Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NC_000913	1,222,233	0	G	A	46.5%	36.4 / 22.0	43	pseudogene (60/75 nt)	ycgH	pseudogene; putative ATP‑binding component of a transport system
Reads supporting (aligned to +/- strand):  ref base G (17/6);  new base A (0/20);  total (17/26)
Fisher's exact test for biased strand distribution p-value = 2.42e-07
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 9.88e-01

GTGAAAGTCGAACAAGATGGGGCGAGTAATTTGGGGGAAATTAAACTTGGCGTAAATGGCAACCTGAATCCAGCGGCCAGCGTCTGGGGAATGTGGGCGTGCAGCTGGGTGATAATGGCTACAATGACACCGCAGTGATGGTGGGCC‑TGAAATATAAGTTCTGATCCCGCCGTTAGCTAAAAAACCGCGTCGTATTCATCGACGCGGTACATATGAAATATTATTTTTTGCCGATAGCACGCATGGTGTCATCAATTGCCGTGATCAACAGCATTTGCGGGTCTTTAGCGCAAACC  >  NC_000913/1222085‑1222380                                                                                                                                                      |                                                                                                                                                    gtgAAAGTCGAACAAGATGGGGCGAGTAATTTGGGGGAAATTAAACTTGGCGTAAATGGCAACCTGAATCCAGCGGCCAGCGTCTGGGGAATGTGGGCGTGCAGCTGGGTGATAATGGCTACAATGACACCGCAGTGATGGTGGGCC‑TGaa                                                                                                                                                   <  2:1265874/151‑1 (MQ=255)         cGAACAAGATGGGGCGAGTAATTTGGGGGAAATTAAACTTGGCGTAAATGGCAACCTGAATCCAGCGGCCAGCGTCTGGGGAATGTGGGCGTGCAGCTGGGAGATAATGGCCACAATGACACCGCAGAGATGGTGGGCC‑TGAAATATAAGt                                                                                                                                           >  1:824862/1‑151 (MQ=255)          gAACAAGATGGGGCGAGTAATTTGGGGGAAATTAAACTTGGCGTAAATGGCAACCTGAATCCAGCGGCCAGCGTCTGGGGAATGTGGGCGTGCAGCTGGGTGATAATGGCTACAATGACACCGCAGTGATGGTGGGCC‑TGAAATATAAGtt                                                                                                                                          <  2:1191851/151‑1 (MQ=255)             cAAGATGGGGCGAGTAATTTGGGTGAAATTAAACTTGGCGTAAATGGCAACCTGAATCCAGCGGCCAGCGTCTGGGGAATGTGGGCGTGCAGCTGGGTGATAATGGCTACAATGACACCGCAGTGATGGCGGGCC‑TGAAATATAAGTTCTg                                                                                                                                       >  1:511872/1‑151 (MQ=255)             cAAGATGGGGCGAGTAATTTGGGGGAAATTAAACTTGGCGTAAATGGCAACCTGAATCCAGCGGCCAGCGTCTGGGGAATGTGGGCGTGCAGCTGGGTGATAATGGCTACAATGACACCGCAGTGATGGTGGGCC‑TGAAATATAAGTTCTg                                                                                                                                       <  2:411176/151‑1 (MQ=255)               aGATGGGGCGAGTAATTTGGGGGAAATTAAACTTGGCGTAAATGGCAACCTGAATCCAGCGGCCAGCGTCTGGGGAATGTGGGCGTGCAGCTGGGTGATAATGGCTACAATGACACCGCAGTGATGGTGGGCC‑TGAAATATAAGTTCTGAt                                                                                                                                     <  2:940308/151‑1 (MQ=255)                            