Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NC_000913	289,275	0	A	G	40.9%	53.5 / 18.0	44	intergenic (‑113/+26)	yagI/argF	CP4‑6 prophage; putative DNA‑binding transcriptional regulator/ornithine carbamoyltransferase 2, chain F; CP4‑6 prophage
Reads supporting (aligned to +/- strand):  ref base A (21/5);  new base G (0/18);  total (21/23)
Fisher's exact test for biased strand distribution p-value = 3.40e-08
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 1.00e+00

CTGCAACGCACGTTCAACAGACTGAATAATCGGCATAATGCTGGCATGTCCACGCTGGAATTAAGGCGAAAACGTACCTTTTTC‑GGGATGAAAAATCAATGAAATGGAGCCGG‑TGTTCTCCCTCTCCC‑T‑GTGGGAGAGGGCCGGGGTGAGG‑G‑C‑A‑CCAACGCGCAGCGGACCCAATCACTCCCCAAGCGTTGCCATCATCACCGCCTTAATCGTATGCATCCGGTTTTCCGCCTGGTCGAACACGATGCTCGCCGCCGACTCAAACACCTCGTCCGTCACCTCCATCCCGCCGTGCA  >  NC_000913/289127‑289422                                                                                                                                                         |                                                                                                                                                        cTGCAACGCACGTTCAACAGACTGAATAATCGGCATAATGCTGGCATGTCCACGCTGGAATTAAGGCGAAAACGTACCTTTTTC‑GGGATGAAAAATCAATGAAATGGAGCCGG‑TGTTCTCCCTCTCCC‑T‑GTGGGAGAGGGCCGGGGTGAgg                                                                                                                                                       >  1:59293/1‑151 (MQ=255)   gCAACGCACGTTCAACAGACTGAATAATCGGCATAATGCTGGCATGTCCACGCTGGAATTAAGGCGAAAACGTACCTTTTTC‑GGGATGAAAAATCAATGAAATGGAGCCGG‑TGTTCTCCCTCTCCC‑T‑GTGGGAGAGGGCCGGGGTGAg                                                                                                                                                        <  1:619699/148‑1 (MQ=255)     aaCGCACGTTCAACAGACTGAATAATCGGCATAATGCTGGCATGTCCACGCTGGAATTAAGGCGAAAACGTACCTTTTTC‑GGGATGAAAAATCAATGAAATGGAGCCGG‑AGTTCTCCCTCTCCC‑T‑GTGGGAGAGGGCCGGGGTGAGG‑G‑C‑A‑c                                                                                                                                               >  1:451163/1‑151 (MQ=255)           ctttCAACAGACTGAATAATCGGCATAATGCTGGCATGTCCACGCTGGAATTAAGGCGAAAACGTACCTTTTTC‑GGGATGAAAAATCAATGAAATGGAGCCGG‑TGTTCTCCCTCTCCC‑T‑GTGGGAGAGGGCCGGGGTGAGG‑G‑C‑A‑CCAAcgc                                                                                                                                         >  2:577307/3‑151 (MQ=255)           cGTTCAACAGACTGAATAATCGGCATAATGCTGGCATGTCCACGCTGGAATTAAGGCGAAAACGTACCTTTTTC‑GGGATGAAAAATCAATGAAATGGAGCCGG‑TGTTCTCCCTCTCCC‑T‑GTGGGAGAGGGCCGGGGTGAGG‑G‑C‑A‑CCAAcgc                                                                                                                                         >  1:554218/1‑151 (MQ=255)              tCAACAGACTGAATAATCGGCATAATGCTGGCATGTCCACGCTGGAATTAAGGCGAAAACGTACCTTTTTC‑GGGATGAAAAATCAATGAAATGGAGCCGG‑TGTTCTCCCTCTCCC‑T‑GTGGGAGAGGGCCGGGGTGAGG‑G‑C‑A‑CCAACgcgc                                                                                                                                       >  2:297427/1‑150 (MQ=255)                         aataatCGGCATAGTGCGGGCTTGCCCCCGTGGAAATTAGGGAAAAAACGT‑CCTTTTTCGGGGATAAAAAACAAGGGAAGGGGGGCCGT‑TTTCCCCCCTCCCCC‑G‑GGGGGGGGGGGCGGGGGGGAGG‑G‑C‑A‑CCAACGCGCAGCGGAcc                                                                                                                               <  1:258847/147‑1 (MQ=255)                          ataatCGGCATAATGCTGGCATGTCCACGCTGGAATTAAGGCGAAAACGTACCTTTTTC‑GGGATGAAAAATCAATGAAATGGAGCCGG‑TGTTCTCCCTCTCCC‑T‑GTGGGAGAGGGCCGGGGTGAGG‑G‑C‑A‑CCAACGCGCAGCGGACCCAATc                                                                                                                          >  1:603749/1‑151 (MQ=255)                            aatCGGCATAATGCTGGCATGTCCACGCTGGAATTAAGGCGAAAACGTACCTTTTTC‑GGGATGAAAAATCAATGAAATGGAGCCGG‑TGTTCTCCCTCTCCC‑T‑GTGGGAGAGGGCCGGGGTGAGG‑G‑C‑A‑CCAACGCGCAGCGGACCCAATCAc                                                                                                                        >  2:164710/1‑151 (MQ=255)                                   aTAATGCTGGCATGTCCACGCTGGAATTAAGGCGAAAACGTACCTTTTTC‑GGGATGAAAAATCAATGAAATGGAGCCGG‑TGTTCTCCCTCTCCC‑T‑GTGGGAGAGGGCCGGGGTGAGG‑G‑C‑A‑CCAACGCGCAGCGGACCCAATCACTCCCCa                                                                                                                  >  1:114116/1‑150 (MQ=255)                                        gCTGGCATGTCCACGCTGGAATTAAGGCGAAAACGTACCTTTTTC‑GGGATGAAAAATCAATGAAATGGAGCCGG‑TGTTCTCCCTCTCCC‑T‑GTGGGAGAGGGCCGGGGTGAGG‑G‑C‑A‑CCAACGCGCAGCGGACCCAATCACTCCCCAAGCGtt                                                                                                            >  1:717808/1‑151 (MQ=255)                                          tGGCATGTCCACGCTGGAATTAAGGCGAAAACGTACCTTTTTC‑GGGATGAAAAATCAATGAAATGGAGCCGG‑TGTTCTCCCTCTCCC‑T‑GTGGGAGAGGGCCGGGGTGAGG‑G‑C‑A‑CCAACGCGCAGCGGACCCAATCACTCCCCAAGCGTTGc                                                                                                          >  1:121115/1‑151 (MQ=255)                                              aTGTCCACGCTGGAATTAAGGCGAAAACGTACCTTTTTC‑GGGATGAAAAATCAATGAAATGGAGCCGG‑TGTTCTCCCTCTCCC‑T‑GTGGGAGAGGGCCGGGGTGAGG‑G‑C‑A‑CCAACGCGCAGCGGACCCAATCACTCCCCAAGCGTTGCcatc                                                                                                      >  1:52499/1‑151 (MQ=255)                                               tGTCCACGCTGGAATTAAGGCGAAAACGTACCTTTTTC‑GGGATGAAAAATCAATGAAATGGAGCCGG‑TGTTCTCCCTCTCCC‑T‑GTGGGAGAGGGCCGGGGTGAGG‑G‑C‑A‑CCAACGCGCAGCGGACCCAATCACTCCCCAAGCGTTGCcatc                                                                                                      >  2:798642/1‑150 (MQ=255)                                                  ccccggtGGAAATAGGGGAAAAACCTTCCTTTTTG‑GGGAAAAAAAAAAAAAGAAAAGGGGCCTG‑TTTTCCCCCCCCCCC‑TGGTGGGGGGGGGCGGGGGTGGGG‑C‑C‑A‑CCAACGCGCAGCGGACCCAATCACTCCCCAAGCGTTGCcatca                                                                                                     <  2:518131/143‑1 (MQ=255)                                                     cgaggaaataagggagAAAACTTCCTTTTTGG‑GGGAAGAAAAATAAAAGAAGGGGGGCCGT‑TTTTTCCCCTCCCCC‑T‑GGGGGAG‑GGGCCGGGGGGGGG‑GCC‑A‑CCAACGCGCAGCGGACCCAATCACTCCCCAAGCGTTGCCATCATCACCg                                                                                               <  1:226730/136‑1 (MQ=255)                                                       cTGGAATTAAGGCGAAAACGTACCTTTTTC‑GGGATGAAAAATCAATGAAATGGAGCCGG‑TGTTCTCCCTCTCCC‑T‑GTGGGAGAGGGCCGGGGTGAGG‑G‑C‑A‑CCAACGCGCAGCGGACCCAATCACTCCCCAAGCGTTGCCATCATCACCGcc                                                                                             >  