Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NC_000913	2,984,718	0	G	C	47.6%	30.2 / 24.9	46	P292R (CCG→CGG)	yqeF	short chain acyltransferase
Reads supporting (aligned to +/- strand):  ref base G (5/17);  new base C (20/0);  total (26/20)
Fisher's exact test for biased strand distribution p-value = 1.08e-07
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 6.77e-01

CCACCATTGACATTGACCCGACGCTCATCCCACTCAAGCATCTTGCCAACCGAAAGCGCCTGTGCAGCAAACGCTTCATTAGCCTCGATAAGATCGACTTCAGCCAACTGCCAGCCTACACGCTCCAGGCAACGGCGGGTCG‑CAT‑ACACCGGCGCAATTC‑CCATCAATGCCGGATCTACACCAACGCTGGCAAATGCGCGAATGCGGGCCAGCACGGGTAAATTCAACGCTCGTGCTTTGGCTTCGCTCATCATCATTACCGCAGCTGCGCCATCGTTTATGGATGATGCATTACCC  >  NC_000913/2984568‑2984864                                                                                                                                                         |                                                                                                                                                    ccaccaTTGACATTGACCCGACGCTCATCCCACTCAAGCATCTTGCCAACCGAAAGCGCCTGTGCAGCAAACGCTTCATTAGCCTCGATAAGATCGACTTCAGCCAACTGCCAGCCTACACGCTCCAGGCAACGGCGGGTCG‑CAT‑ACACCg                                                                                                                                                     <  1:139863/151‑1 (MQ=255)     cattgacattgaCCCGACGCTCATCCCACTCAAGCATCTTGCCAACCGAAAGCGCCTGTGCAGCAAACGCTTCATTAGCCTCGATAAGATCGACTTCAGCCAACTGCCAGCCTACACGCTCCAGGCAACGTCGGGTCG‑CAT‑ACACCGtcgc                                                                                                                                                 <  2:223054/151‑1 (MQ=255)               gacCCGACGCTCATCCCACTCAAGCATCTTGCCAACCGAAAGCGCCTGTGCAGCAAACGCTTCATTAGCCTCGATAAGATCGACTTCAGCCAACTGCCAGCCTACACGCTCCAGGCAACGGCGGGGTG‑CAT‑ACAACCCCGCCATTT‑CCac                                                                                                                                       >  2:479595/1‑149 (MQ=255)                        cTCATCCCACTCAAGCATCTTGCCAACCGAAAGCGCCTGTGCAGCAAACGCTTCATTAGCCTCGATAAGATCGACTTCAGCCAACTGCCAGCCTACACGCTCCAGGCAACGGCGGGTCG‑CCT‑ACACCCGCGCCATTC‑CCATCAATGcc                                                                                                                                >  1:466838/1‑148 (MQ=255)                         tCATCCCACTCAAGCATCTTGCCAACCGAAAGCGCCTGTGCAGCAAACGCTTCATTAGCCTCGATAAGATCGACTTCAGCCAACTGCCAGCCTACACGCTCCAGGCAACGGCGGGGCG‑GCT‑ACACCGGCGCCATTC‑CCCTc                                                                                                                                      >  2:697589/1‑141 (MQ=255)                           aTCCCACTCAAGCATCTTGCCAACCGAAAGCGCCTGTGCAGCAAACGCTTCATTAGCCTCGATAAGATCGACTTCAGCCAACTGCCAGCCTACACGCTCCAGGCAACGGCGGGTGGCCAA‑TAACCGGC‑CCATTC‑CCATCCATgac                                                                                                                                >  1:166472/1‑143 (MQ=255)                           aTCCCACTCAAGCATCTTGCCAACCGAAAGCGCCTGTGCAGCAAACGCTTCATTAGCCTCGATAAGATCGACTTCAGCCAACTGCCAGCCTACACGCTCCAGGCAACGGCGGGTCG‑CAT‑ACACCGGCGCAATTC‑CCATCAATGCCGGATCt                                                                                                                          <  2:107899/151‑1 (MQ=255)                            