Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NC_000913	2,984,718	0	G	C	43.5%	66.6 / 19.5	47	P292R (CCG→CGG)	yqeF	short chain acyltransferase
Reads supporting (aligned to +/- strand):  ref base G (7/19);  new base C (20/0);  total (28/19)
Fisher's exact test for biased strand distribution p-value = 2.49e-07
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 1.00e+00

CACCATTGACATTGACCCGACGCTCATCCCACTCAAGCATCTTGCCAACCGAAAGCGCCTGTGCAGCAAACGCTTCATTAGCCTCGATAAGATCGACTTCAGCCAACTGCCAGCCTACACGCTCCAGGCAACGGCGGGTCGCATACACCGGCGCAATTCCCATCAATGCCGGATCTACACCAACGCTGGCAAATGCGCGAATGCGGGCCAGCACGGGTAAATTCAACGCTCGTGCTTTGGCTTCGCTCATCATCATTACCGCAGCTGCGCCATCGTTTATGGATGATGCATTACC  >  NC_000913/2984569‑2984863                                                                                                                                                      |                                                                                                                                                  caccaTTGACATTGACCCGACGCTCATCCCACTCAAGCATCTTGCCAACCGAAAGCGCCTGTGCAGCAAACGCTTCATTAGCCTCGATAAGATCGACTTCAGCCAACTGCCAGCCTACACGCTCCAGGCAACGGCGGGTCGCATACACCgg                                                                                                                                                  <  2:955354/151‑1 (MQ=255)   ccaTTGACATTGACCCGACGCTCATCCCACTCAAGCATCTTGCCAACCGAAAGCGCCTGTGCAGCAAACGCTTCATTAGCCTCGATAAGATCGACTTCAGCCAACTGCCAGCCTACACGCTCCAGGCAACGGCGGGTCGCATACACCGgc                                                                                                                                                 <  2:954824/150‑1 (MQ=255)        gacattgacCCGACGCTCATCCCACTCAAGCATCTTGCCAACCGAAAGCGCCTGTGCAGCAAACGCTTCATTAGCCTCGATAAGATCGACTTCAGCCAACTGCCAGCCTACACGCTCCAGGCAACGGCGGGTCGCATACACCGGCGCAAtt                                                                                                                                           <  2:183557/151‑1 (MQ=255)          cattgacCCGACGCTCATCCCACTCAAGCATCTTGCCAACCGAAAGCGCCTGTGCAGCAAACGCTTCATTAGCCTCGATAAGATCGACTTCAGCCAACTGCCAGCCTACACGCTCCAGGCAACGGCGGGGCGCATACACCCGCGCAAATc                                                                                                                                          >  2:918269/1‑150 (MQ=255)                cccGACGCTCATCCCACTCAAGCATCTTGCCAACCGAAAGCGCCTGTGCAGCAAACGCTTCATTAGCCTCGATAAGATCGACTTCAGCCAACTGCCAGCCTACACGCTCCAGGCAACGGCGGGGCGCATACACCAGCGCCAATCCCCTCa                                                                                                                                    >  2:39844/1‑150 (MQ=255)                 ccGACGCTCATCCCACTCAAGCATCTTGCCAACCGAAAGCGCCTGTGCAGCAAACGCTTCATTAGCCTCGATAAGATCGACTTCAGCCAACTGCCAGCCTACACGCTCCAGGCAACGGCGGGTCGCATACACCGGCGCAATTCCCATCAAt                                                                                                                                  <  1:799316/151‑1 (MQ=255)                     cGCTCATCCCACTCAAGCATCTTGCCAACCGAAAGCGCCTGTGCAGCAAACGCTTCATTAGCCTCGATAAGATCGACTTCAGCCAACTGCCAGCCTACACGCTCCAGGCAACGGCGGGTGGCATACACCCGCGCCAATCCCCTCAATGcc                                                                                                                               >  2:98483/1‑150 (MQ=255)                     cGCTCATCCCACTCAAGCATCTTGCCAACCGAAAGCGCCTGTGCAGCAAACGCTTCATTAGCCTCGATAAGATCGACTTCAGCCAACTGCCAGCCTACACGCTCCAGGCAACGGCGGGGCGCATACACCCGCGCCAATCCCCTCCAAGcc                                                                                                                               >  1:633682/1‑150 (MQ=255)                       cTCACCCCACTCAAGCATCTTGCCAACCGAAAGCGCCTGTGCAGCAAACGCTTCATTCGCCTCGATAAGATCGACTTCAGCCAACTGCCAGCCTACACGCTCCAGGCAACGGCGGGTCGCATACACCGGCGCAATTCCCATCAATGCCgg                                                                                                                             <  2:56687/150‑1 (MQ=255)                                       aTCTTGCCAACCGAAAGCGCCTGTGCAGCAAACGCTTCATTAGCCTCGATAAGATCGACTTCAGCCAACTGCCAGCCTACACGCTCCAGGCAACGGCGGGATGCACTCAACCGCCCGATTTCCAACAACACCGGGGCTACACCaaaac                                                                                                               >  2:201575/1‑145 (MQ=255)                                           tGCCAACCGAAAGCGCCTGTGCAGCAAACGCTTCATTAGCCTCGATAAGATCGACTTCAGCCAACTGCCAGCCTACACGATCCAGGCAACGGCGGGTCGCATACACCGGCGCAATTCCCATCAATGCCGGATCTACACCAACGCTGGCa                                                                                                          <  2:405730/149‑1 (MQ=255)                                                   gAAAGCGCCTGTGCAGCAAACGCTTCATTAGCCTCGATAAGATCGACTTCAGCCAACTGCCAGCCTACACGCTCCAGGCAACGGCGGGTCGCCTACACCCGCGCCAATCCCATCCATGCCGGGTCTACCCCAAcccccgccaaagcgc                                                                                                   >  2:941291/1‑134 (MQ=255)                                                    aaaGCGCCTGTGCAGCAAACGCTTCATTAGCCTCGATAAGATCGACTTCAGCCAACTGCCAGCCTACACGCTCCAGGCAACGGCGGGGCGCCTACACCCCCGCAAATCCCCTCAAAGCCCGAGATAAACCAACACCGGCAAAAgcgc                                                                                                   >  2:456949/1‑147 (MQ=255)                                                      aGCGCCTGTGCAGCAAACGCTTCATTAGCCTCGATAAGATCGACTTCAGCCAACTGCCAGCCTACACGCTCCAGGCAACGGCGGGGCGCCTACACCCGCGCAAATTCCATCAAAACCGGAGCTACAACAACCCCGGCAAAAGcgcggaag                                                                                              >  2:458767/1‑146 (MQ=255)                                                            tgtgCAGCAAACGCTTCATTAGCCTCGATAAGATCGACTTCAGCCAACTGCCAGCCTACACGCTCCAGGCAACGGCGGGTCGCATACACCCGCGCCATTTCCCTCAATTCCGGATCTACACCAACGCTGGCCAATGCGCGAATGCggggc                                                                                        >  1:993201/1‑148 (MQ=255)                                                             gtgCAGCAAACGCTTCATTAGCCTCGATAAGATCGACTTCAGCCAACTGCCAGCCTACACGCTCCAGGCAACGGCGGGTCGCATACACCGGCGCAATTCCCATCAATGCCGGATCTACACCAACGCTGGCAAATGCGCGAATGCGGGCCa                                                                                       <  2:193927/150‑1 (MQ=255)                                                                cagcaAACGCTTCATTAGCCTCGATAAGATCGACTTCAGCCAACTGCCAGCCTACACGCTCCAGGCAACGGCGGGTCGCATACACCCGCGCAATTCCCATCAATGCCGGATCTACAACAACGCCGGCAAAAGCGCGAATGCGGGCCAGc                                                                                     >  1:264906/1‑149 (MQ=255)                                                                   caAACGCTTCATTAGCCTCGATAAGATCGACTTCAGCCAACTGCCAGCCTACACGCTCCAGGCAACGGCGGGGCGGACACACAGGCGGAAATACCCACAATGCCGGAATTACCCCCACCCTGGGAAATTCGGTGATGAGGGGCAGCACggg                                                                                >  1:187467/1‑151 (MQ=255)                                                                    