Predicted mutation
evidence	seq id	position	mutation	freq	annotation	gene	description
RA	NC_002947	5,816,531	C→G	11.5%	A114G (GCC→GGC)	PP_5092 →	NLP/P60 protein

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NC_002947	5,816,531	0	C	G	11.5%	148.2 / 10.1	52	A114G (GCC→GGC)	PP_5092	NLP/P60 protein
Reads supporting (aligned to +/- strand):  ref base C (24/22);  new base G (3/3);  total (27/25)
Fisher's exact test for biased strand distribution p-value = 1.00e+00
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 8.18e-01

CCATGTCGCCTAAGCAAAGCAGCGATGTGCTGAGCCGTGCGGTAAATGTGCTCGGTACTCCTTATGTTTGGGGCGGCAGCAGCCCGAAAAAAGGCTTTGACTGCAGCGGGCTGGTCAAATACGCCTTCAACGACGTCGCCGACGTCGACCTGCCGCGCACCTCCAATGCCATGGCCCGGGGCCACGGGGTGAAGGTGGCCAAGGGTGATCTGAAGCCTGGCGACCTGATCTTCTTCAACATCAAGAGCCGTCGGGTCAATCACGTAGCCATCTACCTGGGTAACGAC  >  NC_002947/5816393‑5816679                                                                                                                                           |                                                                                                                                                     ccATGTCGCCTAAGCAAAGCAGCGATGTGCTGAGCCGTGCGGTAAATGTGCTCGGTACTCCTTATGTTTGGGGCGGCAGCAGCCCGAAAAAAGGCTTTGACTGCAGCGGGCTGGTCAAATACGCCTTCAACGACGTCGCCGACGTCGAc                                                                                                                                            <  6:83445/149‑1 (MQ=255) ccATGTCGCCTAAGCAAAGCAGCGATGTGCTGAGCCGTGCGGTAAATGTGCTCGGTACTCCTTATGTTTGGGGCGGCAGCAGCCCGAAAAAAGGCTTTGACTGCAGCGGGCTGGTCAAATACGCCTTCAACGACGTCGCCGACGTCGAc                                                                                                                                            <  4:99622/149‑1 (MQ=255)    tGTCGCCTAAGCAAAGCAGCGATGTGCTGAGCCGTGCGGTAAATGTGCTCGGTACTCCTTATGTTTGGGGCGGCAGCAGCCCGAAAAAAGGCTTTGACTGCAGCGGGCTGGTCAAATACGCCTTCAACGACGTCGCCGACGTCGACCTg                                                                                                                                         <  8:76712/149‑1 (MQ=255)      tCGCCTAAGCAAAGCAGCGATGTGCTGAGCCGTGCGGTAAATGTGCTCGGTACTCCTTATGTTTGGGGCGGCAGCAGCCCGAAAAAAGGCTTTGACTGCAGCGGGCTGGTCAAATACGCCTTCAACGACGTCGCCGACGTCGACCTGcc                                                                                                                                       >  8:34722/1‑149 (MQ=255)      tCGCCTAAGCAAAGCAGCGATGTGCTGAGCCGTGCGGTAAATGTGCTCGGTACTCCTTATGTTTGGGGCGGCAGCAGCCCGAAAAAAGGCTTTGACTGCAGCGGGCTGGTCAAATACGCCTTCAACGACGTCGCCGACGTCGACCTGcc                                                                                                                                       >  2:216120/1‑149 (MQ=255)        gCCTAAGCAAAGCAGCGATGTGCTGAGCCGTGCGGTAAATGTGCGCGGTACTCCTTATGTTTGGGGCGGCAGCAGCCCGAAAAAAGGCTTTGACTGCAGCGGGCTGGTCAAATACGCCTTCAACGACGTCGCCGACGTCGACCTGCcgc                                                                                                                                     >  1:271037/1‑149 (MQ=255)        