Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NC_000913	2,984,718	0	G	C	46.3%	36.3 / 23.0	44	P292R (CCG→CGG)	yqeF	short chain acyltransferase
Reads supporting (aligned to +/- strand):  ref base G (4/18);  new base C (19/0);  total (24/20)
Fisher's exact test for biased strand distribution p-value = 5.49e-08
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 9.59e-01

TGACATTGACCCGACGCTCATCCCACTCAAGCATCTTGCCAACCGAAAGCGCCTGTGCAGCAAACGCTTCATTAGCCTCGATAAGATCGACTTCAGCCAACTGCCAGCCTACACGCTCCAGGCAACGGCGGGTCGCATACACCGGCG‑CAATTCCCATCAATGCCGGATCTACACCAACGCTGGCAAATGCGCGAATGCGGGCCAGCACGGGTAAATTCAACGCTCGTGCTTTGGCTTCGCTCATCATCATTACCGCAGCTGCGCCATCGTTTATGGATGATGC  >  NC_000913/2984575‑2984857                                                                                                                                                |                                                                                                                                             tgacattgacCCGACGCTCATCCCACTCAAGCATCTTGCCAACCGAAAGCGCCTGTGCAGCAAACGCTTCATTAGCCTCGATAAGATCGACTTCAGCCAACTGCCAGCCTACACGCTCCAGGCAACGGCGGGTCGCATACACCCGCG‑Caa                                                                                                                                       >  1:414919/1‑150 (MQ=255)   acattgacCCGACGCTCATCCCACTCAAGCATCTTGCCAACCGAAAGCGCCTGTGCAGCAAACGCTTCATTAGCCTCGATAAGATCGACTTCAGCCAACTGCCAGCCTACACGCTCCAGGCAACGGCGGGGCGCCTACACCCgcg‑c                                                                                                                                         >  2:539903/1‑146 (MQ=255)       tgacCCGACGCTCATCCCACTCAAGCATCTTGCCAACCGAAAGCGCCTGTGCAGCAAACGCTTCATTAGCCTCGATAAGATCGACTTCAGCCAACTGCCAGCCTACACGCTCCAGGCAACGGCGGGGCGCCTACAACCGCGCCAATTc                                                                                                                                    >  2:316383/1‑148 (MQ=255)         acCCGACGCTCATCCCACTCAAGCATCTTGCCAACCGAAAGCGCCTGTGCAGCAAACGCTTCATTAGCCTCGATAAGATCGACTTCAGCCAACTGCCAGCCTACACGCTCCAGGCAACGGCGGGTGGCATACACCGGCG‑CAATTccc                                                                                                                                  >  1:752603/1‑147 (MQ=255)           cctaCGCTCATCCCACTCAAGCATCTTGCCAACCGAAAGCGCCTGTGCAGCAAACGCTTCATTAGCCTCGATAAGATCGACTTCAGCCAACTGCCAGCCTACACGCTCCAGGCAACGGCGGGTCGCATACACCGGCG‑CAATTCCCATCAAt                                                                                                                            <  2:299218/148‑1 (MQ=255)              aCGCTCATCCCACTCAAGCATCTTGCCAACCGAAAGCGCCTGTGCAGCAAACGCTTCATTAGCCTCGATAAGATCGACTTCAGCCAACTGCCAGCCTACACGCTCCAGGCAACGGCGGGTCGCATACACCGGCG‑CAATTCCCATCAATGcc                                                                                                                         <  2:578959/151‑1 (MQ=255)                  tCATCCCACTCAAGCATCTTGCCAACCGAAAGCGCCTGTGCAGCAAACGCTTCATTAGCCTCGATAAGATCGACTTCAGCCAACTGCCAGCCTACACGCTCCAGGCAACGGCGGGTCGCCTACACCCGCG‑CCACTCCCATCAATGc                                                                                                                          >  2:150336/1‑146 (MQ=255)                      cccACTCAAGCATCTTGCCAACCGAAAGCGCCTGTGCAGCAAACGCTTCATTAGCCTCGATAAGATCGACTTCAGCCAACTGCCAGCCTACACGCTCCAGGCAACGGCGGGTCGCATACACCGGCG‑CAATTCCCATCAATGCCGGATCTac                                                                                                                 <  1:702218/151‑1 (MQ=255)                            cAAGCATCTTGCCAACCGAAAGCGCCTGTGCAGCAAACGCTTCATTAGCCTCGATAAGATCGACTTCAGCCAACTGCCAGCCTACACGCTCCAGGCAACGGCGGGTCGCATTCTCCGGAG‑TAATTCGCCGCAATGCGGGATCTACACCaa                                                                                                            <  2:314252/150‑1 (MQ=255)                             aaGCATCTTGCCAACCGAAAGCGCCTGTGCAGCAAACGCTTCATTAGCCTCGATAAGATCGACTTCAGCCAACTGCCAGCCTACACGCTCCAGGCAACGGCGGGTCGCATAAACCCGCG‑CAATTCCCATCCATACCGGAACTACACCaa                                                                                                            >  1:683481/1‑149 (MQ=255)                               gCATCTTGCCAACCGAAAGCGCCTGTGCAGCAAACGCTTCATTAGCCTCGATAAGATCGACTTCAGCCAACTGCCAGCCTACACGCTCCAGGCAACGGCGGGTCGCATACACCCGCG‑CAATTCCCCTCAAAGCCGGATCTACACCCACGc                                                                                                         >  1:802722/1‑150 (MQ=255)                                    ttGCCAACCGAAAGCGCCTGTGCAGCAAACGCTTCATTAGCCTCGATAAGATCGACTTCAGCCAACTGCCAGCCTACACGCTCCAGGCAACGGCGGGTCGCATACACCCGCG‑CCAATCCCCTCAAAGCCGGATCTACACCAACCCCGGCa                                                                                                    >  1:803820/1‑150 (MQ=255)                                       ccAACCGAAAGCGCCTGTGCAGCAAACGCTTCATTAGCCTCGATAAGATCGACTTCAGCCAACTGCCAGCCTACACGCTCCAGGCAACGGCGGGTCGCATACACCGGCG‑CAATTCCCATCAATGCCGGATCTACACCAACGCTGGCAAAt                                                                                                 <  1:390045/150‑1 (MQ=255)                                        cAACCGAAAGCGCCTGTGCAGCAAACGCTTCATTAGCCTCGATAAGATCGACTTCAGCCAACTGCCAGCCTACACGCTCCAGGCAACGGCGGGGCCCCTACACCCGCG‑CAATTCCCCCCCATGCCCGCTCTACACCAACCCCTGCaaaaac                                                                                               >  2:714055/1‑148 (MQ=255)                                          aCCGAAAGCGCCTGTGCAGCAAACGCTTCATTAGCCTCGATAAGATCGACTTCAGCCAACTGCCAGCCTACACGCTCCAGGCAACGGCGGGTCGCATACACCCGCG‑CAATTCCCATCAAATCCGGGTCTACACCAAAGCTGGCAAATgcg                                                                                              >  1:242372/1‑150 (MQ=255)                                              aaaGCGCCTGTGCAGCAAACGCTTCATTAGCCTCGATAAGATCGACTTCAGCCAACTGCCAGCCTACACGCTCCAGGCAACGGCGGGTCGCATTCACCGGAG‑CGATACCCCGCAAACCGAGATCTACACCAACGCTGGCAAATGCGCGAAt                                                                                         <  2:432569/151‑1 (MQ=255)                                              aaaGCGCCTGTGCAGCAAACGCTTCATTAGCCTCGATAAGATCGACTTCAGCCAACTGCCAGCCTACACGCTCCAGGCAACGGCGGGTCGCATACACCGGCG‑CAATTCCCATCAATGCCGGATCTACACCAACGCTGGCAAATGCGCGAAt                                                                                         <  1:406813/151‑1 (MQ=255)                                              aaaGCGCCTGTGCAGCAAACGCTTCATTAGCCTCGATAAGATCGACTTCAGCCAACTGCCAGCCTACACGCTCCAGGCAACGGCGGGTCGCATACACCGGCG‑CAATTCCCATCAATGCCGGATCTACACCAACGCTGGCAAATGCGCGAAt                                                                                         <  1:369863/151‑1 (MQ=255)                                                 gcgcCTGTGCAGCAAACGCTTCATTAGCCTCGATAAGATCGACTTCAGCCAACTGCCAGCCTACACGCTCCAGGCAACGGCGGGTCGCATACACCCGCG‑CAATTCCCATCAATGCCGGATCTACACCCACCCTGGCAAAAGCGCGAATGc                                                                                       >  1:645676/1‑150 (MQ=255)                                                  cgcCTGTGCAGCAAACGCTTCATTAGCCTCGATAAGATCGACTTCAGCCAACTGCCAGCCTACACGCTCCAGGCAACGGCGGGTCGCATTCACCGTCG‑CGATACCCAGCACTGCGAGATCTACACCAACGCTGGCAAATGCGCGAATGCgg                                                                                     <  2:802242/151‑1 (MQ=255)                                                       gtgCAGCAAACGCTTCATTAGCCTCGATAAGATCGACTTCAGCCAACTGCCAGCCTACACGCTCCAGGCAACGGCGGGTCGCATACACCCGCG‑CAACTCCCCCCAATGCCCGATCTACACCAACGCCGGCAAAAGCGCGCAAGCGGGcc                                                                                  >  2:32838/1‑149 (MQ=255)                                                          cagcaAACGCTTCATTAGCCTCGATAAGATCGACTTCAGCCAACTGCCAGCCTACACGCTCCAGGCAACGGCGGGTCGCATACACCCGCG‑CAATTCCCATCAATGCCGGGTCTACACCAACGCCGGCAAATGCGCGAATGCGGGcc                                                                                  >  1:97728/1‑146 (MQ=255)                                                          cagcaAACGCTTCATTAGCCTCGATAAGATCGACTTCAGCCAACTGCCAGCCTACACGCTCCAGGCAACGGCGGGTCGCATACAACTGCC‑CCAATCCCCTCAAAAGCAGATCATCCCCCAAACTGGCAAACGCGCGAGTgtg                                                                                      >  2:57764/1‑140 (MQ=255)                                                          cagcaAACGCTTCATTAGCCTCGATAAGATCGACTTCAGCCAACTGCCAGCCTACACGCTCCAGGCAACGGCGGGTCGCATAAAACCGCG‑CAATTCCCATCAATGCCCGATCTAAACCCACACTCGCAAAAGAGCGGAAGCgggggagc                                                                               >  1:428929/1‑144 (MQ=255)                                                           agcaAACGCTTCATTAGCCTCGATAAGATCGACTTCAGCCAACTGCCAGCCTACATGCTCCAGGCAACGGCGGCGCGCATACACCGGCG‑CCAATCCCCTCAATTCCCGATCTACACCCAAGCTGGCAAATGCGCGAAAGCGGGCCAGc                                                                               >  2:49358/1‑148 (MQ=255)                                                              aaaCGCTTCATTTGCCTCGATAAGATCGACTGCAGCCATCTGCCAGCCTATACGCTCCAGGCAACGGCGGGTCGCATACACCGGCG‑CAATTCCCAGGAATGCCGGATCTACACCAACGCTGGCAAATGCGCGAATGCGGGCCAGCACGGGt                                                                         <  2:463030/151‑1 (MQ=255)                                                                  