Predicted mutation
evidence	seq id	position	mutation	freq	annotation	gene	description
RA	NC_002947	5,430,397:1	+A	8.7%	intergenic (‑79/+82)	PP_4769 ← / ← PP_4770	hypothetical protein/hypothetical protein

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NC_002947	5,430,397	1	.	A	8.7%	176.0 / 11.9	46	intergenic (‑79/+82)	PP_4769/PP_4770	hypothetical protein/hypothetical protein
Reads supporting (aligned to +/- strand):  ref base . (18/24);  new base A (2/2);  total (20/26)
Fisher's exact test for biased strand distribution p-value = 1.00e+00
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 2.61e-01

GGCAGCCGTGGGCCTGGCGCACGGTGTAGTAGAGGTTCTGCACATCGGCGAACAGCGCGATCTTTTTCACCTGGGAACCTCATTTTTGGCCTGGAGTGCCGGGGGGC‑TGCTGCGCAG‑ACCTTCGCGGACACGCCCGCTCCCACAGGTAT‑CGCGCGTACACCCGTGGGAGCGGGCGTGCCCGCGAAGGGGCGCAAAGCGCCCCCGGAAATGCCAGCAGTATGCCAGACCTGTCAGACGTAAGAATCGTCGTCCGAGAAGAACCCACCGTCATCGCTGCCAAAACCACCGTCGGCGTAT  >  NC_002947/5430249‑5430545                                                                                                                                                        |                                                                                                                                                     ggCAGCCGTGGGCCTGGCGCACGGTGTAGTAGAGGTTCTGCACATCGGCGAACAGCGCGATCTTTTTCACCTGGGAACCTCATTTTTGGCCTGGAGTGCCGGGGGGC‑TGCTGCGCAG‑ACCTTCGCGGACACGCCCGCTCCCACAGGTAt                                                                                                                                                       >  3:66501/1‑149 (MQ=255)   cAGCCGTGGGCCTGGCGCACGGTGTAGTAGAGGTTCTGCACATCGGCGAACAGCGCGATCTTTTTCACCTGGGAACCTCATTTTTGGCCTGGAGTGCCGGGGGGC‑TGCTGCGCAG‑ACCTTCGCGGACACGCCCGCTCCCACAGGTAT‑cg                                                                                                                                                    <  4:66501/149‑1 (MQ=255)      ccGTGGGCCTGGCGCACGGTGTAGTAGAGGTTCTGCACATCGGCGAACAGCGCGATCTTTTTCACCTGGGAACCTCATTTTTGGCCTGGAGTGCCGGGGGGC‑TGCTGCGCAG‑ACCTTCGCGGACACGCCCGCTCCCACAGGTAT‑cgcgc                                                                                                                                                 >  1:54655/1‑149 (MQ=255)       cGTGGGCCTGGCGCACGGTGTAGTAGAGGTTCTGCACATCGGCGAACAGCGCGATCTTTTTCACCTGGGAACCTCATTTTTGGCCTGGAGTGCCGGGGGGC‑TGCTGCGCAG‑ACCTTCGCGGACACGCCCGCTCCCACAGGTAT‑cgcgcg                                                                                                                                                >  2:262537/1‑149 (MQ=255)        gTGGGCCTGGCGCACGGTGTAGTAGAGGTTCTGCACATCGGCGAACAGCGCGATCTTTTTCACCTGGGAACCTCATTTTTGGCCTGGAGTGCCGGGGGGC‑TGCTGCGCAG‑ACCTTCGCGGACACGCCCGCTCCCACAGGTAT‑CGCGCGt                                                                                                                                               <  5:64631/149‑1 (MQ=255)         tGGGCCTGGCGCACGGTGTAGTAGAGGTTCTGCACATCGGCGAACAGCGCGATCTTTTTCACCTGGGAACCTCATTTTTGGCCTGGAGTGCCGGGGGGC‑TGCTGCGCAG‑ACCTTCGCGGACACGCCCGCTCCCACAGGTAT‑CGCGCGTa                                                                                                                                              <  4:258021/149‑1 (MQ=255)         