Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NC_000913	4,111,747	0	G	T	42.5%	63.5 / 18.5	40	N156K (AAC→AAA)	yiiQ	DUF1454 family putative periplasmic protein
Reads supporting (aligned to +/- strand):  ref base G (22/1);  new base T (0/17);  total (22/18)
Fisher's exact test for biased strand distribution p-value = 2.03e-10
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 1.00e+00

AAAGGCTTTGCTTTTTGTCATTTATTCAAACCTTCAAGCGATTCAGATAGCGCCAGCTTAATCGGTTCAACAGCGAAGGTCAGCCCCTTTT‑CGCC‑GTTGT‑CCGCGACAACATAACGCAGTGCACCTTCTGTCTCGGTGTAATAACGTTTGTTTTT‑CCCCGCCGTTAGTAGCGACTGCAGTTTTTTCTGGCTTTGTGTTTTGGTCATTAATGGGGTGAGTGTGCGGATCACCGCTGCCATGTATTCCTGAGCTTTCGCTTTCGCGGCTTTTTGCTCTGGCCCCTGGATGGGTAGCC  >  NC_000913/4111598‑4111892                                                                                                                                                         |                                                                                                                                                   aaaGGCTTTGCTTTTTGTCATTTATTCAAACCTTCAAGCGATTCAGATAGCGCCAGCTTAATCGGTTCAACAGCGAAGGTCAGCCCCTTTT‑CGCC‑GTTGT‑CCGCGACAACATAACGCAGTGCACCTTCTGTCTCGGTGTAATAACgtttg                                                                                                                                                    <  2:410664/150‑1 (MQ=255) aaaGGCTTTGCTTTTTGTCATTTATTCAAACCTTCAAGCGATTCAGATAGCGCCAGCTTAATCGGTTCAACAGCGAAGGTCAGCCCCTTTT‑CGCC‑GTTGT‑CCGCGACAACATAACGCAGTGCACCTTCTGTCTCGGTGTAATAACgtttg                                                                                                                                                    <  1:204298/150‑1 (MQ=255)      ctttgctttTTGTCATTTATTCAAACCTTCAAGCGATTCAGGTAGCGCCAGCTTAATCGGTTCAACAGCGAAGGTCAGCCCCTCTC‑CGCC‑GTTGT‑CCGCGACAACATAACGCAGTGCACCTTCTGTCTCGGTGTAATAACGTTTGTTTTT‑c                                                                                                                                             >  2:424656/1‑151 (MQ=255)         tgctttTTGTCATTTATTCAAACCTTCAAGCGATTCAGATAGCGCCAGCTTAATCGGTTCAACAGCGAAGGTCAGCCCCTTTT‑CGCC‑GTTGT‑CCGCGACAACATAACGCAGTGCACCTTCTGTCTCGGTGTAATAACGTTTGTTTTT‑cccc                                                                                                                                          >  2:115297/1‑151 (MQ=255)                     tttATTCAAACCTTCAAGCGATTCAGATAGCGCCAGCTTAATCGGTTCAACAGCGAAGGTCAGCCCCTTTT‑CGCC‑GTTGT‑CCGCGACAACATAACGCAGTGCACCTTCTGTCTCGGTGTAATAACGTTTGTTTTT‑CCCCGCCGTTAGTAGc                                                                                                                              >  2:626243/1‑151 (MQ=255)                            aacccTTCAAGCGATTCAAATAGCGCCAGCTTAATCGTTCCAACGGCGAAGGTCAGCCCCTTTT‑CGCC‑GTTGC‑CCGCAACAACATAACGCAGTGCACTTTCTGTCTCGGTGAAATAAGTTTTTTTTTC‑CCCCGCCGTTAGTAGCGACTg                                                                                                                         <  1:156228/146‑1 (MQ=255)                            aaaCCTTCAAGCGATTCAGATAGCGCCAGCTTAATCGGTTCAACAGCGAAGGTCAGCCCCTTTT‑CGCC‑GTTGT‑CCGCGACAACATAACGCAGTGCACCTTCTGTCTCGGTGTAATAACGTTTGTTTTT‑CCCCGCCGTTAGTAGCGACTGc                                                                                                                        >  1:120538/1‑150 (MQ=255)                             acccTTCAAGCGATTCAGATAGCGCCAGCTTAACCGTTTCAACAGCGAAGGCCCCCCCCTTTT‑CGCC‑GTTGC‑CCGCGACAACATAACGCAGTGCCCCTTCTGTCTCGGTGTAATATCGTTTTTTTTC‑CCCCGCCGTTAGTAGCGACTGCa                                                                                                                       <  2:323223/148‑1 (MQ=255)                               ccTTCAAGCGATTCAGATAGCCCCAGCTTAATCGGTTCAACAGCGAGGGTCAGCCCCTTTC‑CGCC‑GTTGT‑CCGCAACAACATAACGCAGTGCCCCTTCTGTCTCGGTTTAATAACTTTTTTTTTC‑CCCCGCCGTTAGTAGCGACTGCAGtt                                                                                                                    <  2:948524/151‑1 (MQ=255)                                 ttCAAGCGATTCAGATAGCGCCAGCTTAATCGGTTCAACAGCGAAGGTCAGCCCCTTTT‑CGCC‑GTTGT‑CCGCGACAACATAACGCAGTGCACCTTCTGTCTCGGTGTAATAACGTTTGTTTTT‑CCCCGCCGTTAGTAGCGACTGCAGtttt                                                                                                                  >  1:534298/1‑151 (MQ=255)                                  tCAAGCGATTGAGATAGCGACAGCTTAATCGGTTCAACAGCGATGGTCAGCCCCTTTT‑CGCC‑GTTGT‑CCGCGACAACATAACGCAGTGCACCTTCTGTCTCGGTGTAATAACGTTTGTTTTT‑CCCCGCCGTTAGTAGCGACTGCAGttttt                                                                                                                 >  1:135752/1‑151 (MQ=255)                                    aaGCGATTCAGATGCCCCCGGTTTAATCGTTCAAACAGCGAAGGTCACCCCTTTTT‑CCCG‑TTTGC‑CCGCGAAAAAATAACGCAGTGCCCCTTCTGTCTCGGTGTAATAACTTTTTTTTTC‑CCCCGCCGTTAGTAGCGACTGCAGttt                                                                                                                   <  2:180287/147‑1 (MQ=255)                                        gATTCAGATAGCGCCAGCTTAATCGGTTCAACAGCGAAGGTCAGCCCCTTTT‑CGCC‑GTTGT‑CCGCGACAACATAACGCAGTGCACCTTCTGTCTCGGTGTAATAACGTTTGTTTTT‑CCCCGCCGTTAGTAGCGACTGCAGTTTTTTCTGGc                                                                                                           >  2:722107/1‑151 (MQ=255)                                             aGATAGCCCCAGTTAAATCGGTAAAACAGGGAAGGCCACCCCCTTTC‑CGCC‑GTTGC‑CCGCAAAAAAATACCGCGGTGCCCCTTCTGTCTCGGTGTAATATCGTTTTTTTTC‑CCCCGCCGTTAGTAGCGACTGCAGTTTTTTCTGGCTTtgt                                                                                                      <  1:466735/151‑1 (MQ=255)                                                   cgcCAGCTTAATCGGTTCAACAGCGAAGGTCAGCCCCTTTT‑CGCC‑GTTGT‑CCGCGACAACATAACGCAGTGCACCTTCTGTCTCGGTGTAATAACGTTTGTTTTT‑CCCCGCCGTTAGTAGCGACTGCAGTTTTTTCTGGCTTTGTGTTTTg                                                                                                >  1:610716/1‑151 (MQ=255)                                                     ccAGTTAAACCGTTTAAACAGCGAGGCTCACCCCTTTTT‑CCCC‑GTTGC‑CCGCCACAACATACCGCTGTGCCCTTTCGGTCTCGGTTTATTATGGTTTTTTTTC‑CCCCGCCGTTAGTAGCGACTGCAGTTTTTTCTGGCTTtgtg                                                                                                     <  1:197272/144‑1 (MQ=255)                                                     ccAGCTTAATCGGTTCAACAGCGAAGGTCAGCCCCTTTT‑CGCC‑GTTGT‑CCGCGACAACATAACGCAGTGCACCTTCTGTCTCGGTGTAATAACGTTTGTTTTT‑CCCCGCCGTTAGTAGCGACTGCAGTTTTTTCTGGCTTTGTGTTTTGGt                                                                                              >  1:573077/1‑151 (MQ=255)                                                        gCTTAATCGGTTCAACAGCGAAGGTCAGCCCCTTTT‑CGCC‑GTTGT‑CCGCGACAACATAACGCAGTGCACCTTCTGTCTCGGTGTAATAACGTTTGTTTTT‑CCCCGCCGTTAGTAGCGACTGCAGTTTTTTCTGGCTTTGTGTTTTg                                                                                                >  1:277080/1‑146 (MQ=255)                                                         ctaaaccgttacAACAGCAAAGCACACCCCTTTTC‑CCCC‑TTTCC‑CCGCAACAACAAACCGCGTTCCCCCTTCTGTCTCGGTGTAAAAACTTTTTTTTTC‑CCCCGCCGTTAGTAGCGACTGCAGTTTTTTCTGGCTTTGTGTTTTGGTCa                                                                                            <  2:573532/138‑1 (MQ=255)                                                          ttAATCGGTTCAACAGCGAAGGTCAGCCCCTTTT‑CGCC‑GTTGT‑CCGCGACAACATAACGCAGTGCACCTTCTGTCTCGGTGTAATAACGTTTGTTTTT‑CCCCGCCGTTAGTAGCGACTGCAGTTTTTTCTGGCTTTGTGTTTTGGTCAtt                                                                                          >  2:3557/1‑150 (MQ=255)                                                           tAATCGGTTCAACAGCGAAGGTCAGCCCCTTTT‑CGCC‑GTTGT‑CCGCGACAACATAACGCAGTGCACCTTCTGTCTCGGTGTAATAACGTTTGTTTTT‑CCCCGCCGTTAGTAGCGACTGCAGTTTTTTCTGGCTTTGTGTTTTGGTCATTa                                                                                         >  1:365224/1‑150 (MQ=255)                                                            aaTGGGTCCAACAGCGAAGG‑CCCCCCCTTTT‑CCCCTTTTGC‑CCGCGAAAACATACCGCAGTCCCCCCCCTGTCTGGGTGTAA‑AACTTTTTTTTTTCCCCCGCCGTTAGTAGCGACTGCAGTTTTTTCTGGCTTTGTGTTTTGGTCAt                                                                                           <  1:384366/147‑1 (MQ=255)                                                                ggTTAAACAGAGAAGGTCCGCCCCTTTC‑CGCG‑GTTGC‑CCGCGACAATAAACCGCTGTGCCCCTTCTGTCTGGTTGAAATAAGTTTTTTTTTT‑CCCCGCCGTTAGTAGCGACTGCAGTTTTTTCTGGCTTTGTGTTTTg                                                                                                <  2:277084/138‑1 (MQ=255)                                                                  ttCAACAGGGAAGTTCACCCCTTTTT‑CGCC‑TTTGC‑CCGCGACAACAAAACGCAGTCCCCTTTCTGTCTGGGTGTAATAAGTTTTTTTTTT‑CCCCGCCGTTAGTAGCGACTGCAGTTTTTTCTGGCTTTGTGTTTTGGTCATTAATg                                                                                      <  2:742345/146‑1 (MQ=255)                                                                  ttCAACAGCGAAGGTCAGCCCCTTTT‑CGCC‑GTTGT‑CCGCGACAACATAACGCAGTGCACCTTCTGTCTCGGTGTAATAACGTTTGTTTTT‑CCCCGCCGTTAGTAGCGACTGCAGTTTTTTCTGGCTTTGTGTTTTGGTCATTAATGGGGTg                                                                                 >  1:519149/1‑151 (MQ=255)                                                                     aaCAGCGAAGGCCACCCCCTTTT‑CGCC‑GTTGC‑CCGCAAAAACATAACGCAGTCCCCCTTCTGTCTCGGTTTAATAATTTTTTTTTTT‑CCCCGCCGTTAGTAGCGACTGCAGTTTTTTCTGGCTTTGTGTTTTGGTCATTAATGGGGTGa                                                                                <  1:198543/149‑1 (MQ=255)                                                                                  aGCCCCTTTT‑CGCC‑GTTGT‑CCGCGACAACATAACGCAGTGCACCTTCTGTCTCGGTGTAATAACGTTTGTTTTT‑CCCCGCCGTTAGTAGCGACTGCAGTTTTTTCTGGCTTTGTGTTTTGGTCATTAATGGGGTGAGTGTGCGGATCACCg                                                                 >  1:125901/1‑151 (MQ=255)                                                                                  aGCCCCTTTT‑CGCC‑GTTGT‑CCGCGACAACATAACGCAGTGCACCTTCTGTCTCGGTGTAATAACGTTTGTTTTT‑CCCCGCCGTTAGTAGCGACTGCAGTTTTTTCTGGCTTTGTGTTTTGGTCATTAATGGGGTGAGTGTGCGGATCACCg                                                                 >  2:123050/1‑151 (MQ=255)                                                                                    ccccTTTTCCGCC‑GTTGC‑CCGCGAAAACAAAACGCAGTGCCCCTTCTGTCTGGGTGTAATAACTTTTTTTTTC‑CCCCGCCGTTAGTAGCGACTGCAGTTTTTTCTGGCTTTGTGTTTTGGTCATTAATGGGGTGAGTGTGCGGATCAc                                                                   <  2:921107/148‑1 (MQ=255)                                                                                     cccTTTT‑CCGC‑GTTTTCCCGCAACAACATAACCCGTTGCCCTTTCGTTCTCGGTTTAAGAATTTTTTTTTTC‑CCCCGCCGTTAGTAGCGACTGCAGTTTTTTCTGGCTTTGTGTTTTGGTCATTAATGGGGTGAGTGTGCGGATCACCGCt                                                               <  1:696838/151‑1 (MQ=255)                                                                                        tttt‑CGCC‑GTTGT‑CCGCGACAACATAACGCAGTGCACCTTCTGTCTCGGTGTAATAACGTTTGTTTTT‑CCCCGCCGTTAGTAGCGACTGCAGTTTTTTCTGGCTTTGTGTTTTGGTCATTAATGGGGTGAGTGTGCGGATCACCGCTGcc                                                            >  2:230033/1‑150 (MQ=255)                                                                                                c‑GTTGT‑CCGCGACAACATAACGCAGTGCACCTTCTGTCTCGGTGTAATAACGTTTGTTTTT‑CCCCGCCGTTAGTAGCGACTGCAGTTTTTTCTGGCTTTGTGTTTTGGTCATTAATGGGGTGAGTGTGCGGATCACCGCTGCCATGTATTc                                                    >  2:814806/1‑151 (MQ=255)                                                                                                  gTTGT‑CCGCGACAACATAACGCAGTGCACCTTCTGTCTCGGTGTAATAACGTTTGTTTTT‑CCCCGCCGTTAGTAGCGACTGCAGTTTTTTCTGGCTTTGTGTTTTGGTCATTAATGGGGTGAGTGTGCGGATCACCGCTGCCATGTATTcc                                                   >  2:253804/1‑151 (MQ=255)                                                                                                        ccGCGACAACATAACGCAGTGCCCTTTCTGTCTGGTTGTAATAGCTTTTTTTTTT‑CCCCGCCGTTAGTAGCGACTGCAGTTTTTTCTGGCTTTGTGTTTTGGTCATTAATGGGGTGAGTGTGCGGATCACCGCTGCCATGTATTCCTGAgc                                              <  1:187346/151‑1 (MQ=255)                                                                                                                             ccccTTCTTTCTCGGTGTAATAACGTTTTTTTTT‑CCCCGCCGTTAGTAGCGACTGCAGTTTTTTCTGGCTTTGTGTTTTGGTCATTAATGGGGTGAGTGTGCGGATCACCGCTGCCATGTATTCCTGAGCTTTCGCTTTCGCGGCttttt                          <  2:945602/148‑1 (MQ=255)                                                                                                                             cACCTTTTTTCGGGGTGTAATATTGTTTTTTTTT‑CCCCGCCGTTAGTAGCGACTGCAGTTTTTTCTGGCTTTGTGTTTTGGTCATTAATGGGGTGAGTGTGCGGATCACCGCTGCCATGTATTCCTGAGCTTTCGCTTTCGCGGCttt                            <  1:722091/148‑1 (MQ=255)                                                                                                                                 ttCTGTCTCGGTGTAATAACGTTTGTTTTT‑CCCCGCCGTTAGTAGCGACTGCAGTTTTTTCTGGCTTTGTGTTTTGGTCATTAATGGGGTGAGTGTGCGGATCACCGCTGCCATGTATTCCTGAGCTTTCGCTTTCGCGGCTTTTTGctct                     >  2:456739/1‑151 (MQ=255)                                                                                                                                            tgtAATAACGTTTGTTTTT‑CCCCGCCGTTAGTAGCGACTGCAGTTTTTTCTGGCTTTGTGTTTTGGTCATTAATGGGGTGAGTGTGCGGATCACCGCTGCCATGTATTCCTGAGCTTTCGCTTTCGCGGCTTTTTGCTCTGGCCCCTGGAt          >  1:647458/1‑151 (MQ=255)                                                                                                                                               aatacCTTTTGTTTTC‑CCCCGCCGTTAGTAGCGACTGCAGTTTTTTCTGGCTTTGTGTTTTGGTCATTAATGGGGTGAGTGTGCGGATCACCGCTGCCATGTATTCCTGAGCTTTCGCTTTCGCGGCTTTTTGCTCTGGCCCCTGGAt          <  2:502661/148‑1 (MQ=255)                                                                                                                                                atatctttttttttC‑CCCCGCCGTTAGTAGCGACTGCAGTTTTTTCTGGCTTTGTGTTTTGGTCATTAATGGGGTGAGTGTGCGGATCACCGCTGCCATGTATTCCTGAGCTTTCGCTTTCGCGGCTTTTTGCTCTGGCCCCt              <  1:34590/137‑1 (MQ=255)                                                                                                                                                ataaCTTTTTTTTTT‑CCCCGCCGTTAGTAGCGACTGCAGTTTTTTCTGGCTTTGTGTTTTGGTCATTAATGGGGTGAGTGTGCGGATCACCGCTGCCATGTATTCCTGAGCTTTCGCTTTCGCGGCTTTTTGCTCTGGCCCCTGGATGGGt      <  2:414616/151‑1 (MQ=255)                                                                                                                                                   aCGTTTGTTTTT‑CCCCGCCGTTAGTAGCGACTGCAGTTTTTTCTGGCTTTGTGTTTTGGTCATTAATGGGGTGAGTGTGCGGATCACCGCTGCCATGTATTCCTGAGCTTTCGCTTTCGCGGCTTTTTGCTCTGGCCCCTGGATGGGTAGc   >  1:802600/1‑151 (MQ=255)                                                                                                                                                    cGTTTGTTTTT‑CCCCGCCGTTAGTAGCGACTGCAGTTTTTTCTGGCTTTGTGTTTTGGTCATTAATGGGGTGAGTGTGCGGATCACCGCTGCCATGTATTCCTGAGCTTTCGCTTTCGCGGCTTTTTGCTCTGGCCCCTGGATGGTTAGcc  >  2:565244/1‑151 (MQ=255)                                                                                                                                                      ttttttttC‑CCCCGCCGTTAGTAGCGACTGCAGTTTTTTCTGGCTTTGTGTTTTGGTCATTAATGGGGTGAGTGTGCGGATCACCGCTGCCATGTATTCCTGAGCTTTCGCTTTCGCGGCTTTTTGCTCTGGCCCCTGGATGGGTa     <  2:120536/146‑1 (MQ=255)                                                                                                                                                      ttttttttC‑CCCCGCCGTTAGTAGCGACTGCAGTTTTTTCTGGCTTTGTGTTTTGGTCATTAATGGGGTGAGTGTGCGGATCACCGCTGCCATGTATTCCTGAGCTTTCGCTTTCGCGGCTTTTTGCTCTGGCCCCTGGATGGGTAGcc  <  2:610731/149‑1 (MQ=255)                                                                                                                                                         |                                                                                                                                                   AAAGGCTTTGCTTTTTGTCATTTATTCAAACCTTCAAGCGATTCAGATAGCGCCAGCTTAATCGGTTCAACAGCGAAGGTCAGCCCCTTTT‑CGCC‑GTTGT‑CCGCGACAACATAACGCAGTGCACCTTCTGTCTCGGTGTAATAACGTTTGTTTTT‑CCCCGCCGTTAGTAGCGACTGCAGTTTTTTCTGGCTTTGTGTTTTGGTCATTAATGGGGTGAGTGTGCGGATCACCGCTGCCATGTATTCCTGAGCTTTCGCTTTCGCGGCTTTTTGCTCTGGCCCCTGGATGGGTAGCC  >  NC_000913/4111598‑4111892

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: ‑