Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NC_000913	357,890	0	C	A	45.8%	9.6 / 10.4	24	L267F (TTG→TTT)	cynR	transcriptional activator of cyn operon; autorepressor
Reads supporting (aligned to +/- strand):  ref base C (7/6);  new base A (0/11);  total (7/17)
Fisher's exact test for biased strand distribution p-value = 5.91e-03
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 9.32e-01

ATAAGCGTAGCGCATCAGGCAATTCCAGCCGCAGACCTGTGTCAGCGGCTACCGT‑GATTCATTTCCGCCAACAACCGCGCATTTATCCAACGCCATGTGCAAAAATGCCTTCGCGGCGGCTGTCTGCCAGCTATTTTTCCGCCGCAACAAAACCGCCGTTCTCTCCAGTAGTGGCGGGGCAAGAGAAATAGCTTTAAGCCCGTCATGTTGTGTGGCAATCGCTGCTGGTAACAATGTGGAAAGGGAAGTGCGGCGAATCAGCTCCAGAACCGCGCTAATTGAGTT  >  NC_000913/357743‑358027                                                                                                                                                     |                                                                                                                                          aTAAGCGTAGCGCATCAGGCAATTCCAGCCGCAGACCTGTGTCAGCGGCTACCGT‑GATTCATTTCCGCCAACAACCGCGCATTTATCCAACGCCATGTGCAAAAATGCCTTCGCGGCGGCTGTCTGCCAGCTATTTTTCCGCCGcaacaa                                                                                                                                         >  1:471173/1‑150 (MQ=255) aTAAGCGTAGCGCATCAGGCAATTCCAGCCGCAGACCTGTGTCAGCGGCTACCGT‑GATTCATTTCCGCCAACAACCGCGCATTTATCCAACGCCATGTGCAAAAATGCCTTCGCGGCGGCTGTCTGCCAGCTATTTTTCCGCCGcaacaa                                                                                                                                         >  1:73510/1‑150 (MQ=255) aTAAGCGTAGCGCATCAGGCAATTCCAGCCGCAGACCTGTGTCAGCGGCTACCGT‑GATTCATTTCCGCCAACAACCGCGCATTTATCCAACGCCATGTGCAAAAATGCCTTCGCGGCGGCTGTCTGCCAGCTATTTTTCCGCCGcaac                                                                                                                                           <  1:489656/148‑1 (MQ=255)      cGTAGCGCATCAGGCAATTCCAGCCGCAGACCTGTGTCAGCGGCTACCGT‑GATTCATTTCCGCCAACAACCGCGCATTTATCCAACGCCATGTGCAAAAATGCCTTCGCGGCGGCTGTCTGCCAGCTATTTTTCCGCCGCAACAAAAccg                                                                                                                                    <  2:732108/150‑1 (MQ=255)       gTAGCGCATCAGGCAATTCCAGCCGCAGACCTGTGTCAGCGGCTACCGT‑GATTCATTTCCGCCAACAACCGCGCATTTATCCAACGCCATGTGCAAAAATGCCTTCGCGGCGGCTGTCTGCCAGCTATTTTTCCGCCGCAACAAAAccg                                                                                                                                    <  1:665387/149‑1 (MQ=255)         accgcgcccggCATTTCCAGCCGCAGACCTGTTTCTGCGCCTTCCGT‑GCTTCTTCTCCCCCACCACCCTCGCTTTTATCCACCCCCCTGTGCAAAACTGCCTTCGCGGCGGCTGTCTGCCAGCTTTTTTTCCGCCGCCACAACAccgcc                                                                                                                                  <  1:568725/140‑1 (MQ=255)                      aTTCCAGCCGCAGACCTGTGTCAGCGGCTACCGT‑GATTCATTTCCGCCAACAACCGCGCATTTATCCAACGCCATGTGCAAAAATGCCTTCGCGGCGGCTGTCTGCCAGCTATTTTTCCGCCGCAACAAAACCGCCGTTCTCTCCagtag                                                                                                                    >  1:413668/1‑150 (MQ=255)                           aGCGGCAGCCCTTTGTCAGCGTCT‑CCGTAGATTCTTTCCCCCCACCACCCGCGCATTTATCCACCGCCATGTTAAAAAATCCCTTCGCGGGGGCTGTCTGCCAGTTTTTTTCCCCCCCCAACAAAACCGCCGTTCTCTCCAGTAGTg                                                                                                                  <  2:587288/147‑1 (MQ=255)                           aGCCGCAGACCTGTGTCAGCGGCTACCGT‑GATTCATTTCCGCCAACAACCGCGCATTTATCCAACGCCATGTGCAAAAATGCCTTCGCGGCGGCTGTCTGCCAGCTATTTTTCCGCCGCAACAAAACCGCCGTTCTCTCCAGTAGTGGCgg                                                                                                              >  2:755216/1‑151 (MQ=255)                             ccGCAGCCCTGTGTCAGCGCCTACCGT‑GTTTCTTTCCCGCCAACACCCGCGCATTTACCCACCCCCATGTCAAAAAATCCCTTCGGGGCGGCTGTCTGCCAGTTTTTTTCCCGCCGCAAAAAAACCGCCGTTCTCTCCAGTAGTGGCg                                                                                                               <  2:123106/148‑1 (MQ=255)                                   aCCTGTGTCAGCGGCTACCGT‑GATTCATTTCCGCCAACAACCGCGCATTTATCCAACGCCATGTGCAAAAATGCCTTCGCGGCGGCTGTCTGCCAGCTATTTTTCCGCCGCAACAAAACCGCCGTTCTCTCCAGTAGTGGCgggg                                                                                                            >  2:412483/1‑145 (MQ=255)                                    ccTGTGTCAGCGGCTACCGT‑GATTCATTTCCGCCAACAACCGCGCATTTATCCAACGCCATGTGCAAAAATGCCTTCGCGGCGGCTGTCTGCCAGCTATTTTTCCGCCGCAACAAAACCGCCGTTCTCTCCAGTAGTGGCggg                                                                                                             >  1:225185/1‑143 (MQ=255)                                        tgtCAGCGGCTACCGT‑GATTCATTTCCGCCAACACCCGAGCATTTATCCAACGACATGTGCAAAAATGCCCTCGCGGCGGCTGTCTGCCAGCTATTTTTCCCCCGCCACAAAACCGCCGTTCTCTCCAGTAGTGGCgtcgagcaat                                                                                                      >  1:490190/1‑137 (MQ=21)                                           cggCGGCTCCCTT‑GTTTCATTCCCCCCAACACCCGCGCTTTTCCCCAACGCCGTGTGCAAAAATGCCTGCGCGGCGTCTGTCGGCCGGCTTTTTTCCCGCCAAAAAAAAACCGCCGTTCTCTCCAGTAGTGGCGGGGCAAGAGAAATAGc                                                                                               <  1:237457/148‑1 (MQ=255)                                               ggCTCCCTT‑GTTTCATTCCCCCAAACCCCCGCGCATTTACCCAGCGCCGGTAAAAAAAATGCCTCCGGGGCGGCTGTCTGCCGGTTTTTTTCCCGCCAAAAAAAAACCGCCGTTCTCTCCAGTAGTGGCGGGGCAAGAGAAATa                                                                                                 <  1:764991/144‑1 (MQ=255)                                               ggCTACCGT‑TATTAATTCCCGCCAACACCCGCGATTTTACCCACCCCCTTGTAAAAAAATGCCTCGGCGGCGGCTGTCTCCCAGTTTTTTTCCCGCCGCAAAAAAACCGCCGTTCTCTCCAGTAGTGGCGGGGCAAGAGAAAt                                                                                                  <  2:371472/143‑1 (MQ=255)                                                        taattcattcCCCCAACCACCCGCTCTTTTACCCAACTCATTGTGAAAAATCGCCTCCGCGGGGTTTGTCTGCCGTTTTTTTTCCCGCCACAAAAAACCCGCCGTTCTCTCCAGTAGTGGCGGGGCAAGAGAAATAGCTTTAAGCCCg                                                                                     <  1:609880/146‑1 (MQ=255)                                                           ttatttcccGCCAAAACCCGCGTTTTTACCCACCGCTTTGTGAAAAAAGCCCTCGGCGGGGGTTGTCTCCCAGCTTTTTTCCCCCCGCAACAAAACCGCCGTTCTCTCCAGTAGTGGCGGGGCAAGAGAAATAGCTTTAAGCCCGTCAt                                                                                 <  2:232778/142‑1 (MQ=255)                                                                