Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NC_000913	357,880	0	T	C	50.0%	24.1 / 20.1	44	K271E (AAA→GAA)	cynR	transcriptional activator of cyn operon; autorepressor
Reads supporting (aligned to +/- strand):  ref base T (15/7);  new base C (0/22);  total (15/29)
Fisher's exact test for biased strand distribution p-value = 1.48e-06
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 1.00e+00

CTCGTAGGCCTGATAAGCGTAGCGCATCAGGCAATTCCAGCCGCAGACCTGTGTCAGCGGCTACCGTGATTCATTTCCGCC‑AACAACCGCGCATTTATCCAACGCC‑ATGTGCAAAAATGCCTTCGCGG‑CGGC‑TGTCTGCCAG‑CTATTTTTCCGCCGCAACAAAACCGCCGTTCTCTCCAGTAGTGGCGGGGCAAGA‑GAAATAGCTTTAAGCCCGTCATGTTGTGTGGCAATCGCTGCTGGTAACAATGTGGAAAGGGAAGTGCGGCGAATCAGCTCCAGAACCGCGCTAAT  >  NC_000913/357731‑358021                                                                                                                                                           |                                                                                                                                               cTCGTAGGCCTGATAAGCGTAGCGCATCAGGCAATTCCAGCCGCAGACCTGTGTCAGCGGCTACCGTGATTCATTTCCGCC‑AACAACCGCGCATTTATCCAACGCC‑ATGTGCAAAAATGCCTTCGCGG‑CGGC‑TGTCTGCCAG‑CTATTTTTc                                                                                                                                               >  2:640643/1‑151 (MQ=255)             aTAAGCGTAGCGCATCAGGCAATTCCAGCCGCAGACCTGTGTCAGCGGCTACCGTGATTCATTTCCGCC‑AACAACCGCGCATTTATCCAACGCC‑ATGTGCAAAAATGCCTTCGCGG‑CGGC‑TGTCTGCCAG‑CTATTTTTCCGCCGcaacaa                                                                                                                                    >  1:817859/1‑150 (MQ=255)               aaGCGTAGCGCATCAGGCAATTCCAGCCGCAGACCTGTGTCAGCGGCTACCGTGATTCATTTCCGCC‑AACAACCGCGCATTTATCCAACGCC‑ATGTGCAAAAATGCCTTCGCGG‑CGGC‑TGTCTGCCAG‑CTATTTTTCCGCCGCAACaaa                                                                                                                                   >  2:409568/1‑149 (MQ=255)                aGCGTAGCGCATCAGGCAATTCCAGCCGCAGACCTGTGTCAGCGGCTACCGTGATTCATTTCCGCC‑AACAACCGCGCATTTATCCAACGCC‑ATGTGCAAAAATGCCTTCGCGG‑CGGC‑TGTCTGCCAG‑CTATTTTTCCGCCGCAACAAAAcc                                                                                                                                <  1:590761/151‑1 (MQ=255)                 gCGTAGCGCATCAGGCAATTCCAGCCGCAGACCTGTGTCAGCGGCTACCGTGATTCATTTCCGCC‑AACAACCGCGCATTTATCCAACGCC‑ATGTGCAAAAATGCCTTCGCGG‑CGGC‑TGTCTGCCAG‑CTATTTTTCCGCCGCAACAAAAccg                                                                                                                               >  2:51724/1‑151 (MQ=255)                 gCGGAGCGCATCATGCAATTCCAGCCGCGGACCCGTGTAAGCGGCTACCGTGATTCATTTCCGCC‑AACAACCGCGCATTTATCCAACGCC‑ATGTGCAAAAATGCCTCCGCGC‑CGCC‑TGTCGGCCAG‑CTATTTTTCCGCCGCAACAAAAcc                                                                                                                                <  2:425425/150‑1 (MQ=18)                    tAGCGAATCAAGCAACTCCAGACGAAGAACTGTGACAGCGGCTACCGTGATTCATTTCCAAC‑AACAAACGCGCATTTATGCAACACC‑AAGGGCAAAAATACCTTCGCGG‑CGGC‑TGTATGACAG‑CTTTTTTTACGACacaacatcaacgc                                                                                                                              >  2:387977/1‑142 (MQ=9)                       cgcATCCGCCAATTCCACCCGCAGTCCGGTCTCAGCTGCTACCGTGATTCATTTCCGCC‑AACAACCGCGCATTTATCCAACGCC‑ATGTGCAAAAATGCCTTCGCGG‑CGGC‑TGTCTGCCGG‑CTATTTTTCCGCCGCAACAAAAccgcc                                                                                                                             <  2:733241/147‑1 (MQ=18)                          aTCAGGCAATTCCAGCCGCAGACCTGTGTCAGCGGCTACCGTGATTCATTTCCGCC‑AACAACCGCGCATTTATCCAACGCC‑ATGTGCAAAAATGCCTTCGCGG‑CGGC‑TGTCTGCCAG‑CTATTTTTCCGCCGCAACAAAACCGCCGTtctct                                                                                                                      >  1:475705/1‑151 (MQ=255)                            cAGGCAATTCCAGCCGCAGACCTGTGTCAGCGGCTACCGTGATTCATTTCCGCC‑AACAACCGCGCATTTATCCAACGCC‑ATGTGCAAAAATGCCTTCGCGG‑CGGC‑TGTCTGCCAG‑CTATTTTTCCGCCGCAACAAAACCGCCGTTCTCTcc                                                                                                                    >  1:773707/1‑151 (MQ=255)                                 attcccAGCCGCAGCCCTGTGCCAGCGCCTACCGTGTTTCATTCCCCCC‑AACAACCGCGCTTTTACCCAACGCC‑ATGTGAAAAAATGCCTTCGGGG‑CGGC‑TGTCGGCCAG‑CTTTTTTCCCGCCGCAACAAAACCGCCGTTCTCTCCagta                                                                                                                <  1:941710/146‑1 (MQ=255)                                     ccAGCCGCAGACCTGTGTCAGCGGCTACCGTGATTCATTTCCGCC‑AACAACCGCGCATTTATCCAACGCC‑ATGTGCAAAAATGCCTTCGCGG‑CGGC‑TGTCTGCCAG‑CTATTTTTCCGCCGCAACAAAACCGCCGTTCTCTCCAGTAGTGGc                                                                                                           >  1:478963/1‑151 (MQ=255)                                     ccACCCGCAGCCTTGTGCCAGGGCCTCCCGGAATTCATTCCCCCC‑AACACCCGCCTATTCACCCACCGCC‑ATCTGAAAAAATGCC‑TCGGGG‑GGGCGTGTCTGCAAT‑CTTTTTTCCCCCCGAAAAAAACCCGCCGTTCTCTCCAGTAGTGGc                                                                                                           <  2:9797/151‑1 (MQ=255)                                          cGCAGACCTGTGTCAGCGGCTACCGTGATTCATTTCCGCC‑AACAACCGCGCATTTATCCAACGCC‑ATGTGCAAAAATGCCTTCGCGG‑CGGC‑TGTCTGCCAG‑CTATTTTTCCGCCGCAACAAAACCGCCGTTCTCTCCAGTAGTGGCgggg                                                                                                       >  1:537332/1‑150 (MQ=255)                                              gACTTGTGTCAGCGGCTACCGTAATTCATTCCCGCC‑AACACCCGCGAATTTAGCCAACTCC‑TGGTGAAAAAAGCCCTTCGCGG‑CGGT‑TTTCTCCCAG‑TTTTTTTCCCGCCGAAAAAAAACCGCCGTTCTCTCCAGTAGTGGCGGGGCaa                                                                                                    <  1:709633/149‑1 (MQ=255)                                                  tgtgTCGGGGGCTCCCGTTTTTCTTTCCCCCC‑AACACCCGCGCTTTTACCCACCGCC‑ATGACAAAAAATCCCTTCGCGG‑GGGC‑TGTCTGCAAG‑TTTTTTTCCCGCCGCAAAAAAACCGCCGTTCTCTCCAGTAGTGGCGGGGc                                                                                                      <  1:796013/143‑1 (MQ=255)                                                   gtgtCAGCGGCTACCGTGATTCATTTCCGCC‑AACAACCGCGCATTTATCCAACGCC‑ATGTGCAAAAATGCCTTCGCGG‑CGGC‑TGTCTGCCAG‑CTATTTTTCCGCCGCAACAAAACCGCCGTTCTCTCCAGTAGTGGCgggg                                                                                                       >  1:101871/1‑141 (MQ=255)                                                     