Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NC_000913	2,984,718	0	G	C	48.3%	29.3 / 13.2	31	P292R (CCG→CGG)	yqeF	short chain acyltransferase
Reads supporting (aligned to +/- strand):  ref base G (1/14);  new base C (14/0);  total (17/14)
Fisher's exact test for biased strand distribution p-value = 2.06e-07
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 1.00e+00

CACCATTGACATTGACCCGACGCTCATCCCACTCAAGCATCTTGCCAACCGAAAGCGCCTGTGCAGCAAACGCTTCATTAGCCTCGATAAGATCGACTTCAGCCAACTGCCAGCCTACACGCTCCAGGCAACGGCGGGTCGCATACACCGGCGCAATTCCCATCAATGCCGGATCTACACCAACGCTGGCAAATGCGCGAATGCGGGCCAGCACGGGTAAATTCAACGCTCGTGCTTTGGCTTCGCTCATCATCATTACCGCAGCTGCGCCATCGTTTATGGAT  >  NC_000913/2984569‑2984852                                                                                                                                                      |                                                                                                                                       caccaTTGACATTGACCCGACGCTCATCCCACTCAAGCATCTTGCCAACCGAAAGCGCCTGTGCAGCAAACGCTTCATTAGCCTCGATAAGATCGACTTCAGCCAACTGCCAGCCTACACGCTCCAGGCAACGGCGGGTCGCATACACCgg                                                                                                                                       <  2:14149/151‑1 (MQ=255)  accaTTGACATTGACCCGACGCTCATCCCACTCAAGCATCTTGCCAACCGAAAGCGCCTGTGCAGCAAACGCTTCATTAGCCTCGATAAGATCGACTTCAGCCAACTGCCAGCCTACACGCTCCAGGCAACGGCGGGTCGCATACACCGgc                                                                                                                                      <  2:41895/151‑1 (MQ=255)  accaTTGACATTGACCCGACGCTCATCCCACTCAAGCATCTTGCCAACCGAAAGCGCCTGTGCAGCAAACGCTTCATTAGCCTCGATAAGATCGACTTCAGCCAACTGCCAGCCTACACGCTCCAGGCAACGGCGGGTCGCATACACCGgc                                                                                                                                      <  2:708271/151‑1 (MQ=255)   ccaTTGACATTGACCCGACGCTCATCCCACTCAAGCATCTTGCCAACCGAAAGCGCCTGTGCAGCAAACGCTTCATTAGCCTCGATAAGATCGACTTCAGCCAACTGCCAGCCTACACGCTCCAGGCAACGGCGGGTCGCATACACCGgcg                                                                                                                                     <  2:399827/151‑1 (MQ=255)         acattgacCCGACGCTCATCCCACTCAAGCATCTTGCCAACCGAAAGCGCCTGTGCAGCAAACGCTTCATTAGCCTCGATAAGATCGACTTCAGCCAACTGCCAGCCTACACGCTCCAGGCAACGGCGGGTCGCATACACCGGCGCAAtt                                                                                                                                <  2:192323/150‑1 (MQ=255)           attgacCCGACGCTCATCCCACTCAAGCATCTTGCCAACCGAAAGCGCCTGTGCAGCAAACGCTTCATTAGCCTCGATAAGATCGACTTCAGCCAACTGCCAGCCTACACGCTCCAGGCAACGGCGGGGCGCATACACCCGGGCCATTtcc                                                                                                                             >  1:379062/1‑151 (MQ=255)                cccGACGCTCATCCCACTCAAGCATCTTGCCAACCGAAAGCGCCTGTGCAGCAAACGCTTCATTAGCCTCGATAAGATCGACTTCAGCCAACTGCCAGCCTACACGCTCCAGGCAACGGCGGGTCGCATACACCGGCGCAATTCCCATCa                                                                                                                         <  2:483665/150‑1 (MQ=255)                cccGACGCTCATCCCACTCAAGCATCTTGCCAACCGAAAGCGCCTGTGCAGCAAACGCTTCATTAGCCTCGATAAGATCGACTTCAGCCAACTGCCAGCCTACACGCTCCAGGCAACGGCGGGGCGGATAAACCCGCGCaacttcc                                                                                                                             >  2:735786/1‑141 (MQ=255)                  cGACGCTCATCCCACTCAAGCATCTTGCCAACCGAAAGCGCCTGTGCAGCAAACGCTTCATTAGCCTCGATAAGATCGACTTCAGCCAACTGCCAGCCTACACGCTCCAGGCAACGGCGGGTCGCATACAACCgcgccacttccc                                                                                                                            >  2:753434/1‑137 (MQ=255)                     