Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NC_000913	357,875	0	A	T	48.0%	43.6 / 28.3	50	N272K (AAT→AAA)	cynR	transcriptional activator of cyn operon; autorepressor
Reads supporting (aligned to +/- strand):  ref base A (16/10);  new base T (0/24);  total (16/34)
Fisher's exact test for biased strand distribution p-value = 1.23e-06
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 1.00e+00

AACTCGTAGGCCTGATAAGCGTAGCGCATCAGGCAATTCCAGCCGCAGACCTGTGTCAGCGGCTACCGTGATTCATTTCCGCCAACAACCGCGCATTTATCCAACGCC‑ATGTGC‑AAAAA‑TGCCTTCGCGGCGGCTGTCTGCCAGCTATTTTT‑CCGCCGCAACAAAACCGCCGTTCTCTCCAGTAGTGGCGGGGCAAGAG‑AAATAGCTTTAAGCCCGTCATGTTGTGTGGCAATCGCTGCT‑GGTAACAATGTGGAAAGGGAAGTGCGGCGAATCAGCTCCAGAACCGC  >  NC_000913/357729‑358015                                                                                                                                                      |                                                                                                                                                aaCTCGTAGGCCTGATAAGCGTAGCGCATCAGGCAATTCCAGCCGCAGACCTGTGTCAGCGGCTACCGTGATTCATTTCCGCCAACAACCGCGCATTTATCCAACGCC‑ATGTGC‑AAAAA‑TGCCTTCGCGGCGGCTGTCTGCCAGCTAtttt                                                                                                                                             >  2:73589/1‑151 (MQ=255)     cGTAGGCCTGATAAGCGTAGCGCATCAGGCAATTCCAGCCGCAGACCTGTGTCAGCGGCTACCGTGATTCATTTCCGCCAACAACCGCGCATTTATCCAACGCC‑ATGTGC‑AAAAA‑TGCCTTCGCGGCGGCTGTCTGCCAGCTATTTTT‑ccg                                                                                                                                        <  1:1005032/151‑1 (MQ=255)     cGTAGGCCTGATAAGCGTAGCGCATCAGGCAATTCCAGCCGCAGACCTGTGTCAGCGGCTACCGTGATTCATTTCCGCCAACAACCGCGCATTTATCCAACGCC‑ATGTGC‑AAAAA‑TGCCTTCGCGGCGGCTGTCTGCCAGCTATTTTT‑ccg                                                                                                                                        <  2:75396/151‑1 (MQ=255)        aGGCCTGATAAGCGTAGCGCATCAGGCAATTCCAGCCGCAGACCTGTGTCAGCGGCTACCGTGATTCATTTCCGCCAACAACCGCGCATTTATCCAACGCC‑ATGTGC‑AAAAA‑TGCCTTCGCGGCGGCTGTCTGCCAGCTATTTTT‑ccgcc                                                                                                                                      <  2:322940/150‑1 (MQ=255)            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                                                                                                                               <  2:451887/151‑1 (MQ=255)              gATAAGCGTAGCGCATCAGGCAATTCCAGCCGCAGACCTGTGTCAGCGGCTACCGTGATTCATTTCCGCCAACAACCGCGCATTTATCCAACGCC‑ATGTGC‑AAAAA‑TGCCTTCGCGGCGGCTGTCTGCCAGCTATTTTT‑CCGCCGcaacaa                                                                                                                               <  1:60702/151‑1 (MQ=255)              gATAAGCGTAGCGCATCAGGCAATTCCAGCCGCAGACCTGTGTCAGCGGCTACCGTGATTCATTTCCGCCAACAACCGCGCATTTATCCAACGCC‑ATGTGC‑AAAAA‑TGCCTTCGCGGCGGCTGTCTGCCAGCTATTTTT‑CCGCCGcaacaa                                                                                                                               <  1:920455/151‑1 (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)                                                                                                                                                      |                                                                                                                                                AACTCGTAGGCCTGATAAGCGTAGCGCATCAGGCAATTCCAGCCGCAGACCTGTGTCAGCGGCTACCGTGATTCATTTCCGCCAACAACCGCGCATTTATCCAACGCC‑ATGTGC‑AAAAA‑TGCCTTCGCGGCGGCTGTCTGCCAGCTATTTTT‑CCGCCGCAACAAAACCGCCGTTCTCTCCAGTAGTGGCGGGGCAAGAG‑AAATAGCTTTAAGCCCGTCATGTTGTGTGGCAATCGCTGCT‑GGTAACAATGTGGAAAGGGAAGTGCGGCGAATCAGCTCCAGAACCGC  >  NC_000913/357729‑358015

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 12 ≤ ATCG/ATCG < 13 ≤ ATCG/ATCG < 27 ≤ ATCG/ATCG < 39 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