Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NC_000913	1,825,031	0	C	T	25.0%	75.2 / 17.0	40	intergenic (‑94/+109)	ves/spy	cold‑ and stress‑inducible protein/periplasmic ATP‑independent protein refolding chaperone, stress‑induced
Reads supporting (aligned to +/- strand):  ref base C (22/8);  new base T (0/10);  total (22/18)
Fisher's exact test for biased strand distribution p-value = 5.16e-05
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 1.00e+00
Rejected as consensus: Frequency below/above cutoff threshold.

CTCCCCATTCGCCGCGATGGATGCAATGCTGGCA‑CGCCAGTAAAAATCACGT‑TTTGCCGGTGGGAACGTGCAAATTTCGCGCGTTTCACCGGCAGCATTTCGCCACAGATTCACCGACATTTTACGCATATCAAAGTATTCCATACTCGCTCCCGGCCCGTTCTTTTCA‑TTGTTATCGTTCAGGTAACCGTGGATGG‑TTAT‑CGGCAACTCGGGTGATTTACGTTAGTGGTGATCAGGCTTTTTTTA‑CAACTGTTT‑GAGAAGAGAAAAGAAAACCGCCGATCCTGTCCACCGCATTACTGCAAGGTAGTGGACAAGACCGGCGGTCTTAAGTTTTTTGGCTGAAAGATTATTCAGCAGTTGCAGGCATTTTACCTTTTGCCGCTGGACGTTCTGTCAGACGC‑TTCTCAAAATTAGCATTAAATTGCTTTTTCTGTTCCGGCGTCAGG  >  NC_000913/1824794‑1825239                                                                                                                                                                                                                                                   |                                                                                                                                                                                                                    cTCCCCATTCGCCGCGATGGATGCAATGCTGGCA‑CGCCAGTAAAAATCACGT‑TTTGCCGGTGGGAACGTGCAAATTTCGCGCGTTTCACCGGCAGCATTTCGCCACAGATTCACCGACATTTTACGCATATCAAAGTATTCCATACTCGCTCCCGGCCCGTTCTTTTCA‑TTGTTATCGTTCAGGTAACCGTGGATGG‑TTAT‑CGGCAACTCGGGTGATTTACGTTAGTGGTGATCAGGCt                                                                                                                                                                                                                    <  1:449312/239‑1 (MQ=255)                     atgCAATGCTGGCA‑CGCCAGTAAAAATCACGT‑TTTGCCGGTGGGAACGTGCAAATTTCGCGCGTTTCACCGGCAGCATTTCGCCACAGATTCACCGACATTTTACGCATATCAAAGTATTCCATACTCGCTCCCGGCCCGTTCTTTTCA‑TTGTTATCGTTCAGGTAACCGTGGATGG‑TTAT‑CGGCAACTCGGGTGATTTACGTTAGTGGTGATCAGGCTTTTTTTA‑CAACTGTTT‑gag                                                                                                                                                                                               <  1:77689/238‑1 (MQ=255)                      tgCAATGCTGGCA‑CGCCAGTAAAAATCACGT‑TTTGCCGGTGGGAACGTGCAAATTTCGCGCGTTTCACCGGCAGCATTTCGCCACAGATTCACCGACATTTTACGCATATCAAAGTATTCCATACTCGCTCCCGGCCCGTTCTTTTCA‑TTGTTATCGTTCAGGTAACCGTGGATGG‑TTAT‑CGGCAACTCGGGTGATTTACGTTAGTGGTGATCAGGCTTTTTTTA‑CAACTGTTT‑gagaa                                                                                                                                                                                             <  1:500253/239‑1 (MQ=255)                       atcaTGCCGGCACCGCCAGTAAAAATC‑CGTGTTTGCCGGTGGGAACTGGCAAATTTCGCGCGTTTCAACAGCAGCATTTCGCCACAGATTCACCGACATTTTACGCATATCAAAGTATTCCATACTCGCTCCCGGCCCGTTCTTTTCA‑TTGTTATCGTTCAGGTAACCGTGGATGG‑TTAT‑CGGCAACTCGGGTGATTTACGTTAGTGGTGATCAGGCTTTTTTTA‑CAACTGTTT‑gagaa                                                                                                                                                                                             <  2:426269/236‑1 (MQ=255)                                                 