gCCTAAGAAAAGCAGCGATGTGCTGAGCCGTGCGGTAAATGTGCTCGGTACTCCTTATGTTTGGGGCGCCAGCAGCCCGAAAAAAGGCTTTGACTGCAGCGGGCTGGTCAAATACGCCTTCAACGACGTCGCCGACGTCGACCTGCcgc                                                                                                                                     >  3:9471/1‑149 (MQ=255)         ccTAAGCAAAGCAGCGATGTGCTGAGCCGTGCGGTAAATGTGCTCGGTACTCCTTATGTTTGGGGCGGCAGCAGCCCGAAAAAAGGCTTTGACTGCAGCGGGCTGGTCAAATACGCCTTCAACGACGTCGCCGACGTCGACCTGCcgcg                                                                                                                                    <  7:57548/149‑1 (MQ=255)          cTAAGCAAAGCAGCGATGTGCTGAGCCGTGCGGTAAATGTGCTCGGTACTCCTTATGTTTGGGGCGGCAGCAGCCCGAAAAAAGGCTTTGACTGCAGCGGGCTGGTCAAATACGCCTTCAACGACGTCGGCGACGTCgttga                                                                                                                                          >  1:31605/1‑138 (MQ=255)          cTAAGCAAAGCAGCGATGTGCTGAGCCGTGCGGTAAATGTGCTCGGTACTCCTTATGTTTGGGGCGGCAGCAGCCCGAAAAAAGGCTTTGACTGCAGCGGGCTGGTCAAATACGCCTTCAACGACGTCGGCGACGTCgttga                                                                                                                                          <  2:31605/142‑5 (MQ=255)              gcaaagcaGCGATGTGCTGAGCCGTGCGGTAAATGTGCTCGGTACTCCTTATGTTTGGGGCGGCAGCAGCCCGAAAAAAGGCTTTGACTGCAGCGGGCTGGTCAAATACGCCTTCAACGACGTCGCCGACGTCGACCTGCCgcgc                                                                                                                                   <  4:199298/145‑1 (MQ=255)              gcaaagcaGCGATGTGCTGAGCCGTGCGGTAAATGTGCTCGGTACTCCTTATGTTTGGGGCGGCAGCAGCCCGAAAAAAGGCTTTGACTGCAGCGGGCTGGTCAAATACGCCTTCAACGACGTCGCCGACGTCGACCTGCCgcgc                                                                                                                                   >  3:199298/1‑145 (MQ=255)                aaagcaGCGATGTGCTGAGCCGTGCGGTAAATGTGCTCGGTACTCCTTATGTTTGGGGCGGCAGCAGCCCGAAAAAAGGCTTTGACTGCAGCGGGCTGGTCAAATACGCCTTCAACGACGTCGCCGACGTCGACCTGCCGCGCACCTcc                                                                                                                             <  4:113978/149‑1 (MQ=255)                   gcagcGATGTGCTGAGCCGTGCGGTAAATGTGCTCGGTACTCCTTATGTTTGGGGCGGCAGCAGCCCGAAAAAAGGCTTTGACTGCAGCGGGCTGGTCAAATACGCCTTCAACGACGTCGCCGACGTCGACCTGCCGCGCACCTCCAAt                                                                                                                          >  3:23840/1‑149 (MQ=255)                      gcGATGTGCTGAGCCGTGCGGTAAATGTGCTCGGTACTCCTTATGTTTGGGGCGGCAGCAGCCCGAAAAAAGGCTTTGACTGCAGCGGGCTGGTCAAATACGCCTTCAACGACGTCGCCGACGTCGACCTGCCGCGCACCTCCAATGcc                                                                                                                       <  4:23840/149‑1 (MQ=255)                              cTGAGCCGTGCGGTAAATGTGCTCGGTACTCCTTATGTTTGGGGCGGCAGCAGCCCGAAAAAAGGCTTTGACTGCAGCGGGCTGGTCAAATACGCCTTCAACGACGTCGCCGACGTCGACCTGCCGCGCACCTCCAATGCCATGGCCCg                                                                                                               <  4:9471/149‑1 (MQ=255)                               tGAGCCGTGCGGTAAATGTGCTCGGTACTCCTTATGTTTGGGGCGGCAGCAGCCCGAAAAAAGGCTTTGACTGCAGCGGGCTGGTCAAATACGCCTTCAACGACGTCGCCGACGTCGACCTGCCGCGCACCTCCAATGCCATGGCCCgg                                                                                                              >  7:102461/1‑149 (MQ=255)                                gAGCCGTGCGGTAAATGTGCTCGGTACTCCTTATGTTTGGGGCGGCAGCAGCCCGAAAAAAGGCTTTGACTGCAGCGGGCTGGTCAAATACGCCTTCAACGACGTCGCCGACGTCGACCTGCCGCGCACCTCCAATGCCATGGCCCggg                                                                                                             >  7:11732/1‑149 (MQ=255)                                 aGCCGTGCGGTAAATGTGCTCGGTACTCCTTATGTTTGGGGCGGCAGCAGCCCGAAAAAAGGCTTTGACTGCAGCGGGCTGGTCAAATACGCCTTCAACGACGTCGCCGACGTCGACCTGCCGCGCACCTCCAATGCCATGGCCCggg                                                                                                             <  2:66071/148‑1 (MQ=255)                                   ccGTGCGGTAAATGTGCTCGGTACTCCTTATGTTTGGGGCGGCAGCAGCCCGAAAAAAGGCTTTGACTGCAGCGGGCTGGTCAAATACGCCTTCAACGACGTCGCCGACGTCGACCTGCCGCGCACCTCCAATGCCATGGCCCGGGGcc                                                                                                          >  4:211468/1‑149 (MQ=255)                                     gTGCGGTAAATGTGCTCGGTACTCCTTATGTTTGGGGCGGCAGCAGCCCGAAAAAAGGCTTTGACTGCAGCGGGCTGGTCAAATACGCCTTCAACGACGTCGCCGACGTCGACCTg                                                                                                                                         >  6:325899/1‑116 (MQ=255)                                     gTGCGGTAAATGTGCTCGGTACTCCTTATGTTTGGGGCGGCAGCAGCCCGAAAAAAGGCTTTGACTGCAGCGGGCTGGTCAAATACGCCTTCAACGACGTCGCCGACGTCGACCTg                                                                                                                                         <  5:325899/116‑1 (MQ=255)                                      tGCGGTAAATGTGCTCGGTACTCCTTATGTTTGGGGCGGCAGCAGCCCGAAAAAAGGCTTTGACTGCAGCGGGCTGGTCAAATACGCCTTCAACGACGTCGCCGACGTCGACCTGCCGCGCACCTCCAATGCCGTGGCCCCGGGCCatg                                                                                                       <  7:34722/149‑3 (MQ=255)                                        cGGTAAATGTGCTCGGTACTCCTTATGTTTGGGGCGGCAGCAGCCCGAAAAAAGGCTTTGACTGCAGCGGGCTGGTCAAATACGCCTTCAACGACGTCGCCGACGTCGACCTGCCGCGCACCTCCAATGCCATGGCCCCGGGCCATgg                                                                                                      <  7:51040/148‑1 (MQ=255)                                          gTAAATGTGCTCGGTACTCCTTATGTTTGGGGCGGCAGCAGCCCGAAAAAAGGCTTTGACTGCAGCGGGCTGGTCAAATACGCCTTCAACGACGTCGCCGACGt                                                                                                                                                <  6:282195/104‑1 (MQ=255)                                          gTAAATGTGCTCGGTACTCCTTATGTTTGGGGCGGCAGCAGCCCGAAAAAAGGCTTTGACTGCAGCGGGCTGGTCAAATACGCCTTCAACGACGTCGCCGACGt                                                                                                                                                >  5:282195/1‑104 (MQ=255)                                                     cGGTACTCCTTATGTTTGGGGCGGCAGCAGCCCGAAAAAAGGCTTTGACTGCAGCGGGCTGGTCAAATACGCCTTCAACGACGTCGCCGACGTCGACCTGCCGCGCACCTCCAATGCCATGGCCC‑GGGCCACGGGGTGAAGGTGGcc                                                                                         >  7:186607/1‑147 (MQ=255)                                                      ggTACTCCTTATGTTTGGGGCGGCAGCAGCCCGAAAAAAGGCTTTGACTGCAGCGGGCTGGTCAAATACGCCTTCAACGACGTCGCCGACGTCGACCTGCCGCGCTCCTCCAATGCCATGGCCCGGGGCCACGGGGTGAAGGTGGcc                                                                                         >  4:280714/1‑147 (MQ=255)                                                          cTCCTTATGTTTGGGGCGGCAGCAGCCCGAAAAAAGGCTTTGACTGCAGCGGGCTGGTCAAATACGCCTTCAACGACGTCGCCGACGTCGACCTGCCGCGCACCTCCAATGCCATGGCCC‑GGGCCACGGGGTGAAGGTGGCCAAGGGt                                                                                   <  8:186607/148‑1 (MQ=255)                                                           tCCTTATGTTTGGGGCGGCAGCAGCCCGAAAAAAGGCTTTGACTGCAGCGGGCTGGTCAAATACGCCTTCAACGACGTCGCCGACGTCGACCTGCCGCGCACCTCCAATGCCATGGCCCGGGGCCACGGGGTGAAGGTGGCCAAGGGt                                                                                   >  1:131211/1‑148 (MQ=255)                                                           tCCTTATGTTTGGGGCGGCAGCAGCCCG‑AAAAAGGCTTTGACTGCAGCGGGCTGGTCAAATACGCCTTCAACGACGTCGCCGACGTCGACCTGCCGCGCACCTCCAATGCCATGGCCCGGGGCCACGGGGTGAAGGTGGCCAAGGGTGa                                                                                 >  7:272367/1‑149 (MQ=255)                                                             cTTATGTTTGGGGCGGCAGCAGCCCGAAAAAAGGCTTTGACTGCAGCGGGCTGGTCAAATACGCCTTCAACGACGTCGCCGACGTCGACCTGCCGCGCACCTCCAATGcc                                                                                                                       >  3:140378/1‑110 (MQ=255)                                                             cTTATGTTTGGGGCGGCAGCAGCCCGAAAAAAGGCTTTGACTGCAGCGGGCTGGTCAAATACGCCTTCAACGACGTCGCCGACGTCGACCTGCCGCGCACCTCCAATGcc                                                                                                                       <  4:140378/110‑1 (MQ=255)                                                             cTTATGTTTGGGGCGGCAGCAGCCCGAAAAAAGGCTTTGACTGCAGCGGGCTGGTCAAATACGCCTTCAACGACGTCGCCGACGTCGACCTGCCGCGCACCTCCAATGCCATGGCCCGGGGCCACGGGGTGAAGGTGGCCAAGGGTGAt                                                                                <  2:131211/149‑1 (MQ=255)                                                              ttATGTTTGGGGCGGCAGCAGCCCGAAAAAAGGCTTTGACTGCAGCGGGCTGGTCAAATACGCCTTCAACGACGTCGCCGACGTCGACCTGCCGCGCACCTCCAATGCCATGGCCCGGGGCCACGGGGTGAAGGTGGCCAAGGGTGATc                                                                               >  6:63056/1‑149 (MQ=255)                                                                       