Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NC_000913	357,887	0	C	A	42.2%	24.7 / 19.8	45	L268F (TTG→TTT)	cynR	transcriptional activator of cyn operon; autorepressor
Reads supporting (aligned to +/- strand):  ref base C (14/12);  new base A (0/19);  total (14/31)
Fisher's exact test for biased strand distribution p-value = 6.22e-05
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 1.00e+00

CTGATAAGCGTAGCGCATCAGGCAATTCCAGCCGCAGACCTGTGTCAGCGGCTACCGTGATTCATTTCCGCCAACAACCGCGCATTTATCCAACGCC‑ATGTGC‑AAAAA‑TGCCTTCGCGGCGGCTGTCTGCCAGCTATTTTT‑CCGCCGCAACAAAACCGCCGTTCTCTCCAGTAGTGGCGGGGCAAGAG‑AAATAGCTTTAAGCCCGTCATGTTGTGTGGCAATCGCTGCT‑GGTAACAATGTGGAAAGGGAAGTGCGGCGAATCAGCTCCAGAACCGCGCTAATTGAGTTCGCCTC  >  NC_000913/357740‑358033                                                                                                                                                        |                                                                                                                                                     cTGATAAGCGTAGCGCATCAGGCAATTCCAGCCGCAGACCTGTGTCAGCGGCTACCGTGATTCATTTCCGCCAACAACCGCGCATTTATCCAACGCC‑ATGTGC‑AAAAA‑TGCCTTCGCGGCGGCTGTCTGCCAGCTATTTTT‑CCGCCGcaac                                                                                                                                                   >  1:32304/1‑151 (MQ=255)  tGATAAGCGTAGCGCATCAGGCAATTCCAGCCGCAGACCTGTGTCAGCGGCTACCGTGATTCATTTCCGCCAACAACCGCGCATTTATCCAACGCC‑ATGTGC‑AAAAA‑TGCCTTCGCGGCGGCTGTCTGCCAGCTATTTTT‑CCGCCGcaac                                                                                                                                                   >  1:12925/1‑150 (MQ=255)   gATAAGCGTAGCGCATCAGGCAATTCCAGCCGCAGACCTGTGTCAGCGGCTACCGTGATTCATTTCCGCCAACAACCGCGCATTTATCCAACGCC‑ATGTGC‑AAAAA‑TGCCTTCGCGGCGGCTGTCTGCCAGCTATTTTT‑CCGCCGcaacaa                                                                                                                                                 <  1:60702/151‑1 (MQ=255)   gATAAGCGTAGCGCATCAGGCAATTCCAGCCGCAGACCTGTGTCAGCGGCTACCGTGATTCATTTCCGCCAACAACCGCGCATTTATCCAACGCC‑ATGTGC‑AAAAA‑TGCCTTCGCGGCGGCTGTCTGCCAGCTATTTTT‑CCGCCGcaacaa                                                                                                                                                 <  1:920455/151‑1 (MQ=255)   gATAAGCGTAGCGCATCAGGCAATTCCAGCCGCAGACCTGTGTCAGCGGCTACCGTGATTCATTTCCGCCAACAACCGCGCATTTATCCAACGCC‑ATGTGC‑AAAAA‑TGCCTTCGCGGCGGCTGTCTGCCAGCTATTTTT‑CCGCCGcaacaa                                                                                                                                                 <  2:451887/151‑1 (MQ=255)         cGTAGCGCATCAGGCAATTCCAGCCGCAGACCTGTGTCAGCGGCTACCGTGATTCATTTCCGCCAACAACCGCGCATTTATCCAACGCC‑ATGTGC‑AAAAA‑TGCCTTCGCGGCGGCTGTCTGCCAGCTATTTTT‑CCGCCGCAACAAAAccgc                                                                                                                                           >  1:113271/1‑151 (MQ=255)          