gCTTCATTAGCCTCGATAAGATCGACTTCAGCCAACTGCCAGCCTACACGCTCCAGGCAACGGCGGGTCGCATACACCCGCG‑CAATTCCCCTCAATTCCGGATCTACACCAACCCTGGCAAATGCGCGAAAGCGGGCCAGCACGGGGaaa                                                                      >  1:385188/1‑150 (MQ=255)                                                                  gCTTCATTAGCCTCGATAAGATCGACTTCAGCCAACTGCCAGCCTACACGCTCCAGGCAACGGCGGGTCCCATACAACCGCC‑CCCTTCCCCTCCATGCCGGCACCACACCCACGCCCGGTAAACAGCGAGTACGCGCCAGCACggggt                                                                        >  2:793167/1‑146 (MQ=255)                                                                    ttCATTAGCCTCGATAAGATCGACTTCAGCCAACTGCCAGCCTACACGCTCCAGGCAACGGCGGGTCGCATACAACGGCG‑CGATTTCCCCCAATACCCGGTCCACAACACCGCTGGCAAACTCGAGAATACGGGCCACCACGGGGaaaat                                                                    >  2:233662/1‑148 (MQ=255)                                                                         tAGCCTCGATAAGATCGACTTCAGCCAACTGCCAGCCTACACGCTCCAGGCAACGGCGGGTCGCATACACCGGCG‑CAATTCCCATCAATGCCGGATCTACACCAACGCTGGCAAATGCGCGAATGCGGGCCAGCACGGGTAAATTCAACg                                                               <  2:145359/150‑1 (MQ=255)                                                                                 aTAAGATCGACTTCAGCCAACTGCCAGCCTACACGCTCCAGGCAACGGCGGGTCGCATACACCGGCG‑CAATTCCCATCAATGCCGGATCTACACCAACGCTGGCAAATGCGCGAATGCGGGCCAGCACGGGTAAATTCAACGCTCGTGCtt                                                      <  1:341354/151‑1 (MQ=255)                                                                                 aTAAGATCGACTTCAGCCAACTGCCAGCCTACACGCTCCAGGCAACGGCGGGTCGCATACACCGGCG‑CAATTCCCATCAATGCCGGATCTACACCAACGCTGGCAAATGCGCGAATGCGGGCCAGCACGGGTAAATTCAACGCTCGTGCtt                                                      <  1:254482/151‑1 (MQ=255)                                                                                 aTAAGATCGACTTCAGCCAACTGCCAGCCTACACGCTCCAGGCAACGGCGGGTCGCATACACCCGCG‑CAAATCCCCTCCATGCCGGGTCTACACCAACGCCGGCAAAAGCGCGGATGCGGGCCCGCACGGGGAAATTCAACGCTCCTGCtt                                                      >  1:846293/1‑151 (MQ=255)                                                                                 aTAAGATCGACTTCAGCCAACTGCCAGCCTACACGCTCCAGGCAACGGCGGGGCGCATACACCCGCG‑CAATTCCCATCAATGCCGGGTCTACACCAACGCTGGCCAATGCGCGAAAGCGGGCCAGCACGGGGAAATTCaa                                                                 >  1:348825/1‑140 (MQ=255)                                                                                                gCCAACTGCCAGCCTACACGCTCCAGGCAACGGCGGGGCGCATACACCCGCG‑CAATTTCCATCAATTCCCGGTCTACACCAACGCAGGCAAATGCGCGAATGCGGGCCAGCACGGGGAAATTCAACACTCCTGCTTTGGCtttcctcctc                                        >  1:254073/1‑142 (MQ=255)                                                                                                 ccAACTGCCAGCCTACACGCTCCAGGCAACGGCGGGTCGCATACACCGGCG‑CAATTCCCATCAATGCCGGATCTACACCAACGCTGGCAAATGCGCGAATGCGGGCCAGCACGGGTAAATTCAACGCTCGTGCTTTGGCTTCGCtcatcat                                      <  2:56492/151‑1 (MQ=255)                                                                                                   