Predicted mutation
evidence	seq id	position	mutation	freq	annotation	gene	description
RA	NC_002947	3,124,491	G→T	8.9%	N254K (AAC→AAA)	PP_2741 ←	membrane protein

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NC_002947	3,124,491	0	G	T	8.9%	170.6 / 3.9	57	N254K (AAC→AAA)	PP_2741	membrane protein
Reads supporting (aligned to +/- strand):  ref base G (22/29);  new base T (3/2);  total (25/32)
Fisher's exact test for biased strand distribution p-value = 6.47e-01
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 9.99e-01

CAGCGGTCAGCCATTTCAACGTGCCCGGGCGTGCCATGCGCCTTAGCACACGCTTGGAGAAGGCGCTGATGCCACGGGCGATGAAGAAGATCGACAGTGCAACGGCCAGGCCGGGCATGGCGCGCAAAATACCGCTGATCAGGTAG‑TTGAGCAGCGCCATCAGGTGGATATTGAGGCTTTCCCCCCAAGACCTTGTGTAGGGGAACTGAGACAGCACGAAGCCCAGCCACTGGTAGCAGAACAACAACACGACCAACCAGTACAGCAGCCAGAGTGAACGGTCGATCAG  >  NC_002947/3124346‑3124634                                                                                                                                                  |                                                                                                                                                 cAGCGGTCAGCCATTTCAACGTGCCCGGGCGTGCCATGCGCCTTAGCACACGCTTGGAGAAGGCGCTGATGCCACGGGCGATGAAGAAGATCGACAGTGCAACGGCCAGGCCGGGCATGGCGCGCAAAATACCGCTGATCAGGTAG‑tt                                                                                                                                               <  4:252169/148‑1 (MQ=255) cAGCGGTCAGCCATTTCAACGTGCCCGGGCGTGCCATGCGCCTTAGCACACGCTTGGAGAAGGCGCTGATGCCACGGGCGATGAAGAAGATCGACAGTGCAACGGCCAGGCCGGGCATGGCGCGCAAAATACCGCTGATCAGGTAG‑tt                                                                                                                                               <  6:223316/148‑1 (MQ=255)         aGCCATTTCAACGTGCCCGGGCGTGCCATGCGCCTTAGCACACGCTTGGAGAAGGCGCTGATGCCACGGGCGATGAAGAAGATCGACAGTGCAACGGCCAGGCCGGGCATGGCGCGCAAAATACCGCTGCTCAACTAC‑CTGATCAgcgg                                                                                                                                      <  6:78062/149‑2 (MQ=255)             aTTTCAACGTGCCCGGGCGTGCCATGCGCCTTAGCACACGCTTGGAGAAGGCGCTGATGCCACGGGCGATGAAGAAGATCGACAGTGCAACGGCCAGGCCGGGCATGGCGCGCAAAATACCGCTGATCAGGTAG‑TTGAGCAGCGCCAt                                                                                                                                   >  6:117055/1‑148 (MQ=255)              tttCAACGTGCCCGGGCGTGCCATGCGCCTTAGCACACGCTTGGAGAAGGCGCTGATGCCACGGGCGATGAAGAAGATCGACAGTGCAACGGCCAGGCCGGGCATGGCGCGCAAAATACCGCTGATCAGGTAG‑TTGAGCAGCGCCAt                                                                                                                                   >  3:131296/1‑147 (MQ=255)                  aaCGTGCCCGGGCGTGCCATGCGCCTTAGCACACGCTTGGAGAAGGCGCTGATGCCACGGGCGATGAAGAAGATCGACAGTGCAACGGCCAGGCCGGGCATGGCGCGCAAAATACCGCTGATCAGGTAG‑TTGAGCAGCGCCATCAGGt                                                                                                                              <  8:105343/148‑1 (MQ=255)                  aaCGTGCCCGCGCGTGCCATGCGCCTTAGCACACGCTTGCAGAAGGCGCTGATGCCACGGGCGATGAAGAAGATCGACAGTGCAACGGCCAGGCCGGGCATGGCGCGCAAAATACCGCTGATCAGGGAG‑TTGACCAGCGCCATCAGGTg                                                                                                                             >  5:367119/1‑149 (MQ=255)                  aaCGTGCACGGGCGTGCCATGCGCCTTAGCACACGCTTGGAGAAGGCGCTGATGCCACGGGCGATGAAGAAGATCGACAGTGCAACGGCCAGGCCGGGCATGGCGCGCAAAATACCGCTGATCAGGTAG‑TTGAGCAGCGCCATCAGGTg                                                                                                                             >  2:59156/1‑149 (MQ=255)                         ccGGGCGTGCCATGCGCCTTAGCACACGCTTGGAGAAGGCGCTGATGCCACGGGCGATGAAGAAGATCGACAGTGCAACGGCCAGGCCGGGCATGGCGCGCAAAATACCGCTGATCAGGTAG‑TTGAGCAGCGCCATCAGGTGGATAtt                                                                                                                       >  6:227469/1‑148 (MQ=255)                          cGGGCGTGCCATGCGCCTTAGCACACGCTTGGAGAAGGCGCTGATGCCACGGGCGATGAAGAAGATCGACAGTGCAACGGCCAGGCCGGGCATGGCGCGCAAAATACCGCTGATCAGGTAG‑TTGAGCAGCGCCATCAGGTGGat                                                                                                                          >  1:198288/1‑144 (MQ=255)                          cGGGCGTGCCATGCGCCTTAGCACACGCTTGGAGAAGGCGCTGATGCCACGGGCGATGAAGAAGATCGACAGTGCAACGGCCAGGCCGGGCATGGCGCGCAAAATACCGCTGATCAGGTAG‑TTGAGCAGCGCCATCAGGTGGat                                                                                                                          <  2:198288/144‑1 (MQ=255)                                          cTTAGCACACGCTTGGAGAAGGCGCTGATGCCACGGGCGATGAAGAAGATCGACAGTGCAACGGCCAGGCCGGGCATGGCGCGCAAAATACCGCTGATCAGGTAG‑TTGAGCAGCGCCATCAGGTGGATATTGAGGCTTTCCCCCCaa                                                                                                       >  6:320094/1‑147 (MQ=255)                                          cTTAGCACACGCTTGGAGAAGGCGCTGATGCCACGGGCGATGAAGAAGATCGACAGTGCAACGGCCAGGCCGGGCATGGCGCGCAAAATACCGCTGATCAGGTAG‑TTGAGCAGCGCCATCAGGTGGATATTGAGGCTTTCCCCCCaa                                                                                                       <  5:320094/147‑1 (MQ=255)                                                acacGCTTGGAGAAGGCGCTGATGCCACGGGCGATGAAGAAGATCGACAGTGCAACGGCCAGGCCGGGCATGGCGCGCAAAATACCGCTGATCAGGTAG‑TTGAGCAGCGCCATCAGGTGGATATTGAGGCTTTCCCACCAAGACCTtgt                                                                                               >  5:123699/1‑149 (MQ=255)                                                  acGCTTGGAGAAGGCGCTGATGCCACGGGCGATGAAGAAGATCGACAGTGCAACGGCCAGGCCGGGCATGGCGCGCAAAATACCGCTGATCAGGTAG‑TTGAGCAGCGCCATCAGGTGGATATTGAGGCTTTCCCCCCAAGACCTtgtg                                                                                              >  4:35421/1‑148 (MQ=255)                                                    gCTTGGAGAAGGCGCTGATGCCACGGGCGATGAAGAAGATCGACAGTGCAACGGCCAGGCCGGGCATGGCGCGCAAAATACCGCTGATCAGGTAG‑TTGAGCAGCGCCATCAGGTGGATATTGAGGCTTTCCCCCCAAGACCTTGTGTAg                                                                                           >  3:210683/1‑149 (MQ=255)                                                     cTTGGAGAAGGCGCTGATGCCACGGGCGATGAAGAAGATCGACAGTGCAACGGCCAGGCCGGGCATGGCGCGCAAAATACCGCTGATCAGGTAG‑TTGAGCAGCGCCATCAGGTGGATATTGAGGCTTTCCCCCCAAGACCTTGTGTAgg                                                                                          <  5:313988/149‑1 (MQ=255)                                                        