Predicted mutation
evidence	seq id	position	mutation	freq	annotation	gene	description
RA	NC_002947	2,817,666	T→A	7.5%	D127V (GAC→GTC)	PP_5526 ←	hypothetical protein

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NC_002947	2,817,666	0	T	A	7.5%	158.8 / 2.6	53	D127V (GAC→GTC)	PP_5526	hypothetical protein
Reads supporting (aligned to +/- strand):  ref base T (27/22);  new base A (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 = 9.97e-01

AAGCCAACTCCATGCCAGAGCGCATTTTGTGCGTTCGTCCTTGTCTTTGAACCAGCTGAAGATCCTGTCTGACCGCGCGTGCTCGGTCCAGGCGTCTGATAGGCGCTTCAATGCACTCTCTTTCTGGCCGAAATCTCTGTCCCAGAGATCGAACAGTGCAATCAGTTGCTCCCTGTCAGTGAGTGTGCGGA‑AGACACTGCTACGTATTCGCAGTCCTGTTTTATTCCCTGCTTGAGCGGCGAGCCATTTTGGTTGTCGTCCGCTTTTTTCGACCCAGCTGAATGCCTC  >  NC_002947/2817527‑2817814                                                                                                                                            |                                                                                                                                                      aaGCCAACTCCATGCCAGAGCGCATTTTGTGCGTTCGTCCTTGTCTTTGAACCAGCTGAAGATCCTGTCTGACCGCGCGTGCTCGGTCCAGGCGTCTGATAGGCGCTTCAATGCACTCTCTTTCTGGCCGAAATCTCTGTCCCagag                                                                                                                                                <  7:134064/147‑1 (MQ=255)      aaCTCCATGCCAGAGCGCATTTTGTGCGTTCGTCCTTGTCTTTGAACCAGCTGAAGATCCTGTCTGACCGCGCGTGCTCGGTCCAGGCGTCTGATAGGCGCTTCAATGCACTCTCTTTCTGGCCGAAATCTCTGTCCCAGAGATCGAAc                                                                                                                                         <  5:197762/149‑1 (MQ=255)        cTCCATGCCAGAGCGCATTTTGTGCGTTCGTCCTTGTCTTTGAACCAGCTGAAGATCCTGTCTGACCGCGCGTGCTCGGTCCAGGCGTCTGATAGGCGCTTCAATGCACTCTCTTTCTGGCCGAAATCTCTGTCCCAGAGATCGAACAg                                                                                                                                       >  8:114683/1‑149 (MQ=255)          ccATGCCAGAGCGCATTTTGTGCGTTCGTCCTTGTCTTTGAACCAGCTGAAGATCCTGTCTGACCGCGCGTGCTCGGTCCAGGCGTCTGATAGGCGCTTCAATGCACTCTCTTTCTGGCCGAAATCTCTGTCCCAGAGATCGAACAGTg                                                                                                                                     >  3:242737/1‑149 (MQ=255)           cATGCCAGAGCGCATTTTGTGCGTTCGTCCTTGTCTTTGAACCAGCTGAAGATCCTGTCTGACCGCGCGTGCTCGGTCCAGGCGTCTGATAGGCGCTTCAATGCACTCTCTTTCTGGCCGAAATCTCTGTCCCag                                                                                                                                                  >  1:41069/1‑135 (MQ=255)           cATGCCAGAGCGCATTTTGTGCGTTCGTCCTTGTCTTTGAACCAGCTGAAGATCCTGTCTGACCGCGCGTGCTCGGTCCAGGCGTCTGATAGGCGCTTCAATGCACTCTCTTTCTGGCCGAAATCTCTGTCCCag                                                                                                                                                  <  2:41069/135‑1 (MQ=255)           cATGCCAGAGCGCATTTTGTGCGTTCGTCCTTGTCTTTGAACCAGCTGAAGATCCTGTCTGACCGCGCGTGCTCGGTCCAGGCGTCTGATAGGCGCTTCAATGCACTCTCTTTCTGGCCGAAATCTCTGTCCCAGAGATCGAACAGTg                                                                                                                                     >  5:116016/1‑148 (MQ=255)           cATGCCAGAGCGCATTTTGTGCGTTCGTCCTTGTCTTTGAACCAGCTGAAGATCCTGTCTGACCGCGCGTGCTCGGTCCAGGCGTCTGATAGGCGCTTCAATGCACTCTCTTTCTGGCCGAAATCTCTGTCCCAGAGATCGAACAGTGc                                                                                                                                    <  3:111634/149‑1 (MQ=255)               ccAGAGCGCATTTTGTGCGTTCGTCCTTGTCTTTGAACCAGCTGAAGATCCTGTCTGACCGCGCGTGCTCGGTCCAGGCGTCTGATAGGCGCTTCAATGCACTCTCTTTCTGGCCGAAATCTCTGTCCCAGAGATCGAACAGTGCAATc                                                                                                                                <  6:116016/149‑1 (MQ=255)                cAGAGCGCATTTTGTGCGTTCGTCCTTGTCTTTGAACCAGCTGAAGATCCTGTCTGACCGCGCGTGCTCGGTCCAGGCGTCTGATAGGCGCTTCAATGCACTCTCTTTCTGGCCGAAATCTCTGTCCCAGAGATCGAACAGTGCAAt                                                                                                                                 >  7:295993/1‑147 (MQ=255)                       cATTTTGTGCGTTCGTCCTTGTCTTTGAACCAGCTGAAGATCCTGTCTGACCGCGCGTGCTCGGTCCAGGCGTCTGATAGGCGCTTCAATGCACTCTCTTTCTGGCCGAAATCTCTGTCCCAGAGATCGAACAGTGCAATCAGTTGCTc                                                                                                                        <  7:62942/149‑1 (MQ=255)                           ttGTGCGTTCGTCCTTGTCTTTGAACCAGCTGAAGATCCTGTCTGACCGCGCGTGCTCGGTCCAGGCGTCTGATAGGCGCTTCAATGCACTCTCTTTCTGGCCGAAATCTCTGTCCCAGAGATCGAACAGTGCAATCAGTTGCTc                                                                                                                        <  8:180826/145‑1 (MQ=255)                           ttGTGCGTTCGTCCTTGTCTTTGAACCAGCTGAAGATCCTGTCTGACCGCGCGTGCTCGGTCCAGGCGTCTGATAGGCGCTTCAATGCACTCTCTTTCTGGCCGAAATCTCTGTCCCAGAGATCGAACAGTGCAATCAGTTGCTc                                                                                                                        >  7:180826/1‑145 (MQ=255)                                 gTTCGTCCTTGTCTTTGAACCAGCTGAAGATCCTGTCTGACCGCGCGTGCTCGGTCCAGGCGTCTGATAGGCGCTTCAATGCACTCTCTTTCTGGCCGAAATCTCTGTCCCAGAGATCGAACAGTGCAATCAGTTGCTCCCTGTCagt                                                                                                               >  1:51336/1‑148 (MQ=255)                                  ttCGTCCTTGTCTTTGAACCAGCTGAAGATCCTGTCTGACCGCGCGTGCTCGGTCCAGGCGTCTGATAGGCGCTTCAATGCACTCTCTTTCTGGCCGAAATCTCTGTCCCAGAGATCGAACAGTGCAATCAGTTGCTCCCTGTCagtga                                                                                                             >  3:85477/1‑149 (MQ=255)                                  ttCGTCCTTGTCTTTGAACCAGCTGAAGATCCTGTCTGACCGCGCGTGCTCGGTCCAGGCGTCTGATAGGCGCTTCAATGCACTCTCTTTCTGGCCGAAATCTCTGTCCCAGAGATCGAACAGTGCAATCAGTTGCTCCCTGTCagtga                                                                                                             <  4:242737/149‑1 (MQ=255)                                        cTTGTCTTTGAACCAGCTGAAGATCCTGTCTGACCGCGCGTGCTCGGTCCAGGCGTCTGATAGGCGCTTCAATGCACTCTCTTTCTGGCCGAAATCTCTGACCCAGAGAt                                                                                                                                              <  3:12089/110‑1 (MQ=255)                                        cTTGTCTTTGAACCAGCTGAAGATCCTGTCTGACCGCGCGTGCTCGGTCCAGGCGTCTGATAGGCGCTTCAATGCACTCTCTTTCTGGCCGAAATCTCTGACCCAGAGAt                                                                                                                                              >  4:7480/1‑110 (MQ=255)                                        cTTGTCTTTGAACCAGCTGAAGATCCTGTCTGACCGCGCGTGCTCGGTCCAGGCGTCTGATAGGCGCTTCAATGCACTCTCTTTCTGGCCGAAATCTCTGACCCAGAGAt                                                                                                                                              <  3:7480/110‑1 (MQ=255)                                        cTTGTCTTTGAACCAGCTGAAGATCCTGTCTGACCGCGCGTGCTCGGTCCAGGCGTCTGATAGGCGCTTCAATGCACTCTCTTTCTGGCCGAAATCTCTGACCCAGAGAt                                                                                                                                              >  4:12089/1‑110 (MQ=255)                                           gTCTTTGAACCAGCTGAAGATCCTGTCTGACCGCGCGTGCTCGGTCCAGGCGTCTGATAGGCGCTTCAATGCACTCTCTTTCTGGCCGAAATCTCTGTCCCAGAGATCGAACAGTGCAATCAGTTGCTCCCTGTCAGTGAGTGTGCgg                                                                                                     >  5:325941/1‑148 (MQ=255)                                            tCTTTGAACCAGCTGAAGATCCTGTCTGACCGCGCGTGCTCGGTCCAGGCGTCTGATAGGCGCTTCAATGCACTCTCTTTCTGGCCGAAATCTCTGTCCCAGAGATCGAACAGTGCAATCAGTTGCTCCCTGTCAGTGAGTGTGCGGa‑a                                                                                                  <  7:114683/149‑1 (MQ=255)                                            tCTTTGAACCAGCTGAAGATCCTGTCTGACCGCGCGTGCTCGGTCCAGGCGTCTGATAGGCGCTTCAATGCACTCTCTTTCTGGCCGAAATCTCTGTCCCAGAGATCGAACAGTGCAATCAGTTGCTCCCTGTCAGTGAGTGTGCGGa‑a                                                                                                  <  2:51336/149‑1 (MQ=255)                                              tttGAACCAGCTGAAGATCCTGTCTGACCGCGCGTGCTCGGTCCAGGCGTCTGATAGGCGCTTCAATGCACTCTCTTTCTGGCCGAAATCTCTGTCCCAGAGATCGAACAGTGCAATCAGTTGCTCCCTGTCAGTGAGTGTGCGGagg                                                                                                  >  1:117327/1‑146 (MQ=255)                                              tttGAACCAGCTGAAGATCCTGTCTGACCGCGCGTGCTCGGTCCAGGCGTCTGATAGGCGCTTCAATGCACTCTCTTTCTGGCCGAAATCTCTGTCCCAGAGATCGAACAGTGCAATCAGTTGCTCCCTGTCAGTGAGTGTGCGGA‑AGa                                                                                                >  8:158716/1‑149 (MQ=255)                                                   aCCAGCTGAAGATCCTGTCTGACCGCGCGTGCTCGGTCCAGGCGTCTGATAGGCGCTTCAATGCACTCTCTTTCTGGCCGAAATCTCTGTCCCAGAGATCGAACAGTGCAATCAGTTGCTCCCTGTCAGTGAGTGTGCGGA‑AGACACTg                                                                                           <  8:295993/149‑1 (MQ=255)                                                    ccAGCTGAAGATCCTGTCTGACCGCGCGTGCTCGGTCCAGGCGTCTGATAGGCGCTTCAATGCACTCTCTTTCTGGCCGAAATCTCTGTCCCAGAGATCGAACAGTGCAATCAGTTGCTCCCTGTCAGTGAGTGTGCGGA‑AGACACTGc                                                                                          >  6:287689/1‑149 (MQ=255)                                                    ccAGCTGAAGATCCTGTCTGACCGCGCGTGCTCGGTCCAGGCGTCTGATAGGCGCTTCAATGCACTCTCTTTCTGGCCGAAATCTCTGTCCCAGAGATCGAACAGTGCAATCAGTTGCTCCCTGTCAGTGAGTCTGCGGA‑AGACACTGc                                                                                          >  5:161501/1‑149 (MQ=255)                                                       gCTGAAGATCCTGTCTGACCGCGCGTGCTCGGTCCAGGCGTCTGATAGGCGCTTCAATGCACTCTCTTTCTGGCCGAAATCTCTGTCCCAGAGATCGAACAGTGCAATCAGTTGCTCCCTGTCAGTGAGTGTGCGGA‑AGACACTGCTAc                                                                                       <  2:149780/149‑1 (MQ=255)                                                        cTGAAGATCCTGTCTGACCGCGCGTGCTCGGTCCAGGCGTCTGATAGGCGCTTCAATGCACTCTCTTTCTGGCCGAAATCTCTGTCCCAGAGATCGAACAGTGCAATCAGTTGCTCCCTGTCAGTGAGTGTGCGGA‑AGACACTGCTACg                                                                                      >  2:73692/1‑149 (MQ=255)                                                               tCCTGTCTGACCGCGCGTGCTCGGTCCAGGCGTCTGATAGGCGCTTCAATGCACTCTCTTTCTGGCCGAAATCTCTGTCCCAGAGATCGAACAGTGCAATCAGTTGCTCCCTGTCAGTGAGTGTGCGGA‑AGACACTGCTACGTATTCg                                                                                <  4:85477/148‑1 (MQ=255)                                                                  tGTCTGACCGCGCGTGCTCGGTCCAGGCGTCTGATAGGCGCTTCAATGCACTCTCTTTCTGGCCGAAATCTCTGTCCCAGAGATCGAACAGTGCAATCAGTTGCTCCCTGTCAGTGAGTGTGCGGA‑AGACACTGCTACGTATTCGCAGt                                                                            >  5:177903/1‑149 (MQ=255)                                                                      tGACCGCGCGTGCTCGGTCCAGGCGTCTGATAGGCGCTTCAATGCACTCTCTTTCTGGCCGAAATCTCTGTCCCAGAGATCGAACAGTGCAATCAGTTGCTCCCTGTCAGTGAGTGTGCGGA‑AGACACTGCTACGTATTCGCAGTCCTg                                                                        >  6:136867/1‑149 (MQ=255)                                                                        aCCGCGCGTGCTCGGTCCAGGCGTCTGATAGGCGCTTCAATGCACTCTCTTTCTGGCCGAAATCTCTGTCCCAGAGATCGAACAGTGCAATCAGTTGCTCCCTGTCAGTGAGTGTGCgg                                                                                                     >  8:138283/1‑119 (MQ=255)                                                                        aCCGCGCGTGCTCGGTCCAGGCGTCTGATAGGCGCTTCAATGCACTCTCTTTCTGGCCGAAATCTCTGTCCCAGAGATCGAACAGTGCAATCAGTTGCTCCCTGTCAGTGAGTGTGCgg                                                                                                     <  7:138283/119‑1 (MQ=255)                                                                           gcgcgTGCTCGGTCCAGGCGTCTGATAGGCGCTTCAATGCACTCTCTTTCTGGCCGAAATCTCTGTCCCAGAGATCGAACAGT‑CAATCAGTTGCTCCCTGTCAGTGAGTGTGCGGA‑AGACACTGCTACGTATTCGCAGTCCTGTTTTAt                                                                  >  8:296828/1‑149 (MQ=255)                                                                               gTGCTCGGTCCAGGCGTCTGATAGGCGCTTCAATGCACTCTCTTTCTGGCCGAAATCTCTGTCCCAGAGATCGAACAGTGCAATCAGTTGCTCCCTGTCAGTGAGTGTGCGGA‑AGACACTGCTa                                                                                        <  6:305195/124‑1 (MQ=255)                                                                               gTGCTCGGTCCAGGCGTCTGATAGGCGCTTCAATGCACTCTCTTTCTGGCCGAAATCTCTGTCCCAGAGATCGAACAGTGCAATCAGTTGCTCCCTGTCAGTGAGTGTGCGGA‑AGACACTGCTa                                                                                        >  5:305195/1‑124 (MQ=255)                                                                                      gTCCAGGCGTCTGATAGGCGCTTCAATGCACTCTCTTTCTGGCCGAAATCTCTGTCCCAGAGATCGAACAGTGCAAt                                                                                                                                 >  4:212381/1‑77 (MQ=255)                                                                                      gTCCAGGCGTCTGATAGGCGCTTCAATGCACTCTCTTTCTGGCCGAAATCTCTGTCCCAGAGATCGAACAGTGCAAt                                                                                                                                 <  3:212381/77‑1 (MQ=255)                                                                                      gTCCAGGCGTCTGATAGGCGCTTCAATGCACTCTCTTTCTGGCCGAAATCTCTGTCCCAGAGATCGAACAGTGCAATCAGTTGCTCCCTGTCAGTGAGTGTGCGGA‑AGACACTGCTACGTATTCGCAGTCCTGTTTTATTCCCTGCtt                                                         >  8:28011/1‑148 (MQ=255)                                                                                         cAGGCGTCTGATAGGCGCTTCAATGCACTCTCTTTCTGGCCGAAATCTCTGTCCCAGAGATCGAGCAGTGCAATCAGTTGCTCCCTGTCAGTGAGTGTGCGGA‑AGACACTGCTACGTATTCGCAGTCCTGTTTAATTCACTGCTTGAgc                                                     >  6:303160/1‑149 (MQ=255)                                                                                                    tAGGCGCTTCAATGCACTCTCTTTCTGGCCGAAATCTCTGTCCCAGAGATCGAACAGTGCAATCAGTTGCTCCCTGTCAGTGACTGTGCGGA‑AGACACTGCTACGTATTCGCAGTCCTGTTTTATTCCCTGCTTGAGCGGCGAGCCAtt                                          <  5:136867/149‑1 (MQ=255)                                                                                                      ggCGCTTCAATGCACTCTCTTTCTGGCCGAAATCTCTGTCCCAGAGATCGAACAGTGCAATCAGTTGCTCCCTGTCAGTGAGTGTGCGGA‑AGACACTGCTACGTATTCGCAGTCCTGTTTTATTCCCTGCTTGAGCGGCGAGCCAttt                                         <  5:287689/148‑1 (MQ=255)                                                                                                       gcgcTTCAATGCACTCTCTTTCTGGCCGAAATCTCTGTCCCAGAGATCGAACAGTGCAATCAGTTGCTCCCTGTCAGTGAGTGTGCGGA‑AGACACTGCTACGTATTCGCAGTCCTGTTTTATTCCCTGCTTGAGCGGCGAGCCATTTTg                                       <  7:207122/149‑1 (MQ=255)                                                                                                           ttCAATGCACTCTCTTTCTGGCCGAAATCTCTGTCCCAGAGATCGAACAGTGCAATCAGTTGCTCCCTGTCAGTGAGTGTGCGGA‑AGACACTGCTACGTATTCGCAGTCCTGTTTTATTCCCTGCTTGAGCGGCGAGCCATTTTGGTTg                                   >  3:198488/1‑149 (MQ=255)                                                                                                               aTGCACTCTCTTTCTGGCCGAAATCTCTGTCCCAGAGATCGAACAGTGCAATCAGTTGCTCCCTGTCAGTGAGTGTGCGGA‑AGACACTGCTACGTATTCGCTGTCCTGTTTTATTCCCTGCTTGAGCGGCGAGCCATTTTGGTTgtcgt                               <  1:73692/149‑1 (MQ=255)                                                                                                                tGCACTCTCTTTCTGGCCGAAATCTCTGTCCCAGAGATCGAACAGTGCAATCAGTTGCTCCCTGTCAGTGAGTGTGCGGA‑AGACACTGCTACGTATTCGCAGTCCTGTTTTATTCCCTGCTTGAGCGGCGAGCCATTTTGGTTgtcgtc                              <  7:28011/149‑1 (MQ=255)                                                                                                                  cACTCTCTTTCTGGCCGAAATCTCTGTCCCAGAGATCGAACAGTGCAATCAGTTGCTCCCTGTCAGTGAGTGTGCGGA‑AGACACTGCTACGTATTCGCAGTCCTGTTTTATTCCCTGCTTGAGCGGCGAGCCATTTTGGTTGTCGTCCg                            >  3:146383/1‑149 (MQ=255)                                                                                                                   aCTCTCTTTCTGGCCGAAATCTCTGTCCCAGAGATCGAACAGTGCAATCAGTTGCTCCCTGTCAGTGAGTGTGCGGA‑AGACACTGCTACGTATTCGCAGTCCTGTTTTATTCCCTGCTTGAGCGGCGAGCCATTTTGGTTGTCGTCCGc                           >  6:17195/1‑149 (MQ=255)                                                                                                                                    aaTCTCTGTCCCAGAGATCGAACAGTGCAATCAGTTGCTCCCTGTCAGTGAGTGTGCGGA‑AGACACTGCTACGTATTCGCAGTCCTGTTTTATTCCCTGCTTGAGCGGCGAGCCATTTTGGTTGTCGTCCGCTTTTTTCGACCCAGCt           <  6:177903/148‑1 (MQ=255)                                                                                                                                     aTCTCTGTCCCAGAGATCGAACAGTGCAATCAGTTGCTCCCTGTCAGTGAGTGTGCGGA‑AGACACTGCTACGTATTCGCAGTCCTGTTTTATTCCCTGCTTGAGCGGCGAGCCATTTTGGTTGTCGTCCGCTTTTTTCGACCCAGCTg          >  3:69788/1‑148 (MQ=255)                                                                                                                                       ctctGTCCCAGAGATCGAACAGTGCAATCAGTTGCTCCCTGTCAGTGAGTGTGCGGAGAGACACTGATACGTATTCGCATACATGTTTTATTCCATCATTGAGCGGCGAGCCATTTTGTTTGTCGTCCGCTTTTTTCGACCAAGATGaa        >  1:256349/1‑149 (MQ=255)                                                                                                                                            tCCCAGAGATCGAACAGTGCAATCAGTTGCTCCCTGTCAGTGAGTGTGCGGA‑AGACACTGCTACGTATTCGCAGTCCTGTTTTATTCCCTGCTTGAGCGGCGAGCCATTTTGGTTGTCGTCCGCTTTTTTCGACCCAGCTGAATGcctc  >  4:172124/1‑149 (MQ=255)                                                                                                                                            tCCCAGAGATCGAACAGTGCAATCAGTTGCTCCCTGTCAGTGAGTGTGCGGA‑AGACACTGCTACGTATTCGCAGTCCTGTTTTATTCCCTGCTTGAGCGGCGAGCCATTTTGGTTGTCGTCCGCTTTTTTCGACCCAGCTGAATGcctc  >  6:35141/1‑149 (MQ=255)                                                                                                                                            |                                                                                                                                                      AAGCCAACTCCATGCCAGAGCGCATTTTGTGCGTTCGTCCTTGTCTTTGAACCAGCTGAAGATCCTGTCTGACCGCGCGTGCTCGGTCCAGGCGTCTGATAGGCGCTTCAATGCACTCTCTTTCTGGCCGAAATCTCTGTCCCAGAGATCGAACAGTGCAATCAGTTGCTCCCTGTCAGTGAGTGTGCGGA‑AGACACTGCTACGTATTCGCAGTCCTGTTTTATTCCCTGCTTGAGCGGCGAGCCATTTTGGTTGTCGTCCGCTTTTTTCGACCCAGCTGAATGCCTC  >  NC_002947/2817527‑2817814

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: ‑