Predicted mutation
evidence	seq id	position	mutation	freq	annotation	gene	description
RA	NC_002947	2,602,279	G→C	9.8%	E15Q (GAG→CAG)	PP_2281 →	capsid assembly protein

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NC_002947	2,602,279	0	G	C	9.8%	144.8 / 6.8	51	E15Q (GAG→CAG)	PP_2281	capsid assembly protein
Reads supporting (aligned to +/- strand):  ref base G (24/22);  new base C (2/3);  total (26/25)
Fisher's exact test for biased strand distribution p-value = 6.68e-01
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 1.53e-01

CGAATACTTCGGTGAGGGCGCAGAGCAAGTTCAATTCAACATCAACCCCCAGGCCAAGCGATACCGAGTGTTCGCTAATGGCCGCGTTCTCGAAGA‑CCTTTAATGGAAAGCATCGAAATCGTATCCCCGAACCCGTCTGCCCCCGAGGGGCATGATGAGGCAATGATTGCCGCCATCGACAAGGCCAATGCTGGCCCGGTAGGCGACAACATCACGACCCCTGCTGAAACCGTAGAGCGCCCCGAAGGCTTGCCCGAAGGCTTCGATTCCTGGGACCAACTGGCGAAAGCCTA  >  NC_002947/2602135‑2602427                                                                                                                                                  |                                                                                                                                                     cGAATACTTCGGTGAGGGCGCAGAGCAAGTTCAATTCAACATCAACCCCCAGGCCAAGCGATACCGAGTGTTCGCTAATGGCCGCGTTCTCGAAGA‑CCTTTAATGGAAAGCATCGAAATCGTATCCCCGAACCCGTCTGCCCCCGAggg                                                                                                                                                  >  3:334130/1‑149 (MQ=255) cGAATACTTCGGTGAGGGCGCAGAGCAAGTTCAATTCAACATCAACCCCCAGGCCAAGCGATACCGAGTGTTCGCTAATGGCCGCGTTCTCGAAGA‑CCTTTAATGGAAAGCATCGAAATCGTATCCCCGAACCCGTCTGCCCCCGAggg                                                                                                                                                  >  2:204807/1‑149 (MQ=255)      aCTTCGGTGAGGGCGCAGAGCAAGTTCAATTCAACATCAACCCCCAGGCCAAGCGATACCGAGTGTTCGCTAATGGCCGCGTTCTCGAAGA‑CCTTTAATGGAAAGCATCGAAATCGTATCCCCGAACCCGTCTGCCCCCGAGGGGCat                                                                                                                                              >  1:182905/1‑148 (MQ=255)       cTTCGGTGAGGGCGCAGAGCAAGTTCAATTCAACATCAACCCCCAGGCCAAGCGATACCGAGTGTTCGCTAATGGCCGCGTTCTCGAAGA‑CCTTTAATGGAAAGCATCGAAATCGTATCCCCGAACCCGTCTGCCCCTCGGGGGCagac                                                                                                                                            <  1:296038/149‑4 (MQ=255)       cTTCGGTGAGGGCGCAGAGCAAGTTCAATTCAACATCAACCCCCAGGCCAAGCGATACCGAGTGTTCGCTAATGGCCGCGTTCTCGAAGA‑CCTTTAATAGAAAGCATCGAAATCGTATCCCCGAACCCGTCTGCCCCTCGGGGGCagac                                                                                                                                            <  4:39468/149‑4 (MQ=255)        ttCGGTGAGGGCGCAGAGCAAGTTCAATTCAACATCAACCCCCAGGCCAAGCGATACCGAGTGTTCGCTAATGGCCGCGTTCTCGAAGA‑CCTTTAATGGAAAGCATCGAAATCGTATCCCCGAACCCGTCTGCCCCTCGGGGGCagac                                                                                                                                            >  2:296038/1‑145 (MQ=255)           ggTGAGGGCGCAGAGCAAGTTCAATTCAACATCAACCCCCAGGCCAAGCGATACCGAGTGTTCGCTAATGGCCGCGTTCTCGAAGA‑CCTTTAATGGAAAGCATCGAAATCGTATCCCCGAACCCGTCTGCCCCCGAGGGGCAtgatga                                                                                                                                         <  5:160621/148‑1 (MQ=255)           ggTGAGGGCGCAGAGCAAGTTCAATTCAACATCAACCCCCAGGCCAAGCGATACCGAGTGTTCGCTAATGGCCGCGTTCTCGAAGA‑CCTTTAATGGAAAGCATCGAAATCGTATCCCCGAACCCGTCTGCCCCCGAGGGGCATGATGAg                                                                                                                                        <  