ggAGAAGGCGCTGATGCCACGGGCGATGAAGAAGATCGACAGTGCAACGGCCAGGCCGGGCATGGCGCGCAAAATACCGCTGATCAGGTAG‑TTGAGCAGCGCCATCAGGTGGATATTGAGGCTTTCCCCCCAAGACCTTGTGTAgggg                                                                                        <  5:227469/148‑1 (MQ=255)                                                        ggAGAAGGCGCTGATGCCACGGGCGATGAAGAAGATCGACAGTGCAACGGCCAGGCCGGGCATGGCGCGCAAAATACCGCTGATCAGGTAG‑TTGAGCAGCGCCATCAGGTGGATATTGAGGCTTTCCCCCCAAGACCTTGTGTAggg                                                                                         <  6:56295/147‑1 (MQ=255)                                                           gaAGGCGCTGATGCCACGGGCGATGAAGAAGATCGACAGTGCAACGGCCAGGCCGGGCATGGCGCGCAAAATACCGCTGATCAGGTAG‑TTGAGCAGCGCCATCAGGTGGATATTTAGGCTTTCCCACCAAGACCTTGTGTAGGGGAACt                                                                                    <  6:123699/149‑1 (MQ=255)                                                           gaAGGCGCTGATGCCACGGGCGATGAAGAAGATCGACAGTGCAACGGCCAGGCCGGGCATGGCGCGCAAAATACCGCTGATCAGGTAG‑TTGAGCAGCGCCATCAGGTGGATATTGAGGCTTTCCCCCCaa                                                                                                       >  2:350480/1‑130 (MQ=255)                                                           gaAGGCGCTGATGCCACGGGCGATGAAGAAGATCGACAGTGCAACGGCCAGGCCGGGCATGGCGCGCAAAATACCGCTGATCAGGTAG‑TTGAGCAGCGCCATCAGGTGGATATTGAGGCTTTCCCCCCaa                                                                                                       <  1:350480/130‑1 (MQ=255)                                                             aGGCGCTGATGCCACGGGCGATGAAGAAGATCGACAGTGCAACGGCCAGGCCGGGCATGGCGCGCAAAATACCGCTGATCAGGTAG‑TTGAGCAGCGCCATCAGGTGGATATTGAGGCTTTCCCCCCAAGACCTTGTGTAGGGGAACTga                                                                                  <  2:17586/149‑1 (MQ=255)                                                             aGGCGCGGATGGCACGGGCGATTCAGATGATCGTCAGTGCTACGGCCCGGCCGGTCAGGGCGCGCAAAATACCGCTGATCAGGTAG‑TTGAGCAGCGCCATCAGGTGGATATTGCGGCTTTCCCCCCAAGACCTTGTGTAGGGGAACTga                                                                                  <  6:367119/149‑1 (MQ=255)                                                                  cTGATGCCACGGGCGATGAAGAAGATCGACAGTGCAACGGCCAGGCCGGGCATGGCGCGCAAAATACCGCTGATCAGGTAG‑TTGagc                                                                                                                                           >  6:348445/1‑87 (MQ=255)                                                                  cTGATGCCACGGGCGATGAAGAAGATCGACAGTGCAACGGCCAGGCCGGGCATGGCGCGCAAAATACCGCTGATCAGGTAG‑TTGagc                                                                                                                                           <  5:348445/87‑1 (MQ=255)                                                                     aTGCCACGGGCGATGAAGAAGATCGACAGTGCAACGGCCAGGCCGGGCATGGCGCGCAAAATACCGCTGATCAGGTAG‑TTGAGCAGCGCCATCAGGTGGATATTGAGGCTTTCCCCCCAAGACCTTGTGTAGGGGAACTGAGACAGCAc                                                                          >  3:126150/1‑149 (MQ=255)                                                                         cACGGGCGATGAAGAAGATCGACAGTGCAACGGCCAGGCCGGGCATGGCGCGCAAAATACCGCTGATCAGGTAG‑TTGAGCAGCGCCATCAGGTGGATATTGAGGCTTTCCCCCCAAGACCTTGTGTAGGGGAACTGAGACAGCACGAAg                                                                      >  7:254656/1‑149 (MQ=255)                                                                           cGGGCGATGAAGAAGATCGACAGTGCAACGGCCAGGCCGGGCATGGCGCGCAAAATACCGCTGATCAGGTAG‑TTGAGCAGCGCCATCAGGTGGATATTGAGGCTTTCCCCCCAAGACCTTGTGTAGGGGAACTGAGACAGCACGAAGcc                                                                    >  3:330870/1‑149 (MQ=255)                                                                             ggCGATGAAGAAGATCGACAGTGCAACGGCCAGGCCGGGCATGGCGCGCAAAATACCGCTGATCAGGTAG‑TTGAGCAGCGCCATCAGGTGGATATTGAGGCTTTCCCCCCAAGACCTTGTGTAGGGGAACTGAGACAGCACGAAGCCCa                                                                  <  2:291564/149‑1 (MQ=255)                                                                              gCGATGAAGAAGATCGACAGTGCAACGGCCAGGCCGGGCATGGCGCGCAAAATACCGCTGATCAGGTAG‑TTGAGCAGCGCCATCAGGTGGATATTGAGGCTTTCCCCCCAAGACCTTGTGTAGGGGAACTGAGACAGCACGAAGCCCAg                                                                 <  5:117055/149‑1 (MQ=255)                                                                                gATGAAGAAGATCGACAGTGCAACGGCCAGGCCGGGCATGGCGCGCAAAATACCGCTGATCAGGTAG‑TTGAGCAGCGCCATCAGGTGGATATTGAGGCTTTCCCCCCAAGACCTTGTGTAGGGGAACTGAGACAGCACGAAGCCCAGc                                                                >  2:344753/1‑148 (MQ=255)                                                                                    aagaagATCGACAGTGCAACGGCCAGGCCGGGCATGGCGCGCAAAATACCGCTGATCAGGTAG‑TTGAGCAGCGCCATCAGGTGGATATTGAGGCTTTCCCCCCAAGACCTTGTGTAGGGTAACTTAGACAGCACGAAGCCCAGCCACTg                                                           <  2:345182/149‑1 (MQ=255)                                                                                    aagaagATCGACAGTGCAACGGCCAGGCCGGGCATGGCGCGCAAAATACCGCTGATCAGGTAG‑TTGAGCAGCGCCATCAGGTGGATATTGAGGCTTTCCCCCCAAGACCTTGTGTAGGGGAACTGAGACAGCACGAAGCCCAGCCACt                                                            <  4:210683/148‑1 (MQ=255)                                                                                      gaagaTCGACAGTGCAACGGCCAGGCCGGGCATGGCGCGCAAAATACCGCTGATCAGGTAG‑TTGa                                                                                                                                             <  4:263672/65‑1 (MQ=255)                                                                                      gaagaTCGACAGTGCAACGGCCAGGCCGGGCATGGCGCGCAAAATACCGCTGATCAGGTAG‑TTGa                                                                                                                                             >  3:263672/1‑65 (MQ=255)                                                                                      gaagaTCGACAGTGCAACGGCCAGGCCGGGCATGGCGCGCAAAATACCGCTGATCAGGTAG‑TTGAGCAGCGCCATCAGGTGGATATTGAGGCTTTCCCCCCAAGACCTTGTGTAGGGGAACTGAGACAGCACGAAGCCCAGCCACTgg                                                          >  6:350952/1‑148 (MQ=255)                                                                                      gaagaTCGACACACCAACTGAAACGCCCGCCAAGGAGCGAAAAATACCGAAGATCAGGTAT‑TATACCAGCGCAATCAGGTGGATATTGAGGCTTTCAACCAAAGAAATTGTGTAGGGTTACTTAGAAAGCAAGAAGACAATCCACTgc                                                          >  4:268258/1‑147 (MQ=255)                                                                                         