Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NC_000913	2,002,825	0	C	T	78.8%	62.9 / 17.0	33	G261E (GGA→GAA)	fliC	flagellar filament structural protein
Reads supporting (aligned to +/- strand):  ref base C (3/4);  new base T (16/10);  total (19/14)
Fisher's exact test for biased strand distribution p-value = 4.22e-01
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 8.75e-01
Rejected as consensus: Frequency below/above cutoff threshold.

CAGCACCAGTAGTTTCATTCACATCCGCAGCGTAAAGATTGCCATTTGTATCTTTAAGCGCATATGTATCGGTATCATTACCCTTGGAATCCTGCAGTTTTACTAAGCTAACAGCACCAAGGTTGGCAGTTGCGGAACCTGCAGTATTATCAATCTGAACAGGTGTACCGCCTGAAGTGATAGTTGTAGCTTTAGTAGTATTTGCATCAGTTACAGTTGCATTTGCCGTTGCTCCAGTCGCCATTGTCACTGTACCATCATTAGCAACTGTTACTGCGTAATACTTCCCATCGTTATCACCACCGGTGATTTTCGCATAGTAATCATTACCATTATCAGTATAAACACCCTCAATTGAAGCTGGGTTAGTTCCGCCAGTATCAGTGGCTGCTTCCGTAGAAAGGGTAATTCCAGTAAGTTTAATATTGTTTGTGGTGGTAGCACCAAAAGCAGTTACTGGAGCACTAGTG  >  NC_000913/2002592‑2003061                                                                                                                                                                                                                                          |                                                                                                                                                                                                                                             cAGCACCAGTAGTTTCATTCACATCCGCAGCGTAAAGATTGCCATTTGTATCTTTAAGCGCATATGTATCGGTATCATTACCCTTGGAATCCTGCAGTTTTACTAAGCTAACAGCACCAAGGTTGGCAGTTGCGGAACCTGCAGTATTATCAATCTGAACAGGTGTACCGCCTGAAGTGATAGTTGTAGCTTTAGTAGTATTTGCATCAGTTACAGTTGCATTTGCCGTTGCTTCAGTCGCCATTGTCACt                                                                                                                                                                                                                             >  1:30447/1‑251 (MQ=255)    cACCAGTCGTTTCATTCACATCCGCAGCGTAAAGATTGCCATTTGTATCTTTAAGCGCATATGTATCGGTATCATTACCCTTGGAATCCTGCAGTTTTACTAAGCTAACAGCACCAAGGTTGGCAGTTGCGGAACCTGCAGTATTATCAATCTGAACAGGTGTACCGCCTGAAGTGATAGTTGTAGCTTTAGTAGTATTTGCATCAGTTACAGTTGCATTTGCCGTTGCTTCAGTCGCCATTGTCACTGt                                                                                                                                                                                                                           >  2:236207/1‑250 (MQ=255)            gtTTCATTCACATCCGCAGCGTAAAGATTGCCATTTGTATCTTTAAGCGCATATGTATCGGTATCATTACCCTTGGAATCCTGCAGTTTTACTAAGCTAACAGCACCAAGGTTGGCAGTTGCGGAACCTGCAGTATTATCAATCTGAACAGGTGTACCGCCTGAAGTGATAGTTGTAGCTTTAGTAGTATTTGCATCAGTTACAGTTGCATTTGCCGTTGCTCCAGTCGCCATTGTCACTGTACCATCAtt                                                                                                                                                                                                                  <  1:232466/251‑1 (MQ=255)                                       ttGCCATTTGTATCTTTAAGCGCATATGTATCGGTATCATTACCCTTGGAATCCTGCAGTTTTACTAAGCTAACAGCACCAAGGTTGGCAGTTGCGGAACCTGCAGTATTATCAATCTGAACAGGTGTACCGCCTGAAGTGATAGTTGTAGCTTTAGTAGTATTTGCATCAGTTACAGTTGCATTTGCCGTTGCTTCAGTCGCCATTGTCACTGTACCATCATTAGCAACTGTTACTGCGTAATACTTccc                                                                                                                                                                                       >  1:128894/1‑251 (MQ=255)                                         gCCATTTGTATCTTTAAGCGCATATGTATCGGTATCATTACCCTTGGAATCCTGCAGTTTTACTAAGCTAACAGCACCAAGGTTGGCAGTTGCGGAACCTGCAGTATTATCAATCTGAACAGGTGTACCGCCTGAAGTGATAGTTGTAGCTTTAGTAGTATTTGCATCAGTTACAGTTGCATTTGCCGTTGCTTCAGTCGCCATTGTCACTGTACCATCATTAGCAACTGTTACTGCGTAATACTTCCCa                                                                                                                                                                                      <  2:30447/250‑1 (MQ=255)                                         gCCATTTGTATCTTTAAGCGCATATGTATCGGTATCATTACCCTTGGAATCCTGCAGTTTTACTAAGCTAACAGCACCAAGGTTGGCAGTTGCGGAACCTGCAGTATTATCAATCTGAACAGGTGTACCGCCTGAAGTGATAGTTGTAGCTTTAGTAGTATTTGCATCAGTTACAGTTGCATTTGCCGTTGCTCCATGCGCCAGTGTCACTGTACCATCATTAGCAACTGTTACTGCGTAATTCTTCCCa                                                                                                                                                                                      <  2:200527/250‑1 (MQ=255)                                                      ttAAGCGCATATGTATCGGTATCATTACCCTTGGAATCCTGCAGTTTTACTAAGCTAACAGCACCAAGGTTGGCAGTTGCGGAACCTGCAGTATTATCAATCTGAACAGGTGTACCGCCTGAAGTGATAGTTGTAGCTTTAGTAGTATTTGCATCAGTTACAGTTGCATTTGCCGTTGCTTCAGTCGCCATTGTCACTGTACCATCATTAGCAACTGTTACTGCGTAATACTTCCCATCGTTATcacc                                                                                                                                                                           <  1:370330/248‑1 (MQ=255)                                                      ttAAGCGCATATGTATCGGTATCATTACCCTTGGAATCCTGCAGTTTTACTAAGCTAACAGCACCAAGGTTGGCAGTTGCGGAACCTGCAGTATTATCAATCTGAACAGGTGTACCGCCTGAAGTGATAGTTGTAGCTTTAGTAGTATTTGCATCAGTTACAGTTGCATTTGCCGTTGCTCCAGTCGCCATTGTCACTGTACCATCATTAGCAACTGTTACTGCGTAATACTTCCCATCGTTATcaccac                                                                                                                                                                         <  2:104644/250‑1 (MQ=255)                                                                atGTATCGGTATCATTACCCTTGGAATCCTGCAGTTTTACTAAGCTAACAGCACCAAGGTTGGCAGTTGCGGAACCTGCAGTATTATCAATCTGAACAGGTGTACCGCCTGAAGTGATAGTTGTAGCTTTAGTAGTATTTGCATCAGTTACAGTTGCATTTGCCGTTGCTCCAGTCGCCATTGTCACTGTACCATCATTAGCAACTGTTACTGCGTAATACTTCCCATCGTTATCACCACCGGTGAtttt                                                                                                                                                               <  1:407486/250‑1 (MQ=255)                                                                          atgattacaattGGAATCCTGCAGTTTTACTAAGCTAACAGCACCAAGGTTGGCAGTTGCGGAACCTGCAGTATTATCAATCTGAACAGGGGTACCGCCTGAAGTGATAGTTGTAGCTTTAGTAGTATTTGCATCAGTTACAGTTGCATTTGCAGTTGCTCCAGTCGCCATTGTCACTGTACCATCATTAGCAACTGTTACTGCGTAATACTTCCCATCGTTATCACCACCGGTGATTTTCGCATAGTatt                                                                                                                                                    >  2:130390/11‑249 (MQ=255)                                                                          aTCATTACCCTTGGAATCCTGCAGTTTTACTAAGCTAACAGCACCAAGGTTGGCAGTTGCGGAACCTGCAGTATTATCAATCTGAACAGGTGTACCGCCTGAAGTGATAGTTGTAGCTTTAGTAGTATTTGCATCAGTTACAGTTGCATTTGCCGTTGCTTCAGTCGCCATTGTCACTGTACCATCATTAGCAACTGTTACTGCGTAATACTTCCCATCGTTATCACCACCGGTGATTTTCGCATAGTAAt                                                                                                                                                    <  1:79516/251‑1 (MQ=255)                                                                                         aTCCTGCAGTTTTACTAAGCTAACAGCACCAAGGTTGGCAGTTGCGGAACCTGCAGTATTATCAATCTGAACAGGTGTACCGCCTGAAGTGATAGTTGTAGCTTTAGTAGTATTTGCATCAGTTACAGTTGCATTTGCCGTTGCTTCAGTCGCCATTGTCACTGTAcc                                                                                                                                                                                                                        <  1:98350/168‑1 (MQ=255)                                                                                         