Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NC_000913_3_bme_pgi	2,866,487	0	G	C	22.9%	74.1 / 20.8	35	intergenic (+22/+72)	ygbN/rpoS	putative transporter/RNA polymerase, sigma S (sigma 38) factor
Reads supporting (aligned to +/- strand):  ref base G (15/12);  new base C (4/4);  total (19/16)
Fisher's exact test for biased strand distribution p-value = 1.00e+00
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 6.96e-01
Rejected as consensus: Frequency below/above cutoff threshold.

TCTGGATTGTGACCAAATATCTGGGGTTGTCGGTAGCAGACGGTCTGAAAACCTGGACAGTGTTAACGACCATTCTCGGTTTTACCGGATTCTTAATTACCTGGTGCGTATGGGCGGTAATTTGACCTTAATAAAAAGGTCCGATGGGCATCGGACCTTTTATTGTGCACAGAAAAGGCCAGCCTCGCTTGAGACTGGCCTTTCTGACAGATGCTTACTTACTCGCGGAACAGCGCTTCGATATTCAGCCCCTGCGTTTGCAGGATTTCGCGCAAACGGCGCAGGCCT  >  NC_000913_3_bme_pgi/2866341‑2866628                                                                                                                                                   |                                                                                                                                              tCTGGATTGTGACCAAATATCTGGGGTTGTCGGTAGCAGACGGTCTGAAAACCTGGACAGTGTTAACGACCATTCTCGGTTTTACCGGATTCTTAATTACCTGGTGCGTATGGGCGGTAATTTGACCTTAATAAAAAGGTCCGATGGGCa                                                                                                                                            >  2:403162/1‑150 (MQ=255)  cTGGATTGTGACCAAATATCTGGGGTTGTCGGTAGCAGACGGTCTGAAAACCTGGACAGTGTTAACGACCATTCTCGGTTTTACCGGATTCTTAATTACCTGGTGCGTATGGGCGGTAATTTGACCTTAATAAAAAGGTCCGATGGGCAt                                                                                                                                           >  3:78795/1‑150 (MQ=255)    ggATTGTGACCAAATATCTGGGGTTGTCGGTAGCAGACGGTCTGAAAACCTGGACAGTGTTAACGACCATTCTCGGTTTTACCGGATTCTTAATTACCTGGTGCGTATGGGCGGTAATTTGACCTTAATAAAAAGGTCCGATGGGCATCg                                                                                                                                         >  3:276656/1‑150 (MQ=255)     gATTGTGACCAAATATCTGGGGTTGTCGGTAGCAGACGGTCTGAAAACCTGGACAGTGTTAACGACCATTCTCGGTTTTACCGGATTCTTAATTACCTGGTGCGTATGGGCGGTAATTTGACCTTAATAAAAAGGTCCGATGGGCAt                                                                                                                                           >  4:289387/1‑147 (MQ=255)     gATTGTGACCAAATATCTGGGGTTGTCGGTAGCAGACGGTCTGAAAACCTGGACAGTGTTAACGACCATTCTCGGTTTTACCGGATTCTTAATTACCTGGTGCGTATGGGCGGTAATTTGACCTTAATAAAAAGGTCCGATGGGCAt                                                                                                                                           <  3:289387/147‑1 (MQ=255)      aTTGTGACCAAATATCTGGGGTTGTCGGTAGCAGACGGTCTGAAAACCTGGACAGTGTTAACGACCATTCTCGGTTTTACCGGATTCTTAATTACCTGGTGCGTATGGGCGGTAATTTGACCTTAATAAAAAGGTCCGATGGGCATCGGa                                                                                                                                       >  3:229715/1‑150 (MQ=255)           gACCAAATATCTGGGGTTGTCGGTAGCAGACGGTCTGAAAACCTGGACAGTGTTAACGACCATTCTCGGTTTTACCGGATTCTTAATTACCTGGTGCGTATGGGCGGTAATTTGACCTTAATAAAAAGGTCCGATGGGCATCGGACCttt                                                                                                                                  >  2:192590/1‑150 (MQ=255)            acaaaaTATCTGTGGTTGTCGCTAGCAGACGGTCTGAAAACCTGGACAGTGTTAACGACCATTCTCGGTTTTACCGGATTCTTAATTACCTGGTGCGTATGGGCGGTAATTTGACCTTAATAAAAATGTCCGATGCCCATCGGACCtttt                                                                                                                                 <  2:327265/147‑1 (MQ=255)                 atatCTGGGGTTGTCGGTAGCAGACGGTCTGAAAACCTGGACAGTGTTAACGACCATTCTCGGTTTTACCGGATTCTTAATTACCTGGTGCGTATGGGCGGTAATTTGACCTTAATAAAAAGGTCCGATGGGCATCGGACCTTTTATtgt                                                                                                                            <  1:192590/150‑1 (MQ=255)                                      aGACGGTCTGAAAACCTGGACAGTGTTAACGACCATTCTCGGTTTTACCGGATTCTTAATTACCTGGTGCGTATGGGCGGTAATTTGACCTTAATAAAAAGGTCCGATGCCCATCGGACCtt                                                                                                                                   >  4:116906/1‑122 (MQ=255)                                      