cACGT‑TTTGCCGGTGGGAACGTGCAAATTTCGCGCGTTTCACCGGCAGCATTTCGCCACAGATTCACCGACATTTTACGCATATCAAAGTATTCCATACTCGCTCCCGGCCCGTTCTTTTCA‑TTGTTATCGTTCAGGTAACCGTGGATGG‑TTAT‑CGGCAACTCGGGTGATTTACGTTAGTGGTGATCAGGCTTTTTTTA‑CAACTGTTT‑GAGAAGAGAAAAGAAAACCGCCGAt                                                                                                                                                                         >  1:539996/1‑233 (MQ=255)                                                         tGCCGGTGGGAACGTGCAAATTTCGCGCGTTTCACCGGCAGCATTTCGCCACAGATTCACCGACATTTTACGCATATCAAAGTATTCCATACTCGCTCCCGGCCCGTTCTTTTCA‑TTGTTATCGTTCAGGTAACCGTGGATGG‑TTAT‑CGGCAACTCGGGTGATTTACGTTAGTGGTGATCAGGCTTTTTTTA‑CAACTGTTT‑gag                                                                                                                                                                                               >  2:220306/1‑204 (MQ=255)                                                         tGCCGGTGGGAACGTGCAAATTTCGCGCGTTTCACCGGCAGCATTTCGCCACAGATTCACCGACATTTTACGCATATCAAAGTATTCCATACTCGCTCCCGGCCCGTTCTTTTCA‑TTGTTATCGTTCAGGTAACCGTGGATGG‑TTAT‑CGGCAACTCGGGTGATTTACGTTAGTGGTGATCAGGCTTTTTTTA‑CAACTGTTT‑gag                                                                                                                                                                                               <  1:220306/204‑1 (MQ=255)                                                               tGGGAACGTGCAAATTTCGCGCGTTTCACCGGCAGCATTTCGCCACAGATTCACCGACATTTTACGCATATCAAAGTATTCCATACTCGCTCCCGGCCCGTTCTTTTCA‑TTGTTATCGTTCAGGTAACCGTGGATGG‑TTAT‑CGGCAACTCGGGTGATTTACGTTAGTGGTGATCAGGCTTTTTTTA‑CAACTGTTT‑GAGAAGAGAAAAGAAAACCGCCGATCCTGTCCACCGCAtt                                                                                                                                                          >  1:32949/1‑235 (MQ=255)                                                                       gtaaactttCGCGTCTTTCACCGGGAGTGTTTCCCCCATGATGCCCCCACTTTTGACTCATATCAAAATTTTCCATCACCGCCCCCGGCCCGTTTTTTTTC‑TTTTTTTCGTTTAGGGTAACGGGGGTGT‑TTTTGCGCAAACGGGGGTGTTTTACGTTAGGGGTGATCAGTTTTTTTTAA‑AATTTGTTG‑GAAAAAAAAAAAAAAAACCGCCGATCCTGTCCACCGCATTACTGCAAGGTa                                                                                                                                               <  2:264234/233‑1 (MQ=255)                                                                        gCAAATTTCGCGCGTTTCCACCGCCGTCTTTCCCCACAATTTCCCCCACATTTTACCCATTTCAAATTTTTCCCATCCCCCCCCCCGCCCGTTTTTTTCATTTTTTATCGTT‑AGGGTACCGTGGGTGGTTTAT‑CGACACCTGGGTTGTTTTAGTTTGGTGGTGA‑CCGGTTTTTTTTACCAATTTTTA‑GAAAAGAAAAAAAAAAACCGCCGATCCTGTCCACCGCATTACTGCAAGGTAg                                                                                                                                              <  2:525016/239‑1 (MQ=255)                                                                                  cgcgTTTCACCGGCAGCATTTCGCCACAGATTCACCGACATTTTACGCATATCAAAGTATTCCATACTCGCTCCCGGCCCGTTCTTTTCA‑TTGTTATCGTTCAGGTAACCGTGGATGG‑TTAT‑CGGCAACTCGGGTGATTTACGTTAGTGGTGATCAGGCTTTTTTTA‑CAACTGTTT‑GAGAAGAGAAAAGAAAACCGCCGATCCTGTCCACCGCATTACTGCAAGGTAGTGGACAAGAc                                                                                                                                    >  1:525016/1‑238 (MQ=255)                                                                                     gtttaccgggCATCTTTACGCCACAGATCCCCCGTCATTTTACGAATATCAAAGTATTCCATACTCGCCCCCGGCCTGTTTTTTTCA‑TTGTTATCGTACAGGTAACGGTGGATGG‑TTAT‑CGGCAACTGGGGTGTTTTACGTTAGTGGTGATCAGGTTTTTTTTA‑CAACTTTTT‑GAAAAGAAAAAAAAAAACCGCCGATCCTGTCCACCGCATTACTGCAAGGTAGTGGACAAGACcgg                                                                                                                                 <  2:539996/230‑1 (MQ=255)                                                                                               cagcaTTTCGCCACAGATTCACCGACATTTTACGCATATCAAAGTATTCCATACTCGCTCCCGGCCCGTTCTTTTCA‑TTGTTATCGTTCAGGTAACCGTGGATGG‑TTAT‑CGGCAACTCGGGTGATTTACGTTAGTGGTGATCAGGCTTTTTTTA‑CAACTGTTT‑GAGAAGAGAAAAGAAAACCGACGATCCTGTCCACCGCa                                                                                                                                                            >  1:719565/1‑201 (MQ=255)                                                                                               cagcaTTTCGCCACAGATTCACCGACATTTTACGCATATCAAAGTATTCCATACTCGCTCCCGGCCCGTTCTTTTCA‑TTGTTATCGTTCAGGTAACCGTGGATGG‑TTAT‑CGGCAACTCGGGTGATTTACGTTAGTGGTGATCAGGCTTTTTTTA‑CAACTGTTT‑GAGAAGAGAAAAGAAAACCGACGATCCTGTCCACCGCa                                                                                                                                                            <  2:719565/201‑1 (MQ=255)                                                                                                        gCCACAGATTCACCGACATTTTACGCATATCAAAGTATTCCATACTCGCTCCCGGCCCGTTCTTTTCA‑TTGTTATCGTTCAGGTAACCGTGGATGG‑TTAT‑CGGCAACTCGGGTGATTTACGTTAGTGGTGATCAGGCTTTTTTTA‑CAACTGTTT‑GAGAAGAGAAAAGAAAACCGCCGATCCTGTCCACCGCATTACTGCAAGGTAGTGGACAAGACCGGCGGGCCTAAGgtttttt                                                                                                                >  2:287891/1‑235 (MQ=255)                                                                                                                   aCCGACATTTTACGCATATCAAAGTATTCCATACTCGCTCCCGGCCCGTTCTTTTCA‑TTGTTATCGTTCAGGTAACCGTGGATGG‑TTAT‑CGGCAACTCGGGTGATTTACGTTAGTGGTGATCAGGCTTTTTTTA‑CAACTGTTT‑GAGAAGAGAAAAGAAAACCGCCGATc                                                                                                                                                                        >  1:232249/1‑169 (MQ=255)                                                                                                                                                         ccccgcccgGTTTTTTTTA‑TTTTTGTCGTGAGGGTAACCGGGGATGT‑TTAT‑GGACAACTGGGGTGTTTTACGTTAGTGTGGATCGGTTTTTTTTTA‑AACTTGTTG‑AAGAAAAAAAAAAAAACCCGCCGATCCTGTCCACCGCATTACTGCAAGGTAGTg                                                                                                                                            <  2:196206/158‑1 (MQ=255)                                                                                                                                                                   ttCTTTTTT‑TTTTTTTCGTGCGGTAAACGGTGGATGT‑TTAC‑CGGAAACTGGGGTGTTTTGCGTTAGGGGGGATCGGTTTTTTTTTA‑AAATTTTTA‑GAAAAGAAAAAAAAAAACCGCCGATCCTGTCCACCGCAt                                                                                                                                                           <  2:691180/134‑1 (MQ=255)                                                                                                                                                                   ttCTTTTCA‑TTGTTATCGTTCAGGTAACCGTGGATGG‑TTAT‑CGGCAACTCGGGTGATTTACGTTAGTGGTGATCAGGCt                                                                                                                                                                                                                    <  2:88579/79‑1 (MQ=255)                                                                                                                                                                   