Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NC_000913	2,984,441	0	A	C	46.9%	66.4 / 18.2	49	G384G (GGT→GGG)	yqeF	short chain acyltransferase
Reads supporting (aligned to +/- strand):  ref base A (24/2);  new base C (0/23);  total (24/25)
Fisher's exact test for biased strand distribution p-value = 5.55e-12
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 1.00e+00

GAGGGAGCCCAGAAAATGTATGTCGACTTGCCAGCCATCATTATTCAACAGATTAATGACGGC‑AGATATTTATCGGTAAGGAGGAAATGCAGAGCTATTCGTCACGTTCAATGGTCAATG‑CCACACCCTGGCCCCCGCCGATACAAAGCGTTGCCAGTCCTTTGCGGGCATTACGTTTCACCATTTCATGAACCAGAGAAACCAGGATTCGGCAACCGGAAGCGCCTATCGGGTGACCGAGTGCGATCGCGCCACCATTGACATTGACCCG  >  NC_000913/2984317‑2984587                                                                                                                               |                                                                                                                                                   gggggACCCAAAAAAATTTATGTCGACTTGCCAGCCTTCATTTTACAAAAGATTAATG‑CGGCAAAATTTTTAGCGTTAAGGAGAAATTGCAGAGTTTTTCGTCCCGTTCAAGGGTCAATC‑CCCCCCCCTGCCCCCCGCCGATACAAAGCGt                                                                                                                          <  2:881351/149‑1 (MQ=255)  aGGGAGCCCAGAAAATGTATGTCGACTTGCCAGCCATCATTATTCAACAGATTAATGACGGC‑AGATATTTATCGGTAAGGAGGAAATGCAGAGCTATTCGTCACGTTCAATGGTCAATG‑CCACACCCTGGCCCCCGCCGATACAAAGCGtt                                                                                                                         >  1:461013/1‑151 (MQ=255)    ggAGCTCAGAAAATGTATGTCGACTTGCCAGCCATCATTATTCAACAGATTAATGA‑GGC‑AGATATTTATCGGTAAGGAGGAAATGCAGAGCTATTCGTCACGTTCAATGGTCAATG‑CCACACCCTGGCCCCCGCCGATACAAAGCGTTGcc                                                                                                                      >  2:146604/1‑151 (MQ=255)    ggAGCCCAGAAAATGTATGTCGACTTGCCAGCCATCATTATTCAACAGATTAATGACGGC‑AGATATTTATCGGTAAGGAGGAAATGCAGAGCTATTCGTCACGTTCAATGGTCAATG‑CCACACCCTGGCCCCCGCCGATACAAAGCGTTGc                                                                                                                       >  2:172555/1‑151 (MQ=255)          cAGAAAATGTATGTCGACTTGCCAGCCATCATTATTCAACAGATTAATGACGGC‑AGATATTTATCGGTAAGGAGGAAATGCAGAGCTATTCGTCACGTTCAATGGTCAATG‑CCACACCCTGGCCCCCGCCGATACAAAGCGTTGCCAGTcc                                                                                                                 >  1:540504/1‑151 (MQ=255)           aaaaaaTGTATTTCGTTTTGCCAGCCATCATTATTAAACAGATAAATGACGGC‑AGATATTTATCGGTAAGGAGAAAATGCAGAGTTTTTCGTCACTTTAATTGGTAAATG‑CCCCCCCCTGGCCCCCGCCGATACAAAGCGTTGCCAGTcc                                                                                                                 <  2:437658/148‑1 (MQ=255)            gAAAATGTATGTCGACTTGCCAGCCATCATTATTCAACAGATTAATGACGGC‑AGATATTTATCGGTAAGGAGGAAATGCAGAGCTATTCGTCACGTTCAATGGTCAATG‑CCACACCCTGGCCCCCGCCGATACAAAGCGTTGCCAGTCCtt                                                                                                               >  1:153965/1‑151 (MQ=255)             aaaaTGTATGTCGACTTGCCAGCCATCATTATTCAACAGATTAATGACGGC‑AGATATTTATCGGTAAGGAGAAAATGCAGAGCTTTTCGTCACTTTCAATGGTCAAGC‑CCACCCCCTGGCCCCCGCCGATACAAAGCGTTGCCAGTCCttt                                                                                                              <  1:552010/151‑1 (MQ=255)              aatggtatgtCTACTGGCCCCCCTTCATATTTCAACAAATTAATGGCGGC‑ATATATTTATCGGTAAGGGGGAAAAGCAGAGATTTTGGCCGCGTTTATTGAACAACG‑CCACCCCCTGGCCCCCGCCGATACAAAGCGTTGCCAGTCCtt                                                                                                               <  1:299718/145‑1 (MQ=255)               aaTGTATGCCGACTTGCCAGCCATCATTATTCAACAGATTAATGACGGC‑ATATATTTAGCGGTAAGGAGAAAATGCAGAGCTTTTCGTCACGTTCAATGGTAAATC‑CCCCCCCCTGGCCCCCGCCGATACAAAGCGTTGCCAGTCCTTTGc                                                                                                            <  2:10194/151‑1 (MQ=255)                   tatgtCGACTTGCCAGCCATCATTATTCAACAGATTAATGACGGC‑AGATATTTATGGGTAAGGAGAAAATGCAGAGCTATTCGTCCCGTTCAATGGTCAATG‑CCACCCCCTGCCCCCCGCCGATACAAAGCGTTGCCAGTCCTTTGCggg                                                                                                         <  2:106404/150‑1 (MQ=255)                   tatgtCGACTTGCCAGCCATCATTATTCAACAGATTAATGACGGC‑AGATATTTATCGGTAAGGAGGAAATGCAGAGCTATTCGTCACGTTCAATGGTCAATG‑CCACACCCTGGCCCCCGCCGATACAAAGCGTTGCCAGTCCTTTGCGGGc                                                                                                        >  1:880476/1‑151 (MQ=255)                   tatgtCGACTTGCCAGCCATCATTATTCAACAGATTAATGACGGC‑AGATATTTAGCGGAAAGGAGAAAATGCAGAGTTTTTCGTCACTTTCAATGGTCAATG‑CCACCCCCGGCCCCCCGCCGATACAAAGCGTTGCCAGTCCTTTGCgg                                                                                                          <  2:658438/149‑1 (MQ=255)                        cGACTTGCCAGCCATCATTATTCAACAGATTAATGACGGC‑AGATATTTATCGGTAGGGAGAAAATGCAGAGCTATTCGTCCCGTTCAATGGTCATTG‑CCCCCCCCTGGCCCCCGCCGATACAAAGCGTTGCCAGTCCTTTGCGGGCATTa                                                                                                    <  2:111510/150‑1 (MQ=255)                         gACTTGCCAGCCATCATTATTCAACAGATTAATGACGGC‑AGATATTTATCGGTAAGGAGGAAATGCAGAGCTATTCGTCACGTTCAATGGTCAATG‑CCACACCCTGGCCCCCGCCGATACAAAGCGTTGCCAGTCCTTTGCGGGCATTACg                                                                                                  >  1:112632/1‑151 (MQ=255)                         gACTTGCCAGCCATCATTATTCAACAGATTAATGACGGC‑AGATATTTATCGGTAAGGAGGAAATGCAGAGCTATTCGTCACGTTCAATGGTCAATG‑CCACACCCTGGCCCCCGCCGATACAAAGCGTTGCCAGTCCTTTGCGGGCATTACg                                                                                                  >  2:235970/1‑151 (MQ=255)                             tGCCAGCCATCATTATTCAACAGATTAATGACGGC‑AGATATTTATCGGTAAGGAGGAAATGCAGAGCTATTCGTCACGTTCAATGGTCAATG‑CCACACCCTGGCCCCCGCCGATACAAAGCGTTGCCAGTCCTTTGCGGGCATTACGTTTc                                                                                              >  1:267104/1‑151 (MQ=255)                               ccagccaTCATTATTCAACAGATAAATGACGGC‑AGATATTTATCGGTAAGGAGAAAATGCAGAGCTATTCGTCACGTTCAATGGTCAATG‑CCCCCCCCGGGCCCCCGCCGATACAAAGCGTTGCCAGTCCTTTGCGGGCATTACGTTTc                                                                                              <  1:840940/149‑1 (MQ=255)                                 agccaTCATTATTCAACAGATTAATGACGGC‑AGATATTTATCGGTAAGGAGGAAATGCAGAGCTATTCGTCACGTTCAATGGTCAATG‑CCACACCCTGGCCCCCGCCGATACAAAGCGTTGCCAGTCCTTTGCGGGCATTACGTTTCAcc                                                                                           >  2:456933/1‑150 (MQ=255)                                  