Predicted mutation
evidence	seq id	position	mutation	freq	annotation	gene	description
RA	NC_002947	5,074,531	G→A	7.1%	D11D (GAC→GAT)	PP_5692 ←	hypothetical protein

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NC_002947	5,074,531	0	G	A	7.1%	159.4 / 2.1	56	D11D (GAC→GAT)	PP_5692	hypothetical protein
Reads supporting (aligned to +/- strand):  ref base G (29/23);  new base A (2/2);  total (31/25)
Fisher's exact test for biased strand distribution p-value = 1.00e+00
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 1.35e-01

CCGCTCGCCCTCGGTAACAATCGCATCAAGGATTACCCAGTCCTGCACGGCGCACAGAGGCATCCATTTATAGATCTTTGAAGCCGCCGCAAACGCATTATCAAGAGGTAGTTCAGACCCCATCAGAGCGATCTCGCGGTCGCTCAACAGGCCATGCTCAATGGGATTCACGCCCTTTTCCCCGCGCTCAGCAATATTTGAGAATTTCCGACATCACCGCCTTAATGCCCCTTTTG‑TAGGCTTCAAACCTTGAACAGTCTGAACGTTTTCGCCTAGATGGACGGA  >  NC_002947/5074393‑5074677                                                                                                                                           |                                                                                                                                                    ccGCTCGCCCTCGGTAACAATCGCATCAAGGATTACCCAGTCCTGCACGGCGCACAGAGGCATCCATTTATAGATCTTTGAAGCCGCCGCAAACGCATTATCAAGAGGTAGTTCAGACCCCATCAGAGCGATCTCGCGGTGGCTCaa                                                                                                                                             >  5:272576/1‑147 (MQ=255) ccGCTCGCCCTCGGTAACAATCGCATCAAGGATTACCCAGTCCTGCACGGCGCACAGAGGCATCCATTTATAGATCTTTGAAGCCGCCGCAAACGCATTATCAAGAGGTAGTTCAGACCCCATCAGAGCGACCGCGAGATCGCTctgat                                                                                                                                           <  5:337437/149‑5 (MQ=255)  cGCTCGCCCTCGGTAACAATCGCATCAAGGATTACCCAGTCCTGCACGGCGCACAGAGGCATCCATTTATAGATCTTTGAAGCCGCCGCAAACGCATTATCAAGAGGTAGTTCAGACCCCATCAGAGCGACCGCGAGATCGCTctgatg                                                                                                                                          <  3:359370/149‑6 (MQ=255)       gCCCTCGGTAACAATCGCATCAAGGATTACCCAGTCCTGCACGGCGCACAGAGGCATCCATTTATAGATCTTTGAAGCCGCCGCAAACGCATTATCAAGAGGTAGTTCAGACCCCATCAGAGCGATCTCGCGGTCGCTCAACAGGCCAt                                                                                                                                     >  1:289889/1‑149 (MQ=255)         ccTCGGTAACAATCGCATCAAGGATTACCCAGTCCTGCACGGCGCACAGAGGCATCCATTTATAGATCTTTGAAGCCGCCGCAAACGCATTATCAAGAGGTAGTTCAGACCCCATCAGAGCGATCTCGCGGTCGCTCAACAGGCCATGc                                                                                                                                   >  1:3120/1‑149 (MQ=255)             ggTAACAATCGCATCAAGGATTACCCAGTCCTGCACGGCGCACAGAGGCATCCATTTATAGATCTTTGAAGCCGCCGCAAACGCATTATCAAGAGGTAGTTCAGACCCCATCAGAGCGATCTCGCGGTCGCTCAACAGGCCATGCTc                                                                                                                                 <  7:295775/147‑1 (MQ=255)                   aaTCGCATCAAGGATTACCCAGTCCTGCACGGCGCACAGAGGCATCCATTTATAGATCTTTGAAGCCGCCGCAAACGCATTATCAAGAGGTAGTTCAGACCCCATCAGAGCGATCTCGCGGTCGCTCAACAGGCCATGCTCAATGGGAt                                                                                                                         >  4:288648/1‑149 (MQ=255)                           cAAGGATTACCCAGTCCTGCACGGCGCACAGAGGCATCCATTTATAGATCTTTGAAGCCGCCGCAAACGCATTATCAAGAGGTACTTCAGTCACAATCAGAGCGATCTCTCGGTCGCTCAACAGTCCATGCTCAATGGGATAAACGccc                                                                                                                 >  7:147224/1‑149 (MQ=255)                            aaGGATTACCCAGTCCTGCACGGCGCACAGAGGCATCCATTTATAGATCTTTGAAGCCGCCGCAAACGCATTATCAAGAGGTAGTTCAGACCCCATCAGAGCGATCTCGCGGTCGCTCAACAGGCGATGCTCAATGGGATTCACGCCCt                                                                                                                >  2:23760/1‑149 (MQ=255)                               gATTACCCAGTCCTGCACGGCGCACAGAGGCATCCATTTATAGATCTTTGAAGCCGCCGCAAACGCATTATCAAGAGGTAGTTCAGACCCCATCAGAGCGATCTCGCGGTCGCTCAACAGGCCATGCTCAATGGGATTCACGCCCtttt                                                                                                             >  3:190441/1‑149 (MQ=255)                               gATTACCCAGTCCTGCACGGCGCACAGAGGCATCCATTTATAGATCTTTGAAGCCGCCGCAAACGCATTATCAAGAGGTAGTTCAGACCCCATCAGAGCGATCTCGCGGTCGCTCAACAGGCCATGCTCAATGGGATTCACGCCCtttt                                                                                                             <  8:129131/149‑1 (MQ=255)                                    cccAGTCCTGCACGGCGCACAGAGGCATCCATTTATAGATCTTTGAAGCCGCCGCAAACGCATTATCAAGAGGTAGTTCAGACCCCATCAGAGCGATCTCGCGGTCGCTCAACAGGCCATGCTCAATGGGATTCACGCCCTTTTCCCcg                                                                                                        >  2:124903/1‑149 (MQ=255)                                     ccAGTCCTGCACGGCGCACAGAGGCATCCATTTATAGATCTTTGAAGCCGCCGCAAACGCATTATCAAGAGGTAGTTCAGACCCCATCAGAGCGATCTCGCGGTCGCTCAACAGGCCATGCTCAATggg                                                                                                                           <  6:358264/129‑1 (MQ=255)                                     ccAGTCCTGCACGGCGCACAGAGGCATCCATTTATAGATCTTTGAAGCCGCCGCAAACGCATTATCAAGAGGTAGTTCAGACCCCATCAGAGCGATCTCGCGGTCGCTCAACAGGCCATGCTCAATGGGATTCCCGCCCTGTTCCCcgc                                                                                                       >  4:348600/1‑149 (MQ=255)                                     ccAGTCCTGCACGGCGCACAGAGGCATCCATTTATAGATCTTTGAAGCCGCCGCAAACGCATTATCAAGAGGTAGTTCAGACCCCATCAGAGCGATCTCGCCGTCGCTCAACAGGCCATGCTCAATggg                                                                                                                           >  5:358264/1‑129 (MQ=255)                                         tCCTGCACGGCGCACAGAGGCATCCATTTATAGATCTTTGAAGCCGCCGCAAACGCATTATCAAGAGGTAGTTCAGACCCCATCAGAGCGATCTCGCGGTCGCTCAACAGGCCATGCTCAATGGGATTCACGCCCTTTTCCCCGCGCTc                                                                                                   <  4:190441/149‑1 (MQ=255)                                            tGCACGGCGCACAGAGGCATCCATTTATAGATCTTTGAAGCCGCCGCAAACGCATTATCAAGAGGTAGTTCAGACCCCATCAGAGCGATCTCGCGGTCGCTCAACAGGCCATGCTCAATGGGATTCACGCCCTTTTCCCCGCGCTCAg                                                                                                 >  1:220066/1‑148 (MQ=255)                                                 