gTAGCGCATCAGGCAATTCCAGCCGCAGACCTGTGTCAGCGGCTACCGTGATTCATTTCCGCCAACAACCGCGCATTTATCCAACGCC‑ATGTGC‑AAAAA‑TGCCTTCGAGGCGGCTGTCTGCCAGCTATTTTT‑CCGCCGCAACAAAAccg                                                                                                                                            >  1:404762/1‑149 (MQ=255)            aGCGCATCAGGCAATTCCAGCCGCAGACCTGTGTCAGCGGCTACCGTGATTCATTTCCGCCAACAACCGCGCATTTATCCAACGCC‑ATGTGC‑AAAAA‑TGCCTTCGCGGCGGCTGTCTGCCAGCTATTTTT‑CCGCCGCAACAAAACCGCCGt                                                                                                                                        >  2:24901/1‑151 (MQ=255)               gcATCAGGCAATTCCAGCCGCAGACCTGTGTCAGCGGCTACCGTGATTCATTTCCGCCAACAACCGCGCATTTATCCAACGCC‑ATGTGC‑AAAAA‑TGCCTTCGCGGCGGCTGTCTGCCAGCTATTTTT‑CCGCCGCAACAAAACCGCCGTtct                                                                                                                                     >  1:353096/1‑151 (MQ=255)                  tCAGGCAATTCCAGCCGCAGACCTGTGTCAGCGGCTACCGTGATTCATTTCCGCCAACAACCGCGCATTTATCCAACGCC‑ATGTGC‑AAAAA‑TGCCTTCGCGGCGGCTGTCTGCCAGCTATTTTT‑CCGCCGCAACAAAACCGCCGTtctctc                                                                                                                                  >  2:810330/1‑151 (MQ=255)                            cccgCCGCAGCCTGGTCTCAGCGCCTCCCGTAATTCTTTCCCGCCAACACCCGCCAATTTACCCAACGCC‑ATGTGA‑AAAAA‑TCCCTTCGCGGCGGCTGTCTGCCAGTTATTTTC‑CCGCCGAAAAAAAACCGCCGTTCTCTCCAGTAGTGGc                                                                                                                        <  2:855163/148‑1 (MQ=255)                            ccaccccccccccTTTGTCGGCGCCACCCGTTTTTCATTCCCCCCAACACCCGCCCTTTTCCCCACCCCC‑ATGTGC‑AAAAA‑TCCCTCCGCGGCGGCTGTCTGCAGGTTTTTTTC‑CCGCCGCAAAAAAACCGCCGTTCTCTCCAGTAGTGGc                                                                                                                        <  1:752131/140‑1 (MQ=255)                             cccccccAGCCCTGTGTCGGCGCCTACCGTGTTTCATTCCCCCCAACACCCGCGCTTTTACCCAACGCC‑ATGGGA‑AAAAA‑GGCCTCCGGGGGGGCTGCCTGCCAGCTTTTTTC‑CCGCCGAAAAAAAACCGCCGTTCTCTCCAGTAGTGGCg                                                                                                                       <  1:282982/145‑1 (MQ=255)                              aGCCGCAGACCTGTGTCAGCGGCTACCGTGATTCATTTCCGCCAACAACCGCGCATTTATCCAACGCC‑ATGTGC‑AAAAA‑TGCCTTCGCGGCGGCTGTCTGCCAGCTATTTTT‑CCGCCGCAACAAAACCGCCGTTCTCTCCAGTAGTGGCgg                                                                                                                      >  1:581674/1‑151 (MQ=255)                               gCCGCAGACCTGTGTCAGCGGCTACCGTGATTCATTTCCGCCAACAACCGCGCATTTATCCAACGCC‑ATGTGC‑AAAAA‑TGCCTTCGCGGCGGCTGTCTGCCAGCTATTTTT‑CCGCCGCAACAAAACCGCCGTTCTCTCCAGTAGTGGCggg                                                                                                                     >  2:197025/1‑151 (MQ=255)                               gCCGCAGACCTGTGTCAGCGGCTACCGTGATTCATTTCCGCCAACAACCGCGCATTTATCCAACGCC‑ATGTGC‑AAAAA‑TGCCTTCGCGGCGGCTGTCTGCCAGCTATTTTT‑CCGCCGCAACAAAACCGCCGTTCTCTCCAGTAGTGGCgg                                                                                                                      >  1:896607/1‑150 (MQ=255)                                               aGCGGCTACCGTGATTCATTTCCGCCAACAACCGCGCATTTATCCAACGCC‑ATGTGC‑AAAAA‑TGCCTTCGCGGCGGCTGTCTGCCAGCTATTTTT‑CCGCCGCAACAAAACCGCCGTTCTCTCCAGTAGTGGCGGGGGCAGAG‑gaaaaaaa                                                                                                     >  2:160438/1‑145 (MQ=255)                                                 cGGCTCCCGTGATTCATTCCCCCCAACACCCGCGCATTTACCCACCGCA‑TTGTGA‑AAAAA‑TCCTTCCGCGGCGGCTGTCTGCCAGTTTTTTTC‑CCGCCGCAAAAAAACCGCCGTTCTCTCCAGTAGTGGCGGGGCAAGAG‑aaa                                                                                                          <  2:252827/143‑1 (MQ=255)                                                  gccTACCGTGATTCTTTCCCCCAAACACCCGCGCTTTTACCCACCCCC‑TTGTGA‑AAAAT‑GGCTTTGGGGGGGGTTGTCGGCCTGTTTTTTTC‑CCGCCGCAAAAAAACCGCCGTTCTCTCCAGTAGTGGCGGGGCAAGAG‑AAATa                                                                                                        <  2:825842/142‑1 (MQ=255)                                                    ccaCCGTTATTCTTTCCCCCCACCACCCGCGCTTTTATCCACCCCC‑ATGTCA‑AAAAA‑CCCCTCCGCGGCGCCTGTCGGCCATTTTTTTTC‑CCGCCAAAAAAAAACCGCCGTTCTCTCCAGTAGTGGCGGGGCAAGAG‑AAATAGCTTTa                                                                                                  <  1:533327/146‑1 (MQ=255)                                                     accgttttttCATTCCCGCAAACACCCGCGCATTTACCCACCCCC‑ATGTAA‑AAAAG‑TGCCTGCGGGGCGGCTGCCGGCCGTGTTTTTTC‑CCGCCCAAAAAAAACCGCCGTTCTCTCCAGTAGTGGCGGGGCAaga                                                                                                               <  1:1024626/127‑1 (MQ=255)                                                       ccGTGTTTCTTTCCCCCCAACACCCGCCCTTTTA‑CCACCCCCAATTTAC‑AAAAT‑TCCCTCCGCGGCGGCTCTC‑GCCCGCTTTTTTTCCCGCCGAAACAAAACCGCCGTTCTCTCCAGTAGTGGCGGGGCAAGAG‑AAATAGCTTTAAg                                                                                                <  2:246470/147‑1 (MQ=255)                                                       ccGTGTTTCATTCCCGCCAACACCCGCGCTTTTACCCACCGCC‑ATGTGA‑AAAAA‑TGCCTTCGCGGCGGCTGTCTGCCAGTTTTTTTC‑CCGCCGCAAAAAAACCGCCGTTCTCTCCAGTAGTGGCGGGGCAAGAG‑AAATAGCTTTAAGcc                                                                                              <  2:552626/149‑1 (MQ=255)                                                       ccGTGTTTCATTCCCCCAAACACCCCCTCTTTTACCCACCGCC‑ATGTGA‑AAAAA‑TGCTTGCGGGGCGGCTGCCTCCCATTTTTTTTC‑CCGCCGAAAAAAAACCGCCGCTCTCTCCAGTAGTGGCGGGGCAAGAG‑AAATAGCTTTAAGcc                                                                                              <  2:739039/149‑1 (MQ=255)                                                       ccGTAATTCTTTCCCCCCAACACCCGCGCATTTACCCACCGCC‑ATTTAA‑AAAAA‑GGCCTCCGGGGGGGCTGTCTGCCAGTTTTTTTC‑CCGCCGAAACAAAACCGCCGTTCTCTCCAGTAGTGGCGGGGCAAGAG‑AAATAGCTTTAAGcc                                                                                              <  2:1008244/149‑1 (MQ=255)                                                         gTGATTCATTTCCGCCAACAACCGCGCATTTATCCAACGCC‑ATGTGC‑AAAAA‑TGCCTTCGCGGCGGCTGTCTGCCAGCTATTTTT‑CCGCCGCAACAAAACCGCCGTTCTCTCCAGTAGTGGCGGGGGAGGGG‑aaaaaaattttaaacc                                                                                             >  2:671732/1‑135 (MQ=25)                                                                 ttcccGCCACCACCCGCCCTTTTACCCACCGCC‑TTTTGA‑AAAAA‑TCCCTTCGGGGCGGCTTTCCGCCAGTTTTTTTC‑CCCCCCCAACAAAACCGCCGTTCTCTCCAGTAGTGGCGGGGCAAGAG‑AAATAGCTTTAAGCCCGTCAtgttgt                                                                                   <  2:675382/147‑1 (MQ=255)                                                                   ccccccAACACCCGCGCATTTATCCACCGCC‑ATGTGA‑AAAAA‑TGCCTTCGCGGCGGCTGTCTGCCAGCTTTTTTC‑CCGCCGCAAAAAAACCGCCGTTCTCTCCAGTAGTGGCGGGGCAAGAG‑AAATAGCTTTAAGCCCGTCATGTtgtg                                                                                  <  2:730887/145‑1 (MQ=255)                                                                    cgccaaacaacCGCGAGTTAACCAAACCCC‑AGGTGA‑AAAAT‑TCCCTCGGGGGCGGTTGTCGGCAAGTTATTTGC‑CCGCCAAAAAAAACCCGCCGTTCTCTCCAGTAGTGGCGGGGCAAGAG‑AAAt                                                                                                         <  1:73582/120‑1 (MQ=255)                                                                    ccaccAACAGCCCCGCATTTGTCAACCGCC‑ATGCGA‑AAAAA‑TGTGCCGGGGGCGCCTGTCACCCACCTATTGAG‑CCGCCAAAAAAAACCCGCCGTTCTCTCCAGTAGTGGCGGGGCAAGAG‑AAATAGCTTTAAGCCCGTCAt                                                                                        <  1:992217/139‑1 (MQ=255)                                                                    ccGCCACCACCCGCGCTTTTACCCACCGCC‑ATTTAA‑AAAAA‑TGCTTTCGCGGCGGCTGTCGCCCAGTTTTTTTC‑CCGCCGAAAAAAAACCGCCGTTCTCTCCAGTAGTGGCGGGGCAAGAG‑AAATAGCTTTAAGCCCGTCATGTtgtgtg                                                                                <  2:190295/150‑1 (MQ=255)                                                                    ccGCCAACACCCGCCTTTTTCTCC‑ACCCC‑AAGTGG‑AAAAAGTGCCTCGGCGGCGGCTTCCTGCCAGTTTTTTTC‑CCGCCGAAAAACATCCGCCGTTCTCTCCAGTAGTGGCGGGGCAAGAG‑AAATAGCTTTAAGCCCGTCATGTtgtgt                                                                                 <  1:40920/149‑1 (MQ=255)                                                                            acccGCGCTTTTACCCAACCCC‑ATGTGC‑AAAAA‑TCCCTCCGGGGCGGCTGTCTGCCAGTTTTTTTC‑CCGCCGCAAAAAAACCGCCGTTCTCTCCAGTAGTGGCGGGGCAAGAG‑AAATAGCTTTAAGCCCGTCATGTTGTGTGGCAATCg                                                                         <  2:339517/147‑1 (MQ=255)                                                                              ccGCGCTTTTCCCAAACCCC‑AT‑TGCAAAAAA‑TGCTTGCGGGGCGGCTTTCTCCCGGTTTTTTTC‑CCGCCAAAAAAAAACCGCCGTTCTCTCCAGTAGTGGCGGGGCAAGAG‑AAATAGCTTTAAGCCCGTCATGTTGTGTGGCAATCgct                                                                       <  1:1022576/149‑1 (MQ=255)                                                                                        acccAACGCT‑ATGTAA‑AAAAT‑TGCCTCCGCGGCGGCTTTCTCCCATCTTTTTTC‑CCGCCGAAAAAAAACCGCCGTTCTCTCCAGTAGTGGCGGGGCAAGAG‑AAATAGCTTTAAGCCCGTCATGTTGTGTGGCAATCGCTGCT‑GGTAAc                                                             <  2:777188/146‑1 (MQ=255)                                                                                        