Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NC_000913	357,890	0	C	A	48.6%	31.2 / 19.4	37	L267F (TTG→TTT)	cynR	transcriptional activator of cyn operon; autorepressor
Reads supporting (aligned to +/- strand):  ref base C (16/3);  new base A (0/18);  total (16/21)
Fisher's exact test for biased strand distribution p-value = 8.71e-08
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 9.50e-01

ATAAGCGTAGCGCATCAGGCAATTCCAGCCGCAGACCTGTGTCAGCGGCTACCGTGATTCATTTCCGCCAA‑CAACCGCGCATTT‑ATCCAACGCCATGTGCAAAAATGCCTT‑CGCGGCGGCTGTCTGCCAGCTATTTTT‑CCGCCGCAACAAAACCGCCGTTCTCTCCAGTAGTGGCGGGGCAAGAG‑AAATAGCTTTAAGCCCGTCATGTTGTGTGGCAATCG‑CTGCTGGT‑AACAATGTGGAAAGGGAAGTGCGGCGAATCAGCTCCAGAACCGCGCTAATTGAGTTCGCCTCA  >  NC_000913/357743‑358034                                                                                                                                                        |                                                                                                                                                    aTAAGCGTAGCGCATCAGGCAATTCCAGCCGCAGACCTGTGTCAGCGGCTACCGTGATTCATTTCCGCCAA‑CAACCGCGCATTT‑ATCCAACGCCATGTGCAAAAATGCCTT‑CGCGGCGGCTGTCTGCCAGCTATTTTT‑CCGCCGcaacaa                                                                                                                                                   >  2:866074/1‑150 (MQ=255)      cGTAGCGCATCAGGCAATTCCAGCCGCAGACCTGTGTCAGCGGCTACCGTGATTCATTTCCGCCAA‑CAACCGCGCATTT‑ATCCAACGCCATGTGCAAAAATGCCTT‑CGCGGCGGCTGTCTGCCAGCTATTTTT‑CCGCCGCAACAAAAccgc                                                                                                                                             >  1:593636/1‑151 (MQ=255)             cATCAGGCAATTCCAGCCGCAGACCTGTGTCAGCGGCTACCGTGATTCATTCCCGCCAA‑CACCCGCGCATTT‑ATCCAACGCCATGTGCAAAAATGCCTT‑CGCGGCGGCTGTCTGCCAGCTATTTTT‑CCGCCGCAACAAAACCGCCGTtc                                                                                                                                        <  2:640297/149‑1 (MQ=255)                   gCAATTCCAGCCGCAGACCTGTGTCAGCGGCTACCGTGATTCATTTCCGCCAA‑CAACCGCGCATTT‑ATCCAACGCCATGTGCAAAAATGCCTT‑CGCGGCGGCTGTCTGCCAGCTATTTTT‑CCGCCGCAACAAAACCGCCGTTCTCTCCagt                                                                                                                                >  1:627264/1‑151 (MQ=255)                    cAATTCCACCCGCAGCCCTGTGTCAGCGGCTCCCGTGATTCATTCCCGCCAA‑CACCCGCGCTTTT‑CCCCAACCCCATGTCAAAAAAGGCCTC‑CGCGGGGGCTGTCTGCCAGCTATTTTT‑CCGCCGCAAAAAACCCGCCGTTCTCTCCagta                                                                                                                               <  2:142691/151‑1 (MQ=255)                      aTTCCAGCCGCAGACCTGTGTCAGCGGCTACCGTGATTCATTTCCGCCAA‑CAACCGCGCATTT‑ATCCAACGCCATGTGCAAAAATGCCTT‑CGCGGCGGCTGTCTGCCAGCTATTTTT‑CCGCCGCAACAAAACCGCCGTTCTCTCCagtagt                                                                                                                             >  2:670598/1‑151 (MQ=255)                         ccACCCGAAGCCCTTTGTAAGCGGCTCCCGTGATTCTTTCCCGCCAA‑CACCCGCGCATTT‑ATCCAACCCCATGTGAAAAAATGCCTC‑CGCGGCGGCTGTCTGCCAGCTATTTTC‑CCGCCGAAAAAAAACCGCCGTTCTCTCCAGTAGTgg                                                                                                                           <  2:25021/150‑1 (MQ=255)                           aGCCGCAGACCTGTGTCAGCGGCTACCGTGATTCATTTCCGCCAA‑CAACCGCGCATTT‑ATCCAACGCCATGTGCAAAAATGCCTT‑CGCGGCGGCTGTCTGCCAGCTATTTTT‑CCGCCGCAACAAAACCGCCGTTCTCTCCAGTAGTGGCgg                                                                                                                        >  2:203811/1‑151 (MQ=255)                                 aGACCTGTGTCAGCGGCTACCGTGATTCATTTCCGCCAA‑CAACCGCGCATTT‑ATCCAACGCCATGTGCAAAAATGCCTT‑CGCGGCGGCTGTCTGCCAGCTATTTTT‑CCGCCGCAACAAAACCGCCGTTCTCTCCAGTAGTGGCggg                                                                                                                       >  1:912010/1‑146 (MQ=255)                                      tgtgTCGGGGGTTCCCGGGTTTCATTCCCCCCAA‑AACCCGCGCATTT‑ACCCAACGCATTGTAAAAAAATGCTTT‑GGGGGGGGCGGTCT‑CCCGCTTTTTTTCCCCCCGCAACAAACCCGCCGTTCTCTCCAGTAGTGGCGGGGCAagag                                                                                                                <  2:770925/148‑1 (MQ=255)                                       gtgtCGGCGCCCCCCGTGTTTCTTTCCCCCCAA‑CACCCGCGTTTTT‑ACCCAACGCCGTGTGAAAAAGTCCCTG‑CGGGGGGGTTGTCGGCCAGTTTTTTTC‑CCGCCGAAAAAAAACCGCCGTTCTCTCCAGTAGTGGCgggg                                                                                                                      <  1:54820/141‑1 (MQ=255)                                       gtgtCAGCGGCTACCGTGATTCATTTCCGCCAA‑CAACCGCGCATTT‑ATCCAACGCCATGTGCAAAAATGCCTT‑CGCGGCGGCTGTCTGCCAGCTATTTTT‑CCGCCGCAACAAAACCGCCGTTCTCTCCAGTAGTGGCggggggaggaaaa                                                                                                             >  1:932656/1‑141 (MQ=255)                                       gtgtCAGCGGCTACCGTGATTCATTTCCGCCAA‑CAACCGCGCATTT‑ATCCAACGCCATGTGCAAAAATGCCTT‑CGCGGCGGCTGTCTGCCAGCTATTTTT‑CCGCCGCAACAAAACCGCCGTTCTCTCCAGTAGTGGCGGGGGGAGAG‑gaa                                                                                                            >  2:207075/1‑150 (MQ=255)                                              cGGCTCCCTTAATTCTTTCCCCCAAA‑CACCCCCCCTTTT‑ACCCACCCCCATTAGAAAAATTGCTTC‑CGCGGCGGTTCTCTGCCTTTTATTTTC‑CCCCCACAAAAAAACCGCCGTTCTCTCCAGTAGTGGCGGGGCAAgag‑a                                                                                                              <  1:133402/141‑1 (MQ=255)                                               gtctcccGTGTTTCTTTCCCGACAA‑CACCCGCGTATTT‑ACCCAACCCCTTGTAC‑AAAATGCCTTCCGGGGCGGTTTTCTGCCGGCTTTTTTC‑CCCCCCCAAAAAACCCGCCGTTCTCTCCAGTAGTGGCGGGGCAagag                                                                                                                <  1:779564/134‑1 (MQ=255)                                                   aCCGTGATTCATTTCCGCCAA‑CAACCGCGCATTT‑ATCCAACGCCATGTGCAAAAATGCCTT‑CGCGGCGGCTGTCTGCCAGCTATTTTT‑CCGCCGCAACAAAACCGCCGTTCTCTCCAGTAGTGGCGGGGGgaaag‑aaaaaaaattaaaacc                                                                                               >  2:967532/1‑138 (MQ=25)                                                    ccttGATTCATTCCCCCCAA‑CACCCGCGCATTT‑CCCCAACGCCATGTGAAAAAATGCCTG‑CGGGGCGGCTTTCTCCCAGTTTTTTTC‑CCGCCGAAAAAAAACCGCCGTTCTCTCCAGTAGTGGCGGGGCAAGAG‑AAATAGCTTTAAGccc                                                                                               <  2:890104/147‑1 (MQ=255)                                                         aTTCATTTCCGCCAA‑CAACCGCGCATTT‑ATCCAACGCCATGTGCAAAAATGCCTT‑CGCGGCGGCTGTCTGCCAGCTATTTTT‑CCGCCGCAACAAAACCGCCGTTCTCTCCAGTAGTGGCGGGGGgaaag‑aaaaaaattttaaacc                                                                                               >  2:855298/1‑132 (MQ=25)                                                             