ggCGCACAGAGGCATCCATTTATAGATCTTTGAAGCCGCCGCAAACGCATTATCAAGAGGTAGTTCAGACCCCATCAGAGCGATCTCGCGGTCGCTCAACAGGCCATGCTTAATGGGATTCACGCCCTTTTCCCCGCGCTCAGCAatat                                                                                           <  8:40578/149‑1 (MQ=255)                                                    gcACAGAGGCATCCATTTATAGATCTTTGAAGCCGCCGCAAACGCATTATCAAGAGGTAGTTCAGACCCCATCAGAGCGATCTCGCGGTCGCTCAACAGGCCATGCTCAATGGGATTCACGCCCTTTTCCCCGCGCTCAGCAATAttt                                                                                         >  3:359991/1‑148 (MQ=255)                                                     cacaGAGGCATCCATTTATAGATCTTTGAAGCCGCCGCAAACGCATTATCAAGAGGTAGTTCAGACCCCATCAGAGCGATCTCGCGGTCGCTCAACAGGCCATGCTCAATGGGATTCACGCCCTTTTCCCCGCGCTCAGCAATATTTga                                                                                       <  1:23760/149‑1 (MQ=255)                                                             cATCCATTTATAGATCTTTGAAGCCGCCGCAAACGCATTATCAAGAGGTAGTTCAGACCCCATCAGAGCGATCTCGCGGTCGCTCAACAGGCCATGCTCAATGGGATTCACGCCCTTTTCCCCGCGCTCAGCAATATTTGAGAATTTcc                                                                               <  6:304391/149‑1 (MQ=255)                                                              aTCCATTTATAGATCTTTGAAGCCGCCGCAAACGCATTATCAAGAGGTAGTTCAGACCCCATCAGAGCGATCTCGCGGTCGCTCAACAGGCCATGCTCAATGGGATTCACGCCCTTTTCCCCGCGCTCAGCAATATTTGAGAATTTcc                                                                               >  2:303013/1‑148 (MQ=255)                                                               tCCATTTATAGATCTTTGAAGCCGCCGCAAACGCATTATCAAGAGGTAGTTCAGACCCCATCAGAGCGATCTCGCGGTCGCTCAACAGGCCATGCTCAATGGGATTCACGCCCTTTTCCCCGCGCTCAGCAATATTTGAGAATTTCCGa                                                                             <  3:288648/149‑1 (MQ=255)                                                                 cATTTATAGATCTTTGAAGCCGCCGCAAACGCATTATCAAGAGGTAGTTCAGACCCCATCAGAGCGATCTCGCGGTCGCTCAACAGGCCATGCTCAATGGGATTCACGCCCTTTTCCCCGCGCTCAGCAATATTTGAGAATTTCCGACa                                                                           >  5:250509/1‑149 (MQ=255)                                                                   tttATAGATCTTTGAAGCCGCCGCAAACGCATTATCAAGAGGTAGTTCAGACCCCATCAGAGCGATCTCGCGGTCGCTCAACAGGCCATGCTCAATGGGATTCACGCCCTTTTCCCCGCGCTCAGCAATATTTGAGAATTTCCGACAt                                                                          >  4:100501/1‑148 (MQ=255)                                                                   tttATAGATCTTTGAAGCCGCCGCAAACGCATTATCAAGAGGTAGTTCAGACCCCATCAGAGCGATCTCGCGGTCGCTCAACAGGCCATGCTCAATGGGATTCACGCCCTTTTCCCCGCGCTCAGCAATATTTGAGAATTTCCGACATc                                                                         <  2:3120/149‑1 (MQ=255)                                                                       taGATCTTTGAAGCCGCCGCAAACGCATTATCAAGAGGTAGTTCAGACCCCATCAGAGCGATCTCGCGGTCGCTCAACAGGCCATGCTCAATGGGATTCACGCCCTTTTCCCCGCGCTCAGCAATATTTGAGAATTTCCGACATCAcag                                                                     >  2:242342/1‑147 (MQ=255)                                                                         gATCTTTGAAGCCGCCGCAAACGCATTATCAAGAGGTAGTTCAGACCCCATCAGAGCGATCTCGCGGTCGCTCAACAGGCCATGCTCAATGGGATTCACGCCCTTTTCCCCGCGCTCAGCAATATTTGAGAATTTCCGACATCACCGcc                                                                   <  1:303013/149‑1 (MQ=255)                                                                         gATCTTTGAAGCCGCCGCAAACGCATTATCAAGAGGTAGTTCAGACCCCATCAGAGCGATCTCGCGGTCGCTCAACAGGCCATGCTCAATGGGATTAACGCCCTTTACCCCGCCCTCAGCAATATTTGAGAATTTCCGACATCAACGca                                                                   >  4:5882/1‑148 (MQ=255)                                                                                gAAGCCGCCGCAAACGCATTATCAAGAGGTAGTTCAGACCCCATCAGAGCGATCTCGCGGTCGCTCAACAGGCCATGCTCAATGGGATTCACGCCCTTTTCCCCGCGCTCAGCAATATTTGAGAATTTCCGACATCACCGCCTTAATGc                                                            >  7:220859/1‑149 (MQ=255)                                                                                    ccgccgCAAACGCATTATCAAGAGGTAGTTCAGACCCCATCAGAGCGATCTCGCGGTGGCTCAACAGGCCATGCTCAATGGGATTCACGCCCTTTTCCCCGCGCTCAGCAATATTTGAGAATTTCCGACATCACCGCCTTAATGCCCCt                                                        <  6:272576/149‑1 (MQ=255)                                                                                       ccgcAAACGCATTATCAAGAGGTAGTTCAGACCCCATCAGAGCGATCTCGCGGTCGCTCAACAGGCCATGCTCAATGGGATTCACGCCCTTTTCCCCGCGCTCAGCAATATTTGAGAATTTCCGACATCACCGCCTTAATGCCCCtttt                                                     <  6:250509/149‑1 (MQ=255)                                                                                         gcAAACGCATTATCAAGAGGTAGTTCAGACCCCATCAGAGCGATCTCGCGGTCGCTCAACAGGCCATGCTCAATGGGATTCACGCCCTTTTCCCCGCGCTCAGCAATATTTGAGAATTTCCGACATCACCGCCTTAATGCCCCTTTTg                                                    >  6:6650/1‑148 (MQ=255)                                                                                          cAAACGCATTATCAAGAGGTAGTTCAGACCCCATCAGAGCGATCTCGCGGTCGCTCAACAGGCCATGCTCAATGGGATTCACGCCCTTTTCCCCGCGCTCAGCAATATTTGAGAATTTCCGACATCACCGCCTTAATGCCCCTTTTG‑Ta                                                 <  2:220066/149‑1 (MQ=255)                                                                                               gCATTATCAAGAGGTAGTTCAGACCCCATCAGAGCGATCTCGCGGTCGCTCAACAGGCCATGCTCAATGGGATTCACGCCCTTTTCCCCGCGCTCAGCAATATTTGAGAATTTCCGACATCACCGCCTTAATGCCCCTTTTG‑TAGGCt                                             >  4:152217/1‑148 (MQ=255)                                                                                                   tATCAAGAGGTAGTTCAGACCCCATCAGAGCGATCTCGCGGTCGCTCAACAGGCCATGCTCAATGGGATTCACGCCCTTTTCCCCGCGCTCAGCAATATTTGAGAATTTCCGa                                                                             >  5:64475/1‑113 (MQ=255)                                                                                                   tATCAAGAGGTAGTTCAGACCCCATCAGAGCGATCTCGCGGTCGCTCAACAGGCCATGCTCAATGGGATTCACGCCCTTTTCCCCGCGCTCAGCAATATTTGAGAATTTCCGa                                                                             <  6:64475/113‑1 (MQ=255)                                                                                                       aaGAGGTAGTTCAGACCCCATCAGAGCGATCTCGCGGTCGCTCAACAGGCCATGCTCAATGGGATTCACGACCTTTTCCCCGCTCTCAGCAATATTTGAGAATTTCCGACATCACCGCCTTAATGCCCCTTTTG‑TAGGCTTCAAACCtt                                    <  1:242342/149‑1 (MQ=255)                                                                                                            