Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NC_000913	1,825,061	0	G	A	46.5%	33.6 / 31.5	44	intergenic (‑124/+79)	ves/spy	cold‑ and stress‑inducible protein/periplasmic ATP‑independent protein refolding chaperone, stress‑induced
Reads supporting (aligned to +/- strand):  ref base G (20/3);  new base A (0/20);  total (20/24)
Fisher's exact test for biased strand distribution p-value = 2.32e-09
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 1.00e+00

GCATATCAAAGTATTCCATACTCGCTCCCGGCCCGTTCTTTTCATTGTTATCGTTCAGGTAACCGT‑GGATGGTTATCGGCAACTCGGGTGATTT‑ACGTTAGTGGTGATCAGGCTTTTTTTACAACTG‑TTT‑GAGAAGAGAAAAGAAAACCGCCGATCCTGTCCACCGCATTACTGCAAGGTAGTGGACAAGACCGGCGGTCTTAAGTTTTTTGGCTGAAAGATTATTCAGCAGTTGCAGGCATTTTACCTTTTGCCGCTGGACGTTCTGTCAGACGCTTCTCAAAATTAGCATT  >  NC_000913/1824919‑1825211                                                                                                                                                   |                                                                                                                                                       gCATATCAAAGTATTCCATACTCGCTCCCGGCCCGTTCTTTTCATTGTTATCGTTCAGGTAACCGT‑GGATGGTTATCGGCAACTCGGGTGATTT‑ACGTTAGTGGTGATCAGGCTTTTTTTACAACTG‑TTT‑GAGAAGAGAAAAGAAAAcc                                                                                                                                                  >  1:298095/1‑149 (MQ=255)       cAAAGTATTCCATACTCGCTCCCGGCCCGTTCTTTTCATTGTTATCGTTCAGGTAACCGT‑GGATGGTTATCGGCAACTCGGGTGATTT‑ACGTTAGTGGTGATCAGGCTTTTTTTACAACTG‑TTT‑GAGAAGAGAAAAGAAAACCGCCGATcc                                                                                                                                          >  2:504950/1‑151 (MQ=255)           gTATTCCATACTCGCTCCCGGCCCGTTCTTTTCATTGTTATCGTTCAGGTAACCGT‑GGATGGTTATCGGCAACTCGGGTGATTT‑ACGTTAGTGGTGATCAGGCTTTTTTTACAACTG‑TTT‑GAGAAGAGAAAAGAAAACCGCCGATCCTGTc                                                                                                                                      >  2:337937/1‑151 (MQ=255)             aTTCCATACTCGCTCCCGGCCCGTTCTTTTCATTGTTATCGTTCAGGTAACCGT‑GGATGGTTATCGGCAACTCGGGTGATTT‑ACGTTAGTGGTGATCAGGCTTTTTTTACAACTG‑TTT‑GAGAAGAGAAAAGAAAACCGCCGATCCTGTcc                                                                                                                                     >  1:350735/1‑150 (MQ=255)               tCCATACTCGCTCCCGGCCCGTTCTTTTCATTGTTATCGTTCAGGTAACCGT‑GGATGGTTATCGGCAACTCGGGTGATTT‑ACGTTAGTGGTGATCAGGCTTTTTTTACAACTG‑TTT‑GAGAAGAGAAAAGAAAACCGCCGATCCTGTCCAcc                                                                                                                                  >  2:186837/1‑151 (MQ=255)                  atccccGCCCCCGGCCTTTTTTTTTCTTTTTTTTCGTTAGGGTACCCGT‑GGATGGTTATCGGCAACTGGGGTGTTTT‑ACGTTAGTGGTGACCAGGTTTTTTTAACATCTT‑TTT‑GAAAAGAGAAAAAAAAACCGCCGATCCTGTcc                                                                                                                                     <  