Predicted mutation
evidence	seq id	position	mutation	freq	annotation	gene	description
RA	NC_002947	5,041,249	T→A	6.8%	intergenic (+227/‑435)	PP_5680 → / → PP_4447	Cro/CI family transcriptional regulator/hypothetical protein

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NC_002947	5,041,249	0	T	A	6.8%	173.5 / 2.3	59	intergenic (+227/‑435)	PP_5680/PP_4447	Cro/CI family transcriptional regulator/hypothetical protein
Reads supporting (aligned to +/- strand):  ref base T (29/26);  new base A (2/2);  total (31/28)
Fisher's exact test for biased strand distribution p-value = 1.00e+00
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 7.42e-01

TCCACAGAGGGTTAGGGATAGCCTTAAGGCGTAATTGTCTGATACCAACACCTCTGCGATGAGGACATGACCTCTTCATCGGCGCGCCTTAAGCCCGCCGAGAAGAGCCAGAGACCCCGAGCAAGACCCCTAACCGCCTTATGGCGGTTTCTCTGCCTCCCAGTCTGCTGCGAAGGCCGATAGCCGA‑GTCCAACCAATTCTATTTTTCGACCTGGCCTGACCGCAGTAGAGCGTGTGCTATCAGAGAAAAGTGGTATCAATATCAGCCCCCCACCGA  >  NC_002947/5041111‑5041387                                                                                                                                           |                                                                                                                                            tCCACAGAGGGTTAGGGATAGCCTTAAGGCGTAATTGTCTGATACCAACACCTCTGCGATGAGGACATGACCTCTTCATCGGCGCGCCTTAAGCCCGCCGAGAAGAGCCAGAGACCCCGAGCAAGACCCCTAACCGCCTTATGGCGGtt                                                                                                                                   >  2:6630/1‑149 (MQ=255)   cacaGAGGGTTAGGGATAGCCTTAAGGCGTAATTGTCTGATACCAACACCTCTGCGATGAGGACATGACCTCTTCATCGGCGCGCCTTAAGCCCGCCGAGAAGAGCCAGAGACCCCGAGCAAGACCCCTAACCGCCTTATGGCGGTTtc                                                                                                                                 >  2:296975/1‑149 (MQ=255)    acaGAGGGTTAGGGATAGCCTTAAGGCGTAATTGTCTGATACCAACACCTCTGCGACGAGGACATGACCTCTTCATCGGCGCGCCTTAAGCCCGCCGAGAAGAGCCAGAGACCCCGAGCAAGACCCCTAACCGCCTTATGGc                                                                                                                                       >  2:88350/1‑142 (MQ=255)    acaGAGGGTTAGGGATAGCCTTAAGGCGTAATTGTCTGATACCAACACCTCTGCGACGAGGACATGACCTCTTCATCGGCGCGCCTTAAGCCCGCCGAGAAGAGCCAGAGACCCCGAGCAAGACCCCTAACCGCCTTATGGc                                                                                                                                       <  1:88350/142‑1 (MQ=255)      agagGGTTAGGGATAGCCTTAAGGCGTAATTGTCTGATACCAACACCTCTGCGATGAGGACATGACCTCTTCATCGGCGCGCCTTAAGCCCGCCGAGAAGAGCCAGAGACCCCGAGCAAGACCCCTAACCGCCTTATGGCGGTTTctct                                                                                                                              <  7:300225/149‑1 (MQ=255)           gTTAGGGATAGCCTTAAGGCGTAATTGTCTGATACCAACACCTCTGCGATGAGGACATGACCTCTTCATCGGCGCGCCTTAAGCCCGCCGAGAAGAGCCAGAGACCCCGAGCAAGACCCCTAACCGCCATAAGGCGGttag                                                                                                                                 >  8:86993/1‑139 (MQ=255)           gTTAGGGATAGCCTTAAGGCGTAATTGTCTGATACCAACACCTCTGCGATGAGGACATGACCTCTTCATCGGCGCGCCTTAAGCCCGCCGAGAAGAGCCAGAGACCCCGAGCAAGACCCCTAACCGCCATAAGGCGGttag                                                                                                                                 <  7:86993/141‑3 (MQ=255)            ttAGGGATAGCCTTAAGGCGTAATTGTCTGATACCAACACCTCTGCGATGAGGACATGACCTCTTCATCGGCGCGCCTTAAGCCCGCCGAGAAGAGCCAGAGACCCCGAGCAAGACCCCTAACCGCCATAAGGCGGttagg                                                                                                                                >  1:246339/1‑138 (MQ=255)            ttAGGGATAGCCTTAAGGCGTAATTGTCTGATACCAACACCTCTGCGATGAGGACATGACCTCTTCATCGGCGCGCCTTAAGCCCGCCGAGAAGAGCCAGAGACCCCGAGCAAGACCCCTAACCGCCATAAGGCGGttagg                                                                                                                                <  2:246339/141‑4 (MQ=255)                ggATAGCCTTAAGGCGTAATTGTCTGATACCAACACCTCTGCGATGAGGACATGACCTCTTCATCGGCGCGCCTTAAGCCCGCCGAGAAGAGCCAGAGACCCCGAGCAAGACCCCTAACCGCCTTATGGCGGTTTCTCTGCCTCCCAGt                                                                                                                    >  2:297382/1‑149 (MQ=255)                 gATAGCCTTAAGGCGTAATTGTCTGATACCAACACCTCTGCGATGAGGACATGACCTCTTCATCGGCGCGCCTTGAGCCCGCCGAGAAGAGCCAGAGACCCCGAGCAAGACCCCTAACCGCCTTATGGCGGTTtctc                                                                                                                               >  4:279441/1‑137 (MQ=255)                 gATAGCCTTAAGGCGTAATTGTCTGATACCAACACCTCTGCGATGAGGACATGACCTCTTCATCGGCGCGCCTTGAGCCCGCCGAGAAGAGCCAGAGACCCCGAGCAAGACCCCTAACCGCCTTATGGCGGTTtctc                                                                                                                               <  3:279441/137‑1 (MQ=255)                       cTTAAGGCGTAATTGTCTGATACCAACACCTCTGCGATGAGGGCATGACCTCTTCATCGGCGCGCCTTAAGCCCGCCGAGAAGAGCCAGAGACCCCGAGCAAGACCCCTAACCGCCTTATGGCGGTTTCTCTGCCTCCCAGTctgct                                                                                                               <  3:342499/147‑1 (MQ=255)                       cTTAAGGCGTAATTGTCTGATACCAACACCTCTGCGATGAGGGCATGACCTCTTCATCGGCGCGCCTTAAGCCCGCCGAGAAGAGCCAGAGACCCCGAGCAAGACCCCTAACCGCCTTATGGCGGTTTCTCTGCCTCCCAGTctgct                                                                                                               >  4:342499/1‑147 (MQ=255)                       cTTAAGGCGTAATTGTCTGATACCAACACCTCTGCGATGAGGACATGACCTCTTCATCGGCGCGCCTTAAGCCCGCCGAGAAGAGCCAGAGACCCCGAGCAAGACCCCTAACCGCCTTATGGCGGTTTCTCTGCCTCCCAGTCtgctgc                                                                                                             >  3:219692/1‑149 (MQ=255)                        ttAAGGCGTAATTGTCTGATACCAACACCTCTGCGATGAGGACATGACCTCTTCATCGGCGCGCCTTAAGCCCGCCGAGAAGAGCCAGAGACCCCGAGCAAGACCCCTAACCGCCTTATGGCgg                                                                                                                                     <  5:298896/124‑1 (MQ=255)                        ttAAGGCGTAATTGTCTGATACCAACACCTCTGCGATGAGGACATGACCTCTTCATCGGCGCGCCTTAAGCCCGCCGAGAAGAGCCAGAGACCCCGAGCAAGACCCCTAACCGCCTTATGGCgg                                                                                                                                     >  6:298896/1‑124 (MQ=255)                                      tCTGATACCAACACCTCTGCGATGAGGACATGACCTCTTCATCGGCGCGCCTTAAGCCCGCCGAGAAGAGCCAGAGACCCCGAGCAAGACCCCTAACCGCCTTATGGCGGTTTCTCTGCCTCCCAGTCTGCTGCGAAGGCCGATAGcc                                                                                               >  2:258950/1‑148 (MQ=255)                                        tGATACCAACACCTCTGCGATGAGGACATGACCTCTTCATCGGCGCGCCTTAAGCCCGCCGAGAAGAGCCAGAGACCCCGAGCAAGACCCCTAACCGCCTTATGGCGGTTTCTCTGcc                                                                                                                           <  5:300844/118‑1 (MQ=255)                                        tGATACCAACACCTCTGCGATGAGGACATGACCTCTTCATCGGCGCGCCTTAAGCCCGCCGAGAAGAGCCAGAGACCCCGAGCAAGACCCCTAACCGCCTTATGGCGGTTTCTCTGcc                                                                                                                           >  6:300844/1‑118 (MQ=255)                                             ccAACACCTCTGCGATGAGGACATGACCTCTTCATCGGCGCGCCTTAAGCCCGCCGAGCAGAGCCAGAGACCCCGAGCAAGACCCCTAACCGCCTTATGGCGGTTTCTCTGCCTCCCAGTCTGCTGCGAAGGCCGATAGCCGA‑GTccaa                                                                                      >  5:258776/1‑149 (MQ=255)                                             ccAACACCTCTGCGATGAGGACATGACCTCTTCATCGGCGCGCCTTAAGCCCGCCGAGAAGAGCCAGAGACCCCGAGCAAGACCCCTAACCGCCTTATGGCGGTTTCTCTGCCTCCCAGTCTGCTGCGAAGGCCGATAGCCGA‑GTccaa                                                                                      >  2:81751/1‑149 (MQ=255)                                              cAACACCTCTGCGATGAGGACATGACCTCTTCATCGGCGCGTCTTAAGCCCGCCGAGAAGAGCCAGAGACCCCGAGCAAGACCCCTAACCGCCTTATGGCGGTTTCTCTGCCTCCCAGTCTGCTGCGAAGGCCGATAGCCGA‑GTccaac                                                                                     <  1:297382/149‑1 (MQ=255)                                              cAACACCTCTGCGATGAGGACATGACCTCTTCATCGGCGCGCCTTAAGCCCGCCGAGAAGAGCCAGAGACCCCGAGCAAGACCCCTAACCGCCTTATGGCGGTTTCTCTGCCTCCCAGTCTGCTGCGAAGGCCGATAGCCGA‑GTccaac                                                                                     >  6:80070/1‑149 (MQ=255)                                                    ctctGCGATGAGGACATGACCTCTTCATCGGCGCGCCTTAAGCCCGCCGAGAAGAGCCAGAGACCCCGAGCAAGACCCCTAACCGCCTTATGGCGGTTTCTCTGCCTcc                                                                                                                        >  2:289188/1‑109 (MQ=255)                                                    ctctGCGATGAGGACATGACCTCTTCATCGGCGCGCCTTAAGCCCGCCGAGAAGAGCCAGAGACCCCGAGCAAGACCCCTAACCGCCTTATGGCGGTTTCTCTGCCTcc                                                                                                                        <  1:289188/109‑1 (MQ=255)                                                         cGATGAGGACATGACCTCTTCATCGGCGCGCCTTAAGCCCGCCGAGAAGAGCCAGAGACCCCGAGCAAGACCCCTAACCGCCTTATGGCGGTTTCTCTGCCTCCCAGTCTGCTGCGAAGGCCGATAGCCGA‑GTCCAACCAATTCTAtt                                                                           <  1:309253/148‑1 (MQ=255)                                                          gATGAGGACATGACCTCTTCATCGGCGCGCCTTAAGCCCGCCGAGAAGAGCCAGAGACCCCGAGCAAGACCCCTAACCGCCTTATGGCGGTTTCTCTGCCTCCCAGTCTGCTGCGAAGGCCGATAGCCGA‑GTCCAACCAATTCTAtttt                                                                         <  7:10140/149‑1 (MQ=255)                                                              aGGACATGACCTCTTCATCGGCGCGCCTTAAGCCCGCCGAGAAGAGCCAGAGACCCCGAGCAAGACCCCTAACCGCCTTATGGCGGTTTCTCTGCCTCCCAGTCTGCTGCGAAGGCCGATAGCCGA‑GTCCAACCAATTCTATTTTTCGa                                                                     <  4:219692/149‑1 (MQ=255)                                                                    tGACCTCTTCATCGGCGCGCATTAAGCCCGCCGAGAAGAGCCAGAGACCCCGAGCAAGACCCCTATCCGCCTTATGGCGGTTTCTCTGCCTCCCAGTCTGCTGCGAAGGCCGATAGCCGA‑GTCCAACCAATTCTATTTTTCGACCTGGc                                                               <  6:258776/149‑1 (MQ=255)                                                                     gACCTCTTCATCGGCGCGCCTTAAGCCCGCCGAGAAGAGCCAGAGACCCCGAGCAAGACCCCTAACCGCCTTATGGc                                                                                                                                       <  4:307954/77‑1 (MQ=255)                                                                     gACCTCTTCATCGGCGCGCCTTAAGCCCGCCGAGAAGAGCCAGAGACCCCGAGCAAGACCCCTAACCGCCTTATGGc                                                                                                                                       >  3:307954/1‑77 (MQ=255)                                                                      aCCTCTTCATCGGCGCGCCTTAAGCCCGCCGAGAAGAGCCAGAGACCCCGAGCAAGACCCCTAACCGCCTTATGGCGGTTTCTCTGCCTCCCAGTCTGCTGCGAAGGCCGATAGCCGA‑GTCCAACCAATTCTATTTTTCGACCTGGCCt                                                             <  5:80070/149‑1 (MQ=255)                                                                          ctTCATCGGCGCGCCTTAAGCCCGCCGAGAAGAGCCAGAGACCCCGAGCAAGACCCCTAACCGCCTTATGGCGGTTTCTCTGCCTCCCAGTCTGCTGCGAAGGCCGATAGCCGA‑GTCCTAGCATTTGAATTTATGGACCTGGCCTGagc                                                         >  2:140786/1‑147 (MQ=255)                                                                           ttCATCGGCGCGCCTTAAGCCCGCCGAGAAGAGCCAGAGACCCCGAGCAAGACCCCTAACCGCCTTATGGCGGTTTCTCTGCCTCCCAGTCTGCTGCGAAGGCCGATAGCCGA‑GTccaaccaa                                                                                  <  4:308620/123‑1 (MQ=255)                                                                           ttCATCGGCGCGCCTTAAGCCCGCCGAGAAGAGCCAGAGACCCCGAGCAAGACCCCTAACCGCCTTATGGCGGTTTCTCTGCCTCCCAGTCTGCTGCGAAGGCCGATAGCCGA‑GTccaaccaa                                                                                  >  3:308620/1‑123 (MQ=255)                                                                              aTCGGCGCGCCTTAAGCCCGCCGAGAAGAGCCAGAGACCCCGAGCAAGACCCCTAACCGCCTTATGGCGGTTTCTCTGCCTCCCAGTCTGCTGCGAAGGCCGATAGCCGA‑GTCCAACCAATTCTATTTTTCGACCTGGCCTGACCGCAg                                                     <  1:296975/149‑1 (MQ=255)                                                                                  gcgcgcCTTAAGCCCGCCGAGAAGAGCCAGAGACCCCGAGCAAGACCCCTAACCGCCTTATGGCGGTTTCTCTGCCTCCCAGTCTGCTGCGAAGGCCGATAGCCGA‑GTCCAACCAATTCTATTTTTCGACCTGGCCTGACCGCAGTa                                                   >  1:314704/1‑147 (MQ=255)                                                                                    gcgcCTTAAGCCCGCCGAGAAGAGCCAGAGACCCCGAGCAAGACCCCTAACCGCCTTATGGCGGTTTCTCTGCCTCCCAGTCTGCTGCGAAGGCCGATAGCCGA‑GTCCAACCAATTCTATTTTTCGACCTGGCCTGACCGCAg                                                     <  7:97726/143‑1 (MQ=255)                                                                                    gcgcCTTAAGCCCGCCGAGAAGAGCCAGAGACCCCGAGCAAGACCCCTAACCGCCTTATGGCGGTTTCTCTGCCTCCCAGTCTGCTGCGAAGGCCGATAGCCGA‑GTCCAACCAATTCTATTTTTCGACCTGGCCTGACCGCAg                                                     >  8:97726/1‑143 (MQ=255)                                                                                       ccTTAAGCCCGCCGAGAAGAGCCAGAGACCCCGAGCAAGACCCCTAACCGCCTTATGGCGGTTTCTCTGCCTCCCAGTCTGCTGCGAAGGCCGATAGCCGACGTCCAACCAATTCTATTTTTCGACCTGGCCTGACCGCAGTAGAGCgt                                             <  1:258950/149‑1 (MQ=255)                                                                                           aaGCCCGCCGAGAAGAGCCAGAGACCCCGAGCAAGACCCCTAACCGCCTTATGGCGGTTTCTCTGCCTCCCAGTCTGCTGCGAAGGCCGATAGCCGA‑GTCCAACCAATTCTATTTTTCGACCTGGCCTGACCGCAGTAGAGCGTGTGc                                         <  1:6630/148‑1 (MQ=255)                                                                                              cccGCCGAGAAGAGCCAGAGACCCCGAGCAAGACCCCTAACCGCCTTATGGCGGTTTCTCTGCCTCCCAGTCTGCTGCGAAGGCCGATAGCCGA‑GTCCAACCAATTCTATTTTTCGACCTGGCCTGACCGCAGTAGAGCGTGTGCTAt                                      >  2:45189/1‑148 (MQ=255)                                                                                               ccgccgAGAAGAGCCAGAGACCCCGAGCAAGACCCCTAACCGCCTTATGGCGGTTTCTCTGCCTCCCAGTCTGCTGCGAAGGCCGATAGCCGA‑GTCCAACCAATTCTATTTTTCGACCTGGCCTGACCGCAGTAGAGCGTGTGCTATCa                                    <  1:140786/149‑1 (MQ=255)                                                                                                      gaagaGCCAGAGACCCCGAGCAAGACCCCTAACCGCCTTATGGCGGTTTCTCTGCCTCCCAGTCTGCTGCGAAGGCCGATAGCCGA‑GTCCAACCAATTCTATTTTTCGACCTGGCCTGACCGCAGTAGAGCGTGTGCTATCAGAGaaaa                             <  1:81751/149‑1 (MQ=255)                                                                                                       aagaGCCAGAGACCCCGAGCAAGACCCCTAACCGCCTTATGGCGGTTTCTCTGCCTCCCAGTCTGCTGCGAAGGCCGATAGCCGA‑GTCCAACCAATTCTATTTTTCGACCTGGCCTGACCGCAGTAGAGCGTGTGCTATCAGAGAAAAg                            <  1:45189/149‑1 (MQ=255)                                                                                                          agCCAGAGACCCCGAGCAAGACCCCTAACCGCCTTATGGCGGTTTCTCTGCCTCCCAGTCTGCTGCGAAGGCCGATAGCCGA‑GTCCAACCAATTCTATTTTTCGACCTGGCCTGACCGCAGTAGAGCGTGTGCTATCAGAGAAAAGTgg                         >  5:176712/1‑149 (MQ=255)                                                                                                              agagACCCCGAGCAAGACCCCTAACCGCCTTATGGCGGTTTCTCTGCCTCCCAGTctgct                                                                                                               >  6:100977/1‑60 (MQ=255)                                                                                                              agagACCCCGAGCAAGACCCCTAACCGCCTTATGGCGGTTTCTCTGCCTCCCAGTctgct                                                                                                               <  5:100977/60‑1 (MQ=255)                                                                                                                    cccGAGCAAGACCCCTAACCGCCTTATGGCGGTTTCTCTGCCTCCCAGTCTGCTGCGAAGGCCGATAGCCGA‑GTCCAACCAATTCTATTTTTCGACCTGGCCTGACCGCAGTAGAGCGTGTGCTATCAGAGAAAAGTGGTATCAatat                >  4:76575/1‑148 (MQ=255)                                                                                                                    