Predicted mutation
evidence	seq id	position	mutation	freq	annotation	gene	description
RA	NC_002947	3,553,796	A→G	7.5%	S155G (AGC→GGC)	PP_3138 →	VirK domain‑containing protein

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NC_002947	3,553,796	0	A	G	7.5%	150.4 / 3.0	53	S155G (AGC→GGC)	PP_3138	VirK domain‑containing protein
Reads supporting (aligned to +/- strand):  ref base A (27/22);  new base G (2/2);  total (29/24)
Fisher's exact test for biased strand distribution p-value = 1.00e+00
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 8.95e-01

GAGGCTGTGTGACCTGTCCAGCCACTCGCCGGGCTGTTGCCTGGTGCTGGACCGGCCAATCTGGTTCAAGCGCGAAGGCGAGCTGGTGCTGAACCTGTTCCAGGCCGACCTGCGTGTGGCATCCCTTGCCTTCACCCTGGGCCGCAG‑CCAGGGTGAAACCTGCCTGTTCATTGGTGCGGTGCAGGGCATCCACAAAGGTATCGACAGCGAAACCTCGCTGGCCATCTACCGTGACCTGACCAAGGACTTCGAAGGGCTGCGGCCACGCAGCCTGTTGCTCGAAGCGTTGA  >  NC_002947/3553651‑3553940                                                                                                                                                  |                                                                                                                                                  gAGGCTGTGTGACCTGTCCAGCCACTCGCCGGGCTGTTGCCTGGTGCTGGACCGGCCAATCTGGTTCAAGCGCGAAGGCGAGCTGGTGCTGAACCTGTTCCAGGCCGACCTGCGTGTGGCATCCCTTGCCTTCACCCTGGGCCGCAG‑c                                                                                                                                                >  3:26215/1‑148 (MQ=255)         gtgACCTGTCCAGCCACTCGCCGGGCTGTTGCCTGGTGCTGGACCGGCCAATCTGGTTCAAGCGCGAAGGCGAGCTGGTGCTGAACCTGTTCCAGGCCGACCTGCGTGTGGCATCCCTTGCCTTCACCCT‑GGCTGCGGCCCAGGGTGaa                                                                                                                                       <  1:4323/149‑1 (MQ=255)          tgACCTGTCCAGCCACTCGCCGGGCTGTTGCCTGGTGCTGGACCGGCCAATCTGGTTCAAGCGCGAAGGCGAGCTGGTGCTGAACCTGTTCCAGGCCGACCTGCGTGTGGCATCCCTTGCCTTCACCCTGGGCCGCAG‑CCAGGGt                                                                                                                                          >  1:258972/1‑145 (MQ=255)          tgACCTGTCCAGCCACTCGCCGGGCTGTTGCCTGGTGCTGGACCGGCCAATCTGGTTCAAGCGCGAAGGCGAGCTGGTGCTGAACCTGTTCCAGGCCGACCTGCGTGTGGCATCCCTTGCCTTCACCCTGGGCCGCAG‑CCAGGGt                                                                                                                                          <  2:258972/145‑1 (MQ=255)          tgACCTGTCCAGCCACTCGCCGGGCTGTTGCCTGGTGCTGGACCGGCCAATCTGGTTCAAGCGCGAAGGCGAGCTGGTGCTGAACCTGTTCCAGGCCGACCTGCGTGTGGCATCCCTTGCCTTCACCCTGGGCCGCAG‑CCAGGGTGaaa                                                                                                                                      >  3:297898/1‑149 (MQ=255)                gTCCAGCCACTCGCCGGGCTGTTGCCTGGTGCTGGACCGGCCAATCTGGTTCAAGCGCGAAGGCGAGCTGGTGCTGAACCTGTTCCAGGCCGACCTGCGTGTGGCATCCCTTGCCTTCACCCTGGGCCGCAG‑CCAGGGTGAAAcctgcc                                                                                                                                >  7:11504/1‑149 (MQ=255)                