Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NC_000913	289,263	0	A	G	41.0%	60.7 / 12.0	41	intergenic (‑101/+38)	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 (20/3);  new base G (0/16);  total (20/21)
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

CGAGGATCTGCAACGCACGTTCAACAGACTGAATAATCGGCATAATGCTGGCATGTCCACGCTGGAATTAAGGCGAAAACGTACCTTTTTC‑GGGATGAAAAATCAATGAAATGGAGCCGG‑TGTTCTCCCTCTCCC‑T‑GTGGGAGAGGGCCGGGGTGAGG‑G‑C‑ACCAACGCGCAGCGGACCCAATCACTCCCCAAGCGTTGCCATCATCACCGCCTTAATCGTATGCATCCGGTTTTCCGCCTGGTCGAACACGATGCTCGCCGCCGACTCAAACACCTCGTCCGTCACCTC  >  NC_000913/289120‑289408                                                                                                                                                    |                                                                                                                                                     cGAGGATCTGCAACGCACGTTCAACAGACTGAATAATCGGCATAATGCTGGCATGTCCACGCTGGAATTAAGGCGAAAACGTACCTTTTTC‑GGGATGAAAAATCAATGAAATGGAGCCGG‑TGTTCTCCCTCTCCC‑T‑GTGGGAGAGGGCCg                                                                                                                                                <  1:643620/150‑1 (MQ=255)        cTGCAACGCACGTTCAACAGACTGAATAATCGGCATAATGCTGGCATGTCCACGCTGGAATTAAGGCGAAAACGTACCTTTTTC‑GGGATGAAAAATCAATGAAATGGAGCCGG‑TGTTCTCCCTCTCCC‑T‑GTGGGAGAGGGCCGGGGTGAgg                                                                                                                                        >  1:59293/1‑151 (MQ=255)          gCAACGCACGTTCAACAGACTGAATAATCGGCATAATGCTGGCATGTCCACGCTGGAATTAAGGCGAAAACGTACCTTTTTC‑GGGATGAAAAATCAATGAAATGGAGCCGG‑TGTTCTCCCTCTCCC‑T‑GTGGGAGAGGGCCGGGGTGAg                                                                                                                                         <  1:619699/148‑1 (MQ=255)          gCAACGCACGTTCAACAGACTGAATAATCGGCATAATGCTGGCATGTCCACGCTGGAATTAAGGCGAAAACGTACCTTTTTC‑GGGATGAAAAATCAATGAAATGGAGCCGG‑TGTTCTCCCTCACCC‑T‑GTGGGAGAGGGCCGGGGTg                                                                                                                                           <  1:78660/146‑1 (MQ=255)            aaCGCACGTTCAACAGACTGAATAATCGGCATAATGCTGGCATGTCCACGCTGGAATTAAGGCGAAAACGTACCTTTTTC‑GGGATGAAAAATCAATGAAATGGAGCCGG‑AGTTCTCCCTCTCCC‑T‑GTGGGAGAGGGCCGGGGTGAGG‑G‑C‑Ac                                                                                                                                 >  1:451163/1‑151 (MQ=255)                  ctttCAACAGACTGAATAATCGGCATAATGCTGGCATGTCCACGCTGGAATTAAGGCGAAAACGTACCTTTTTC‑GGGATGAAAAATCAATGAAATGGAGCCGG‑TGTTCTCCCTCTCCC‑T‑GTGGGAGAGGGCCGGGGTGAGG‑G‑C‑ACCAAcgc                                                                                                                           >  2:577307/3‑151 (MQ=255)                  