aTTTCCGCCAA‑CAACCGCGCATTT‑ATCCAACGCCATGTGCAAAAATGCCTT‑CGCGGCGGCTGTCTGCCAGCTATTTTT‑CCGCCGCAACAAAACCGCCGTTCTCTCCAGTAGTGGCGGGGCCAAGG‑AAAAAACTTTAAACCCCTcccgtttt                                                                                     >  2:424503/1‑144 (MQ=25)                                                               ttCCCCCAACCACCCGCCCATTT‑ACCAACCGCCATGTGAAAAAATGCCTT‑CGGGGCGGCTGTCTCCCATTTTTTTTC‑CCGCCGCAAAAAAACCGCCGTTCTCTCCAGTAGTGGCGGGGCAAGAG‑AAATAGCTTTAAGCCCGTCAtgtt                                                                                       <  2:887244/148‑1 (MQ=255)                                                                 ccaccAA‑CACCCGC‑CATTTAATCCCACGCCTTGTGAAAAAATGCTTT‑CCCGGGGCGTGTCGCCCATTTTTTTTC‑CCGCCCAAAAAAATCCGCCGTTCTCTCCAGTAGTGGCGGGGCAAGAG‑AAATAGCTTTAAGCCCGTCATGTTGTGTgg                                                                                 <  1:97670/148‑1 (MQ=255)                                                                                          caccGCTATGTAAAAAATTCCCTT‑CGCGGCGTCTTTCTCCCATCTTTTTTC‑CCGCCGCAAAAAAACCGCCGTTCTCTCCAGTAGTGGCGGGGCAAGAG‑AAATAGCTTTAAGCCCGTCATGTTGTGTGGCAATCG‑CTGCTGGT‑AACa                                                             <  2:213772/143‑1 (MQ=255)                                                                                               ccttgtgAAAAAATGCCTG‑CGGGGCGGCTGTCTGCCATTTTTTTTC‑CCGCCGCAAAAAAACCGCCGTTCTCTCCAGTAGTGGCGGGGCAAGAG‑AAATAGCTTTAAGCCCGTCATGTTGTGTGGCAATCG‑CTGCTGGT‑AACAATGTGGAAAg                                                   <  1:871560/148‑1 (MQ=255)                                                                                                   gtgAAAAAATCCCTC‑CGCGGCGGCTGTCTGCCAGTTTTTTTC‑CCGCCGAAAAAAAACCGCCGTTCTCTCCAGTAGTGGCGGGGCAAGAG‑AAATAGCTTTAAGCCCGTCATGTTGTGTGGCAATCG‑CTGCTGGT‑AACAATGTgg                                                       <  1:191377/143‑1 (MQ=255)                                                                                                    tgCAAAAATGCCTT‑CGCGGCGGCTGTCTGCCAGCTATTTTT‑CCGCCGCAACAAAACCGCCGTTCTCTCCAGTAGTGGCGGGGCAAGAG‑AAAAAACTTTTAAACCCCCCTGTTGTGTGGGCATCT‑CTGCTGGG‑TACAAAGTGGGAAggg                                                 >  2:154025/1‑148 (MQ=255)                                                                                                       aaaaaTGCCTT‑CGCGGCGGCTGTCTGCCAGCTATTTTT‑CCGCCGCAACAAAACCGCCGTTCTCTCCAGTAGTGGCGGGGGGAGGG‑GAAAAAATTTTAACCCGCCCTGTTTTTTGGGGATCG‑CTGGCGGTAAAAAATGGGGGAAGGGagagg                                            >  2:616993/1‑147 (MQ=255)                                                                                                       aaaaaTGCCTT‑CGCGGCGGCTGTCTGCCAGCTATTTTT‑CCGCCGCAACAAAACCGCCGTTCTCTCCAGTAGTGGCGGGGGGAGAGAAAAAAATTTTAAACCCG‑CCTGTTTTGTGGGGATCG‑CTGGTGGG‑GAAAAAGTGGGAAGGGGAgggg                                           >  2:761214/1‑148 (MQ=255)                                                                                                          attGCCTT‑CGCGGCGGCTTTCTGCCAGTTTTTTTC‑CCGCCGCAAAAAAACCGCCGTTCTCTCCAGTAGTGGCGGGGCAAGAG‑AAATAGCTTTAAGCCCGTCATGTTGTGTGGCAATCG‑CTGCTGGT‑AACAATGTGGAAAGGGAAGTgcggc                                        <  2:125156/149‑1 (MQ=255)                                                                                                           aTGCCTT‑CGCGGCGGCTGTCTGCCAGCTATTTTT‑CCGCCGCAACAAAACCGCCGTTCTCTCCAGTAGTGGCGGGGCAAGAG‑AAAAAGATTTTATACCCTCATATTTTGTGGGTATAGCCTGTTGG‑‑GACAAAGTGGAAAGGGGAGGgcgg                                         >  2:76092/1‑149 (MQ=255)                                                                                                              