gTCCAGCCACTCGCCGGGCTGTTGCCTGGTGCTGGACCGGCCAATCTGGTTCAAGCGCGAAGGCGAGCTGGTGCTGAACCTGTTCCAGGCCGACCTGCGTGTGGCATCCCTTGCCTTCACCCTGGGCCGCAG‑CCAGGGTGAAAcctgc                                                                                                                                 >  4:227779/1‑148 (MQ=255)                gTCCAGCCACTCGCCGGGCTGTTGCCTGGTGCTGGACCGGCCAATCTGGTTCAAGCGCGAAGGCGAGCTGGTGCTGAACCTGTTCCAGGCCGACCTGCGTGTGGCATCCCTTGCCTTCACCCTGGGCCGCAG‑CCAGGGTGAAAcctgc                                                                                                                                 <  3:227779/148‑1 (MQ=255)                 gccAGCCACTCGCCGGGCTGTTGCCTGGTGCTGGACCGGCCAATCTGGTTCAAGCGCGAAGGCGAGCTGGTGCTGAACCTGTTCCAGGCCGACCTGCTTGTGGCATCCCTTGCCTTCACCCTGGGCCGCAG‑CCAGGGTGAAAcctgc                                                                                                                                 <  7:305621/146‑1 (MQ=255)                   cAGCCACTCGCCGGGCTGTTGCCTGGTGCTGGACCGGCCAATCTGGTTCAAGCGCGAAGGCGAGCTGGTGCTGAACCTGTTCCAGGCCGACCTGCGTGTGGCATCCCTTGCCTTCACCCTGGGCCGCAG‑CCAGGGTGAAACCTGCCTGt                                                                                                                             >  5:183071/1‑149 (MQ=255)                   cAGCCACTCGCCGGGCTGTTGCCTGGTGCTGGACCGGCCAATCTGGTTCAAGCGCGAAGGCGAGCTGGTGCTGAACCTGTTCCAGGCCGACCTGCGTGTGGCATCCCTTGCCTTCACCCT‑GGCTGCGGCCCAGGGTGaag                                                                                                                                      <  1:276649/140‑2 (MQ=255)                   cAGCCACTCGCCGGGCTGTTGCCTGGTGCTGGACCGGCCAATCTGGTTCAAGCGCGAAGGCGAGCTGGTGCTGAACCTGTTCCAGGCCGACCTGCGTGTGGCATCCCTTGCCTTCACCCT‑GGCTGCGGCCCAGGGTGaag                                                                                                                                      >  2:276649/1‑139 (MQ=255)                    aGCCACTCGCCGGGCTGTTGCCTGGTGCTGGACCGGCCAATCTGGTTCAAGCGCGAAGGCGAGCTGGTGCTGAACCTGTTCCAGGCCGACCTGCGTGTGGCATCCCTTGCCTTCACCCTGGGCCGCAG‑CCAGGGTGAAACCTGCCTGtt                                                                                                                            <  5:98006/149‑1 (MQ=255)                          tCGCCGGGCTGTTGCCTGGTGCTGGACCGGCCAATCTGGTTCAAGCGCGAAGGCGAGCTGGTGCTGAACCTGTTCCAGGCCGACCTGCGTGTGGCATCCCTTGCCTTCACCCTGGGCCGCAG‑CCAGGGTGAAACCTGCCTGTTCATTgg                                                                                                                      >  6:259496/1‑149 (MQ=255)                           cGCCGGGCTGTTGCCTGGTGCTGGACCGGCCAATCTGGTTCAAGCGCGAAGGCGAGCTGGTGCTGAACCTGTTCCAGGCCGACCTGCGTGTGGCATCCCTTGCCTTCACCCTGGGCCGCAG‑CCAGGGTGAAACCTGCCTGTTCATTggt                                                                                                                     >  8:125372/1‑149 (MQ=255)                            gCCGGGCTGTTGCCTGGTGCTGGACCGGCCAATCTGGTTCAAGCGCGAAGGCGAGCTGGTGCTGAACCTGTTCCAGGCCGACCTGCGTGTGGCATCCCTTGCCTTCACCCTGGGCCGCAG‑CCAGGGTGAAACCTGCCTGTTCATTggt                                                                                                                     <  4:26215/148‑1 (MQ=255)                                     ttGCCTGGTGCTGGACCGGCCAATCTGGTTCAAGCGCGAAGGCGAGCTGGTGCTGAACCTGTTCCAGGCCGACCTGCGTGTGGCATCCCTTGCCTTCACCCTGGGCCGCAG‑CCAGGGTGAAACCTGCCTGTTCATTGGTGCGGTGCAgg                                                                                                           <  6:219055/149‑1 (MQ=255)                                       gCCTGGTGCTGGACCGGCCAATCTGGTTCAAGCGCGAAGGCGAGCTGGTGCTGAACCTGTTCCAGGCCGACCTGCGTGTGGCATCCCTTGCCTTCACCCTGGGCCGCAG‑CCAGGGTGAAACCTGCCTGTTCATTGGTGCGGTGCAggg                                                                                                          <  7:42775/148‑1 (MQ=255)                                        ccTGGTGCTGGACCGGCCAATCTGGTTCAAGCGCGAAGGCGAGCTGGTGCTGAACCTGTTCCAGGCCGACCTGCGTGTGGCATCCCTTGCCTTCACCCTGGGCCGCAG‑CCAGGGTGAAACCTGCCTGTTCATTGGTGCGGTGCAGGGc                                                                                                         <  7:125372/148‑1 (MQ=255)                                            gTGCTGGACCGGCCAATCTGGTTCAAGCGCGAAGGCGAGCTGGTGCTGAACCTGTTCCAGGCCGACCTGCGTGTGGCATCCCTTGCCTTCACCCTGGGCCGCAG‑CCAGGGTGAAACCTGCCTGTTCATTGGTGCGGTGCAGGGCATc                                                                                                      <  5:259496/147‑1 (MQ=255)                                            gTGCTGGACCGGCCAATCTGGTTCAAGCGCGAAGGCGAGCTGGTGCTGAACCTGTTCCAGGCCGACCTGCGTGTGGCATCCCTTGCCTTCACCCTGGGCCGCAG‑CCAGGGTGAAACCTGCCTGTTCATTGGTGCGGTGCAGGGCATc                                                                                                      <  6:68104/147‑1 (MQ=255)                                               cTGGACCGGCCAATCTGGTTCAAGCGCGAAGGCGAGCTGGTGCTGAACCTGTTCCAGGCCGACCTGCGTGTGGCATCCCTTGCCTTCACCCTGGGCCGCAG‑CCAGGGTGAAACCTGCCTGTTCATTGGTGCGGTGCAGGGCATCCACaa                                                                                                 <  6:183071/149‑1 (MQ=255)                                                  gACCGGCCAATCTGGTTCAAGCGCGAAGGCGAGCTGGTGCTGAACCTGTTCCAGGCCGACCTGCGTGTGGCATCCCTTGCCTTCACCCTGGGCCGCAG‑CCAGGGTGAAACCTGCCTGTTCATTGGTGCGGTGCAGGGCATCCACAAAgg                                                                                              >  2:176628/1‑149 (MQ=255)                                                      ggCCAATCTGGTTCAAGCGCGAAGGCGAGCTGGTGCTGAACCTGTTCCAGGCCGACCTGCGTGTGGCATCCCTTGCCTTCACCCTGGGCCGCAG‑CCAGGGTGAAACCTGCCTGTTCATTGGTGAGGTGCAGGGCATCCACAAAGCTATc                                                                                          >  3:38230/1‑149 (MQ=255)                                                          aaTCTGGTTCAAGCGCGAAGGCGAGCTGGTGCTGAACCTGTTCCAGGCCGACCTGCGTGTGGCATCCCTTGCCTTCACCCTGGGCCGCAG‑CCAGGGTGAAACCTGCCTGTTCATTGGTGCGGTGCAGGGCATCCACAAAGGTATCGa                                                                                        >  5:252173/1‑147 (MQ=255)                                                              tGGTTCAAGCGCGAAGGCGAGCTGGTGCTGAACCTGTTCCAGGCCGACCTGCGTGTGGCATCCCTTGCCTTCACCCTGGGCCGCAG‑CCAGGGTGAAACCTGCCTGTTCAtt                                                                                                                        >  4:120968/1‑111 (MQ=255)                                                                gTTCAAGCGCGAAGGCGAGCTGGTGCTGAACCTGTTCCAGGCCGACCTGCGTGTGGCATCCCTTGCCTTCACCCTGGGCCGCAG‑CCAGGGTGAAACCTGCCTGTTCATTGGTGCGGTGCAgg                                                                                                           >  3:36963/1‑122 (MQ=255)                                                                gTTCAAGCGCGAAGGCGAGCTGGTGCTGAACCTGTTCCAGGCCGACCTGCGTGTGGCATCCCTTGCCTTCACCCTGGGCCGCAG‑CCAGGGTGAAACCTGCCTGTTCATTGGTGCGGTGCAgg                                                                                                           <  4:36963/122‑1 (MQ=255)                                                                    aaGCGCGAAGGCGAGCTGGTGCTGAACCTGTTCCAGGCCGACCTGCGTGTGGCATCCCTTGCCTTCACCCTGGGCCGCAG‑CCAGGGTGAAACCTGCCTGTTCATTGGTGCGGTGCAGGGCATCCACAAAGGTATCGACAGCGAAACCt                                                                             <  8:11504/148‑1 (MQ=255)                                                                       cgcgAAGGCGAGCTGGTGCTGAACCTGTTCCAGGCCGACCTGCGTGTGGCATCCCTTGCCTTCACCCTGGGCCGCAG‑CCAGGGTGAAACCTGCCTGTTCATTGGTGCGGTGCAGGGCATCCACAAAGGTATCGACAGCGAAACCTCGCt                                                                         <  5:71788/149‑1 (MQ=255)                                                                           aaGGCGAGCTGGTGCTGAACCTGTTCCAGGCCGACCTGCGTGTGGCATCCCTTGCCTTCACCCTGGGCCGCAG‑CCAGGGTGAAACCTGCCTGTTCATTGGTGCGGTGCAGGGCATCCACAAAGGTATCGACAGCGAAACCTCGCTGGc                                                                      >  3:119214/1‑148 (MQ=255)                                                                            aGGCGAGCTGGTGCTGAACCTGTTCCAGGCCGACCTGCGTGTGGCATCCCTTGCCTTCACCCTGGGCCGCAG‑CCAGGGTGAAACCTGCCTGTTCATTGGTGCGGTGCAGGGCATCAACAAAGGTATCGACAGCGAAACCTCGCTGGCCa                                                                    >  2:241125/1‑149 (MQ=255)                                                                                       tGCTGAACCTGTTCCAGGCCGACCTGCGTGTGGCATCCCTTGCCTTCACCCTGGGCCGCAG‑CCAGGGTGAAACCTGCCTGTTCATTGGTGCGGTGCAGGGCATCCACAAAGGTATCGACAGCGAAACCTCGCTGGCCATCTACCGtgac                                                         <  6:194252/149‑1 (MQ=255)                                                                                          ttatgcTGTTACAGGCAGACCTGCGTGTGGCATCCCTTGCCTTCTCGCTGGGCCGCAG‑CCAGTGTGAAACCTTCCTGTTCATTTGTGCGGTGCATGGCATCGACAAAGGTATATACAGCGAAACCTCGCTGGGCATCTACCGtgtcctg                                                      <  4:38230/144‑1 (MQ=255)                                                                                             aCCTGTTCCAGGCCGACCTGCGTGTGGCATCCCTTGCCTTCACCCTGGGCCGCAG‑CCAGGGTGAAACCTGCCTGTTCATTGGTGCGGTGCAGGGCATCCACAAAGGTATCGACAGCGAAACCTCGCTGGCCATCTACCGtgacctgacc                                                   <  5:312894/149‑1 (MQ=255)                                                                                                 gTTCCAGGCCGACCTGCGTGTGGCATCCCTTGCCTTCACCCTGGGCCGCAG‑CCAGGGTGAAACCTGCCTGTTCATTGGTGCGGTGCAGGGCATCCACAAAGGTATCGACAGCGAAACCTCGCTGGCCATCTACCGTGACCTGACCAAg                                                >  3:119397/1‑148 (MQ=255)                                                                                                  ttCCAGGCCGACCTGCGTGTGGCATCCCTTGCCTTCACCCTGGGCCGCAG‑CCAGGGTGAAACCTGCCTGTTCATTGGTGCGGTGCAGGGCATCCACAAAGGTATCGACAGCGAAACCTCGCTGGCCATCTACCGTGACCTGACCAAg                                                <  6:252173/147‑1 (MQ=255)                                                                                                     cAGGCCGACCTGCGTGTGGCATCCCTTGCCTTCACCCTGGGCCGCAG‑CCAGGGTGAAACCTGCCTGTTCATTGGTGCGGTGCAgg                                                                                                           >  6:58657/1‑85 (MQ=255)                                                                                                       ggCCGACCTGCGTGTGGCATCCCTTGCCTTCACCCTGGGCCGCAG‑CCAGGGTGAAACCTGCCTGTTCATTGGTGCGGTGCAGGGCATCCACAAAGGTATCGACAGCGAAACCTCGCTGGCCATCTACCGTGACCTGACCAAGGACTTc                                          >  3:332975/1‑148 (MQ=255)                                                                                                       ggCCGACCTGCGTGTGGCATCCCTTGCCTTCACCCTGGGCCGCAG‑CCAGGGTGAAACCTGCCTGTTCATTGGTGCGGTGCAGGGCATCCACAAAGGTATCGACAGCGAAACCTCGCTGGCCATCTACCGTGACCTGACCAAGGACTTCg                                         <  4:119214/149‑1 (MQ=255)                                                                                                        gCCGACCTGCGTGTGGCATCCCTTGCCTTCACCCTGGGCCGCAG‑CCAGGGTGAAACCTGCCTGTTCATTGGTGCGGTGCAGGGCATCCACAAAGGTATCGACAGCGAAACCTCGCTGGCCATCTACCGTGACCTGACCAAGGatcaccc                                        >  1:166511/1‑143 (MQ=255)                                                                                                                          tCCCTTGCCTTCACCCTGGGCCGCAG‑CCAGGGTGAAACCTGCCTGTTCATTGGTGCGGTGCAGGGCATCCACAAAGGTATCGACAGCGAAACCTCGCTGGCCATCTACCGTGACCTGACCAAGGACTTCGAAGGGCTGCGGCCACGCAg                      >  5:114156/1‑149 (MQ=255)                                                                                                                            ccTTGCCTTCACCCTGGGCCGCAG‑CCAGGGTGAAACCTGCCTGTTCATTGGTGCGGTGCAGGGCATCCACAAAGGTATCGACAGCGAAACCTCGCTGGCCATCTACCGTGACCTGACCAAGGACTTCGAAGGGCTGCGGCCACGCAGcc                    >  2:278275/1‑149 (MQ=255)                                                                                                                              caggtttCACCCT‑GGCTGCGGCCCAGGGTGAAACCTGCCTGTTCATTGGTGCGGTGCAGGGCATCCACAAAGGTATCGACAGCGAAACCTCGCTGGCCATCTACCGTGACCTGACCAAGGACTTCGAAGGGCTGCGGCCACGCAGCCTg                  >  6:202672/6‑149 (MQ=255)                                                                                                                                 ccTTCACCCTGGGCCGCAG‑CCAGGGTGAAACCTGCCTGTTCAt                                                                                                                         <  4:128247/43‑1 (MQ=255)                                                                                                                                 ccTTCACCCTGGGCCGCAG‑CCAGGGTGAAACCTGCCTGTTCAt                                                                                                                         >  3:128247/1‑43 (MQ=255)                                                                                                                                 ccTTCACCCTGGGCCGCAG‑CCAGGGTGAAACCTGCCTGTTCATTGGTGCGGTGCAGGGCATCCACAAAGGTATCGACAGCGAAACCTCGCTGGCCATCTACCGTGACCTGACCAAGGACTTCGAAGGGCTGCGGCCACGCAGCCTGTTg               >  3:223586/1‑149 (MQ=255)                                                                                                                                  cTTCACCCTGGGCCGCAG‑CCAGGGTGAAACCTGCCTGTTCATTGGTGCGGTGCAGGGCATCCACAAAGGTATCGACAGCGAAACCTCGCTGGCCATCTACCGTGACCTGACCAAGGACTTCGAAGGGCTGCGGCCACGCAGCCTGTTGc              >  3:91027/1‑149 (MQ=255)                                                                                                                                   ttCACCCTGGGCCGCAG‑CCAGGGTGAAACCTGCCTGTTCATTGGTGCGGTGCAGGGCATCCACAAAGGTATCGACAGCGAAACCTCGCTGGCCATCTACCGTGACCTGACCAAGGACTTCGAAGGGCTGCGGCCACGCAGCCTGTTGCt             >  4:50660/1‑149 (MQ=255)                                                                                                                                            ggCCGCAG‑CCAGGGTGAAACCTGCCTGTTCATTGGGGCGGTGCAGGGCATCCACAAAGGTATCGACAGCGAAACCTCGCTGGCCATCTACCGTGACCTGACCAAGGACTTCGAAGGGCTGCGGCCACGCAGCCTGTTGCTCGAAGCGt     <  1:176628/148‑1 (MQ=255)                                                                                                                                              ccGCAG‑CCAGGGTGAAACCTGCCTGTTCATTGGTGCGGTGCAGGGCATCCACAAAGGTATCGACAGCGAAACCTCGCTGGCCATCTACCGTGACCTGACCAAGGACTTCGAAGGGCTGCGGCCACGCAGCCTGTTGCTCGAAGCGTTg   >  4:48172/1‑148 (MQ=255)                                                                                                                                              ccGCAG‑CCAGGGTGAAACCTGCCTGTTCATTGGTGCGGTGCAGGGCATCCACAAAGGTATCGACAGCGAAACCTCGCTGGCCATCTACCGTGACCTGACCAAGGACTTCGAAGGGCTGCGGCCACGCAGCCTGTTGCTCGAAGCGTTGa  <  1:278275/149‑1 (MQ=255)                                                                                                                                               cGCAG‑CCAGGGTGAAACCTGCCTGTTCATTGGTGCGGTGCAGGGCATCCACAAAGGTATCGACAGCGAAACCTCGCTGGCCATCTACCGTGACCTGACCAAGGACTTCGAAGGGCTGCGGCCACGCAGCCTGTTGCTCGAAGCGTTGa  >  2:15080/1‑148 (MQ=255)                                                                                                                                                  aG‑CCAGGGTGAAACCTGCCTGTTCATTGGTGCGGTGCAGGGCATCCACAAAGGTATCGACAGCGAAACCTCGCTGGCCATCTACCGTGACCTGACCAAGGACTTCGAAGGGCTGCGGCCACGCAGCCTGtt                <  4:276700/131‑1 (MQ=255)                                                                                                                                                  aG‑CCAGGGTGAAACCTGCCTGTTCATTGGTGCGGTGCAGGGCATCCACAAAGGTATCGACAGCGAAACCTCGCTGGCCATCTACCGTGACCTGACCAAGGACTTCGAAGGGCTGCGGCCACGCAGCCTGtt                >  3:276700/1‑131 (MQ=255)                                                                                                                                                  |                                                                                                                                                  GAGGCTGTGTGACCTGTCCAGCCACTCGCCGGGCTGTTGCCTGGTGCTGGACCGGCCAATCTGGTTCAAGCGCGAAGGCGAGCTGGTGCTGAACCTGTTCCAGGCCGACCTGCGTGTGGCATCCCTTGCCTTCACCCTGGGCCGCAG‑CCAGGGTGAAACCTGCCTGTTCATTGGTGCGGTGCAGGGCATCCACAAAGGTATCGACAGCGAAACCTCGCTGGCCATCTACCGTGACCTGACCAAGGACTTCGAAGGGCTGCGGCCACGCAGCCTGTTGCTCGAAGCGTTGA  >  NC_002947/3553651‑3553940

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: ‑