gTAGTTCAGACCCCATCAGAGCGATCTCGCGGTCGCTCAACAGGCCATGCTCAATGGGATTCACGCCCTTTTCCCCGCGCTCAGCAATATTTGAGAATTTCCGACATCACCGCCTTAATGCCCCTTTTG‑TAGGCTTCAAACCtt                                    <  7:142652/144‑1 (MQ=255)                                                                                                            gTAGTTCAGACCCCATCAGAGCGATCTCGCGGTCGCTCAACAGGCCATGCTCAATGGGATTCACGCCCTTTTCCCCGCGCTCAGCAATATTTGAGAATTTCCGACATCACCGCCTTAATGCCCCTTTTG‑TAGGCTTCAAACCtt                                    >  8:142652/1‑144 (MQ=255)                                                                                                            gTAGTTCAGACCCCATCAGAGCGATCTCGCGGTCGCTCAACAGGCCATGCTCAATGGGATTCACGCCCTTTTCCCCGCGCTCAGCAATATTTGAGAATTTCCGACATCACCGCCTTAATGCCCCTTTTG‑TAGGCTTCAAACCTTGaa                                 >  2:85237/1‑147 (MQ=255)                                                                                                            gTAGTTCAGACCCCATCAGAGCGATCTCGCGGTCGCTCAACAGGCCATGCTCAATGGGATTCACGCCCTTTTCCCCGCGCTCAGCAATATTTGAGAATTTCCGACATCACCGCCTTAATGCCCCTTTTG‑TAGGCTTCAAACCTTGAACa                               <  3:100501/149‑1 (MQ=255)                                                                                                             tAGTTCAGACCCCATCAGAGCGATCTCGCGGTCGCTCAACAGGCCATGCTCAATGGGATTCACGCCCTTTTCCCCGCGCTCAGCAATATTTGAGAATTTCCGACATCACCGCCTTAATGCCCCTTTTG‑TAGGCTTCAAACCTTGAACAg                              <  4:153365/149‑1 (MQ=255)                                                                                                             tAGTTCAGACCCCATCAGAGCGATCTCGAGGTCGCTCAACAGGCCATGCTCAATGGGATTCACGCCCTTTTCCCCGAGCTCAGCAATATTTGAGAATTTCCGACATCACAGCCTTAATGCCCCTTTTG‑TAGGCTTCAAACCTTGAACAg                              >  7:262711/1‑149 (MQ=255)                                                                                                                ttCAGACCCCATCAGAGCGATCTCGCGGTCGCTCAACAGGCCATGCTCAATGGGATTCACGCCCTTTTCCCCGCGCTCAGCAATATTTGACAATTTCCGACATCACCGCCTTAATGCCCCTTTTG‑TAGGCTTCAAACCTTGAACAGTCt                           >  8:170666/1‑149 (MQ=255)                                                                                                                       cccATCAGAGCGATCTCGCGGTCGCTCAACAGGCCATGCTCAATGGGATTCAc                                                                                                                     >  5:84706/1‑53 (MQ=255)                                                                                                                       cccATCAGAGCGATCTCGCGGTCGCTCAACAGGCCATGCTCAATGGGATTCAc                                                                                                                     <  6:84706/53‑1 (MQ=255)                                                                                                                        ccATCAGAGCGATCTCGCGGTCGCTCAACAGGCCATGCTCAATGGGATTCACGCCCTTTTCCCCGCGCTCAGCAATATTTGAGAATTTCCGACATCACCGCCTTAATGCCCCTTTTG‑TAGGCTTCAAACCTTGAACAGTCTGAACGttt                   >  2:315176/1‑149 (MQ=255)                                                                                                                          tgttgagCGACCGCGAGATCGCTCAACAGGCCATGCTCAATGGGATTCACGCGCTTTTCCCCGCGCTCAGCAATATTTGAGAATTTCCGACATCACCGCCTTAATGCCCCTTTTG‑TAGGCTTCAAACCTTGAACAGTCTGAACGTTTTc                 >  