Predicted mutation
evidence	seq id	position	mutation	freq	annotation	gene	description
RA	NC_002947	5,963,846	T→G	10.4%	Y216D (TAT→GAT)	PP_5229 →	hypothetical protein

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NC_002947	5,963,846	0	T	G	10.4%	156.1 / 3.9	53	Y216D (TAT→GAT)	PP_5229	hypothetical protein
Reads supporting (aligned to +/- strand):  ref base T (26/21);  new base G (4/2);  total (30/23)
Fisher's exact test for biased strand distribution p-value = 6.87e-01
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 1.00e+00

TGTTCGGTGAAGAACAGCGCCGGGAAGTAGGCTCCAGCGCCGTGGCAGCTCTTGAGTACCAGGGGCTGCATGGGGTTCTGGCCATCGGCAGCCGCGACCCGCAACACTA‑CAAGAGCAGCGTCGGTACCCTTTTCCTCGGCTATATCGCCGAGGTGCTTGGCCGCGTTGTGCCACGCGTCACCCAGACCCTGCGCCCGGTACGCTGATGAAACGCCAGCTGGAGGCTTATTGCGCACACCTGCGCAACGAGCGCCAGGTGTCGGAGCACACCTCGCAGGGCTACCGTC  >  NC_002947/5963706‑5963992                                                                                                                                              |                                                                                                                                                   tGTTCGGTGAAGAACAGCGCCGGGAAGTAGGCTCCAGCGCCGTGGCAGCTCTTGAGTACCAGGGGCTGCATGGGGTTCTGGCCATCGGCAGCCGCGACCCGCAACACTA‑CAAGAGCAGCGTCGGTACCCTTTTCCTCGGCGATATAGcc                                                                                                                                            >  6:42731/1‑149 (MQ=255) tGTTCGGTGAAGAACAGCGCCGGGAAGTAGGCTCCAGCGCCGTGGCAGCTCTTGAGTACCAGGGGCTGCATGGGGTTCTGGCCATCGGCAGCCGCGACCCGCAACACTA‑CAAGAGCAGCGTCGGTACCCGTTTCCTCGGCTATTTCGcc                                                                                                                                            >  6:72892/1‑149 (MQ=255)        tGAAGAACAGCGCCGGGAAGTAGGCTCCAGCGCCGTGGCAGCTCTTGAGTACCAGGGGCTGCATGGGGTTCTGGCCATCGGCAGCCGCGACCCGCAACACTA‑CAAGAGCAGCGTCGGTACCCTTTTCCTCGGCTATATCGCCGAGGTGc                                                                                                                                     <  4:127647/149‑1 (MQ=255)          aagaaCAGCGCCGGGAAGTAGGCTCCAGCGCCGTGGCAGCTCTTGAGTACCAGGGGCTGCATGGGGTTCTGGCCATCGGCAGCCGCGACCCGCAACACTA‑CAAGAGCAGCGTCGGTACCCTTTTCCTCGGCGATATAGCCGAggaaaa                                                                                                                                    <  5:42731/148‑5 (MQ=255)                 gcgcCGGGAAGTAGGCTCCAGCGCCGTGGCAGCTCTTGAGTACCAGGGGCTGCATGGGGTTCTGGCCATCGGCAGCCGCGACCCGCAACACTA‑CAAGAGCAGCGTCGGTACCCTTTTCCTCGGCTATATCGCCGAGGTGCTTGGCcgcg                                                                                                                            <  1:301928/149‑1 (MQ=255)                         aaGTAGGCTCCAGCGCCGTGGCAGCTCTTGAGTACCAGGGGCTGCATGGGGTTCTGGCCATCGGCAGCCGCGACCCGCAACACTA‑CAAGAGCAGCGTGGGTACCCTTTTCCTCGGCTATATCGCCGAGGTGCTTGGCCGCGTTGTGCCa                                                                                                                    >  2:311975/1‑149 (MQ=255)                         aaGTAGGCTCCAGCGCCGTGGCAGCTCTTGAGTACCAGGGGCTGCATGGGGTTCTGGCCATCGGCAGCCGCGACCCGCAACACTA‑CAAGAGCAGCGTCGGTACCCTTTTCCTCGGCTTTATCGCCGAGGTGCTTGGCCGCGTTGTGCCa                                                                                                                    >  3:59362/1‑149 (MQ=255)                          aGTAGGCTCCAGCGCCGTGGCAGCTCTTGAGTACCAGGGGCTGCATGGGGTTCTGGCCATCGGCAGCCGCGACCCGCAACACTA‑CAAGAGCAGCGTCGGTACCCTTTTCCTCGGCTATATCGCCGAGGTGCTTGGCCGCGTTGTGCCAc                                                                                                                   <  1:40299/149‑1 (MQ=255)                           