cGTTCAACAGACTGAATAATCGGCATAATGCTGGCATGTCCACGCTGGAATTAAGGCGAAAACGTACCTTTTTC‑GGGATGAAAAATCAATGAAATGGAGCCGG‑TGTTCTCCCTCTCCC‑T‑GTGGGAGAGGGCCGGGGTGAGG‑G‑C‑ACCAAcgc                                                                                                                           >  1:554218/1‑151 (MQ=255)                     tCAACAGACTGAATAATCGGCATAATGCTGGCATGTCCACGCTGGAATTAAGGCGAAAACGTACCTTTTTC‑GGGATGAAAAATCAATGAAATGGAGCCGG‑TGTTCTCCCTCTCCC‑T‑GTGGGAGAGGGCCGGGGTGAGG‑G‑C‑ACCAACgcgc                                                                                                                         >  2:297427/1‑150 (MQ=255)                                aataatCGGCATAGTGCGGGCTTGCCCCCGTGGAAATTAGGGAAAAAACGT‑CCTTTTTCGGGGATAAAAAACAAGGGAAGGGGGGCCGT‑TTTCCCCCCTCCCCC‑G‑GGGGGGGGGGGCGGGGGGGAGG‑G‑C‑ACCAACGCGCAGCGGAcc                                                                                                                 <  1:258847/147‑1 (MQ=255)                                 ataatCGGCATAATGCTGGCATGTCCACGCTGGAATTAAGGCGAAAACGTACCTTTTTC‑GGGATGAAAAATCAATGAAATGGAGCCGG‑TGTTCTCCCTCTCCC‑T‑GTGGGAGAGGGCCGGGGTGAGG‑G‑C‑ACCAACGCGCAGCGGACCCAATc                                                                                                            >  1:603749/1‑151 (MQ=255)                                   aatCGGCATAATGCTGGCATGTCCACGCTGGAATTAAGGCGAAAACGTACCTTTTTC‑GGGATGAAAAATCAATGAAATGGAGCCGG‑TGTTCTCCCTCTCCC‑T‑GTGGGAGAGGGCCGGGGTGAGG‑G‑C‑ACCAACGCGCAGCGGACCCAATCAc                                                                                                          >  2:164710/1‑151 (MQ=255)                                          aTAATGCTGGCATGTCCACGCTGGAATTAAGGCGAAAACGTACCTTTTTC‑GGGATGAAAAATCAATGAAATGGAGCCGG‑TGTTCTCCCTCTCCC‑T‑GTGGGAGAGGGCCGGGGTGAGG‑G‑C‑ACCAACGCGCAGCGGACCCAATCACTCCCCa                                                                                                    >  1:114116/1‑150 (MQ=255)                                               gCTGGCATGTCCACGCTGGAATTAAGGCGAAAACGTACCTTTTTC‑GGGATGAAAAATCAATGAAATGGAGCCGG‑TGTTCTCCCTCTCCC‑T‑GTGGGAGAGGGCCGGGGTGAGG‑G‑C‑ACCAACGCGCAGCGGACCCAATCACTCCCCAAGCGtt                                                                                              >  1:717808/1‑151 (MQ=255)                                                 tGGCATGTCCACGCTGGAATTAAGGCGAAAACGTACCTTTTTC‑GGGATGAAAAATCAATGAAATGGAGCCGG‑TGTTCTCCCTCTCCC‑T‑GTGGGAGAGGGCCGGGGTGAGG‑G‑C‑ACCAACGCGCAGCGGACCCAATCACTCCCCAAGCGTTGc                                                                                            >  1:121115/1‑151 (MQ=255)                                                     aTGTCCACGCTGGAATTAAGGCGAAAACGTACCTTTTTC‑GGGATGAAAAATCAATGAAATGGAGCCGG‑TGTTCTCCCTCTCCC‑T‑GTGGGAGAGGGCCGGGGTGAGG‑G‑C‑ACCAACGCGCAGCGGACCCAATCACTCCCCAAGCGTTGCcatc                                                                                        >  1:52499/1‑151 (MQ=255)                                                      tGTCCACGCTGGAATTAAGGCGAAAACGTACCTTTTTC‑GGGATGAAAAATCAATGAAATGGAGCCGG‑TGTTCTCCCTCTCCC‑T‑GTGGGAGAGGGCCGGGGTGAGG‑G‑C‑ACCAACGCGCAGCGGACCCAATCACTCCCCAAGCGTTGCcatc                                                                                        >  2:798642/1‑150 (MQ=255)                                                         ccccggtGGAAATAGGGGAAAAACCTTCCTTTTTG‑GGGAAAAAAAAAAAAAGAAAAGGGGCCTG‑TTTTCCCCCCCCCCC‑TGGTGGGGGGGGGCGGGGGTGGGG‑C‑C‑ACCAACGCGCAGCGGACCCAATCACTCCCCAAGCGTTGCcatca                                                                                       <  2:518131/143‑1 (MQ=255)                                                            cgaggaaataagggagAAAACTTCCTTTTTGG‑GGGAAGAAAAATAAAAGAAGGGGGGCCGT‑TTTTTCCCCTCCCCC‑T‑GGGGGAG‑GGGCCGGGGGGGGG‑GCC‑ACCAACGCGCAGCGGACCCAATCACTCCCCAAGCGTTGCCATCATCACCg                                                                                 <  1:226730/136‑1 (MQ=255)                                                              cTGGAATTAAGGCGAAAACGTACCTTTTTC‑GGGATGAAAAATCAATGAAATGGAGCCGG‑TGTTCTCCCTCTCCC‑T‑GTGGGAGAGGGCCGGGGTGAGG‑G‑C‑ACCAACGCGCAGCGGACCCAATCACTCCCCAAGCGTTGCCATCATCACCGcc                                                                               >  1:33350/1‑151 (MQ=255)                                                                    ttAAGGCGAAAACGTACCTTTTTC‑GGGATGAAAAATCAATGAAATGGAGCCGG‑TGTTCTCCCTCTCCC‑T‑GTGGGAGAGGGCCGGGGTGAGG‑G‑C‑ACCAACGCGCAGCGGACCCAATCACTCCCCAAGCGTTGCCATCATCACCGCCTTAATc                                                                         >  1:490999/1‑151 (MQ=255)                                                                    ataacggcaaaaCGATCCTTTTTT‑GGGAAAAAAAACAAAATAAAGGGGGGCGGTTTTTCCCCCCCCCCT‑T‑GGGGGAGGGGGCGGGGGGGGGG‑C‑C‑ACCAACGCGCAGCGGACCCAATCACTCCCCAAGCGTTGCCATCATCACCGc                                                                                <  2:276715/137‑1 (MQ=255)                                                                           gAAAACGTACCTTTTTC‑GGGATGAAAAATCAATGAAATGGAGCCGG‑TGTTCTCCCTCTCCC‑T‑GTGGGAGAGGGCCGGGGTGAGG‑G‑C‑ACCAACGCGCAGCGGACCCAATCACTCCCCAAGCGTTGCCATCATCACCGCCTTAATCGTATGc                                                                   >  2:38191/1‑150 (MQ=255)                                                                            aaaaCCTTCTTTTTTG‑GGGAAAAAAAAAAAAAGAAAGGGGGCCGG‑TTTTCCCCCCCCCCC‑T‑GGGGGGGGGGGCGGGGGGGGGG‑GCC‑ACCAACGCGCAGCGGACCCAATCACTCCCCAAGCGTTGCCATCATCACCGCCTTAATCGTa                                                                      <  2:111614/147‑1 (MQ=255)                                                                             aaaCGT‑CCTTTTTG‑GGGAAAAAAAAACAAAGAAAGGGGGCCGG‑TTTTCCCCCCCCCCC‑T‑GGGGGGAGGGGCCGGGGGGGGG‑GCC‑ACCAACGCGCAGCGGACCCAATCACTCCCCAAGCGTTGCCATCATCACCGCCTTAATCGTATGCATc                                                                <  2:116293/151‑1 (MQ=255)                                                                                cgtccttttttG‑GGGAAAAAAAACAAAAGAATGGGAGCGGT‑TTTTCCCCCCCCCCC‑T‑GGGGGAGGGGCCGGGGGTGGGG‑C‑C‑ACCAACGCGCAGCGGACCCAATCACTCCCCAAGCGTTGCCATCATCACCGCCTTAATCGTATGCATCCgg                                                             <  1:156985/145‑1 (MQ=255)                                                                                        tttgggggaaaaaaaaTAAAAGAAAGGGCGCTGT‑TGTCCTCCCTCCCCC‑G‑GGGGGAGGGGCCGGGGGTGGGG‑C‑C‑ACCAACGCGCAGCGGACCCAATCACTCCCCAAGCGTTGCCATCATCACCGCCTTAATCGTATGCATCCGGTTTTcc                                                       <  1:243488/139‑1 (MQ=255)                                                                                                      aaacaaaaaaaGGGGGCCGG‑T‑TTCCCCCCCCCCC‑G‑GGGGGGGGGGGGCGGGGGGGGG‑GCC‑ACCAACGCGCAGCGGACCCAATCACTCCCCAAGCGTTGCCATCATCACCGCCTTAATCGTATGCATCCGGTTTTCCGCCTGGTCGAACACg                                        <  1:103347/143‑1 (MQ=255)                                                                                                         aaaaaaaaGGGGGCGGG‑TTTTCCCCCCCCCCC‑G‑GGGGGGGGGGGCGGGGGGGGGG‑GAA‑ACCAACGCGCAGCGGACCCAATCACTCCCCAAGCGTTGCCATCATCACCGCCTTAATCGTATGCATCCGGTTTTCCGCCTGGTCGAACACGAt                                      <  2:297115/146‑1 (MQ=255)                                                                                                             gAAATGGAGCCGG‑TGTTCTCCCTCTCCC‑T‑GTGGGAGAGGGCCGGGGTGAGG‑G‑C‑ACCAACGCGCAGCGGACCCAATCACTCCCCAAGCGTTGCCATCATCACCGCCTTAATCGTATGCATCCGGTTTTCCGCCTGGTCGAACACGATGCTcg                                 >  2:442162/1‑151 (MQ=255)                                                                                                                    gcgcGG‑TTTTCCCCCTTTCCC‑G‑GTGGGGGCGGGCGGGGGGGGGG‑GCC‑ACCAACGCGCAGCGGACCCAATCCCTCCCCAAGCGTTGCCATCATCACCGCCTTAATCGTATGCATCCGGTTTTCCGCCTGGTCGAACACGAt                                      <  1:626615/137‑1 (MQ=255)                                                                                                                       cGG‑TGTTCTCCCTCTCCC‑T‑GTGGGAGAGGGCCGGGGTGAGG‑G‑C‑ACCAACGCGCAGCGGACCCAATCACTCCCCAAGCGTTGCCATCATCACCGCCTTAATCGTATGCATCCGGTTTTCCGCCTGGTCGAACACGATGCTCGCCGCCGACTc                       >  2:284470/1‑151 (MQ=255)                                                                                                                         gtggtTCCCCCCCCCCT‑T‑GGGGGGGGGGGGGGGGTTGGGG‑C‑C‑ACCAACGCGCAGCGGACCCAATCACTCCCCAAGCGTTGCCATCATCACCGCCTTAATCGTATGCATCCGGTTTTCCGCCTGGTCGAACACGATGCTCGCCGCCGACTCa                      <  1:211130/148‑1 (MQ=255)                                                                                                                             tttcccccctcccgT‑GGGGGGGGGGGGCGGGGTGGGGCG‑C‑ACCAACGCGCAGCGGACCCAACCACTCCCCAAGCGTTGCCATCATCACCGCCTTAATCGTATGCATCCGGTTTTCCGCCTGGTCGAACACGATGCTCGCCGCCGACTCa                      <  1:409292/145‑1 (MQ=255)                                                                                                                                 ccccccccc‑t‑GGGGGGGGGGGGCGGGGGGGGG‑GCC‑ACCAACGCGCAGCGGACCCAATCCCTCCCCAAGCGTTGCCATCATCACCGCCTTAATCGTATGCATCCGGTTTTCCGCCTGGTCGAACACGATGCTCGCCGCCGACTCAAacac                 <  