Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NC_000913	3,029,965	0	A	C	44.6%	82.3 / 21.9	56	L323V (TTA→GTA)	ygfT	putative oxidoreductase, Fe‑S subunit/nucleotide‑binding subunit
Reads supporting (aligned to +/- strand):  ref base A (27/4);  new base C (0/25);  total (27/29)
Fisher's exact test for biased strand distribution p-value = 4.32e-12
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 1.00e+00

CGCCGCTGGCTTAATACCGTTTTATCGAGTTTGAAAGGAGGAATGCCAAAAGTCAGCATACCGCCAATTTCTGGATGGCGATCAAAGACATCGACCTGAACTCCTGCGCGCGCCAGAATATCAGCACACCCTAACCCTGCAG‑GCCCAGCGCCAATCACCGCCACTTTTTCGCTACGGGGAACAACTTTGCTGACATCGGGACGCCAGCCCATCGCCAGCGCGGTATCGGTGATGTAGCGTTCCAGATTACCGATAGAGACTGCGCCCGAGTGATCTTTCAA  >  NC_000913/3029832‑3030112                                                                                                                                      |                                                                                                                                                     cgccgcTGGCTTAATACCGTTTTATCGAGTTTGAAAGGAGGAATGCCAAAAGTCAGCATACCGCCAATTTCTGGATGGCGATCAAAGACATCGACCTGAACTCCTGCGCGCGCCAGAATATCAGCACACCCTAACCCTGCAG‑GCCCAgc                                                                                                                                      <  2:843669/149‑1 (MQ=255) cgccgcTGGCTTAATACCGTTTTATCGAGTTTGAAAGGAGGAATGCCAAAAGTCAGCATACCGCCAATTTCTGGATGGCGATCAAAGACATCGACCTGAACTCCTGCGCGCGCCAGAATATCAGCACACCCTAACCCTGCAG‑GCCCAgc                                                                                                                                      <  2:54258/149‑1 (MQ=255)           ttAATACCGTTTTATCGAGTTTGAAAGGAGGAATGCCAAAAGTCAGCATACCGCCAATTTCTGGATGGCGATCAAAGACATCGACCTGAACTCCTGCGCGCGCCAGAATATCAGCACACCCTAACCCTGCAG‑GCCCAGCGCCAATCACCGc                                                                                                                          >  1:630523/1‑151 (MQ=255)             aaTACCGTTTTATCGAGTTTGAAAGGAGGAATGCCAAAAGTCAGCATACCGCCAATTTCTGGATGGCGATCAAAGACATCGACCTGAACTCCTGCGCGCGCCAGAATATCAGCACACCCTAACCCTGCAG‑GCCCAGCGCCAATCACCGCCa                                                                                                                        <  1:1044752/151‑1 (MQ=255)                 cctttttATCGAGTTTGAAAGGAGGAATGCCAAAAGTCAGCATCCCGCCAATTTCTGGATGGCGATCAAAGACATCGACCTGAACTCCTGCGCGCGCCAGAATATCAGCACACCCTACCCCTGCAG‑GCCCAGCGCCAATCACCGCCACtt                                                                                                                     <  2:465897/147‑1 (MQ=255)                     tttATCGAGTTTGAAAGGAGGAATGCCAAAAGTCAGCATACCGCCAATTTCTGGATGGCGATCAAAGACATCGACCTGAACTCCTGCGCGCGCCAGAATATCAGCACACCCTAACCCTGCAG‑GCCCAGCGCCAATCACCGCCACTTTTTCg                                                                                                                >  1:582436/1‑151 (MQ=255)                        aTCGAGTTTGAAAGGAGGAATGCCAAAAGTCAGCATACCGCCAATTTCTGGATGGCGATCAAAGACATCGACCTGAACTCCTGCGCGCGCCAGAATATCAGCACACCCTAACCCTGCAG‑GCCCAGCGCCAATCACCGCCACTTTTTCGCt                                                                                                              >  1:1128185/1‑150 (MQ=255)                         tCGAGTTTGAAAGGAGGAATGCCAAAAGTCAGCATACCGCCAATTTCTGGATGGCGATCAAAGACATCGACCTGAACTCCTGCGCGCGCCAGAATATCAGCACACCCTAACCCTGCAG‑GCCCAGCGCCAATCACCGCCACTTTTTCGCTAc                                                                                                            >  2:1106290/1‑151 (MQ=255)                           gAGTTTGAAAGGAGGAATGCCAAAAGTCAGCATACCGCCAATTTCTGGATGGCGATCAAAGACATCGACCTGAACTCCTGCGCGCGCCAGAATATCAGCACACCCTAACCCTGCAG‑GCCCAGCGCCAATCACCGCCACTTTTTCGCTACgg                                                                                                          >  1:1097031/1‑151 (MQ=255)                           gAGTTTGAAAGGAGGAATGCCAAAAGTCAGCATACCGCCAATTTCTGGATGGCGATCAAAGACATCGACCTGAACTCCTGCGCGCGCCAGAATATCAGCACACCCTAACCCTGCAG‑GCCCAGCGCCAATCACCGCCACTTTTTCGCTACgg                                                                                                          >  1:264705/1‑151 (MQ=255)                             gTTTGAAAGGAGGAATGCCAAAAGTCAGCATACCGCCAATTTCTGGATGGCGATCAAAGACATCGACCTGAACTCCTGCGCGCGCCAGAATATCAGCACACCCTAACCCTGCAG‑GCCCAGCGCCAATCACCGCCACTTTTTCGCTACgggg                                                                                                        >  2:80421/1‑151 (MQ=255)                                tGAAAGGAGGAATGCCAAAAGTCAGCATACCGCCAATTTCTGGATGGCGATCAAAGACATCGACCTGAACTCCTGCGCGCGCCAGAATATCAGCACACCCTAACCCTGCAG‑GCCCAGCGCCAATCACCGCCACTTTTTCGCTACGGGGaac                                                                                                     >  2:346901/1‑151 (MQ=255)                                  aaaGGAGAAATGCAAAAAGCCAGCACCCCGCAATTTTCTGGATGGCGATAAAAGACACCGCCCTGACCCCCTGCGCGCGCAAGAATACCACCCCCCCCAACCCCTGCGG‑GCCCAGCGCCAATCCCCGCCACTTTTTCGCTACGGGGaac                                                                                                     <  2:989910/149‑1 (MQ=255)                                   aaGGAGGAATGCCAAAAGTCAGCATACCGCCAATTTCTGGATGGCGATCAAAGACATCGACCTGAACTCCTGCGCGCGCCAGAATATCAGCACACCCTAACCCTGCAG‑GCCCAGCGCCAATCACCGCCACTTTTTCGCTACGGGGaacaac                                                                                                  >  2:38730/1‑151 (MQ=255)                                        gaaatccaaaaaGTCACCATCCCGCCATTTTCTGGATGGCGATAAAAGACACCGACCTAAACTCCGGCGCGCGCAAGAATATCAGCACCCCCTACCCCGGCAG‑CCCCAGCGCAAATCACCGCCACTTTTTCGCTACGGGGAACAACttt                                                                                               <  1:9041/141‑1 (MQ=255)                                         gaATGCCAAAAGTCAGCATACCGCCAATTTCTGGATGGCGATCAAAGACATCGACCTGAACTCCTGCGCGCGCCAGAATATCAGCACACCCTAACCCTGCAG‑GCCCAGCGCCAATCACCGCCACTTTTTCGCTACGGGGAACAACTTTGCt                                                                                            >  1:472292/1‑151 (MQ=255)                                                 aaaGCCAGCATCCCCCCATTTTCTGGATGGCGATAAAAGCCACCGCCCTAACCTCCGGCGCGCGCAAGAATACCACCACCCCCTACCCCGGCAG‑GCCCAGCGCAAATCACCGCCACTTTTTCGCTACGGGGAACAACTTTGCTGACATCgg                                                                                    <  1:1069053/151‑1 (MQ=255)                                                   