 (MQ=255)                      aGCCGACTGCGTCCTGCACCAGGCGGGTAAAGCGCGCCAGGTCCTCGGCACCCCACGGTGCCCGCGTGGTATCGCCTGTGGCCGGGTCGATCTTGACCTGGTCGTCCACCACCACCGCTACCGACAGGCGGGCCAt                                                                                                             <  1:425804/136‑1 (MQ=255)                             tGCGTCCTGCACCAGGCGGGTAAAGCGCGCCAGGTCCTCGGCACCACACGGTGCCAGCGTGGTATCGCCTGTGGCCGGGTCGATCTTGACCTGGTCGTCCACAACCACCGCTACCGACAGGCGGGCCATGCGcccc                                                                                                      >  1:425431/1‑136 (MQ=255)                             tGCGTCATGCACCAGGCGGGTAAAGCGCGCCAGGTCCTCGGCACCACACGGTGCCAGCGTGGTATCGCCTGTGGCCGGGTCGATCTTGACCTGGTCGTCCACAACCACCGCTACCGACAGGCGGGCCATGCGcccc                                                                                                      >  1:42935/1‑136 (MQ=255)                                  ccTGCACCAGGCGGGTAAAGCGCGCCAGGTCCTCGGCACCCCACGGTGCCCGCGTGGTATCGCCTGTGGCCGGGTCGATCTTGACCTGGTCGTCCACCACCACCGCTACCGACAGGCGGGCCATGCGCCCctgctg                                                                                                 <  2:410608/136‑1 (MQ=255)                                                                        ccccACGGTGCCCGCGTGGTATCGCCTGTGGCCGGGTCGATCTTGACCTGGTCGTCCACCACCACCGCTACCGACAGGCGGGCCATGCGCCCCTGCTGCTGGCGGGTGTGGCTGATGGAACGGTCCAGCTCGAAAt                                                           <  1:11981/136‑1 (MQ=255)                                                                        ccccACGGTGCCCGCGTGGTATCGCCTGTGGCCGGGTCGATCTTGACCTGGTCGTCCACCACCACCGCTACCGACAGGCGGGCCATGCGCCCCTGCTGCTGGCGGGTGTGGCTGATGGAACGGTCCAGCTCGAAAt                                                           <  1:9402/136‑1 (MQ=255)                                                                             cGGTGCCAGCGTGGTATCGCCTGTGGCCGGGTCGATCTTGACCTGGTCGTCCACAACCACCGCTACCGACAGGCGGGCCATGCGCCCCTGCTGCTGGCGGGTGTGGCTGATGGAACGGTCCAGCTCGAAATTCTTg                                                      <  2:425431/136‑1 (MQ=255)                                                                             cGGTGCCAGCGTGGTATCGCCTGTGGCCGGGTCGATCTTGACCTGGTCGTCCACAACCACCGCTACCGACAGGCGGGCCATGCGCCCCTGCTGCTGGCGGGTGTGGCTGATGGAACGGTCCAGCTCGAAATTCTTg                                                      <  2:42935/136‑1 (MQ=255)                                                                               gTGCCCGCGTGGTATCGCCTGTGGCCGGGTCGATCTTGACCTGGTCGTCCACCACCACCGCTACCGACAGGCGGGCCATGCGCCCCTGCTGCTGGCGGGTGTGGCTGATGGAACGGTCCAGCTCGAAATTCTTGGt                                                    <  1:425828/136‑1 (MQ=255)                                                                               gTGCCCGCGTGGTATCGCCTGTGGCCGGGTCGATCTTGACCTGGTCGTCCACCACCACCGCTACCGACAGGCGGGCCATGCGCCCCTGCTGCTGGCGGGTGTGGCTGATGGAACGGTCCAGCTCGAAATTCTTGGt                                                    <  1:129585/136‑1 (MQ=255)                                                                                         ggTATCGCCTGTGGCCGGGTCGATCTTGACCTGGTCGTCCACCACCACCGCTACCGACAGGCGGGCCATGCGCCCCAGCTGCTGGCGGGTGTGGCTGATGGAACGGTCCAGCTCGAAATTCTTGGTGCTTTGCTgt                                          >  1:376670/1‑135 (MQ=255)                                                                                                       ccGGGTCGATCTTGACCTGGTCGTCCACCACCACCGCTACCGACAGGCGGGCCATGCGCCCCTGCTGCTGGCGGGTGTGGCTGATGGAACGGTCCAGCTCGAAATTCTTGGTGCTTTGCTGACGTTTGTCTGACgg                            >  1:269982/1‑136 (MQ=255)                                                                                                            gcGATCTTGACCTGGTCGTCCACCACCACCGCTACCGACAGGCGGGCCATGCGCCCCTGCTGCTGGCGGGTGTGGCTGATGGAACGGTCCAGCTCGAAATTCTTGGTGCTTTGCTGACGTTTGTCTGACGGGTACg                       <  1:213215/135‑1 (MQ=255)                                                                                                                                 accaccaccGCTACCGACAGGCGGGCCATGCGCCCCTGCTGCTGGCGGGTGTGGCTGATGGAACGGTCCAGCTCGAAATTCTTGGTGCTTTGCTGACGTTTGTCTGACGGGTACGGCGCGAGCATCGGCTGACCgg  >  1:275297/1‑136 (MQ=255)                                                                                                                                   |                                                                                                                                      TGTCGCCACGGCTGGCATCGAAGCCGACTGCGTCCTGCACCAGGCGGGTAAAGCGCGCCAGGTCCTCGGCACCCCACGGTGCCCGCGTGGTATCGCCTGTGGCCGGGTCGATCTTGACCTGGTCGTCCACCACCACCGCTACCGACAGGCGGGCCATGCGCCCCTGCTGCTGGCGGGTGTGGCTGATGGAACGGTCCAGCTCGAAATTCTTGGTGCTTTGCTGACGTTTGTCTGACGGGTACGGCGCGAGCATCGGCTGACCGG  >  NC_002947/4964087‑4964350

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 21 ≤ ATCG/ATCG < 32 ≤ ATCG/ATCG < 36 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