Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NC_000913	1,649,295	0	T	G	46.5%	62.9 / 15.3	43	intergenic (+254/‑314)	ydfC/dicB	uncharacterized protein, Qin prophage/Qin prophage; cell division inhibition protein
Reads supporting (aligned to +/- strand):  ref base T (2/21);  new base G (20/0);  total (22/21)
Fisher's exact test for biased strand distribution p-value = 2.62e-10
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 1.00e+00

GATATTTCCCTGAAAAGTCAGACCATAACGCGAAAGCGCATGGCGAGGTAGCTGGTTCATAGATAGCCTGTCGTTAAATTTTCGTCGACCGTGCGCTTCCGGTTGTGGCAACCCGCGAAATGGCGCGGCGGTAAGTATGGC‑GGGGTTA‑TTCCTTCCCCGTTGAGGACACCGGGTTGT‑CAGGTTGACCATACGCTTAAGTGACAACCCCGCTGCAACGCCCTCTGTTATCAA‑TTTTCTGGTGACGTTTGGCGGTATCAGTTTTACTCCGTGACTGCTCTGCCGCCCTTTTTAAAG  >  NC_000913/1649150‑1649443                                                                                                                                                   |                                                                                                                                                        gATATTTCCCTGAAAAGTCAGACCATAACGCGAAAGCGCATGGCGAGGTAGCTGGTTCATAGATAGCCTGTCGTTAAATTTTCGTCGACCGTGCGCTTCCGGTTGTGGCAACCCGCGAAATGGCGCGGCGGTAAGTATGGC‑GGGGGTA‑tt                                                                                                                                                    >  1:750910/1‑150 (MQ=255)  atatTTCCCTGAAAAGTCAGACCATAACGCGAAAGCGCATGGCGAGGTAGCTGGTTCATAGATAGCCTGTCGTTAAATTTTCGTCGACCGTGCGCTTCCGGTTGTGGCAACCCGCGAAATGGCGCGGCGGTAAGTATGGC‑GGGGGTA‑tt                                                                                                                                                    >  1:469387/1‑149 (MQ=255)    atTTCCCTGAAAAGTCAGACCATAACGCGAAAGCGCATGGCGAGGTAGCTGGTTCATAGATAGCCTGTCGTTAAATTTTCGTCGACCGTGCGCTTCCGGTTGTGGCAACCCGCGAAATGGCGCGGCGGTAAGTATGGC‑GGGGGTT‑tttctt                                                                                                                                                >  1:240898/1‑151 (MQ=255)        cccTGAAAAGTCAGACCATAACGCGAAAGCGCATGGCGAGGTAGCTGGTTCATAGATAGCCTGTCGTTAAATTTTCGTCGACCGTGCGCTTCCGGTTGTGGCAACCCGCGAAATGGCGCGGCGGTAAGTATGGC‑GGGGTTA‑TTCCTTccc                                                                                                                                             <  1:186595/150‑1 (MQ=255)           tGAAAAGTCAGACCATAACGCGAAAGCGCATGGCGAGGTAGCTGGTTCATAGATAGCCTGTCGTTAAATTTTCGTCGACCGTGCGCTTCCGGTTGTGGCAACCCGCGAAATGGCGCGGCGGTAAGTATGGC‑GGGGGTT‑TTTCTTTCCCGtt                                                                                                                                         >  1:168722/1‑151 (MQ=255)              aaaGTCAGACCATAACGCGAAAGCGCATGGCGAGGTAGCTGGTTCATAGATAGCCTGTCGTTAAATTTTCGTCGACCGTGCGCTTCCGGTTGTGGCAACCCGCGAAATGGCGCGGCGGTAAGTATGGC‑GGGGGTT‑TTCCTTCCCCgcttgg                                                                                                                                      >  1:324819/1‑146 (MQ=255)                 