gaTCGACAGTGCAACGGCCAGGCCGGGCATGGCGCGCAAAATACCGCTGATCAGGTAGNTTGAGCAGCGCCATCAGGTGGATATTGAgg                                                                                                                   <  1:33253/89‑1 (MQ=255)                                                                                         gaTCGACAGTGCAACGGCCAGGCCGGGCATGGCGCGCAAAATACCGCTGATCAGGTAG‑TTGAGCAGCGCCATCAGGTGGATATTGAgg                                                                                                                   >  2:33253/1‑88 (MQ=255)                                                                                              aCAGTGCAACGGCCAGGCCGGGCATGGCGCGCAAAATACCGCTGATCAGGTAG‑TTGAGCAGCGCCATCAGGTGGATATTGAGGCTTTCCCCCCAAGACCTTGTGTAGGGGAACTGAGACAGCACGAAGCCCAGCCACTGGTAGCAGaac                                                 <  1:344753/149‑1 (MQ=255)                                                                                                    cAACGGCCAGGCCGGGCATGGCGCGCAAAATACCGCTGATCAGGTAG‑TTGAGCAGCGCCATCAGGTGGATATTGAGGCTTTCCCCCCAAGACCTTGTGTAGGGGAACTGAGACAGCACGAAGCCCAGCCACTGGTAGCAGaacaacaa                                            <  4:131296/148‑1 (MQ=255)                                                                                                          ccAGGCCGGGCATGGCGCGCAAAATACCGCTGATCAGGTAG‑TTGAGCAGCGCCATCAGGTGGATATTGAGGCTTTCCCCCCAAGACCTTGTGTAGGGGAACTgaga                                                                                >  1:170713/1‑106 (MQ=255)                                                                                                          ccAGGCCGGGCATGGCGCGCAAAATACCGCTGATCAGGTAG‑TTGAGCAGCGCCATCAGGTGGATATTGAGGCTTTCCCCCCAAGACCTTGTGTAGGGGAACTgaga                                                                                <  2:170713/106‑1 (MQ=255)                                                                                                            aGGCCGGGCATGGCGCGGAAAATACCGCTGATCAGGTAG‑TTGAGCAGCGCCATCAGGTGGATATTGAGGCTTTCCCCCCAAGACCTTGTGTAGGGGAACTGAGACAGCACGAAGCCCAGCCACTGGTAGCAGAACAACAACACGaccaa                                   <  1:59156/149‑1 (MQ=255)                                                                                                             ggCCGGGCATGGCGCGCAAAATACCGCTGATCAGGTAG‑TTGAGCAGCGCCATCAGGTGGATATTGAGGCTTTCCCCCCAAGACCTTGTGTAGGGGAACTGAGACAGCACGAAGCCCAGCCACTGGTAGCAGAACAACAACACGaccaac                                  <  4:330870/149‑1 (MQ=255)                                                                                                                  ggCATGGCGCGCAAAATACCGCTGATCAGGTAG‑TTGAGCAGCGCCATCAGGTGGATATTGAGGCTTTCCCCCCAAGACCTTGTGTAGGGGAACTGAGACAGCACGAAGCCCAGCCACTGGTAGCAGAACAACAACACGACCAACCAGTa                             >  1:91183/1‑149 (MQ=255)                                                                                                                       ggCGCGCAAAATACCGCTGATCAGGTAG‑TTGAGCAGCGCCATCAGGTGGATATTGAGGCTTTCCCCCCAAGACCTTGTGTAGGGGAACTGAGACAGCACGAAGCCCAGCCACTGGTAGCAGAACAACAACACGACCAACCAGTAcag                          >  3:15785/1‑147 (MQ=255)                                                                                                                        gcgcgcAAAATACCGCTGATCAGGTAG‑TTGAGCAGCGCCATCAGGTGGATATTGAGGCTTTCACCCCAAGACCTTGTGTAGGGGAACTGAGACAGCACGAAGCCCAGCCACTGGTAGCAGAACAACAACACGACCAACCAGTAcagca                        <  