aaTTTGGGGGAAATTAAACTTGGCGTAAATGGCAACCTGAATCCAGCGGCCAGCGTCTGGGGAATGTGGGCGTGCAGCTGGGTGATAATGGCTACAATGACACCGCAGTGATGGTGGGCC‑TGAAATATAAGTTCTGATCCCGCCGTTAGCt                                                                                                                        >  1:57299/1‑151 (MQ=255)                             aTTTGGGGGAAATTAAACTTGGCGTAAATGGCAACCTGAATCCAGCGGCCAGCGTCTGGGGAATGTGGGCGTGCAGCTGGGTGATAATGGCTACAATGACACCGCAGTGATGGTGGGCC‑TGAAATATAAGTTCTGATCCCGCCGTTAGCt                                                                                                                        >  2:380673/1‑150 (MQ=255)                                  gggaAAATTAATTTTGGGTAAAATGGCACCCTGACCCCGGCGGCCAGGTTCTGGGAAGTGTGGGTGTGCGGTGGGGTAAAAATGTCTACAAGCCCCCCGCAGTGTTGGTGGGCC‑TAAAAAAAATTTTCTGTTCCCGCCGTTAGCTaaaaaa                                                                                                                  <  1:795885/151‑1 (MQ=255)                                           aaccTTGGCGTAAATGCCACCCGGAACCCAGCGGCCGGCGTCTGGGAAATGTGGGCGTGCAGCTGGGTGATAATGCCAACAATCACCCCGCGTTGATGGTGGGCC‑TAAAATATAAGTTCTGATCCCGCCGTTAGCTAAAAAACCGcgtcg                                                                                                          <  2:1249643/147‑1 (MQ=255)                                           aaaCTTGGCGTAAAGGGCAACCTGAATCCAGCGGCCAGCGTCGGGGGAATGGGGGCGTGCAGCTGGGTAATAATGCCTCAAATGCCCCCGCAGTGAGGGTGGGCC‑TAAAATATAAGTTCTGATCCCGCCGTTAGCTAAAAAACCGcgtcgt                                                                                                         <  1:561176/151‑1 (MQ=255)                                              cTTGGCGTAAATGGCAACCTGAATCCAGCGGCCAGCGTCTGGGGAATGTGGGCGTGCAGCTGGGTGATAATGGCTACAATGACACCGCAGTGATGGTGGGCC‑TGAAATATAAGTTCTGATCCCGCCGTTAGCTAAAAAACCGCGCCGTAtt                                                                                                      >  2:113713/1‑151 (MQ=255)                                                   cGTAAATGGCAACCTGAATCCAGCGGCCAGCGTCTGGGGAATGTGGGCGTGCAGCTGGGTGATAATGGCTACAATGACACCGCAGTGATGGTGGGCC‑TGAAATATAAGTTCTGATCCCGCCGTTAGCTAAAAAACCGCGTCGTATTCATCg                                                                                                 >  1:1289260/1‑151 (MQ=255)                                                   cGTAAATGGCAACCTGAATCCAGCGGCCAGCGTCTGGGGAATGTGGGCGTGCAGCTGGGTGATAATGGCTACAATGACACCGCAGTGATGGTGGGCC‑TGAAATATAAGTTCTGATCCCGCCGTTAGCTAAAAAACCGCGTCGTATTCATCg                                                                                                 >  1:1124171/1‑151 (MQ=255)                                                    gTAAATGGCAACCTGAATCCAGCGGCCAGCGTCTGGGGAATGTGGGCGTGCAGCTGGGTGATAATGGCTACAATGACACCGCAGTGATGGTGGGCC‑TGAAATATAAGTTCTGATCCCGCCGTTAGCTAAAAAACCGCGTCGTATTCATCg                                                                                                 >  2:17128/1‑150 (MQ=255)                                                      aaaTGGCAACTTAAATCCAGCGCCGAGCGTCGGGGAAATGTGGGCGGGCAGGGGGGTGAAAATGCCTAAAATGCCCCCGTGGTGAGGGTGGGCC‑AAAAATAAAGTTTCAGTCCCCGCCGTTAGCTAAAAAACCGCGTCGTATTCATc                                                                                                  <  1:1115477/147‑1 (MQ=255)                                                      