gTCAGACCATAACGCGAAAGCGCATGGCGAGGTAGCTGGTTCATAGATAGCCTGTCGTTAAATTTTCGTCGACCGTGCGCTTCCGGTTGTGGCAACCCGCGAAATGGCGCGGCGGTAAGTATGGC‑GGGGTTA‑TTCCTTCCCCGTTGAGGac                                                                                                                                   <  1:898322/151‑1 (MQ=255)                  tCAGACCATAACGCGAAAGCGCATGGCGAGGTAGCTGGTTCATAGATAGCCTGTCGTTAAATTTTCGTCGACCGTGCGCTTCCGGTTGTGGCAACCCGCGAAATGGCGCGGCGGTAAGTATGGC‑GGGGGTA‑TTTCTTTCCCGCTGAgg                                                                                                                                     >  1:339208/1‑148 (MQ=255)                     gACCATAACGCGAAAGCGCATGGCGAGGTAGCTGGTTCATAGATAGCCTGTCGTTAAATTTTCGTCGACCGTGCGCTTCCGGTTGTGGCAACCCGCGAAATGGCGCGGCGGTAAGTATGGCGGGGGGTT‑TTCTTTCCCCGtgtgg                                                                                                                                      >  2:824715/1‑141 (MQ=255)                         aTAACGCGAAAGCGCATGGCGAGGTAGCTGGTTCATAGATAGCCTGTCGTTAAATTTTCGTCGACCGTGCGCTTCCGGTTGTGGCAACCCGCGAAATGGCGCGGCGGTAAGTATGGC‑GGGGTTA‑TTCCTTCCCCGTTGAGGACACCGGGtt                                                                                                                           <  2:802358/151‑1 (MQ=255)                            aCGCGAAAGCGCATGGCGAGGTAGCTGGTTCATAGATAGCCTGTCGTTAAATTTTCGTCGACCGTGCGCTTCCGGTTGTGGCAACCCGCGAAATGGCGCGGCGGTAAGTATGGC‑GGGGTTA‑ATCCTTCCCCGTTGAGGACACCGGGTTGT‑c                                                                                                                       <  2:428459/151‑1 (MQ=255)                            aCGCGAAAGCGCATGGCGAGGTAGCTGGTTCATAGATAGCCTGTCGTTAAATTTTCGTCGACCGTGCGCTTCCGGTTGTGGCAACCCGCGAAATGGCGCGGCGGTAAGTATGGC‑GGGGGTA‑TTTCTTTCCCCGTGGGGAAACCcgg                                                                                                                             >  1:573044/1‑146 (MQ=255)                                gAAAGCGCATGGCGAGGTAGCTGGTTCATAGATAGCCTGTCGTTAAATTTTCGTCGACCGTGCGCTTCCGGTTGTGGCAACCCGCGAAATGGCGCGGCGGTAAGTATGGC‑GGGGTTA‑TTCCTTCCCCGTTGAGGACACCGGGTTGT‑CAGGt                                                                                                                   <  1:447645/151‑1 (MQ=255)                                gAAAGCGCATGGCGAGGTAGCTGGTTCATAGATAGCCTGTCGTTAAATTTTCGTCGACCGTGCGCTTCCGGTTGTGGCAACCCGCGAAATGGCGCGGCGGTAAGTATGGC‑GGGGGTA‑TTTCTTCCCCCCTGAGGACACCCGGGTGT‑CAgg                                                                                                                    >  1:262867/1‑150 (MQ=255)                                           gCGAGGTAGCTGGTTCATAGATAGCCTGTCGTTAAATTTTCGTCGACCGTGCGCTTCCGGTTGTGGCAACCCGCGAAATGGCGCGGCGGTAAGTATGGC‑GGGGTTA‑TTCCTTCCCCGTTGAGGACACCGGGTTGT‑CAGGTTGACCATACGc                                                                                                        <  2:30792/151‑1 (MQ=255)                                                         tCATAGATAGCCTGTCGTTAAATTTTCGTCGACCGTGCGCTTCCGGTTGTGGCAACCCGCGAAATGGCGCGGCGGTAAGTATGGC‑GGGGGTT‑TTTTTTTCCCCCGGTGGGCCCCGGGGTGT‑TAGGGTGTACATACGccttattggacaa                                                                                            >  2:9188/1‑137 (MQ=255)                                                             