Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NC_000913	3,875,532	0	A	T	28.6%	48.9 / 12.2	28	H32L (CAT→CTT)	yidX	putative lipoprotein YidX
Reads supporting (aligned to +/- strand):  ref base A (9/11);  new base T (8/0);  total (17/11)
Fisher's exact test for biased strand distribution p-value = 9.68e-03
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 9.72e-01
Rejected as consensus: Frequency below/above cutoff threshold.

GTACTACAATTTAGATCACAAAAAGAACAATGCATAAAAAAATGACATGCGTCGGGCAGAAATCTGAAAAGGGATATCAGGCGCTAAACAGGAGGGAAAGAAGAGTATGCTTTCAACGGCTTAGCTACTCGTTTAAAGGATTAATCATGAAGTTGAATTTTAAGGGATTTTTTAAGGCTGCCGGTTTATTCCCACTGGCGCTGATGCTTTCAGGCTGTATCTCGTATGCTCTGGTTTCCCATACCGCAAAGGGTAGTTCAGGAAAGTATCAATCGCAGTCAGACACCATCACTGGGCTATCGCAGGCAAAAGATAGTAATGGAACAAAAGGCTATGTTTTTGTAGGGGAATCGCTGGATTACCTTATCACTG‑ATGGTGCCGATGACATCGTTAAGATGCTCAATGATCCAGCACTTAACCGGCACAATATTCAGGTTGCCGATGACG  >  NC_000913/3875292‑3875738                                                                                                                                                                                                                                                 |                                                                                                                                                                                                                gtACTACAATTTAGATCACAAAAAGAACAATGCATAAAAAAATGACATGCGTCGGGCAGAAATCTGAAAAGGGATAGCAGGCGCTAAACAGGAGGGAAAGAAGAGTATGCTTTCAACGGCTTAGCTACTCGTTTAAAGGATTAATCATGAAGTTGAATTTTAAGGGATTTTTTAAGGCTGCCGGTTTATTCCCACTGGCGCTGATGCTTTCAGGCTGTATCTCGTATGCTCTGGTTTCCCATACCGCAAAg                                                                                                                                                                                                       <  1:40486/251‑1 (MQ=255)                             aaTGCATAAAAAAATGACATGCGTCGGGCAGAAATCTGAAAAGGGATATCAGGCGCTAAACAGGAGGGAAAGAAGAGTATGCTTTCAACGGCTTAGCTACTCGTTTAAAGGATTAATCATGAAGTTGAATTTTAAGGGATTTTTTAAGGCTGCCGGTTTATTCCCACTGGCGCTGATGCTTTCAGGCTGTATCTCGTATGCTCTGGTTTCCCTTACCGCAAAGGGTAGTTCAGGAAAGTATCAATCGCAGt                                                                                                                                                                           >  1:395919/1‑251 (MQ=255)                                                                  gAAAAGGGATATCAGGCTCTAAACAGGAGGGAAAGAAGAGTATGCTTTCAACGGCTTAGCTACTCGTTTAAAGGATTAATCATGAAGTTGAATTTTAAGGGATTTTTTAAGGCTGCCGGTTTATTCCCACTGGCGCTGATGCTTTCAGGCTGTATCTCGTATGCTCTGGTTTCCCATACCGCAAAGGGTAGTTCAGGAAAGTATCAATCGCAGTCAGACACCATCACTGGGCTATCGCAGGCAAAAGATa                                                                                                                                       <  2:95767/250‑1 (MQ=255)                                                                    aaaGGGATATCAGGCGCTAAACAGGAGGGAAAGAAGAGTATGCTTTCAACGGCTTAGCTACTCGTTTAAAGGATTAATCATGAAGTTGAATTTTAAGGGATTTTTTAAGGCTGCCGGTTTATTCCCACTGGCGCTGATGCTTTCAGGCTGTATCTCGTATGCTCTGGTTTCCCATACCGCAAAGGGTAGTTCAGGAAAGTATCAATCGCAGTCAGACACCATCACTGGGCTATCGCAGGCAAAAGATAGTa                                                                                                                                    <  1:300212/251‑1 (MQ=255)                                                                               aggtgcTAAACAGGAGGGAAAGAAGAGTATGCTTTCAACGGCTTAGCTACTCATTTAAAGGATTAATCATGAAGTTGAATTTTAAGGGATATTTTAAGGCGGCCGGTTTATTCCCACTGGCGCTGATGCTTTCAGGCTGTATCTCGTATGCTCTGGTTTCCCAGACCGCAAAGGGTAGTTCAGGAAAGTATTAATCGCAGTCAGACACCATCACTGGGCTATCGCAGGCAAAAGATAGTAATGGTACaaaa                                                                                                                         <  2:367808/247‑1 (MQ=255)                                                                                  cgatAAACAGGAGGAAAAGAAGAGTATGCTTTCAACGACTTAGCTACTCGTTAAAAGGATTAATTATGAAGATGAAGTTTAAGGGATTTTTGAAGGCTGCCAGTTTATTCCCGCAGGCGCTGATGCTGTCAGGCTGTATCTCGTATGCTCTGGTTTCCCATACCGCAAAGGGTAGTTCAGGAAAGTATCAATCGCAGTCAGACTCCAGCACTGGGCTATCGCAGGCAAAAGATAGTAATGGAACAAAAGGc                                                                                                                      <  1:261832/248‑1 (MQ=255)                                                                                   gcTAAACAGGAGGGAAAGAAGAGTATGCTTTCAACGGCTTAGCTACTCGTTTAAAGGATTAATCATGAAGTTGAATTTTAAGGGATTTTTTAAGGCTGCCGGTTTATTCCCACTGGCGCTGATGCTTTCAGGCTGTATCTCGTATGCTCTGGTTTCCCATACCGCAAAGGGTAGTTCAGGAAAGTATCAATCGCAGTCAGACACCATCACTGGGCTATCGCAGGCAAAAGATAGTAATGGAACAAAAGGCt                                                                                                                     >  2:86589/1‑251 (MQ=255)                                                                                      aaaCAGGAGGGAAAGAAGAGTATGCTTTCAACGGCTTAGCTACTCGTTTAAAGGATTAATCATGAAGTTGAATTTTAAGGGATTTTTTAAGGCTGCCGGTTTATTCCCACTGGCGCTGATGCTTTCAGGCTGTATCTCGTATGCTCTGGTTTCCCATACCGCAAAGGGTAGTTCAGGAAAGTATCAATCGCAGTCAGACACCATCACTGGGCTATCGCAGGCAAAAGATAGTAATGGAACAAAAGGCTAt                                                                                                                   <  1:86589/250‑1 (MQ=255)                                                                                                gAAAGAAGAGTATGCTTTCAACGGCTTAGCTACTCGTTTAAAGGATTAATCATGAAGTTGAATTTTAAGGGATTTTTTAAGGCTGCCGGTTTATTCCCACTGGCGCTGATGCTTTCAGGCTGTATCTCGTATGCCGTCTTCTGCTTTACAACAAAGGGTAGTTCAGGAAAGTATCAATCGCAGTCAGACACCATCACTGGGCTATCGCAGGCAAAAGATAGTAATGGAACAAAAGGCTATGTTTTTGTAgg                                                                                                        >  1:141770/1‑251 (MQ=255)                                                                                                  aagaagAGTATGCTTTCAACGGCTTAGCTACTCGTTTAAAGGATTAATCATGAAGTTGAATTTTAAGGGATTTTTTAAGGCTGCCGGTTTATTCCCACTGGCGCTGATGCTTTCAGGCTGTATCTCGTATGCCGTCTTCTGCTTGAAAAAAAAGGGTAGTTCAGGAAAGTATCAATCGCAGTCAGACACCATCACTGGGCTATCGCAGGCAAAAGATAGTAATGGAACAAAAGGCTATGTTTTTGTAgggg                                                                                                      >  1:349944/1‑251 (MQ=255)                                                                                                              