tttggCTCCAGCGCCGTGGCAGCTCTTTAGTACCACGGGCTGCATGGGGTTCTGGCCATCGGCAGCCGCGACCCGCAACACTACCAAGAGCAGCGTCGGTACCCTTTTCCTCGGCTATATCGCCGAGGTGCTTGGCCGCGTTGTGCCa                                                                                                                    <  1:96198/145‑1 (MQ=255)                                 tCCAGCGCCGTGGCAGCTCTTGAGTACCAGGGGCTGCATGGGGTTCTGGCCATCGGCAGCCGCGACCCGCAACACTA‑CAAGAGCAGCGTCGGTACCCTTTTCCTCGGCTATATCGCCGAGGTGCTTGGCCGCGTTGTGCCACGCGTCAc                                                                                                            >  8:173966/1‑149 (MQ=255)                                         cGTGGCAGCTCTTGAGTACCAGGGGCTGCATGGGGTTCTGGCCATCGGCAGCCGCGACCCGCAACACTA‑CAAGAGCAGCGTCGGTACCCTTTTCCTCGGCTATATCGCCGAGGTGCTTGGcc                                                                                                                               <  1:52673/122‑1 (MQ=255)                                         cGTGGCAGCTCTTGAGTACCAGGGGCTGCATGGGGTTCTGGCCATCGGCAGCCGCGACCCGCAACACTA‑CAAGAGCAGCGTCGGTACCCTTTTCCTCGGCTATATCGCCGAGGTGCTTGGcc                                                                                                                               >  2:52673/1‑122 (MQ=255)                                             gCAGCTCTTGAGTACCAGGGGCTGCATGGGGTTCTGGCCATCGGCAGCCGCGACCCGCAACACTA‑CAAGAGCAGCGTCGGTACCCTTTTCCTCGGCTATATCGCCGAGGTGCTTGGCCGCGTTGTGCCACGCGTCCCCCCGACCCTgcg                                                                                                >  8:104245/1‑149 (MQ=255)                                                  tctTGAGTACCAGGGGCTGCATGGGGTTCTGGCCATCGGCAGCCGCGACCCGCAACACTA‑CAAGAGCAGCGTCGGTACCCTTTTCCTCGGCTATATCGCCGAGGTGCTTGGCCGCGTTGTGCCACGCGTCAc                                                                                                            >  3:47529/1‑132 (MQ=255)                                                  tctTGAGTACCAGGGGCTGCATGGGGTTCTGGCCATCGGCAGCCGCGACCCGCAACACTA‑CAAGAGCAGCGTCGGTACCCTTTTCCTCGGCTATATCGCCGAGGTGCTTGGCCGCGTTGTGCCACGCGTCAc                                                                                                            <  4:47529/132‑1 (MQ=255)                                                    ttGAGTACCAGGGGCTGCATGGGGTTCTGGCCATCGGCAGCCGCGACCCGCAACACTA‑CAAGAGCAGCGTCGGTACCCTTTTCCTCGGCTATATCGCCGAGGTGCTTGGCCGCGTTGTGCCACGCGTCACCCAGACCCTGCGCCCgg                                                                                           <  7:101450/147‑1 (MQ=255)                                                      gAGTACCAGGGTCTGCATGGGTTTCTGGCCATCGGCAGCCGCGACCCGCAACACTA‑CAAGAGCAGCGTCGGTACCCTTTTCCTCGGCTATATCGCCGAGGTGCTTGGCCGCGTTGTGCCACGCGTCACCCAGACCCTGCGCCCGGTa                                                                                         <  6:248867/147‑1 (MQ=255)                                                         tACCAGGGGCTGCATGGGGTTCTGGCCATCGGCAGCCGCGACCCGCAACACTA‑CAAGAGCAGCGTCGGTACCCTTTTCCTCGGCTATATCGCCGAGGTGCTTGGCCGCGTTGTGCCACGCGTCACCCAGACCCTGCGCCCGGTACGCt                                                                                     >  7:10824/1‑148 (MQ=255)                                                                ggCTGCATGGGGTTCTGGCCATCGGCAGCCGCGACCCGCAACACTA‑CAAGAGCAGCGTTGGTACCCTTTTCCTCGGCTATATCGCCGAGGTGCTTGGCCGCGTTGTGCCACGCGTCACCCAGACCCTGCGCCCGGTACGCTGATGAAAc                                                                             <  1:311975/149‑1 (MQ=255)                                                                ggCTGCATGGGGTTCTGGCCATCGGCAGCCGCGACCCGCAACACTA‑CAAGAGCAGCGTCGGTACCCTTTTCCTCGGCTATATCGCCGAGGTGCTTGGCCGCGTTGTGCCACGCGTCACCCAGACCCTGCGCCCGGTACGCTGATGAAAc                                                                             <  4:228212/149‑1 (MQ=255)                                                                  cTGCATGGGGTTCTGTCCATCGGCAGCCGCGACCCGCAACACTA‑CAAGAGCAGCGTCGGTACCCTTTTCCTCGGCTATATCGCCGAGGTGCTTGGCCGCGTTGTGCCACGCGTCACCCAGACCCTGCGCCCGGTACGCTGATGAAACGc                                                                           <  6:101148/149‑1 (MQ=255)                                                                    gCATGGGGTTCTGGCCATCGGCAGCCGCGACCCGCAACACTA‑CAAGAGCAGCGTCGGTACCCTTTTCCTCGGCTATATCGCCGAGGTGCTTGGCCGCGTTGTGCCACGCGTCACCCAGACCCTGCGCCCGGTACGCTGATGAAACGc                                                                           >  4:127171/1‑147 (MQ=255)                                                                     cATGGGGTTCTGGCCATCGGCAGCCGCGACCCGCAACACTA‑CAAGAGCAGCGTCGGTACCCTTTTCCTCGGCTATATCGCCGAGGTGCTTgg                                                                                                                                 >  2:119114/1‑92 (MQ=255)                                                                     cATGGGGTTCTGGCCATCGGCAGCCGCGACCCGCAACACTA‑CAAGAGCAGCGTCGGTACCCTTTTCCTCGGCTATATCGCCGAGGTGCTTgg                                                                                                                                 <  1:119114/92‑1 (MQ=255)                                                                                    aTCGGCAGCCGCGACCCGCAACACTA‑CAAGAGCAGCGTCGGTACCCTTTTCCTCGGCGATATAGCCGAg                                                                                                                                         <  5:140008/69‑1 (MQ=255)                                                                                    aTCGGCAGCCGCGACCCGCAACACTA‑CAAGAGCAGCGTCGGTACCCTTTTCCTCGGCGATATAGCCGAg                                                                                                                                         >  6:140008/1‑69 (MQ=255)                                                                                              gcgACCCGCAACACTA‑CAAGAGCAGCGTCGGTACCCTTTTCCTCGGCTATATCGCCGAGGTGCTTGGCCGCGTTGTGCCACGCGTCACCCAGACCCTGCGCCCGGTACGCTGATGAAACGCCAGCTGGAg                                                                  >  6:221706/1‑130 (MQ=255)                                                                                              gcgACCCGCAACACTA‑CAAGAGCAGCGTCGGTACCCTTTTCCTCGGCTATATCGCCGAGGTGCTTGGCCGCGTTGTGCCACGCGTCACCCAGACCCTGCGCCCGGTACGCTGATGAAACGCCAGCTGGAg                                                                  <  5:221706/130‑1 (MQ=255)                                                                                                  cccGCAACACTA‑CAAGAGCAGCGTCGGTACCCTTTTCCTCGGCTATATCGCCGAGGTGCTTGGCCGCGTTGTGCCACGCGTCACCCAGACCCTGCGCCCGGTACGCTGATGaa                                                                               >  8:59271/1‑113 (MQ=255)                                                                                                  cccGCAACACTA‑CAAGAGCAGCGTCGGTACCCTTTTCCTCGGCTATATCGCCGAGGTGCTTGGCCGCGTTGTGCCACGCGTCACCCAGACCCTGCGCCCGGTACGCTGATGaa                                                                               <  7:59271/113‑1 (MQ=255)                                                                                                   ccGCAACACTA‑CAAGAGCAGCGTCGGTACCCTTTTCCTCGGCTATATCGCCGAGGTGCTTGGCCGCGTTGTGCCACGCGTCACCCAGACCCTGCGCCCGGTACGCTGATGAAACGCCAGCTGGAGGCTTATTGCGCACACCTGCGCAAc                                          >  3:135530/1‑149 (MQ=255)                                                                                                           