cGCTCATCCCACTCAAGCATCTTGCCAACCGAAAGCGCCTGTGCAGCAAACGCTTCATTAGCCTCGATAAGATCGACTTCAGCCAACTGCCAGCCTACACGCTCCAGGCAACGGCGGGTCGCATACACCGGCGCAATTCCCATCAATGCCg                                                                                                                   <  2:579976/151‑1 (MQ=255)                      gCTCATCCCACTCAAGCATCTTGCCAACCGAAAGCGCCTGTGCAGCAAACGCTTCATTAGCCTCGATAAGATCGACTTCAGCCAACTGCCAGCCTACACGCTCCAGGCAACGGCGGGGTGCATCCACCCGCGCACTTCCCATCCATGCCg                                                                                                                   >  1:78350/1‑150 (MQ=255)                      ccTCATCCCACGCAAGGATCTTGCCAACCGAAAGCGCCTGTGCAGCAACCGCTTCATTAGCCTCGATATGATCGACTCCAGCCAACTGCCAGCCTACACGCTCCTGGCAACGGCGGGTCGCATACAGCGGCGCAATTCCCATCAATGCCgg                                                                                                                  <  2:652909/150‑1 (MQ=255)                          aTCCCACTCAAGCATCTGGCCAACCGAAAGCGCCTGTGCAGCAAACGCTTCATTAGCCTCGATAAGATCGACTTCAGCCAACTGCCAGCCTACACGCTCCAGTCAACGGCGGGTCGCATACCCCGGCGCAATGCCCATCAATGCCGGATcg                                                                                                              <  2:668038/151‑2 (MQ=255)                              cACTCAAGCATCTTGCCAACCGAAAGCGCCTGTGCAGCAAACGCTTCATTAGCCTCGATAAGATCGACTTCAGCCAACTGCCAGCCTACACGCTCCAGGCAACGGCGGGTCGCATACACCGGCGCAATTCCCATCAATGCCGGATCTacac                                                                                                          <  1:601452/151‑1 (MQ=255)                                           tGCCAACCGAAAGCGCCTGTGCAGCAAACGCTTCATTAGCCTCGATAAGATCGACTTCAGCCAACTGCCAGCCTACACGCTCCAGGCAACGGCGGGTCGCATACACCGGCGCAATTCCCATCAATGCCGGATCTACACCAACGCTGGCa                                                                                               <  1:589193/149‑1 (MQ=255)                                               aaCCGAAAGCGCCTGTGCAGCAAACGCTTCATTAGCCTCGATAAGATCGACTTCAGCCAACTGCCAGCCTACACGCTCCAGGCAACGGCGGGTCGCATACACCCGCGCAATTTCCATCAAAGCCGGATCTACACCAACGCTGGCAAATggg                                                                                         >  1:79617/1‑149 (MQ=255)                                                             gtgCAGCAAACGCTTCATTAGCCTCGATAAGATCGACTTCAGCCAACTGCCAGCCTACACGCTCCAGGCAACGGCGGGTCGCATACACCGGCGCAATTCCCATCAATGCCGGATCTACACCAACGCTGGCAAATGCGCGAATGCGGGcc                                                                             <  1:70913/149‑1 (MQ=255)                                                              tgCAGCAAACGCTTCATTAGCCTCGATAAGATCGACTTCAGCCAACTGCCAGCCTACACGCTCCAGGCAACGGCGGGGCGCATACACCAGCGCAAATCCCCTCCCAACCCGACCTACACCCACGCCCGCAAATGCGCGGATGCggggc                                                                             >  2:395297/1‑146 (MQ=255)                                                                       cGCTTCATTAGCCTCGATAAGATCGACTTCAGCCAACTGCCAGCCTACACGCTCCAGGCAACGGCGGGTCGCATACAACCGCGCAAATCCCCTCAATACCGGATCTACACCACCGCTGGGAAAAACGCGAAAGCGGGCCAGCACGGGGaa                                                                  >  2:32597/1‑150 (MQ=255)                                                                           tCATTAGCCTCGATAAGATCGACTTCAGCCAACTGCCAGCCTACACGCTCCAGGCAACGGCGGGTCGCCCACCCCCGCGCAATTTCCACCAATGCCGGCACTACACCAACACCGGCAAAAGCGCGAATGCGGGCCCGCCCGGGGAAATTc                                                              >  2:596238/1‑150 (MQ=255)                                                                                     cGATAAGATCGACTTCAGCCAACTGCCAGCCTACACGCTCCAGGCAACGGCGGGTCGCATACACCCGCGCAAATCCCATCAATTCCGGATCTACACCCACGCTGGCAAAAGCGCGAATGCGGGCCAGCACGGGGAAATTCAAAGCCCGTGc                                                   >  1:328489/1‑151 (MQ=255)                                                                                          aGATCGACTTCAGCCAACTGCCAGCCTACACGCTCCAGGCAACGGCGGGTCGCATACACCCCCGCAAATCCCCTCCAAGCCGGAGCTACACCAACACTGGGAAAAGCGCGAAAGCGGGCCAGCCCGGGGAAATTTAAAACTCGGGCttt                                                >  2:768534/1‑149 (MQ=255)                                                                                            aTCGACTTCAGCCAACTGCCAGCCTACACGCTCCAGGCAACGGCGGATCGCCAAAACCCGCCCCATTTCCCTCAAAACCGGACCTAAACCCACACCGGCAAAAAGGCGGATGGCGGGCAACACGGGGGAATTCaaaccccgggcct                                                 >  2:86797/1‑135 (MQ=255)                                                                                             tCGACTTCAGCCAACTGCCAGCCTACACGCTCCAGGCAACGGCGGGTCGCATACACCGGCGCCATTCCCCTCAATGCCGGATCTACACCAACGCTGGCAAATGCGCGAATGCGGGCCAGCACGGGTAAAATCAACGCCCCTGCttt                                                >  1:501625/1‑146 (MQ=255)                                                                                               gACTTCAGCCAACTGCCAGCCTACACGCTCCAGGCAACGGCGGGTCGCATACACCCGCCCAAATCCCCACAATTACGGGTCTACACCAAAGCCGGGAAAAGCGCGGAAGCGGGGCCGCACGGGGAAAATTAAAGCTCCTGCttttg                                              >  1:560118/1‑144 (MQ=255)                                                                                               gACTTCAGCCAACTGCCAGCCTACACGCTCCAGGCAACGGCGGGTCGCATAAACCCGCGCCATTCCCCTCAATGCCCGATCTACACCAACGCTGGCAAAAGCGCGAAAGCGGGGCCACACGGGGAAAATCAACGCCCGTGCTTTTGCtt                                           >  1:52468/1‑149 (MQ=255)                                                                                                        cAACTGCCAGCCTACACGCTCCAGGCAACGGCGGGCCGCATTCAACAGCGCAAATCCCCCCAATGACGGCAATACACCAACACCGGCAAAAATGCGGATGGGGGGCAGCACGGGGACATTCTACACCCCTGCTTTGGGCTCGCtcatc                                   >  2:173348/1‑148 (MQ=255)                                                                                                                        cGCTCCAGGCAACGGCGGGTCGCATACACCGGCGCAATTCCCATCAATGCCGGATCTACACCAACGCTGGCAAATGCGCGAATGCGGGCCAGCACGGGTAAATTCAACGCTCGTGCTTTGGCTTCGCTCATCATCATTACCGCAGCTgcg                 <  2:244195/150‑1 (MQ=255)                                                                                                                         gCTCCAGGCAACGGCGGGTCGCCTACACCCGCGCAATTCCCATCAATGCCGGGTCTACACCAACGCTGGCAAATGCGCGAATGCGGGCCAGCACGGGGAAATTTAAAGCCCGTGCTTTTGCTTCGCCCATCATCATTACCGCCGCCGCGcc               >  1:441833/1‑151 (MQ=255)                                                                                                                            ccAGGCAACGGCGGGGCGCATACACCCGCGCCATTTCCATCACTGCCGGATCTACACCCACCCTGGCAAAAGCGCGAAAGCGGGCCAGCACGGGGAAAATCAAACCCTTTGCTTTGGCTTCGCCCATCATCATTACCGCAGCTGCGCCCTc            >  2:444403/1‑151 (MQ=255)                                                                                                                             cAGGCAACGGCGGGTCGCATACACCGGCGCAATTCCCATCAATGCCGGATCTACACCAACGCTGGCAAATGCGCGAATGCGGGCCAGCACGGGTAAATTCAACGCTCGTGCTTTGGCTTCGCTCATCATCATTACCGCAGCTGCGCCATCg           <  2:492153/151‑1 (MQ=255)                                                                                                                                      gcggGTCGCATACACCGGCGCAATTCCCATCAATGCCGGATCTACACCAACGCTGGCAAATGCGCGAATGCGGGCCAGCACGGGTAAATTCAACGCTCGTGCTTTGGCTTCGCTCATCATCATTACCGCAGCTGCGCCATCGTTTATGgat  <  1:70475/151‑1 (MQ=255)                                                                                                                                                      |                                                                                                                                       CACCATTGACATTGACCCGACGCTCATCCCACTCAAGCATCTTGCCAACCGAAAGCGCCTGTGCAGCAAACGCTTCATTAGCCTCGATAAGATCGACTTCAGCCAACTGCCAGCCTACACGCTCCAGGCAACGGCGGGTCGCATACACCGGCGCAATTCCCATCAATGCCGGATCTACACCAACGCTGGCAAATGCGCGAATGCGGGCCAGCACGGGTAAATTCAACGCTCGTGCTTTGGCTTCGCTCATCATCATTACCGCAGCTGCGCCATCGTTTATGGAT  >  NC_000913/2984569‑2984852

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 12 ≤ ATCG/ATCG < 14 ≤ ATCG/ATCG < 29 ≤ ATCG/ATCG < 39 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