cTTTCAACGGCTTAGCTACTCGTTTAAAGGATTAATCATGAAGTTGAATTTTAAGGGATTTTTTAAGGCTGCCGGTTTATTCCCACTGGCGCTGATGCTTTCAGGCTGTATCTCGTATGCCGTCTTCTGCTTGAAAAAAAAATGAAGATCAGGAAAAAATCAATCGCAGACAGACACCATCAATGGGCTATCGCAGGCAAAAGACAGTAATGGAACAAATTCATATGTTCTTAAAGAGGAATCGCTGGAtt                                                                                          >  1:388606/1‑251 (MQ=255)                                                                                                                        cTTAGCTACTCGTTTAAAGGATTAATCATGAAGTTGAATTTTAAGGGATTTTTTAAGGCTGCCGGTTTATTCCCACTGGCGCTGATGCTTTCAGGCTGTATCTCGTATGCTCTGTTTTCCCTTACCGCAAAGGGTAGTTCAGGAAAGTATCAATCGCAGTCAGACACCATCACTGGGCTATCGCAGGCAAAAGATAGTAATGGAACAAAAGGCTATGTTTTTGTAGGGGAATCGCTGGATTACCTTATCAc                                                                                >  1:83627/1‑251 (MQ=255)                                                                                                                           aGCTACTCGTTTAAAGGATTAATCATGAAGTTGAATTTTAAGGGATTTTTTAAGGCTGCCGGTTTATTCCCACTGGCGCTGATGCTTTCAGGCTGTATCTCGTATGCTCTGGTTTCCCATACCGCAAAGGGTAGTTCAGGAAAGTATCAATCGCAGTCAGACACCATCACTGGGCTATCGCAGGCAAAAGATAGTAATGGAACAAAAGGCTATGTTTTTGTAGGGGAATCGCTGGATTACCTTATCACTg                                                                              >  1:255810/1‑250 (MQ=255)                                                                                                                                  cGTTTAAAGGATTAATCATGAAGTTGAATTTTAAGGGATTTTTTAAGGCTGCCGGTTTATTCCCACTGGCGCTGATGCTTTCAGGCTGTATCTCGTATGCCGTCTTCTGCTTGAAAAAAAAAAGAAGATCAGGAAAGTATAAATCACATTCAGACACCATCACTGGGATATCGCAGGCACAAGATAGTAATGTCACAAAAGACTATGCTTGTGTAGGGGATTCGCCGGAATACCTTAGCACCG‑Atagaga                                                                      >  1:372531/1‑245 (MQ=255)                                                                                                                                                aTCATGAAGTTGAATTTTAAGGGATTTTTTAAGGCTGCCGGTTTATTCCCACTGGCGCTGATGCTTTCAGGCTGTATCTCGTATGCTCTGGTTTCCCATACCGCAAAGGGTAGTTCAGGAAAGTATCAATCGCAGTCAGACACCATCACTGGGCTATCGCAGGCAAAAGATAGTAATGGAACAAAAGGCTATGTTTTTGTAGGGGAATCGCTGGATTACCTTATCACTG‑ATGGTGCCGATGACATCGTTa                                                        >  2:299371/1‑250 (MQ=255)                                                                                                                                                 tCATGAAGTTGAATTTTAAGGGATTTTTTAAGGCTGCCGGTTTATTCCCACTGGCGCTGATGCTTTCAGGCTGTATCTCGTATGCTCTGGTTTCCCATACCGCAAAGGGTAGTTCAGGAAAGTATCAATCGCAGTCAGACACCATCACTGGGCTATCGCAGGCAAAAGATAGTAATGGAACAAAAGGCTATGTTTTTGTAGGGGAATCGCTGGATTACCTTATCACTG‑ATGGTGCCGATGACATCGTTa                                                        >  1:20992/1‑249 (MQ=255)                                                                                                                                                       aGTTGAATTTTAAGGGATTTTTTAAGGCTGCCGGTTTATTCCCACTGGCGCTGATGCTTTCAGGCTGTATCTCGTATGCTCTGGTTTCCCATACCGCAAAGGGTAGTTCAGGAAAGTATCAATCGCAGTCAGACACCATCACTGGGCTATCGCAGGCAAAAGATAGTAATGGAACAAAAGGCTATGTTTTTGTAGGGGAATCGCTGGATTACCTTATCACTG‑ATGGTGCCGATGACATCGTTAAGATGCTc                                                >  2:216623/1‑251 (MQ=255)                                                                                                                                                                ttAAGGGATTTTTTAAGGCTGCCGGTTTATTCCCACTGGCGCTGATGCTTTCAGGCTGTATCTCGTATGCTCTGGTTTCCCATACCGCAAAGGGTAGTTCAGGAAAGTATCAATCGCAGTCAGACACCATCACTGGGCTATCGCAGGCAAAAGATAGTAATGGAACAAAAGGCTa                                                                                                                    <  1:103975/175‑1 (MQ=255)                                                                                                                                                                ttAAGGGATTTTTTAAGGCTGCCGGTTTATTCCCACTGGCGCTGATGCTTTCAGGCTGTATCTCGTATGCTCTGGTTTCCCATACCGCAAAGGGTAGTTCAGGAAAGTATCAATCGCAGTCAGACACCATCACTGGGCTATCGCAGGCAAAAGATAGTAATGGAACAAAAGGCTa                                                                                                                    >  2:103975/1‑175 (MQ=255)                                                                                                                                                                            ttacttcttcctttttATTCCCACTGGCGCTGATGCTTTCAGGCTGTATCTCGTATGCCCTGTTTTGCCTTACCACAAAGGGTAGCTCAGGAAAGTATCAATCGCAGTCAGACACCTTCACTGGGCTATCGCAGGCAAAAGATAGACATGTAACAAAAGGCTATGTTTTTGTAGGGGAATCGCTGGATTACCTTAT‑ACTTTCAGGAGCCGCTGCCATCGTTAAGATGCTCAATGATACAGCACTTAACCgg                           >  1:190004/14‑251 (MQ=255)                                                                                                                                                                                   tGCCGGTTTATTCCCACTGGCGCTGATGCTTTCAGGCTGTATCTCGTATGCTCTGGTTTCCCATACCGCAAAGGGTAGTTCAGGAAAGTATCAATCGCAGTCAGACACCATCACTGGGCTATCGCAGGCAAAAGATAGTAATGGAACAAAAGGCTATGTTTTTGTAGGGGCATCGCTGGATTACCTTATCACTG‑ATGGTGCCGATGACATCGTTAAGATGCTCAATGATCCAGCACTTAACCGGCACAat                     >  2:97558/1‑250 (MQ=255)                                                                                                                                                                                       ggtttataacaaCTGGCGCTTATGCTTTCAGGCTGTATCTCATATGCTCTGGTATCCCAAACCGCAAAGGGTAGTTCAGGAAAGTATCAATCGCAGTCAGACACCATCACTGGGCTATCGCAGGCAAAAGATAGTAATGGAACAAAAGGCTATGTTTTTGTAGGGGAAACTCTGGATTACCTTATCACTG‑ATGGTGCCGATGACATCGTTAAGATGCTCAATGATCCAGCACTTAACCGGCACAATATTCa                <  1:37045/240‑1 (MQ=255)                                                                                                                                                                                          ttATTCCCACTGGCGCTGATGCTTTCAGGCTGTATCTCGTATGCCCTGGTCTCCCTTACCGCAAAGGGTAGTTCAGGAAAGTATCAATCGCAGTCAGACACCATCACTGGGCTATCGCAGGCAAAAGATAGTAATGGAACAAAAGGCTATGTTTTTGTAGGGGAATCGCTGGATTACCTTATCACTG‑ATGGTGCCGATGACATCGTTAAGATGCTCAATGATCCAGCACTTAACCGGCACAATATTCAGGt             >  1:218137/1‑251 (MQ=255)                                                                                                                                                                                           