Predicted mutation
evidence	seq id	position	mutation	freq	annotation	gene	description
RA	CP009273	1,597,224	T→A	12.2%	V493D (GTC→GAC)	lsrA →	autoinducer 2 import ATP‑binding protein

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	CP009273	1,597,224	0	T	A	12.2%	102.0 / 4.9	40	V493D (GTC→GAC)	lsrA	autoinducer 2 import ATP‑binding protein
Reads supporting (aligned to +/- strand):  ref base T (18/16);  new base A (3/2);  total (21/19)
Fisher's exact test for biased strand distribution p-value = 1.00e+00
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 9.34e-01

ACCAGCAAAAAATCCTCATTGCCAAATGCTTGGAAGCTTCGCCGCAAGTATTGATTGTCGATGAGCCGACGCGCGGCGTGGATGTCTCGGCCCGTAATGATATCTACCAGCTGTTGCGCAGCATCGCCGCACAAAATGTGGCTGTGCTGCTTATCTCCTCCGACCTGGAAGAGATCGAACTGATGGCAGATCGTGTGTATGTGATGCATCAGGGCGAAATTACCCACTCTGCACTGACCGAGCGCGATATTAATGTCGAGACTATTATGCGCGTTGCCTTCGGCGATAGTCAGCGTCAGGAGGCGTCATGCTGAAGTTTATTCAGAACAACCGTGAAATCACGGCACTGCTGGCGGTGGTGCTGCTGTTTGTATTACCCGGTTTTCTCGACCGCCAGTATTTAAGTGTGCAAACGCTGACCATGGTTTATAGCAGCGCGCAAATCCTGATCCTGCTGGCAATGGGCGCGACGCTGGTAATGCTTACGCGCAATATTGATGTTTCAGTGGGTTCGATTACCGGA  >  CP009273/1596969‑1597491                                                                                                                                                                                                                                                                |                                                                                                                                                                                                                                                                            aCCAGCAAAAAATCCTCATTGCCAAATGCTTGGAAGCTTCGCCGCAAGTATTGATTGTCGATGAGCCGACGCGCGGCGTGGATGTCTCGGCCCGTAATGATATCTACCAGCTGTTGCGCAGCATCGCCGCACAAAATGTGGCTGTGCTGCTTATCTCCTCCGACCTGGAAGAGATCGAACTGATGGCAGCTCGAGTGTATGTGATGCATCAGGACGAAATTACCCACTCTGCACTGACCGAGCGCGATATTAATGACGAGATTNTTATGCCCGt                                                                                                                                                                                                                                                           >  2:76156/1‑274 (MQ=255)     gCAAAATATCCTCATTGCCAAATGCTTGGAAGCTTCGCCGTAAGTATTGATTGTCGATGAGCCGACGCGCGGCGTGGATGTCTCGGCCCGTAATGATATCTACCAGCTGTTGCGCAGCATCGCCGCACAAAATGTGGCTGTGCTGCTTATCTCCTCCGACCTGGAAGAGATCGAACTGATGGCAGATCGTGTGTATGTGATGCATCAGGGCGAAATTACCCACTCTGCACTGACCGAGCGCGATATTAATGACGAGACTATTATGCGCGTTGcc                                                                                                                                                                                                                                                       <  1:76156/274‑1 (MQ=255)                                                           cGATGAGCCGACGCGCGGCGTGGATGTCTCGGCCCGTAATGATATCTACCAGCTGTTGCGCAGCATCGCCGCACAAAATGTGGCTGTGCTGCTTATCTCCTCCGACCTGGAAGAGATCGAACTGATGGCAGATCGTGTGTATGTGATGCATCAGGGCGAAATTACCCACTCTGCACTTACCGACCGCGATATTAATGTCGAGACTATTATGCGCGTTGCCTTCGTCGa                                                                                                                                                                                                                                               >  1:729626/1‑228 (MQ=255)                                                                         gcggcgTGGATGTCTCGGCCCGTAATGATANCTACCAGCTGGTGCGCAGCATCGCCGCTCAAAATGTGGCTGTGCTGCTTATCTCCTCCGACCGGGAAGAGATCGAACTGATGGCAGATCGTGTGTATGTGATGCATCAGGGCGAAATTACCCACTCTGCACTGACCGAGCGCGATATTAATGTCgaga                                                                                                                                                                                                                                                                        <  1:742664/189‑1 (MQ=255)                                                                                                   gATATCTACCAGCTGTTGCGCAGCATCGCCTCACAAAATGTGGCTGTGCTGCTTATCTCCTCCGACCTGGAAGAGATCGAACTGATGGCAGATCGTGTGTATGTGATGCATCAGGGCGAAATTACCCACTCTGCACTGACCGAGCGCGATATTAATGTCGAGACTATTATGCGCGTTGCCTTCGGCGATAGTCAGCGTCAGGAGGCGt                                                                                                                                                                                                                           <  1:432304/208‑1 (MQ=255)                                                                                                         tACCAGCTGTTGCGCAGCATCGCCGCACAAAATGTGGCTGTGCTGCTTATCTCCTCCGACCTGGAAGAGATCGAACTGATGGCAGATCGTGTGTATGTGATGCATCAGGGCGAAATTACCCACTCTGCACTGACCGAGCGCGATATTAATGTCGAGACTATTATGCGCGTTGCCTTCGGCGATAGTCAGCGTCAGGAGGCGTCATGCTGAAGCTTATTCAGAACAACCGTGAAATCACGGCACAGCTGGCGGTGGTGCGGCGGTTTGTATTAcc                                                                                                                                                   >  1:341946/1‑274 (MQ=255)                                                                                                           ccAGCTTTTTCGCAGCATCGCCGCACAAAATGTGGCTGTGCTGCTTATCTCCTCCGACCTGGAAGAGATCGAACTGATGGCAGATCGTGTGTATGTGATGCATCAGGGCGAAATTACCCACTCTGCACTGACCGAGCGCGATATTAATGTCGAGACTATTATGCGCGTTGCCTTCGGCGATAGTCAGCGTCAGGAGGCGTCATGCTGAAGTTTATTCAGAACAACCGTGAAATCACGGCACTGCTGGCGGTGGTGCTGCTGTTTGTATTACCCg                                                                                                                                                 <  1:661777/274‑1 (MQ=255)                                                                                                               cTGTTGCGCAGCATCGCCGCACAAAATGTGGCTGTGCTGCTTATCTCCTCCGACCTGGAAGAGATCGAACTGATGGCAGATCGTGTGTATGTGATGCATCAGGGCGAAATTACCCACTCTGCACTGACCGAGCGCGATATTAATGACGAGACTATTATGCGCGTTGCCTTCGGCGATAGTCAGCGt                                                                                                                                                                                                                                     >  1:405461/1‑186 (MQ=255)                                                                                                                   tGCGCAGCATCGCCGCACAAAATGTGGCTGTGCTGCTTATCTCCTCCGACCTGGAAGAGATCGAACTGATGGCAGATCGTGTGTATGTGATGCATCAGGGCGAAATTACCCACTCTGCACTGACCGAGCGCGATATTAATGACGAGACTATTATGCGCGTTGCCTTCGGCGATAGTCAGCGTCagg                                                                                                                                                                                                                                 <  2:405456/186‑1 (MQ=255)                                                                                                                                                    tgctTATCTCCTCCGAACTGTAAGAGATCGAACGGATGGCAGATCGTGTGTATGTGATGCATCAGGGCGAAATTACCCACTCTGCACTGACCGAGCGCGATATTAATGGCGAGACGATTATGCGCGTTGCCTTCGGCGATAGTCAGCGTCAGGAGGCGTCATGCTGAAGTTTATTCAGAACAACCGTGAAATCACGGCACTGCTGGCGGTGGTGCTGCTGTTTGTATTACCCGGTTTTCTCGACCGCCAGTATTTAAGTGTGCAAACGCTGACCa                                                                                                       <  1:112412/275‑1 (MQ=255)                                                                                                                                                                ccGACCTGGAAGAGATCGAACTGATGGCAGATCGTGTGTATGTGATGCATCAGGGCGAAATTACCCACTCTGCACTGACCGAGCGCGATATTAATGTCGAGACTATTATGCGCGTTGCCTTCGGCGAt                                                                                                                                                                                                                                              >  1:42233/1‑128 (MQ=255)                                                                                                                                                                    ccTGGAAGAGATCGAACTGATGGCAGATCGTGTGTATGTGATGCATCAGGGCGAAATTACCCACTCTGCACTGACCGAGCGCGATATTAATGTCGAGACTATTATGCGCGTTGCCTTCGGCGATAGTc                                                                                                                                                                                                                                          <  2:42233/128‑1 (MQ=255)                                                                                                                                                                                                     