ccTT‑CGCGGCGTCTTTCTGCCATTTATTTTC‑CCCCAACAAAAAAACCGCCGTTCTCTCCAGTAGTGGCGGGGCAAGAG‑AAATAGCTTTAAGCCCGTCATGTTGTGTGGCAATCG‑CTGCTGGT‑AACAATGTGGAAAGGGAAGTGCGGCGAAt                                    <  1:909602/151‑1 (MQ=255)                                                                                                                              tctcCCAGTTTTTTTC‑CCGCCGAAAAAAAACCGCCGTTCTCTCCAGTAGTGGCGGGGCAAGAG‑AAATAGCTTTAAGCCCGTCATGTTGTGTGGCAATCG‑CTGCTGGT‑AACAATGTGGAAAGGGAAGTGCGGCGAATCAGCTCCAGAAc                        <  2:702898/148‑1 (MQ=255)                                                                                                                                     gCTATTTTT‑CCGCCGCAACAAAACCGCCGTTCTCTCCAGTAGTGGC‑GGGTTAGCG‑AAAAAACTTTAAACCCCCCCTGTTGTGTGGGCAACT‑CTGCTGGT‑AACAATGGGGGAAGGGAAGGGCGGGGGATCCACTCCCGGAACCCGCCAAtt              >  1:91907/1‑150 (MQ=255)                                                                                                                                      cTATTTTT‑CCGCCGCAACAAAACCGCCGTTCTCTCCAGTAGTGGCGGTGCCAGGG‑AAAAAAAATTAAAACCCTCCCGTTGTTTGGCGAGCG‑CCGCTGGG‑GAAAAAGTGGGGAGGGAGAGGGGGGGGAGCAGCTCCCGAAccac                     >  1:81605/1‑141 (MQ=255)                                                                                                                                         ttttc‑CCGCCGCAAAAAAACCGCCGTTCTCTCCAGTAGTGGCGGGGCAAGAG‑AAATAGCTTTAAGCCCGTCATGTTGTGTGGCAATCG‑CTGCTGGT‑AACAATGTGGAAAGGGAAGTGCGGCGAATCAGCTCCAGAACCGCGCTAATTg             <  2:963467/148‑1 (MQ=255)                                                                                                                                         ttttc‑CCCCCGCAAAAAAACCGCCGTTCTCTCCAGTAGTGGCGGGGCAAGAG‑AAATAGCTTTAAGCCCGTCATGTTGTGTGGCAATCG‑CTGCTGGT‑AACAATGTGGAAAGGGAAGTGCGGCGAATCAGCTCCAGAACCGCGCTAATTGa            <  1:200078/149‑1 (MQ=255)                                                                                                                                              cccgccgAAAAAAACCCGCCGTTCTCTCCAGTAGTGGCGGGGCAAGAG‑AAATAGCTTTAAGCCCGTCATGTTGTGTGGCAATCG‑CTGCTGGT‑AACAATGTGGAAAGGGAAGTGCGGCGAATCAGCTCCAGAACCGCGCTAATTGAGTTc        <  1:99342/148‑1 (MQ=255)                                                                                                                                                  ccgcAACAAAACCGCCGTTCTCTCCAGTAGTGGCGGGGCAAGAG‑AAATAGCTTTAAGCCCGTCATGTTGTGTGGCAATCG‑CTGCTGGT‑AACAATGTGGAAAGGGAAGTGCGGCGAATCAGCTCCAGAACCGCGCTAATTGAGTTCGCCTCa  <  2:627363/151‑1 (MQ=255)                                                                                                                                                  ccgcAAAAAAACCGCCGTTCTCTCCAGTAGTGGCGGGGCAAGAG‑AAATAGCTTTAAGCCCGTCATGTTGTGTGGCAATCG‑CTGCTGGT‑AACAATGTGGAAAGGGAAGTGCGGCGAATCAGCTCCAGAACCGCGCTAATTGAGTTCGCCTCa  <  2:279195/151‑1 (MQ=255)                                                                                                                                                        |                                                                                                                                                    ATAAGCGTAGCGCATCAGGCAATTCCAGCCGCAGACCTGTGTCAGCGGCTACCGTGATTCATTTCCGCCAA‑CAACCGCGCATTT‑ATCCAACGCCATGTGCAAAAATGCCTT‑CGCGGCGGCTGTCTGCCAGCTATTTTT‑CCGCCGCAACAAAACCGCCGTTCTCTCCAGTAGTGGCGGGGCAAGAG‑AAATAGCTTTAAGCCCGTCATGTTGTGTGGCAATCG‑CTGCTGGT‑AACAATGTGGAAAGGGAAGTGCGGCGAATCAGCTCCAGAACCGCGCTAATTGAGTTCGCCTCA  >  NC_000913/357743‑358034

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: ‑