tATTCCCACTGGCGCTGATGCTTTCAGGATGTATCTCGTATGCTCTGGTTTCCCATACCGCAAAGGGTAGTTCAGGAAAGTATCAATCGCAGTCAGACTCCATCACTGGGCTATCGCAGGCAAAAGATAGTAATGGAACAAAAGGCTATGTTTTTGTAGGGGAATCGCTGGATTACCTTATCAGTG‑ATGGTGCCGATGACATCGTTAAGATGCTCAATGATCCAGCACTTAACCGGCACAATATTGAGGt             <  2:141770/250‑1 (MQ=255)                                                                                                                                                                                                    gggCGCTGATGTTTTCAGGCTGTATCTCGTATGCTCTGGTTTCCCATACCGCAAAGGGTAGTTCAGGAAAGTATCAATCGCAGTCAGACACCATCACTGGGCTATCACAGGCAAAAGATAGTAATGGAACAAAAGGCTATGTTTTTGTAGGGGAATCGCTGGATTACCTTATCACTG‑ATGGTGCCGATGACATCGTTAAGATGCTCAATGATCCAGCACTTAACCGGCACAATATTCAGGTGGCCGAttac   <  2:234123/250‑4 (MQ=255)                                                                                                                                                                                                     ggCGCTGATGCTTTCAGGCTGTATCTCGTATGCTCTGGTTTCCCATACCGCAAAGGGTAGTTCAGGAAAGTATCAATCGCAGTCAGACACCATCACTGGGCTATCGCAGGCAAAAGATAGTAATGGAACAAAAGGCTATGTTTTTGTAGGGGAATCGCTGGATTACCTTATCACTG‑ATGGTGCCGATGACATCGTTAAGATGCTCAATGATCCAGCACTTAACCGGCACAATATTCAGGTTGCCGATGACg  >  1:79018/1‑251 (MQ=255)                                                                                                                                                                                                         cTGATGCTTTCAGGCTGTATCTCGTATGCTCTGGTTTCCCATACCGCAAAGGGTAGTTCAGGAAAGTATCAATCGCAGTCAGACACCATCACTGGGCTATCGCAGGCAAAAGATAGTAATGGAACAAAAGGCTATGTTTTTGTAGGGGAATCGCTGGATTACCTTATCACTG‑ATGGTGCCGATGACATCGTTAAGATGCTCAATGATCCAGCACTTAACCGGCACAATATTCAg               >  2:17658/1‑234 (MQ=255)                                                                                                                                                                                                         cTGATGCTTTCAGGCTGTATCTCGTATGCTCTGGTTTCCCATACCGCAAAGGGTAGTTCAGGAAAGTATCAATCGCAGTCAGACACCATCACTGGGCTATCGCAGGCAAAAGATAGTAATGGAACAAAAGGCTATGTTTTTGTAGGGGAATCGCTGGATTACCTTATCACTG‑ATGGTGCCGATGACATCGTTAAGATGCTCAATGATCCAGCACTTAACCGGCACAATATTCAg               <  1:17658/234‑1 (MQ=255)                                                                                                                                                                                                                                                 |                                                                                                                                                                                                                GTACTACAATTTAGATCACAAAAAGAACAATGCATAAAAAAATGACATGCGTCGGGCAGAAATCTGAAAAGGGATATCAGGCGCTAAACAGGAGGGAAAGAAGAGTATGCTTTCAACGGCTTAGCTACTCGTTTAAAGGATTAATCATGAAGTTGAATTTTAAGGGATTTTTTAAGGCTGCCGGTTTATTCCCACTGGCGCTGATGCTTTCAGGCTGTATCTCGTATGCTCTGGTTTCCCATACCGCAAAGGGTAGTTCAGGAAAGTATCAATCGCAGTCAGACACCATCACTGGGCTATCGCAGGCAAAAGATAGTAATGGAACAAAAGGCTATGTTTTTGTAGGGGAATCGCTGGATTACCTTATCACTG‑ATGGTGCCGATGACATCGTTAAGATGCTCAATGATCCAGCACTTAACCGGCACAATATTCAGGTTGCCGATGACG  >  NC_000913/3875292‑3875738

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 14 ≤ ATCG/ATCG < 16 ≤ ATCG/ATCG < 34 ≤ ATCG/ATCG < 39 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