cccGAGCAAGACCCCTAACCGCCTTATGGCGGTTTCTCTGCCTCCCAGTCTGCTGCGAAGGCCGATAGCCGA‑GTCCAACCAATTCTATTTTTCGACCTGGCCTGACCGCAGTAGAGCGTGTGCTATCAGAGAAAAGTGGTATCAATATc               >  7:276492/1‑149 (MQ=255)                                                                                                                    cccGAGCAAGACACCTAACCGCCTTATGGCGGTTTCTCTGCCTCCCAGTCTGCTGCGAAGGCCGATAGCCGA‑GTCCAACCAATTCTATTTTTCGACCTGGCCTGACCGCAGTAGAGCGTGTGCTATCAGAGAAAAGTGGTATCAatat                >  4:309067/1‑148 (MQ=255)                                                                                                                      cGAGCAAGACCCCTAACCGCCTTATGGCGGTTTCTCTGCCTCCCGGTCTGCTGCGAAGGCCGATAGCCGA‑GTCCAACCAATTCTATTTTTCGACCTGGCCTGACCGCAGTAGAGCGTGTGCTATCAGAGAAAAGTGGTATCAATATCAg             >  5:206980/1‑149 (MQ=255)                                                                                                                         gCAAGACCCCTAACCGCCTTATGGCGGTTTCTCTGCCTCCCAGTCTGCTGCGAAGGCCGATAGCCGA‑GTCCAACCAATTCTATTTTTCGACCTGGCCTGACCGCAGTAGAGCGTGTGCTATCAGAGAAAAGTGGTATCAATATCAGccc          <  2:314704/149‑1 (MQ=255)                                                                                                                            aGACCCCTAACCGCCTTATGGCGGTTTCTCTGCCTCCCAGTCTGCTGCGAAGGCCGATAGCCGA‑GTCCAACCAATTCTATTTTTCGACCTGGCCTGACCGCAGTAGAGCGTGTGCTATCAGAGAAAAGTGGTATCAATATCAGccccc        >  8:172529/1‑148 (MQ=255)                                                                                                                                cccTAACCGCCTTATGGCGGTTTCTCTGCCTCCCAGTCTGCTGCGAAGGCCGATAGCCGA‑GTCCAACCAATTCTATTTTTCGACCTGGCCTGACCGCAGTAGAGCGTGTGCTATCAGAGAAAAGTGGTATCAATATCCGCCCCCCAcc    >  7:45670/1‑148 (MQ=255)                                                                                                                                cccTAACCGCCTTATGGCGGTTTCTCTGCCTCCCAGTCTGCTGCGAAGGCCGATAGCCGA‑GTCCAACCAATTCTATTTTTCGACCTGGCCTGACCGCAGTAGAGCGTGTGCTATCAGAGAAAAGTGGTATCAATATCAGCCCCCCAcc    >  4:332098/1‑148 (MQ=255)                                                                                                                                cacTAACCGGCTTATGGAGGTTTCTCTGCCTCGCATTCTGCTGCGAAGGCCGATAGCCGA‑GTCCAACCAATTCTATTTTTCGACCTGGCGTGACCGCAGTAGAGCGTGTGCTATCAGAGAAAAGTGGTATCAATATCAGCCCCCCACCg   <  5:211911/147‑1 (MQ=255)                                                                                                                                 ccTAACCCCCTTATTGCTGTTTCTCTGCCACCCAGTCTGCTGCGAAGGCCGATAGCCGA‑GTCCAACCAATTCTATTTTTCGACCTGGCCTGACCGCAGTAGAGCGTGTGCTATCAGAGAAAAGTGGTATCAATATCAGCCCCCCACCGa  <  8:276492/149‑1 (MQ=255)                                                                                                                                           |                                                                                                                                            TCCACAGAGGGTTAGGGATAGCCTTAAGGCGTAATTGTCTGATACCAACACCTCTGCGATGAGGACATGACCTCTTCATCGGCGCGCCTTAAGCCCGCCGAGAAGAGCCAGAGACCCCGAGCAAGACCCCTAACCGCCTTATGGCGGTTTCTCTGCCTCCCAGTCTGCTGCGAAGGCCGATAGCCGA‑GTCCAACCAATTCTATTTTTCGACCTGGCCTGACCGCAGTAGAGCGTGTGCTATCAGAGAAAAGTGGTATCAATATCAGCCCCCCACCGA  >  NC_002947/5041111‑5041387

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 14 ≤ ATCG/ATCG < 27 ≤ ATCG/ATCG < 32 ≤ ATCG/ATCG < 36 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