1:33350/1‑151 (MQ=255)                                                             ttAAGGCGAAAACGTACCTTTTTC‑GGGATGAAAAATCAATGAAATGGAGCCGG‑TGTTCTCCCTCTCCC‑T‑GTGGGAGAGGGCCGGGGTGAGG‑G‑C‑A‑CCAACGCGCAGCGGACCCAATCACTCCCCAAGCGTTGCCATCATCACCGCCTTAATc                                                                                       >  1:490999/1‑151 (MQ=255)                                                             ataacggcaaaaCGATCCTTTTTT‑GGGAAAAAAAACAAAATAAAGGGGGGCGGTTTTTCCCCCCCCCCT‑T‑GGGGGAGGGGGCGGGGGGGGGG‑C‑C‑A‑CCAACGCGCAGCGGACCCAATCACTCCCCAAGCGTTGCCATCATCACCGc                                                                                              <  2:276715/137‑1 (MQ=255)                                                                    gAAAACGTACCTTTTTC‑GGGATGAAAAATCAATGAAATGGAGCCGG‑TGTTCTCCCTCTCCC‑T‑GTGGGAGAGGGCCGGGGTGAGG‑G‑C‑A‑CCAACGCGCAGCGGACCCAATCACTCCCCAAGCGTTGCCATCATCACCGCCTTAATCGTATGc                                                                                 >  2:38191/1‑150 (MQ=255)                                                                     aaaaCCTTCTTTTTTG‑GGGAAAAAAAAAAAAAGAAAGGGGGCCGG‑TTTTCCCCCCCCCCC‑T‑GGGGGGGGGGGCGGGGGGGGGG‑GCC‑A‑CCAACGCGCAGCGGACCCAATCACTCCCCAAGCGTTGCCATCATCACCGCCTTAATCGTa                                                                                    <  2:111614/147‑1 (MQ=255)                                                                      aaaCGT‑CCTTTTTG‑GGGAAAAAAAAACAAAGAAAGGGGGCCGG‑TTTTCCCCCCCCCCC‑T‑GGGGGGAGGGGCCGGGGGGGGG‑GCC‑A‑CCAACGCGCAGCGGACCCAATCACTCCCCAAGCGTTGCCATCATCACCGCCTTAATCGTATGCATc                                                                              <  2:116293/151‑1 (MQ=255)                                                                         cgtccttttttG‑GGGAAAAAAAACAAAAGAATGGGAGCGGT‑TTTTCCCCCCCCCCC‑T‑GGGGGAGGGGCCGGGGGTGGGG‑C‑C‑A‑CCAACGCGCAGCGGACCCAATCACTCCCCAAGCGTTGCCATCATCACCGCCTTAATCGTATGCATCCgg                                                                           <  1:156985/145‑1 (MQ=255)                                                                                 tttgggggaaaaaaaaTAAAAGAAAGGGCGCTGT‑TGTCCTCCCTCCCCC‑G‑GGGGGAGGGGCCGGGGGTGGGG‑C‑C‑A‑CCAACGCGCAGCGGACCCAATCACTCCCCAAGCGTTGCCATCATCACCGCCTTAATCGTATGCATCCGGTTTTcc                                                                     <  1:243488/139‑1 (MQ=255)                                                                                               aaacaaaaaaaGGGGGCCGG‑T‑TTCCCCCCCCCCC‑G‑GGGGGGGGGGGGCGGGGGGGGG‑GCC‑A‑CCAACGCGCAGCGGACCCAATCACTCCCCAAGCGTTGCCATCATCACCGCCTTAATCGTATGCATCCGGTTTTCCGCCTGGTCGAACACg                                                      <  1:103347/143‑1 (MQ=255)                                                                                                  aaaaaaaaGGGGGCGGG‑TTTTCCCCCCCCCCC‑G‑GGGGGGGGGGGCGGGGGGGGGG‑GAA‑A‑CCAACGCGCAGCGGACCCAATCACTCCCCAAGCGTTGCCATCATCACCGCCTTAATCGTATGCATCCGGTTTTCCGCCTGGTCGAACACGAt                                                    <  2:297115/146‑1 (MQ=255)                                                                                                      gAAATGGAGCCGG‑TGTTCTCCCTCTCCC‑T‑GTGGGAGAGGGCCGGGGTGAGG‑G‑C‑A‑CCAACGCGCAGCGGACCCAATCACTCCCCAAGCGTTGCCATCATCACCGCCTTAATCGTATGCATCCGGTTTTCCGCCTGGTCGAACACGATGCTcg                                               >  2:442162/1‑151 (MQ=255)                                                                                                             gcgcGG‑TTTTCCCCCTTTCCC‑G‑GTGGGGGCGGGCGGGGGGGGGG‑GCC‑A‑CCAACGCGCAGCGGACCCAATCCCTCCCCAAGCGTTGCCATCATCACCGCCTTAATCGTATGCATCCGGTTTTCCGCCTGGTCGAACACGAt                                                    <  1:626615/137‑1 (MQ=255)                                                                                                                cGG‑TGTTCTCCCTCTCCC‑T‑GTGGGAGAGGGCCGGGGTGAGG‑G‑C‑A‑CCAACGCGCAGCGGACCCAATCACTCCCCAAGCGTTGCCATCATCACCGCCTTAATCGTATGCATCCGGTTTTCCGCCTGGTCGAACACGATGCTCGCCGCCGACTc                                     >  2:284470/1‑151 (MQ=255)                                                                                                                  gtggtTCCCCCCCCCCT‑T‑GGGGGGGGGGGGGGGGTTGGGG‑C‑C‑A‑CCAACGCGCAGCGGACCCAATCACTCCCCAAGCGTTGCCATCATCACCGCCTTAATCGTATGCATCCGGTTTTCCGCCTGGTCGAACACGATGCTCGCCGCCGACTCa                                    <  1:211130/148‑1 (MQ=255)                                                                                                                      tttcccccctcccgT‑GGGGGGGGGGGGCGGGGTGGGGCG‑C‑A‑CCAACGCGCAGCGGACCCAACCACTCCCCAAGCGTTGCCATCATCACCGCCTTAATCGTATGCATCCGGTTTTCCGCCTGGTCGAACACGATGCTCGCCGCCGACTCa                                    <  1:409292/145‑1 (MQ=255)                                                                                                                          ccccccccc‑t‑GGGGGGGGGGGGCGGGGGGGGG‑GCC‑A‑CCAACGCGCAGCGGACCCAATCCCTCCCCAAGCGTTGCCATCATCACCGCCTTAATCGTATGCATCCGGTTTTCCGCCTGGTCGAACACGATGCTCGCCGCCGACTCAAacac                               <  1:169829/143‑1 (MQ=255)                                                                                                                               cccc‑t‑GGGGGGGGGGGCCGGGGGGGGG‑G‑CAA‑CCAACGCGCAGCGGACCCAATCACTCCCCAAGCGTTGCCATCATCACCGCCTTAATCGTATGCATCCGGTTTTCCGCCTGGTCGAACACGATGCTCGCCGCCGACTCAAACACCTcgt                          <  2:588783/148‑1 (MQ=255)                                                                                                                                    t‑gtgGGAGAGGGCCGGGGTGAGG‑G‑C‑A‑CCAACGCGCAGCGGACCCAATCACTCCCCAAGCGTTGCCATCATCACCGCCTTAATCGTATGCATCCGGTTTTCCGCCTGGTCGAACACGATGCTCGCCGCCGACTCAAACACCTCGTCCGTCAc                   >  1:704332/1‑151 (MQ=255)                                                                                                                                      gggggAGGGGGCGGGGGTGGGG‑C‑C‑A‑CCAACGCGCAGCGGACCCAATCACTCCCCAAGCGTTGCCATCATCACCGCCTTAATCGTATGCATCCGGTTTTCCGCCTGGTCGAACACGATGCTCGCCGCCGACTCAAACACCTCGTCCGTCAcc                  <  1:463762/149‑1 (MQ=255)                                                                                                                                       tgGGAGAGGGCCGGGGTGAGG‑G‑C‑A‑CCAACGCGCAGCGGACCCAATCACTCCCCAAGCGTTGCCATCATCACCGCCTTAATCGTATGCATCCGGTTTTCCGCCTGGTCGAACACGATGCTCGCCGCCGACTCAAACACCTCGTCCGTCACCt                 >  1:285186/1‑151 (MQ=255)                                                                                                                                       ggggAGGGGGGCGGGGGGGGG‑GCC‑A‑CCAACGCGCAGCGGACCCAATCACTCCCCAAGCGTTGCCATCATCACCGCCTTAATCGTATGCATCCGGTTTTCCGCCTGGTCGAACACGATGCTCGCCGCCGACTCAAACACCTcgtccgtc                     <  2:338041/147‑1 (MQ=255)                                                                                                                                        