Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NC_000913	357,873	0	C	T	41.9%	21.4 / 14.9	31	S273N (AGC→AAC)	cynR	transcriptional activator of cyn operon; autorepressor
Reads supporting (aligned to +/- strand):  ref base C (12/6);  new base T (0/13);  total (12/19)
Fisher's exact test for biased strand distribution p-value = 1.42e-04
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 1.00e+00

GAACTCGTAGGCCTGATAAGCGTAGCGCATCAGGCAATTCCAGCCGCAGACCTGTGTCAGCGGCTACCGTGATTCATTT‑CCGCC‑AACAACCGCGCATTTATCCAACGCCAT‑GTGCAAAAATGCC‑TT‑C‑GCGGCGGCTGTCTGCCAGCTATTTTTCCG‑CCGCAACAAAACCGCCGTTCTCTCCAGTAGTGGCGGGGC‑AAGAGAAATAGCTTTAAGCCCGTCATGTTGTGTGGCAATCGCTGCTGGTAACAATGTGGAAAGGGAAGTGCGGCGAATCAGCTCCAGAACCG  >  NC_000913/357728‑358014                                                                                                                                                        |                                                                                                                                                gAACTCGTAGGCCTGATAAGCGTAGCGCATCAGGCAATTCCAGCCGCAGACCTGTGTCAGCGGCTACCGTGATTCATTT‑CCGCC‑AACAACCGCGCATTTATCCAACGCCAT‑GTGCAAAAATGCC‑TT‑C‑GCGGCGGCTGTCTGCCAGCTAt                                                                                                                                              <  2:1067161/149‑1 (MQ=255)        tccgCCTGATAAGCGTAGCGCATCAGGCAATTCCAGCCGCAGACCTGTGTCAGCGGCTACCGTGATTCATTT‑CCGCC‑AACAACCGCGCATTTATCCAACGCCAT‑GTGCAAAAATGCC‑TT‑C‑GCGGCGGCTGTCTGCCAGCTATTTTTccg‑cc                                                                                                                                    >  2:186984/4‑151 (MQ=255)         aGGCCTGATAAGCGTAGCGCATCAGGCAATTCCAGCCGCAGACCTGTGTCAGCGGCTACCGTGATTCATTT‑CCGCC‑AACAACCGCGCATTTATCCAACGCCAT‑GTGCAAAAATGCC‑TT‑C‑GCGGCGGCTGTCTGCCAGCTATTTTTccg‑ccg                                                                                                                                   <  2:884357/151‑1 (MQ=255)             cTGATAAGCGTAGCGCATCAGGCAATTCCAGCCGCAGACCTGTGTCAGCAGCTACCGTGATTCATTT‑CCGCC‑AAAAACCGCGCATTTATCCAACGCCAT‑GTGCAAAAATGCC‑TT‑C‑GCGGCGGCTGTCTGCCAGCTATTTTTCCG‑CCGcaac                                                                                                                               >  1:472883/1‑151 (MQ=255)                aTAAGCGTAGCGCATCAGGCAATTCCAGCCGCAGACCTGTGTCAGCGGCTACCGTGATTCATTT‑CCGCC‑AACAACCGCGCATTTATCCAACGCCAT‑GTGCAAAAATGCC‑TT‑C‑GCGGCGGCTGTCTGCCAGCTATTTTTCCG‑CCGcaacaa                                                                                                                             <  1:532080/150‑1 (MQ=255)                      gTAGCGCATCAGGCAATTCCAGCCGCAGACCTGTGTCAGCGGCTACCGTGATTCATTT‑CCGCC‑AACAACCGCGCATTTATCCAACGCCAT‑GTGCAAAAATGCC‑TG‑C‑GCGGCGGCTGTCTGCCAGCTATTTTTCCG‑ACGCAACAAAAccgcc                                                                                                                      >  2:47916/1‑151 (MQ=255)                        aGCGCATCAGGCAATTCCAGCCGCAGACCTGTGTCAGCGGCTACCGTGATTCATTT‑CCGCC‑AACAACCGCGCATTTATCCAACGCCAT‑GTGCAAAAATGCC‑TT‑C‑GCGGCGGCTGTCTGCCAGCTATTTTTCCG‑CCGCAACAAAAccgccg                                                                                                                     >  2:202169/1‑150 (MQ=255)                             aTCAGGCAATTCCAGCCGCAGACCTGTGTCAGCGGCTACCGTGATTCATTT‑CCGCC‑AACAACCCCGCATTTATCCAACGCCAT‑GTGCAAAAATGCC‑TT‑C‑GCGGCGGCTGTCTGCCAGCTATTTTTCCG‑CCGCAACAAAACCGCCGTtctct                                                                                                               >  2:160559/1‑151 (MQ=255)                                   cAATTCCAGCCGCAGACCTGTGTCAGCGGCTACCGTGATTCATTT‑CCGCC‑AACAACCGCGCATTTATCCAACGCCAT‑GTGCAAAAATGCC‑TT‑C‑GCGGCGGCTGTCTGCCAGCTATTTTTCCG‑CCGCAACAAAACCGCCGTTCTCTCCagt                                                                                                          >  1:1132002/1‑150 (MQ=255)                                            ccGCAGTCTTGTGGCAGCGGCTCCGGTAATTCATTC‑CCGCC‑ACCACCCGCACTTATACCCCGC‑CCTT‑GTTGAAAAATTCCTTT‑C‑GGGGCGTTTCCCTGCGTTTTTTTTTCCCG‑CCGCAAAAAAGCCGCCGTTCTCTCCAGTAGTGGCgg                                                                                                  <  1:736265/149‑1 (MQ=255)                                                agccttgtgTCGGCGCCTCCCGTTTTTCTTTC‑CCGCC‑AACACCCGCGTTTTTA‑CCCACCCCATGGTGAAAAAATGCC‑TC‑C‑GGGGGGGCTGTCTCCCAGTTTTTTTCCCG‑CCGCAAAAAAACCGCCGTTCTCTCCAGTAGTGGCGGGGc                                                                                               <  1:400497/143‑1 (MQ=255)                                                aGACCTGTGTCAGCGGCTACCGTGATTCATTT‑CCGCC‑AACAACCGCGCATTTATCCAACGCCAT‑GTGCAAAAATGCC‑TT‑C‑GCGGCGGCTGTCTGCCAGCTATTTTTCCG‑CCGCAACAAAACCGCCGTTCTCTCCAGTAGTGGCggtggcc                                                                                             >  2:362509/1‑145 (MQ=255)                                                       tgccggCGGCTCCGGTGATTCTTTC‑CCCCT‑AACACCCGCGCATTTACCCACCGCCAT‑GTGAAAAAATGCT‑TC‑C‑GCGGCGGCTGTCTGCCAGCTTTTTTCCCG‑CCGCAAAAAAACCGCCGTTCTCTCCAGTAGTGGCGGGGC‑AAGAGAAAt                                                                                     <  1:674863/145‑1 (MQ=255)                                                         tcggcggcgACCGT‑ATTCATTTCCCCCC‑ACCACCCGCTCTTTTCACCCGCGCAAG‑GTG‑AAAAATTCC‑TT‑CGGGGGGGGGTGTCCCCCACCT‑TTTTTCCGCCCGAAAAAAAACCGCCGTTCTCTCCAGTAGTGGCGGGGC‑AAGAGAAATAg                                                                                   <  1:644299/147‑1 (MQ=255)                                                           aGCGGCTACCGTGATTCATTT‑CCGCC‑AACAACCGCGCATTTATCCAACGCCAT‑GTGCAAAAATGCC‑TT‑C‑GCGGCGGCTGTCTGCCAGCTATTTTTCCG‑CCGCAACAAAACCGCCGTTCTCTCCAGTAGTGGCGGCGG‑CAGAGaaaa                                                                                     >  1:38025/1‑145 (MQ=255)                                                                          ttcttt‑CCCCCAAACACCCCCGCTTTTACCAACCCCCAG‑GTGAAAAAATCCC‑TC‑C‑GCGGCGGCGGTCTGCCCGTTTTTTTCCCG‑CCGCAAAAAAACCGCCGTTCTCTCCAGTAGTGGCGGGGC‑AAGAGAAATAGCTTTAAGCCCGTCAtg                                                                   <  1:568129/147‑1 (MQ=255)                                                                              ttcccccc‑AACACCCCCGCTTTTACCCACCCCCAG‑GTGAAAAAGTCCC‑TC‑C‑GGGGGGGCTTTCGCCAAGTTTTTTTCCCG‑CCAAAAAAAAACCGCCGTTCTCTCCAGTAGTGGCGGGGC‑AAGAGAAATAGCTTTAAGCCCGTCAtgttg                                                                <  1:870330/143‑1 (MQ=255)                                                                                cccccc‑AACACCCGCGTTTTAATCCACCCCAAT‑GTGAAAAAAGGCC‑TC‑C‑GGGGCGGCTTTCTGCCAGTTTTTTTCCCG‑CCCAAAAAAACCCGCCGTTCTCTCCAGTAGTGGCGGGGC‑AAGAGAAATAGCTTTAAGCCCGTCATGTtgtgt                                                             <  1:1080326/146‑1 (MQ=255)                                                                                cccGCA‑AACACCCGCGATTTTACCCACCCCCAT‑GTAAAAAAATCCC‑TG‑C‑GGGGCGGCTGTCGCCCAGTTTTTTTCCCG‑CCGCAAAAAAACCGCCGTTCTCTCCAGTAGTGGCGGGGC‑AAGAGAAATAGCTTTAAGCCCGTCAtgtt                                                                 <  1:550202/145‑1 (MQ=255)                                                                                        acaacCGCGCATTTATCCAACGCCAT‑GTGCAAAAATGCC‑TT‑C‑GCGGCGGCTGTCTGCCAGCTATTTTTCCG‑CCGCAACAAAACCGCCGTTCTCTCCAGTAGTGGCGGGGG‑GAGAGAAAAAACTTTTAAACCGTCCTGTTTTGTgggga                                                        >  1:521945/1‑145 (MQ=25)                                                                                            ccccgttttcccccACCGCAAT‑GTG‑AAAAATGCC‑TTCC‑GGGGGGCCGGTCTCCCGTTTTTTTTCCCG‑CCACAAAAAAACCGCCGTTCTCTCCAGTAGTGGCGGGGC‑AAGAGAAATAGCTTTAAGCCCGTCATGTTGTGTGGCAATCgctg                                                  <  2:428878/138‑1 (MQ=255)                                                                                                   tttcccaaccGCCAG‑GAGAAAAATTCCC‑TT‑C‑GGGGCGGTTGTCGGCCATTTTTTTTCCCG‑CCGAAAAAAACCCGCCGTTCTCTCCAGTAGTGGCGGGGC‑AAGAGAAATAGCTTTAAGCCCGTCATGTTGTGTGGCAATCGCTGCTGGTaa                                           <  2:1131927/141‑1 (MQ=255)                                                                                                   tttACCCCACGCCCT‑GCCAAAAACTGCT‑TC‑C‑GCGGCGGCTGTCGCCCATTTTTTTCCCCC‑CCGCAAAAAAACCGCCGTTCTCTCCAGTAGTGGCGGGGC‑AAGAGAAATAGCTTTAAGCCCGTCATGTTGTGTGGCAATCGCTGCTGGTa                                            <  1:201607/149‑1 (MQ=255)                                                                                                    ttATCCAACGCCAT‑GTGCAAAAATGCC‑TT‑C‑GCGGCGGCTGTCTGCCAGCTATTTTTCCG‑CCGCAACAAAACCGCCGTTCTCTCCAGTAGTGGCGGGGG‑CGGAGAAAAAGCCTTAAGAACCCCATGTTGTGTGGGaaacagcgctcgtaac                                          >  1:1108577/1‑136 (MQ=25)                                                                                                           aCGCCAT‑GTGCAAAAATGCC‑TT‑C‑GCGGCGGCTGTCTGCCAGCTATTTTTCCG‑CCGCAACAAAACCGCCGTTCTCTCCAGTAGTGGCGGGGA‑GCAAGAAAAAAATTTATATCCCCCCTGTTGTGTGGGGGTCGCCGCTGGTGACAAtgt                                     >  1:326037/1‑148 (MQ=21)                                                                                                                aT‑GTGCAAAAATGCC‑TC‑C‑GCGGCGGCTGTCTGCCACTTTTTTTCCCC‑CCAAAAAAAAACCGCCGTTCTCTCCAGTAGTGGCGGGGC‑AAGAGAAATAGCTTTAAGCCCGTCATGTTGTGTGGCAATCGCTGCTGGTAACAATGTgg                                   <  1:1174346/145‑1 (MQ=255)                                                                                                                       aaaaaTCCC‑TT‑C‑CCGGCGGCTCTCTCCCATTTTTTTTCCCC‑CCGCAAAAAAACCGCCGTTCTCTCCAGTAGTGGCGGGGC‑AAGAGAAATAGCTTTAAGCCCGTCATGTTGTGTGGCAATCGCTGCTTGTAACAATGTGGAAAGGGAAGTgc                       <  1:975767/151‑1 (MQ=255)                                                                                                                                      gcggcgGCTGTCTGCCAGCTATTTTTCCG‑CCGCAACAAAACCGCCGTTCTCTCCAGTAGTGGCGGGGCGAAGGGAAAAAAATTAAAAGCCGACCGGTTTTGGGGAATTCCCTCTGGGGAACAAGGTGGAAAGGGaaaggggggaaggcg              >  2:528509/1‑136 (MQ=255)                                                                                                                                         gcgtcTGCCTGCCGGTTTTTTCGCCG‑CCGCAAAAAACCCGCCGTTCTCTCCAGTAGTGGCGGGGC‑AAGAGAAATAGCTTTAAGCCCGTCATGTTGTGTGGCAATCGCTGCTGGTAACAATGTGGAAAGGGAAGTGCGGCGAATCAGCTc          <  2:233374/149‑1 (MQ=255)                                                                                                                                              tGTCTCCCACCTTTTTTCCCC‑CCAAAAAAAAACCGCCGTTCTCTCCAGTAGTGGCGGGGC‑AAGAGAAATAGCTTTAAGCCCGTCATGTTGTGTGGCAATCGCTGCTGGTAACAATGTGGAAAGGGAAGTGCGGCGAATCAGCTCCAGaa     <  1:63934/149‑1 (MQ=255)                                                                                                                                                    ccAGTTTTTTTCCCC‑CCACAAAAAAACCGCCGTTCTCTCCAGTAGTGGCGGGGC‑AAGAGAAATAGCTTTAAGCCCGTCATGTTGTGTGGCAATCGCTGCTGGTAACAATGTGGAAAGGGAAGTGCGGCGAATCAGCTCCAGAACcg  <  1:1035921/146‑1 (MQ=255)                                                                                                                                                        |                                                                                                                                                GAACTCGTAGGCCTGATAAGCGTAGCGCATCAGGCAATTCCAGCCGCAGACCTGTGTCAGCGGCTACCGTGATTCATTT‑CCGCC‑AACAACCGCGCATTTATCCAACGCCAT‑GTGCAAAAATGCC‑TT‑C‑GCGGCGGCTGTCTGCCAGCTATTTTTCCG‑CCGCAACAAAACCGCCGTTCTCTCCAGTAGTGGCGGGGC‑AAGAGAAATAGCTTTAAGCCCGTCATGTTGTGTGGCAATCGCTGCTGGTAACAATGTGGAAAGGGAAGTGCGGCGAATCAGCTCCAGAACCG  >  NC_000913/357728‑358014

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: ‑