gggCGGCAGCAGCCCGAAAAAAGGCTTTGACTGCAGCGGGCTGGTCAAATACGCCTTCAACGACGTCGCCGACGTCGACCTGCCGCGCACCTCCAATGCCATGGCCCGGGGCCACGGGGTGAAGGTGGCCAAGGGTGATCTGAAGCCTg                                                                      <  1:216120/149‑1 (MQ=255)                                                                         gcggcAGCAGCCCGAAAAAAGGCTTTGACTGCAGCGGGCTGGTCAAATACGCCTTCAACGACGTCGCCGACGTCGACCTGCCGCGCACCTCCAATGCCATGGCCCGGGGCCACGGGGTGAAGGTGGCCAAGGGTGATCTGAAGCCTGGc                                                                    <  2:186331/149‑1 (MQ=255)                                                                            gcagcaGCCCGAAAAAAGGCTTTGACTGCAGCGGGCTGGTCAAATACGCCTTCAACGACGTCGCCGACGTCGACCTGCCGCGCACCTCCAATGCCATGGCCCGGGGCCACGGGGTGAAGGTGGCCAAGGGTGATCTGAAGCCTGGCGAc                                                                 <  3:211468/149‑1 (MQ=255)                                                                               gcagcCCGAAAAAAGGCGTTGACTGCAGCGTGCTGGTCAAATACGCCTTCAACGACGTCGCCGACGTCGACCTGCCGCGCACCTCCAATGCCATGGCCCGGGGCCACGGGGTGAAGGTGGCCAAGGGTGATCTGAAGCCTGGCGACCTg                                                              <  3:190675/149‑1 (MQ=255)                                                                                  gcCCGAAAAAAGGCTTTGACTGCAGCGGGCTGGTCAAATACGCCTTCAACGACGTCGCCGACGTCGACCTGCCGCGCACCTCCAATGCCATGGCCCGGGGCCACGGGGTGAAGGTGGCCAAGGGTGATCTGAAGCCTGGCGACCTGAtc                                                           <  8:102461/149‑1 (MQ=255)                                                                                   cccGAAAAAAGGCTTTGACTGCAGCGGGCTGGTCAAATACGCCTTCAACGACGTCGCCGACGTCGACCTGCCGCGCACCTCCAATGCCATGGCCCGGGGCCACGGGGTGAAGGTGGCCAAGGGTGATCTGAAGCCTGGCGACCTGAtct                                                          >  1:315997/1‑149 (MQ=255)                                                                                                                         aCGCCTTCAACGACGTCGCCGACGTCGACCTGCCGCGCACCTCCAATGCCATGGCCCGGGGCCACGGGGTGAAGGTGGCCAAGGGTGATCTGAAGCCTGGCGACCTGATCTTCTTCAACATCAAGAGCCGTCGGGTCAATCACGTa                       >  7:287897/1‑146 (MQ=255)                                                                                                                         aCGCCTTCAACGACGTCGCCGACGTCGACCTGCCGCGCACCTCCAATGCCATGGCCCGGGGCCACGGGGTGAAGGTGGCCAAGGGTGATCTGAAGCCTGGCGACCTGATCTTCTTCAACATCAAGAGCCGTCGGGTCAATCACGTa                       <  8:287897/146‑1 (MQ=255)                                                                                                                             cTTCAACGACGTCGCCGACGTCGACCTGCCGCGCACCTCCAATGCCATGGCCCGGGGCCACGGGGTGAAGGTGGCCAAGGGTGATCTGAAGCCTGGCg                                                                   >  8:179331/1‑98 (MQ=255)                                                                                                                             cTTCAACGACGTCGCCGACGTCGACCTGCCGCGCACCTCCAATGCCATGGCCCGGGGCCACGGGGTGAAGGTGGCCAAGGGTGATCTGAAGCCTGGCGACCTGATCTTCTTCAACATCAAGAGCCGTCGGGTCAATCACGTAGCCATc                 >  7:100391/1‑148 (MQ=255)                                                                                                                              