3:294285/148‑1 (MQ=255)                                                                                                                             cAAAATACCGCTGATCAGGTAG‑TTGAGCAGCGCCATCAGGTGGATATTGAGGCTTTCCCCCCAAGACCTTGTGTAGGGGAACTGAGACAGCACGAAGCCCAGCCACTGGTAGCAGAACAACAACACGACCAACCAGTACAGCAGCCaga                  <  8:254656/149‑1 (MQ=255)                                                                                                                              aaaaTACCGCTGATCAGGTAT‑TTGAGCAGCGCCATCAGGTGGATATTGAGGCTTTCCCCCCAAGACCTTGTGTAGGGGAACTGAGACAGCACGAAGCCCAGCCACTGGTAGCAGAACAACAACACGACCAACCAGTACAGCAGCCa                    <  7:197476/146‑1 (MQ=255)                                                                                                                              aaaaTACCGCTGATCAGGTAT‑TTGAGCAGCGCCATCAGGTGGATATTGAGGCTTTCCCCCCAAGACCTTGTGTAGGGGAACTGAGACAGCACGAAGCCCAGCCACTGGTAGCAGAACAACAACACGACCAACCAGTACAGCAGCCa                    <  7:202746/146‑1 (MQ=255)                                                                                                                              aaaaTACCGCTGATCAGGTAT‑TTGAGCAGCGCCATCAGGTGGATATTGAGGCTTTCCCCCCAAGACCTTGTGTAGGGGAACTGAGACAGCACGAAGCCCAGCCACTGGTAGCAGAACAACAACACGACCAACCAGTACAGCAGCCa                    >  8:197476/1‑146 (MQ=255)                                                                                                                              aaaaTACCGCTGATCAGGTAT‑TTGAGCAGCGCCATCAGGTGGATATTGAGGCTTTCCCCCCAAGACCTTGTGTAGGGGAACTGAGACAGCACGAAGCCCAGCCACTGGTAGCAGAACAACAACACGACCAACCAGTACAGCAGCCa                    >  8:202746/1‑146 (MQ=255)                                                                                                                                           tCAGGTAG‑TTGAGCAGCGCCATCAGGTGGATATTGAGGCTTTCCCCCCAAGACCTTGTGTAGGGGAACTGAGACAGCACGAAGCCCAGCCACTGGTAGCAGAACAACAACACGACCAACCAGTACAGCAGCCAGAGTGAACGGTCGAt     <  3:35421/148‑1 (MQ=255)                                                                                                                                           tCAGGTAG‑TTGAGCAGCGCCATCAGGTGGATATTGAGGCTTTCCCCCCAAGACCTTGTGTAGGGGAACTGAGACAGCACGAAGCCCAGCCACTGGTAGCAGAACAACAACACGACCAACCAGTACAGCAGCCAGAGTGAACGGTCGATc    <  4:15785/149‑1 (MQ=255)                                                                                                                                             aGGTAG‑TTGAGCAGCGCCATCAGGTGGATATTGAGTCTTTCCCCCCAAGACCTTGTGTAGGGGAACTGAGACAGCACGAAGCCCAGCCACTGGTAGCAGAACAACAACACGACCAACCAGTACAGCAGCCAGAGTGAACGGTCGATCAg  <  5:303870/149‑1 (MQ=255)                                                                                                                                                  |                                                                                                                                                 CAGCGGTCAGCCATTTCAACGTGCCCGGGCGTGCCATGCGCCTTAGCACACGCTTGGAGAAGGCGCTGATGCCACGGGCGATGAAGAAGATCGACAGTGCAACGGCCAGGCCGGGCATGGCGCGCAAAATACCGCTGATCAGGTAG‑TTGAGCAGCGCCATCAGGTGGATATTGAGGCTTTCCCCCCAAGACCTTGTGTAGGGGAACTGAGACAGCACGAAGCCCAGCCACTGGTAGCAGAACAACAACACGACCAACCAGTACAGCAGCCAGAGTGAACGGTCGATCAG  >  NC_002947/3124346‑3124634

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 14 ≤ ATCG/ATCG < 21 ≤ ATCG/ATCG < 32 ≤ ATCG/ATCG < 36 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