2:716556/140‑1 (MQ=255)                   tACTCGCTCCCGGCCCGTTCTTTTCATTGTTATCGTTCAGGTAACCGT‑GGATGGTTATCGGCAACTGGGGTGATTT‑ACGTTAGTGGTGATCAGGCTTTTTTTACAACTG‑TTT‑GAGAAGAGAAAAGAAAACCGCCGATCCTGTCCACCGCAt                                                                                                                              >  2:44652/1‑151 (MQ=255)                   tACTCGCTCCCGGCCCGTTCTTTTCATTGTTATCGTTCAGGTAACCGT‑GGATGGTTATCGGCAACTCGGGTGATTT‑ACGTTAGTGGTGATCAGGCTTTTTTTACAACTG‑TTT‑GAGAAGAGAAAAGAAAACCGCCGATCCTGTCCACCGCAt                                                                                                                              >  1:438104/1‑151 (MQ=255)                           cccGGCCCGTTCTTTTATTTGTTATCGTTCAGGTACCCGT‑GGATGGTTAGGGGCAACTGGGGTAATTT‑CCGTTGGTGGTGATCGGCTTTTTTTTACAACTG‑TTA‑GAAAAGAGAAAAGAAAACCGCCGATCCTGTCCACCGCATTACTGCaa                                                                                                                      <  1:364905/151‑1 (MQ=255)                             cGGCCCGTTCTTTTCATTGTTATCGTTCAGGTAACCGT‑GGATGGTTATCGGCAACTCGGGTGATTT‑ACGTTAGTGGTGATCAGGCTTTTTTTACAACTG‑TTT‑GAGAAGAGAAAAGAAAACCGCCGATCCTGTCCACCGCATTACTGCAAgg                                                                                                                    >  2:13627/1‑151 (MQ=255)                                  cGTTCTTTTCATTGTTATCGTTCAGGTAACCGT‑GGATGGTTATCGGCAACTCGGGTGATTT‑ACGTTAGTGGTGATCAGGCTTTTTTTACAACTG‑TTT‑GAGAAGAGAAAAGAAAACCGCCGATCCTGTCCACCGCATTACTGCAAGGTAGTg                                                                                                               >  1:384573/1‑151 (MQ=255)                                        tttCATTTTTATCGTTCAGGTACCGGT‑GGATGGTTATCGGCAACTGGGGTGTTTT‑ACGTTAGTGGTGATCAGGTTTTTTTTAAAATTG‑TTT‑GAGAAGAAAAAAAAAAACCGCCGATCCTGTCCACCGCATTACTGCAAGGTAGTGGACaa                                                                                                          <  1:627343/150‑1 (MQ=255)                                        tttCATTGTTATCGTTCAGGTAACCGT‑GGATGGTTATCGGCAACTCGGGTGATTT‑ACGTTAGTGGTGATCAGGCTTTTTTTACAACTG‑TTT‑GAGAAGAGAAAAGAAAACCGCCGATCCTGTCCACCGCATTACTGCAAGGAAGTGGACa                                                                                                           >  2:377900/1‑149 (MQ=255)                                           tttttttATCTTTCGGGT‑ACCGTGGGGTGTTTATCGACATCTGGGTTGTTTT‑GTGTAAGTGGTAATCGGGTTTTTTTTTCAACTT‑TTA‑GAAAAGAAAAAAAAAAACCGCCGATCCTGTCCACCGCATTACTGCAAGGTAGTGGACAAGa                                                                                                        <  1:310887/144‑1 (MQ=255)                                               gTTATCGTTCAGGTAACCGT‑GGATGGTTATCGGCAACTCGGGTGATTT‑ACGTTAGTGGTGATCAGGCTTTTTTTACAACTG‑TTT‑GAGAAGAGAAAAGAAAACCGCCGATCCTGTCCACCGCATTACTGCAAGGTAGTGGACAAGACcggcg                                                                                                  >  1:319266/1‑151 (MQ=255)                                                 