ttCAACGACGTCGCCGACGTCGACCTGCCGCGCACCTCCAATGCCATGGCCCGGGGCCACGGGGTGAAGGTGGCCAAGGGTGATCTGAAGCCTGGCGACCTGATCTTCTTCAACATCAAGAGCCGTCGGGTCAATCACGTAGCCATCTa               >  6:110114/1‑149 (MQ=255)                                                                                                                                 gtcgacgTCGGCGACGTCGACCTGCCGCGCACCTCCAATGCCATGGCCCGGGGCCACGGGGTGAAGGTGGCCAAGGGTGATCTGAAGCCTGGCGACCTGATCTTCTTCAACATCAAGAGCCGTCGGGTCAATCACGt                        >  3:144660/3‑137 (MQ=255)                                                                                                                                 gtcgacgTCGGCGACGTCGACCTGCCGCGCACCTCCAATGCCATGGCCCGGGGCCACGGGGTGAAGGTGGCCAAGGGTGATCTGAAGCCTGGCGACCTGATCTTCTTCAACATCAAGAGCCGTCGGGTCAATCACGt                        <  4:149538/135‑1 (MQ=255)                                                                                                                                 gtcgacgTCGGCGACGTCGACCTGCCGCGCACCTCCAATGCCATGGCCCGGGGCCACGGGGTGAAGGTGGCCAAGGGTGATCTGAAGCCTGGCGACCTGATCTTCTTCAACATCAAGAGCCGTCGGGTCAATCACGt                        <  4:144660/135‑1 (MQ=255)                                                                                                                                 gtcgacgTCGGCGACGTCGACCTGCCGCGCACCTCCAATGCCATGGCCCGGGGCCACGGGGTGAAGGTGGCCAAGGGTGATCTGAAGCCTGGCGACCTGATCTTCTTCAACATCAAGAGCCGTCGGGTCAATCACGt                        >  3:149538/3‑137 (MQ=255)                                                                                                                                 aaCGACGTCGCCGACGTCGACCTGCCGCGCACCTCCAATGCCATGGCCCGGGGCCACGGGGTGAAGGTGGCCAAGGGTGATCTGAAGCCTGGCGACCTGATCTTCTTCAACATCAAGAGCCGTCGGGTCAATCACGTAGCCATCTACCt            >  8:53883/1‑149 (MQ=255)                                                                                                                                       gTCGCCGACGTCGACCTGCCGCGCACCTCCAATGCCATGGCCCGGGGCCACGGGGTGAAGGTGGCCAAGGGTGATCTGAAGCCTGGCGACCTGATCTTCTTCAACATCAAGAGCCGTCGGGTCAATCACGTAGCCATCTACCTGGGTaa      >  8:160271/1‑149 (MQ=255)                                                                                                                                           ccGACGTCGACCTGCCGCGCACCTCCAATGCCATGGCCCGGGGCCACGGGGTGAAGGTGGCCAAGGGTGATCTGAAGCCTGGCGACCTGATCTTCTTCAACATCAAGAGCCGTCGGGTCAATCACGTAGCCATCTACCTGGGTAACGAc  <  5:63056/149‑1 (MQ=255)                                                                                                                                           |                                                                                                                                                     CCATGTCGCCTAAGCAAAGCAGCGATGTGCTGAGCCGTGCGGTAAATGTGCTCGGTACTCCTTATGTTTGGGGCGGCAGCAGCCCGAAAAAAGGCTTTGACTGCAGCGGGCTGGTCAAATACGCCTTCAACGACGTCGCCGACGTCGACCTGCCGCGCACCTCCAATGCCATGGCCCGGGGCCACGGGGTGAAGGTGGCCAAGGGTGATCTGAAGCCTGGCGACCTGATCTTCTTCAACATCAAGAGCCGTCGGGTCAATCACGTAGCCATCTACCTGGGTAACGAC  >  NC_002947/5816393‑5816679

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: ‑