1:204807/149‑1 (MQ=255)            gTGAGGGCGCAGAGCAAGTTCAATTCAACATCAACCCCCAGGCCAAGCGATACCGAGTGTTCGCTAATGGCCGCGTTCTCGAAGA‑CCTTTAATGGAAAGCATCGAAATCGTATCCCCGAACCCGTCTGCCCCCGAGGGGCATGATGAgg                                                                                                                                       <  2:182905/149‑1 (MQ=255)                    gcAGAGCAAGTTCAATTCAACATCAACCCCCAGGCCAAGCGATACCGAGTGTTCGCTAATGGCCGCGTTCTCGAAGA‑CCTTTAATGGAAAGCATCGAAATCGTATCCCCGAACCCGTCTGCCCCTCGGGGGCagacg                                                                                                                                           <  5:132233/137‑5 (MQ=255)                    gcAGAGCAAGTTCAATTCAACATCAACCCCCAGGCCAAGCGATACCGAGTGTTCGCTAATGGCCGCGTTCTCGAAGA‑CCTTTAATGGAAAGCATCGAAATCGTATCCCCGAACCCGTCTGCCCCTCGGGGGCagacg                                                                                                                                           >  6:132233/1‑133 (MQ=255)                     cAGAGCAAGTTCAATTCAACCTCACCCCCCAGGCCCATCGATCCCGAGTGTTCGCTAATGGCCGCGTTCTCGAAGA‑ACTTTAATGGAAAGCATCGAAATAGTAGCCCCGAACCCGTCTGCCCCCGAGGGGCATGATGAGGCAATGATTg                                                                                                                              <  7:307472/149‑1 (MQ=255)                          cAAGTTCAATTCAACATCAACCCCCAGGCCAAGCGATACCGAGTGTTCGCTAATGGCCGCGTTCTCGAAGA‑CCTTTAATGGAAAGCATCGAAATCGTATCCCCGAACCCGTCTGCCCCCGAGGGGCATGATGAGGCAATGATTgccgcc                                                                                                                         <  6:69905/149‑1 (MQ=255)                                caattcaaCATCAACCCCCAGGCCAAGCGATACCGAGTGTTCGCTAATGGCCGCGTTCTCGAAGA‑CCTTTAATGGAAAGCATCGAAATCGTATCCCCGAACCCGTCTGCCCCCGAGGGGCATGATGAGGCAATGATTGCCGCCATCGa                                                                                                                    <  1:101318/148‑1 (MQ=255)                                   ttcaaCATCAACCCCCAGGCCAAGCGATACCGAGTGTTCGCTAATGGCCGCGTTCTCGAAGA‑CCTTTAATGGAAAGCATCGAAATCGTATCCCCGAACCCGTCTGCCCCCGAGGGGCATGATGAGGCAATGATTGCCGCCATCGACAAg                                                                                                                >  3:341693/1‑149 (MQ=255)                                   ttcaaCATCAACCCCCAGGCCAAGCGATACCGAGTGTTCGCTAATGGCCGCGTTCTCGAAGA‑CCTTTAATGGAAAGCATCGAAATCGTATCCCCGAACCCGTCTGCCCCCGAGGGGCATGATGAGGCAATGATTGCCGCCATCGACAAg                                                                                                                >  3:148490/1‑149 (MQ=255)                                        cATCAACCCCCAGGCCAAGCGATACCGAGTGTTCGCTAATGGCCGCGTTCTCGAAGA‑CCTTTAATGGAAAGCATCGAAATCGTATCCCCGAACCCGTCTGCCCCCGAGGGGCATGATGAGGCAATGATTGCCGCCATCGACAAGGCCaa                                                                                                           >  1:292716/1‑149 (MQ=255)                                         aTCAACCCCCAGGCCAAGCGATACCGAGTGTTCGCTAATGGCCGCGTTCTCGAAGA‑CCTTTAATGGAAAGCATCGAAATCGTATCCCCGAACCCGTCTGCCCCCGAGGGGCATGATGAGGCAATGATTGCCGCCATCGACAAGGCCAAt                                                                                                          >  1:362484/1‑149 (MQ=255)                                          tCAACCCCCAGGCCAAGCGATACCGAGTGTTCGCTAATGGCCGCGTTCTCGAAGA‑CCTTTAATGGAAAGCATCGAAATCGTATCCCCGAACCCGTCTGCCCCCGAGGGGCATGATGAGGCAATGATTGCCGCCATCGACAAGGCCAATg                                                                                                         >  1:139174/1‑149 (MQ=255)                                             