tCCCACTCAAGCATCTTGCCAACCGAAAGCGCCTGTGCAGCAAACGCTTCATTAGCCTCGATAAGATCGACTTCAGCCAACTGCCAGCCTACACGCTCCAGGCAACGGCGGGTCG‑CCT‑AAACCCGCGCCATTC‑CCCTCAATGCCCGATCt                                                                                                                          >  2:296001/1‑150 (MQ=255)                               cACTCAAGCATCTTGCCAACCGAAAGCGCCTGTGCAGCAAACGCTTCATTAGCCTCGATAAGATCGACTTCAGCCAACTGCCAGCCTACACGCTCCAGGCAACGGCGGGGCG‑CGA‑CCACCCGCGCAAATA‑CCATCAATACCGGATCTac                                                                                                                        >  1:497309/1‑149 (MQ=255)                                aCTCAAGCATCTTGCCAACCGAAAGCGCCTGTGCAGCAAACGCTTCATTAGCCTCGATAAGATCGACTTCAGCCATCTGCCAGCCTACACGCTCCAGGCAACGGCGTGTCG‑CAT‑ACACCGGCGCAATTC‑CCATCAATGCCGGATCt                                                                                                                          <  2:368672/146‑1 (MQ=255)                                aCTCAAGCATCTTGCCAACCGAAAGCGCCTGTGCAGCAAACGCTTCATTAGCCTCGATAAGATCGACTTCAGCCAACTGCCAGCCTACACGCTCCAGGCAACGGCGGGTCC‑CAT‑ACACCGGCGCAAATC‑CCATTGATACCGGTACTATAcc                                                                                                                     >  1:258181/1‑151 (MQ=255)                                      gCATCTTGCCAACCGAAAGCGCCTGTGCAGCAAACGCTTCATTAGCCTCGATAAGATCGACTTCAGCCAACTGCCAGCCTACACGCTCCAGGCAACGGCGGGTCG‑CAT‑ACACCGGCGCAATTC‑CCATCAATGCCGGATCTACACCAACGCt                                                                                                               <  1:619040/151‑1 (MQ=255)                                      gCATCTTGCCAACCGAAAGCGCCTGTGCAGCAAACGCTTCATTAGCCTCGATAAGATCGACTTCAGCCAACTGCCAGCCTACACGCTCCAGGCAACGGCGGGTCG‑CAT‑ACACCCCCGCCATTT‑CCCTCAATGCCCGATCTACACCAACGc                                                                                                                >  1:465669/1‑150 (MQ=255)                                        aTCTTGCCAACCGAAAGCGCCTGTGCAGCAAACGCTTCATTAGCCTCGATAAGATCGACTTCAGCCAACTGCCAGCCTACACGCTCCAGGCAACGGCGGGGCG‑CAT‑ACACCCGCGCAATTC‑CCATCAATACCGGAACTACACCAAcac                                                                                                                >  1:567029/1‑146 (MQ=255)                                            tGCCAACCGAAAGCGCCTGTGCAGCAAACGCTTCATTAGCCTCGATAAGATCGACTTCAGCCAACTGCCAGCCTACACGCTCCAGGCAACGGCGGGTCG‑CAT‑ACACCGGCGCAATTC‑CCATCAATGCCGGATCTACACCAACGCTgg                                                                                                             <  1:637469/147‑1 (MQ=255)                                            tGCCAACCGAAAGCGCCTGTGCAGCAAACGCTTCATTAGCCTCGATAAGATCGACTTCAGCCAACTGCCAGCCTACACGCTCCAGGCAACGGCGGGTCG‑CAT‑ACACCGGCGCAATTC‑CCATCAATGCCGGATCTACACCAACGCTGGCa                                                                                                           <  1:538435/149‑1 (MQ=255)                                                   cGAAAGCGCCTGTGCAGCAAACGCTTCATTAGCCTCGATAAGATCGACTTCAGCCAACTGCCAGCCTACACGCTCCAGGCAACGGCGGGTCG‑CAT‑ACACCCGCGCCATTC‑CCCTCAAAGCCGGAGCTACACCAACCCCTGCAAATgcg                                                                                                     >  2:417334/1‑148 (MQ=255)                                                     aaaGCGCCTGTGCAGCAAACGCTTCATTAGCCTCGATAAGATCGACTTCAGCCAACTGCCAGCCTACACGCTCCAGGCAACGGCGGGTCG‑CCT‑ACACCCGCGCAATTT‑CCCTCAATTCCGGGTCTACACCAACCCTGGCAAAAGCGCGaa                                                                                                 >  1:285214/1‑150 (MQ=255)                                                     aaaGCGCCTGTGCAGCAAACGCTTCATTAGCCTCGATAAGATCGACTTCAGCCAACTGCCAGCCTACACGCTCCAGGCAACGGCGGGTCG‑CAT‑ACACCCGCGCAATTC‑CCCTCAATGCCGGATCTACACCAACGCTGGCAAAAGCGCGaa                                                                                                 >  1:439779/1‑150 (MQ=255)                                                         cgcCTGTGCAGCAAACGCTTCATTAGCCTCGATAAGATCGACTTCAGCCAACTGCCAGCCTACACGCTCCAGGCAACGGCGGGTCG‑CATAACACC‑GCCCCATTC‑CCCCCCATGCCCGCGCTACACCCACCCTGGCAAAAGCGCGCAAGCg                                                                                             >  2:180631/1‑150 (MQ=255)                                                         cgcCTGTGCAGCAAACGCTTCATTAGCCTCGATAAGATCGACTTCAGCCAACTGCCAGCCTACACGCTCCAGGCAACGGCGGGTCG‑CAT‑ACACCCGCGCCATTC‑CCCTCCATGCCGGATCTACACCAACGCTGGCAAATGCGCGAATGc                                                                                              >  2:243110/1‑149 (MQ=255)                                                               tgCAGCAAACGCTTCATTAGCCTCGATAAGATCGACTTCAGCCAACTGCCAGCCTACACGCTCCAGGCAACGGCGGGCCG‑CAT‑ACACCCGCGCAAATC‑CCATCCAAACCGGGACTACACCAACCCTGGCAAAAGCGCGAATGGGGGCCa                                                                                        >  1:521425/1‑149 (MQ=255)                                                                   gcaAACGCTTCATTAGCCTCGATAAGATCGACTTCAGCCAACTGCCAGCCTACACGCTCCAGGCAACGGCGGGTCG‑CAT‑ACACCCGCGCCATTC‑CCCTCAATACCGGCACTACACCAACGCTGGCAAAAGCGCGAATGCGGGCCAGCACgg                                                                                  >  1:167578/1‑151 (MQ=255)                                                                   caaaaCGCTTCATTGGCCTCGATAAGGTCGACTTAGTCCAGCTTCCAGCCGTCACGCTCCAGTCGACGGCGGGGAG‑CTT‑TCGTTTTGACGATAC‑CGCGCCCAACCGGATCTACACCAACGCTGGCAAATGCGCGAATGCGGGCCAGc                                                                                      <  2:683345/145‑1 (MQ=255)                                                                    caAACGCTTCATTAGCCTCGATAAGATCGACTTCAGCCAACTGCCAGCCTACACGCTCCAGGCAACGGCGGGTCG‑CAC‑AAACCCGCGCACCTC‑CCCCCCATGCCCGGTCTACACCCACCCCGGCCAAATCGCGCAAGCGGGCCAGCCCggg                                                                                 >  2:310336/1‑151 (MQ=255)                                                                     aaaCGCTGAATTAGCCGCGATAAGATCGACTTCAGCAAACTACCAGCCTACACGCTCCAGGCAACGGCGGGTCG‑CAT‑ACACCGGCGCGATAC‑CGAGCACTGCCGGATCTACACCAACGCTGGCAAATGCGCGAATGCGGGCCAGCa                                                                                     <  2:241479/146‑1 (MQ=255)                                                                         gCTTCATTAGCCTCGATAAGATCGACTTCAGCCAACTGCCAGCCTACACGCTCCAGGCAACGGCGGGTCG‑CAT‑ACACCGGCGCAATTC‑CCATCAATGCCGGATCTACACCAACGCTGGCAAATGCGCGAATGCGGGCCAGCACGGGTAAAt                                                                            <  1:313498/151‑1 (MQ=255)                                                                          cTTCATTAGCCTCGATAAGATCGACTTCAGCCAACTGCCAGCCTACACGCTCCAGGCAACGGCGGGTCG‑CAT‑ACACCGCCGCCAATC‑CCATCAAAGCCCGATCCACACCAAAGCTGGCCAAAACGCGAATGCGGGCCCACACGGGGAAAtt                                                                           >  2:457364/1‑151 (MQ=255)                                                                            