gtCAGCGGCTACCGTGATTCATTTCCGCC‑AACAACCGCGCATTTATCCAACGCC‑ATGTGCAAAAATGCCTTCGCGG‑CGGC‑TGTCTGCCAG‑CTATTTTTCCGCCGCAACAAAACCGCCGTTCTCTCCAGTAGTGGCGGGGCCAAA‑Gaaa                                                                                             >  1:127158/1‑148 (MQ=255)                                                         gCGGCTCCCGTTATTCTTTCCCGCA‑AACACCCGTCAATTAACCCAACGCC‑TGTTGAAAAAATCCCTCCGGGG‑GGTT‑GGCCTGCCGG‑GTATTTTTCCCCCGCAAAAAAACCGCCGTTCTCTCCAGTAGTGGc                                                                                                           <  2:153858/131‑1 (MQ=255)                                                          cGGCTACCGTGATTCATTTCCGCC‑AACAACCGCGCATTTATCCAACGCC‑ATGTGCAAAAATGCCTTCGCGG‑CGGC‑TGTCTGCCAG‑CTATTTTTCCGCCGCAACAAAACCGCCGATCTCTCCAGTAGGGGCggggggaacgcactttcc                                                                                         >  2:613558/1‑134 (MQ=21)                                                           ggCTACGGTGTTTCATTTCCCCC‑AAAACCCGCTCTTTTCCCCACCGCC‑TTGGGCAAAAAGGCTTTCGGGG‑CGGC‑TGTCTCCCAG‑TTTTTTTTCCGCCGCAAAAAAACCGCCGTTCTCTCCAGTAGTGGCGGGGCAaga‑g                                                                                                <  1:590245/139‑1 (MQ=255)                                                           ggCTACCGTGTTTCTTCCCCCCA‑AACACCCGCCCTTTTACCCACCCCA‑TTGTGAAAAAATCCTTTCGCGG‑CGGC‑TGTTTCCAGG‑TTTTTTTTCCCCCGCAAAAAAACCGCCGTTCTCTCCAGTAGTGGCGGGGCAAGA‑GAAATAGCtt                                                                                       <  1:901401/148‑1 (MQ=255)                                                             caaCCGTGATTAGTCCCCACC‑AACACCCGCCCATTTA‑CCAAAGCCAAGGTGAAAAAATGCCTTCGGGG‑CGGT‑TGTCGCCCAT‑CTATTTTCCCGCCGCAAAAAAACCGCCGTTCTCTCCAGTAGTGGCGGGGCAAGA‑GAAATAGc                                                                                         <  1:463634/142‑1 (MQ=255)                                                                  gtgtTTCTTTCCCCCC‑AACACCCGCGTTTTTACCCACCCCC‑GTGTCCAAAAATGCTTCCGCGG‑CTGC‑TCCCGGCCAT‑ATTTTTTCCCCCCGCAACAAAACCGCCGTTCTCTCCAGTAGTGGCGGGGCAAGA‑GAAATAGCTTTAAGccc                                                                                <  1:834166/148‑1 (MQ=255)                                                                      ttCTTTCCCCCC‑AACACCCGCGATTTTACCCACCCCC‑ATGTAAAAAAATGCTTCCGCGG‑CGGT‑TGTCTCCCAG‑TTTTTTTCCCGCCGCAAAAAAACCGCCGTTCTCTCCAGTAGTGGCGGGGCAAGA‑GAAATAGCTTTAAGCCCGTCa                                                                            <  1:1017609/148‑1 (MQ=255)                                                                       ttctttCCCCCAAACACCCGCGTTTTTACCCACCCCC‑ATGTGAAAAAATGCCTCCGGGG‑CGTC‑TGTCGCCCAT‑CTATTTTCCCGCCAAAAAAAAACCGCCGTTCTCTCCAGTAGTGGCGGGGCAAGA‑GAAATAGCTTTAAGCCCGt                                                                              <  2:478888/143‑1 (MQ=255)                                                                       tCATTTCCGCC‑AACAACCGCGCATTTATCCAACGCC‑ATGTGCAAAAATGCCTTCGCGG‑CGGC‑TGTCTGCCAG‑CTATTTTTCCGCCGCAACAAAACCGCCGTTCTCTCCAGTAGTGGCGGGGGGAGA‑GGAAAAACTTTTAAccccgcccgtt                                                                        >  2:997772/1‑143 (MQ=25)                                                                            