1:169829/143‑1 (MQ=255)                                                                                                                                      cccc‑t‑GGGGGGGGGGGCCGGGGGGGGG‑G‑CAACCAACGCGCAGCGGACCCAATCACTCCCCAAGCGTTGCCATCATCACCGCCTTAATCGTATGCATCCGGTTTTCCGCCTGGTCGAACACGATGCTCGCCGCCGACTCAAACACCTcgt            <  2:588783/148‑1 (MQ=255)                                                                                                                                           t‑gtgGGAGAGGGCCGGGGTGAGG‑G‑C‑ACCAACGCGCAGCGGACCCAATCACTCCCCAAGCGTTGCCATCATCACCGCCTTAATCGTATGCATCCGGTTTTCCGCCTGGTCGAACACGATGCTCGCCGCCGACTCAAACACCTCGTCCGTCAc     >  1:704332/1‑151 (MQ=255)                                                                                                                                             gggggAGGGGGCGGGGGTGGGG‑C‑C‑ACCAACGCGCAGCGGACCCAATCACTCCCCAAGCGTTGCCATCATCACCGCCTTAATCGTATGCATCCGGTTTTCCGCCTGGTCGAACACGATGCTCGCCGCCGACTCAAACACCTCGTCCGTCAcc    <  1:463762/149‑1 (MQ=255)                                                                                                                                              tgGGAGAGGGCCGGGGTGAGG‑G‑C‑ACCAACGCGCAGCGGACCCAATCACTCCCCAAGCGTTGCCATCATCACCGCCTTAATCGTATGCATCCGGTTTTCCGCCTGGTCGAACACGATGCTCGCCGCCGACTCAAACACCTCGTCCGTCACCt   >  1:285186/1‑151 (MQ=255)                                                                                                                                              ggggAGGGGGGCGGGGGGGGG‑GCC‑ACCAACGCGCAGCGGACCCAATCACTCCCCAAGCGTTGCCATCATCACCGCCTTAATCGTATGCATCCGGTTTTCCGCCTGGTCGAACACGATGCTCGCCGCCGACTCAAACACCTcgtccgtc       <  2:338041/147‑1 (MQ=255)                                                                                                                                               gggAGGGGGCGGGGGTGAGG‑C‑C‑ACCAACGCGCAGCGGACCCAATCACTCCCCAAGCGTTGCCATCATCACCGCCTTAATCGTATGCATCCGGTTTTCCGCCTGGTCGAACACGATGCTCGCCGCCGACTCAAACACCTCGTCCGTCACCTc  <  1:297695/151‑1 (MQ=255)                                                                                                                                               gggAGAGGGCCGGGGTGAGG‑G‑C‑ACCAACGCGCAGCGGACCCAATCACTCCCCAAGCGTTGCCATCATCACCGCCTTAATCGTATGCATCCGGTTTTCCGCCTGGTCGAACACGATGCTCGCCGCCGACTCAAACACCTCGTCCGTCACCTc  >  1:755126/1‑151 (MQ=255)                                                                                                                                                    |                                                                                                                                                     CGAGGATCTGCAACGCACGTTCAACAGACTGAATAATCGGCATAATGCTGGCATGTCCACGCTGGAATTAAGGCGAAAACGTACCTTTTTC‑GGGATGAAAAATCAATGAAATGGAGCCGG‑TGTTCTCCCTCTCCC‑T‑GTGGGAGAGGGCCGGGGTGAGG‑G‑C‑ACCAACGCGCAGCGGACCCAATCACTCCCCAAGCGTTGCCATCATCACCGCCTTAATCGTATGCATCCGGTTTTCCGCCTGGTCGAACACGATGCTCGCCGCCGACTCAAACACCTCGTCCGTCACCTC  >  NC_000913/289120‑289408

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: ‑