Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NC_000913	1,435,718	0	G	A	43.2%	58.3 / 22.2	44	intergenic (‑99/+42)	uspF/ompN	stress‑induced protein, ATP‑binding protein/outer membrane pore protein N, non‑specific
Reads supporting (aligned to +/- strand):  ref base G (21/4);  new base A (0/19);  total (21/23)
Fisher's exact test for biased strand distribution p-value = 6.43e-09
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 1.00e+00

TTCTGAATCGGAAATATCGATAGGGACAAGAATCGTTCTGTTCATAAAACCTCCTGTTTTAGTATCCGCATAAAGTGTAACGCCAGATGACACTTTTTGTG‑TAATGACGGAGTTCACATTTTTAATTTAGATC‑AAAGGAGGAAGAATAAGCAGAAAAAG‑CCCGCCATAACAGCGGGCAGGAGGATTTAGAACTGATAAACCAGACCTAAAGCGACAATATCATCGGTAGAGATGCCATTGGCAGCGTAGAAGCTGTCATCTTCATCCAACAGGTTGATTTTAT  >  NC_000913/1435575‑1435857                                                                                                                                                  |                                                                                                                                             ttCTGAATCGGAAATATCGATAGGGACAAGAATCGTTCTGTTCATAAAACCTCCTGTTTTAGTATCCGCATAAAGTGTAACGCCAGATGACACTTTTTGTG‑TAATGACGGAGTTCACATTTTTAATTTAGATC‑AAAGGAGGAAGAATAAGc                                                                                                                                       >  2:639822/1‑151 (MQ=255)     gAATCGGAAATATCGATAGGGACAAGAATCGTTCTGTTCATAAAACCTCCTGTTTTAGTATCCGCATAAAGTGTAACGCCAGATGACACTTTTTGTG‑TAATGACGGAGTTCACATTTTTAATTTAGATC‑AAAGGAGGAAGAATAAGCAg                                                                                                                                     <  1:531766/149‑1 (MQ=255)          ggAAATATCGATAGGGACAAGAATCGTTCTGTTCATAAAACCTCCTGTTTTAGTATCCGCATAAAGTGTAACGCCAGATGACACTTTTTGTG‑TAATGACGGAGTTCACATTTTTAATTTAGATC‑AAAGGAGGAAGAATAAGCAGAAAAAG‑c                                                                                                                             >  1:168538/1‑151 (MQ=255)          ggAAATATCGATAGGGACAAGAATCGTTCTGTTCATAAAACCTCCTGTTTTAGTATCCGCATAAAGTGTAACGCCAGATGACACTTTTTGTG‑TAATGACGGAGTTCACATTTTTAATTTAGATC‑AAAGGAGGAAGAATAAGCAGAAAAAG‑c                                                                                                                             >  1:505311/1‑151 (MQ=255)              atatCGATAGGGACAAGAATCGTTCTGTTCATAAAACCTCCTGTTTTAGTATCCGCATAAAGTGTAACGCCAGATGACACTTTTTGTG‑TAATGACGGAGTTCACATTTTTAATTTAGATC‑AAAGGAGGAAGAATAAGCAGAAAAAG‑CCCGc                                                                                                                         <  2:462573/151‑1 (MQ=255)              atatCGATAGGGACAAGAATCGTTCTGTTCATAAAACCTCCTGTTTTAGTATCCGCATAAAGTGTAACGCCAGATGACACTTTTTGTG‑TAATGACGGAGTTCACATTTTTAATTTAGATC‑AAAGGAGGAAGAATAAGCAGAAAAAG‑CCCGc                                                                                                                         <  1:746988/151‑1 (MQ=255)                     tAGGGACAAGAATCGTTCTGTTCATAAAACCTCCTGTTTTAGTATCCGCATAAAGTGTAACGCCAGATGACACTTTTTGTG‑TAATGACGGAGTTCACATTTTTAATTTAGATC‑AAAGGAGGAAGAATAAGCAGAAAAAG‑CCCGCCATAAc                                                                                                                   >  2:444421/1‑150 (MQ=255)                          aaaaGAATCGTTCTTTTAAAAAACCCTCCTTTTTTAGTACCCGAAAAAAGTTTAACGCCAGATGACTTTTTTTGTG‑TAAGGACGGATTTCACATTTTTAATTTAGATA‑AAGGGAGAAAAAAAAAGCAAAAAAAG‑CCCGCCATAACAGCggg                                                                                                             <  1:452004/149‑1 (MQ=255)                          aCAAGAATCGTTCTGTTCATAAAACCTCCTGTTTTAGTATCCGCATAAAGTGTAACGCCAGATGACACTTTTTGTG‑TAATGACGGAGTTCACATTTTTAATTTAGATC‑AAAGGAGGAAGAATAAGCAGAAAAAG‑CCCGCCATAACAGCggg                                                                                                             >  1:782675/1‑151 (MQ=255)                            aaGAATTTTTCTGTACAAAAACCCTCTTGTTTTATTATCCAAAAAAAGTGTAACGCAAGAAAACTTTTTTTGTG‑AAATGACGGATTTCACATTTTTAATTAAGAGA‑AAGGGAGAAAAAATAAGAAAAAAAAG‑CCCGCCATAACAGCg                                                                                                               <  2:1036836/147‑1 (MQ=255)                              aaaTCTTTCTGTTAAAAAACCCCCTTGTTTAATTATCCGAAAAAGGTGTACCCCCAGATGACTTTTTTTTTG‑TAATGAGGGATTTCACTTTTTTAATTAAGAAA‑AAAGGAGAAAAAAAAAGAAAAAAAAG‑CCCGCCATAACAGCGGGCagg                                                                                                         <  1:581287/150‑1 (MQ=255)                                    ttttGTTAATAAACCCTCCTTTTTTTGTACCCGAAAAAAGTGTACCGCCAGATGACTTTTTTTGTG‑TAATGACGGATTTCATTTTTTTAATTTAAAAC‑AAAGGAGAAAAAAAAAGCAAAAAAAG‑CCCGCCATAACAGCGGGCaggagg                                                                                                      <  1:639831/145‑1 (MQ=255)                                     tCTGTTCATAAAACCTCCTGTTTTAGTATCCGCATAAAGTGTAACGCCAGATGACACTTTTTGTG‑TAATGACGGAGTTCACATTTTTAATTTAGATC‑AAAGGAGGAAGAATAAGCAGAAAAAG‑CCCGCCATAACAGCGGGCAGGAGGAttt                                                                                                  >  2:441024/1‑151 (MQ=255)                                            aaaaacCCTCTTTTTTTAGTATCCGCAAAAAGTGAACCGCCAGATGACATTTTTTGTG‑TAAGGACGGATTCCATATTTTTAATTTAGAAA‑AAGGGAGAAAAAAAAAGAAAAAAAAG‑CCCGCCATAACAGCGGGCAGGAGGATTTAGaa                                                                                              <  1:195787/146‑1 (MQ=255)                                             aaaacCCTCTTGTTTTAGTACCCGAAAAAAGTGAAACCCCAGATGACTCTTTTTGTG‑AAAGGACGGATTTCACTTTTTTAATTTAAACA‑AAAGGAGGAAGAAAAAGAAAAAAAAG‑CCCGCCATAACAGCGGGCAGGAGGATTTAGAACTGa                                                                                          <  1:539399/150‑1 (MQ=255)                                               aaaCCTCCTGTTTTAGTATCCGCATAAAGTGTAACGCCAGATGACACTTTTTGTG‑TAATGACGGAGTTCACATTTTTAATTTAGATC‑AAAGGAGGAAGAATAAGCAGAAAAAG‑CCCGCCATAACAGCGGGCAGGAGGATTTAGAACTGAt                                                                                         >  2:807766/1‑150 (MQ=255)                                                     cctGTTTTAGTATCCGCATAAAGTGTAACGCCAGATGACACTTTTTGTG‑TAATGACGGAGTTCACATTTTTAATTTAGATC‑AAAGGAGGAAGAATAAGCAGAAAAAG‑CCCGCCATAACAGCGGGCAGGAGGATTTAGAACTGATAAAcc                                                                                    >  1:749891/1‑149 (MQ=255)                                                         ttttAGTATCCGCAAAAAGTGTAACGCAAGATAACTCTTTTTGTG‑TAAGGCGGGAGTTCACATTTTTAATTTAGATA‑AAAGGAGAAAAAAAAACAAAAAAAAC‑CCCGCCATAACAGCGGGCAGGAGGATTTAGAACTGATAAACCAGAcc                                                                               <  2:642975/150‑1 (MQ=255)                                                         ttttAGTACCCGAATAAAGTGTAACGCAAGATGACCTTTTTTGTG‑TAAGGACGGAGTCCACTTTTTTAATTAAGAAA‑AAAGGAGAAAAAAAAAGAAAAAAAAG‑CCCGCCATAACAGCGGGCAGGAGGATTTAGAACTGATAAACCAGAc                                                                                <  1:34648/149‑1 (MQ=255)                                                                aTCCGCATAAAGTGTAACGCCAGATGACACTTTTTGTG‑TAATGACGGAGTTCACATTTTTAATTTAGATC‑AAAGGAGGAAGAATAAGCAGAAAAAG‑CCCGCCATAACAGCGGGCAGGAGGATTTAGAACTGATAAACCAGACCTAAAGCg                                                                        >  1:276166/1‑150 (MQ=255)                                                                     cATAAAGTGTAACGCCAGATGACACTTTTTGTG‑TAATGACGGAGTTCACATTTTTAATTTAGATC‑AAAGGAGGAAGAATAAGCAGAAAAAG‑CCCGCCATAACAGCGGGCAGGAGGATTTAGAACTGATAAACCAGACCTAAAGCGACAat                                                                   >  1:653951/1‑150 (MQ=255)                                                                        aaaGTGTAACGCCAGATGACACTTTTTGTG‑TAATGACGGAGTTCACATTTTTAATTTAGATC‑AAAGGAGGAAGAATAAGCAGAAAAAG‑CCCGCCATAACAGCGGGCAGGAGGATTTAGAACTGATAAACCAGACCTAAAGCGACAATatc                                                                >  2:790944/1‑150 (MQ=255)                                                                           gtgtAACGCCAGATGACACTTTTTGTG‑TAATGACGGAGTTCACATTTTTAATTTAGATC‑AAAGGAGGAAGAATAAGCAGAAAAAG‑CCCGCCATAACAGCGGGCAGGAGGATTTAGAACTGATAAACCAGACCTAAAGCGACAATATCATCg                                                            >  1:57914/1‑151 (MQ=255)                                                                             gaaaCGCCAGATGACTTTTTTTGTG‑TAATGACGGAGTTCACTTTTTAAATTAAGAAA‑AAAGGAGAAAAAAAAAGAAAAAAAAG‑CCCGCCATAACAGCGGGCAGGAGGATTTAGAACTGATAAACCAGACCTAAAGCGACAATATCATCg                                                            <  1:653644/147‑1 (MQ=255)                                                                               aaCCCCAGATAAC‑CTTTTTTTGTTAATGACGGATTTAACTTTTTTAATTAAGAGA‑AAAGGAGAAAAAAAAAGAAAAAAAAG‑CCCGCCATAACAGCGGGCAGGAGGATTTAGAACTGATAAACCAGACCTAAAGCGACAATATCATCGGTag                                                        <  1:941315/151‑1 (MQ=255)                                                                                 cGCCAAATAACATTTTTGGTG‑AAATGAGGAAATACACTTTTTTATTTAAGAAA‑AAGGGAGGAAAAAAAAGAAAAAAACC‑ACCGCCATAACAGCGGGCAGGAGGATTTAGAACTGATAAACCAGACCTAAAGCGACAATATCATCGGTa                                                         <  2:226851/148‑1 (MQ=255)                                                                                    