aaaCGCTTCATTAGCCTCGATAAGATCGACTTCAGCCAACTGCTAGCCTACACGCTCCAGGCAACGGCGGGTTGCATACACCCGCGCAATTTCCCTCAATGCCGGGTCTACACCAACGCCGGCAAAAACGCGAATGCGGGCCCGCAAggg                                                                                >  1:337324/1‑150 (MQ=255)                                                                       cGCTTCATTAGCCTCGATAAGATCGACTTCAGCCAACTGCCAGCCTACACGCTCCAGGCAACGGCGGGTCGCATACAACCGCGCAAATCCCCCCAATGCCGGCAATACACCCACACCGGCCAAAGCGCGCAAGCGGGCCCGCCCGGGGaa                                                                             >  2:716266/1‑150 (MQ=255)                                                                       cGCTTCATTAGCCTCGATAAGATCGACTTCAGCCAACTGCCAGCCTACACGCTCCAGGCAACGGCGGGTCGCATAAACCCGCGCAATTTCCATCAAAGCCGGATCTACACCAACGCTGGCAAATGCGCGAAAGCGGGGCAACACGGGGaa                                                                             >  1:784040/1‑150 (MQ=255)                                                                        gCTTCATTAGCCTCGATAAGATCGACTTCAGCCAACTGCCAGCCTACACGCTCCAGGCAACGGCGGGTCGCATACACCGGCGCAATTCCCATCAATGCCGGATCTACACCAACGCTGGCAAATGCGCGAATGCGGGCCAGCACGGGTAAAt                                                                           <  1:687011/151‑1 (MQ=255)                                                                           tCATTAGCCTCGATAAGATCGACTTCAGCCAACTGCCAGCCTACACGCTCCGGGCAACGGCGGGGCGCATACACCGGCGCAATTCCCATCAATTCCGGATCTACACCAAAGCTGGCAAATGCGCGAATGCGGGGCAGGACGGGGAAAtt                                                                          >  1:547739/1‑149 (MQ=255)                                                                           tCATTAGCCTCGATAAGATCGACTTCAGCCAACTGCCAGCCTACACGCTCCAGGCAATGGCGGGTCGCATACACCGGCGCCATTCCCATCAATGCCGGATCTACACCAACGCTGGCAAATGCGCGAATGCGGGCCAGCACGGGGAAAtt                                                                          >  1:114619/1‑149 (MQ=255)                                                                           tCATTAGCCTCGATAAGATCGACTTCAGCCAACTGCCAGCCTACACGCTCCAGGCAACGGCGGGGCGCCTACACCCGCGCAAATCCCCCCAAATCCCGATCTACACCAACGCTGGCAAAAGGGCGGATTCGGGGCAGCACGGGGaaa                                                                            >  2:969425/1‑147 (MQ=255)                                                                            cATTAGCCTCGATAAGATCGACTTCAGCCAACTGCCAGCCTACACGCTCCAGGCAACGGCGGGTCGCATACACCGGCGCAATTCCCATCAATGCCGGATCTACACCAACGCTGGCAAATGCGCGAATGCGGGCCAGCACGGGTAAATTCaa                                                                       <  1:498062/151‑1 (MQ=255)                                                                             aTTAGCCTCGATAAGATCGACTTCAGCCAACTGCCAGCCTACACGCTCCAGGCAACGGCGGGTCGCATACACCGGCGCAATTCCCATCAATGCCGGATCTACACCAACGCTGGCAAATGCGCGAATGCGGGCCAGCACGGGTAAATTCAAc                                                                      <  1:39846/151‑1 (MQ=255)                                                                             aTTAGCCTCGATAAGATCGACTTCAGCCAACTGCCAGCCTACACGCTCCAGGCAACGGCGGGTCGCATACACCGGCGCAATTCCCATCAATGCCGGATCTACACCAACGCTGGCAAATGCGCGAATGCGGGCCAGCACGGGTAAATTCAAc                                                                      <  1:296565/151‑1 (MQ=255)                                                                                   cTCGATAAGATCGACTTCAGCCAACTGCCAGCCTACACGCTCCAGGCAACGGCGGGTCGCATACACCCGCGCCATTCCCCTCAATGCCGGATCTACACCCACCCCGGCAAAAGCGCGCAAGCGGGCCAGCACGGGGAAAATTAACGccc                                                                  >  2:784/1‑147 (MQ=255)                                                                                   cTCGATAAGATCGACTTCAGCCAACTGCCAGCCTACACGCTCCAGGCAACGGCGGGGCGCCCACACCCGCGCAATTCCCCTCAATGCCGGGTCTACACCAACGCCGGCAAATGCGCGCATGCGGGCCCGCACGGGGAAATTTAACGccc                                                                  >  1:643917/1‑147 (MQ=255)                                                                                     cGATAAGATCGACTTCAGCCAACTGCCAGCCTACACGCTCCAGGCAACGGCGGGTCGCATACACCGGCGCAATTCCCCTCAATGCCGGGTCTACACCAACGCTGGCAAATGCGCGAATGCGGGCCAGCACGGGGAAATTCAACGCTCGTg                                                               >  1:655360/1‑150 (MQ=255)                                                                                         aaGATCGACTTCAGCCAACTGCCAGCCTACACGCTCCAGGCAACGGCGGGTCGCATACACCGGCGCAATTCCCATCAATGCCGGATCTACACCAACGCTGGCAAATGCGCGAATGCGGGCCAGCACGGGTAAATTCAACGCTCGTGCttt                                                           <  1:146599/150‑1 (MQ=255)                                                                                         aaGATCGACTTCAGCCAACTGCCAGCCTACACGCTCCAGGCAACGGCGGGGCGCCCACAACCGCGCAATTCCCACCAATGCCGGATCTACACCAACGCTGGCAAATGCGAGAATGCGGGGCCGCACGGGGAAATTTaaaccccgggcgtt                                                           >  2:545194/1‑138 (MQ=255)                                                                                         aaGATCGACTTCAGCCAACTGCCAGCCTACACGCTCCAGGCAACGGCGGGGCGCATACACCCGCGCAATTTCCCTCAATGCCGGGCCTACACCAACCCCGGCAAAAGCGCGGATGCGGGCCAGCCCGGGGAAATTTAACGCTCGTGCttt                                                           >  2:1037194/1‑150 (MQ=255)                                                                                                aCTTCAGCCAACTGCCAGCCTACACGCTCCAGGCAACGGCGGGTCGCATACACCGGCGCAATTCCCATCAATGCCGGATCTACACCAACGCTGGCAAATGCGCGAATGCGGGCCAGCACGGGTAAATTCAACGCTCGTGCTTTGGCTTCGc                                                   <  1:457080/151‑1 (MQ=255)                                                                                                    cAGCCAACTGCCAGCCTACACGCTCCAGGCAACGGCGGGTCGCATACACCGGCGCAATTCCCATCAATGCCGGATCTACACCAACGCTGGCAAATGCGCGAATGCGGGCCAGCACGGGTAAATTCAACGCTCGTGCTTTGGCTTCGCtca                                                <  2:993156/150‑1 (MQ=255)                                                                                                        cAACTGCCAGCCTACACGCTCCAGGCAACGGCGGGTCGCATACACCGGCGCAATTCCCATCAATGCCGGATCTACACCAACGCTGGCAAATGCGCGAATGCGGGCCAGCACGGGTAAATTCAACGCTCGTGCTTTGGCTTCGCtcatcatc                                           <  1:404205/151‑1 (MQ=255)                                                                                                             gCCAGCCTACACGCTCCAGGCAACGGCGGGGCGCATACACCCGCGCAAATTCCCTCAAAACCGGAACTACACCAACGCTGGGAAAAGCGCGGATGCGGGCCCGCACCGGGAAATTCAAAGCCCGTGCTTTTGGTTCGCtcct                                               >  2:694501/1‑140 (MQ=255)                                                                                                                   cTACACGCTCCAGGCAACGGCGGGTCGCCTACACCCGCCCAACTCCCCTCCAAGACGGGTCTTCACCAACACTGGCAAAAAGGCGAAAGCGGGCCAGCACGGGGGAATTTAACCCCCGTGCTTTGGCCTCGCTCATTATCAATACCGc                                   >  2:458014/1‑148 (MQ=255)                                                                                                                     acacGCTCCAGGCAACGGCGGGTCGCATACACCGGCGCAATTCCCATCAATGCCGGATCTACACCAACGCTGGCAAATGCGCGAATGCGGGCCAGCACGGGTAAATTCAACGCTCGTGCTTTGGCTTCGCTCATCATCATTACCGCAGCTg                              <  1:172135/151‑1 (MQ=255)                                                                                                                          cTCCAGGCAACGGCGGGTCGCATACACCCGCGCCAATCCCCTCAAAACCCGATCTACACCCAACCTCGCAAATGCGCGAATGCCGGCCAGCCCCGGGAAATTTAACCCCCGTGCTTTTGCTTCGCCCATCATCATTACCGCAGCCGCGcc                          >  2:963175/1‑150 (MQ=255)                                                                                                                              aGGCAACGGCGGGTCGCATACACCGGCGCAATTCCCATCAATGCCGGATCTACACCAACGCTGGCAAATGCGCGAATGCGGGCCAGCACGGGTAAATTCAACGCTCGTGCTTTGGCTTCGCTCATCATCATTACCGCAGCTGCGCCATCGt                     <  1:52569/151‑1 (MQ=255)                                                                                                                               ggCAACGGCGGGTCGCATACACCGGCGCAATTCCCATCAATGCCGGATCTACACCAACGCTGGCAAATGCGCGAATGCGGGCCAGCACGGGTAAATTCAACGCTCGTGCTTTGGCTTCGCTCATCATCATTACCGCAGCTGCGCCATCGtt                    <  2:860283/151‑1 (MQ=255)                                                                                                                                    cggcggGTCGCATACACCGGCGCAATTCCCATCAATGCCGGATCTACACCAACGCTGGCAAATGCGCGAATGCGGGCCAGCACGGGTAAATTCAACGCTCGTGCTTTGGCTTCGCTCATCATCATTACCGCAGCTGCGCCATCGTTTATgg               <  2:792357/151‑1 (MQ=255)                                                                                                                                     ggcggGTCGCATACACCGGCGCAATTCCCATCAATGCCGGATCTACACCAACGCTGGCAAATGCGCGAATGCGGGCCAGCACGGGTAAATTCAACGCTCGTGCTTTGGCTTCGCTCATCATCATTACCGCAGCTGCGCCATCGTTTATgg               >  1:928827/1‑150 (MQ=255)                                                                                                                                      gcggGTCGCATACACCGGCGCAATTCCCATCAATGCCGGATCTACACCAACGCTGGCAAATGCGCGAATGCGGGCCAGCACGGGTAAATTCAACGCTCGTGCTTTGGCTTCGCTCATCATCATTACCGCAGCTGCGCCATCGTTTATGgat             <  2:313376/151‑1 (MQ=255)                                                                                                                                        gggTCGCATACACCGGCGCAATTCCCATCAATGCCGGATCTACACCAACGCTGGCAAATGCGCGAATGCGGGCCAGCACGGGTAAATTCAACGCTCGTGCTTTGGCTTCGCTCATCATCATTACCGCAGCTGCGCCATCGTTTATGgatg            >  2:372076/1‑150 (MQ=255)                                                                                                                                                 acacCGGCGCAATTCCCATCAATGCCGGATCTACACCAACGCTGGCAAATGCGCGAATGCGGGCCAGCACGGGTAAATTCAACGCTCGTGCTTTGGCTTCGCTCATCATCATTACCGCAGCTGCGCCATCGTTTATGGATGATGCATTAcc  >  1:696219/1‑151 (MQ=255)                                                                                                                                                      |                                                                                                                                                  CACCATTGACATTGACCCGACGCTCATCCCACTCAAGCATCTTGCCAACCGAAAGCGCCTGTGCAGCAAACGCTTCATTAGCCTCGATAAGATCGACTTCAGCCAACTGCCAGCCTACACGCTCCAGGCAACGGCGGGTCGCATACACCGGCGCAATTCCCATCAATGCCGGATCTACACCAACGCTGGCAAATGCGCGAATGCGGGCCAGCACGGGTAAATTCAACGCTCGTGCTTTGGCTTCGCTCATCATCATTACCGCAGCTGCGCCATCGTTTATGGATGATGCATTACC  >  NC_000913/2984569‑2984863

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 12 ≤ ATCG/ATCG < 14 ≤ ATCG/ATCG < 33 ≤ ATCG/ATCG < 39 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