Predicted mutation
evidence	seq id	position	mutation	annotation	gene	description
RA	NC_002947	336,125	+T	coding (210/237 nt)	PP_0278 →	hypothetical protein

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NC_002947	336,124	1	.	T	98.0%	151.5 / ‑5.6	50	D70V (GAT→GTT)	PP_0278	hypothetical protein
Reads supporting (aligned to +/- strand):  ref base . (1/0);  major base T (23/25);  minor base C (0/1);  total (24/26)
Fisher's exact test for biased strand distribution p-value = 1.00e+00
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 1.00e+00

AACCCATCCCTCAATCTCCTACGCGTAGAGCCCGGCGTCCCCGTCGACGCGGCCTACGAGCATGTCTCGATCCTGATGGGCTACATCAAGCACCTGGTGCGCGAGGGCGATATGGAGGACGACCATAAATTCCTGGGGGCAGCCGA‑TACCTGTGCGACATGGCCAAGGCGCTGATGAACGATATCGAGATCGCCAAGGGTAAGGCGCATTAGGCATTGACGCG‑GTCATTTGTGGGAGCGGCCTTGCGTCGCGAATGGGCTGCAAAGCAGCCCCGGCGATTTCA  >  NC_002947/335979‑336261                                                                                                                                                   |                                                                                                                                           aaCCCATCCCTCAATCTCCTACGCGTAGAGCCCGGCGTCCCCGTCGACGCGGCCTACGAGCATGTCTCGATCCTGATGGGCTACATCAAGCACCTGGTGCGCGAGGGCGATATGGAGGACGACCATAAATTCCTGGGGGCAGCCGA‑tta                                                                                                                                         >  6:192109/1‑147 (MQ=255) aaCCCATCCCTCAATCTCCTACGCGTAGAGCCCGGCGTCCCCGTCGACGCGGCCTACGAGCATGTCTCGATCCTGATGGGCTACATCAAGCACCTGGTGCGCGAGGGCGATATGGAGGACGACCATAAATTCCTGGGGGCAGCCGA‑tt                                                                                                                                          <  7:348123/148‑2 (MQ=255)   cccATCCCTCAATCTCCTACGCGTAGAGCCCGGCGTCCCCGTCGACGCGGCCTACGAGCATGTCTCGATCCTGATGGGCTACATCAAGCACCTGGTGCGCGAGGGCGATATGGAGGACGACCATAAATTCCTGGGGGCAGCCGA‑ttacc                                                                                                                                       >  1:287108/1‑145 (MQ=255)    ccATCCCTCAATCTCCTACGCGTAGAGCCCGGCGTCCCCGTCGACGCGGCCTACGAGCATGTCTCGCTCCGGATGGGCGCCATCACGCCCCGGGTGCGCGAGGGCGCGATGGCGGACGACCAAAAATTCAGGGGGGCAGCCGA‑TAccct                                                                                                                                      >  8:150044/1‑147 (MQ=255)    ccATCCCTCAATCTCCTACGCGTAGAGCCCGGCGTCCCCGTCGACGCGGCCTACGAGCATGTCTCGATCCTGATGGGCTACATCAAGCACCTGGTGCGCGAGGGCGATATGGAGGACGACCATAAATTCCTGGGGGCAGCCGA‑ttacct                                                                                                                                      <  6:215582/149‑6 (MQ=255)    ccATCCCTCAATCTCCTACGCGTAGAGCCCGGCGTCCCCGTCGACGCGGCCTACGAGCATGTCTCGATCCTGATGGGCTACATCAAGCACCTGGTGCGCGAGGGCGATATGGAGGACGACCATAAATTCCTGGAGGCAGCCGA‑ttacct                                                                                                                                      <  6:272875/149‑6 (MQ=255)         ccTCAATCTCCTACGCGTAGAGCCCGGCGTCCCCGTCGACGCGGCCTACGAGCATGTCTCGATCCTGATGGGCTACATCAAGCACCTGGTGCGCGAGGGCGATATGGAGGACGACCATAAATTCCTGGGGGCAGCCGATTACCTGTGc                                                                                                                                   >  7:169658/1‑148 (MQ=255)             aaTCTCCTACGCGTAGAGCCCGGCGTCCCCGTCGACGCGGCCTACGAGCATGTCTCGATCCTGATGGGCTACATCAAGCACCTGGTGCGCGAGGGCGATATGGAGGACGACCATAAATTCCTGGGGGCAGCCGATTACCTGTGCGACAt                                                                                                                              >  7:328067/1‑149 (MQ=255)                ctcCTACGCGTAGAGCCCGGCGTCCCCGTCGACGCGGCCTACCAGCATGTCTCGATCCTGATGGGCTACATCAAGCACCTGGTGCGCGAGGGCGATATGTAGGACGACCAAAAATTCCTGGTTGCAACCGATTACCTGAGCCACATGGc                                                                                                                           >  8:283687/1‑149 (MQ=255)                      cgcgTAGAGCCCGGCGTCCCCGTCGACGCGGCCTACGAGCATGTCTCGATCCTGATGGGCTACATCAAGCACCTGGTGCGCGAGGGCGATATGGAGGACGACCATAAATTCCTGGGGGCAGCCGATTACCTGTGCGACATGGCCAAgg                                                                                                                      <  8:169658/148‑1 (MQ=255)                       gggTAGAGCCCGGCGTCCCCGTCGACGCGGACTACGAGCATGTCTCGATCCTGATGGGCTACATCAAGCACCTGGTGCGCGAGGGCGATATGGAGGACGACCATAAATTCCTGGGGGCAGCCGATTACCTGTGCGACATGGCCAAGgcg                                                                                                                    <  4:349811/147‑1 (MQ=255)                               cccGGCGTCCCCGTCGACGCGGCCTACGATCATGTCTCGATCCTGATGGGCTACATCAAGCACCTGGTGCGCGAGGGCGATATGGAGGACGACCATAAATTCCTGGGGGCAGCCGATTACCTGTGCGACATGGCCAAGGCGCTGATGaa                                                                                                            <  8:328631/149‑1 (MQ=255)                                   gCGTCCCCGTCGACGCGGCCTACGAGCATGTCTCGATCCTGATGGGCTACATCAAGCACCTGGTGCGCGAGGGCGATATGGAGGACGACCATAAATTCCTGGGGGCAGCCGATTACCTGTGCGACATGGCCAAGGCGCTGATGAACGat                                                                                                        <  2:287108/149‑1 (MQ=255)                                        cccGTCGACGCGGCCTACGAGCATGTCTCGATCCTGATGGGCTACATCAAGCACCTGGTGCGCGAGGGCGATATGGAGGACGACCATAAATTCCTGGGGGCAGCCGATTACCTGTGCGACATGGCCAAGGCGCTGATGAACGATATCga                                                                                                   <  5:192109/149‑1 (MQ=255)                                         ccGTCGACGCGGCCTACGAGCATGTCTCGATCCTGATGGGCTACATCAAGCACCTGGTGCGCGAGGGCGATATGGAGGACGACCATAAATTCCTGGGGGCAGCCGATTACCTGTGCGACATGGCCAAGGCGCTGATGAACGATATc                                                                                                     >  2:43895/1‑146 (MQ=255)                                          cGTCGACGCGGCCTACGAGCATGTCTCGATCCTGATGGGCTACATCAAGCACCTGGTGCGCGAGGGCGATATGGAGGACGACCATAAATTCCTGGGGGCAGCCGATTACCTGTGCGACATGGCCAAGGCGCTGATGAACGATATc                                                                                                     >  2:376696/1‑145 (MQ=255)                                              gACGCGGCCTACGAGCATGTCTCGATCCTGATGGGCTACATCAAGCACCTGGTGCGCGAGGGCGATATGGAGGACGACCATAAATTCCTGGGGGCAGCCGATTACCTGTGCGACATGGCCAAGGCGCTGATGAACGATATCGAGATCGc                                                                                             <  8:328067/149‑1 (MQ=255)                                               aCGCGGCCTACGAGCATGTCTCGATCCTGATGGGCTACATCAAGCACCTGGTGCGCGAGGGCGATATGGAGGACGACCATAAATTCCTGGGGGCAGCCGATTACCTGTGCGACATGGCCAAGGCGCTGATGAACGATATCGAGATCGc                                                                                             >  3:364861/1‑148 (MQ=255)                                                 gcgGCCTACGAGCACGTCTCGATCCTGATGGGCTACATCAAGCACCTGGTGCGCGAGGGCGATATGGAGGACGACCATAAATTCCTGGGGGCAGCCGATTACCTGTGCGACATGGCCAAGGCGCTGATGAACGATATCGAGATCGcc                                                                                            >  8:167354/1‑147 (MQ=255)                                                                 tctcGATCCTGATGGGCTACATGAAGCACCTGGTGCGCGAGGGCGATATGGAGGTCGACCATAAATTCCTGGGGGCAGCCGATTTCCTGTGCGACATGGCCAAGGCGCTGATGAACGATATCGAGATCGCCAAGGGTAAGGCGCATTa                                                                           <  7:283687/148‑1 (MQ=255)                                                                   tcGATCCTGATGGGCTACATCAAGCACCTGGTGCGCGAGGGCGATATGGAGGACGACCATAAATTCCTGGGGGCAGCCGATTACCTGTGCGACATGGCCAAGGCGCTGATGAACGATATCgag                                                                                                  >  1:192309/1‑123 (MQ=255)                                                                   tcGATCCTGATGGGCTACATCAAGCACCTGGTGCGCGAGGGCGATATGGAGGACGACCATAAATTCCTGGGGGCAGCCGATTACCTGTGCGACATGGCCAAGGCGCTGATGAACGATATCgag                                                                                                  <  2:192309/123‑1 (MQ=255)                                                                   tcGATCCTGATGGGCTACATCAAGCACCTGGTGCGCGAGGGCGATATGGAGGACGACCATAAATTCCTGGGGGCAGCCGATTACCTGTGCGACATGGCCAAGGCGCTGATGAACGATATCGAGATCGCCAAgg                                                                                        >  3:266997/1‑133 (MQ=255)                                                                   tcGATCCTGATGGGCTACATCAAGCACCTGGTGCGCGAGGGCGATATGGAGGACGACCATAAATTCCTGGGGGCAGCCGATTACCTGTGCGACATGGCCAAGGCGCTGATGAACGATATCGAGATCGCCAAgg                                                                                        <  4:266997/133‑1 (MQ=255)                                                                       tCCTGATGGGCTACATCAAGCACCTGGTGCGCGAGGGCGATATGGAGGACGACCATAAATTCCTGGGGGCAGCCGATTACCTGTGCGACATGGCCAAGGCGCTGATGAACGATATCGAGATCGCCaa                                                                                          >  3:135235/1‑127 (MQ=255)                                                                       tCCTGATGGGCTACATCAAGCACCTGGTGCGCGAGGGCGATATGGAGGACGACCATAAATTCCTGGGGGCAGCCGATTACCTGTGCGACATGGCCAAGGCGCTGATGAACGATATCGAGATCGCCaa                                                                                          <  4:135235/127‑1 (MQ=255)                                                                          tGATGGGCTACATCAAGCACCTGGTGCGCGAGGGCGATATGGAGGACGACCATAAATTCCTGGGGGCAGCCGATTACCTGTGCGACATGGCCAAGGCGCTGATGAACGATATCGAGATCGCCAAGGGTAAGGCGCATTAGGCATTGAcg                                                                 >  2:399060/1‑149 (MQ=255)                                                                             tGGGCTACATCAAGCACCTGGTGCGCGAGGGCGATATGGAGGACGACCATAAATTCCTGGGGGCAGCCGATTACCTGTGCGACATGGCCAAGGCGCTGATGAACGATATCGAGATCGCCAAGGGTAAGGCGCATTAGGCATTGAcgcg                                                               <  5:53524/148‑1 (MQ=255)                                                                             tGGGCTACATCAAGCACCTGGTGCGCGAGGGCGATATGGAGGACGACCATAAATTCCTGGGGGCAGCCGATTACCTGTGCGACATGGCCAAGGCGCTGATGAACGATATCGAGATCGCCAAGGGTAAGGCGCATTAGGCATTGACGCg‑g                                                             >  8:285170/1‑149 (MQ=255)                                                                              gggCTACATCAAGCACCTGGTGCGCGAGGGCGATATGGAGGACGACCATAAATTCCTGGGGGCAGCCGATTACCTGTGCGACATGGCCAAGGCGCTGATGAACGATATCGAGATCGCCAAGGGTAAGGCGCATTAGGCATTGACGCG‑Gt                                                            >  2:296465/1‑149 (MQ=255)                                                                                gCTACATCAAGCACCTGGTGCGCGAGGGCGATATGGAGGACGACCATAAATTCCTGGGGGCAGCCGATTACCTGTGCGACATGGCCAAGGCGCTGATGAACGATATCGAGATCGCCAAGGGTAAGGCGCATTAGGCATTGACGCG‑GTCa                                                          <  7:167354/149‑1 (MQ=255)                                                                                 cTACATCAAGCACCTGGTGCGCGAGGGCGATATGGAGGACGACCATAAATTCCTGGGGGCAGCCGATTACCTGTGCGACATGGCCAAGGCGCTGATGAACGATATCGAGATCGCCAAGGGTAAGGCGCATTAGGCATTGACGCG‑GTCAt                                                         >  8:351347/1‑149 (MQ=255)                                                                                        aaGCACCTGGTGCGCGAGGGCGATATGGATGACGACCATAAATTCCTGGGGGCAGCCGATTACCTGTGCGACATGGCCAAGGCGCTGATGAACGATATCGAGATCGCCAAGGGTAAGGCGCATTAGGCATTGACGCG‑GTCATTTGTgg                                                   <  6:427882/148‑1 (MQ=255)                                                                                        aaGCACCTGGTGCGCGAGGGCGATATGGAGGACGACCATAAATTCCTGGGGGCAGCCGATTACCTGTGCGACATGGCCAAGGCGCTGATGAACGATATc                                                                                                     <  5:31503/99‑1 (MQ=255)                                                                                        aaGCACCTGGTGCGCGAGGGCGATATGGAGGACGACCATAAATTCCTGGGGGCAGCCGATTACCTGTGCGACATGGCCAAGGCGCTGATGAACGATATc                                                                                                     >  6:31503/1‑99 (MQ=255)                                                                                        aaGCACCTGGTGCGCGAGGGCGATATGGAGGACGACCATAAATTCCTGGGGGCAGCCGATTACCTGTGCGACATGGCCAAGGCGCTGATGAACGATATCGAGATCGCCAAGGGTAAGGCGCATTAGGCATTGACGCG‑GTCATTTGTgg                                                   >  5:432538/1‑148 (MQ=255)                                                                                         aGCACCTGGTGCGCGAGGGCGATATGGAGGACGACCATAAATTCCTGGGGGCAGCCGATTACCTGTGCGACATGGCCAAGGCGCTGATGAACGATATCGAGATCGCCAAGGGTAAGGCGCATTAGGCATTGACGCG‑GTCATTTGTgg                                                   >  1:168775/1‑147 (MQ=255)                                                                                                 gTGCGCGAGGTCGATATGGAGGTCGACCATAAATTCCTGGGGGCAGCCGATTACCTGTGCGACATGGCCAAGGCGCTGATGAACGATATCGAGATCGCCAAGGGTAAGGCGCATTAGGCATTGACGCG‑GTCATTTGTGGGAGCGGcc                                           <  8:110414/147‑1 (MQ=255)                                                                                                        aGGGCGATATGGAGGCCGACCCTCAATTCCTGGGGGCCTCCGACTACCTGTGAGACATGGCCCAGGCGCTGCTGAACGATATCGAGATCGCCAAGGGTCAGGCGCATTAGGCATTGCCGCG‑GGCCTTTGTGGGAGCGGCCGGGCGTcgc                                  <  7:150044/149‑1 (MQ=255)                                                                                                            cGATATGGAGGACGACCATAAATTCCTGGGGGCAGCCGATTACCTGTGCGACATGGCCAAGGCGCTGATGAACGATATCGAGATCGCCAAGGGTAAGGCGCATTAGGCATTGACGCG‑GTCATTTGTGGGAGCGGCCTTGCGTCGCGAAt                              <  1:399060/149‑1 (MQ=255)                                                                                                             gATATGGAGGACGACCATAAATTCCTGGGGGCAGCCGATTACCTGTGCGACATGGCCAAGGCGCTGATGAACGATATCGAGATCGCCAAGGGTAAGGCGCATTAGGCATTGACGCG‑GTCATTTGTGGGAGCGGCCTTGCGTCGCGAATg                             <  6:64793/149‑1 (MQ=255)                                                                                                                   gaggaCGACCATAAATTCCTGGGGGCAGCCGATTACCTGTGCGACATGGCCAAGGCGCTGATGAACGATATCGAGATCGCCAAGGGTAAGGCGCATTAGGCATTGACGCG‑GTCATTTGTGGGAGCGGCCTTGCGTCGCGAATGGGCTg                        <  7:285170/148‑1 (MQ=255)                                                                                                                      gacgacCATAAATTCCTGGGGGCAGCCGATTACCTGTGCGACATGGCCAAGGCGCTGATGAACGATATCGAGATCGCCAAGGGTAAGGCGCATTAGGCATTGACGCG‑GTCATTTGTGGGAGCGGCCTTGCGTCGCGAATGGGCTGCaaa                    <  4:364861/149‑1 (MQ=255)                                                                                                                         gacCATAAATTCCTGGGGGCAGCCGATTACCTGTGCGACATGGCCAAGGCGCTGATGAACGATATCGAGATCGCCAAGGGTAAGGCGCATTAGGCATTGACGCG‑GTCATTTGTGGGAGCGGCCTTGCGTCGCGAAAGGGCCGCAAagcg                 >  1:290022/1‑148 (MQ=255)                                                                                                                          acCATAAATTCCTGGGGGCAGCCGATTACCTGTGCGACATGGCCAAGGCGCTGATGAACGATATCGAGATCGCCAAGGGTAAGGCGCATTAGGCATTGACGCGCATCATTTGTGGGAGCGGCCTTGCGTCGCGAATGGGCTGCAAagca                 <  1:296465/149‑1 (MQ=255)                                                                                                                           ccATAAATTCCTGGGGGCAGCCGATTACCTGTGCGACATGGCCAAGGCGCTGATGAACGATATCGAGATCGCCAAGGGTAAGGCGCATTAGGCATTGACGCG‑GTCATTTGTGGGAGCGGc                                            <  1:199385/120‑1 (MQ=255)                                                                                                                           ccATAAATTCCTGGGGGCAGCCGATTACCTGTGCGACATGGCCAAGGCGCTGATGAACGATATCGAGATCGCCAAGGGTAAGGCGCATTAGGCATTGACGCG‑GTCATTTGTGGGAGCGGc                                            >  2:199385/1‑120 (MQ=255)                                                                                                                           