tATCGTTCAGGTAACCGT‑GGATGGTTATCGGCAACTCGGGTGATTT‑ACGTTAGTGGTGATCAGGCTTTTTTTACAACTG‑TTT‑GAGAAGAGAAAAGAAAACCGCCGATCCTGTCCACCGCATTACTGCAAGGTAGTGGACAAGACcggcgg                                                                                                 >  1:265650/1‑150 (MQ=255)                                                          ggTAACCGT‑GGATGGTTATCGGAAACGCGGGTGATTT‑CCGTTAGTGGTGATCAGGTTTTTTTTACAACTG‑TTT‑GAGAAGAGAAAAAAAAACCGCCGATCCTGTCCACCGCATTACTGCAAGGTAGTGGACAAGACCGGCGGTCTTAAg                                                                                          <  1:85137/148‑1 (MQ=255)                                                              aCCGT‑GGATGGTTATCGGCAACTCGGGTGATTT‑ACGTTAGTGGTGATCAGGCTTTTTTTACAACTG‑TTT‑GAGAAGAGAAAAGAAAACCGCCGATCCTGTCCACCGCATTACTGCAAGGTAGTGGACAAGACCGGCGGTCTTAAGtttttt                                                                                    >  1:651132/1‑150 (MQ=255)                                                               ccGT‑GGATGGGTATCGGCAACTCGGGTGATTT‑ACGTTAGTGGGGATCAGGCTTTTTTTACAACTG‑TTT‑GAGAAGAGAAAAGAAAACCGCCGATCCTGTCCACCGCATTACTGCAAGGTAGTGGACAAGACCGGCGGGCTTTAGtttttttg                                                                                  >  1:137689/1‑149 (MQ=255)                                                                               ggCAACGCGGGTGATTT‑ACGTTAGTGGTGATCAGGTTTTTTTTACAACTG‑TTT‑GAAAAGAAAAAAAAAAACCGCCGATCCTGTCCACCGCATTACTGCAAGGTAGTGGACAAGACCGGCGGTCTTAAGTTTTTTGGCTGAAAGattatt                                                                     <  2:266237/149‑1 (MQ=255)                                                                                gacaaccGGGTTATTTAACATTAGTGGTAATC‑GGTTTTTTTTAACACTT‑TTTAGAAAAGAAAAAAAAAAGCCGCCGATCCTGTCCACCGCATTACTGCAAGGTAGTGGACAAGACCGGCGGTCTTAAGTTTTTTGGCTGAAAGATTATTc                                                                    <  1:4056/144‑1 (MQ=255)                                                                                gCAACTCGGGTGATTT‑ACGTTAGTGGTGATCATGCTTTTTTTACAACTG‑TTT‑GAGAAGAGAAAAGAAAACCGCCGATCCTGTCCACCGCCTTACTGCAAGGTAGTGGACAAGACCGGCGGCCCTAAGATTTCTGGCCGAAAGATTTTTc                                                                    >  2:477918/1‑149 (MQ=255)                                                                                gCAACTCGGGTGATTT‑ACGTTAGTGGTGATCAGGCTTTTTTTACAACTG‑TTT‑GAGAAGAGAAAAGAAAACCGCCGATCCTGTCCACCGCATTACTGCAAGGTAGTGGACAAGACCGGCGGTCTTAAGTTTTTTGGCTGAAAGATTATTc                                                                    >  1:204599/1‑149 (MQ=255)                                                                                  acctgggttgtttt‑ACGTAAGTGGTGACCAGGTTTTTTTTACAACTT‑TTT‑GAGAAAAAAAAAAAAAACCGCCGATCCTGTCCACCGCATTACTGCAAGGTAGTGGACAAGACCGGCGGTCTTAAGTTTTTTGGCTGAAAGATTATTcag                                                                  <  2:261287/138‑1 (MQ=255)                                                                                   