Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NC_000913	357,890	0	C	A	51.6%	0.7 / 32.6	31	L267F (TTG→TTT)	cynR	transcriptional activator of cyn operon; autorepressor
Reads supporting (aligned to +/- strand):  ref base C (12/3);  new base A (0/16);  total (12/19)
Fisher's exact test for biased strand distribution p-value = 3.22e-06
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 9.42e-04

CTGATAAGCGTAGCGCATCAGGCAATTCCAGCCGCAGACCTGTGTCAGCGGCTACCGTGATTCATTT‑CCGCC‑AACAACCGCGCATTTATCCAACGCCAT‑GTGCAAAAATGCC‑TT‑C‑GCGGCGGCTGTCTGCCAGCTATTTTTCCG‑CCGCAACAAAACCGCCGTTCTCTCCAGTAGTGGCGGGGC‑AAGAG‑AAATAGCTTTAAGCCCGTCATGTTGTGTGGCAATCGCTGCTGGTAACAATGTGGAAAGGGAAGTGCGGCGAATCAGCTCCAGAACCGCGCTAATTGAGTTCGCCT  >  NC_000913/357740‑358032                                                                                                                                                              |                                                                                                                                                 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‑AAGAG‑AAAt                                                                                                       <  1:674863/145‑1 (MQ=255)                                             tcggcggcgACCGT‑ATTCATTTCCCCCC‑ACCACCCGCTCTTTTCACCCGCGCAAG‑GTG‑AAAAATTCC‑TT‑CGGGGGGGGGTGTCCCCCACCT‑TTTTTCCGCCCGAAAAAAAACCGCCGTTCTCTCCAGTAGTGGCGGGGC‑AAGAG‑AAATAg                                                                                                     <  1:644299/147‑1 (MQ=255)                                               aGCGGCTACCGTGATTCATTT‑CCGCC‑AACAACCGCGCATTTATCCAACGCCAT‑GTGCAAAAATGCC‑TT‑C‑GCGGCGGCTGTCTGCCAGCTATTTTTCCG‑CCGCAACAAAACCGCCGTTCTCTCCAGTAGTGGCGGCGG‑CAGAG‑aaaa                                                                                                       >  1:38025/1‑145 (MQ=255)                                                              ttcttt‑CCCCCAAACACCCCCGCTTTTACCAACCCCCAG‑GTGAAAAAATCCC‑TC‑C‑GCGGCGGCGGTCTGCCCGTTTTTTTCCCG‑CCGCAAAAAAACCGCCGTTCTCTCCAGTAGTGGCGGGGC‑AAGAG‑AAATAGCTTTAAGCCCGTCAtg                                                                                     <  1:568129/147‑1 (MQ=255)                                                                  ttcccccc‑AACACCCCCGCTTTTACCCACCCCCAG‑GTGAAAAAGTCCC‑TC‑C‑GGGGGGGCTTTCGCCAAGTTTTTTTCCCG‑CCAAAAAAAAACCGCCGTTCTCTCCAGTAGTGGCGGGGC‑AAGAG‑AAATAGCTTTAAGCCCGTCAtgttg                                                                                  <  1:870330/143‑1 (MQ=255)                                                                    cccccc‑AACACCCGCGTTTTAATCCACCCCAAT‑GTGAAAAAAGGCC‑TC‑C‑GGGGCGGCTTTCTGCCAGTTTTTTTCCCG‑CCCAAAAAAACCCGCCGTTCTCTCCAGTAGTGGCGGGGC‑AAGAG‑AAATAGCTTTAAGCCCGTCATGTtgtgt                                                                               <  1:1080326/146‑1 (MQ=255)                                                                    cccGCA‑AACACCCGCGATTTTACCCACCCCCAT‑GTAAAAAAATCCC‑TG‑C‑GGGGCGGCTGTCGCCCAGTTTTTTTCCCG‑CCGCAAAAAAACCGCCGTTCTCTCCAGTAGTGGCGGGGC‑AAGAG‑AAATAGCTTTAAGCCCGTCAtgtt                                                                                   <  1:550202/145‑1 (MQ=255)                                                                            acaacCGCGCATTTATCCAACGCCAT‑GTGCAAAAATGCC‑TT‑C‑GCGGCGGCTGTCTGCCAGCTATTTTTCCG‑CCGCAACAAAACCGCCGTTCTCTCCAGTAGTGGCGGGGG‑GAGAG‑AAAAAACTTTTAAACCGTCCTGTTTTGTgggga                                                                          >  1:521945/1‑145 (MQ=25)                                                                                ccccgttttcccccACCGCAAT‑GTG‑AAAAATGCC‑TTCC‑GGGGGGCCGGTCTCCCGTTTTTTTTCCCG‑CCACAAAAAAACCGCCGTTCTCTCCAGTAGTGGCGGGGC‑AAGAG‑AAATAGCTTTAAGCCCGTCATGTTGTGTGGCAATCgctg                                                                    <  2:428878/138‑1 (MQ=255)                                                                                       tttcccaaccGCCAG‑GAGAAAAATTCCC‑TT‑C‑GGGGCGGTTGTCGGCCATTTTTTTTCCCG‑CCGAAAAAAACCCGCCGTTCTCTCCAGTAGTGGCGGGGC‑AAGAG‑AAATAGCTTTAAGCCCGTCATGTTGTGTGGCAATCGCTGCTGGTaa                                                             <  2:1131927/141‑1 (MQ=255)                                                                                       tttACCCCACGCCCT‑GCCAAAAACTGCT‑TC‑C‑GCGGCGGCTGTCGCCCATTTTTTTCCCCC‑CCGCAAAAAAACCGCCGTTCTCTCCAGTAGTGGCGGGGC‑AAGAG‑AAATAGCTTTAAGCCCGTCATGTTGTGTGGCAATCGCTGCTGGTa                                                              <  1:201607/149‑1 (MQ=255)                                                                                        ttATCCAACGCCAT‑GTGCAAAAATGCC‑TT‑C‑GCGGCGGCTGTCTGCCAGCTATTTTTCCG‑CCGCAACAAAACCGCCGTTCTCTCCAGTAGTGGCGGGGG‑CGGAG‑AAAAAGCCTTAAGAACCCCATGTTGTGTGGGaaacagcgctcgtaac                                                            >  1:1108577/1‑136 (MQ=25)                                                                                               aCGCCAT‑GTGCAAAAATGCC‑TT‑C‑GCGGCGGCTGTCTGCCAGCTATTTTTCCG‑CCGCAACAAAACCGCCGTTCTCTCCAGTAGTGGCGGGGA‑GCAAG‑AAAAAAATTTATATCCCCCCTGTTGTGTGGGGGTCGCCGCTGGTGACAAtgt                                                       >  1:326037/1‑148 (MQ=21)                                                                                                    aT‑GTGCAAAAATGCC‑TC‑C‑GCGGCGGCTGTCTGCCACTTTTTTTCCCC‑CCAAAAAAAAACCGCCGTTCTCTCCAGTAGTGGCGGGGC‑AAGAG‑AAATAGCTTTAAGCCCGTCATGTTGTGTGGCAATCGCTGCTGGTAACAATGTgg                                                     <  1:1174346/145‑1 (MQ=255)                                                                                                           aaaaaTCCC‑TT‑C‑CCGGCGGCTCTCTCCCATTTTTTTTCCCC‑CCGCAAAAAAACCGCCGTTCTCTCCAGTAGTGGCGGGGC‑AAGAG‑AAATAGCTTTAAGCCCGTCATGTTGTGTGGCAATCGCTGCTTGTAACAATGTGGAAAGGGAAGTgc                                         <  1:975767/151‑1 (MQ=255)                                                                                                                          gcggcgGCTGTCTGCCAGCTATTTTTCCG‑CCGCAACAAAACCGCCGTTCTCTCCAGTAGTGGCGGGGCGAAGGG‑AAAAAAATTAAAAGCCGACCGGTTTTGGGGAATTCCCTCTGGGGAACAAGGTGGAAAGGGaaaggggggaaggcg                                >  2:528509/1‑136 (MQ=255)                                                                                                                             