Predicted mutation
evidence	seq id	position	mutation	freq	annotation	gene	description
RA	NC_000913	3,217,530	T→C	23.6%	intergenic (+128/+26)	yqjI → / ← aer	PadR family putative transcriptional regulator/fused signal transducer for aerotaxis sensory component/methyl accepting chemotaxis component

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NC_000913	3,217,530	0	T	C	23.6%	66.2 / 2.7	37	intergenic (+128/+26)	yqjI/aer	PadR family putative transcriptional regulator/fused signal transducer for aerotaxis sensory component/methyl accepting chemotaxis component
Reads supporting (aligned to +/- strand):  ref base T (23/3);  new base C (2/7);  total (25/12)
Fisher's exact test for biased strand distribution p-value = 5.26e-04
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 1.00e+00

ATATCAGTGATGCACAAATAAAAAAGATCATTGCGGTGATCGACCGCGCCGCTTTTGATATTACGCAACTGGATTAATCGCC‑GCATCCGCCAGTGGCGCGGTGCAATT‑GCCGGATGCGACGCTTGAC‑GCGCCTTATCCGGCCTACACCCG‑CTACACACCCCGC‑AGGCCTGATAAGATGCG‑CCAGCATCGCATCAGGCATTGTG‑CTCCAACCGCCGGATCCGGCATACCGATTAATGCAGTACCGTCACCGCGTCTTCCAGTCGGCTGGCGCGGTGTTTCACCATCGCCGACACCTGCGCACTCTCTTCCACCAGCTCGGCATTTTTCTGGGTGATCAGGTTAAGCTCATCCACTGCACGGGTCAGGCTGGAAAGCCCATCGGCCTGTTCCAGCGTTGAATGGCTAATCTGGGCGATCAACTGGGTGACGT  >  NC_000913/3217326‑3217755                                                                                                                                                                                                                    |                                                                                                                                                                                                                                  atatCAGTGATGCACAAATAAAAAAGATCATTGCGGTGATCGACCGCGCCGCTTTTGATATTACGCAACTGGATTAATCGCC‑GCATCCGCCAGTGGCGCGGTGCAATT‑GCCGGATGCGACGCTTGAC‑GCGCCTTATCCGGCCTACACCCG‑CTACACACCCCGC‑AGGCCTGATAAGATGCG‑CCAGCATCGCATCAGGCATTGTG‑CTCCACCCCCCGGATCCGGCATAcc                                                                                                                                                                                                            >  1:187792/1‑228 (MQ=255)          ttgcaaacaaaaaaaaGATCAGTGGGCACAGCGCCCGGCCCGATTTTGATACTCCGCAAGGAAAGTAGTCGCC‑GCACCCGCCAGTGGCGGGGTGCAATG‑CCCGGATCGGCCGCTGTAC‑CACCCTTACCCGGCCTACCCCCG‑CTACACCCCCCGC‑AGGCCTGATAGTACGGG‑CCAGCATCGAACCGGGAATTGTG‑CTCCAACCGCCGGATCCGGCATACCGATTAATGc                                                                                                                                                                                                   <  2:469846/218‑1 (MQ=255)            gCACAAATAAAAAAGATCATTGCGGTGATCGACCGCGCCGCTTTTGATATTACGCAACTGGATTAATCGCC‑GCATCCGCCAGTGGCGCGGTGCAATT‑GCCGGATGCGACGCTTGAC‑GCGCCTTATCCGGCCTACACCCG‑CTACACACCCCGC‑AGGCCTGCTAAGATGCG‑CCAGCATCGCATCAGGCATTGTG‑CTCCAACCGCCGGATCCAGCATACCGATTAATGCa                                                                                                                                                                                                  >  1:426778/1‑227 (MQ=255)                                       