aTCCAACGCC‑ATGTGC‑AAAAA‑TGCCTTCGCGGCGGCTGTCTGCCAGCTATTTTT‑CCGCCGCAACAAAACCGCCGTTCTCTCCAGTAGTGGCGGCGCGGGAG‑AAAAAGATTTTATACCCTCCTGTTGTTTGGGGATCCCGGCT‑gggtaca                                                            >  2:902798/1‑144 (MQ=21)                                                                                          ccAACGCC‑ATGTGA‑AAAAA‑GGCCTCCGCGGCGGCTGTCTGCCGGTTTTTTTC‑CCGCCGAAAAAAAACCGCCGTTCTCTCCAGTAGTGGCGGGGCAAGAG‑AAATAGCTTTAAGCCCGTCATGTTGTGTGGCAATCGCTGCT‑GGTAACAAt                                                          <  1:541393/149‑1 (MQ=255)                                                                                                cc‑ATGTGA‑AAAAA‑TCCCTTCGGGGCGGCTGTCTGCCAGTTTTTTTC‑CCGCCGCAAAAAAACCGCCGTTCTCTCCAGTAGTGGCGGGGCAAGAG‑AAATAGCTTTAAGCCCGTCATGTTGTGTGGCAATCGCTGCT‑GGTAACAATGTGGAAAg                                                  <  2:566398/151‑1 (MQ=255)                                                                                                 c‑ATGTGC‑AAAAA‑TGCCTTCGCGGCGGCTGTCTGCCAGCTATTTTT‑CCGCCGCAACAAAACCGCCGTTCTCTCCAGTAGTGGCGGGGGGAAAG‑AAAAAAATTTAAACCCCCCCTGTTGTGTGGGGATAGCCGCT‑ggggaaaaagtggg                                                     >  2:674067/1‑135 (MQ=25)                                                                                                          aaaaa‑TGCCTTCGCGGCGGCTGTCTGCCAGCTATTTTT‑CCGCCGCAACAAAACCGCCGTTCTCTCCAGTAGTGGCGGGGGCAGAGAAAAAAAATTTAACCCCG‑CCTGTTTTGGGGGAATTGCCGCTGGGTAAAAAGTGGGAAAGGGagggg                                           >  2:879188/1‑147 (MQ=255)                                                                                                          aaaaa‑GCCCTCCGCGGCGCCTGTCTGCAATTTATTTTC‑CCCCCGCAAAAAACCCGCCGTTCTCTCCAGTAGTGGCGGGGCAAGAG‑AAATAGCTTTAAGCCCGTCATGTTGTGTGGCAATCGCTGCT‑GGTAACAATGTGGAAAGGGAAGTgc                                          <  1:552585/151‑1 (MQ=255)                                                                                                            aaa‑TGCCTCCGCGGCGGCTGTCTGCCAGCTTTTTTC‑CCGCCGAAAAAAAACCGCCGTTCTCTCCAGTAGTGGCGGGGCAAGAG‑AAATAGCTTTAAGCCCGTCATGTTGTGTGGCAATCGCTGCT‑GGTAACAATGTGGAAAGGGAAGTgcgg                                        <  2:798479/151‑1 (MQ=255)                                                                                                                  ccTCCGGGGCGATTGTCCCCCAGCTTTTTCC‑CCGCCGAAAAAAAACCGCCGTTCTCTCCATTAGTGGCGGGGCAAGAG‑AAATAGCTTTAAGCCCGTCATGTTGTGTGGCAATCGCTGCT‑GGTAACAATGTGGAAAGGGAAGTGCGGCGAAt                                   <  2:769384/151‑1 (MQ=255)                                                                                                                       gcgggggtttccTGCCAGTTTTTTCC‑CCGCCAAAAAAAAACCGCCGTTCTCTCCAGTAGTGGCGGGGCAAGAG‑AAATAGCTTTAAGCCCGTCATGTTGTGTGGCAATCGCTGCT‑GGTAACAATGTGGAAAGGGAAGTGCGGCGaa                                    <  1:275165/134‑1 (MQ=255)                                                                                                                          gcgccTGTCGGCGAGTTTTTTTT‑CCGCCCCAAAAAAGCCGCCGTTCTCTCCAGTAGTGGCGGGGCAAGAG‑AAATAGCTTTAAGCCCGTCATGTTGTGTGGCAATCGCTGCT‑GGTAACAATGTGGAAAGGGAAGTGCGGCGAATCAGCTc                             <  2:846779/149‑1 (MQ=255)                                                                                                                                  ctccctgCTTTTTTC‑CCGCCGCAAAAAAACCGCCGTTCTCTCCAGTAGTGGCGGGGCAAGAG‑AAATAGCTTTAAGCCCGTCATGTTGTGTGGCAATCGCTGCT‑GGTAACAATGTGGAAAGGGAAGTGCGGCGAATCAGCTCCAGAACcgc                    <  2:802040/144‑1 (MQ=255)                                                                                                                                            ttttc‑CCGCCGAAAAAAAACCGCCGTTCTCTCCAGTAGTGGCGGGGCAAGAG‑AAATAGCTTTAAGCCCGTCATGTTGTGTGGCAATCGCTGCT‑GGTAACAATGTGGAAAGGGAAGTGCGGCGAATCAGCTCCAGAACCGCGCTAATTGAg          <  2:534353/150‑1 (MQ=255)                                                                                                                                            ttttc‑CCGCCACAAAAAAACCGCCGTTCTCTCCAGTAGTGGCGGGGCAAGAG‑AAATAGCTTTAAGCCCGTCATGTTGTGTGGCAATCGCTGCT‑GGTAACAATGTGGAAAGGGAAGTGCGGCGAATCAGCTCCAGAACCGCGCTAAt              <  1:425864/146‑1 (MQ=255)                                                                                                                                            ttttc‑CCCCCGAAAAAAAACCGCCGTTCTCTCCAGTAGTGGCGGGGCAAGAG‑AAATAGCTTTAAGCCCGTCATGTTGTGTGGCAATCGCTGCT‑GGTAACAATGTGGAAAGGGAAGTGCGGCGAATCAGCTCCAGAACCGCGCTAATTGa           <  1:179343/149‑1 (MQ=255)                                                                                                                                                t‑CCGCCGCAACAAAACCGCCGTTCTCTCCAGTAGTGGCGGGGGCAGGG‑GAAAAAATTTTAGCCCCTCCTGTTGTGTGGGGATCGCTGCT‑GGGGACAATGTGGGAAGGGGAGGGGGGGGGAACAGCTCCCGAAACCCGCCAATTGAGttt       >  1:474192/1‑148 (MQ=255)                                                                                                                                                 ccctccgaAAAAAAACCGCCGTTCTCTCCAGTAGTGGCGGGGCAAGAG‑AAATAGCTTTAAGCCCGTCATGTTGTGTGGCAATCGCTGCT‑GGTAACAATGTGGAAAGGGAAGTGCGGCGAATCAGCTCCAGAACCGCGCTAATTGAGTTc       <  1:51262/145‑1 (MQ=255)                                                                                                                                                     ccgaAAAAAAACCGCCGTTCTCTCCAGTAGTGGCGGGGCAAGAG‑AAATAGCTTTAAGCCCGTCATGTTGTGTGGCAATCGCTGCT‑GGTAACAATGTGGAAAGGGAAGTGCGGCGAATCAGCTCCAGAACCGCGCTAATTGAGTTCGCCTc  <  2:761555/150‑1 (MQ=255)                                                                                                                                                        |                                                                                                                                                     CTGATAAGCGTAGCGCATCAGGCAATTCCAGCCGCAGACCTGTGTCAGCGGCTACCGTGATTCATTTCCGCCAACAACCGCGCATTTATCCAACGCC‑ATGTGC‑AAAAA‑TGCCTTCGCGGCGGCTGTCTGCCAGCTATTTTT‑CCGCCGCAACAAAACCGCCGTTCTCTCCAGTAGTGGCGGGGCAAGAG‑AAATAGCTTTAAGCCCGTCATGTTGTGTGGCAATCGCTGCT‑GGTAACAATGTGGAAAGGGAAGTGCGGCGAATCAGCTCCAGAACCGCGCTAATTGAGTTCGCCTC  >  NC_000913/357740‑358033

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 12 ≤ ATCG/ATCG < 13 ≤ ATCG/ATCG < 26 ≤ ATCG/ATCG < 39 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