cTA‑CAAGAGCAGCGTCGGTACCCTTTTCCTCGGCTATATCGCCGAGGTGCTTGGCCGCGTTGTGCCACGCGTCACCCAGACCCTGCGCCCGGTACGCTGATGAAACGCCAGCTGGAGGCTTATTGCGCACACCTGCGCAACGAGCGCCa                                  <  8:10824/149‑1 (MQ=255)                                                                                                            tA‑CAAGAGCAGCGTCGGTACCCTTTTCCTCGGCTATATCGCCGAGGTGCTTGGCCGCGTTGTGCCACGCGTCACCCAGACCCTGCGCCCGGTACGCTGATGAAACGCCAGCTGGAGGCTTATTGCGCACACCTGCGCAACGAGCGCCAg                                 >  4:55264/1‑149 (MQ=255)                                                                                                                aaGAGCAGCGTCGGTACCCTTTTCCTCGGCTATATCGCCGAGGTGCTTGGCCGCGTTGTGCCACGCGTCACCCAGACCCTGCGCCCGGTACGCTGATGAAACGCCAGCTGGAGGCTTATTGCGCACACCTGCGCAACGa                                        >  6:55563/1‑139 (MQ=255)                                                                                                                aaGAGCAGCGTCGGTACCCTTTTCCTCGGCTATATCGCCGAGGTGCTTGGCCGCGTTGTGCCACGCGTCACCCAGACCCTGCGCCCGGTACGCTGATGAAACGCCAGCTGGAGGCTTATTGCGCACACCTGCGCAACGa                                        <  5:55563/139‑1 (MQ=255)                                                                                                                aaGAGCAGCGTCGGTACCCTTTTCCTCGGCTATATCGCCGAGGTGCTTGGCCGCGTTGTGCCACGCGTCACCCAGACCCTGCGCCCGGTACGCTGATGAAACGCCAGCTGGAGGCTTATTGCGCACACCTGCGCAACGAGCGCCAGgtg                              >  5:127463/1‑149 (MQ=255)                                                                                                                aaGAGCAGCGTCGGTACCCTTTTCCTCGGCTATATCGCCGAGGTGCTTGGCCGCGTTGTGCCACGCGTCACCCAGACCCTGCGCCCGGTACGCTGATGAAACGCCAGCTGGAGGCTTATTGCGCACACCTGCGCAACGAGCGCCAGgtg                              >  3:85016/1‑149 (MQ=255)                                                                                                                  gagCAGCGTCGGTACCCTTTTCCTCGGCTATATCGCCGAGGTGCTTGGCCGCGTTGTGCCACGCGTCACCCAGACCCTGCGCCCGGTACGCTGATGAAACGCCAGCTGGAGGCTTATTGCGCACACCTGCGCAACGAgc                                      <  8:89077/139‑1 (MQ=255)                                                                                                                  gagCAGCGTCGGTACCCTTTTCCTCGGCTATATCGCCGAGGTGCTTGGCCGCGTTGTGCCACGCGTCACCCAGACCCTGCGCCCGGTACGCTGATGAAACGCCAGCTGGAGGCTTATTGCGCACACCTGCGCAACGAgc                                      >  7:89077/1‑139 (MQ=255)                                                                                                                  gagCAGCGTCGGTACCCTTTTCCTCGGCGATATCGCCGCGGTGCTTGGCCGCGTTGTGCCACGCGTCCCCCAGACCCTGCGCCCGGTACGCTGATGACACGCCAGCTGGCGGCTTATTGCGCACACCTGCGCAACGCGCGCCAGGGGTc                            >  4:41892/1‑149 (MQ=255)                                                                                                                        cGTCGGTACCCTTTTCCTCGGCTATATCGCCGAGGTGCTTGGCCGCGTTGTGCCACGCGTCACCCAGACCCTGCGCCCGGTACGCTGATGAAACGCCAGCTGGAGGCTTATTGCGCACACCTGCGCAACGAGCGCCAGGTGTCGGAGca                      >  7:177071/1‑149 (MQ=255)                                                                                                                           cGGTACCCTTTTCCTCGGCTATATCGCCGAGGTGCTTGGCCGCGTTGTGCCACGCGTCACCCAGACCCTGCGCCCGGTACGCTGATGAAACGCCAGCTGGAGGCTTATTGCGCACACCTGCGCAACGAGCGCCAGGTGTCGGAGCacac                   >  7:113085/1‑149 (MQ=255)                                                                                                                            ggTACCCTTTTCCTCGGCTATATCGCCGAGGTGCTTGGCCGCGTTGTGCCACGCGTCACCCAGACCCTGCGCCCGGTACGCTGATGAAACGCCAGCTGGAGGCTTATTGCGCACACCTGCGCAACGAGCGCCAGGTGTCGGAGCACAcc                  >  4:229733/1‑149 (MQ=255)                                                                                                                             