aaaGGGCAACCGGAACCCGGGGGCCAGCGTCTGGGGAAGGTGGGCGGGCAGTTGGGTGATAATGGCTACAATGACCCCGGAGTGAGGGTGGGCT‑TAAAATATAATTTCTGATCCCGCCGTTAGCTAAAAAACCGCGTCGTATTCATc                                                                                                  <  2:569481/147‑1 (MQ=255)                                                       aagggcacccaaacaccAGCGCCAAGGGTCGGGGAAAGGTGGGCGTGCTGCAGGGTAATATTGCTTAAAAGCGCCCCGCAGGGGTGGTGGACT‑TAAAATATAATTTCGAACCCCGCCGTTAGCTAAAAAACCGCGTCGTATTCATCGAcgc                                                                                             <  1:800548/136‑1 (MQ=255)                                                          ggaacccTAAACCCAGGGGCCGGGGTCGGGGGAAGGGGGGCGTGCAGCGGGGTGATAAGGGCTACAATGACACCGCGGTGATGGTGGGCT‑TAAAATATAAGTTCTGATCCCGCCGTTAGCTAAAAAACCGCGTCGTATTCATCGAcgcg                                                                                            <  2:293686/144‑1 (MQ=255)                                                              aCCTGAATCCAGCGGCCAGCGTCTGGGGAATGTGGGCGTGCAGCTGGGTGATAATGGCTACAATGACACCGCAGTGATGGTGGGCC‑TGAAATATAAGTTCTGATCCCGCCGTTAGCTAAAAAACCGCGTCGTATTCATCGACGCGGTACat                                                                                      >  1:382523/1‑151 (MQ=255)                                                               ccgaaaTCCAGCGGCCAGCGTGGGGGAAATGGGGGCGTGCTGTTGGGTGATAAGGGCTAAAATGACACCTAAGTGAGGGGGGGCT‑TAAAATATAATTTCTTTCCCCGCCGTTAGCTAAAAAACCGCGTCGTATTCATCGACGCGGTa                                                                                         <  2:967957/143‑1 (MQ=255)                                                               ccTGAATCCAGCGGCCAGCGTCTGGGGAATGTGGGCGTGCAGCTGGGTGATAATGGCTACAATGACACCGCAGTGATGGTGGGCC‑TGAAATATAAGTTCTGATCCCGCCGTTAGCTAAAAAACCGCGTCGTATTCATCGACGCGGTACat                                                                                      >  1:193982/1‑150 (MQ=255)                                                               ccTGAATCCAGCGGCCAGCGTCGGGGGAATGGGGGCGTGCAGCTGGGTGATAATGGCTACAATGACCCCGCAGTGAGGGGGGGCC‑TAAAATATAAGTTCTGACCCCGCCGTTAGCTAAAAAACCGCGTCGTATTCATCGACGCGGTACata                                                                                     <  2:172070/151‑1 (MQ=255)                                                                         ggggCCGGCGTCTGGGGATTGGGGGCGTGCCGGTGGGTAATAAGGACTAAAATGACCCCGCAGTGATGGTGGGCC‑CAAAATATAATTTCTGATCCCGCCGTTAGCTAAAAAACCGCGTCGTATTCATCGACGCGGTACATATGAAatat                                                                             <  2:36489/147‑1 (MQ=255)                                                                           ggCCAGCGTCTGGGGAATGTGGGCGTGCAGCTGGGTGATAATGGCTACAATGACACCGCAGTGATGGTGGGCC‑TGAAATATAAGTTCTGATCCCGCCGTTAGCTAAAAAACCGCGTCGTATTCATCGACGCGGTACATATGAAATattatt                                                                         >  2:850618/1‑151 (MQ=255)                                                                           ggCCAGCGTCGGGGAAATGGGGGCGTGCGGCGGGGTGATAAGGGCTACAATGACCCCGCGGTGAGGGTGGGCT‑TAAAATATAATTTCTGATCCCGCCGTTAGCTAAAAAACCGCGTCGTATTCATCGACGCGGTACATATGAAAtatt                                                                            <  2:1039807/148‑1 (MQ=255)                                                                             ccAGCGTCGGGGAATTGGGGGGGTGCAGTTGGGTGATAATGGCTACAATGCCACCGAAGTTATGGGGGGCC‑TAAAATATAAGTTCTGATCCCGCCGTTAGCTAAAAAACCGCGTCGTATTCATCGACGCGGTACATATGAAATATTAtttt                                                                       <  2:1632/151‑1 (MQ=255)                                                                              cAGCGTCGGGGGAATGGGGGCGTGCAGTTGGGTGATAATGGCTACAATACCCCCGGAGTGATGGTGGGCT‑TAAAATATAAGTTCTGATCCCGCCGTTAGCTAAAAAACCGCGTCGTATTCATCGACGCGGTACATATGAAATATTAttt                                                                        <  2:1287971/149‑1 (MQ=255)                                                                                  gtggggggAATGGGGGGGTGCAGTTGGGTGATAAGGGCTAAAATGACCCCGCAGTGATGGGGGGCT‑TAAAAAATAATTTCTGATCCCGCCGTTAGCTAAAAAACCGCGTCGTATTCATCGACGCGGTACATATGAAATATTATTTTTTGc                                                                   <  2:17461/146‑1 (MQ=255)                                                                                  gTCTGGGGAATGTGGGCGTGCAGCTGGGTGATAATGGCTACAATGACACCGCAGTGATGGTGGGCC‑TGAAATATAAGTTCTGATCCCGCCGTTAGCTAAAAAACCGCGTCGTATTCATCGACGCGGTACATATGAAATATTATTTTTTGcc                                                                  >  2:58522/1‑151 (MQ=255)                                                                                          atggtgGGCGTGCAGGTGGGTGATAAGGCCAAAAAGGACACCGC‑GTTGTGGGGGGCCTTAAAATATAATTTCTGTCCCCGCCGTTAGCTAAAAAACCGCGTCGTATTCATCGACGCGGTACATATGAAATATTATTTTTTGCCGATAGCa                                                           <  2:961731/147‑1 (MQ=255)                                                                                              gggggGTGCAGCGGGGTGATAAGGGTTAAAATGACCCCCCGGTGTTGGGGGGCC‑TAAAATATAAGTTCTGACCCCGCCGTTAGCTAAAAAACCGCGTCGTATTCATCGACGCGGTACATATGAAATATTATTTTTTGCCGATAGCACGCAt                                                      <  2:506854/150‑1 (MQ=255)                                                                                               gggCGTGCGGGTGGGTGATAAGCGCAAAAATGACCCCGAGGTGATGGGGGCCG‑TAAAATAGAATTTTTTCTCCCGCCGTTAGCTAAAAAACCGCGTCGTATTCATCGACGCGGTACATATGAAATATTATTTTTTGCCGATAGCACg                                                         <  1:1041006/147‑1 (MQ=255)                                                                                                   gtggaggggggTGATAGTGCATACAAGGCCGCCGCAGTGATGGGGGGCA‑TAAAATATAAGTTTTGCTCCCGCCGTTAGCTAAAAAACCGCGTCGTATTCATCGACGCGGTACATATGAAATATTATTTTTTGCCGATAGCACGCATGgtgt                                                 <  2:668765/143‑1 (MQ=255)                                                                                                           ggttGAAAATGGCTAAAACACCCCCGGAGTGAGGGGGGGTG‑TAAAATAAAGGTTTTGACCCCGCCGTTAGCTAAAAAACCGCGTCGTATTCATCGACGCGGTACATATGAAATATTATTTTTTGCCGATAGCACGCATGGTGtcatca                                            <  2:179361/145‑1 (MQ=255)                                                                                                             