gggAGGGGGCGGGGGTGAGG‑C‑C‑A‑CCAACGCGCAGCGGACCCAATCACTCCCCAAGCGTTGCCATCATCACCGCCTTAATCGTATGCATCCGGTTTTCCGCCTGGTCGAACACGATGCTCGCCGCCGACTCAAACACCTCGTCCGTCACCTc                <  1:297695/151‑1 (MQ=255)                                                                                                                                        gggAGAGGGCCGGGGTGAGG‑G‑C‑A‑CCAACGCGCAGCGGACCCAATCACTCCCCAAGCGTTGCCATCATCACCGCCTTAATCGTATGCATCCGGTTTTCCGCCTGGTCGAACACGATGCTCGCCGCCGACTCAAACACCTCGTCCGTCACCTc                >  1:755126/1‑151 (MQ=255)                                                                                                                                           gggggcggggggggAGG‑C‑G‑A‑CCAACGCGCAGCGGACCCAATCACTCCCCAAGCGTGGCCATCATCACCGCCTTAATCGTATGCATCCGGTTTTCCGCCTGGTCGAACACGATGCTCGCCGCCGACTCAAACACCTCGTCCGTCACCTCCAt             <  2:467404/143‑1 (MQ=255)                                                                                                                                                  gggggTGGGG‑C‑C‑A‑CCAACGCGCAGCGGACCCAACCACTCCCCAAGCGTTGCCATCATCACCGCCTTAATCGTATGCATCCGGTTTTCCGCCTGGTCGAACACGATGCTCGCCGCCGACTCAAACACCTCGTCCGTCACCTCCATCccgccg      <  2:767291/150‑1 (MQ=255)                                                                                                                                                    gggTGGGG‑G‑G‑ACCCAACGCGCAGCGGACCCAATCACTCCCCAAGCGTTGCCATCATCACCGCCTTAATCGTATGCATCCGGTTTTCCGCCTGGTCGAACACGATGCTCGCCGCCGACTCAAACACCTCGTCCGTCACCTCCAt             <  2:610075/143‑1 (MQ=255)                                                                                                                                                     ggTGAGG‑G‑C‑A‑CCAACGCGCAGCGGACCCAATCACTCCCCAAGCGTTGCCATCATCACCGCCTTAATCGTATGCATCCGGTTTTCCGCCTGGTCGAACACGATGCTCGCCGCCGACTCAAACACCTCGTCCGTCACCTCCATCCCGCCGTGc   <  2:704271/151‑1 (MQ=255)                                                                                                                                                      gTGAGG‑G‑C‑A‑CCAACGCGCAGCGGACCCAATCACTCCCCAAGCGTTGCCATCATCACCGCCTTAATCGTATGCATCCGGTTTTCCGCCTGGTCGAACACGATGCTCGCCGCCGACTCAAACACCTCGTCCGTCACCTCCATCCCGCCGTGc   >  2:488566/1‑150 (MQ=255)                                                                                                                                                         aGG‑G‑C‑A‑CCAACGCGCAGCGGACCCAATCACTCCCCAAGCGTTGCCATCATCACCGCCTTAATCGTATGCATCCGGTTTTCCGCCTGGTCGAACACGATGCTCGCCGCCGACTCAAACACCTCGTCCGTCACCTCCATCCCGCCGTGCa  >  1:324311/1‑148 (MQ=255)                                                                                                                                                         |                                                                                                                                                        CTGCAACGCACGTTCAACAGACTGAATAATCGGCATAATGCTGGCATGTCCACGCTGGAATTAAGGCGAAAACGTACCTTTTTC‑GGGATGAAAAATCAATGAAATGGAGCCGG‑TGTTCTCCCTCTCCC‑T‑GTGGGAGAGGGCCGGGGTGAGG‑G‑C‑A‑CCAACGCGCAGCGGACCCAATCACTCCCCAAGCGTTGCCATCATCACCGCCTTAATCGTATGCATCCGGTTTTCCGCCTGGTCGAACACGATGCTCGCCGCCGACTCAAACACCTCGTCCGTCACCTCCATCCCGCCGTGCA  >  NC_000913/289127‑289422

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 12 ≤ ATCG/ATCG < 14 ≤ ATCG/ATCG < 34 ≤ ATCG/ATCG < 39 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