3:242219/5‑149 (MQ=255)                                                                                                                           tCAGATCGATCTCGCGGTCGCTCAACAGGCCATGCTCAATGGGATTCACGCCCTTTTCCCCGCGCTCAGCAATATTTGAGAATTTCCGACATCACCGCCTTAATGCCCCTTTTG‑TAGGCTTCAAACCTTGAACAGTCTGAACGTTTTCg                <  5:6650/149‑1 (MQ=255)                                                                                                                           gttgagCGACCGCGAGATCGCTCAACAGGCCATGCTCAATGGGATTCACGCCCTTTTCCCCGCGCTCAGCAATATTTGAGAATTTCCGACATCACCGCCTTAATGCCCCTTTTG‑TAGGCTTCAAACCTTGAACAGTCTGAACGTTTTCg                >  4:227298/4‑149 (MQ=255)                                                                                                                              gagCGATCTCGCGGTCGCTCAACAGGCCATGCTCAATGGGATTCACGCCCTTTTCCCCGCGCTCAGCAATATTTGAGAATTTCCGACATCACCGCCTTAATGCCCCTTTTG‑TAGGCTTCAAACCTTGAACAGTCTGAACGTTTTCGcc              >  6:144351/1‑148 (MQ=255)                                                                                                                              gagCGATCTCGCGGTCGCTCAACAGGCCATGCTCAATGGGATTCACGCCCTTTTCCCCGCGCTCAGCAATATTTGAGAATTTCCGACATCACCGCCTTAATGCCCCTTTTG‑TAGGCTTCAAACCTTGAACAGTCTGAACGTTTTCGcc              >  4:137879/1‑148 (MQ=255)                                                                                                                                        tctgTCGCTAAACAGGCCATGCTCAATTGGATTCACTCCCTTTTCCCCGCGCTCATCAATATTTGAGAATTTCCGACATCAACGCCTTAATGCACCTTTTG‑TAGGCTTCAAAACTTGAACAGTATGAACGTTTTCGCCTAGATGGAc     <  8:262711/144‑1 (MQ=255)                                                                                                                                        gcgGTCGCTTAAAACGGCATTCTCAATTGGATTCACGGCCTTTTCCCCGCGCTCATCAATATTTTAGAATTTCCGTCATCACCGCCTTAATGCCCCTTTTGCTAGGCTTCAAACCTTGAACAGTCTGAACGTTTTCGCCTAGATGGAc     <  1:85237/148‑1 (MQ=255)                                                                                                                                        gcgGTCGCTCAACAGGCCATGCTCAATGGGATTCACGCCCTTTTCCCCGCGCTCAGCAATATTTGAGAATTTCCGACATCACCGCCTTAATGCCCCTTTTG‑TAGGCTTCAAACCTTGAACAGTCTGAACGTTTTCGCCTAGATGGAc     <  3:152217/147‑1 (MQ=255)                                                                                                                                         cgGTCGCTCAACAGGCCATGCTCAATGGGATTCACGCCCTTTTCCCCGCGCTCAGCAATATTTGAGAATTTCCGACATCACCGCCTTAATGCCCCTTTTG‑TAGGCTTCAAACCTTGAACAGTCTGAACGTTTTCGCCTAGATGGACGGa  <  2:289889/149‑1 (MQ=255)                                                                                                                                           |                                                                                                                                                    CCGCTCGCCCTCGGTAACAATCGCATCAAGGATTACCCAGTCCTGCACGGCGCACAGAGGCATCCATTTATAGATCTTTGAAGCCGCCGCAAACGCATTATCAAGAGGTAGTTCAGACCCCATCAGAGCGATCTCGCGGTCGCTCAACAGGCCATGCTCAATGGGATTCACGCCCTTTTCCCCGCGCTCAGCAATATTTGAGAATTTCCGACATCACCGCCTTAATGCCCCTTTTG‑TAGGCTTCAAACCTTGAACAGTCTGAACGTTTTCGCCTAGATGGACGGA  >  NC_002947/5074393‑5074677

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 14 ≤ ATCG/ATCG < 21 ≤ ATCG/ATCG < 32 ≤ ATCG/ATCG < 36 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