gtATGTGATGCATCAGGGCGAAATTACCCACTCTGCACTGACCGAGCGCGATATTAATGt                                                                                                                                                                                                                                                                             <  2:788484/60‑1 (MQ=255)                                                                                                                                                                                                     gtATGTGATGCATCAGGGCGAAATTACCCACTCTGCACTGACCGAGCGCGATATTAATGTCGAGACTATTATGCGCGTTGCCTTCGGCGATAGTCAGCGTCAGGAGGCGTCATGCTGAAGTTTATTCAGAACAACCGTGAAATCACGGCACTGCTGGCGGTGGTGCTGCTGTTTGTATTAACCGGTTTTCTCGACCGCCAGTATTTAAGTGTGCAAACGCTGACCATGGTTTATagcag                                                                                          <  1:15690/239‑1 (MQ=255)                                                                                                                                                                                                      aaggggcagCATCAGGGCGAAATTACCCACTCTGCACTGACCGAGCGCGATATTAATGTAGAGACTATTATGCGCGTTGCCTACGGCGATAGTCAGCGTCAGGAGGCGTCATGCTGAAGTTTATTCAGAACAACCGTTAAAGCACGGACCTGCTGGCGGTGGTGCTGCTGTTTGTATTACCCGGTATTCTCGACCGCCAGTATTTAAGTGTGCAAACGCTGACCATGGTTTATAGCAGCGCGCAAATCCTGATCCTGCTGGCAATGGGCGCGAc                                                      <  1:124705/266‑1 (MQ=255)                                                                                                                                                                                                            aTGCATCAGGGCGAAATTACCCACTCTGCACTGACCGAGCGCGATATTAATGTCGAGACTATTATTCGCGTTGCCTTCGGCGATAGTCAGCGTCAGGAGGCGTCATGCTGAAGTTTATTCAGAACAACCGTGAAATCACGGCACTGCTGGCGGTGGTGCTGCTGTTTGTATTACCCGGTTTTCTCGACCGCCAGTATTTAAGTGTGCAAACGCTGACCATGGTTTATAGCAGCGCGCAAATCCCGATCCGGCTTGCAATGGCCGCGAGGCTgttg                                               >  2:703577/1‑272 (MQ=255)                                                                                                                                                                                                            aTGCATCAGGGCGAAATTACCCACTCTGCACTGACCGAGCGCGATATTAATGTCGAGACTATTATGCGCGTTGCCTTCGGCGATAGTCAGCGTCAGGAGGCGTCATGCTGAAGTTTATTCAGAACAACCGTGAAATCACGGCACTGCTGGCGGTGGTGCTGCTGTTTGTATTACCCGGTTTTCTCGACCGCCAGTATTTAAGTGTGCAAACGCTg                                                                                                           >  1:308339/1‑215 (MQ=255)                                                                                                                                                                                                             tGCATCAGGGCGAAATTACCCACTCTGCACTGACCGAGCGCGATATTAATGTCGAGACTATTATGCGCGTTg                                                                                                                                                                                                                                                         >  2:460873/1‑72 (MQ=255)                                                                                                                                                                                                                aTCAGGGCGAAATTACCCACTCTGCACTGACCGAGCGCGATATTAATGTCGAGACTATTATGCGCGTTg                                                                                                                                                                                                                                                         >  2:285530/1‑69 (MQ=255)                                                                                                                                                                                                                aTCAGGGCGAAATTACCCACTCTGCACTGACCGAGCGCGATATTAATGTCGAGACTATTATGCGCGTTGCCTTCGGCTATAGTCAGCGTAAGGGGGCGTCATGCTGAAGTTTATTCAGAACAACCGTGAAATCACGGCACTGCTGGCGGTGGTGCTGCTGTTTGTATTACCCGGTTTTCTCGACCGCCAGTATTTAAGTGTGCACACGCTGACCATGGTTTATAGCAGCGCGCAAATCCTGATCCTGCTTGCACTGTGCGGGCCGCTGGtcttgt                                           >  2:228606/1‑270 (MQ=255)                                                                                                                                                                                                                aTCAGGGCGAAATTACCCACTCTGCACTGACCGAGCGCGATATTAATGTCGAGACTATTATGCGCGTTGCCTTCGGCGATAGTCAGCGTCAGGAGGCGTCATGCTGAAGTTTATTCAGAACAACCGTGAAATCACGGCACTGCTGGCGGTGGTGCTGCTGTTTGTATTACCCGGTTTTCTCGACCGCCAGTATTTAAGTGTGCAAACGCTGACCa                                                                                                       <  2:308335/215‑1 (MQ=255)                                                                                                                                                                                                                aTCAGGGCGAAATTACACACTCTGCACTGACCGAGCGCGATATTAATGTCGAGACTATTATGCGCGTTGCCTTCGGCGATAGTCAGCGTCAGTAGGCGTCATGCTGAAGTTTATTCAGAACAACCGTGAAATCACGGCACTGCTGGCGATGGTGCTGCTGTTTGTATTACCCGGTTTTCTCGACCGACAGTCTTTAAGTGTGCAAACGCTGCCCATGGTTTATAGCAGCGCGCAAATCCTGCTACTGCTGGCAGTCGGCGATACGCTGGTAAGGc                                           >  2:248726/1‑275 (MQ=255)                                                                                                                                                                                                                 tCAGGGCGAAATTACCCACTCTGCACTGACCGAGCGCGATATTAATGTCGAGACTATTATGCGCGTTGCCtt                                                                                                                                                                                                                                                     <  1:460878/72‑1 (MQ=255)                                                                                                                                                                                                                    gggCGAAATTACCCACTCTGCACTGACCGAGCGCGATATTAATGTCGAGACTATTATGCGCGTTGCCtt                                                                                                                                                                                                                                                     <  1:285534/69‑1 (MQ=255)                                                                                                                                                                                                                          aaTTACCCACTCTGCACTGACCGAGCGCGATATTAATGTCGAGAGTATGATCTGCGTTGCCTCCGGCGATAGGCAGCGTCAGGAGGCGTCATGCTGATGTTTAGTCAGCACAATCGTGAAATCACGGCACTGCTGGCGGTGGTGCTGCAGTTTGTATTACCCGGTTTTCTCGACCGGCAGGATTTAGGTGTGCAAACGCTGACCCGGGGTTATAGCAGCGCGCACATCCTGATCATGATGTCAGGGGGAGTGCGGCGGGTAATGccggactaggc                                 >  2:124705/1‑265 (MQ=255)                                                                                                                                                                                                                              tcccACTCTGCACGTACCGAGCGCGATATTTTTGTGGAGACTATTATGCGCGTTGCCTTCGGCGATAGTCAGCGTCAGGAGGCGTCATGCTGAAGTTTATTCATAACAACCGTGAAATCACGGCACTGCTGGCGGTGGTGCTGCTGTTTGTATTACCCGGTTTTCTCGACCGCCAGTATTTAAGTGTGCAAACGCTGACCATGGTTTATAGCAGCGCGCAAATCCTGATCCTGCTGGCACTGGGCGCGACGCTGGTAATGCTTACGCGCAatat                              <  1:500260/273‑1 (MQ=255)                                                                                                                                                                                                                                             aCCGAGCGCGATATTAATGTCGAGACTATTATGCGCGTTGCCTTCGGCGa                                                                                                                                                                                                                                               >  1:119745/1‑50 (MQ=255)                                                                                                                                                                                                                                             aCCGAGCGCGATATTAATGTCGAGACTATTATGCGCGTTGCCTTCGGCGATAGTCAGCGTCagga                                                                                                                                                                                                                                >  1:169934/1‑65 (MQ=255)                                                                                                                                                                                                                                             aCCGAGCGCGATATTAATGTCGAGACTATTATGCGCGTTGCCTTCGGCGATAGTCAGCGTCAGGAGGCGTCATGCTGAAGTTTATTCAGAACAACCGTGAAATCACGGCACTGCTGGCGGTGGTGCTGCTGTTTGTATTACCCGGTTTTCTCGa                                                                                                                                       >  2:163031/1‑154 (MQ=255)                                                                                                                                                                                                                                             aCCGAGCGCGATATTAATGTCGAGACTATTATGCGCGTTGCCTTCGGCGATAGTCAGCGTCAGGAGGCGTCATGCTGAAGTTTATTCAGAACAACCGTGAAATCACGGCACTGCTGGCGGTGGTGCTGCTGTTTGTATTACCCGGTTTTCTCGACCGCCAGTATTTAAGTGTGCAAAGGCTGACCATGGTTTATAGCAGCGCGCAAATCCTGATCCTGCTGGCAATGGGCGCGACGCTGGTAATGCTTACGCGCAATATTGATGTTTCAGTGGGt              >  1:455428/1‑275 (MQ=255)                                                                                                                                                                                                                                             aCCGAGCGCGATATTAATGTCGAGACTATTATGCGCGTTGCCTTCGGCGATAGTCAGCGTCAGGAGGCGTCATGCTGAAGTTTATTCAGAACAACCGTGAAATCACGGCACTGCTGGCGGTGGTGCTGCTGTTTGTATTACCCGGTTTTCTCGACCGCCAGTATTTAAGTGTGCAAACGCTGACCATGGTTTATAGCAGCGCGCAAATCCTTATCCTGCTGGCAATGGGCGCGACGCTGGTCATGCTTACGCGCAATATTGCTTTTTTAGTgggg              >  2:4241/1‑274 (MQ=255)                                                                                                                                                                                                                                             aCCGAGCGCGATATTAATGTCGAGACTATTATGCGCGTTGCCTTCGGCGATAGTCAGCGTCAGGAGGCGTCATGCTGAAGTTTATTCAGAACAACCGTGAAATCACGGCACTGCTGGCGGTGGTGCTGCTGTTTGTATTACCCGGTTTTCTCGACCGCCAGTATTGAAGTGTGCAAACGCTGACAATGGTTTATAGCAGCGCGCAAATCCTGATCCTGCTGGCAATGGGCGCGACGCTGGTAATGCTTACGCGCAATATTGATGTTTCAGTg                 >  1:672723/1‑272 (MQ=255)                                                                                                                                                                                                                                             aCCGAGCGCGATATTAATGTCCAGACTATTATGCGCGTTGCCTTCGGCGATAGTCAGCGTCAGGAGGCGTCATGCTGAAGTTTATTCAGAACAACCGTGAAATCACGGCAc                                                                                                                                                                                  >  1:569906/1‑111 (MQ=255)                                                                                                                                                                                                                                             aCCGAGCGCGATATTAATGACGAGACTATTATGCGCGTTGCCTTCGGCGATAGTCAGCGTCAGGAGGCGTCATGCTGAAGTTTATTCAGAACAACCGTGAAATCACGGCACTGCTGGCGGTGGTGCTGCTGTTTGTATTACCCGGTTTTCTCGACCGCCAGTATTTAAGTGTGCAAACGCTGACCATGGTTTATAGCAGCGCGCAAATCCTGATCCTGCTGGCAATGGGCGCGACGCTGGTAATGCTTACGCGCAATATTGATGTTTCAGTGGGt              >  1:655848/1‑275 (MQ=255)                                                                                                                                                                                                                                                 aGCGCGATATTAATGTCGAGACTATTATGCGCGTTGCCTTCGGCGATAGt                                                                                                                                                                                                                                           <  2:119745/50‑1 (MQ=255)                                                                                                                                                                                                                                                 