ttCCGCCAACAACCGCGCATTTATCCAACGCCATGTGCAAAAATGCCTTCGCGGCGGCTGTCTGCCAGCTATTTTTCCGCCGCAACAAAACCGCCGTTCTCTCCAGTAGTGGCGGGGGAAGAGAGAAAACttttaaaccaccctgt                                                                               >  1:493217/1‑133 (MQ=25)                                                                          acccGCGCTTTTCCCAAACCCCATGTGAAAAATTGCCTCCGCGGCGGCTGTCTGCCAGCTATTTTCCCCCCGCAAAAAAACCGCCGTTCTCTCCAGTAGTGGCGGGGCAAGAGAAATAGCTTTAAGCCCGTCATGTTGTGTGGCAATCgc                                                                 <  2:677083/148‑1 (MQ=255)                                                                                 cATTTATCCAACGCCATGTGCAAAAATGCCTTCGCGGCGGCTGTCTGCCAGCTATTTTTCCGCCGCAACAAAACCGCCGTTCTCTCCAGTAGTGGCGGGGGGAGAGAAAAAGATTTAAAACCCTCCTTTTGTGTGGGAATTgctg                                                               >  2:168565/1‑145 (MQ=37)                                                                                   tttACCCACCGCCTTGTAAAAAAATGCCTCCGCGGCGGCTGTCTGCCAGTTTTTTTCCCGCCGCAAAAAAACCGCCGTTCTCTCCAGTAGTGGCGGGGCAAGAGAAATAGCTTTAAGCCCGTCATGTTGTGTGGCAATCGCTGCTGGTaa                                                        <  2:177450/150‑1 (MQ=255)                                                                                                 tgaaaaaaagTGCCTGCGGGGCGTCTGCGTGCAGGTTTTTTTCCCGCCGCAAAAAATCCGCCGTTCTCTCCAGTAGTGGCGGGGCAAGAGAAATAGCTTTAAGCCCGTCATGTTGTGTGGCAATCGCTGCTGGTAACAATGTGGAAAggg                                          <  1:103737/145‑1 (MQ=255)                                                                                                                  gcggcgGTTTTCTGCCAGTTTTTTTCCCGCCGCAACAAAGCCGCCGTTCTCTCCAGTAGTGGCGGGGCAAGAGAAATAGCTTTAAGCCCGTCATGTTGTGTGGCAATCGCTGCTGGTAACAATGTGGAAAGGGAAGTgcggcg                                <  1:159995/143‑1 (MQ=255)                                                                                                                                ccAGTTTTTTTCCCGCCGCAAAAAAACCGCCGTTCTCTCCAGTAGTGGCGGGGCAAGAGAAATAGCTTTAAGCCCGTCATGTTGTGTGGCAATCGCTGCTGGTAACAATGTGGAAAGGGAAGTGCGGCGAATCAGCTCCAGAAcc                <  2:223254/145‑1 (MQ=255)                                                                                                                                       ttttcCCGCCGCAAAAAAACCGCCGTTCTCTCCAGTAGTGGCGGGGCAAGAGAAATAGCTTTAAGCCCGTCATGTTGTGTGGCAATCGCTGCTGGTAACAATGTGGAAAGGGAAGTGCGGCGAATCAGCTCCAGAACCGCGCTAATTGa     <  2:449410/149‑1 (MQ=255)                                                                                                                                            ccgcggCAAAAAAACCGCCGTTCTCTCCAGTAGTGGCGGGGCAAGAGAAATAGCTTTAAGCCCGTCATGTTGTGTGGCAATCGCTGCTGGTAACAATGTGGAAAGGGAAGTGCGGCGAATCAGCTCCAGAACCGCGCTAATTGAGtt  <  1:93437/147‑1 (MQ=255)                                                                                                                                                     |                                                                                                                                          ATAAGCGTAGCGCATCAGGCAATTCCAGCCGCAGACCTGTGTCAGCGGCTACCGT‑GATTCATTTCCGCCAACAACCGCGCATTTATCCAACGCCATGTGCAAAAATGCCTTCGCGGCGGCTGTCTGCCAGCTATTTTTCCGCCGCAACAAAACCGCCGTTCTCTCCAGTAGTGGCGGGGCAAGAGAAATAGCTTTAAGCCCGTCATGTTGTGTGGCAATCGCTGCTGGTAACAATGTGGAAAGGGAAGTGCGGCGAATCAGCTCCAGAACCGCGCTAATTGAGTT  >  NC_000913/357743‑358027

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 12 ≤ ATCG/ATCG < 13 ≤ ATCG/ATCG < 25 ≤ ATCG/ATCG < 39 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