Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NC_000913	1,649,295	0	T	G	43.9%	62.9 / 10.6	41	intergenic (+254/‑314)	ydfC/dicB	uncharacterized protein, Qin prophage/Qin prophage; cell division inhibition protein
Reads supporting (aligned to +/- strand):  ref base T (3/20);  new base G (18/0);  total (21/20)
Fisher's exact test for biased strand distribution p-value = 7.52e-09
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 1.00e+00

ATATTTCCCTGAAAAGTCAGACCATAACGCGAAAGCGCATGGCGAGGTAGCTGGTTCATAGATAGCCTGTCGTTAAATTTTCGTCGACCGTGCGCTTCCGGTTGTGGCAACCCGCGAAATGGCGCGGCGGTAAGTATGGC‑GGGGTTATTCCTTCCCCGTTGAGGA‑CACCGGGTTGTC‑AGGTTGACCATACG‑C‑TTAAGT‑GAC‑AACCCCGCTGCAACGCCCTCTG‑TTATCAATTTTCTGGTGACGTTTGGCGGTATCAGTTTTACTCCGTGACTGCTCTGCCGCCCTTTTTAAAG  >  NC_000913/1649151‑1649443                                                                                                                                                  |                                                                                                                                                            atatTTCCCTGAAAAGTCAGACCATAACGCGAAAGCGCATGGCGAGGTAGCTGGTTCATAGATAGCCTGTCGTTAAATTTTCGTCGACCGTGCGCTTCCGGTTGTGGCAACCCGCGAAATGGCGCGGCGGTAAGTATGGC‑GGGGGTAtt                                                                                                                                                         >  2:697133/1‑149 (MQ=255)   atTTCCCTGAAAAGTCAGACCATAACGCGAAAGCGCATGGCGAGGTAGCTGGTTCATAGATAGCCTGTCGTTAAATTTTCGTCGACCGTGCGCTTCCGGTTGTGGCAACCCGCGAAATGGCGCGGCGGTAAGTATGGC‑GGGGTTAttcctt                                                                                                                                                     <  1:734671/151‑1 (MQ=255)     ttCCCTGAAAAGTCAGACCATAACGCGAAAGCGCATGGCGAGGTAGCTGGTTCATAGATAGCCTGTCGTTAAATTTTCGTCGACCGTGCGCTTCCGGTTGTGGCAACCCGCGAAATGGCGCGGCGGTAAGTATGGC‑GGGGTTAttccttc                                                                                                                                                    <  1:452222/150‑1 (MQ=255)       cccTGAAAAGTCAGACCATAACGCGAAAGCGCATGGCGAGGTAGCTGGTTCATAGATAGCCTGTCGTTAAATTTTCGTCGACCGTGCGCTTCCGGTTGTGGCAACCCGCGAAATGGCGCGGCGGTAAGTATGGC‑GGGGTTATTCCTTccc                                                                                                                                                  <  1:534282/150‑1 (MQ=255)        ccTGAAAAGTCAGACCATAACGCGAAAGCGCATGGCGAGGTAGCTGGTTCATAGATAGCCTGTCGTTAAATTTTCGTCGACCGTGCGCTTCCGGTTGTGGCAACCCGCGAAATGGCGCGGCGGTAAGTATGGC‑GGGGGTATTTCTTtcccc                                                                                                                                                >  2:497252/1‑150 (MQ=255)           gAAAAGTCAGACCATAACGCGAAAGCGCATGGCGAGGTAGCTGGTTCATAGATAGCCTGTCGTTAAATTTTCGTCGACCGTGCGCTTCCGGTTGTGGCAACCCGCGAAATGGCGCGGCGGTAAGTATGGC‑GGGGTTATTCCTTCCCCGTTg                                                                                                                                             <  2:142687/151‑1 (MQ=255)                      