Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NC_000913	357,875	0	A	T	52.5%	17.1 / 53.8	40	N272K (AAT→AAA)	cynR	transcriptional activator of cyn operon; autorepressor
Reads supporting (aligned to +/- strand):  ref base A (12/7);  new base T (0/21);  total (12/28)
Fisher's exact test for biased strand distribution p-value = 9.02e-06
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 5.04e-05

GAACTCGTAGGCCTGATAAGCGTAGCGCATCAGGCAATTCCAGCCGCAGACCTGTGTCAGCGGCTACCGTGATTCATTTCCGCCAACAACCGCGCATTTATCCAACGCCATGTGCAAAAA‑TGCCT‑TCGCGGCGGCTGTCTGCCAGCTATTTTT‑CCGCCGCAACAAAACCGCCGTTCTCTCCAGTAGTGGC‑GGGGCAAGAGAAATAGC‑TTTAAGCCCGTCATGTTGTGTGGCAATCGCTGCTGGTAACAATGTGGAAAGGGAAGTGCGGCGAATCAGCTCC  >  NC_000913/357728‑358007                                                                                                                                                      |                                                                                                                                        gAACTCGTAGGCCTGATAAGCGTAGCGCATCAGGCAATTCCAGCCGCAGACCTGTGTCAGCGGCTACCGTGATTCATTTCCGCCAACAACCGCGCATTTATCCAACGCCATGTGCAAAAA‑TGCCT‑TCGCGGCGGCTGTCTGCCAGCTAttt                                                                                                                                      >  1:552543/1‑151 (MQ=255) gAACTCGTAGGCCTGATAAGCGTAGCGCATCAGGCAATTCCAGCCGCAGACCTGTGTCAGCGGCTACCGTGATTCATTTCCGCCAACAACCGCGCATTTATCCAACGCCATGTGCAAAAA‑TGCCT‑TCGCGGCGGCTGTCTGCCAGCTAtt                                                                                                                                       <  1:171291/150‑1 (MQ=255)        tAGGCCTGATAAGCGTAGCGCATCAGGCAATTCCAGCCGCAGACCTGTGTCAGCGGCTACCGTGATTCATTTCCGCCAACAACCGCGCATTTATCCAACGCCATGTGCAAAAA‑TGCCT‑TCGCGGCGGCTGTCTGCCAGCTATTTTT‑ccgcc                                                                                                                              >  1:701924/1‑151 (MQ=255)            ccTGATAAGCGTAGCGCATCAGGCAATTCCAGCCGCAGACCTGTGTCAGCGGCTACCGTGATTCATTTCCGCCAACAACCGCGCATTTATCCAACGCCATGTGCAAAAA‑TGCCT‑TCGCGGCGGCTGTCTGCCAGCTATTTTT‑CCGCCGcaa                                                                                                                          <  1:848348/151‑1 (MQ=255)                aTAAGCGTAGCGCATCAGGCAATTCCAGCCGCAGACCTGTGTCAGCGGCTACCGTGATTCATTTCCGCCAACAACCGCGCATTTATCCAACGCCATGTGCAAAAA‑TGCCT‑TCGCGGCGGCTGTCTGCCGGCTATTTTT‑CCGCCGcaacaa                                                                                                                       <  2:814195/150‑1 (MQ=255)                     cGTAGCGCATCAGGCAATTCCAGCCGCAGACCTGTGTCAGCGGCTACCGTGATTCATTTCCGCCAACAACCGCGCATTTATCCAACGCCATGTGCAAAAA‑TGCCT‑TCGCGGCGGCTGTCTGCCAGCTATTTTT‑CCGCCGCAACAAAAccgc                                                                                                                 >  1:1009120/1‑151 (MQ=255)                      gTAGCGCATCAGGCAATTCCAGCCGCAGACCTGTGTCAGCGGCTACCGTGATTCATTTCCGCCAACAACCGCGCATTTATCCAACGCCATGTGCAAAAA‑TGCCT‑TCGCGGCGGCTGTCTGCCAGCTATTTTT‑CCGCCGCAACAAAAccgcc                                                                                                                <  2:168112/151‑1 (MQ=255)                        aGCGCATCAGGCAATTCCAGCCGCAGACCTGTGTCAGCGGCTACCGTGATTCATTTCCGCCAACAACCGCGCATTTATCCAACGCCATGTGCAAAAA‑TGCCT‑TCGCGGCGGCTGTCTGCCAGCTATTTTT‑CCGCCGCAACAAAACCGCCGt                                                                                                              >  2:226140/1‑151 (MQ=255)                            cATCGGGCAATTCCAGCCGCAGACCTGTGTCAGCGGCTACCGTGATTCATTCCCGCCAACACCCGCGCATTTATCCAACGCCATGTGCAAAAA‑GGCCT‑TCGCGGCGGCTGTCTGCCAGCTATTTTT‑CCGCCGCAACAAAAccgccg                                                                                                               <  2:150198/146‑1 (MQ=255)                                    attcccAGCCGAAGCCTTGTGTCGGCGGCTCCCGTGTTTCATTCCCCCCAACACCCGCGCTTTTACCCACCCCCATGTGAAAAAA‑GCCCT‑CCGCGGCGGCTTTCTCCCAGTTTTTTTC‑CCGCCGCAAAAAAACCGCCGTTCTCTCCagta                                                                                                   <  2:478763/146‑1 (MQ=255)                                    aaTTCCAGCCGCAGACCTGTGTCAGCGGCTACCGTGATTCATTTCCGCCAACAACCGCGCATTTATCCAACGCCATGTGCAAAAA‑TGCCT‑TCGCGGCGGCTGTCTGCCAGCTATTTTT‑CCGCCGCAACAAAACCGCCGTTCTCTCCagt                                                                                                    >  1:92199/1‑149 (MQ=255)                                       tCCAGCCGCAGACCTGTGTCAGCGGCTCCAGTGATTCATTTCCGCCAACAACCGCGCATTTATCCAACGCCATGTGCAAAAA‑TGCCT‑TCGCGGCGGCTGTCTGCCAGCTATTTTT‑CCGCCGCAACAAAACCGACGTTCTCTCCagtag                                                                                                  >  1:1049213/1‑148 (MQ=255)                                       cccggCCCCAGCCCTGTGCCGGCGGCTCCGGTTATTCATCCCCCCCAACACCCGCCCATTTACCAACCGCCATTCAAAAAAA‑GGCCT‑CCGGGGCGGCTCTCGGCCATTTTTTTTC‑CCGCCGAAAAAAAACCGCCGTTCTCTCCagtagt                                                                                                 <  1:254438/145‑1 (MQ=255)                                          aGCCGCAGACCTGTGTCAGCGGCTACCGTGATTCATTTCCCCCAACAACCGCGCATTTATCCAACGCCATGTGCAAAAA‑TGCCT‑TCGCGGCGGCTGTCTGCCAGCTATTTTT‑CCGCCGCAACAAAACCGCCGTTCTCTCCAGTAGTGGC‑gg                                                                                           >  1:736617/1‑151 (MQ=255)                                           gCCGCAGACTTGTGTCGGCGGCTACCGTGTTTCATTCCCGCCAACACCCGCGCTTTTATCCACCGCCTTGTGAAAAAA‑TGCCT‑TCGCGGCGGCTGTCTGCCAGTTTTTTTC‑CCGCCGCAAAAAAACCGCCGTTCTCTCCAGTAGTGGC‑ggg                                                                                          <  2:946317/151‑1 (MQ=255)                                               cAGACCTGTGTCAGCGGCTACCGTGATTCATTTCCGCCAACAACCGCGCATTTATCCAACGCCATGTGCAAAAA‑TGCCT‑TCGCGGCGGCTGTCTGCCAGCTATTTTT‑CCGCCGCAACAAAACCGCCGTTCTCTCCAGTAGTGGC‑gg                                                                                           >  1:491814/1‑146 (MQ=255)                                                 gACCTGTGTCAGCGGCTACCGTGATTCATTTCCGCCAACAACCGCGCATTTATCCAACGCCATGTGCAAAAA‑TGCCT‑TCGCGGCGGCTGTCTGCCAGCTATTTTT‑CCGCCGCAACAAAACCGCCGTTCTCTCCAGTAGTGGC‑gggg                                                                                         >  1:1039360/1‑146 (MQ=255)                                                           aGCGGCTACCGTGATTCATTTCCGCCAACAACCGCGCATTTATCCAACGCCATGTGCAAAAA‑TGCCT‑TCGCGGCGGCTGTCTGCCAGCTATTTTT‑CCGCCGCAACAAAACCGCCGTTCTCTCCAGTAGTGGCGGGGGCAAGAGAACTaagt                                                                           >  1:714642/1‑148 (MQ=255)                                                            gCGGCTCCCGTGTTTCTTTCCCCCAAACACCCGCGCTTTTACCCAACCCCTTGTGAAAAAA‑TGCCT‑TCGGGGCGGCTGTCGGCCAGTTTTTTTC‑CCGCCGCAAAAAAACCGCCGTTCTCTCCAGTAGTGGC‑GGGGCAAGAGAAATAGC‑ttt                                                                        <  2:1019753/151‑1 (MQ=255)                                                              ggctccgtcaaTTCTTTCCCGCCACCACCCGCCCTTTTACCCAGCCCCATGGAAAAAAG‑TGCCG‑CCGCGGCGGTTGTCGGCCATTTTTTTTC‑CCGCGGAAAAAAAACCGCCGTTCTCTCCAGTAGTGGC‑GGGGCAAGAGAAATAGC‑t                                                                          <  1:525196/137‑1 (MQ=255)                                                              ggCTCCCGTGATTCTTTCCCGCAAACACCCGCGCATTTACCCACCGCCATGGGAAAAAA‑TCCCT‑TCGCGGCGGCTGTCTGCCACTTTTTTTC‑CCGCCGAAAAAAAACCGCCGTTCTCTCCAGTAGTGGC‑GGGGCAAGAGAAATAGC‑TTTaa                                                                      <  2:552642/151‑1 (MQ=255)                                                              gcctcccttGATTCTTTCCCCCAAACACCCGCGAATTTACCCACCGCCTTGTGAAAAAA‑GGCCT‑TCGCGGCGGCTGTCTGCAAGCTTTTTTC‑CCGCCGCAAAAAAACCGCCGTTCTCTCCAGTAGTGGC‑GGGGCAaga                                                                                    <  2:1017708/130‑1 (MQ=255)                                                                ctcccttGATTCATTCCCCCCAACACCCGCACTTTTACCCACCCCCATGTACAAAAT‑TGCTT‑TCGGGGCGTCTGTCTGCAATATTTTTTT‑CCGCCGAAAAAAAACCGCCGTTCTCTCCAGTAGTGGC‑GGGGCAAGAGAAATAGC‑TTTAAg                                                                     <  1:901104/144‑1 (MQ=255)                                                                             ttccccccAACACCCGCGCATTTACCCAACGCAATGTGAAAAAA‑TCCCT‑CCGCGGCGGCTGTCTGCCAGCTTTTTTC‑CCGCCGCAAAAAAACCGCCGTTCTCTCCAGTAGTGGC‑GGGGCAAGAGAAATAGC‑TTTAAGCCCGTCAtgttgt                                                        <  2:350993/144‑1 (MQ=255)                                                                             ttccccccAACACCCGCGAATTTACCCACCCCCATG‑GCAAAAAGGGCTT‑TCGGGGCGGCTGTCTGCCAGTTATTTTC‑CCGCCGCAAAAAAACCGCCGTTCTCTCCAGTAGTGGC‑GGGGCAAGAGAAATAGC‑TTTAAGc                                                                    <  2:144483/132‑1 (MQ=255)                                                                             ttcccccaaacaccCGCGCATTTACCCACCGCAATGTGAAAAAA‑TCCTT‑TCGGGGCGGCTGTCTGCCTGTTTTTTTC‑CCGCCGCAAAAAAACCGCCGTTCTCTCCAGTAGTGGC‑GGGGCAAGAGAAATAGC‑TTTAAGCCCGTCAtgttgt                                                        <  2:536495/142‑1 (MQ=255)                                                                               cccGCAACCACCCGCGCATTTACCCACCGCCATGTGCAAAAA‑TGCCT‑TCGCGGCGGCTGTCGGCCATTTTTTTTC‑CCGCCGCAAAAAATCCGCCGTTCTCTCCAGTAGTGGC‑GGGGCAAGAGAAATAGC‑TTTAAGCCCGTCATGTtgtg                                                       <  1:997673/148‑1 (MQ=37)                                                                                      acaccCGCGCTTTTACCAAACCCCATGGGAAAAAA‑TGCCT‑CCGCGGGGGCTGTCGGCCAGTTTTTTTC‑CCGCCAAAAAAAATCCGCCGTTCTCTCCAGTAGTGGC‑GGGGCAAGAGAAATAGC‑TTTAAGCCCGTCATGTTGTGTGGCAATc                                               <  1:226076/150‑1 (MQ=255)                                                                                                 tttACCCACCGCCTTGTGAAAAAA‑TGCCT‑CCGGGGCGGCTGCCTGCATTTTTTTTTC‑CCGCCGCAAAAAAACCGCCGTTCTCTCCAGTAGTGGC‑GGGGCAAGAGAAATAGC‑TTTAAGCCCGTCATGTTGTGTGGCAATCGCTGCTGGTaa                                    <  1:513382/150‑1 (MQ=255)                                                                                                 tttACCCACCGCCATGTGCAAAAT‑TCTTT‑TCGGGGGGGCGGTCTGCCTTTTTTTTTC‑CCGCCAAAAAAAATCCGCCGTTCTCTCCAGTAGTGGC‑GGGGCAAGAGAAATAGC‑TTTAAGCCCGTCATGTTGTGTGGCAATCGCTGCTGGTa                                     <  2:155124/149‑1 (MQ=255)                                                                                                   tATCCAACGCCATGTGCAAAAA‑TGCCT‑TCGCGGCGGCTGTCTGCCAGCTATTTTT‑CCGCCGCAACAAAACCGCCGTTCTCTCCAGTAGTGGC‑GGGGGGAGAGAAAAAACATTTAAACCC‑CCCTGTTTTGTGGGGATAGCTGCTgg                                       >  2:724348/1‑145 (MQ=25)                                                                                                     cccACCGCCATGTGAAAAAA‑TGCTT‑TCGCGGCGCCTGTCTGCCGGTTTTTTTC‑CCGCCGCAACAAAACCGCCGTTCTCTCCAGTAGTGGC‑GGGGCAAGAGAAATAGC‑TTTAAGCCCGTCATGTTGTGTGGCAATCGCTGCTGGTAACAAt                                <  2:894008/149‑1 (MQ=255)                                                                                                        accGCCATGTGAAAAAA‑GGCCT‑CCGGGGGGGCTGTCCCCCAGTTTTTTTC‑CCGCCGCAAAAAAACCGCCGTTCTCTCCAGTAGTGGC‑GGGGCAAGAGAAATAGC‑TTTAAGCCCGTCATGTTGTGTGGCAATCGCTGCTGGTAACaa                                 <  2:260193/144‑1 (MQ=255)                                                                                                          ccccgtgtgCAAAAA‑TTCTG‑GCGGGGCGGTTGTCGGCCAGCTTTTTTC‑CCGCCGCAAAAAAACCGCCGTTCTCTCCAGTAGTGGC‑GGGGCAAGAGAAATAGC‑TTTAAGCCCGTCATGTTGTGTGGCAATCGCTGCTGGTAACAAtgtg                             <  1:617588/143‑1 (MQ=255)                                                                                                          cGCCATGTACAAAAT‑GGCTT‑CCGCGGGTTCTGTCCGCCAGTTTTTTTC‑CCGCCAAAAAAAACCCGCCGTTCTCTCCAGTAGTGGC‑GGGGCAAGAGAAATAGC‑TTTAAGCCCGTCATGTTGTGTGGCAATCGCTGCTGGTAACAATGTGGa                           <  1:883731/150‑1 (MQ=255)                                                                                                          cGCCATGT‑CAAAAA‑ACCCTCTCGGGGGGGCTGTCGCCCACCTTTTTTC‑CCGCGGAAACAAAACCGCCGTTCTCTCCAGTAGTGGC‑GGGGCAAGAGAAATAGC‑TTTAAGCCCGTCATGTTGTGTGGCAATCGCTGCTGGTAACAATGTGGaa                          <  2:285669/151‑1 (MQ=255)                                                                                                                    aaaaa‑TCCCT‑TCGCGGCGCCGGTCT‑CCAGGTATTTTTCCCGCCACAACAAAACCGCCGTTCTCTCCAGTAGTGGC‑GGGGCAAGAGAAATAGC‑TTTAAGCCCGTCATGTTGTGTGGCAATCGCTGCTGGTAACAATGTGGAAAGGGAAGt                  <  1:832533/149‑1 (MQ=255)                                                                                                                                    ggcggcTGTCTGCCATCTTTTTTC‑CCGCCGAAAAAAAACCGCCGTTCTCTCCAGTAGTGGC‑GGGGCAAGAGAAATAGC‑TTTAAGCCCGTCATGTTGTGTGGCAATCGCTGCTGGTAACAATGTGGAAAGGGAAGTGCGGCGAATCAg      <  2:94984/147‑1 (MQ=255)                                                                                                                                    ggcggcTGTCTCCCGGCTTTTTTC‑CCGCCGCAAAAAAACCGCCGTTCTCTCCAGTAGTGGC‑GGGGCAAGAGAAATAGC‑TTTAAGCCCGTCATGTTGTGTGGCAATCGCTGCTGGTAACAATGTGGAAAGGGAAGTGCGGCGAATCAGCTcc  <  2:983871/151‑1 (MQ=255)                                                                                                                                      cggcTGTCTGCCAGCTATTTTT‑CCGCCGCAACAAAACCGCCGTTCTCTCCAGTAGTGGC‑GGGGGGAGAGAAAAAAC‑ATTTACCCCCCCCCGTTGTGTGGGGATCGCTGCTGGGGAAAAAGTGGGAAGGGGAgagggggg            >  1:553290/1‑132 (MQ=255)                                                                                                                                                      |                                                                                                                                        GAACTCGTAGGCCTGATAAGCGTAGCGCATCAGGCAATTCCAGCCGCAGACCTGTGTCAGCGGCTACCGTGATTCATTTCCGCCAACAACCGCGCATTTATCCAACGCCATGTGCAAAAA‑TGCCT‑TCGCGGCGGCTGTCTGCCAGCTATTTTT‑CCGCCGCAACAAAACCGCCGTTCTCTCCAGTAGTGGC‑GGGGCAAGAGAAATAGC‑TTTAAGCCCGTCATGTTGTGTGGCAATCGCTGCTGGTAACAATGTGGAAAGGGAAGTGCGGCGAATCAGCTCC  >  NC_000913/357728‑358007

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: ‑