aTCCTGCAGTTTTACTAAGCTAACAGCACCAAGGTTGGCAGTTGCGGAACCTGCAGTATTATCAATCTGAACAGGTGTACCGCCTGAAGTGATAGTTGTAGCTTTAGTAGTATTTGCATCAGTTACAGTTGCATTTGCCGTTGCTTCAGTCGCCATTGTCACTGTAcc                                                                                                                                                                                                                        >  2:98350/1‑168 (MQ=255)                                                                                                       cTAAGCTAACAGCACCAAGGTTGGCAGTTGCGGAACCTGCAGTATTATCAATCTGAACAGGTGTACCGCCTGAAGTGATAGTTGTAGCTTTAGTAGTATTTGCATCAGTTACAGTTGCATTTGCCGTTGCTTCAGTCGCCATTGTCACTGTACCATCATTAGCAACTGTTACTGCGTAATACTTCCCATCGTTATCACCACCGGTGATTTTCGCATAGTAATCATTACCATTATCAGTATAAACACCCTc                                                                                                                        >  1:18717/1‑250 (MQ=255)                                                                                                         aaGCTAACAGCACCAAGGTTGGCAGTTGCGGAACCTGAAGGATTATCAATCTGAACAGGTGTACCGCCTGAAGTGATAGTTGTAGCTTTAGTAGTATTTGCATCAGTTACAGTTGCATTTGCCGTTGCTTCAGTAGCCATTGTCACTGTACCATCATTAGCAACTGTTACTGCGTAATACTTCCCATCTTTATCACCACCGGTGATTTTCGCATAGTAATCATTACCATTATCAGTATAAACACCCTCa                                                                                                                       <  2:112464/249‑1 (MQ=255)                                                                                                                    aCCAAGGTTGGCAGTTGCGGAACCTGCAGTATTATCAATCTGAACAGGCGTAACGCCTGAAGTGATAGTTGTAGCTTTAGTAGTATTTGCATCAGTTACAGTTGCATTTGCCGTTGCTTCAGTCGCCATTGTCACTGTACCATCATTAGCAACTGTTACTGCGTAATACTTCCCATCGTTATCACCACCGGTGATTTTCGCATAGTCATCATTACCATTATCAGTATAAACACCCTCAATTGAAGCTGGGt                                                                                                          >  1:41353/1‑251 (MQ=255)                                                                                                                     ccAAGGTTGGCAGTTGCGGAACCTGCAGTATTATCAATCTGAACAGGTGTACCGCCTGAAGTGATAGTTGTAGCTTTAGTAGTATTTGCATCAGTTACAGTTGCATTTGCCGTTGCTTCAGTCGCCATTGTCACTGTACCATCATTAGCAACTGTTACTGCGTAATACTTCCCATCGTTATCACCACCGGTGATTTTCGCATAGTAATCATTACCATTATCAGTATAAACACCCTCAATTGAAGCTGGGtt                                                                                                         >  2:144912/1‑251 (MQ=255)                                                                                                                            tggcaatggtggcaCCTCCAGTATTACCAATCTGAACAGGTGTACCGCCTGAAGTGATAGTTGAAGCTTTAGTAGTATTTGCATAAGTTACAGTTGCATTTGCCGTTGCTTCAGTCGCCATTGTCACTGTATCATCATTAGCAATTGTTACTGCGTAATACTTCCCATCGTTATCACCACCGGTGATTTGCGCATAGTAATAATTACTATTATCAGTATAAACACCCTCAATTGAAGCTGGGTTAGTTCCg                                                                                                  >  2:404853/14‑251 (MQ=255)                                                                                                                                               aGTATTATCAATCTGAACAGGTGTACCGCCTGAAGTGATAGTTGTAGCTTTAGTAGTATTTGCATCAGTTACAGTTGCATTTGCCGTTGCTTCAGTCGCCATTGTCACTGTACCATCATTAGCAACTGTTACTGCGTAATACtt                                                                                                                                                                                          >  1:132617/1‑144 (MQ=255)                                                                                                                                               aGTATTATCAATCTGAACAGGTGTACCGCCTGAAGTGATAGTTGTAGCTTTAGTAGTATTTGCATCAGTTACAGTTGCATTTGCCGTTGCTTCAGTCGCCATTGTCACTGTACCATCATTAGCAACTGTTACTGCGTAATACtt                                                                                                                                                                                          <  2:132617/144‑1 (MQ=255)                                                                                                                                               aGTATTATCAATCTGAACAGGTGTACCGCCTGAAGTGATAGTTGTAGCTTTAGTAGTATTTGCATCAGTTACAGTTGCATTTGCCGTTGCTTCAGTCGCCATTGTCACTGTACCATCATTAGCAACTGTTACTGCGTAATACTTCCCATCGTTATCACCACCGGTGATTTTCGCATAGTAATCATTACCATTATCAGTATAAACACCCTCAATTGAAGCTGGGTTAGtt                                                                                                     <  1:427457/229‑1 (MQ=255)                                                                                                                                               aGTATTATCAATCTGAACAGGTGTACCGCCTGAAGTGATAGTTGTAGCTTTAGTAGTATTTGCATCAGTTACAGTTGCATTTGCCGTTGCTTCAGTCGCCATTGTCACTGTACCATCATTAGCAACTGTTACTGCGTAATACTTCCCATCGTTATCACCACCGGTGATTTTCGCATAGTAATCATTACCATTATCAGTATAAACACCCTCAATTGAAGCTGGGTTAGtt                                                                                                     >  2:427457/1‑229 (MQ=255)                                                                                                                                                    tatCAATCTGAACAGGTGTACCGCCTGAAGTGATAGTTGTAGCTTTAGTAGTATTTGCATCAGTTACAGTTGCATTTGCCGTTGCTCCAGTCGCCATTGTCACTGTACCATCATTAGCAACTGTTACTGCGTAATACTTCCCATCGTTATCACCACCGGTGATTTTCGCATAGTAATCATTACCATTATCAGTATAAACACCCTCACTTGAAGCTGGGTTAGTTCCGCCAGTATCAGTGGCTGCTTCCGt                                                                           >  1:453186/1‑250 (MQ=255)                                                                                                                                                         aTCTGAACAGGTGTACCGCCTGAAGTGATAGTTGTAGCTTTAGTAGTATTTGCATCAGTTACAGTTGCATTTGCCGTTGCTTCAGTCGCCATTGTCACTGTACCATCATTAGCAACTGTTACTGCGTAATACTTCCCATCGTTATCACCACCGGTGATTTTCGCATAGTAATCATTACCATTATCAGTATAAACACCCTCAATTGAAGCTGGGTTAGTTCCGCCAGTATCAGTGGCTGCTTcc                                                                             <  2:385311/243‑1 (MQ=255)                                                                                                                                                         aTCTGAACAGGTGTACCGCCTGAAGTGATAGTTGTAGCTTTAGTAGTATTTGCATCAGTTACAGTTGCATTTGCCGTTGCTTCAGTCGCCATTGTCACTGTACCATCATTAGCAACTGTTACTGCGTAATACTTCCCATCGTTATCACCACCGGTGATTTTCGCATAGTAATCATTACCATTATCAGTATAAACACCCTCAATTGAAGCTGGGTTAGTTCCGCCAGTATCAGTGGCTGCTTcc                                                                             >  1:385311/1‑243 (MQ=255)                                                                                                                                                            tGAACAGGTGTACCGCCTGAAGGGATAGTTGTAGCTTTAGTAGTATTTGCATCAGTTACAGTTGCATTTGCCGTTGCTTCAGACGCCATTGTCACTGTACCATCATTAGCAACTGTTACTGCGTAATACTTCCCATCGTTATCACCACCGGAGATTTTCGCATAGTAATCATTACCATTATCAGTATAAACACCCTCAATTGAAGCTGGGTTAGTTCCGCCCGAATCAGTGGATGCTTCCGTAgcacgggg                                                                  >  2:342695/1‑244 (MQ=255)                                                                                                                                                                               aaGTGATAGTTGTAGCTTTAGTAGTATTTGCATCAGTTACAGTTGCATTTGCCGTTGCTTCAGTCGCCATTGTCACTGTACCATCATTAGCAACTGTTACTGCGTAATACTTCCCATCGTTATCACCACCGGTGATTTTCGCATAGTAATCATTACCATTATCAGTATAAACACCCTCAATTGAAGCTGGGTTAGTTCCGCCAGTATCAGTGGCTGCTTCCGTAGAAAGGGTAATTCCAGTACGTTTAat                                                >  1:435573/1‑250 (MQ=255)                                                                                                                                                                                          