aGCGCGATATTAATGTCGAGACTATTATGCGCGTTGCCTTCGGCGATAGTCAGCGTCAGGAGGCg                                                                                                                                                                                                                            <  2:169934/65‑1 (MQ=255)                                                                                                                                                                                                                                                 aGCGCGATATTAATGTCGAGACTATTATGCGCGTTGCCTTCGGCGATAGTCAGCGTCAGGAGGCGTCATGCTGAAGTTTATTCAGAACAACCGTGAAATCACGGCActgct                                                                                                                                                                              <  2:569901/111‑1 (MQ=255)                                                                                                                                                                                                                                                 aGCGCGATATTAATGTCGAGACTATTATGCGCGTTGCCTTCGGCGATAGTCAGCGTCAGGAGGCGTCATGCTGAAGTTTATTCAGAACAACCGTGAAATCACGGCACTGCTGGCGGTGGTGCTGCTGTTTGTATTACCCGGTTTTCTCGACCGc                                                                                                                                   <  1:163031/154‑1 (MQ=255)                                                                                                                                                                                                                                                       atatTAATGTCGAGACTATTATGCGCGTTGCCTTCGGCGATAGTCAGCGTCAGGAGGCGTCa                                                                                                                                                                                                                         >  1:647528/1‑62 (MQ=255)                                                                                                                                                                                                                                                          ttAATGTCGAGCATATTATGGGCTTTGCCTTCGGCGATAGTCAGCGTCCGGAGGCGTTATGGTGAATTTTATTCAGAACAACCGTGACATCACGGCACTGCTGGCGGTGGTGGTGCTGTTTGTATTACCCGGTTTTCTCGACCGCCAGTATTTAAGTGTGCAAACGCTGACCATGGTTTATAGCAGCGCGCAAATCCTGATCCTGCTGGCAATGGGCGCGACGCTGGTAATGCTTACGCGCAATATTGATGTTTCAGTGGGTTCGATTACCGGa  <  2:341942/274‑1 (MQ=255)                                                                                                                                                                                                                                                           tAATGTCGAGACTATTATGCGCGTTGCCTTCGGCGATAGTCAGCGTCAGGAGGCGTCATGCt                                                                                                                                                                                                                     <  2:647521/62‑1 (MQ=255)                                                                                                                                                                                                                                                                |                                                                                                                                                                                                                                                                            ACCAGCAAAAAATCCTCATTGCCAAATGCTTGGAAGCTTCGCCGCAAGTATTGATTGTCGATGAGCCGACGCGCGGCGTGGATGTCTCGGCCCGTAATGATATCTACCAGCTGTTGCGCAGCATCGCCGCACAAAATGTGGCTGTGCTGCTTATCTCCTCCGACCTGGAAGAGATCGAACTGATGGCAGATCGTGTGTATGTGATGCATCAGGGCGAAATTACCCACTCTGCACTGACCGAGCGCGATATTAATGTCGAGACTATTATGCGCGTTGCCTTCGGCGATAGTCAGCGTCAGGAGGCGTCATGCTGAAGTTTATTCAGAACAACCGTGAAATCACGGCACTGCTGGCGGTGGTGCTGCTGTTTGTATTACCCGGTTTTCTCGACCGCCAGTATTTAAGTGTGCAAACGCTGACCATGGTTTATAGCAGCGCGCAAATCCTGATCCTGCTGGCAATGGGCGCGACGCTGGTAATGCTTACGCGCAATATTGATGTTTCAGTGGGTTCGATTACCGGA  >  CP009273/1596969‑1597491

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 9 ≤ ATCG/ATCG < 17 ≤ ATCG/ATCG < 34 ≤ ATCG/ATCG < 38 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