Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NC_000913	1,222,233	0	G	A	46.4%	17.0 / 12.9	28	pseudogene (60/75 nt)	ycgH	pseudogene; putative ATP‑binding component of a transport system
Reads supporting (aligned to +/- strand):  ref base G (12/3);  new base A (0/13);  total (12/16)
Fisher's exact test for biased strand distribution p-value = 1.54e-05
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 9.40e-01

GTGAAAGTCGAACAAGATGGGGCGAGTAATTTGGGGGAAATTAAACTTGGCGTAAATGGCAACCTGAATCCAGCGG‑CCAGCGTCTGGGGAATGTGGGCGTGCAGCTGGGTGATAATGGCTACAATGACACCGCAGTGATGGTGGGCCTGAAATATAAGTTCTGATCCCGCCGTTAGCTAAAAAACCGCGTCGTATTCATCGACGCGGTACATATGAAATATTATTTTTTGCCGATAGCACGCATGGTGTCATCAATTGCCGTGATCAACAGCATTTGCGGGTCTTTAG  >  NC_000913/1222085‑1222372                                                                                                                                                      |                                                                                                                                            gtgAAAGTCGAACAAGATGGGGCGAGTAATTTGGGGGAAATTAAACTTGGCGTAAATGGCAACCTGAATCCAGCGG‑CCAGCGTCTGGGGAATGTGGGCGTGCAGCTGGGTGATAATGGCTACAATGACACCGCAGTGATGGTGGGCCTGa                                                                                                                                            >  2:104285/1‑150 (MQ=255)                           tAATTTGGGGGAAATTAAACTTGGCGTAAATGGCAACCTGAATACAGCGG‑CCAGCGTCTGGGGAATGTGGGCGTGCAGCTGGGTGATAATGGCTACAATGACACCGCAGTGATGGTGGGCCTGAAATATAAGTTCTGATCCCGCCGTTAGc                                                                                                                 >  2:282391/1‑151 (MQ=255)                            aaTTTGGGGGAAATTAAACTTGGCGTAAATGGCAACCTGAATCCAGCGG‑CCAGCGTCTGGGGAATGTGGGCGTGCAGCTGGGTGATAATGGCTACAATGACACCGCAGTGATGGTGGGCCTGAAATATAAGTTCTGATCCCGCCGTTAGCt                                                                                                                >  2:647859/1‑151 (MQ=255)                                           aaccTTGGCAAAAAGGGCACCCAGAA‑CCCGCGGCCCAGCTTATGGGGAGTGTGGGCGTGCAGCTGGTTGAAAATGGCAACACTCCCCCCCCGGTGAGGGTCGGCCTAAAATAAACTTCCTCATCCCGCCGTTAGCTAAAAAACCGcgt                                                                                                    <  2:66924/145‑1 (MQ=255)                                           aaaCTTGGCGTAAAGGGCACCCTGAATCCAGCGG‑CCAGCGTGGGGGGAATGGGGGCGTGCAGCGGGGTGATAAGGGCTACAATGACCCCGCAGTGATGGTGGGCCTGAAATATAAGTTCTGACCCCGCCGTTAGCTAAAAAACCGcgtcg                                                                                                  <  1:446967/150‑1 (MQ=255)                                           aaaCTGGGCGAAAAGGGCACCCTGAACCCGGCGG‑CCGGCGTCGGGGAAATGGGGGGGTGCAGCTGGGTAATAATGGCTAAAATGACCCCGAAGTGAGGGTGGGCCTAAAATATAATTTCTGACCCCGCCGTTAGCTAAAAAACCGcgtcgt                                                                                                 <  1:296186/151‑1 (MQ=255)                                                tGGCGTAAATGGCAACCTGAATCCAGCGG‑CCAGCGTCTGGGGAATGTGGGCGTGCAGCTGGGTGATAATGGCTACAATGACACCGCAGTGATGGTGGGCCTGAAATATAAGTTCTGATCCCGCCGTTAGCTAAAAAACCGCGTCGTATTc                                                                                             >  1:265311/1‑150 (MQ=255)                                                  gCGTAAATGGCAACCTGAATCCAGCGG‑CCAGCGTCTGGGGAATGTGGGCGTGCAGCTGGGTGATAATGGCTACAATGACACCGCAGTGATGGTGGGCCTGAAATATAAGTTCTGATCCCGCCGTTAGCTAAAAAACCGCGTCGTATTCATc                                                                                          >  1:29179/1‑151 (MQ=255)                                                      aaaTGGCACCCTGAATCCGGCGG‑CCAGCGTCGGGGGAATGGGGGCGTGCAGCGGGGTGATAATGGCTACAATGACCCCGCGGTGAGGGTGGGCCTAAAATATAAGTTCTGACCCCGCCGTTAGCTAAAAAACCGCGTCGTATTCATCGAcg                                                                                      <  1:204352/151‑1 (MQ=255)                                                      aaaTGGCAACCTGAACCCAGCGG‑CCAGCGTCGGGGGAATGTGGGCGTGCAGCGGGGTGATAATGGCTACAATGACCCCGCAGTGAGGGTGGGCCTAAAATATAAGTTCTGATCCCGCCGTTAGCTAAAAAACCGCGTCGTATTCATCGa                                                                                        <  1:711207/149‑1 (MQ=255)                                                       aatgcaacccTAAACCCGGCGG‑CCAGCGTCTGGGGATGGGGGGGGTGCAGCTGGGTAATAAGGCCTAAAACGCCCCCGCAGTGATGGTGGGCCTAAAATATAATTTCTGATCCCGCCGTTAGCTAAAAAACCGCGTCGTATTCATCGAcgc                                                                                     <  1:50758/143‑1 (MQ=255)                                                                           gg‑CCAGCGTCTGGGGAATGTGGGCGTGCAGCTGGGTGATAATGGCTACAATGACACCGCAGTGATGGTGGGCCTGAAATATAAGTTCTGATCCCGCCGTTAGCTAAAAAACCGCGTCGTATTCATCGACGCGGTACATATGAAATattatt                                                                 >  2:328043/1‑151 (MQ=255)                                                                                    tCTGGGGAATGTGGGCGTGCAGCTGGGTGATAATGGCTACAATGACACCGCAGTGATGGTGGGCCTGAAATATAAGTTCTGATCCCGCCGTTAGCTAAAAAACCGCGTCGTATTCATCGACGCGGTACATATGAAATATTATTTTTTGCCg                                                         >  2:109166/1‑151 (MQ=255)                                                                                      tGGGGAATGTGGGCGTGCAGCTGGGTGATAATGGCTACAATGACACCGCAGTGATGGTGGGCCTGAAATATAAGTTCTGATCCCGCCGTTAGCTAAAAAACCGCGTCGTATTCATCGACGCGGTACATATGAAATATTATTTTTTGCCGAt                                                       >  1:192618/1‑151 (MQ=255)                                                                                       ggggATTGGGGGGGTGCAGTTGGGAAAAAATGGCTACAATGACACCGAGGTTATGGTGGGCATGAAATAAATTTTCTGATCCCGCCGTTAGCTAAAAAACCGCGTCGTATTCATCGACGCGGTACATATGAAATATTATTTTTTg                                                            <  2:422005/145‑1 (MQ=255)                                                                                         ggAATGTGGGCGTGCAGCTGGGTGATAATGGCTACCATGACACCGCAGTGATGGTGGGCCTGAAATATAAGTTCTGATCCCGCCGTTAGCTAAAAAACCGCGTCGTATTCATCGACGCGGTCCATATGAAATATTATTTTTTGCCGATAGc                                                    >  2:359606/1‑151 (MQ=255)                                                                                              gtgGGGGGGCAGTGGGGTGATAATGTCTACAATCACCCCGAGGTGGTGGGGGTCCTAAAATATAATTTCTGACCCCGCCGTTAGCTAAAAAACCGCGTCGTATTCATCGACGCGGTACATATGAAATATTATTTTTTGCCGATAGc                                                    <  2:56036/146‑1 (MQ=255)                                                                                              gggggCGTGCAGTTGGGTAATAAGGGATACAATGCCCCCGTAGAGGGGGGGGGCCTAAATGATAATTGCGGTTCCCGCCGTTAGCTAAAAAACCGCGTCGTATTCATCGACGCGGTACATATGAAATATTATTTTTTGCCGATAGCACGCa                                               <  2:121578/149‑1 (MQ=255)                                                                                                    gTGCAGCTGGGTGATAATGGCTACAATGACACCGCAGTGATGGTGGGCCTGAAATATAAGTTCTGATCCCGCCGTTAGCTAAAAAACCGCGTCGTATTCATCGACGCGGTACATATGAAATATTATTTTTTGCCGATAGCACGCATGgtgt                                         >  2:311266/1‑151 (MQ=255)                                                                                                    