cAGATGACACTTTTTGTG‑TAATGACGGAGTTCACATTTTTAATTTAGATC‑AAAGGAGGAAGAATAAGCAGAAAAAG‑CCCGCCATAACAGCGGGCAGGAGGATTTAGAACTGATAAACCAGACCTAAAGCGACAATATCATCGGTAGAGATg                                                   >  1:100527/1‑151 (MQ=255)                                                                                         gACACTTTTTGTG‑TAATGACGGAGTTCACATTTTTAATTTAGATC‑AAAGGAGGAAGAATAAGCAGAAAAAG‑CCCGCCATAACAGCGGGCAGGAGGATTTAGAACTGATAAACCAGACCTAAAGCGACAATATCATCGGTAGAGATGCCAtt                                              >  2:83070/1‑151 (MQ=255)                                                                                              tttttGTG‑AAAGGAGGGGTTTCATTTTTTAAATTAAGAAA‑AAAGGAGAAAAAAAAAGAAAAAAAAG‑CCCGCCATAACAGCGGGCAGGAGGATTTAGAACTGATAAACCAGACCTAAAGCGACAATATCATCGGTAGAGATGCCAtt                                              <  2:920475/146‑1 (MQ=255)                                                                                                tttGTG‑TAAGGAGGGAGTTCATTTTTTAAATTAAGAAA‑AAGGGAGAAAAAAAAAGAAAAAAAAC‑CCCGCCATAACAGCGGGCAGGAGGATTTAGAACTGATAAACCAGACCTAAAGCGACAATATCATCGGTAGAGATGCCATTGGCAGc                                        <  2:803138/150‑1 (MQ=255)                                                                                                       tAATGACGGAGTTCACATTTTTAATTTAGATC‑AAAGGAGGAAGAATAAGCAGAAAAAG‑CCCGCCATAACAGCGGGCAGGAGGATTTAGAACTGATAAACCAGACCTAAAGCGACAATATCATCGGTAGAGATGCCATTGGCAGCGTAGa                                   >  2:754139/1‑149 (MQ=255)                                                                                                         attgccggagtcctaTTTTTAATTTAAAACAAAAGGAGAAAAAATAGGAAAAAAAAT‑CCCGCCATAACAGCGGGCAGGAGGATTTAGAACTGATAAACCAGACCTAAAGCGACAATATCATCGGTAGAGATGCCATTGGCAGCGTAGaa                                  <  2:673976/135‑1 (MQ=255)                                                                                                            acgaggTTCACATTTTTAATTTA‑AAC‑AAAGAAGGAAAAAAAAGAAAAAAAAGCCCCGCCATAACAGCGGGCAGGAGGATTTAGAACTGATAAACCAGACCTAAAGCGACAATATCATCGGTAGAGATGCCATTGGCAGCGTAGAAGCTGt                             <  1:402705/145‑1 (MQ=255)                                                                                                             cGGAGTTCACATTTTTAATTTAGATC‑AAAGGAGGAAGAATAAGCAGAAAAAG‑CCCGCCATAACAGCGGGCAGGAGGATTTAGAACTGATAAACCAGACCTAAAGCGACAATATCATCGGTAGAGATGCCATTGGCAGCGTAGAAGCTGTc                            >  1:1008123/1‑150 (MQ=255)                                                                                                                 gTTCACATTTTTAATTTAGATC‑AAAGGAGGAAGAATAAGCAGAAAAAG‑CCCGCCATAACAGCGGGCAGGAGGATTTAGAACTGATAAACCAGACCTAAAGCGACAATATCATCGGTAGAGATGCCATTGGCAGCGTAGAAGCTGTCATCtt                       >  2:349648/1‑151 (MQ=255)                                                                                                                        tttttAATTAAGATA‑AAGGAAAGAAAAATAACGAAAAAAAC‑CCCGCCATAACAGCGGGCAGGAGGATTTAGAACTGATAAACCAGACCTAAAGCGACAATATCATCGGTAGAGATGCCATTGGCAGCGTAGAAGCTGTCATCTTCATCCa                 <  2:301045/150‑1 (MQ=255)                                                                                                                            