aaCGGCCAGCCTACACGCTCCAGGCAACGGCGGGTCGCATACACCTGCG‑CGATTCCCAGCAATGCCGGATCTACACCAACGCTGGCAAATGCGCGAATGCGGGCCAGCACGGGTAAATTCAACGCTCGTGCTTTGGCTTCGCtcatcatca                                    <  2:525691/151‑1 (MQ=255)                                                                                                        ccAGCCTACACGCTCCAGGCAACGGCGGGTCGCATACACCGGCG‑CAATTCCCATCAATGCGAGATCTACACCAACGCTGGCAAATGCGCGAATGCGGGCCAGCACGGGTAAATTCAACGCTCGTGCTTTGGCTTCGCTCATCATCATTAcc                               <  2:5991/151‑1 (MQ=255)                                                                                                                       cAGGCAACGGCGGGTCGCATACACCGGCG‑CAATTCCCCTCACTGCCGGATCTACACCAACGCTGGCAAATGCGCGAATGCGGGCCAGCACGGGTAAATTCAACGCTCGTGCTTTGGCTTCGCTCATCATCATTACCGCAGCTGCGCCATCg                <  2:544051/151‑1 (MQ=255)                                                                                                                       cAGGCAACGGCGGGTCGCATAAACCCGCG‑CCATTCCCCTCCATGCCGGATCTCCACCCACGCCGGGAAAAGCGCGAAAGCCGGCCAGCCCCGGGAAATTCAACCCTCGCGCTTTTGCTTCGCTCCTCATCATTACCGCCGCCGccccccc                 >  2:378649/1‑147 (MQ=255)                                                                                                                                   ggTCGCATACACCGGCG‑CAATTCCCATCAATGCCGGATCTACACCAACGCTGGCAAATGCGCGAATGCGGGCCAGCACGGGTAAATTCAACGCTCGTGCTTTGGCTTCGCTCATCATCATTACCGCAGCTGCGCCATCGTTTATGgatgat    <  1:642943/151‑1 (MQ=255)                                                                                                                                     tCGCATACACCGGCG‑CAATTCCCATCAATGCCGGATCTACACCAACGCTGGCAAATGCGCGAATGCGGGCCAGCACGGGTAAATTCAACGCTCGTGCTTTGGCTTCGCTCATCATCATTACCGCAGCTGCGCCATCGTTTATGGATGATGc  >  1:656592/1‑151 (MQ=255)                                                                                                                                      cGCATACGCCTGAA‑CAATTCCGAGCAATGCCAGATCTACACCAACGCTGGCAAATGCGCGAATGCGGGCCAGCACGGGTAAATTCAACGCTCGTGCTTTGGCTTCGCTCATCATCATTACCGCAGCTGCGCCATCGTTTATGgat       <  2:297565/145‑1 (MQ=255)                                                                                                                                      cGCATACACCGGCG‑CAATTCCCATCAATGCCGGATCTACACCAACGCTGGCAAATGCGCGAATGCGGGCCAGCACGGGTAAATTCAACGCTCGTGCTTTGGCTTCGCTCATCATCATTACCGCAGCTGCGCCATCGTTTATGGATGATGc  <  1:32843/150‑1 (MQ=255)                                                                                                                                                |                                                                                                                                             TGACATTGACCCGACGCTCATCCCACTCAAGCATCTTGCCAACCGAAAGCGCCTGTGCAGCAAACGCTTCATTAGCCTCGATAAGATCGACTTCAGCCAACTGCCAGCCTACACGCTCCAGGCAACGGCGGGTCGCATACACCGGCG‑CAATTCCCATCAATGCCGGATCTACACCAACGCTGGCAAATGCGCGAATGCGGGCCAGCACGGGTAAATTCAACGCTCGTGCTTTGGCTTCGCTCATCATCATTACCGCAGCTGCGCCATCGTTTATGGATGATGC  >  NC_000913/2984575‑2984857

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: ‑