aTCGACCGCGCCGCTTTTGATATTACGCAACTGGATTAATCGCC‑GCATCCGCCAGTGGCGCGGTGCAATT‑GCCGGATGCGACGCTTGAC‑GCGCCTTATCCGGCCTACACCCG‑CTACACACCCCGC‑AGGCCTGATAAGATGCG‑CCAGCATCGCATCAGGCATTGTG‑CTCCAACCGCCGGATCCGGCATACCGATTAATGCAGGACCGTCACCGCGGCTTCCCGTCGCCt                                                                                                                                                                      >  1:513965/1‑228 (MQ=255)                                               cgccgcTTTTGATATTACGCAACTGGATTAATCGCC‑GCATCCGCCAGTGGCGCGGTGCAATT‑GCCGGATGCGACGCTTGCC‑GCGCCTTATCCGGCCTCCACCCG‑CTCCACACCCCGC‑CGGCCCGATAAGTTGCG‑CCACCCTCTCACCAGGCCATGTC‑CCACTACCGCCGGACTCGGCATCCCGATTGATGCGGTCCCGCCCCCCCGCCCTCCACCCGGCCTGcgcgc                                                                                                                                                               >  2:195675/1‑226 (MQ=19)                                                               aCGCAACTGGATTAATCGCC‑GCATCCGCCAGTGGCGCGGTGCAATT‑GCCGGATGCGACGCTTGAC‑GCGCCTTATCCGGCCTACACCCG‑CTACACACCCCGC‑AGGCCTGATAAGATGCG‑CCAGCATCGCATCAGGCATTGTG‑CTCCAACCGCCGGATCCGGCATACCGATTAATGCAGTACCGTCACCGCGTCTTCCAGTCGGCTGGCCCGGTGTTTCACCATCGCCg                                                                                                                                               >  1:28875/1‑227 (MQ=255)                                                               aCGCAACTGGATTAATCGCC‑GCATCCGCCAGTGGCGCGGTGCAATT‑GCCGGATGCGACGCTTGAC‑GCGCCTTATCCGGCCTACACCCG‑CTACACACCCCGC‑AGGCCTGATAAGATGCG‑CCAGCATCGCATCAGGCATTGGG‑CTCCAACCGCCGGATCCGGCAACCCGATTAATGCAGTACCTTCACCGCGCCTTCCGGTCGCCTGCCCCGGGGTTTCACCACTGCCg                                                                                                                                               >  1:473530/1‑227 (MQ=38)                                                                  cAAGTGGATTAACCCCCAGCCCCCGCAGGTGGC‑CGGTGCAATTGGCCGGAT‑CGACCTGTGGCGGCGCCTTGACCGG‑CTCCACCCGATTACCCCACCCGC‑GGGCCTTATAAGATGCG‑ACAGCAGCTAAGCAGGCGTTGGG‑CACCAACCTCCGGATCCGGCATACCGATTAATGCAGTACCGTCACCGCGTCTTCCAGTCGGCTGGCGCGGTGTTTCACCATCGCCGaca                                                                                                                                            <  2:168687/228‑1 (MQ=255)                                                                        gATTAATCGCC‑GCATCCGCCAGTGGCGCGGTGCAATT‑GCCGGATGCGACGCTTGAC‑GCGCCTTATCCGGCCTACACCCG‑CTACACACCCCGC‑AGGCCTGATAAGATGCG‑CCAGCATCGCATCAGGCATTGTG‑CTCCAACCGCCGGATCCGGCATACCGATTAATGCAGTACCGTCACCGCGTCTTCCAGTCGGCTGGCGCGGTGGTTCACCATCGCCGACCCCTgcg                                                                                                                                      >  1:14252/1‑227 (MQ=255)                                                                               cgcc‑gcATCCGCCAGTGGCGCGGTGCAATT‑GCCGGATGCGACGCTTGAC‑GCGCCTTATCCGGCCTACACCCG‑CTACACACCCCGC‑AGGCCTGATAAGATGCG‑CCAGCATCGCATCAGGCATTGTG‑CTCCAACCGCCGGATCCGGCATACCGCTTAATGCAGGCCCGTCCCCCCGTCTTCCCGTCGGCTGCCGCGGGGTTTCACCACACCCGACCCCCgcgccccccct                                                                                                                              >  2:340499/1‑221 (MQ=38)                                                                                  c‑gcATCCGCCAGTGGCGCGGTGCAATT‑GCCGGATGCGACGCTTGAC‑GCGCCTTATCCGGCCTACACCCG‑CTACACACCCCGC‑AGGCCTGATAAGATGCG‑CCAGCATCGCATCAGGCATTGTG‑CTCCAACCGCCGGATCCGGCATACCGATTAATGCAGTACCGTCACCCCGTCTTCCAGTCGCCTGGCGCGGGGTTTCACCATACCCGACACCTTCGCACCCCCTTc                                                                                                                            >  1:280533/1‑227 (MQ=39)                                                                                               tGGCGCGGTGCAATT‑CCCGGATGCGCCGCTTGAC‑GCGCCTTATCCGGCCTACACCCG‑CTACACACCCCGC‑AGGCCTGATAAGATGCG‑CCAGCATCGCATCAGGCATTGTC‑CTCCAACCGCCGGCTCCGGCATCCCGATTAATGCAGTACCGTCACCGCGTCGTCCAGTCGGCTGCCCCGCTGTTTCACCATCGCCCACACCTGCGCCCTCCCCTCCCCCACCCCGGCa                                                                                                               >  2:164486/1‑228 (MQ=255)                                                                                                                ccGGATGCGACGCTTGAC‑GCGCCTTATCCGGCCTACACCCG‑CTACACACCCCGC‑AGGCCTGATAAGATGCG‑CCAGCATCGCATCAGGCATTGTG‑CCCCAACCGCCGGATCCGGCATACCGa                                                                                                                                                                                                          >  1:205805/1‑121 (MQ=255)                                                                                                                 cGGATGCGACGCTTGAC‑GCGCCTTATCCGGCCTACACCCG‑CTACACACCCCGC‑AGGCCTGATAAGATGCG‑CCAGCATCGCATCAGGCATTGTG‑CCCCAACCGCCGGATCCGGCATACCGAt                                                                                                                                                                                                         <  2:205805/121‑1 (MQ=255)                                                                                                                  ggATGCGACGCTTGAC‑GCGCCTTATCCGGCCTACACCCG‑CTACACACCCCGC‑AGGCCTGATAAGATGCG‑CCAGCATCGCATCAGGCATTCTC‑CTCCAACCGCCGGAACCGGCACACCGCTTAATGCAGCACCGTCACCGCTTCTTCCAGTCGGCTGGCGCGGCGGTTCACCCTCGCCGCCACCTGCGCACACTCTCCCACCAGCCCGGCGTTTTTCTGGGCGACCAg                                                                                              >  2:536138/1‑227 (MQ=255)                                                                                                                                     gcCTTACCCGGCCTACCCCCG‑CTACACACCCCGC‑AGGCCTGATAAGATGCG‑CCAGCCTCGAATGAGGCATTGGG‑CTCCAACCGCCGGATCCGGCATACCGATTAATGCAGTACCGTCACCGCGTCTTCCAGTCGGCTGGCGCGGTGTTTCACCATCGCCGACACCTGCGCACTCTCTTCCACCAGCTCGGCATTTTTCTGGGTGATCAGGTTAAGCTCATCCACTGc                                                                            <  1:409489/227‑1 (MQ=255)                                                                                                                                      ccTTATCCGGCCTACACCCG‑CTACACACCCCGC‑AGGCCTGATAAGATGCG‑CCAGCATCGCATCAGGCATTGTG‑CTCCAACCGCCGGATCCGGCATACCGATTAATGCAGTACCGTCACCGCGTCTTCCAGTCGGCTGGCGCGGTGTTTCACCATCGCCGACACCTGCGCACTCTCTTCCACCAGCTCGGCATTTTTCTGGGTGATCAGGTTAAGCTCATCCACTGCAc                                                                          >  1:487449/1‑228 (MQ=255)                                                                                                                                                ccTACACCCG‑CTACACACCCCGC‑AGGCCTGATAAGATGCG‑CCAGCCTCGCATCAGGCATTGTG‑CTCCAACCGCCGGATCCGGCATACCGATTAATGCAGTACCGTCACCCCGTCTTCCAGTCGGCTGGGCCGGTGTTTCACCATCTCCGCCACCTGCCCACTCCCTCCCACCCACTCGCCATTGTTCCGGTGGATCAGGTTAAGCTCACCCCCCCGACGGGTccccct                                                                >  2:516467/1‑223 (MQ=255)                                                                                                                                                   acccccG‑CTACACTCCCCGC‑AGGCCTGATAAGAGGCG‑CAAGACTCGCATCAGGCTTTGTG‑CTCCAACCGCCGGATCCGGCATACCGATTAATGCAGTACCGTCACCGCGTCTTCCAGTCGGCTGGCGCGGTGTTTCACCATCGCCGACACCTGCGCACTCTCTTCCACCAGCTCGGCATTTTTCTGGGTGATCAGGTTAAGCTCATCCACTGCACGGGTCAGGCTGGa                                                             <  1:232546/225‑1 (MQ=255)                                                                                                                                                            cacacccCCCAC‑GTGCCTGAAAAGCTGCC‑CCAGCATCGCATCAGGCATTGTG‑CCCCAACCGCCGGATCCGGCATACCGATTAATGCAGTACCGTCACCGCGTCTTCCAGTCGGCTGGCGCGGTGTTTCACCATCGCCGACACCTGCGCACTCTCTTCCACCAGCTCGGCATTTTTCTGGGTGATCAGGTTAAGCTCATCCACTGCACGGGTCAGGCTGGAAAGCCCAt                                                     <  1:536138/227‑1 (MQ=255)                                                                                                                                                              ccgcccccccaaGGCCTG‑TAAGAAGGGCCCAGCATCGCATCAGGAATTGTG‑CCCCAACCGCCGGATCCGGCATACCGATTAATGCAGTACCGTCCCCGCGTCTTCCAGTCGGCTGGCGCGGTGTTTCCCCATCGCCGACACCTGCGCACTCTCTTCCACCAGCTCGGCATTTTTCTGGGTGATCAGGTTAAGCTCATCCACTGCACGGGTCAGGCTGGAAAGCCCAt                                                     <  1:555866/216‑1 (MQ=255)                                                                                                                                                                  ccccGCAAGGCCGTATAAAATGCC‑CCAGAACCGCATAAGGCA‑TGTGCCACCATCCGCCGGATCCGGCATACCGATTAATGCAGTACCGTCACCGCGTCTTCCAGTCGGCTGGCGCGGTGTTTCACCATCGCCGACACCTGCGCACTCTCTTCCACCAGCTCGGCATTTTTCTGGGTGATCAGGTTAAGCTCATCCACTGCACGGGTCAGGCTGGAAAGCCCATCGGcc                                                <  1:340499/228‑1 (MQ=255)                                                                                                                                                                  ccccGC‑AGGCCTGATAAGATGCG‑CCAGCATCGCATCAGGCATTGTG‑CTCCAACCGCCGGATCCGGCATACCGATTAATGCAGTACCGTCACCGCGTCTTCCAGTCGGCTGGCGCGGGGTTTCACCATCGCCGACACCTGCGCACTCTCTTCCACCAGCTCGGCATTTTTCTGGGGGATCAGGTTAAGCTCCTCCACTGCCCGGGTCAGGCCGGAAAGCCCATCGGCCt                                               >  1:573284/1‑228 (MQ=255)                                                                                                                                                                      gC‑AGGCCTGATAAGATGCG‑CCAGCATCGCATCAGGCATTGTG‑CTCCAACCGCCGGATCCGGCATACCGATTAATGCAGTACCGTCACCGCGTCTTCCAGTCGGCTGGCGCGGTGTTTCACCATCGCCGCAACCTGCGCCACCTCTTCCACCCACTCGGCATTTTTCTGGGGGATCCGGTTAAGCCCATCCACTCCCCGGTTCAGCCTGTAAACCCCAGCGGCCGGTTc                                           >  2:488414/1‑228 (MQ=255)                                                                                                                                                                      gC‑AGGCCTGATAAGATGCG‑CCAGCATCGCATCAGGCATTGTG‑CTCCAACCGCCGGATCCGGCATACCGATTAATGCAGTACCGTCACCGCGTCTTCCAGTCGGCTGGCGCGGTGTTTCACCATCGCCGACACCTGCGCACTCTCTTCCACCAGCTCGGCATTTTTCTGGGTGATCAGGTTAAGCTCATCCCCTGCACGGGTCAGGCTGGAAAGCCCATCGGCCTTTTc                                           >  1:207271/1‑228 (MQ=255)                                                                                                                                                                      gC‑AGGCCTGATAAGATGCG‑CCAGCATCGCATCAGGCATTGTG‑CTCCAACCGCCGGATCCGGCATACCGATTAATGCAGTACCGTCACCGCGTCTTCCAGTCGGCTGGCGCGGTGTTTCACCATCGCCGACACCTGCGCACTCTCTTCCACCAGCTCGGCATTTTTCTGGGTGATCAGGTTAAGCTCATCCACTCCACGGGTCAGGCTGGAAAGCCCATCGGCCCGTTc                                           >  1:390427/1‑228 (MQ=255)                                                                                                                                                                      gC‑AGGCCTGATAAGATGCG‑CCAGCATCGCATCAGGCATTGTG‑CTCCAACCGCCGGATCCGGCATACCGATTAATGCAGTACCGTCACCGCGTCTTCCAGTCGGCTGGCGCGGTGTTTCACCATCGCCGACACCTGCGCACTCTCTTCCACCAGCTCGGCATTTATCTGGGTGATCAGGTTCAGCTCATCCACTGCACGGGTCAGGCTGGAAAGCCCATCGGCCTCTTc                                           >  1:294720/1‑228 (MQ=255)                                                                                                                                                                      gC‑AGGCCGGATGAGATGCG‑CCAGCCGCGCATCGGGCTTTGGT‑CCCCACCCGCCGGATCCGGCATACCGATTAATGCAGTTCCGTCACCGCGTCTTCCAGTCGGCTGGCGCGGTGTTTCACCATCGCCGACACCTGCGCACTCTCTTCCACCAGCTCGGCATTTTTCTGGGTGATCAGGTTAAGCTCATCCACTGCACGGGTCAGGCTGGAAAGCCCATCGGCCTGTTc                                           <  1:516467/228‑1 (MQ=255)                                                                                                                                                                         aGGCCTGATAAGATGCG‑CCAGCATCGCATCAGGCATTGTG‑CTCCAACCGCCGGATCCGGCATACCGCTTAATGCAGTACCGTCACCGCGTCTTCCAGTCGGCTGGCGCGGTGGTTCACCATCGCCGACACCTGCGCACTCTCTTCCACCAGCTCGGCATTTTTCTGGGGGATCAGGTTAAGCTCATCCACTGCACGGGGCCGGCGGGGAACGCACTCGGCCTGTTccg                                         >  2:373752/1‑227 (MQ=255)                                                                                                                                                                              tGATAAGATGCG‑CCAGCATCGCATCAGGCATTGTG‑CTCCAACCGCCGGATCCGGCATACCGATTAATGCAGTACCGTCACCGCGTCTTCCAGTCGGCTGGCGCGGTGTTTCACCATCGCCGACACCTGCGCACTCTCTTCCACCAGCTCGGCATTTTTCTTGGTGATCAGGTTAAGCTCATCCACTCCACGGGTCAGGCTGGCAAGCCCATCTGCCTGTTCCACCGt                                     >  1:664953/1‑227 (MQ=255)                                                                                                                                                                                     aTGCG‑CCAGCATCGCATCAGGCATTGTG‑CTCCAACCGCCGGATCCGGCATACCGATTAATGCAGTACCGTCACCGCGTCTTCCAGTCGGCTGGCGCGGTGTTTCACCATCGCCGACACCTGCGCACTCTCTTCCACCAGCTCGGCATTTTTCTGGGTGATCAGGGTAACCTCCTCCACTGCACGGGTACGGATGGGAAGCCCATCGCCCTGTCCCCGCGTTGCATGGc                             >  2:587988/1‑228 (MQ=255)                                                                                                                                                                                     aTGCG‑CCAGCATCGCATCAGGCATTGTG‑CTCCAACCGCCGGATCCGGCATACCGATTAATGCAGTACCGTCACCGCGTCTTCCAGTCGACTGGCGCGGTGTTTCACCATCGCCGACACCTGCGCACTCTCTTCCACCAGCTCGCCATTTTTCTGGGTGTTCAGGTTAAGCTCATCCACTGCACGGTCCAGCCGGGCAAGCCCATCGGCCTGTTCCACCGTTGAATgga                             >  1:91546/1‑227 (MQ=255)                                                                                                                                                                                            cagctcccgctcAGGCTTTGTG‑CCCCAACCGCCGGATCCGGCATTCCGATTAATGCAGTACCGGCACCGCGTCTTCCAGTCGGCTGGCGCGGTGTTTCACCATCGCCGACACCTGCGCACTCTCTTCCACCAGCTCGGCATTTTTCTGGGTGATCAGGTTAAGCTCATCCACTGCACGGGTCAGGCTGGAAAGCCCATCGGCCTGTTCCAGCGTTGAATGGCTAATCt                       <  1:373752/218‑1 (MQ=255)                                                                                                                                                                                                              tgtg‑CTCCAACCGCCGGATCCGGCATACCGATTAATGCAGTACCGTCACCGCGTCTTCCAGTCGGCTGGCGCGGTGTTTCACCATCCCCGCCACCTGCGCAACCTCTTCACCCCGCTCGGCATTTTTCTGGGTGCTCAGGTTAAGCCCATCCCCTGACCCGGTCAGGCTGGACAGCCACTCGGCCGTTTCCAACGTTGAATGGCTCATCTGGGCGGTCAACCggggg      >  2:438818/1‑225 (MQ=255)                                                                                                                                                                                                              tgtg‑CCCCACCCGCCGGATCCGGCGTACGGTTTAATGCCGTACCGTCACCGCGTCTTCCAGTCGGCTGGCGCGGTGTTTCACCATCGCCGACACCTGCGCACTCTCTTCCACCAGCTCGGCATTTTTCTGGGTGATCAGGTTAAGCTCATCCACTGCACGGGTCAGGCTGGAAAGCCCATCGGCCTGTTCCAGCGTTGAATGGCTAATCTGGGCGATCAACTGGGTGa     <  2:22323/228‑1 (MQ=255)                                                                                                                                                                                                               gtg‑CCCCACCCGCCGGATCCGGCATGCCGAGTAAGGCAGTACCGTCACCGCGTCTTCCAGTCGGCTGGCGCGGTGTTTCACCATCGCCGACACCTGCGCAATCTCTTCCTCCAGCTCGGCATTTTTCTGGGTGATCAGGTTAAGCTCATCCACTGCACGGGTCAGGCTGGAAAGCCCATCGGCCTGTTCCATCGTTGAATGGCTAATCTGGGCGATCAACTGGGTGa     <  1:438818/227‑1 (MQ=255)                                                                                                                                                                                                                   cTCCAACCGCCGGATCCGGCATACCGATTAATGCAGTACCGTCACCGCGTCTTCCAGTCGGCTGGCGCGGTGTTTCACCATCGCCGACACCTGCGCACTCTCTTCCACCAGCTCGGCATTTTTCTGGGTGATCAGGTTAAGCTCATCCACTGCACGGGTCAGCCTGGCAAGCCCATCGGCCTGTTCCAGCGTTGAATGGATAATCTGGGCGACCACCTGGGTGACGt  >  1:613835/1‑227 (MQ=255)                                                                                                                                                                                                                    |                                                                                                                                                                                                                                  ATATCAGTGATGCACAAATAAAAAAGATCATTGCGGTGATCGACCGCGCCGCTTTTGATATTACGCAACTGGATTAATCGCC‑GCATCCGCCAGTGGCGCGGTGCAATT‑GCCGGATGCGACGCTTGAC‑GCGCCTTATCCGGCCTACACCCG‑CTACACACCCCGC‑AGGCCTGATAAGATGCG‑CCAGCATCGCATCAGGCATTGTG‑CTCCAACCGCCGGATCCGGCATACCGATTAATGCAGTACCGTCACCGCGTCTTCCAGTCGGCTGGCGCGGTGTTTCACCATCGCCGACACCTGCGCACTCTCTTCCACCAGCTCGGCATTTTTCTGGGTGATCAGGTTAAGCTCATCCACTGCACGGGTCAGGCTGGAAAGCCCATCGGCCTGTTCCAGCGTTGAATGGCTAATCTGGGCGATCAACTGGGTGACGT  >  NC_000913/3217326‑3217755

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 12 ≤ ATCG/ATCG < 13 ≤ ATCG/ATCG < 24 ≤ ATCG/ATCG < 38 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