agatagCCTGTCGTTAAATTTTCGTCGACCGTGCGCTTCCGGTTGTGGCAACCCGCGAAATGGCGCGGCGGTAAGTATGGC‑GGGGTTA‑TTCCTTCCCCGTTGAGGACACCGGGTTGT‑CAGGTTGACCATACGCTTAAGTGACAACCCCGCt                                                                                      <  1:837177/151‑1 (MQ=255)                                                             agatagCCTGTCGTTAAATTTTCGTCGACCGTGCGCTTCCGGTTGTGGCAACCCGCGAAATGGCGCGGCGGTAAGTATGGC‑GGGGGTA‑TTTCTTCCCCGCTGAGGACACCCGGGTGG‑CAGGGTGACCATACCCCTAAATGACAAaccccc                                                                                       >  1:178588/1‑148 (MQ=255)                                                                  gCCTGTCGTTAAATTTTCGTCGACCGTGCGCTTCCGGTTGTGGCAACCCGCGAAATGGCGCGGCGGTAAGTATGGC‑GGGGTTA‑TTCCTTCCCCGTTGAGGACACCGGGTTGT‑CAGGTTGACCATACGCTTAAGTGACAACCCCGCTGCAAc                                                                                 <  2:620522/151‑1 (MQ=255)                                                                        cGTTAAATTTTCGTCGACCGTGCGCTTCCGGTTGTGGCAACCCGCGAAATGGCGCGGCGGTAAGTATGGC‑GGGGTTA‑TTCCTTCCCCGTTGAGGACACCGGGTTGT‑CAGGTTGACCATACGCTTAAGTGACAACCCCGCTGCAACGCCctc                                                                           <  1:513124/151‑1 (MQ=255)                                                                        cGTTAAATTTTCGTCGACCGTGCGCTTCCGGTTGTGGCAACCCGCGAAATGGCGCGGCGGTAAGTATGGC‑GGGGGTATTTCTTTCCCCCTTG‑GGAAACCCGGGTGTCCGGGTTGA‑CAAACGCCTAAGAGACAACCCCCCCGCAAACCCctc                                                                           >  1:503731/1‑151 (MQ=255)                                                                                   cgtcgACCGTGCGCTTCCGGTTGTGGCAACCCGCGAAATGGCGCGGCGGTAAGTATGGC‑GGGGTTA‑TTCCTTCCCCGTTGAGGACACCGGGTTGT‑CAGGTTAACCATACGCTTAAGTGACAACCCCGCTGCAACGCCCTCTGTTATCAA‑tt                                                               <  2:469909/151‑1 (MQ=255)                                                                                   cgtcgACCGTGCGCTTCCGGTTGTGGCAACCCGCGAAATGGCGCGGCGGTAAGTATGGC‑GGGGGTG‑TTTCTTCCCCCCTTAGGGAACCCCGGTGT‑CAGGGTGACCCAACCCCTAAGTGACCACCCCCCCGCCACCCCCCCCGTTAttcatt                                                                >  2:905569/1‑146 (MQ=255)                                                                                    gtcgACCGTGCGCTTCCGGTTGTGGCAACCCGCGAAATGGCGCGGCGGTAAGTATGGC‑GGTGTTA‑TTCCTTCCCCGTTGAGGACGCCGGGTTGT‑CAGGTTGACCATACGCTTAAGTGACAACCCCGCTGCAACGCCCTCTGTTATCAA‑ttt                                                              <  2:629415/151‑1 (MQ=255)                                                                                       gACCGTGCGCTTCCGGTTGTGGCAACCCGCGAAATGGCGCGGCGGTAAGTATGGCGGGGGTTT‑TTTCTTCCCGCTGTGGGGCACCGGGTGTG‑CAGG‑TGAACATACGCTTTAGAGAAAAACCCCCCGCCACGCCCCCTCTTTTTCA‑tttttt                                                           >  2:586709/1‑149 (MQ=255)                                                                                       gACCGTGCGCTTCCGGTTGTGGCAACCCGCGAAATGGCGCGGCGGTAAGTATGGC‑GGGGGTA‑TTTCTTCCCCGTTGAGGGCACCCGGGTGG‑CAGGTTGACCATACGCTTAAATGACAAACCCCCCGCCACGCCCTCTGTTTTCAA‑tttttt                                                           >  