gTGCAGCTGGGTGATAATGGCTACAATGACACCGCAGTGATGGTGGGCCTGAAATATAAGTTCTGATCCCGCCGTTAGCTAAAAAACCGCGTCGTATTCATCGACGCGGTACATATGAAATATTATTTTTTGCCGATAGCACGCATGgtgt                                         >  1:247681/1‑151 (MQ=255)                                                                                                                          aCAATGACCCCGGAGTGTGGGTGGCCTTAAAATATATTTTCTGATCCCGCCGTTAGCTAAAAAACCGCGTCGTATTCATCGACGCGGTACATATGAAATATTATTTTTTGCCGATAGCACGCATGGTGTCATCAATTGCCGTGATCAACa                    <  2:586715/150‑1 (MQ=255)                                                                                                                            aaTGACCCCGCAGTGAGGGGGGGCTAAAAATATAATTTCTGACCCCGCCGTTAGCTAAAAAACCGCGTCGTATTCATCGACGCGGTACATATGAAATATTATTTTTTGCCGATAGCACGCATGGTGTCATCAATTGCCGTGATCAACAGCa                 <  1:656142/151‑1 (MQ=255)                                                                                                                             aTGACCCCGCAGTGATGGGGGGCCTAAAATATAAGTTCTGACCCCGCCGTTAGCTAAAAAACCGCGTCGTATTCATCGACGCGGTACATATGAAATATTATTTTTTGCCGATAGCACGCATGGTGTCATCAATTGCCGTGATCAACAGCAt                <  1:93147/151‑1 (MQ=255)                                                                                                                             aTGACACCGCAGTGATGGTGGGCCTGAAATATAAGTTCTGATCCCGCCGTTAGCTAAAAAACCGCGTCGTATTCATCGACGCGGTACATATGAAATATTATTTTTTGCCGATAGCACGCATGGTGTCATCAATTGCCGTGATCAACAGCAt                >  2:620213/1‑151 (MQ=255)                                                                                                                                 cgcctaggttaTGGGGGTCCAGAAATAAATTTCCTGGTCCCGCCGTTAGCTAAAAAACCGCGTCGTATTCATCGACGCGGTACATATGAAATATTATTTTTTGCCGATAGCACGCATGGTGTCATCAATTGCCGTGATCAACAGCAt                <  2:425443/137‑1 (MQ=255)                                                                                                                                             ggtggCCATAAAATATATGTTCTGTTCCCGCCGTTAGCTAAAAAACCGCGTCGTATTCATCGACGCGGTACATATGAAATATTATTTTTTGCCGATAGCACGCATGGTGTCATCAATTGCCGTGATCAACAGCATTTGCGGGTCTTTa   <  1:185476/148‑1 (MQ=255)                                                                                                                                             ggggggCATAAAATATAAGTTCTGATCCCGCCGTTAGCTAAAAAACCGCGTCGTATTCATCGACGCGGTACATATGAAATATTATTTTTTGCCGATAGCACGCATGGTGTCATCAATTGCCGTGATCAACAGCATTTGCGGGTCTTTAg  <  1:622088/146‑1 (MQ=255)                                                                                                                                                gggCTTAAAATTTATCTTCTCATCCCGCCGTTAGCTAAAAAACCGCGTCGTATTCATCGACGCGGTACATATGAAATATTATTTTTTGCCGATAGCACGCATGGTGTCATCAATTGCCGTGATCAACAGCATTTGCGGGTCTTTa   <  2:590401/145‑1 (MQ=255)                                                                                                                                                      |                                                                                                                                            GTGAAAGTCGAACAAGATGGGGCGAGTAATTTGGGGGAAATTAAACTTGGCGTAAATGGCAACCTGAATCCAGCGG‑CCAGCGTCTGGGGAATGTGGGCGTGCAGCTGGGTGATAATGGCTACAATGACACCGCAGTGATGGTGGGCCTGAAATATAAGTTCTGATCCCGCCGTTAGCTAAAAAACCGCGTCGTATTCATCGACGCGGTACATATGAAATATTATTTTTTGCCGATAGCACGCATGGTGTCATCAATTGCCGTGATCAACAGCATTTGCGGGTCTTTAG  >  NC_000913/1222085‑1222372

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 12 ≤ ATCG/ATCG < 14 ≤ ATCG/ATCG < 31 ≤ ATCG/ATCG < 39 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