gTGATAATGGCTACAATGACACCGCAGTGATGGTGGGCC‑TGAAATATAAGTTCTGATCCCGCCGTTAGCTAAAAAACCGCGTCGTATTCATCGACGCGGTACATATGAAATATTATTTTTTGCCGATAGCACGCATGGTGTCATCAATTGc                                       >  2:804977/1‑151 (MQ=255)                                                                                                                   aTGGCTACAATGACACCGCAGTGATGGTGGGCC‑TGAAATATAAGTTCTGATCCCGCCGTTAGCTAAAAAACCGCGTCGTATTCATCGACGCGGTACATATGAAATATTATTTTTTGCCGATAGCACGCATGGTGTCATCAATTGCCGTGAt                                 >  1:392546/1‑151 (MQ=255)                                                                                                                      gCTACAATGACACCGCAGTGATGGTGGGCC‑TGAAATATAAGTTCTGATCCCGCCGTTAGCTAAAAAACCGCGTCGTATTTATTGACCCGGTACATATGAAATATTATTTTTTGCCGATAGCACGCATGGCGTCATAAATTACCGCGATc                                >  2:244708/1‑149 (MQ=255)                                                                                                                                  ccGCAGTGATGGGGGGCC‑TGAAATATAATTTCTGATCCCGCCGTTAGCTAAAAAACCGCGTCGTATTCATCGACGCGGTACATATGAAATATTATTTTTTGCCGATAGCACGCATGGTGTCATCAATTGCCGTGATCAACAGCATTTg                     <  2:241055/148‑1 (MQ=255)                                                                                                                                            ggtggtCT‑TAAAATATAGTTTCTGATCCCGCCGTTAGCTAAAAAACCGCGTCGTATTCATCGACGCGGTACATATGAAATATTATTTTTTGCCGATAGCACGCATGGTGTCATCAATTGCCGTGATCAACAGCATTTGCGGGTCTTTAgc         <  1:686614/150‑1 (MQ=255)                                                                                                                                            ggtggGCT‑TGAAATAAAATTTCTAACCCCGCCGTTAGCTAAAAAACCGCGTCGTATTCATCGACGCGGTACATATGAAATATTATTTTTTGCCGATAGCACGCATGGTGTCATCAATTGCCGTGATCAACAGCATTTGCggg                 <  1:291131/142‑1 (MQ=255)                                                                                                                                                ggCC‑TGAAATATAAGTTCTGATCCCGCCGTTAGCTAAAAAACCGCGTCGTATTCATCGACGCGGTACATATGAAATATTATTTTTTGCCGATAGCACGCATGGTGTCATCAATTGCCGTGATCAACAGCATTTGCGGGTCTTTAGCGCaa     >  1:593635/1‑150 (MQ=255)                                                                                                                                                  cc‑TGAAATATAAGTTCTGATCCCGCCGTTAGCTAAAAAACCGCGTCGTATTCATCGACGCGGTACATATGAAATATTATTTTTTGCCGATAGCACGCATGGTGTCATCAATTGCCGTGATCAACAGCATTTGCGGGTCTTTAGCGCAAAcc  >  2:667459/1‑151 (MQ=255)                                                                                                                                                      |                                                                                                                                                    GTGAAAGTCGAACAAGATGGGGCGAGTAATTTGGGGGAAATTAAACTTGGCGTAAATGGCAACCTGAATCCAGCGGCCAGCGTCTGGGGAATGTGGGCGTGCAGCTGGGTGATAATGGCTACAATGACACCGCAGTGATGGTGGGCC‑TGAAATATAAGTTCTGATCCCGCCGTTAGCTAAAAAACCGCGTCGTATTCATCGACGCGGTACATATGAAATATTATTTTTTGCCGATAGCACGCATGGTGTCATCAATTGCCGTGATCAACAGCATTTGCGGGTCTTTAGCGCAAACC  >  NC_000913/1222085‑1222380

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: ‑