agcaagacccccGCCATTTTGGGGAGGGCGAAAAAAGACACCGCCCTAACCCCCGGCGCGCGCAAAAATACCACCCCCCCCAACCCCGGCAG‑GCCCGGCGCCAATCACCGCCACTTTTTCGCTACGGGGAACAACTTTGCTGACATCGGGa                                                                                  <  2:708968/141‑1 (MQ=255)                                                    gTCAGCATACCGCCAATTTCTGGATGGCGATCAAAGACATCGACCTGAACTCCTGCGCGCGCCAGAATATCAGCACACCCTAACCCTGCAG‑GCCCAGCGCCAATCACCGCCACTTTTTCGCTACGGGGAACAACTTTGCTGACATCGGGAc                                                                                 >  2:889155/1‑151 (MQ=255)                                                      cAGCATCCCGCCATTTTCTGGATGGCAAAAAAAGACATCGCCCTGACCTCCTGCGCGCGCAAGAATATCAGCCCCCCCTACCCCTGCAG‑CCCCAGCCCCAATCCCCGCCACTTTTTCGCTACGGGGAACAACTTTGCTGACATCGGGACg                                                                                <  1:739008/150‑1 (MQ=255)                                                       acatccccGCAATTTTCGGGAGGGCGACAAAAACCACCGCCCTGAACCCCGGCCCCCGCAAGAATATCACCACCCCCAACCCCGGCAG‑GCCAGGCCCAAATCACCGCCACTTTTTCGCTACGGGGAACAACTTTGCTGACATCGGGACg                                                                                <  2:186871/143‑1 (MQ=255)                                                           tccccccAATTTGTGGATGGCAATAAAAGACCTCTACTGCACCCCCCGCGCGCGAAAGAATATCAGCACCCTCACCCCCTACAGCCCCCAGC‑AAAATCACCGCCACTTTTTCGCTACGGGGAACAACTTTGCTGACATCggg                                                                                   <  2:1126382/137‑1 (MQ=255)                                                           tACCGCCAATTTCTGGATGGCGATCAAAGACATCGACCTGAACTCCTGCGCGCGCCAGAATATCAGCACACCCTAACCCTGCAG‑GCCCAGCGCCAATCACCGCCACTTTTTCGCTACGGGGAACAACTTTGCTGACATCGGGACGCCAGcc                                                                          >  2:751455/1‑151 (MQ=255)                                                             ccGCAATTTTCTGGATGGCGATAAAAGACACCGCCCTGAACCCCGGCGCGCGCAAAAATATAAGCCCCCCCTACCCCTGCAG‑GCCCAGCGCCAATCACCGCCACTTTTTCGCTACGGGGAACAACTTTGCTGACATCGGGACGCCAg                                                                            <  1:125970/147‑1 (MQ=255)                                                                ccAATTTCTGTATGCCAAACAAACACATCGCCCTAACCTCCTGCGCGCGCCAAAATATCACCCCCCCCAACCCCTGCGG‑GCCCAGCGCAAACCACCGCCACTTTTTCGCTACGGGGAACAACTTTGCTGACATCGGGACGCCAGCCCATCg                                                                     <  1:619478/151‑1 (MQ=255)                                                                    tttCTGGATGGCGATCAAAGACATCGACCTGAACTCCTGCGCGCGCCAGAATATCAGCACACCCTAACCCTGCAG‑GCCCAGCGCCAATCACCGCCACTTTTTCGCTACGGGGAACAACTTTGCTGACATCGGGACGCCAGCCCATCGcc                                                                   >  2:269970/1‑149 (MQ=255)                                                                      tCTGGATGGCAATCAAAAACACCGCCGTGCCCCCCCGCGCGCGCAAAAATACCCCCCCCCCCTACCCCTGCAG‑CCCCGGCCCCAACCACCGCCACTTTTTCGCTACGGGGAACAACTTTGCTGACATCGGGACGCCAGCCCATCGCCAgc                                                                <  2:361074/150‑1 (MQ=255)                                                                        tGGATGGCGATCAAAGACATCGACCTGAACTCCTGCGCGCGCCAGAATATCAGCACACCCTAACCCTGCAG‑GCCCAGCGCCAATCACCGCCACTTTTTCGCTACGGGGAACAACTTTGCTGACATCGGGACGCCAGCCCATCGCCAGcgcg                                                             >  2:499956/1‑151 (MQ=255)                                                                        tGGATGGCGATCAAAGACATCGACCTGAACTCCTGCGCGCGCCAGAATATCAGCACACCCTAACCCTGCAG‑GCCCAGCGCCAATCACCGCCACTTTTTCGCTACGGGGAACAACTTTGCTGACATCGGGACGCCAGCCCATCGCCAGcgcg                                                             >  1:186387/1‑151 (MQ=255)                                                                         ggATGGCGATAAAAGACATCGCCCTGACCTCCTGCGCGCGCAAAAATATCAGCCCACCCTACCCCGGCAG‑GCCCAGCGCCAATCACCGCCACTTTTTCGCTACGGGGAACAACTTTGCTGACATCGGGACGCCAGCCCATCGCCAGcgcg                                                             <  1:497494/150‑1 (MQ=255)                                                                             ggCGATCAAAGACATCGACCTGACCTCCTGCGCGCGCAAGAATAACAGCACCCCCAACCCCGGCAG‑GCCCCGCGCAAATCACCGCCACTTTTTCGCTACGGGGAACAACTTTGCTGACATCGGGACGCCAGCCCATCGCCAGCGCGGTATc                                                        <  2:1096695/151‑1 (MQ=255)                                                                             ggCAATCAAAAACACCGACCTGAACCCCTGCGCGCGCCAGAATACCAGCACCCCCAACCCCTGCAG‑TCCCAGCTCAAATCACCGCCACTTTTTCGCTACGGGGAACAACTTTGCTGACATCGGGACGCCAGCCCATCGCCAGCGCGGTATc                                                        <  1:1043182/151‑1 (MQ=255)                                                                             ggCAATAAAAGCCACCGCCCTGACCCCCGGCGCGCCACAAAATACCACCACCCCCCACCCCCCAAG‑GCCCAGCCCAAAACACCGCCACTTTTTCGCTACGGGGAACAACTTTGCTGACATCGGGACGCCAGCCCATCGCCAGCGCGGTATc                                                        <  2:264647/151‑1 (MQ=255)                                                                              gCGATCAAAGACATCGACCTGAACTCCTGCGCGCGCCAGAATATCAGCACACCCTAACCCTGCAG‑GCCCAGCGCCAATCACCGCCACTTTTTCGCTACGGGGAACAACTTTGCTGACATCGGGACGCCAGCCCATCGCCAGCGCGGTATCg                                                       >  2:672371/1‑151 (MQ=255)                                                                               cGAACAAAGCCATCGCCCGGACCTCGCGCGCGCGAAATATTACCACCCCCCCCAACCCCCGCGG‑CCCCAGCGCAAATCACCGCCACTTTTTCGCTACGGGGAACAACTTTGCTGACATCGGGACGCCAGCCCATCGCCAGCGCGGTATCg                                                       <  2:1059666/150‑1 (MQ=255)                                                                                   aaaaGCCACCGCCCTGACCCCCCGCGCGCGCCAAAATATCACCACCCCCTACCCCTGCGG‑CCCAAGCCCCAATCACCGCCACTTTTTCGCTACGGGGAACAACTTTGCTGACATCGGGACGCCAGCCCATCGCCAGCGCGGTATCGGTGAt                                                  <  2:112776/150‑1 (MQ=255)                                                                                      aGACATCGACCTGAACTCCTGCGCGCGCCAGAATATCAGCACACCCTAACCCTGCAG‑GCCCAGCGCCAATCACCGCCACTTTTTCGCTACGGGGAACAACTTTGCTGACATCGGGACGCCAGCCCATCGCCAGCGCGGTATCGGTGATGt                                                >  1:155840/1‑150 (MQ=255)                                                                                            cGACCTGAACTCCTGCGCGCGCCAGAATATCAGCACACCCTAACCCTGCAG‑GCCCAGCGCCAATCACCGCCACTTTTTCGCTACGGGGAACAACTTTGCTGACATCGGGACGCCAGCCCATCGCCAGCGCGGTATCGGTGATGTAGCGTTc                                         >  2:4330/1‑151 (MQ=255)                                                                                               ccTGACCTCCGGCGCGCGCAAAAATACCACCCCCCCCTACCCCTGCAG‑GCCCAGCGCAAACCACCGCCACTTTTTCGCTACGGGGAACAACTTTGCTGACATCGGGACGCCAGCCCATCGCCAGCGCGGTATCGGTGATGTAGCGTTc                                         <  1:671685/148‑1 (MQ=255)                                                                                               ccTGACCCCCTGCGCGCACAAAAATACAAGCCCCCCCTACCCCGGCGG‑CCCCAGCGCAAACCACCGCCACTTTTTCGCTACGGGGAACAACTTTGCTGACATCGGGACGCCAGCCCATCGCCAGCGCGGTATCGGTGATGTAGCGTTc                                         <  2:971569/148‑1 (MQ=255)                                                                                                   aaCTCCTGCGCGCGCCAGAATATCAGCACACCCTAACCCTGCAG‑GCCCAGCGCCAATCACCGCCACTTTTTCGCTACGGGGAACAACTTTGCTGACATCGGGACGCCAGCCCATCGCCAGCGCGGTATCGGTGATGTAGCGTTCCAGAtt                                   >  2:965828/1‑150 (MQ=255)                                                                                                    aCTCCTGCGCGCGCCAGAATATCAGCACACCCTAACCCTGCAG‑GCCCAGCGCCAATCACCGCCACTTTTTCGCTACGGGGAACAACTTTGCTGACATCGGGACGCCAGCCCATCGCCAGCGCGGTATCGGTGATGTAGCGTTCCAGATTAc                                 >  1:844906/1‑151 (MQ=255)                                                                                                     cTCCTGCGCGCGCCAGAATATCAGCACACCCTAACCCTGCAG‑GCCCAGCGCCAATCACCGCCACTTTTTCGCTACGGGGAACAACTTTGCTGACATCGGGACGCCAGCCCATCGCCAGCGCGGTATCGGTGATGTAGCGTTCCAGATTAcc                                >  1:489177/1‑151 (MQ=255)                                                                                                           cgcgcgcAAGAATACCAGCCCCCCCTACCCCGGCGG‑CCCCGGCGCCAATCACCGCCACTTTTTCGCTACGGGGAACAACTTTGCTGACATCGGGACGCCAGCCCATCGCCAGCGCGGTATCGGTGATGTAGCGTTCCAGATTACCGATa                            <  2:409833/149‑1 (MQ=255)                                                                                                            gcgcgcCAGAATATCAGCACACCCTAACCCTGCAG‑GCCCAGCGCCAATCACCGCCACTTTTTCGCTACGGGGAACAACTTTGCTGACATCGGGACGCCAGCCCATCGCCAGCGCGGTATCGGTGATGTAGCGTTCCAGATTACCGATag                           >  1:1103256/1‑149 (MQ=255)                                                                                                               cgcaaaaaTATCACCCCCCCCAACCCCGCCGG‑GCCCACCCCCAACCACCGCCACTTTTTCGCTACGGGGAACAACTTTGCTGACATCGGGACGCCAGCCCATCGCCAGCGCGGTATCGGTGATGTAGCGTTCCAGATTACCGATAGAGACt                      <  2:518491/145‑1 (MQ=255)                                                                                                               cgcCAGAATATCAGCACCCCCTACCCCTGCGG‑CCCCACCGCCAATCACCGCCACTTTTTCGCTACGGGGAACAACTTTGCTGACATCGGGACGCCAGCCCATCGCCAGCGCGGTATCGGTGATGTAGCGTTCCAGATTACCGATAgaga                        <  1:833042/149‑1 (MQ=255)                                                                                                                gcCAGAATATCAGCACACCCTAACCCTGCAG‑GCCCAGCGCCAATCACCGCCACTTTTTCGCTACGGGGAACAACTTTGCTGACATCGGGACGCCAGCCCATCGCCAGCGCGGTATCGGTGATGTAGCGTTCCAGATTACCGATAGAGACTg                     >  1:848335/1‑151 (MQ=255)                                                                                                                      atatCAGCACACCCTAACCCTGCAG‑GCCCAGCGCCAATCACCGCCACTTTTTCGCTACGGGGAACAACTTTGCTGACATCGGGACGCCAGCCCATCGCCAGCGCGGTATCGGTGATGTAGCGTTCCAGATTACCGATAGAGACTGCGCCCg               >  2:954207/1‑151 (MQ=255)                                                                                                                           aGCACCCCCAACCCCTGCGG‑GCCCAGCGCCAATCCCCGCCACTTTTTCGCTACGGGGAACAACTTTGCTGACATCGGGACGCCAGCCCATCGCCAGCGCGGTATCGGTGATGTAGCGTTCCAGATTACCGATAGAGACTGCGCCCGAGTg           <  1:110789/150‑1 (MQ=255)                                                                                                                           aGCACACCCTAACCCTGCAG‑GCCCAGCGCCAATCACCGCCACTTTTTCGCTACGGGGAACAACTTTGCTGACATCGGGACGCCAGCCCATCGCCAGCGCGGTATCGGTGATGTAGCGTTCCAGATTACCGATAGAGACTGCGCCCGAGTg           >  1:626838/1‑150 (MQ=255)                                                                                                                           aGCACACCCTAACCCTGCAG‑GCCCAGCGCCAATCACCGCCACTTTTTCGCTACGGGGAACAACTTTGCTGACATCGGGACGCCAGCCCATCGCCAGCGCGGTATCGGTGATGTAGCGTTCCAGATTACCGATAGAGACTGCGCCCGAGTg           >  1:610173/1‑150 (MQ=255)                                                                                                                             caccCCCTACCCCGGCAG‑CCCCACCGCAAACCTCCGCCACTTTTTCGCTACGGGGAACAACTTTGCTGACATCGGGACGCCAGCCCATCGCCAGCGCGGTATCGGTGATGTAGCGTTCCAGATTACCGATAGAGACTGCGCCCGAGTGATc        <  1:824923/151‑1 (MQ=255)                                                                                                                             caccCCCAACCCCGGCAG‑GCCCAGCGCCAATCACCGCCACTTTTTCGCTACGGGGAACAACTTTGCTGACATCGGGACGCCAGCCCATCGCCAGCGCGGTATCGGTGATGTAGCGTTCCAGATTACCGATAGAGACTGCGCCCg               <  1:209231/144‑1 (MQ=255)                                                                                                                                 ccatAACCCTCCGG‑CCCAAACCCCAATCACCGCCACTTTTTCGCTACGGGGAACAACTTTGCTGACATCGGGACGCCAGCCCATCGCCAGCGCGGTATCGGTGATGTAGCGTTCCAGATTACCGATAGAGACTGCGCCCGa              <  2:1127837/138‑1 (MQ=255)                                                                                                                                    tAACCCTGCAG‑GCCCAGCGCCAATCACCGCCACTTTTTCGCTACGGGGAACAACTTTGCTGACATCGGGACGCCAGCCCATCGCCAGCGCGGTATCGGTGATGTAGCGTTCCAGATTACCGATAGAGACTGCGCCCGAGTGATCTTTCaa  >  2:515110/1‑150 (MQ=255)                                                                                                                                      |                                                                                                                                                     CGCCGCTGGCTTAATACCGTTTTATCGAGTTTGAAAGGAGGAATGCCAAAAGTCAGCATACCGCCAATTTCTGGATGGCGATCAAAGACATCGACCTGAACTCCTGCGCGCGCCAGAATATCAGCACACCCTAACCCTGCAG‑GCCCAGCGCCAATCACCGCCACTTTTTCGCTACGGGGAACAACTTTGCTGACATCGGGACGCCAGCCCATCGCCAGCGCGGTATCGGTGATGTAGCGTTCCAGATTACCGATAGAGACTGCGCCCGAGTGATCTTTCAA  >  NC_000913/3029832‑3030112

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 12 ≤ ATCG/ATCG < 14 ≤ ATCG/ATCG < 34 ≤ ATCG/ATCG < 39 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