gccaTCATTATTCAACAGATTAATGACGGC‑AGATATTTATCGGTAAGGAGGAAATGCAGAGCTATTCGTCACGTTCAATGGTCAATG‑CCACACCCTGGCCCCCGCCGATACAAAGCGTTGCCAGTCCTTTGCGGGCATTACGTTTCACCAt                                                                                         >  2:554039/1‑151 (MQ=255)                                   ccaTCTTTATTCAACAGATTAATGACGGC‑AGATATTTATCGGTAAGGAGAAAATGCAGAGTTATTCGTCCCTTTAAATGGTCAATG‑CCCCCCCCTGGCCCCCGCCGATACAAAGCGTTGCCAGTCCTTTGCGGGCATTACGTTTCACCAt                                                                                         <  1:499433/150‑1 (MQ=255)                                            ttCAACAGATTAATGACGGC‑AGATATTTATCGGTAAGGAGGAAATGCAGAGCTTTTCGTCACTTTAAATGGTCAATG‑CCACCCCCGGGCCCCCGCCGATACAAAGCGTTGCCAGTCCTTTGCGGGCATTACGTTTCACCATTTCATGaa                                                                                 <  1:224721/149‑1 (MQ=255)                                            ttCAACAGATAAATGACGGC‑AGATATTTATCGGTAAGGAGGAAATGCAGAGCTTTTCGTCACTTTCAATGGTAAATG‑CCACCCCCTGGCCCCCGCCGATACAAAGCGTTGCCAGTCCTTTGCGGGCATTACGTTTCACCATTTCATGaa                                                                                 <  1:333937/149‑1 (MQ=255)                                                      tAATGACGGC‑AGATATTTATCGGTAAGGAGGAAATGCAGAGCTATTCGTCACGTTCAATGGTCAATG‑CCACACCCTGGCCCCCGCCGATACAAAGCGTTGCCAGTCCTTTGCGGGCATTACGTTTCACCATTTCATGAACCAGAGAAAcc                                                                      >  2:452337/1‑150 (MQ=255)                                                       aaTGCCGGC‑AAATATTTATCGGTAAGGAGAAAATGCAGAGCTTTTCGTCACGTTAAATGGTCAATC‑CCCCCCCCGGGCCCCCGCCGATACAAAGCGTTGCCAGTCCTTTGCGGGCATTACGTTTCACCATTTCATGAACCAGAGAAAcc                                                                      <  1:798885/149‑1 (MQ=255)                                                             ggC‑AGATATTTATCGGAAGGGAGAAAATGCAGAGTTTTTCGTCACGTTCAATGGTAAATC‑CCCCCCCCTGGCCCCCGCCGATACAAAGCGTTGCCAGTCCTTTGCGGGCATTACGTTTCACCATTTCATGAACCAGAGAAACCAGGAtt                                                                <  2:537616/149‑1 (MQ=255)                                                              gC‑AGATTTTTATCGGTAAGGAGGAAATGCAGAGCTTTTCGTCACTTTCAATGGTCAATG‑CCACCCCCTGCCCCCCGCCGATACAAAGCGTTGCCAGTCCTTTGCGGGCATTACGTTTCACCATTTCATGAACCAGAGAAACCAGGATTCgg                                                             <  1:497783/151‑1 (MQ=255)                                                                 aGATATTTACCGGTAAGGAGAAAATGCAGAGCTTTTCGTCCCGTTAAATGTCCAATG‑CCCCCCCCTGCCCCCCGCCGATACAAAGCGTTGCCAGTCCTTTGCGGGCATTACGTTTCACCATTTCATGAACCAGAGAAACCAGGATTCGGc                                                            <  2:363397/150‑1 (MQ=255)                                                                      tttATCGGTAAGGAGGAAATGCAGAGCTATTCGTCACGTTCAATGGTCAATG‑CCACACCCTGGCCCCCGCCGATACAAAGCGTTGCCAGTCCTTTGCGGGCATTACGTTTCACCATTTCATGAACCAGAGAAACCAGGATTCGGCAAcc                                                        >  1:126452/1‑149 (MQ=255)                                                                            ggTAGGGAGAAAATGCAGAGCTATTGGTCACGTTCAATGGTCAATG‑CCCCCCCCTGCCCCCCGCCGATACAAAGCGTTGCCAGTCCTTTGCGGGCATTACGTTTCACCATTTCATGAACCAGAGAAACCAGGATTCGGCAACCGGAAgcg                                                 <  2:86072/150‑1 (MQ=255)                                                                            