tAATTTAGATC‑AAAGGAGGAAGAATAAGCAGAAAAAG‑CCCGCCATAACAGCGGGCAGGAGGATTTAGAACTGATAAACCAGACCTAAAGCGACAATATCATCGGTAGAGATGCCATTGGCAGCGTAGAAGCTGTCATCTTCATCCAACAgg            >  1:572770/1‑151 (MQ=255)                                                                                                                             aaTTAAGAAA‑AAAGGAGAAAAAAAAAGAAAAAAACG‑CCCGCCATAACAGCGGGCAGGAGGATTTAGAACTGATAAACCAGACCTAAAGCGACAATATCATCGGTAGAGATGCCATTGGCAGCGTAGAAGCTGTCATCTTCATCCAACAGGt           <  2:198247/151‑1 (MQ=255)                                                                                                                              aTTAAGATA‑AAAGGAGAAAAAAAAAGAAAAAAAAG‑CCCGCCATAACAGCGGGCAGGAGGATTTAGAACTGATAAACCAGACCTAAAGCGACAATATCATCGGTAGAGATGCCATTGGCAGCGTAGAAGCTGTCATCTTCATCCAACAGGtt          <  2:612899/151‑1 (MQ=255)                                                                                                                               tttAGATC‑AAAGGAGGAAGAATAAGCAGAAAAAG‑CCCGCCATAACAGCGGGCAGGAGGATTTAGAACTGATAAACCAGACCTAAAGCGACAATATCATCGGTAGAGATGCCATTGGCAGCGTAGAAGCTGTCATCTTCATCCAACAGGTTg         >  1:1030809/1‑151 (MQ=255)                                                                                                                                  aGATA‑AAAGGAGGAAAAATAAGAAAAAAAAG‑CCCGCCATAACAGCGGGCAGGAGGATTTAGAACTGATAAACCAGACCTAAAGCGACAATATCATCGGTAGAGATGCCATTGGCAGCGTAGAAGCTGTCATCTTCATCCAACAGGTTGAt       <  1:865611/150‑1 (MQ=255)                                                                                                                                    aTC‑AAAGGAGGAAGAATAAGCAGAAAAAG‑CCCGCCATAACAGCGGGCAGGAGGATTTAGAACTGATAAACCAGACCTAAAGCGACAATATCATCGGTAGAGATGCCATTGGCAGCGTAGAAGCTGTCATCTTCATCCAACAGGTTGAtttt    >  1:991453/1‑151 (MQ=255)                                                                                                                                        aaaGGAGGAAGAATAAGCAGAAAAAG‑CCCGCCATAACAGCGGGCAGGAGGATTTAGAACTGATAAACCAGACCTAAAGCGACAATATCATCGGTAGAGATGCCATTGGCAGCGTAGAAGCTGTCATCTTCATCCAACAGGTTGATTTtat  >  2:829473/1‑150 (MQ=255)                                                                                                                                        aaaGGAGAAAAAAAAAGCAAAAAAAG‑CCCGCCATAACAGCGGGCAGGAGGATTTAGAACTGATAAACCAGACCTAAAGCGACAATATCATCGGTAGAGATGCCATTGGCAGCGTAGAAGCTGTCATCTTCATCCAACAGGTTGATTTtat  <  1:145865/150‑1 (MQ=255)                                                                                                                                                  |                                                                                                                                             TTCTGAATCGGAAATATCGATAGGGACAAGAATCGTTCTGTTCATAAAACCTCCTGTTTTAGTATCCGCATAAAGTGTAACGCCAGATGACACTTTTTGTG‑TAATGACGGAGTTCACATTTTTAATTTAGATC‑AAAGGAGGAAGAATAAGCAGAAAAAG‑CCCGCCATAACAGCGGGCAGGAGGATTTAGAACTGATAAACCAGACCTAAAGCGACAATATCATCGGTAGAGATGCCATTGGCAGCGTAGAAGCTGTCATCTTCATCCAACAGGTTGATTTTAT  >  NC_000913/1435575‑1435857

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 14 ≤ ATCG/ATCG < 16 ≤ ATCG/ATCG < 35 ≤ ATCG/ATCG < 39 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