gTACCCTTTTCCTCGGCTATATCGCCGAGGTGCTTGGCCGCGTTGTGCCACGCGTCACCCAGACCCTGCGCCCGGTACGCTGATGAAACGCCAGCTGGAGGCTTATTGCGCACACCTGCGCAACGAGCGCCAGGTGTCGGAGCACACCt                 >  3:137217/1‑149 (MQ=255)                                                                                                                                cccTTTTCCTCGGCTATATCGCCGAGGTGCTTGGCCGCGTTGTGCCACGCGTCACCCAGACCCTGCGCCCGGTACGCTGATGAAACGCCAGCTGGAGGCTTATTGCGCACACCTGCGCAACGAGCGCCAGGTGTCGGAGCACACCTCg               <  3:55264/148‑1 (MQ=255)                                                                                                                                   ttttCCTCGGCTATATCGCCGAGGTGCTTGGCCGCGTTGTGCCACGCGTCACCCAGACCCTGCGCCCGGTACGCTGATGAAACACCAGCTGGAGGCTTATTGCGCACACCTGCGCAACGAGCGcc                                   <  2:76759/125‑1 (MQ=255)                                                                                                                                   ttttCCTCGGCTATATCGCCGAGGTGCTTGGCCGCGTTGTGCCACGCGTCACCCAGACCCTGCGCCCGGTACGCTGATGAAACACCAGCTGGAGGCTTATTGCGCACACCTGCGCAACGAGCGcc                                   >  1:76759/1‑125 (MQ=255)                                                                                                                                       ccTCGGCGATATAGCCGAGGTGCTTGGCCGCGTTGTGCCACGCGTCACCCAGACCCTGCGCCCGGTACGCTGATGAAACGCCAGCTGGAGGCTTATTGCGCACACCTGCGCAACGAGCGCCAGGTGTCGGAGCACACCTCGCAGGGCTa       >  2:131967/1‑149 (MQ=255)                                                                                                                                         tCGGCTATATCGCCGAGGTGCTTGGCCGCGTTGTGCCACGCGTCACCCAGACCCTGCGCCCGGTACGCTGATGAAACGCCAGCTGGAGGCTTATTGCGCACACCTGCGCAACGAGCGCCAGGTGTCGGAGCACACCTCGCAGGGc         >  6:50805/1‑145 (MQ=255)                                                                                                                                         tCGGCTATATCGCCGAGGTGCTTGGCCGCGTTGTGCCACGCGTCACCCAGACCCTGCGCCCGGTACGCTGATGAAACGCCAGCTGGAGGCTTATTGCGCACACCTGCGCAACGAGCGCCAGGTGTCGGAGCACACCTCGCAGGGc         <  5:50805/145‑1 (MQ=255)                                                                                                                                         tCGGCTATATCGCCGAGGTGCTTGGCCGCGTTGTGCCACGCGTCACCCAGACCCTGCGCCCGGTACGCTGATGAAACGCCAGCTGGAGGCTTATTGCGCACACCTGCGCAACGAGCGCCAGGTGTCGGAGCACACCTCGCAGGGCTAcc     >  3:187903/1‑149 (MQ=255)                                                                                                                                         tCGGCTATATCGCCGAGGTGCTTGGCCGCGTTGTGCCACGCGTCACCCAGACCCTGCGCCCGGTACGCTGATGAAACGCCAGCTGGAGGCTTATTGCGCACACCTGCGCAACGAGCGCCAGGTGTCGGAGCACACCTCGCAGGGCTAcc     >  1:321290/1‑149 (MQ=255)                                                                                                                                            gCTATATCGCCGAGGTGCTTGGCCGCTTTGTGCCACGCGTCACCCAGACCCTGCGCCCGGTACGCTGATGAAACGCCAGCTGGAGGCTTATTGCGCACACCTGCGCAACGAGCGCCAGGTGTCGGAGCACACCTCGCAGGGCTACCGTc  <  7:153980/149‑1 (MQ=255)                                                                                                                                              |                                                                                                                                                   TGTTCGGTGAAGAACAGCGCCGGGAAGTAGGCTCCAGCGCCGTGGCAGCTCTTGAGTACCAGGGGCTGCATGGGGTTCTGGCCATCGGCAGCCGCGACCCGCAACACTA‑CAAGAGCAGCGTCGGTACCCTTTTCCTCGGCTATATCGCCGAGGTGCTTGGCCGCGTTGTGCCACGCGTCACCCAGACCCTGCGCCCGGTACGCTGATGAAACGCCAGCTGGAGGCTTATTGCGCACACCTGCGCAACGAGCGCCAGGTGTCGGAGCACACCTCGCAGGGCTACCGTC  >  NC_002947/5963706‑5963992

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: ‑