aCCCCCAGGCCAAGCGATACCGAGTGTTCGCTAATGGCCGCGTTCTCGAAGA‑CCTTTAATGGAAAGCATCGAAATCGTATCCCCGAACCCGTCTGCCCCCGAGGGGCATGATGAGGCAATGATTGCCGCCATCGACAAGGCCAATGCTg                                                                                                      >  6:363176/1‑149 (MQ=255)                                               ccccAGGCCAAGCGATACCGAGTGTTCGCTAATGGCCGCGTTCTCGAAGA‑CCTTTAATGGAAAGCATCGAAATCGTATCCCCGAACCCGTCTGCCCCCGAGGGGCatga                                                                                                                                            >  3:15825/1‑109 (MQ=255)                                               ccccAGGCCAAGCGATACCGAGTGTTCGCTAATGGCCGCGTTCTCGAAGA‑CCTTTAATGGAAAGCATCGAAATCGTATCCCCGAACCCGTCTGCCCCCGAGGGGCatga                                                                                                                                            <  4:15825/109‑1 (MQ=255)                                                   aGGCCAAGCGATACCGAGTGTTCGCTAATGGCCGCGTTCTCGAAGA‑CCTTTAATGGAAAGCATCGAAATCGTATCCCCGAACCCGTCTGCCCCCGAGGGGCATGATGAGGCAATGATTGCCGCCATCGACAAGGCCAATGCTGGCCCgg                                                                                                <  4:148490/149‑1 (MQ=255)                                                    ggCCAAGCGATACCGAGTGTTCGCTAATGGCCGCGTTCTCGAAGAGCCTTTAATGGAAAGCATCGAAATCGTATCCCCGAACCCGTCTGCCCCCGAGGGGCATGATGAGGCAATGATTGCCGCCATCGACAAGGCCAATGCTGGCCCgg                                                                                                >  1:269203/1‑149 (MQ=255)                                                       cAAGCGATACCGAGTGTTCGCTAATGGCCGCGTTCTCGAAGA‑CCTTTAATGGAAAGCATCGAAATCGTATCCCCGAACCCGTCTGCCCCCGAGGGGCATGATGAGGCAATGATTGCCGCCATCGACAAGGCCAATGCTGGCCCGGTAgg                                                                                            <  3:186618/149‑1 (MQ=255)                                                                 cGAGTGTTCGCTAATGGCCGCGTTCTCGAAGA‑CCTTTAATGGAAAGCATCGAAATCGTATCCCCGAACCCGTCTGCCCCCGAGGGGCATGATGAGGCaa                                                                                                                                    <  8:271713/99‑1 (MQ=255)                                                                 cGAGTGTTCGCTAATGGCCGCGTTCTCGAAGA‑CCTTTAATGGAAAGCATCGAAATCGTATCCCCGAACCCGTCTGCCCCCGAGGGGCATGATGAGGCaa                                                                                                                                    >  7:271713/1‑99 (MQ=255)                                                                 cGAGTGTTCGCTAATGGCCGCGTTCTCGAAGA‑CCTTTAATGGAAAGCATCGAAATCGTATCCCCGAACCCGTCTGCCCCCGAGGGGCATGATGAGGCAATGATTGCCGCCATCGACAAGGCCAATGCTGGCCCGGTAGGCGACAACAt                                                                                   >  1:61651/1‑148 (MQ=255)                                                                 cGAGTGTTCGCTAATGGCCGCGTTCTCGAAGA‑CCTTTAATGGAAAGCATCGAAATCGTATCCCCGAACCCGTCTGCCCCCGAGGGGCATGATGAGGCAATGATTGCCGCCATCGACAAGGCCAATGCTGGCCCGGTAGGCGACAACATc                                                                                  <  2:269203/149‑1 (MQ=255)                                                                   aGTGTTCGCTAATGGCCGCGTTCTCGAAGA‑CCTTTAATGGAAAGCATCGAAATCGTATCCCCGAACCCGTCTGCCCCCGAGGGGCATGATGAGGCAATGATTGCCGCCATCGACAAGGCCAATGCTGGCCCGGTAGGCGa                                                                                         >  6:324585/1‑140 (MQ=255)                                                                   aGTGTTCGCTAATGGCCGCGTTCTCGAAGA‑CCTTTAATGGAAAGCATCGAAATCGTATCCCCGAACCCGTCTGCCCCCGAGGGGCATGATGAGGCAATGATTGCCGCCATCGACAAGGCCAATGCTGGCCCGGTAGGCGa                                                                                         <  5:324585/140‑1 (MQ=255)                                                                       ttCGCTAATGGCCGCGTTCTCGAAGA‑CCTTTAATGGAAAGCATCGAAATCGTATCCCCGAACCCGTCTGCCCCCGAGGGGCATGATGAGGCAATGATTGCCGCCATCGACAAGGCCAATGCTGGCCCGGTAGGCGACAACATCACGAcc                                                                            >  2:152623/1‑149 (MQ=255)                                                                          gCTAATGGCCGCGTTCTCGAAGA‑CCTTTAATGGAAAGCATCGAAATCGTATCCCCGAACCCGTCTGCCCCCGAGGGGCATGATGAGGCAATGATTGCCGCCATCGACAAGGCCAATGCTGGCCCGGTAGGCGACAACATCACGAccc                                                                           >  6:352815/1‑147 (MQ=255)                                                                             aaTGGCCGCGTTCTCGAAGA‑CCTTTAATGGAAAGCATCGAAATCGTATCCCCGAACCCGTCTGCCCCCGAGGGGCATGATGAGGCAATGATTGCCGCCATCGACAAGGCCAATGCTGGCCCGGTAGGCGACAACATCACGACCCctgct                                                                      >  8:246801/1‑149 (MQ=255)                                                                               tGGCCGCGTTCTCGAAGA‑CCTTTAATGGAAAGCATCGAAATCGTATCCCCGAACCCGTCTGCCCCCGAGGGGCATGATGAGGCAATGATTGCCGCCATCGACAAGGCCAATGCTGGCCCGGTAGGCGACAACATCACGACCCctgctg                                                                     >  1:322263/1‑148 (MQ=255)                                                                                 gCCGCGTTCTCGAAGA‑CCTTTAATGGAAAGCATCGAAATCGTATCCCCGAACCCGTCTGCCCCCGAGGGGCATGATGAGGCAATGATTGCCGCCATCGACAAGGCCAATGCTGGCCCGGTAGGCGACAACATCACGACCCCTGCTGaaa                                                                  <  7:246801/149‑1 (MQ=255)                                                                                  ccGCGTTCTCGAAGA‑CCTTTAATGGAAAGCATCGAAATCGTATCCCCGAACCCGTCTGCCCCCGAGGGGCATGATGAGGCAATGATTGCCGCCATCGACAAGGCCAATGCTGGCCCGGTAGGCGACAACATCACGACCCCTGCTGAAAc                                                                 >  6:889/1‑149 (MQ=255)                                                                                         ctcGAAGA‑CCTTTAATGGAAAGCATCGAAATCGTATCCCCGAACCCGTCTGCCCCCGAGGGGCATGATGAGGCAATGATTGCCGCCATCGACAAGGCCAATGCTGGCCCGGTAGGCGACAACATCACGACCCCTGCTGAAACCGTaga                                                           <  2:61651/148‑1 (MQ=255)                                                                                            gAAGA‑CCTTTAATGGAAAGCATCGAAATCGTATCCCCGAACCCGTCTGCCCCCGAGGGGCATGATGAg                                                                                                                                        >  8:171918/1‑68 (MQ=255)                                                                                            gAAGA‑CCTTTAATGGAAAGCATCGAAATCGTATCCCCGAACCCGTCTGCCCCCGAGGGGCATGATGAg                                                                                                                                        <  7:171918/68‑1 (MQ=255)                                                                                                               gCATCGAAATCGTATCCCCGAACCCGTCTGCCCCCGAGGGGCATGATGAGGCAATGATTGCCGCCATCGACAAGGCCAATGCTGGCCCGGTAGGCGACAACATCACGACCCCTGCTGAAACCGTAGAGCGCCCCGAAGGCTTGCCCGaa                                     <  5:889/149‑1 (MQ=255)                                                                                                               gCATCGAAATCGTATCCCCGAACCCGTCTGCCCCCGAGGGGCATGATGAGGCAATGATTGCCGCCATCGACAAGGCCAATGCTGGCCCGGTAGGCGACAACATCACGACCCCTGCTGAAACCGTAGAGCGCCCCGAAGGCTTGCCCGaa                                     <  4:341693/149‑1 (MQ=255)                                                                                                               