gcgtcTGCCTGCCGGTTTTTTCGCCG‑CCGCAAAAAACCCGCCGTTCTCTCCAGTAGTGGCGGGGC‑AAGAG‑AAATAGCTTTAAGCCCGTCATGTTGTGTGGCAATCGCTGCTGGTAACAATGTGGAAAGGGAAGTGCGGCGAATCAGCTc                            <  2:233374/149‑1 (MQ=255)                                                                                                                                  tGTCTCCCACCTTTTTTCCCC‑CCAAAAAAAAACCGCCGTTCTCTCCAGTAGTGGCGGGGC‑AAGAG‑AAATAGCTTTAAGCCCGTCATGTTGTGTGGCAATCGCTGCTGGTAACAATGTGGAAAGGGAAGTGCGGCGAATCAGCTCCAGaa                       <  1:63934/149‑1 (MQ=255)                                                                                                                                        ccAGTTTTTTTCCCC‑CCACAAAAAAACCGCCGTTCTCTCCAGTAGTGGCGGGGC‑AAGAG‑AAATAGCTTTAAGCCCGTCATGTTGTGTGGCAATCGCTGCTGGTAACAATGTGGAAAGGGAAGTGCGGCGAATCAGCTCCAGAACcg                    <  1:1035921/146‑1 (MQ=255)                                                                                                                                          acttATTTTCCCG‑CCCAAACAAAACCGCCGTTCTCTCCAGTAGTGGCGGGGC‑AAGAG‑AAATAGCTTTAAGCCCGTCATGTTGTGTGGCAATCGCTGCTGGTAACAATGTGGAAAGGGAAGTGCGGCGAATCAGCTCCAGAACCGCGCTAAt             <  1:281345/148‑1 (MQ=255)                                                                                                                                             ttttttcCCG‑CCGCAACAAAACCGCCGTTCTCTCCAGTAGTGGCGGGGC‑AAGAG‑AAATAGCTTTAAGCCCGTCATGTTGTGTGGCAATCGCTGCTGGTAACAATGTGGAAAGGGAAGTGCGGCGAATCAGCTCCAGAACCGCGCTAAt             <  2:281903/146‑1 (MQ=255)                                                                                                                                                    ccg‑cccCAACAAAACCGCCGTTCTCTCCAGTAGTGGCGGGGC‑AAGAG‑AAATAGCTTTAAGCCCGTCATGTTGTGTGGCAATCGCTGCTGGTAACAATGTGGAAAGGGAAGTGCGGCGAATCAGCTCCAGAACCGCGCTAATTGAGTTCGc    <  1:1072985/150‑1 (MQ=255)                                                                                                                                                     cg‑ccgcAACAAAACCGCCGTTCTCTCCAGTAGTGGCGGGGC‑CAGAGAAAAAACCTTTAAACCC‑CCATGTTTTGTGGGGATCGCTGCTGGGAAAAAAGTGGGAAGGGGAATGTGGGGGACCAGCTCCAGAACCCCGCTAATTGAGTTCGCCt  >  1:789499/1‑151 (MQ=255)                                                                                                                                                         cgcAACAAAACCGCCGTTCTCTCCAGTAGTGGCGGGGG‑AAAAG‑AAAAAAATTTAAACCCCCCCTGGTGTGTGGGGAAGGCTACCGGTGACAATAGGGTAAGGGAAGGGGGGGGGAGCAGCTCCACAAACGCGCCAATTTAGGTTGCCt  >  1:822462/1‑148 (MQ=255)                                                                                                                                                              |                                                                                                                                                 CTGATAAGCGTAGCGCATCAGGCAATTCCAGCCGCAGACCTGTGTCAGCGGCTACCGTGATTCATTT‑CCGCC‑AACAACCGCGCATTTATCCAACGCCAT‑GTGCAAAAATGCC‑TT‑C‑GCGGCGGCTGTCTGCCAGCTATTTTTCCG‑CCGCAACAAAACCGCCGTTCTCTCCAGTAGTGGCGGGGC‑AAGAG‑AAATAGCTTTAAGCCCGTCATGTTGTGTGGCAATCGCTGCTGGTAACAATGTGGAAAGGGAAGTGCGGCGAATCAGCTCCAGAACCGCGCTAATTGAGTTCGCCT  >  NC_000913/357740‑358032

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: ‑