ggTAAGGAGAAAATGCAGAGCTTTTCGTCACGTTAAATGGTAAATC‑CCCCCCCCTGCCCCCCGCCGATACAAAGCGTTGCCAGTCCTTTGCGGGCATTACGTTTCACCATTTCATGAACCAGAGAAACCAGGATTCGGCAACCGGAAgcgc                                                <  2:505141/151‑1 (MQ=255)                                                                              tAAGGAGGAAATGCAGAGCTATTCGTCACGTTCAATGGTCAATG‑CCACACCCTGGCCCCCGCCGATACAAAGCGTTGCCAGTCCTTTGCGGGCATTACGTTTCACCATTTCATGAACCAGAGAAACCAGGATTCGGCAACCGGAAGCGCCt                                              >  2:883481/1‑151 (MQ=255)                                                                               aaGGAGGAAATGCAGAGCTATTCGTCACGTTCAATGGTCAATG‑CCACACCCTGGCCCCCGCCGATACAAAGCGTTGCCAGTCCTTTGCGGGCATTACGTTTCACCATTTCATGAACCAGAGACACCAGGATTCGGCAACCGGAAGCGCCt                                              >  2:482392/1‑150 (MQ=255)                                                                                 ggaggaAATGCAGAGCTTTTCGTCACTTTCAATGGTCAATG‑CCACCCCCTGGCCCCCGCCGATACAAAGCGTTGCCAGTCCTTTGCGGGCATTACGTTTCACCATTTCATGAACCAGAGAAACCAGGATTCGGCAACCGGAAGCGCCTATc                                           <  1:418476/151‑1 (MQ=255)                                                                                      aaaTGCAGTGCTATTCTCCACGTTCAATGTCCAATG‑CCCCACCCTGCCCCCCGCCGATACAAAGCGTTGCCAGTCCTTTGCGGGCATTACGTTTCACCATTTCATGAACCAGAGAAACCAGGATTCGGCAACCGGAAGCGCCTATCGGGTg                                      <  2:595325/151‑1 (MQ=255)                                                                                       aaTGCAGAGCTATTCGTCACGTTCAATGGTCAATG‑CCACACCCTGGCCCCCGCCGATACAAAGCGTTACCTGTCCTTTGCGGGCATTACGTTTCACCATTTCATGAACCAGAGAAACCAGGATTCGGCAACCGGAAGCGCCTATCGGGTg                                      >  2:806402/1‑150 (MQ=255)                                                                                            agagCTATTCGTCACGTTCAATGGTCAATG‑CCACACCCTGGCCCCCGCCGATACAAAGCGTTGCCAGTCCTTTGCGGGCATTACGTTTCACCATTTCATGAACCAGAGAAACCAGGATTCGGCAACCGGAAGCGCCTATCGGGTGACCg                                  >  1:878709/1‑149 (MQ=255)                                                                                            agagCTATTCGTCACGTTCAATGGTCAATG‑CCACACCCTGGCCCCCGCCGATACAAAGCGTTGCCAGTCCTTTGCGGGCATTACGTTTCACCATTTCATGAACCAGAGAAACCAGGATTCGGCAACCGGAAGCGCCTATCGGGTGACCg                                  >  2:679794/1‑149 (MQ=255)                                                                                             gagCTATTCGTCACGTTCAATGGTCAATG‑CCACACCCTGGCCCCCGCCGATACAAAGCGTTGCCAGTCCTTTGCGGGCATTACGTTTCACCATTTCATGAACCAGAGAAACCAGGATTCGGCAACCGGAAGCGCCTATCGGGTGACCGAGt                               >  1:294835/1‑151 (MQ=255)                                                                                               gCTATTCGTCACGTTCAATGGTCAATG‑CCACACCCTGGCCCCCGCCGATACAAAGCGTTGCCAGTCCTTTGCGGGCATTACGTTTCACCATTTCATGAACCAGAGAAACCAGGATTCGGCAACCGGAAGCGCCTATCGGGTGACCGAGTGc                             >  1:603721/1‑151 (MQ=255)                                                                                                 ttttCGTCACGTTAAAGGTTCAATC‑CCCCCCCCGGCCCCCCGCCGATACAAAGCGTTGCCAGTCCTTTGCGGGCATTACGTTTCACCATTTCATGAACCAGAGAAACCAGGATTCGGCAACCGGAAGCGCCTATCGGGTGACCGAGTGc                             <  2:984441/147‑1 (MQ=255)                                                                                                    