gCATCGAAATCGTATCCCCGAACCCGTCTGCCCCCGAGGGGCATGATGAGGCAATGATTGCCGCCATCGACAAGGCCAATGCTGGCCCGGTAGGCGACAACATCACGACCCCTGCTGAAACCGTAGAGCGCCCCGAAGGCTTGCCCGaa                                     <  2:139174/149‑1 (MQ=255)                                                                                                                               cccGAACCCGTCTGCCCCCGAGGGGCATGATGAGGCAATGATTGCCGCCATCGACCAGGCCAATGCTGGCCCGGTAGGCGCCAACCTCACGACCCCTGCTGAACCCGTAGAGCGCCCCGAAGGCTTGCCCGAAGGCTGCGAGTCCTggg                     >  5:241370/1‑149 (MQ=255)                                                                                                                                      ccGTCTGCCCCCGAGGGGCATGATGAGGCAATGATTGCCGCCATCGACAAGGCCAATGCTGGCCCGGTAGGCGACAACATCACGACCCCTGCTGAAACCGTAGAGCGCCCCGAAGGCTTGCCCGAAGGCtt                                <  5:293466/131‑1 (MQ=255)                                                                                                                                      ccGTCTGCCCCCGAGGGGCATGATGAGGCAATGATTGCCGCCATCGACAAGGCCAATGCTGGCCCGGTAGGCGACAACATCACGACCCCTGCTGAAACCGTAGAGCGCCCCGAAGGCTTGCCCGAAGGCtt                                >  6:293466/1‑131 (MQ=255)                                                                                                                                        gTCTGCCCCCGAGGGGCATGATGAGGCAATGATTGCCGCCATCGACAAGGCCAATGCTGGCCCGGTAGGCGACAACATCACGACCCCTGCTGAAACCGTAGAGCGCCCCGAAGGCTTg                                           <  7:187696/118‑1 (MQ=255)                                                                                                                                        gTCTGCCCCCGAGGGGCATGATGAGGCAATGATTGCCGCCATCGACAAGGCCAATGCTGGCCCGGTAGGCGACAACATCACGACCCCTGCTGAAACCGTAGAGCGCCCCGAAGGCTTg                                           >  8:187696/1‑118 (MQ=255)                                                                                                                                         tCTGCCCCCGAGGGGCATGATGAGGCAATGATTGCCGCCATCGACAAGGCCAATGCTGGCCCGGTAGGCGACAACATCACGACCCCTGTTGAAACCGTAGAGCGCCCCGAAGGCTTGCCCGAAGGCTTCGATTCCTGGGACCAACTGGc           <  5:363176/149‑1 (MQ=255)                                                                                                                                         tCTGCCCCCGAGGGGCATGATGAGGCAATGATTGCCGCCATCGACAAGGCCAATGCTGGCCCGGTAGGCGACAACATCACGACCCCTGCTGAAACCGTAGAGCGCCCCGAAGGCTTGCCCGAAGGCTTCGATTCCTGGGACCAACTGGc           <  5:352815/149‑1 (MQ=255)                                                                                                                                             cccccGAGGGGCATGATGAGGCAATGATTGCCGCCATCGACAAGGCCAATGCTGGCCCGGTAGGCGACAACATCACGACCCCTGCTGAAACCGTAGAGCGCCCCGAAGGCTTGCCCGAAGGCTTCGATTCCTGGGACCAACTGGCGa         >  1:300404/1‑147 (MQ=255)                                                                                                                                                  gAGGGGCATGATGAGGCAATGATTGCCGCCATCGACAAGGCCAATGCTGGCCCGGTAGGCGACAACATCACGACCCCTGCTGAAACCGTAGAGCGCCCCGAAGGCTTGCCCGAAGGCTTCGATTCCTGGGACCAACTGGCGAAAGCCTa  >  4:252668/1‑149 (MQ=255)                                                                                                                                                  |                                                                                                                                                     CGAATACTTCGGTGAGGGCGCAGAGCAAGTTCAATTCAACATCAACCCCCAGGCCAAGCGATACCGAGTGTTCGCTAATGGCCGCGTTCTCGAAGA‑CCTTTAATGGAAAGCATCGAAATCGTATCCCCGAACCCGTCTGCCCCCGAGGGGCATGATGAGGCAATGATTGCCGCCATCGACAAGGCCAATGCTGGCCCGGTAGGCGACAACATCACGACCCCTGCTGAAACCGTAGAGCGCCCCGAAGGCTTGCCCGAAGGCTTCGATTCCTGGGACCAACTGGCGAAAGCCTA  >  NC_002947/2602135‑2602427

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: ‑