ccATAACGCGAAAGCGCATGGCGAGGTAGCTGGTTCATAGATAGCCTGTCGTTAAATTTTCGTCGACCGTGCGCTTCCGGTTGTGGCAACCCGCGAAATGGCGCGGCGGTAAGTATGGC‑GGGGTTATTCCTTCCCCGTTGAGGA‑CACCgg                                                                                                                                  <  1:657395/150‑1 (MQ=255)                      ccATAACGCGAAAGCGCATGGCGAGGTAGCTGGTTCATAGATAGCCTGTCGTTAAATTTTCGTCGACCGTGCGCTTCCGGTTGTGGCAACCCGCGAAATGGCGCGGCGGTAAGTATGGC‑GGGGGTTTTTCTTTCCCCTTgggggaacccgg                                                                                                                                  >  2:21032/1‑143 (MQ=255)                        aTAACGCGAAAGCGCATGGCGAGGTAGCTGGTTCATAGATAGCCTGTCGTTAAATTTTCGTCGACCGTGCGCTTCCGGTTGTGGCAACCCGCGAAATGGCGCGGCGGTAAGTATGGC‑GGGGTTATTCCTTCCCCGTTGAGGA‑CACCGGGtt                                                                                                                               <  1:837986/151‑1 (MQ=255)                           aCGCGAAAGCGCATGGCGAGGTAGCTGGTTCATAGATAGCCTGTCGTTAAATTTTCGTCGACCGTGCGCTTCCGGTTGTGGCAACCCGCGAAATGGCGCGGCGGTAAGTATGGC‑GGGGTTATTCCTTCCCCGTTGAGGA‑CACCGGGTTGt                                                                                                                             <  1:792796/150‑1 (MQ=255)                                 aaGCGCATGGCGAGGTAGCTGGTTCATAGATAGCCTGTCGTTAAATTTTCGTCGACCGTGCGCTTCCGGTTGTGGCAACCCGCGAAATGGCGCGGCGGTAAGTATGGC‑GGGGTTATTCCTTCCCCGTTGAGGA‑CACCGGGTTGTC‑AGGTTg                                                                                                                     <  2:182703/151‑1 (MQ=255)                                    cgcATGGCGAGGTAGCTGGTTCATAGATAGCCTGTCGTTAAATTTTCGTCGACCGTGCGCTTCCGGTTGTGGCAACCCGCGAAATGGCGCGGCGGTAAGTATGGC‑GGGGGTATTTCTTCCCCCCTGAGGG‑CACCCGGGTGTG‑AGGGTTAcc                                                                                                                  >  2:772126/1‑151 (MQ=255)                                      cATGGCGAGGTAGCTGGTTCATAGATAGCCTGTCGTTAAATTTTCGTCGACCGTGCGCTTCCGGTTGTGGCAACCCGCGAAATGGCGCGGCGGTAAGTATGGCGGGGGTTTTTCTTCCCCCCTTGGGGA‑‑ACCGGGGTGTC‑AGGGTGAcc                                                                                                                  >  1:437281/1‑149 (MQ=255)                                           cGAGGTAGCTGGTTCATAGATAGCCTGTCGTTAAATTTTCGTCGACCGTGCGCTTCCGGTTGTGGCAACCCGCGAAATGGCGCGGCGGTAAGTATGGC‑GGGGGTATTTCTTTCCCCGTGGGGG‑GACCgggggggcgggggggc                                                                                                                    >  1:937990/1‑130 (MQ=255)                                           cGAGGTAGCTGGTTCATAGATAGCCTGTCGTTAAATTTTCGTCGACCGTGCGCTTCCGGTTGTGGCAACCCGCGAAATGGCGCGGCGGTAAGTATGGC‑GGGGGTATTTCTTCCCCCGTGAGGG‑CACCCGGgtgttcgggtggcc                                                                                                                   >  2:224187/1‑134 (MQ=255)                                              