tCATTAGCCTCGATAAGATCGACTTCAGCCAACTGCCAGCCTACACGCTCCAGGCAACGGCGGGTCG‑CAT‑ACACCGGCGCAATTC‑CCATCAATGCCGGATCTACACCAACGCTGGCAAATGCGCGAATGCGGGCCAGCACGGGTAAAtt                                                                           <  1:246804/149‑1 (MQ=255)                                                                               ttAGCCTCGATAAGATCGACTTCAGCCAACTGCCAGCCTACACGCTCCAGGCAACGGCGGGTTG‑CCT‑ACACCCGCGCAATTC‑CCATCAAAGCCCGGTCTTCACCAACGCCGGCAAAAGCGCGAATGAGGGGCCGCCCGGGGAAATTCaa                                                                        >  1:255709/1‑149 (MQ=255)                                                                                tAGCCTCGATAAGATCGACTTCAGCCAACTGCCAGCCTACACGCTCCAGGCAACGGCGGGGCG‑CAC‑ACCACCGCGCCATTC‑CCCTCCACGGCCGGTCTACACCCAACCTGGCCAAAGCGCGAAAGCGGGCCAGCCCGGGGaaaattcactc                                                                     >  2:559901/1‑143 (MQ=255)                                                                                      cGATAAGATCGACTTCAGCCAACTGCCAGCCTACACGCTCCAGGCAACGGCGGGTCG‑CAT‑ACACCGGCGCAATTC‑CCCGCAATGCCGGATCTACACCAACGCTGGCAAATGCGCGAATGCGGGCCAGCACGGGTAAATTCAACGCTCGTg                                                                <  2:182194/150‑1 (MQ=255)                                                                                      cGATAAGATCGACTTCAGCCAACTGCCAGCCTACACGCTCCAGGCAACGGCGGGTCG‑CAT‑ACACCGGCGCAATTC‑CCATCAATGCCGGATCTACACCAACGCTGGCAAATGCGCGAATGCGGGCCAGCACGGGTAAATTCAACGCTCGTg                                                                <  1:548313/150‑1 (MQ=255)                                                                                       gATAAGATCGACTTCAGCCAACTGCCAGCCTACACGCTCCAGGCAACGGCGGGTCG‑CCT‑ACACCCGCGCAAATC‑CCATCAATGCCGGATCTACACCAACGCTGGCCAATGCGCGCATGCGGGCCAGCACGGGGAAATTCAACGCTCGTGCt                                                              >  2:217915/1‑151 (MQ=255)                                                                                        aTAAGATCGACTTCAGCCAACTGCCAGCCTACACGCTCCAGGCAACGGCGGGTCG‑CAT‑TATTTGTAATGATACGCCGACCA‑CCGAGATCTACACCAACGCTGGCAAATGCGCGAATGCGGGCCAGCACGGGTAAATTCAACGCTCGTGCtt                                                             <  2:662593/151‑1 (MQ=255)                                                                                            gATCGACTGCAGCCGACTGCCAGCCTACACGCGCCAGGCAACGGCGGGTCG‑TAT‑TCTTCTTAATAATAC‑GGCGACCTCCGAGATCTACACCAACGCTGGCAAATGCGCGAATGCGGGCCAGCACGGGTAAATTCAACGCTCGTGCTTTg                                                           <  2:644094/149‑1 (MQ=255)                                                                                             aTCGACTTCAGCCAACTGCCAGCCTACACGCTCCAGGCAACGGCGGGTCG‑CAT‑ACACCCGCGCCATTC‑CCATCAATGCCGGATCTACACCAACGCTGGCAAAAGCGCGAAAGCGGGCCAGCACGGGGAAATTCAAAGCCCGTGCttt                                                            >  1:156045/1‑147 (MQ=255)                                                                                               cGACTTCAGCCAACTGCCAGCCTACACGCTCCAGGCAACGGCGGGTCG‑CAT‑ACACCGGCGCAATTC‑CCATCAATGCCGGATCTACACCAACGCTGGCAAATGCGCGAATGCGGGCCAGCACGGGTAAATTCAACGCTCGTGCTTTGGCTTc                                                      <  1:616425/151‑1 (MQ=255)                                                                                                       gCCAACTGCCAGCCTACACGCTCCAGGCAACGGCGGGTCG‑CAT‑ACACCGGCGCAATTC‑CCATCAATGCCGGATCTACACCAACGCTGGCAAATGCGCGAATGCGGGCCAGCACGGGTAAATTCAACGCTCGTGCTTTGGCTTCGCtcatca                                              <  1:239785/151‑1 (MQ=255)                                                                                                              gCCAGCCTACACGCTCCAGGCAACGGCGGGTCG‑CAT‑ACACCTGAGCGATAC‑GCCGTACTGCCGGATCTACACCAACGCTGGCAAATGCGCGAATGCGGGCCAGCACGGGTAAATTCAACGCTCGTGCTTTGGCTTCGCTCATCATCATTa                                        <  2:154050/150‑1 (MQ=255)                                                                                                              gCCAGCCTACACGCTCCAGGCAACGGCGGGTCG‑CAT‑ACACCGGCGCAATTC‑CCACCAATTCCGGGTCTACACCAACCCTGGCAAATGCGCGGATGCGGGCCAGCACGGGGAAAATCAAAGCCCGTGCTTTTGCTTCGCTCATCAttatta                                        >  1:397318/1‑150 (MQ=255)                                                                                                                 aGCCTACACGCTCCAGGCAACGGCGGGGCG‑CAT‑ACACCCGCGCCATTT‑CCCTCCATACCGGGTCTCCACCAACGCCGGCAAAAGCGCGAAAGCGGGCCAGCCCGGGGAAAATCAACACTCCTGCTTTGGCTTCGCCCCTCATCATTTcc                                      >  2:198255/1‑149 (MQ=255)                                                                                                                          gCTCCAGGCAACGGCGGGTCG‑CCT‑AAACCCGCGCAATTC‑CCCCCAAAGCCGGATCTCCACCCACGCTGGCAAATGCGCGAATGCGGGCCAGCACGGGGAAATACAAAGCCCGCGCCTTTGCCTCGCCCCTCCTCATTACCCCAGCCGAGcc                           >  2:533688/1‑151 (MQ=255)                                                                                                                               aGGCAACGGCGGGGCG‑CAT‑AAACCCGGGCCATTC‑CCCTCAATGCCCGAACTACCCCAACGATGGCAAATGCGCGAATGCGGGCCAGCCCGGGGAAATTCAACACCCGGGCTTTTGCCTCGCTCCACATCATTACCGCAACTGCGcc                           >  2:605892/1‑146 (MQ=255)                                                                                                                                 gCAACGGCGGGTCG‑CAT‑ACACCGGCGCAATGC‑CCATCAATGCCGGATCTACACCAACGCTGGCAAATGCGCGAATGCGGGCCAGCACGGGTAAATTCAACGCTCGTGCTTTGGCTTCGCTCATCATCATTACCGCAGCTGCGCCATCGttt                    <  2:484036/151‑1 (MQ=255)                                                                                                                                      ggcggGTCG‑CAT‑ACACCGGCGCAATTC‑CCATCAATGCCGGATCTACACCAACGCTGGCAAATGCGCGAATGCGGGCCAGCACGGGTAAATTCAACGCTCGTGCTTTGGCTTCGCTCATCATCATTACCGCAGCTGCGCCATCGTTTATGga               <  1:456693/151‑1 (MQ=255)                                                                                                                                                     cacCGGCGCAATTC‑CCATCAATGCCGGATCTACACCAACGCTGGCAAATGCGCGAATGCGGGCCAGCACGGGTAAATTCAACGCTCGTGCTTTGGCTTCGCTCATCATCATTACCGCAGCTGCGCCATCGTTTATGGATGATGCATTAccc  <  1:296074/151‑1 (MQ=255)                                                                                                                                                         |                                                                                                                                                    CCACCATTGACATTGACCCGACGCTCATCCCACTCAAGCATCTTGCCAACCGAAAGCGCCTGTGCAGCAAACGCTTCATTAGCCTCGATAAGATCGACTTCAGCCAACTGCCAGCCTACACGCTCCAGGCAACGGCGGGTCG‑CAT‑ACACCGGCGCAATTC‑CCATCAATGCCGGATCTACACCAACGCTGGCAAATGCGCGAATGCGGGCCAGCACGGGTAAATTCAACGCTCGTGCTTTGGCTTCGCTCATCATCATTACCGCAGCTGCGCCATCGTTTATGGATGATGCATTACCC  >  NC_000913/2984568‑2984864

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: ‑