1:107107/1‑149 (MQ=255)                                                                                        aCCGTGCGCTTCCGGTTGTGGCAACCCGCGAAATGGCGCGGCGGTAAGTATGGC‑GGGGTTA‑TTCCTTCCCCGTTGAGGACACCGGGTTGT‑CAGGTTGACCATACGCTTAAGTGACAACCCCGCTGCAACGCCCTCTGTTATCAA‑TTTTCTg                                                          <  1:464683/151‑1 (MQ=255)                                                                                        aCCGTGCGCTTCCGGTTGTGGCAACCCGCGAAATGGCGCGGCGGTAAGTATGGC‑GGGGGTT‑TTTCTTTCCCCCTGGGGGCACCCGGGTTT‑CCGGGTGGCCACACACCTAAATGACAAACCCCCCCCAACGCCCCCCGTTTTTAA‑attttt                                                           >  1:875041/1‑148 (MQ=255)                                                                                           gTGCGCTTCCGGTTGTGGCAACCCGCGAAATGGCGCGGCGGTAAGTATGGC‑GGGGGTG‑TTTCTTTCCCGGTGAGGACACCCGGGTGG‑CAGGGTGAACATACGCCTTAGAGAAAAACCCCCCGCCACGCCCCCTGTTTTTAA‑attt                                                             >  2:262320/1‑145 (MQ=255)                                                                                                 ttCCGGTTGTGGCAACCCGCGAAATGGCGCGGCGGTAAGTATGGC‑GGGGGTA‑TTTTTTTCCCCCTTAGGGGACCCGGGGGT‑CATGGTGACCATACGCCTAAAGGAAAACCCCCCCGCCACGCCCCCTGTTTTTAA‑TTTTTTTGTGGCGtt                                                  >  2:499455/1‑150 (MQ=255)                                                                                                      gTTGTGGCAACCCGCGAAATGGCGCGGCGGTAAGTATGGC‑GGGGTTA‑TTCCTTCCCCGTTGAGGACACCGGGTTGT‑CAGGTTGACCATACGCTTAAGTGACAACCCCGCTGCAACGCCCTCTGTTATCAA‑TTTTCTGGTGACGTTTGGCgg                                            <  2:881318/151‑1 (MQ=255)                                                                                                           ggCAACCCGCGAAATGGCGCGGCGGTAAGTATGGC‑GGGGTTA‑TTCCTTCCCCGTTGAGGACACCGGGTTGT‑CAGGTTGACCATACGCTTAAGTGACAACCCCGCTGCAACGCCCTCTGTTATCAA‑TTTTCTGGTGACGTTTGGCGGTATc                                        <  1:612872/150‑1 (MQ=255)                                                                                                           ggCAACCCGCGAAATGGCGCGGCGGTAAGTATGGC‑GGGGTTA‑TTCCTTCCCCGTTGAGGACACCGGGTTGT‑CAGGTTGACCATACGCTTAAGTGACAACCCCGCTGCAACGCCCTCTGTTATCAA‑TTTTCTGGTGACGTTTGGCGGTATc                                        <  2:826978/150‑1 (MQ=255)                                                                                                              aaCCCGCGAAATGGCGCGGCGGTAAGTATGGC‑GGGGGTA‑TTCCTTCCCCGGTGAGGACACCGGGGTGT‑TCGGGTGACCATTCGCCTTAATGGCAACACCCCCGGCACGCCCTCTGTTATTAA‑TTTTTTGGTGACGGTTTGGGGGATTAGtt                                    >  1:267819/1‑151 (MQ=255)                                                                                                                  cgcgAAATGGCGCGGCGGTAAGTATGGC‑GGGGGTT‑TTTCTTCCCCCTTTAGGACACCCGGGTGT‑CAGGGTTGCCCTACGCTTAAATGAAAAACCCCCTGCAACGCCCCCTTTTTTTAA‑TTTTTTTGTGGCGTTTTGCGGGATCCGtttt                                  >  1:424804/1‑149 (MQ=255)                                                                                                                     gAAATGGCGCGGCGGTAAGTATGGC‑GGGGTTA‑TTCCTTCCCCGTTGAGGACACCGGGTTGT‑CAGGTTGACCATACGCTTAAGTGACAACCCCGCTGCAACGCCCTCTGTTATCAA‑TTTTCTGGTGACGTTTGGCGGTATCAGTTTTACTcc                             <  2:219079/151‑1 (MQ=255)                                                                                                                     gAAATGGCGCGGCGGTAAGTATGGC‑GGGGGTA‑TTTCTTTCCCCTTGAGGACACCCGGGTGT‑CAGGGTGAACATAAGCTTAAGGGACAAACCCCCCGCAAAGCCCCCTGTTTTTAATTTTTTTGGGGAGGTTTGG‑GGGATCAGtttttatcc                             >  1:774659/1‑146 (MQ=255)                                                                                                                          ggCGCGGCGGTAAGTATGGC‑GGGGTTA‑TTCCTTCCCCGTTGAGGACACCGGGTTGT‑CAGGTTGACCATACGCTTAAGTGACAACCCCGCTGCAACGCCCTCTGTTATCAA‑TTTTCTGGTGACGTTTGGCGGTATCAGTTTTACTCCGTGAc                        <  1:257994/151‑1 (MQ=255)                                                                                                                           gcgcGGCGGTAAGTATGGC‑GGGGTTA‑TTCCTTCCCCGTTGAGGACACCGGGTTGT‑CAGGTTGACCATACGCTTAAGTGACAACCCCGCTGCAACGCCCTCTGTTATCAA‑TTTTCTGGTGACGTTTGGCGGTATCAGTTTTACTCCGTGACt                       <  1:189678/151‑1 (MQ=255)                                                                                                                                     aaGTATGGC‑GGGGTTA‑TTCCTTCCCCGTTGAGGACACCGGGTTGT‑CAGGTTGACCATACGCTTAAGTGACAACCCCGCTGCAACGCCCTCTGTTATCAA‑TTTTCTGGTGACGTTTGGCGGTATCAGTTTTACTCCGTGACTGCTCTgccg              <  2:468424/150‑1 (MQ=255)                                                                                                                                            gC‑GGGGTTA‑TTCCTTCCCCGTTGAGGACACCGGGTTGT‑CAGGTTGACCATACGCTTAAGTGACAACCCCGCTGCAACGCCCTCTGTTATCAA‑TTTTCTGGTGACGTTTGGCGGTATCAGTTTTACTCCGTGACTGCTCTGCCGCCCttttt      <  1:504689/151‑1 (MQ=255)                                                                                                                                                 ggTTA‑TTCCTTCCCCGTTGAGGACACCGGGTTGT‑CAGGTTGACCATACGCTTAAGTGACAACCCCGCTGCAACGCCCTCTGTTATCAA‑TTTTCTGGTGACGTTTGGCGGTATCAGTTTTACTCCGTGACTGCTCTGCCGCCCTTTTTaa    >  2:627280/1‑149 (MQ=255)                                                                                                                                                 ggTTA‑TTCCTTCCCCGTTGAGGACACCGGGTTGT‑CAGGTTGACCATACGCTTAAGTGACAACCCCGCTGCAACGCCCTCTGTTATCAA‑TTTTCTGGTGACGTTTGGCGGTATCAGTTTTACTCCGTGACTGCTCTGCCGCCCTTTTTAAAg  <  2:491232/151‑1 (MQ=255)                                                                                                                                                   |                                                                                                                                                        GATATTTCCCTGAAAAGTCAGACCATAACGCGAAAGCGCATGGCGAGGTAGCTGGTTCATAGATAGCCTGTCGTTAAATTTTCGTCGACCGTGCGCTTCCGGTTGTGGCAACCCGCGAAATGGCGCGGCGGTAAGTATGGC‑GGGGTTA‑TTCCTTCCCCGTTGAGGACACCGGGTTGT‑CAGGTTGACCATACGCTTAAGTGACAACCCCGCTGCAACGCCCTCTGTTATCAA‑TTTTCTGGTGACGTTTGGCGGTATCAGTTTTACTCCGTGACTGCTCTGCCGCCCTTTTTAAAG  >  NC_000913/1649150‑1649443

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 12 ≤ ATCG/ATCG < 14 ≤ ATCG/ATCG < 35 ≤ ATCG/ATCG < 39 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