aatggggTGATTT‑ACTTAAGTGGTGATCGGTGTTTTTATAAATTTT‑TTA‑GAGAAGAAAAAAAAAAACCGCCGATCCTGTCCACCGCATTACTGCAAGGTAGTGGACAAGACCGGCGGTCTTAAGTTTTTTGGCTGAAAGattattt                                                                    <  2:346609/142‑2 (MQ=255)                                                                                     ctggggtattttcggTTGGTGGTAATCAGTTTTTTTTTAAACTTT‑TTT‑GAGAAGAAAAAAAAAAACCGCCGATCCTGTCCACCGCATTACTGCAAGGTAGTGGACAAGACCGGCGGTCTTAAGTTTTTTGGCTGAAAGATTATTcagcag                                                               <  1:265162/136‑1 (MQ=255)                                                                                       gggTGTTTT‑ATGTTAGTGGTGATCGGGTTTTTTTTACAATTT‑TTG‑GAGAAGAAAAAAGAAAACCGCCGATCCTGTCCACCGCATTACTGCAAGGTAGTGGACAAGACCGGCGGTCTTAAGTTTTTTGGCTGAAAGATTATTCAGCAGt                                                              <  2:159137/148‑1 (MQ=255)                                                                                          tGATTT‑ACGTTAGTGGTGATCAGGCTTTTTTTACAACTG‑TTT‑GAGAAGAGAAAAGAAAACCGCCGATCCTGTCCACCGCATTACTGCAAGGTAGTGGACAAGACCGGCGGTCTTAAGTTTTTTGGCTGAAAGATTATTCAGCAGTTGCAgg                                                        >  2:615439/1‑151 (MQ=255)                                                                                             ttt‑ACGTTAGTGTTGATCAGTTTTTTTTTACAATTT‑TTT‑GAAAAGAAAAAAAAAAACCGCCGATCCTGTCCACCGCATTACTGCAAGGTAGTGGACAAGACCGGCGGTCTTAAGTTTTTTGGCTGAAAGATTATTCAGCAGTTGCAGGc                                                       <  2:25205/149‑1 (MQ=255)                                                                                                         ggtaaccggtttttttttACAATTT‑TTT‑AAAAAAAAAAAAAAAAACCGCCGATCCTGTCCACCGCATTACTGCAAGGTAGTGGACAAGACCGGCGGTCTTAAGTTTTTTGGCTGAAAGATTATTCAGCAGTTGCAGGCATTTTACCTTTTg                                          <  1:701588/140‑1 (MQ=255)                                                                                                              tCAGGCTTTTTTTACAACTG‑TTT‑GAGAAGAGAAAAGAAAACCGCCGATCCTGTCCACCGCATTACTGCAAGGTAGTGGACAAGACCGGCGGTCTTAAGTTTTTTGGCTGAAAGATTATTCAGCAGTTGCAGGCATTTTACCTTTTGCCGCt                                     >  1:129454/1‑151 (MQ=255)                                                                                                               cagtttttttttACATCTT‑TTG‑AAAAAGAAAAAAAAAACCCGCCGATCCTGTCCACCGCATTACTGCAAGGTAGTGGACAAGACCGGCGGTCTTAAGTTTTTTGGCTGAAAGATTATTCAGCAGTTGCAGGCATTTTACCTTTTGc                                         <  2:27882/141‑1 (MQ=255)                                                                                                               cagtttttttttACAACTT‑TTT‑GAAAAAAAAAAAGAAAACCGCCGATCCTGTCCACCGCATTACTGCAAGGTAGTGGACAAGACCGGCGGTCTTAAGTTTTTTGGCTGAAAGATTATTCAGCAGTTGCAGGCATTTTACCTTTTGCCg                                       <  1:490154/143‑1 (MQ=255)                                                                                                                    tttttttAAAATTTTTTT‑GAAAAGAAAAAACAAAACCGCCGATCCTGTCCACCGCATTACTGCAAGGTAGTGGACAAGACCGGCGGTCTTAAGTTTTTTGGCTGAAAGATTATTCAGCAGTTGCAGGCATTTTACCTTTTGCCGCTg                                    <  2:724799/147‑1 (MQ=255)                                                                                                                        tttACACCTG‑TTG‑AAGAAGAAAAAAAAAAACCGCCGATCCTGTCCACCGCATTACTGCAAGGTAGTGGACAAGACCGGCGGTCTTAAGTTTTTTGGCTGAAAGATTATTCAGCAGTTGCAGGCATTTTACCTTTTGCCGCTGGACGTTCt                            <  2:297825/150‑1 (MQ=255)                                                                                                                          aacacCTG‑TTG‑AAAAAGAAAAAAAAAAACCGCCGATCCTGTCCACCGCATTACTGCAAGGTAGTGGACAAGACCGGCGGTCTTAAGTTTTTTGGCTGAAAGATTATTCAGCAGTTGCAGGCATTTTACCTTTTGCCGCTGGACGTTCTGt                          <  2:395473/149‑1 (MQ=255)                                                                                                                                  ttttagagaaaaaaaAAAAAAACCGCCGATCCTGTCCACCGCATTACTGCAAGGTAGTGGACAAGACCGGCGGTCTTAAGTTTTTTGGCTGAAAGATTATTCAGCAGTTGCAGGCATTTTACCTTTTGCCGCTGGACGTTCTGTCAGAc                     <  2:256871/144‑1 (MQ=255)                                                                                                                                   tttcgataaaagaaaaaaaaCCCGCCGATCCTGTCCACCGCATTACTGCAAGGTAGTGGACAAGACCGGCGTTCTTAAGTTTTTTGGCTGAAAGATTATTCAGCAGTTGCAGGCATTTTTCCTTTTGCCGCTGGACGTTCTGTCAGAc                     <  2:107276/138‑1 (MQ=255)                                                                                                                                   ttt‑GAAAAAAAAAAAAAAAACCGCCGATCCTGTCCACCGCATTACTGCAAGGTAGTGGACAAGACCGGCGGTCTTAAGTTTTTTGGCTGAAAGATTATTCAGCAGTTGCAGGCATTTTACCTTTTGCCGCTGGACGTTCTGTc                         <  2:170335/143‑1 (MQ=255)                                                                                                                                        agaagaaaaAAAAAAACCGCCGATCCTGTCCACCGCATTACTGCAAGGTAGTGGACAAGACCGGCGGTCTTAAGTTTTTTGGCTGAAAGATTATTCAGCAGTTGCAGGCATTTTACCTTTTGCCGCTGGACGTTCTGTCAGACGCTtct               <  2:438063/149‑1 (MQ=255)                                                                                                                                        agaagaaaaAAAAAAACCGCCGATCCTGTCCACCGCATTACTGCAAGGTAGTGGACAAGACCGGCGGTCTTAAGTTTTTTGGCTGAAAGATTATTCAGCAGTTGCAGGCATTTTACCTTTTGCCGCTGGACGTTCTGTCAGACGCTtct               <  1:528060/149‑1 (MQ=255)                                                                                                                                        agaaaaaaaAAAAAAACCGCCGATCCTGTCCACCGCATTACTGCAAGGTAGTGGACAAGACCGGCGGTCTTAAGTTTTTTGGCTGAAAGATTATTCAGCAGTTGCAGGCATTTTACCTTTTGCCGCTGGACGTTCTGTCAGACGCTtctc              <  1:720839/150‑1 (MQ=255)                                                                                                                                          aagagaaAAGAAAACCGCCGATCCTGTCCACCGCATTACTGCAAGGTAGTGGACAAGACCGGCGGTCTTAAGTTTTTTGGCTGAAAGATTATTCAGCAGTTGCAGGCATTTTACCTTTTGCCGCTGGACGTTCTGTCAGACGCTTCTCaa            >  2:154414/1‑150 (MQ=255)                                                                                                                                           agagaaAAGAAAACCGCCGATCCTGTCCACCGCATTACTGCAAGGTAGTGGACAAGACCGGCGGTCTTAAGTTTTTTGGCTGAAAGATTATTCAGCAGTTGCAGGCATTTTACCTTTTGCCGCTGGACGTTCTGTCAGACGCTTCTCaaa           >  1:577248/1‑150 (MQ=255)                                                                                                                                           agaaaaAAAAAAACCGCCGATCCTGTCCACCGCATTACTGCAAGGTAGTGGACAAGACCGGCGGTCTTAAGTTTTTTGGCTGAAAGATTATTCAGCAGTTGCAGGCATTTTACCTTTTGCCGCTGGACGTTCTGTCAGACGCTtctc              <  2:337362/147‑1 (MQ=255)                                                                                                                                             aaaaaaaaaaaCCGCCGATCCTGTCCACCGCATTACTGCAAGGTAGTGGACAAGACCGGCGGTCTTAAGTTTTTTGGCTGAAAGATTATTCAGCAGTTGCAGGCATTTTACCTTTTGCCGCTGGACGTTCTGTCAGACGCTTCTCAAAAt         <  1:651839/148‑1 (MQ=255)                                                                                                                                               aaaagaaagCCGCCGATCCTGTCCACCGCATTACTGCAAGGTAGTGGACAAGACCGGCGGTCTTAAGTTTTTTGGCTGAAAGATTATTCAGCAGTTGCAGGCATTTTACCTTTTGCCGCTGGACGTTCTGTCAGACGCTTCTCAAAATTAg      <  1:138240/151‑1 (MQ=255)                                                                                                                                               aaaagaaaaCCGCCGATCCTGTCCACCGCATTACTGCAAGGTAGTGGACAAGACCGGCGGTCTTAAGTTTTTTGGCTGAAAGATTATTCAGCAGTTGCAGGCATTTTACCTTTTGCCGCTGGACGTTCTGTCAGACGCTTCTCAAAAtt        >  1:593114/1‑149 (MQ=255)                                                                                                                                               aaaaaaaaaCCGCCGATCCTGTCCACCGCATTACTGCAAGGTAGTGGACAAGACCGGCGGTCTTAAGTTTTTTGGCTGAAAGATTATTCAGCAGTTGCAGGCATTTTACCTTTTGCCGCTGGACGTTCTGTCAGACGCTTCTCAAAATTAg      <  1:224454/151‑1 (MQ=255)                                                                                                                                                   gaaaaCCGCCGATCCTGTCCACCGCATTACTGCAAGGTAGTGGACAAGACCGGCGGTCTTAAGTTTTTTGGCTGAAAGATTATTCAGCAGTTGCAGGCATTTTACCTTTTGCCGCTGGACGTTCTGTCAGACGCTTCTCAAAATTAGCAtt  >  1:4297/1‑151 (MQ=255)                                                                                                                                                   |                                                                                                                                                       GCATATCAAAGTATTCCATACTCGCTCCCGGCCCGTTCTTTTCATTGTTATCGTTCAGGTAACCGT‑GGATGGTTATCGGCAACTCGGGTGATTT‑ACGTTAGTGGTGATCAGGCTTTTTTTACAACTG‑TTT‑GAGAAGAGAAAAGAAAACCGCCGATCCTGTCCACCGCATTACTGCAAGGTAGTGGACAAGACCGGCGGTCTTAAGTTTTTTGGCTGAAAGATTATTCAGCAGTTGCAGGCATTTTACCTTTTGCCGCTGGACGTTCTGTCAGACGCTTCTCAAAATTAGCATT  >  NC_000913/1824919‑1825211

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 13 ≤ ATCG/ATCG < 16 ≤ ATCG/ATCG < 34 ≤ ATCG/ATCG < 39 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