aGACGGTCTGAAAACCTGGACAGTGTTAACGACCATTCTCGGTTTTACCGGATTCTTAATTACCTGGTGCGTATGGGCGGTAATTTGACCTTAATAAAAAGGTCCGATGCCCATCGGACCtt                                                                                                                                   <  3:116906/122‑1 (MQ=255)                                      aGACGGTCTGAAAACCTGGACAGTGTTAACGACCATTCTCGGTTTTACCGGATTCTTAATTACCTGGTGCGTATGGGAGGTAATTTGACCTTAATAAAAAGGTCCGATGGGCATCGGACCTTTTATTGTGCACAGAAAAGGCCAGCCTCg                                                                                                       >  3:218608/1‑150 (MQ=255)                                         cGGTCTGAAAACCTGGACAGTGTTAACGACCATTCTCGGTTTTACCGGATTCTTAATTACCTGGTGCGTATGGGCGGTAATTTGACCTTAATAAAAAGGTCCGATGGGCATCGGACCTTTTATTGTGCACAGAAAAGGCCAGtctcaagc                                                                                                    <  2:165291/150‑5 (MQ=255)                                              tGAAAACCTGGACAGTGTTAACGACCATTCTCGGTTTTACCGGATTCTTAATTACCTGGTGCGTATGGGCGGTAATTTGACCTTAATAAAAAGGTCCGATGGGCATCGGACCtt                                                                                                                                   <  4:16444/114‑1 (MQ=255)                                              tGAAAACCTGGACAGTGTTAACGACCATTCTCGGTTTTACCGGATTCTTAATTACCTGGTGCGTATGGGCGGTAATTTGACCTTAATAAAAAGGTCCGATGGGCATCGGACCtt                                                                                                                                   >  3:16444/1‑114 (MQ=255)                                               gAAAACCTGGACAGTGTTAACGACCATTCTCGGTTTTACCGGATTCTTAATTACCTGGTGCGTATGGGCGGTAATTTGACCTTAATAAAAAGGTCCGATGGGCATCGGACCTTTTATTGTGCACAGAAAAGGCCAGCCTCGCTTGAGACt                                                                                              >  4:83353/1‑150 (MQ=255)                                                aaaaCCTGGACAGTGTTAACGACCATTCTCGGTTTTACCGGATTCTTAATTACCTGGTGCGTATGGGCGGTAATTTGACCTTAATAAAAAGGTCCGATGGGCATCGGACCTTTTATTGTGCACAGAAAAGGCCAGCCTCGCTTGAGACTg                                                                                             <  4:78795/150‑1 (MQ=255)                                                 aaaCCTGGACAGTGTTAACGACCATTCTCGGTTTTACCGGATTCTTAATTACCTGGTGCGTATGGGCGGTAATTTGACCTTAATAAAAAGGTCCGATGGGCATCGGACCTTTTATTGTGCACAGAAAAGGCCAGCCTCGCTTGAGACTgg                                                                                            <  1:403162/150‑1 (MQ=255)                                                       ggACAGTGTTAACGACCATTCTCGGTTTTACCGGATTCTTAATTACCTGGTGCGTATGGGCGGTAATTTGACCTTAATAAAAAGGTCCGATGGGCATCGGACCTTTTATTGTGCACAGAAAAGGCCAGCCTCGCTTGAGACTGGCCTTTc                                                                                      <  3:83353/150‑1 (MQ=255)                                                                    gACCATTCTCGGTTTTACCGGATTCTTAATTACCTTGTGCGTATGGGCGGTAATTTGACCTTAATAAAAAGGACCGATGGGCATCGGACCTTTTATTGTGCACAGAAAAGGCCAGCCTCGCTTGAGACTGGCCTTTCTGACAGATGctta                                                                         >  3:142663/1‑150 (MQ=255)                                                                              ggTTTTACCGGATTCTTAATTACCTGGTGCGTATGGGCGGTAATTTGACCTTAATAAAAAGGTCCGATGCCCATCGGAc                                                                                                                                      >  1:359497/1‑79 (MQ=39)                                                                              ggTTTTACCGGATTCTTAATTACCTGGTGCGTATGGGCGGTAATTTGACCTTAATAAAAAGGTCCGATGCCCATCGGAc                                                                                                                                      <  2:359497/79‑1 (MQ=39)                                                                               gTTTTACCGGATTCTTAATTACCTGGTGCGTATGGGCGGTAATTTGACCTTAATAAAAAGGTCCGATGGGCATCGGACCTTTTATTGTGCACAGAAAAGGCCAGCCTCGCTTga                                                                                                  <  3:5284/114‑1 (MQ=255)                                                                               gTTTTACCGGATTCTTAATTACCTGGTGCGTATGGGCGGTAATTTGACCTTAATAAAAAGGTCCGATGGGCATCGGACCTTTTATTGTGCACAGAAAAGGCCAGCCTCGCTTga                                                                                                  >  4:5284/1‑114 (MQ=255)                                                                                  ttACCGGATTCTTAATTACCTGGTGCGTATGGGCGGTAATTTGACCTTAATAAAAAGGTCCGATGGGCATCGGACCTTTTATTGTGCACAGAAAAGGCCa                                                                                                             >  4:1291/1‑100 (MQ=255)                                                                                  ttACCGGATTCTTAATTACCTGGTGCGTATGGGCGGTAATTTGACCTTAATAAAAAGGTCCGATGGGCATCGGACCTTTTATTGTGCACAGAAAAGGCCa                                                                                                             <  3:1291/100‑1 (MQ=255)                                                                                              tAATTACCTGGTGCGTATGGGCGGTAATTTGACCTTAATAAAAAGGTCCGATGGGc                                                                                                                                             >  3:78024/1‑56 (MQ=255)                                                                                              tAATTACCTGGTGCGTATGGGCGGTAATTTGACCTTAATAAAAAGGTCCGATGGGc                                                                                                                                             <  4:78024/56‑1 (MQ=255)                                                                                                                             aCCTTAATAAAAAGGTCCGATGGGCATCGGACCTTTTATTGTGCACAGAAAAGGCCAGCCTCGCTTGAGACTGGCCTTTCTGACAGATGCTTACTTACTCGCGGAACAGCGCTTCGATATTCAGCCCCTGCGTTTGCAGGATTTCGCGCa                >  3:201101/1‑150 (MQ=255)                                                                                                                                   aataaaaGGTCCGATGCCCATCGGACCTTTTATTGTGCACAGAAAAGGCCAGCCTCGCTTGAGACTGGCCTTTCTGACAGATGCTTACTTACTCGCGGAACAGCGCTTCGATATTCAGCCCCTGCGt                                 >  4:281481/4‑127 (MQ=255)                                                                                                                                   aataaaaGGTCCGATGCCCATCGGACCTTTTATTGTGCACAGAAAAGGCCAGCCTCGCTTGAGACTGGCCTTTCTGACAGATGCTTACTTACTCGCGGAACAGCGCTTCGATATTCAGCCCCTGCGt                                 <  3:281481/124‑1 (MQ=255)                                                                                                                                       aaaGGTCCGATGGGCATCGGACCTTTTATTGTGCACAGAAAAGGCCAGCCTCGCTTGAGACTGGCCTTTCTGACAGATGCttacttac                                                                    >  2:405596/1‑88 (MQ=255)                                                                                                                                       aaaGGTCCGATGGGCATCGGACCTTTTATTGTGCACAGAAAAGGCCAGCCTCGCTTGAGACTGGCCTTTCTGACAGATGCttacttac                                                                    <  1:405596/88‑1 (MQ=255)                                                                                                                                         aGGTCCGATGGGCATCGGACCTTTTATTGTGCACAGAAAAGGCCAGCCTCGCTTGAGACTGGCCTTTCTGACAGATGCTTACTTACTCGCGGAACAGCGCTTCGATATTCAGCCCCTGCGTTTGCAGGATTTCGCGCAAACGGCGCAGGc    <  4:218608/150‑1 (MQ=255)                                                                                                                                           gTCCGATGCCCATCGGACCTTTTATTGTGCACAGAAAAGGCCAGCCTCGCTTGAGACTGGCCTTTCTGACAGATGCTTACTTACTCGCGGAACAGCGCTTCGATATTCAGCCCCTGCGTTTGCAGGATTTCGCGCAAACGGCGCAGGCCt  >  2:361564/1‑150 (MQ=255)                                                                                                                                                   |                                                                                                                                              TCTGGATTGTGACCAAATATCTGGGGTTGTCGGTAGCAGACGGTCTGAAAACCTGGACAGTGTTAACGACCATTCTCGGTTTTACCGGATTCTTAATTACCTGGTGCGTATGGGCGGTAATTTGACCTTAATAAAAAGGTCCGATGGGCATCGGACCTTTTATTGTGCACAGAAAAGGCCAGCCTCGCTTGAGACTGGCCTTTCTGACAGATGCTTACTTACTCGCGGAACAGCGCTTCGATATTCAGCCCCTGCGTTTGCAGGATTTCGCGCAAACGGCGCAGGCCT  >  NC_000913_3_bme_pgi/2866341‑2866628

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 12 ≤ ATCG/ATCG < 32 ≤ ATCG/ATCG < 41 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