Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NC_000913	1,649,308	0	G	C	43.6%	62.1 / 17.9	40	intergenic (+267/‑301)	ydfC/dicB	uncharacterized protein, Qin prophage/Qin prophage; cell division inhibition protein
Reads supporting (aligned to +/- strand):  ref base G (3/19);  new base C (17/0);  total (21/19)
Fisher's exact test for biased strand distribution p-value = 2.57e-08
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 1.00e+00

GAAAAGTCAGACCATAACGCGAAAGCGCATGGCGAGGTAGCTGGTTCATAGATAGCCTGTCGTTAAATTTTCGTCGACCGTGCGCTTCCGGTTGTGGCAACCCGCGAAATGGCGCGGCGGTAAGTATGGC‑GGGGTTATTCCTTCCCCGTTGAGGA‑CACCGGGTTGTC‑AGGTTGACCATACG‑C‑TTAAGT‑GAC‑AACCCCGCTGCAACGCCCTCTG‑TTATCAATTTTCTGGTGACGTTTGGCGGTATCAGTTTTACTCCGTGACTGCTCTGCCGCCCTTTTTAAAGTGAATTTTGTGATG  >  NC_000913/1649161‑1649457                                                                                                                                                     |                                                                                                                                                             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                                                                                               <  1:475120/151‑1 (MQ=255)                                                       gCCTGTCGTTAAATTTTCGTCGACCGTGCGCTTCCGGTTGTGGCAACCCGCGAAATGGCGCGGCGGTAAGTATGGC‑GGGGTTATTCCTTCCCCGTTGAGGA‑CACCGGGTTGTC‑AGGTTGACCATACG‑C‑TTAAGT‑GAC‑AACCCCGCTGCAAc                                                                                               <  2:295219/151‑1 (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)                                                                                                                                         tATTCCTTCCCCGTTGAGGA‑CACCGGGTTGTC‑AGGTTGACCATACG‑C‑TTAAGT‑GAC‑AACCCCGCTGCAACGCCCTCTG‑TTATCAATTTTCTGGTGACGTTTGGCGGTATCAGTTTTACTCCGTGACTGCTCTGCCGCCCTTTTTAAAGTg              >  2:129693/1‑150 (MQ=255)                                                                                                                                                 ccccGTTGAGGA‑CACCGGGTTGTC‑AGGTTGACCATACG‑C‑TTAAGT‑GAC‑AGCCCCGCTGCAACGCCCTCTG‑TTATCAATTTTCTGGTGACGTTTGGCGGTATCAGTTTTACTCCGTGACTGCGCTGCCGCCCTTTTTAAAGTGAATTTtgtg     <  1:261538/151‑1 (MQ=255)                                                                                                                                                  cccGTTGAGGA‑CACCGGGTTGTC‑AGGTTGACCATACG‑C‑TTAAGT‑GAC‑AACCCCGCTGCAACGCCCTCTG‑TTATCAATTTTCTGGTGACGTTTGGCGGTATCAGTTTTACTCCGTGACTGCTCTGCCGCCCTTTTTAGAGTGAATTTTGTGa    <  1:365802/151‑1 (MQ=255)                                                                                                                                                    cGTTGAGGA‑CACCGGGTTGTC‑AGGTTGACCATACG‑C‑TTAAGT‑GAC‑AACCCCGCTGCAACGCCCTCTG‑TTATCAATTTTCTGGTGACGTTTGGCGGTATCAGTTTTACTCCGTGACTGCTCTGCCGCCCTTTTTAAAGTGAATTTTGTGAtg  >  1:266207/1‑151 (MQ=255)                                                                                                                                                     |                                                                                                                                                             GAAAAGTCAGACCATAACGCGAAAGCGCATGGCGAGGTAGCTGGTTCATAGATAGCCTGTCGTTAAATTTTCGTCGACCGTGCGCTTCCGGTTGTGGCAACCCGCGAAATGGCGCGGCGGTAAGTATGGC‑GGGGTTATTCCTTCCCCGTTGAGGA‑CACCGGGTTGTC‑AGGTTGACCATACG‑C‑TTAAGT‑GAC‑AACCCCGCTGCAACGCCCTCTG‑TTATCAATTTTCTGGTGACGTTTGGCGGTATCAGTTTTACTCCGTGACTGCTCTGCCGCCCTTTTTAAAGTGAATTTTGTGATG  >  NC_000913/1649161‑1649457

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 12 ≤ ATCG/ATCG < 14 ≤ ATCG/ATCG < 32 ≤ ATCG/ATCG < 39 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