gTAGCTTTAGTAGTATTTGCATCAGTTACAGTTGCATTTGCCGTTGCTCCAGTCGCCATTGTCACTGTACCATCATTAGCAACTGTTACTGCGTAATACTTCCCATCGTTATCACCACCGGTGATTTTCGCATAGTAATCATTACCATTATCAGTATAAACACCCTCAATTGAAGCTGGGTTAGTTCCGCCAGTATCAGTGGCTGCTTCCGTAGAAAGGGTAATTCCAGTAAGTTTAATATTGTTTgtggt                                    >  2:326988/1‑251 (MQ=255)                                                                                                                                                                                               tttAGTAGTATTTGCATCAGTTACAGTTGCATTTGCCGTTGCTTCAGTCGCCATTGTCACTGTACCATCATTAGCAACTGTTACTGCGTAATACTTCCCATCGTTATCACCACCGGTGATTTTCGCATAGTAATCATTACCATTATCAGTATAAACACCCTCAATTGAAGCTGGGTTAGTTCCGCCAGTATCAGTGGCTGCTTCCGTAGAAAGGGTAATTCCAGTAAGTTTAATATTGTTTGTggtggt                                 >  1:365720/1‑249 (MQ=255)                                                                                                                                                                                                        aTTTGCATCAGTTACAGTTGCATTTGCCGTTGCTTCAGTCGCCATTGTCACTGTACCATCATTAGCAACTGTTACTGCGTAATACTTCCCATCGTTATCACCACCGGTGATTTTCGCATAGTAATCATTACCATTATCAGTATAAACACCCTCAATTGAAGCTGGGTTAGTTCCGCCAGTATCAGTGGCTGCTTCCGTAGAAAGGGTAATTCCAGTAAGTTTAATATTGTTTGTGGTGGTAGCACCaaaa                       <  2:128894/250‑1 (MQ=255)                                                                                                                                                                                                                  gTTACAGTTGCATTTGCCGTTGCTTCAGTCGCCATTGTCACTGTACCATCATTAGCAACTGTTACTGCGTAATACTTCCCATCGTTATCACCACCGGTGATTTTCGCATAGTAATCATTACCATTATCAGTATAAACACCCTCAATTGAAGCTGGGTTAGTTCCGCCAGTATCAGTGGCTGCTTCCGTAGAAAGGGTAATTCCAGTAAGTTTAATATTGTTTGTGGTGGTAGCACCAAAAGCAGTTACTgg            >  2:284083/1‑251 (MQ=255)                                                                                                                                                                                                                     aCAGTTGCATTTGCCGTTGCTTCAGTCGCCATTGTCACTGTACCATCATTAGCAACTGTTACTGCGTAATACTTCCCATCGTTATCACCACCGGTGATTTTCGCATAGTAATCATTACCATTATCAGTATAAACACCCTCAATTGAAGCTGGGTTAGTTCCGCCAGTATCAGTGGCTGCTTCCGTAGAAAGGGTAATTCCAGTAAGTTTAATATTGTTTGTGGTGGTAGCACCAAAAGCAGTTACTGGAGc         >  1:2273/1‑251 (MQ=255)                                                                                                                                                                                                                            cATTTGCCGTTGCTTCAGTCGCCATTGTCACTGTACCATCATTAGCAACTGTTACTGCGTAATACTTCCCATCGTTATCACCACCGGTGATTTTCGCATAGTAATCATTACCATTATCAGTATAAACACCCTCAATTGAAGCTGGGTTAGTTCCGCCAGTATCAGTGGCTGCTTCCGTAGAAAGGGTAATTCCAGTAAGTTTAATATTGTTTGTGGTGGTAGCACCAAAAGCAGTTACTGGAGCACTAGTg  <  1:355973/251‑1 (MQ=255)                                                                                                                                                                                                                                          |                                                                                                                                                                                                                                             CAGCACCAGTAGTTTCATTCACATCCGCAGCGTAAAGATTGCCATTTGTATCTTTAAGCGCATATGTATCGGTATCATTACCCTTGGAATCCTGCAGTTTTACTAAGCTAACAGCACCAAGGTTGGCAGTTGCGGAACCTGCAGTATTATCAATCTGAACAGGTGTACCGCCTGAAGTGATAGTTGTAGCTTTAGTAGTATTTGCATCAGTTACAGTTGCATTTGCCGTTGCTCCAGTCGCCATTGTCACTGTACCATCATTAGCAACTGTTACTGCGTAATACTTCCCATCGTTATCACCACCGGTGATTTTCGCATAGTAATCATTACCATTATCAGTATAAACACCCTCAATTGAAGCTGGGTTAGTTCCGCCAGTATCAGTGGCTGCTTCCGTAGAAAGGGTAATTCCAGTAAGTTTAATATTGTTTGTGGTGGTAGCACCAAAAGCAGTTACTGGAGCACTAGTG  >  NC_000913/2002592‑2003061

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 15 ≤ ATCG/ATCG < 26 ≤ ATCG/ATCG < 37 ≤ ATCG/ATCG < 39 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