cccGCC‑ACAACCCGCGCATTTAACCACCGCC‑ATGTCAAAAAATGCCTCCGCGG‑CGGC‑TGTCTGCCAC‑CTTTTTTCCCCCCCCAAAAAAACCGCCGTTCTCTCCAGTAGTGGCGGGGCAAGA‑GAAATAGCTTTAAGCCCGTCATGTtgtgtg                                                                   <  1:274704/150‑1 (MQ=255)                                                                             ccccc‑AACACCCGCCCTTTTACCCACCGCA‑ATGTGAAAAAATCCCTCCGCGG‑CGGC‑TGTCTGCAAG‑TTTTTTTCCCGCCGCAACAAAACCGCCGTTCTCTCCAGTAGTGGCGGGGCAAGA‑GAAATAGCTTTAAGCCCGTCATGTtgtgtg                                                                   <  1:187959/147‑1 (MQ=255)                                                                                   aacaccCGCGCATTTACCCACCGCT‑GGGGGAAAAATTTCCTGCGCGG‑CGGT‑TGTCTCCCAG‑TTTTTTTTCCGCCGAAAAAAAACCGCCGTTCTCTCCAGTAGTGGCGGGGCAAGA‑GAAATAGCTTTAAGCCCGTCAt                                                                           <  1:877037/137‑1 (MQ=255)                                                                                      acccgccctttttcccAACGCC‑ATGTGAAAAAATCCTTCCGGGG‑GTTC‑GTTCGGCCTG‑TTTTTTTCCCGCCGCAAAAAAACCGCCGTTCTCTCCAGTAGTGGCGGGGCAAGA‑GAAATAGCTTTAAGCCCGTCATGTTGTGTGGCAATc                                                             <  2:984385/134‑1 (MQ=255)                                                                                           cgattttACCCACCCCA‑ATGTAAAAAAGTGCCTCGGGGG‑CGGC‑TGTCTCCCAG‑TTTTTTTCCCGCCGAAAAAAAACCGCCGTTCTCTCCAGTAGTGGCGGGGCAAGA‑GAAATAGCTTTAAGCCCGTCATGTTGTGTGGCAATCGCTGCTgg                                                     <  1:775644/147‑1 (MQ=255)                                                                                               tttACCCACCGCC‑ATGTGAAAAAATCCCTCCGGGG‑GGTC‑TGTCTGCCAT‑TTTTTTTCCCCCCGCAAAAAACCCGCCGTTCTCTCCAGTAGTGGCGGGGCAAGA‑GAAATAGCTTTAAGCCCGTCATGTTGTGTGGCAATCGCTGCTGGt                                                    <  1:350705/148‑1 (MQ=255)                                                                                                   tCCAACGCC‑ATGTGCAAAAATGCCTTCGCGG‑CGGC‑TGTCTGCCAG‑CTATTTTTCCGCCGCAACAAAACCGCCGTTCTCTCCAGTAGTGGCGGAGGGAGAGGAAAACACTTTAATACCG‑CCTATTGTGTGGCTAATGCCGCTGGTaatga                                               >  1:194407/1‑146 (MQ=21)                                                                                                       acccccttgtgAAAAAATGCCTTCGGGG‑GGTC‑TTTCTGCCAG‑TTTTTTTCCCGCCGAAAAAAAACCGCCGTTCTCTCCAGTAGTGGCGGGGCAAGA‑GAAATAGCTTTAAGCCCGTCATGTTGTGTGGCAATCGCTGCTGGTAACaa                                               <  1:873928/139‑1 (MQ=255)                                                                                                          cc‑ATTTGAAAAATCGCTTTCGCGG‑GGGA‑TGTCT‑CCAGTCTTTTTTCCCCCCAAAAAAAAACCGCCGTTCTCTCCAGTAGTGGCGGGGCAAGA‑GAAATAGCTTTAAGCCCGTCATGTTGTGTGGCAATCGCTGCTGGTAACAATGTGGa                                         <  1:120313/148‑1 (MQ=255)                                                                                                                  aaaaatTGCTTCCGGGG‑CGGC‑TGTCTCCCAG‑TTTTTTTCCCGCCGAAAAAAAACCGCCGTTCTCTCCAGTAGTGGCGGGGCAAGA‑GAAATAGCTTTAAGCCCGTCATGTTGTGTGGCAATCGCTGCTGGTAACAATGTGGAAAGGGAAGTg                               <  1:940449/150‑1 (MQ=255)                                                                                                                   