ttCTTTTCA‑TTGTTATCGTTCAGGTAACCGTGGATGG‑TTAT‑CGGCAACTCGGGTGATTTACGTTAGTGGTGATCAGGCt                                                                                                                                                                                                                    >  1:88579/1‑79 (MQ=255)                                                                                                                                                                   ttCTTTTCA‑TTGTTATCGTTCAGGTAACCGTGGATGG‑TTAT‑CGGCAACTCGGGTGATTTACGTTAGTGGTGATCAGGCTTTTTTTA‑CAACTGTTT‑GAGAAGAGAAAAGAAAACCGCCGATCCTGTCCACCGCATTACTGCAAGGTAGTGGACAAGACcg                                                                                                                                  >  1:196206/1‑159 (MQ=255)                                                                                                                                                                   ttCTTTTCA‑TTGTTATCGTTCAGGTAACCGTGGATGG‑TTAT‑CGGCAACTCGGGTGATTTACGTTAGTGGTGATCAGGCTTTTTTTA‑CAACTGTTT‑GAGAAGAGAAAAGAAAACCGCCGATCCTGTCCACCGCATTACTGCAAGGTAGTGGACAAGACCGGCGGTCTTAAGTTTTTTTGCTGAAAGATTATTCAGCAGTTTCAGGCATTTTACCTTTTTTCGCTGGGCGGTCTGTCAGAc                                                  >  1:13115/1‑239 (MQ=255)                                                                                                                                                                              tGTTATCGTTCAGGTAACCGTGGATGG‑TTAT‑CGGCAACTCGGGTGATTTACGTTAGTGGTGATCAGGCTTTTTTTA‑CAACTGTTT‑GAGAAGAGAAAAGAAAACCGCCGATCCTGTCCACCGCATTACTGCAAgg                                                                                                                                                 >  1:691180/1‑134 (MQ=255)                                                                                                                                                                                  aTCGTTCAGGTAACCGTGGATGG‑TTAT‑CGGCAACTCGGGTGATTTACGTTAGTGGTGATCAGGCTTTTTTTA‑CAACTGTTT‑gagaaga                                                                                                                                                                                           >  1:394135/1‑88 (MQ=255)                                                                                                                                                                                  aTCGTTCAGGTAACCGTGGATGG‑TTAT‑CGGCAACTCGGGTGATTTACGTTAGTGGTGATCAGGCTTTTTTTA‑CAACTGTTT‑gagaaga                                                                                                                                                                                           <  2:394135/88‑1 (MQ=255)                                                                                                                                                                                   tcgtcaaGGTACCCGTGGTTGT‑TTAT‑CGGAACCTGGGTTGTTTTACTTTAGTGGTAATCAGGTTTTTTTTA‑‑AACCGTTTGGAAAAGAAAAAAGAAAACCGCCGATCCTGTCCACCGCATTACTGCAAGGTAGTGGACAAGACCGGCGGTCTTAAGTTTTTTGGCTGAAAGATTATTCAGCAGTTGCAGGCATTTTACCTTTTGCCGCTGGACGTTCTGTCAGACGC‑TTCTCAAAATTAg                                  <  1:347132/233‑1 (MQ=255)                                                                                                                                                                                   tCGTTGAGTTACCGGTGGATGT‑TTAG‑GGGCAACTGGGTTGTTTTACGTTAGTGGTGATCAGGTTTTTTTAA‑CAATTGTTG‑GAAAAGAAAAAAGAAAACCGCCGATCCTGTCCACCGCATTACTGCAAGGTAGTGGACAAGACCGGCGGTCTTAAGTTTTTTGGCTGAAAGATTATTCAGCAGTTGCAGGCATTTTACCTTTTGCCGCTGGACGTTCTGTCAGACGC‑TTCTCAAAATTAg                                  <  1:187119/239‑1 (MQ=255)                                                                                                                                                                                   tCGTTCAGGTAACGGTGGTTGT‑TTAC‑CGCCAACTGGGGTTTTTTCCGTTGGGGGTGATCGGTTTTTTTTTA‑CACCTTTTG‑GAAAAGAAAAAAAAAAACCGCCGATCCTGTCCACCGCATTACTGCa                                                                                                                                                    <  2:726892/126‑1 (MQ=255)                                                                                                                                                                                    cGTTCAGGTACCCGTGGATGT‑TTAT‑CGGCAACTGGGGTGATTTACGTTAGTGGTGATCAGGTTTTTTTTA‑CAACTTTTG‑GAGAAGAAAAAAAAAAACCGCCGATCCTGTc                                                                                                                                                                   <  1:432578/110‑1 (MQ=255)                                                                                                                                                                                          ggTAACCGTGGATGG‑TTAT‑CGGCAACTCGGGTGATTTACGTTAGTGGTGATCAGGCTTTTTTTA‑CAACTGTTT‑GAGAAGAGAAAAGAAAACCGCCGATCCTGTCCACCGCATTACTGCAAGGTAGTGGACAAGACCGGCGGTCTTTAGTTTTTTTGCTGAAAGATTATTCATCAGTTGCAGGGATTTTACCTTTTTCCGCTGGACGGTCTGTCCGACGCTTTCTCaaattagaacttaa                            >  2:583036/1‑228 (MQ=255)                                                                                                                                                                                             aaCCGTGGATGG‑TTAT‑CGGCAACTCGGGTGATTTACGTTAGTGGTGATCAGGCTTTTTTTA‑CAACTGTTT‑GAGAAGAGAAAAGAAAACCGCCGATCCTGTCCACCGCATTACTGCAAGGTAGTGGa                                                                                                                                          >  1:726892/1‑126 (MQ=255)                                                                                                                                                                                              aCCGTGGATGG‑TTAT‑CGGCAACTCGGGTGATTTACGTTAGTGGTGATCAGGCTTTTTTTA‑CAACTGTTT‑GAGAAGAGAAAAGAAAACCGCCGATCCTGTCCACCGCATTa                                                                                                                                                         >  2:432578/1‑110 (MQ=255)                                                                                                                                                                                                cGTGGATGG‑TTAT‑CGGCAACTCGGGTGATTTACGTTAGTGGTGATCAGGCTTTTTTTA‑CAACTGTTT‑GAGAAGAGAAAAGAAAACCGCCGATCCTGTCCACCGCATTACTGCAAGGTAGTGGACAAGACCGGCGGTCTTAAGTTTTTTGGCTGAAAGATTATTCAGCAGTTGCAGGCATTTTACCTTTTGc                                                                      >  1:233809/1‑191 (MQ=255)                                                                                                                                                                                                   ggATGG‑TTAT‑CGGCAACTCGGGTGATTTACGTTAGTGGTGATCAGGCTTTTTTTA‑CAACTGTTT‑GAGAAGAGAAAAGAAAACCGCCGATCCTGTCCACCGCATTACTGCAAGGTAGTGGACAAGACCGGCGGGCTTAAGGTTTTTGGCTGAAAGATTATTCAGCAGGTGCAGGGATTTTACCTTTTGTCGCTGGACGTTCTTTTATGAGC‑TTCTCGAAATTAGCCTTTAAtt                         >  2:336839/1‑232 (MQ=255)                                                                                                                                                                                                    gATGG‑TTAT‑CGGCAACTCGGGTGATTTACGTTAGTGGTGATCAGGCTTTTTTTA‑CAACTGTTT‑GAGAAGAGAAAAGAAAACCGCCGATCCTGTCCACCGCATTACTGCAAGGTAGTGGACAAGACCGGCGGTCTTAAGTTTTTTGGCTGAAAGATTATTCAGCAGTTGCAGGCCTTTTACCTTTTTCCGCTGGACGTTCTGTCAGACGC‑TTCTCAAAATTAGCATTTAAtt                         >  1:459810/1‑231 (MQ=255)                                                                                                                                                                                                           ttacgggCACCTGGGGTAATTTACGTTGGTGGTAACCAGGTTTTTTTAA‑CACTTTTTG‑GAGAAGAAAAAAGAAAACCGCCGATCCTGTCCACCGCATTACTGCAAGGTAGTGGACAAGACCGGCGGTCTTAAGTTTTTTGGCTGAAAGATTATTCAGCAGTTGCAGGCATTTTACCTTTTGCCGCTGGACGTTCTGTCAGACGC‑TTCTCAAAAt                                     <  1:398056/209‑1 (MQ=255)                                                                                                                                                                                                            aT‑CGGCAACTCGGGTGATTTACGTTAGTGGTGATCAGGCTTTTTTTA‑CAACTGTTT‑GAGAAGAGAAAAGAAAACCGCCGATCCTGTCCACCGCATTACTGCAAGGTAGTGGACAAGACCGGCGGTCTTAAGTTTTTTGGCTGAAAGATTATTCAGCAGTTGCAGGCATTTTACCTTTTGCCGCTGGACGTTCTGTCAGACGC‑TTCTCAAAATTAGCATTAAATTGCTTTTTCTGTTCCg          >  1:736010/1‑239 (MQ=255)                                                                                                                                                                                                                     cTCGGGTGATTTACGTTAGTGGTGATCAGGCTTTTTTTA‑CAACTGTTT‑GAGAAGAGAAAAGAAAACCGCCGATCCTGTCCACCGCATTACTGCAAGGTAGTGGACAAGACCGGCGGTCTTAAGTTTTTTTGCTGAAAGATTATTCAGCAGTTGCAGGCATTTTACCTTTTGCCGCTGGGCGGTCTGTCTGGCGC‑TTCTCAAAATTAGCATTCAATTGGCTTTTTTTTTTCGGCGTCAgt  >  2:178728/1‑238 (MQ=255)                                                                                                                                                                                                                     cTCGGGTGATTTACGTTAGTGGTGATCAGGCTTTTTTTA‑CAACTGTTT‑GAGAAGAGAAAAGAAAACCGCCGATCCTGTCCACCGCATTACTGCAAGGTAGTGGACAAGACCGGCGGTCTTAAGTTTTTTGGCTGAAAGATTATTCAGCAGTTGCAGGCATTTTACCTTTTGCCGCTGGACGTTCTGTCAGACGC‑TTCTCAAAATTAGCATTAAAATGCTTTTTCTGTTTCGGCGTCAgg  >  1:280304/1‑239 (MQ=255)                                                                                                                                                                                                                                   gTTAGTGGTGATCAGGCTTTTTTTA‑CAACTGTTT‑GAGAAGAGAAAAGAAAACCGCTGATc                                                                                                                                                                        >  2:669457/1‑60 (MQ=255)                                                                                                                                                                                                                                                   |                                                                                                                                                                                                                    CTCCCCATTCGCCGCGATGGATGCAATGCTGGCA‑CGCCAGTAAAAATCACGT‑TTTGCCGGTGGGAACGTGCAAATTTCGCGCGTTTCACCGGCAGCATTTCGCCACAGATTCACCGACATTTTACGCATATCAAAGTATTCCATACTCGCTCCCGGCCCGTTCTTTTCA‑TTGTTATCGTTCAGGTAACCGTGGATGG‑TTAT‑CGGCAACTCGGGTGATTTACGTTAGTGGTGATCAGGCTTTTTTTA‑CAACTGTTT‑GAGAAGAGAAAAGAAAACCGCCGATCCTGTCCACCGCATTACTGCAAGGTAGTGGACAAGACCGGCGGTCTTAAGTTTTTTGGCTGAAAGATTATTCAGCAGTTGCAGGCATTTTACCTTTTGCCGCTGGACGTTCTGTCAGACGC‑TTCTCAAAATTAGCATTAAATTGCTTTTTCTGTTCCGGCGTCAGG  >  NC_000913/1824794‑1825239

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 8 ≤ ATCG/ATCG < 9 ≤ ATCG/ATCG < 32 ≤ ATCG/ATCG < 40 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