ccATAAATTCCTGGGGGCAGCCGATTACCTGTGCGACATGGCCAAGGCGCTGATGAACGATATCGAGATCGCCAAGGGTAAGGCGCATTAGGCATTGACGCG‑GTCATTTGTGGGAGCGGCCTTGCGTCGCGAATGGGCTGCAAagcagc               <  7:351347/149‑1 (MQ=255)                                                                                                                           ccATAAATTCCTGGGGGCAGCCGATTACCTGTGCGACATGGCCAAGGCGCTGATGAACGATATCGAGATCGCCAAGGGTAAGGCGCATTAGGCATTGACGCG‑GTCATTTGTGGGAGCGGCCTTGCGTCGCGAATGGGCTGCAAagcagc               >  7:344507/1‑149 (MQ=255)                                                                                                                            cATAAATTCCTGGGGGCAGCCGATTACCTGTGCGACATGGCCAAGGCGCTGATGAACGATATc                                                                                                     <  2:125376/63‑1 (MQ=255)                                                                                                                            cATAAATTCCTGGGGGCAGCCGATTACCTGTGCGACATGGCCAAGGCGCTGATGAACGATATc                                                                                                     >  1:125376/1‑63 (MQ=255)                                                                                                                             aTAAATTCCTGGGGGCAGCCGATTACCTGTGCGACATGGCCAAGGCGCTGATGAACGATAGCGAGATCGCCAAGGGGAAGGCGCATTAGGCATTGACGCG‑GTCATTTGTGGGAGCGGCCTTGCGTCGCGAATGGGCTGCAAAGCAGccc             <  1:43895/149‑1 (MQ=255)                                                                                                                                 aTTCCTGGGGGCAGCCGATTACCTGTGCGACATGGCCAAGGCGCTGATGAACGATATCGAGATCGCCAAGGGTAAGGCGCATTAGGCATTGACGCG‑GTCATTTGTGGGAGCGGCCTTGCGTCGCGAATGGGCTGCAAAGCAGCCCCGGc         >  1:153242/1‑149 (MQ=255)                                                                                                                                        ggggCAGCCGATTACCTGTGCGACATGGCCAAGGCGCTGATGAACGATATCGAGATCGCCAAGGGTAAGGCGCATTAGGCATTGACGCG‑GTCATTTGTGGGAGCGGCCTTGCGTCGCGAATGGGCTGCAAAGCAGCCCCGGCGAttt    >  6:74221/1‑147 (MQ=255)                                                                                                                                        ggggCAGCCGATTACCTGTGCGACATGGCCAAGGCGCTGATGAACGATATCGAGATCGCCAAGGGTAAGGCGCATTAGGCATTGACGCG‑GTCATTTGTGGGAGCGGCCTTGCGTCGCGAATGGGCTGCAAAGCAGCCCCGGCGATTTCa  <  2:168775/149‑1 (MQ=255)                                                                                                                                                   |                                                                                                                                           AACCCATCCCTCAATCTCCTACGCGTAGAGCCCGGCGTCCCCGTCGACGCGGCCTACGAGCATGTCTCGATCCTGATGGGCTACATCAAGCACCTGGTGCGCGAGGGCGATATGGAGGACGACCATAAATTCCTGGGGGCAGCCGA‑TACCTGTGCGACATGGCCAAGGCGCTGATGAACGATATCGAGATCGCCAAGGGTAAGGCGCATTAGGCATTGACGCG‑GTCATTTGTGGGAGCGGCCTTGCGTCGCGAATGGGCTGCAAAGCAGCCCCGGCGATTTCA  >  NC_002947/335979‑336261

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 14 ≤ ATCG/ATCG < 15 ≤ ATCG/ATCG < 32 ≤ ATCG/ATCG < 36 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