ggTAGCTGGTTCATAGATAGCCTGTCGTTAAATTTTCGTCGACCGTGCGCTTCCGGTTGTGGCAACCCGCGAAATGGCGCGGCGGTAAGTATGGC‑GGGGTTATTCCTTCCCCGTTGAGGA‑CACCGGGTTGTC‑AGGTTGACCATACG‑C‑TTaa                                                                                                      <  1:20815/151‑1 (MQ=255)                                               gTAGCTGGTTCATAGATAGCCTGTCGTTAAATTTTCGTCGACCGTGCGCTTCCGGTTGTGGCAACCCGCGAAATGGCGCGGCGGTAAGTATGGC‑GGGGTTATTCCTTCCCCGTTGAGGA‑CACCGGGTTGTC‑AGGTTGACCATACG‑C‑TTAAg                                                                                                     <  2:294525/151‑1 (MQ=255)                                                   cTGGTTCATAGATAGCCTGTCGTTAAATTTTCGTCGACCGTGCGCTTCCGGTTGTGGCAACCCGCGAAATGGCGCGGCGGTAAGTATGGC‑GGGGGGATTCCTTCCCCCCTCAGGC‑GACCGGGGTGGC‑AGGGTGGCCCTACC‑C‑tt                                                                                                        >  1:230809/1‑144 (MQ=255)                                                      gTTCATAGATAGCCTGTCGTTAAATTTTCGTCGACCGTGCGCTTCCGGTTGTGGCAACCCGCGAAATGGCGCGGCGGTAAGTATGGC‑GGGGTTATTCCTTCCCCGTTGAGGA‑CACCGGGTTGTC‑AGGTTGACCATACG‑C‑TTAAGT‑GAC‑AAc                                                                                            <  1:439882/151‑1 (MQ=255)                                                            agatagCCTGTCGTTAAATTTTCGTCGACCGTGCGCTTCCGGTTGTGGCAACCCGCGAAATGGCGCGGCGGTAAGTATGGC‑GGGGTTATTCCTTCCCCGTTGAGGA‑CACCGGGTTGTC‑AGGTTGACCATACG‑C‑TTAAGT‑GAC‑AACCCCGCt                                                                                      <  1:337353/151‑1 (MQ=255)                                                            agatagCCTGTCGTTAAATTTTCGTCGACCGTGCGCTTCCGGTTGTGGCAACCCGCGAAATGGCGCGGCGGTAAGTATGGC‑GGGGGATTTTCTTCCCCCCTGGGGG‑GACCGGGGTGGCAAGGTTG‑CCATAAC‑C‑CTAAAA‑GAC‑AAaccccc                                                                                       >  2:133384/1‑148 (MQ=255)                                                                 gCCTGTCGTTAAATTTTCGTCGACCGTGCGCTTCCGGTTGTGGCAACCCGCGAAATGGCGCGGCGGTAAGTATGGC‑GGGGTTATTCCTTCCCCGTTGAGGA‑CACCGGGTTGTC‑AGGTTGACCATACG‑C‑TTAAGT‑GAC‑AACCCCGCTGCAAc                                                                                 <  2:295219/151‑1 (MQ=255)                                                                 gCCTGTCGTTAAATTTTCGTCGACCGTGCGCTTCCGGTTGTGGCAACCCGCGAAATGGCGCGGCGGTAAGTATGGC‑GGGGTTATTCCTTCCCCGTTGAGGA‑CACCGGGTTGTC‑AGGTTGACCATACG‑C‑TTAAGT‑GAC‑AACCCCGCTGCAAc                                                                                 <  1:475120/151‑1 (MQ=255)                                                                                 tcgtcgACCGTGCGCTTCCGGTTGTGGCAACCCGCGAAATGGCGCGGCGGTAAGTATGGC‑GGGGGTATTTCTTCCCCCTTTAGGG‑AACCCGGGTGTT‑AGGGTGACCCTACG‑C‑TTTAAG‑GAA‑AAACCCCCCGCAAAGCCCCCTT‑TTAt                                                                    >  2:883823/1‑147 (MQ=255)                                                                                    tcgACCGTGCGCTTCCGGTTGTGGCAACCCGCGAAATGGCGCGGCGGTAAGTATGGC‑GGGGGTTTTTCTTTCCCCTTTAGGA‑CACCCGGGTGTC‑AGGGTGACCCTACG‑C‑CTAAAA‑GACAAACCCCCCGGCAA‑GCCCTCCGTTTTTCAAttt                                                              >  2:347499/1‑151 (MQ=255)                                                                                          gTGCGCTTCCGGTTGTGGCAACCCGCGAAATGGCGCGGCGGTAAGTATGGC‑GGGGGTATTTCCTCCCCCTTGGGGA‑CACCCGGTTGTC‑AGGTTGTCCATAAG‑C‑CTAAAT‑GAA‑AACCCCCCCGCCAAGCCCCCCG‑TTTTTAAtttttt                                                           >  2:859554/1‑145 (MQ=255)                                                                                            gcgcTTCCGGTTGTGGCAACCCGCGAAATGGCGCGGCGGTAAGTATGGC‑GGGGTTATTCCTTCCCCGTTGAGGA‑CACCGGGTTGTC‑AGGTTGACCATACG‑C‑TTAAGT‑GAC‑AACCCCGCTGCAACGCCCTCTG‑TTATCAATTTTCTGGTGa                                                      <  2:690381/150‑1 (MQ=255)                                                                                               cTTCCGGTTGTGGCAACCCGCGAAATGGCGCGGCGGTAAGTATGGC‑GGGGGTATTTCTTCCCCCGTTTGGA‑AACCCGGGTGTT‑AGGGTTACCATAAGCC‑TTAAG‑‑GAC‑AAACCCCCCGCAACGCCCCCCT‑TTTTTAAtttttttggtacggt                                                  >  2:774855/1‑140 (MQ=255)                                                                                                ttCCGGTTGTGGCAACCCGCGAAATGGCGCGGCGGTAAGTATGGCGGGGGTTTTTCTTTCCCCTTTGGGGG‑CCCCGGG‑TGTC‑AGGGTGAGCCTACC‑C‑CTTAGTGGCC‑AACCCCCCCGC‑ACGCCCCCTG‑TTTTTAAATTTTTTGGGGCGttt                                                 >  1:478344/1‑151 (MQ=255)                                                                                                    ggTTGTGGCAACCCGCGAAATGGCGCGGCGGTAAGTATGGC‑GGGGGTTTTTCTTCCCCCCTTAGGACCACCAGG‑TGTC‑AGGGTGACCATAAG‑CTTTAAGT‑AAA‑AACCCC‑CCGCAAAGCCCCCCGTTTTTAAATTTTTTGGGGCGGTTTggg                                              >  2:520506/1‑150 (MQ=255)                                                                                                          ggCAACCCGCGAAATGGCGCGGCGGTAAGTATGGC‑GGGGTTATTCCTTCCCCGTTGAGGA‑CACCGGGTTGTC‑AGGTTGACCATACG‑C‑TTAAGT‑GAC‑AACCCCGCTGCAACGCCCTCTG‑TTATCAATTTTCTGGTGACGTTTGGCGGTATCa                                       <  1:461584/151‑1 (MQ=255)                                                                                                                 cgcgAAATGGCGCGGCGGTAAGTATGGC‑GGGGGTTTTTCTTCCCCCCTGGGGG‑GACCGGGGGGTG‑AGGGTGGCCAATAG‑C‑TTTAAT‑GAC‑AACCCCCCCGCCAACCCCCCTG‑GTTTTCATTTTTTGGGGGGGGTTGGGGGGCTCAGttttt                                 >  1:626624/1‑149 (MQ=255)                                                                                                                      aaTGGCGCGGCGGTAAGTATGGC‑GGGGGTTTTTCTTCCCCCCTGAGGG‑CACCGGGGTGTC‑AGGGTGACCATACGCC‑TTAAG‑‑GAC‑AAACCCCCCGCAACGCCCCCTT‑TTATTCATTTTTTTGGGACGTTTTGCGGGGTTAGttttttttc                             >  2:74261/1‑144 (MQ=255)                                                                                                                      aaTGGCGCGGCGGTAAGTATGGC‑GGGGGTATTTCTTTCCCCCTTAGGA‑CACCCGGGTGTT‑AGGGTGGGCAAACC‑C‑TTTATT‑GGA‑AAACCCCCCGCCACGCCCCCTC‑TTTTTAATTTTTTTGTGGCGTTTGGGGGGATAAGgttttttcc                             >  1:569055/1‑144 (MQ=255)                                                                                                                        tGGCGCGGCGGTAAGTATGGC‑GGGGGTATTTCTTTCCCCTTGAGGA‑CACCCGGGTGTG‑AGGGTGACCATAAGCC‑TTAAG‑‑GAC‑AACCCCCCCGCAACCCCCCCTG‑TTTTTAATTTTTTTGGGACGTTTTGCggggaccattttttt                               >  2:179273/1‑132 (MQ=255)                                                                                                                                 ggTAAGTATGGC‑GGGGGTATTTCTTTCCCCCTGAGGA‑CACCCGGGTGTT‑AGGGTGACCCTACG‑C‑TTAAGT‑GAC‑AACCCCGCCGCAAACCCCCCTG‑TTATTAATTTTCTTGTGGCGGTTGGCGGGATCAGTTTTTCTCCCTGACTg                      >  1:10981/1‑145 (MQ=255)                                                                                                                                      gTATGGC‑GGGGTTATTCCTTCCCCGTTGAGGA‑CACCGGGTTGTC‑AGGTTGACCATACG‑C‑TTAAGT‑GAC‑AACCCCGCTGCAACGCCCTCTG‑TTATCAATTTTCTGGTGACGTTTGGCGGTATCAGTTTTACTCCGTGACTGCTCTGCCGccc           <  1:593225/151‑1 (MQ=255)                                                                                                                                      gTATGGC‑GGGGTTATTCCTTCCCCGTTGAGGA‑CACCGGGTTGTC‑AGGTTGACCATACG‑C‑TTAAGT‑GAC‑AACCCCGCTGCAACGCCCTCTG‑TTATCAATTTTCTGGTGACGTTTGGCGGTATCAGTTTTACTCCGTGACTGCTCTGCCGccc           <  1:495117/151‑1 (MQ=255)                                                                                                                                                ggTTATTCCTTCCCCGTTGAGGA‑CACCGGGTTGTC‑AGGTTGACCATACG‑C‑TTAAGT‑GAC‑AACCCCGCTGCAACGCCCTCTG‑TTATCAATTTTCTGGTGACGTTTGGCGGTATCAGTTTTACTCCGTGACTGCTCTGCCGCCCTTTTTaa    >  2:663030/1‑149 (MQ=255)                                                                                                                                                ggTTATTCCTTCCCCGTTGAGGA‑CACCGGGTTGTC‑AGGTTGACCATACG‑C‑TTAAGT‑GAC‑AACCCCGCTGCAACGCCCTCTG‑TTATCAATTTTCTGGTGACGTTTGGCGGTATCAGTTTTACTCCGTGACTGCTCTGCCGCCCTTTTTAAAg  <  2:295524/151‑1 (MQ=255)                                                                                                                                                ggTTATTCCTTCCCCGTTGAGGA‑CACCGGCTTGTC‑AGGTTGACCATACG‑C‑TTAAGT‑GAC‑AACCCCGCTGCAACGCCCTCTG‑TTATCAATTTTCTGGTGACGTTTGGCGGTATCAGTTTTACTCCGTGACTGCTCTGCCGCCCTTTTTaaa   <  1:242962/150‑1 (MQ=255)                                                                                                                                                  |                                                                                                                                                            ATATTTCCCTGAAAAGTCAGACCATAACGCGAAAGCGCATGGCGAGGTAGCTGGTTCATAGATAGCCTGTCGTTAAATTTTCGTCGACCGTGCGCTTCCGGTTGTGGCAACCCGCGAAATGGCGCGGCGGTAAGTATGGC‑GGGGTTATTCCTTCCCCGTTGAGGA‑CACCGGGTTGTC‑AGGTTGACCATACG‑C‑TTAAGT‑GAC‑AACCCCGCTGCAACGCCCTCTG‑TTATCAATTTTCTGGTGACGTTTGGCGGTATCAGTTTTACTCCGTGACTGCTCTGCCGCCCTTTTTAAAG  >  NC_000913/1649151‑1649443

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 12 ≤ ATCG/ATCG < 14 ≤ ATCG/ATCG < 33 ≤ ATCG/ATCG < 39 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