aaaaaTGCCTTCCCGGCCGCC‑TTTCTCCCAT‑GTATGTTCCCGCCGCAACAAAACCGCCGTTCTCTCCAGTAGTGTCGGGGCAAGA‑GAAATAGCTTTAAGCCCGTCATGTTGTGTGGCAATCGCTGCTGGTAACAATGTGGAAAgg                                     <  2:209116/145‑1 (MQ=255)                                                                                                                    aaaaTGCCTGCGCGG‑GGGC‑TGTCGGCCAG‑CTTTTTTCCCGCCGCAACAAAACCGCCGTTCTCTCCAGTAGTGGCGGGGCAAGA‑GAAATAGCTTTAAGCCCGTCATGTTGTGTGGCAATCGCTGCTGGTAACAATGTGGAAAGGGAAGTgcg                             <  2:104203/151‑1 (MQ=255)                                                                                                                               gggg‑cggc‑TGTCTGCCAG‑CTATTTTCCCGCCGAAAAAAATCCGCCGTTCTCTCCAGTAGTGGCGGGGCAAGA‑GAAATAGCTTTAAGCCCGTCATGTTGTGTGGCAATCGCTGCTGGTAACAATGTGGAAAGGGAAGTGCGGCGa                         <  2:47390/142‑1 (MQ=255)                                                                                                                                     ggc‑TGTCTGCAAG‑TTTTTTTCCCGCCGCAAAAAAACCGCCGTTCTCTCCAGTAGTGGCGGGGCAAGA‑GAAATAGCTTTAAGCCCGTCATGTTGTGTGGCAATCGCTGCTGGTAACAATGTGGAAAGGGAAGTGCGGCGAATCAGCTCCAg              <  1:508863/150‑1 (MQ=255)                                                                                                                                      ggttGTCTCCAAG‑TTTTTTTCCCGCCGAAAAAAAACCGCCGTTCTCTCCAGTAGTGGCGGGGCAAGA‑GAAATAGCTTTAAGCCCGTCATGTTGTGTGGCAATCGCTGCTGGTAACAATGTGGAAAGGGAAGTGCGGCGAATc                      <  2:887245/139‑1 (MQ=255)                                                                                                                                          gTCTGCCAG‑CTATTTTTCCGCCGCAACAAAACCGCCGTTCTCTCCAGTAGTGGCGGGGGGAGA‑GGAAAAAATTTAAAACCCGCACGATGTTTGGCACTCGGTGCTCGTAACAAAGTGGGGAGGGGAGAGGGGGGGAGCAGCTcc                >  2:517025/1‑144 (MQ=255)                                                                                                                                               ccAG‑CTTTTTTCCCGCCGCAAAAAAACCGCCGTTCTCTCCAGTAGTGGCGGGGCAAGA‑GAAATAGCTTTAAGCCCGTCATGTTGTGTGGCAATCGCTGCTGGTAACAATGTGGAAAGGGAAGTGCGGCGAATCAGCTCCAGAACCGCGCTa    <  1:251279/151‑1 (MQ=255)                                                                                                                                                  agtttttttcCCGCCGAAAAAAAACCGCCGTTCTCTCCAGTAGTGGCGGGGCAAGA‑GAAATAGCTTTAAGCCCGTCATGTTGTGTGGCAATCGCTGCTGGTAACAATGTGGAAAGGGAAGTGCGGCGAATCAGCTCCAGAACCGCGCTAAt  <  2:305311/146‑1 (MQ=255)                                                                                                                                                           |                                                                                                                                               CTCGTAGGCCTGATAAGCGTAGCGCATCAGGCAATTCCAGCCGCAGACCTGTGTCAGCGGCTACCGTGATTCATTTCCGCC‑AACAACCGCGCATTTATCCAACGCC‑ATGTGCAAAAATGCCTTCGCGG‑CGGC‑TGTCTGCCAG‑CTATTTTTCCGCCGCAACAAAACCGCCGTTCTCTCCAGTAGTGGCGGGGCAAGA‑GAAATAGCTTTAAGCCCGTCATGTTGTGTGGCAATCGCTGCTGGTAACAATGTGGAAAGGGAAGTGCGGCGAATCAGCTCCAGAACCGCGCTAAT  >  NC_000913/357731‑358021

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 12 ≤ ATCG/ATCG < 13 ≤ ATCG/ATCG < 24 ≤ ATCG/ATCG < 39 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