tCGTCACGTTCAATGTTCAATG‑CCCCACCCTGCCCCCCGCCGATACAAAGCGTTGCCAGTCCTTTGCGGGCATTACGTTTCACCATTTCATGAACCAGAGAAACCAGGATTCGGCAACCGGAAGCGCCTATCGGGTGACCGAGTGCGATc                         <  1:641186/150‑1 (MQ=255)                                                                                                               aagggTCAAGG‑CCCCCCCCGGGCCCCCGCCGATACAAAGCGTTGCCAGTCCTTTGCGGGCATTACGTTTCACCATTTCATGAACCAGAGAAACCAGGATTCGGCAACCGGAAGCGCCTATCGGGTGACCGAGTGCGATCGCGCCACcattg             <  1:824495/148‑1 (MQ=255)                                                                                                                  tggcAATGCCCACCCCCTGGCCCCCGCCGATACAAAGCGTTGCCAGTCCTTTGCGGGCATTACGTTTCACCATTTCATGAACCAGAGAAACCAGGATTCGGCAACCGGAAGCGCCTATCGGGTGACCGAGTGCGATCGCGCCACcat               <  1:466236/144‑1 (MQ=255)                                                                                                                    tCAATG‑CCACACCCTGGCCCCCGCCGATACAAGGCGTTGCCAGTCCTTTGCGGGCATTACGTTTCACCATTTCATGAACCAGAGAAACCAGGATTCGGCAACCGGAAGCGCCTATCGGGTGACCGAGTGCGATCGCGCCACcattgacatt        >  2:688551/1‑151 (MQ=255)                                                                                                                    tCAATG‑CCACACCCTGGCCCCCGCCGATACAAAGCGTTGCCAGTCCTTTGCGGGCATTACGTTTCACCATTTCATGAACCAGAGAAACCAGGATTCGGCAACCGGAAGCGCCTATCGGGTGACCGAGTGCGATCGCGCCACcattgacatt        >  1:274703/1‑151 (MQ=255)                                                                                                                      aaTG‑CCACCCCCGGCCCCCCGCCGATACAAAGCGTTGCCAGTCCTTTGCGGGCATTACGTTTCACCATTTCATGAACCAGAGAAACCAGGATTCGGCAACCGGAAGCGCCTATCGGGTGACCGAGTGCGATCGCGCCACcattgacatt        <  1:379193/149‑1 (MQ=255)                                                                                                                      aaTG‑CCACACCCTGGCCCCCGCCGATACAAAGCGTTGCCAGTCCTTTGCGGGCATTACGTTTCACCATTTCATGAACCAGAGAAACCAGGATTCGGCAACCGGAAGCGCCTATCGGGTGACCGAGTGCGATCGCGCCACcattgacattg       >  2:607055/1‑150 (MQ=255)                                                                                                                      aaTG‑CCACACCCTGGCCCCCGCCGATACAAAGCGTTGCCAGTCCTTTGCGGGCATTACGTTTCACCATTTCATGAACCAGAGAAACCAGGATTCGGCAACCGGAAGCGCCTATCGGGTGACCGAGTGCGATCGCGCCACcattgacattg       >  2:412574/1‑150 (MQ=255)                                                                                                                            cacaCCCTGGCCCCCGCCGATACAAAGCGTTGCCAGTCCTTTGCGGGCATTACGTTTCACCATTTCATGAACCAGAGAAACCAGGATTCGGCAACCGGAAGCGCCTATCGGGTGACCGAGTGCGATCGCGCCACCATTGACATTGACCCg  >  2:806010/1‑150 (MQ=255)                                                                                                                               |                                                                                                                                                   GAGGGAGCCCAGAAAATGTATGTCGACTTGCCAGCCATCATTATTCAACAGATTAATGACGGC‑AGATATTTATCGGTAAGGAGGAAATGCAGAGCTATTCGTCACGTTCAATGGTCAATG‑CCACACCCTGGCCCCCGCCGATACAAAGCGTTGCCAGTCCTTTGCGGGCATTACGTTTCACCATTTCATGAACCAGAGAAACCAGGATTCGGCAACCGGAAGCGCCTATCGGGTGACCGAGTGCGATCGCGCCACCATTGACATTGACCCG  >  NC_000913/2984317‑2984587

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 13 ≤ ATCG/ATCG < 14 ≤ ATCG/ATCG < 33 ≤ ATCG/ATCG < 39 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