tGGGCCTGGCGCACGGTGTAGTAGAGGTTCTGCACATCGGCGAACAGCGCGATCTTTTTCACCTGGGAACCTCATTTTTGGCCTGGAGTGCCGGGGGGC‑TGCTGCGCAG‑ACCTTCGCGGACACGCCCGCTCCCACAGGTAT‑CGCGCGTa                                                                                                                                              <  7:21039/149‑1 (MQ=255)             ccTGGCGCACGGTGTAGTAGAGGTTCTGCACATCGGCGAACAGCGCGATCTTTTTCACCTGGGAACCTCATTTTTGGCCTGGAGTGCCGGGGGGC‑TGCTGCGCAG‑ACCTTCGCGGACACGCCCGCTCCCACAGGTAT‑CGCGCGTACAcc                                                                                                                                          <  1:37723/149‑1 (MQ=255)                  cgcACGGTGTAGTAGAGGTTCTGCACATCGGCGAACAGCGCGATCTTTTTCACCTGGGAACCTCATTTTTGGCCTGGAGTGCCGGGGGGC‑TGCTGCGCAG‑ACCTTCGCGGACACGCCCGCTCCCACAGGTAT‑CGCGCGTACACCCGTgg                                                                                                                                     <  7:113140/149‑1 (MQ=255)                   gcACGGTGTAGTAGAGGTTCTGCACATCGGCGAACAGCGCGATCTTTTTCACCTGGGAACCTCATTTTTGGCCTGGAGTGCCGGGGGGC‑TGCTGCGCAG‑ACCTTCGCGGACACGCCCGCTCCCACAGGTAT‑CGCGCGTACACCCGTggg                                                                                                                                    >  6:287528/1‑149 (MQ=255)                        gtgtAGTAGAGGTTCTGCACATCGGCGAACAGCGCGATCTTTTTCACCTGGGAACCTCATTTTTGGCCTGGAGTGCCGGGGGGC‑TGCTGCGCAG‑ACCTTCGCGGACACGCCCGCTCCCACAGGTAT‑CGCGCGTACACCCGTGGGAGCgg                                                                                                                               <  2:265932/149‑1 (MQ=255)                           tagtagAGGTTCTGCACATCGGCGAACAGCGCGATCTTTTTCACCTGGGAACCTCATTTTTGGCCTGGAGTGCCGGGGGGC‑TGCTGCGCAG‑ACCTTCGCGGACACGCCCGCTCCCACAGGTAT‑CGCGCGTACACCCGTGGGAGCGGGCg                                                                                                                            >  5:324193/1‑149 (MQ=255)                             gtagAGGTTCTGCACATCGGCGAACAGCGCGATCTTTTTCACCTGGGAACCTCATTTTTGGCCTGGAGTGCCGGGGGGC‑TGCTGCGCAG‑ACCTTCGCGGACACGCCCGCTCCCACGGGTGTACGCGCG‑ATACCTGTGGGAGCGGGCGt                                                                                                                           <  4:174666/148‑1 (MQ=37)                             gtagAGGTTCTGCACATCGGCGAACAGCGCGATCTTTTTCACCTGGGAACCTCATTTTTGGCCTGGAGTGCCGGGGGGC‑TGCTGCGCAG‑ACCTTCGCGGACACGCCCGCTCCCACAGGTAT‑CGCGCGTACACCCGTGGGAGCGGGCGt                                                                                                                           <  5:287528/148‑1 (MQ=255)                             gtagAGGTTCTGCACATCGGCGAACAGCGCGATCTTTTTCACCTGGGAACCTCATTTTTGGCCTGGAGTGCCGGGGGGC‑TGCTGCGCAG‑ACCTTCGCGGACACGCCCGCTCCCACAGGTAT‑CGCGCGTACACCCGTGGGAGCGGGCGTg                                                                                                                          >  5:215460/1‑149 (MQ=255)                                         cacaTCGGCGAACAGCGCGATCTTTTTCACCTGGGAACCTCATTTTTGGCCTGGAGTGCCGGGGGGC‑TGCTGCGCAG‑ACCTTCGCGGACACGCCCGCTCCCACAGGTAT‑CGCGCGTACACCCGTGGGAGCGGGCGTGCCCGCGAAgg                                                                                                                <  3:84308/147‑1 (MQ=255)                                         cacaTCGGCGAACAGCGCGATCTTTTTCACCTGGGAACCTCATTTTTGGCCTGGAGTGCCGGGGGGC‑TGCTGCGCAG‑ACCTTCGCGGACACGCCCGCTCCCACAGGTAT‑CGCGCGTACACCCGTGGGAGCGGGCGTGCCCGCGAAg                                                                                                                 <  6:324193/146‑1 (MQ=255)                                         cacaTCGGCGAACAGCGCGATCTTTTTCACCTGGGAACCTCATTTTTGGCCTGGAGTGCCGGGGGGC‑TGCTGCGCAG‑ACCTTCGCGGACACGCCCGCTCCCACAGGTAT‑CGCCCGTACACCCGTGGGAGCGGGCGTGCCCGCGAAgggg                                                                                                              >  8:74470/1‑149 (MQ=255)                                           caTCGGCGAACAGCGCGATCTTTTTCACCTGGGAACCTCATTTTTGGCCTGGAGTGCCGGGGGGC‑TGCTGCGCAG‑ACCTTCGCGGACACGCCCGCTCCCACAGGTAT‑CGCGCGTa                                                                                                                                              >  3:113479/1‑115 (MQ=255)                                           caTCGGCGAACAGCGCGATCTTTTTCACCTGGGAACCTCATTTTTGGCCTGGAGTGCCGGGGGGC‑TGCTGCGCAG‑ACCTTCGCGGACACGCCCGCTCCCACAGGTAT‑CGCGCGTa                                                                                                                                              <  4:113479/115‑1 (MQ=255)                                            aTCGGCGAACAGCGCGATCTTTTTCACCTGGGAACCTCATTTTTGGCCTGGAGTGCCGGGGGGC‑TGCTGCGCAG‑ACCTTCGCGGACACGCCCGCTCCCACAGGTAT‑cgc                                                                                                                                                   >  5:370970/1‑109 (MQ=255)                                            aTCGGCGAACAGCGCGATCTTTTTCACCTGGGAACCTCATTTTTGGCCTGGAGTGCCGGGGGGC‑TGCTGCGCAG‑ACCTTCGCGGACACGCCCGCTCCCACAGGTAT‑cgc                                                                                                                                                   <  6:370970/109‑1 (MQ=255)                                                     cAGCGCGATCTTTTTCACCTGGGAACCTCATTTTTGGCCTGGAGTGCCGGGGGGC‑GGCTGCGCAG‑ACCTTCGCGGACACGCCCGCTCCCACAGGTAT‑CGCGCGTACACCCGTGGGAGCGGGCGTGCCCGCGAAGGGGCGCAAAGCGccc                                                                                                  <  8:42274/149‑1 (MQ=255)                                                          cgATCTTTTTCACCTGGGAACCTCATTTTTGGCCTGGAGTGCCGGGGGGC‑TGCTGCGCAG‑ACCTTCGCGGACACGCCCGCTCCCACAGGTAT‑CGCGCGTACACCCGTGGGAGCGGGCGTGCCCGCGAAGGGGCGCAAAGCGCCCCCgg                                                                                              >  3:287943/1‑148 (MQ=255)                                                             tCTTTTTCACCTGGGAACCTCATTTTTGGCCTGGAGTGCCGGGGGGC‑TGCTGCGCAG‑ACCTTCGCGGACACGCCCGCTCCCACAGGTAT‑CGCGCGTACACCCGTGGGAGCGGGCGTGCCCGCGAAGGGGCGCAAAGCGCCCCCGGAAAt                                                                                          >  7:251165/1‑149 (MQ=255)                                                               tttttCACCTGGGAACCTCATTTTTGGCCTGGAGTGCCGGGGGGC‑TGCTGCGCAG‑ACCTTCGCGGACACGCCCGCTCCCACAGGTAT‑CGCGCGTACACCCGTGGGAGCGGGCGTGCCCGCGAAGGGGCGCAAAGCGCCCCCGGAAATGc                                                                                        >  3:121089/1‑149 (MQ=255)                                                               tttttCACCTGGGAACCTCATTTTTGGCCTGGAGTGCCGGGGGGC‑TGCTGCGCAG‑ACCTTCGCGGACACGCCCGCTCCCACAGGTAT‑CGCGCGTACACCCGTGGGAGCGGGCGTGCCCGCGAAGGGGCGCAAAGCGCCCCCGGAAATGc                                                                                        >  8:42091/1‑149 (MQ=255)                                                               tttttCACCTGGGAACCTCATTTTTGGCCTGGAGTGCCGGGGGGC‑TGCTGCGCAG‑ACCTTCGCGGACACGCCCGCTCCCACAGGTAT‑CGCGCGTACACCCGTGGGAGCGGGCGTGCCCGCGAAGGGGCGCAAAGCGCCCCCGGAAATGc                                                                                        >  1:17157/1‑149 (MQ=255)                                                                   tCACCTGGGAACCTCATTTTTGGCCTGGAGTACCGGGGGGC‑TGCTGCGCAG‑ACCTTCGCGGACACGCCCGCTCCCACAGGTAT‑CGCGCGTACACCCGTGGGAGCGGGCGTGCCCGCGAAGGGGCGCAAAGCGCCCCCGGAAATGCcag                                                                                     >  5:203425/1‑148 (MQ=255)                                                                     acgtGGGAACGTGATTTTTGGCCTGGAGTGCCGGGGGGC‑TGCTGCGCAG‑ACCTTTGCGGACACGCCCGCTCGCACAGGTAT‑CGCGCGTACAGCCGTGGGAGCGGGCGTGccc                                                                                                                       <  2:279581/109‑1 (MQ=255)                                                                     aCCTGGGAACCTCATTTTTGGACTGGAGTTCAGGGGGGC‑TGCTGCGCAGAACATTCCCGGACACGCCCCCTCCCACAGGTAT‑CGCGCGTACACACTTTGGAGCGGGCGTcccc                                                                                                                       >  1:279581/1‑113 (MQ=255)                                                                          ggAACCTCATTTTTGGCCTGGAGTGCCGGGGGGC‑TGCTGCGCAG‑ACCTTCGCGGACACGCCCGCTCCCACAGGTAT‑CGCGCGTACCCCCGTGGGAGCGGGCGTGCCCGCGAAGGGGCGCAAAGCGCCCCCGGAAATGCCAGCAGTAt                                                                               <  8:310025/147‑1 (MQ=255)                                                                          ggAACCTCATTTTTGGCCTGGAGTGCCGGGGGGC‑TGCTGCGCAG‑ACCTTCGCGGACACGCCCGCTCCCACAGGTAT‑CGCGCGTACACCCGTGGGAGCGGGCGTGCCCGCGAAGGGGCGCAAAGCGCCCCCGGAAATGCCAGCAGTATGc                                                                             <  1:165899/149‑1 (MQ=255)                                                                               cTCATTTTTGGCCTGGAGTGCCGGGGGGCTTGCTGCGCAG‑ACCTTCGCGGACACGCCCGCTCCCACAGGTAT‑CGCGCGTACACCCGTGGGAGCGGGCGTGCCCGCGAAGGGGCGCAAAGCGCCCCCGGAAATGCCAGCAGTATGCCAGa                                                                         >  1:225937/1‑149 (MQ=255)                                                                                 cATTTTTGGCCTGGAGTGCCGGGGGGC‑TGCTGCGCAG‑ACCTTCGCGGACACGCCCGCTCCCACAGGTAT‑CGCGCGTACACCCGTGGGAGCGGGCGTGCCCGCGAAGGGGCGCAAAGCGCCCCCGGAAATGCCAGCAGTATGCCAGACCt                                                                      >  4:260531/1‑149 (MQ=255)                                                                                  aTTTTTGGCCTGGAGTGCCGGGGGGC‑TGCTGCGCAG‑ACCTTCGCGGACACGCCCGCTCCCACAGGTAT‑CGCGCGTACACCCGTGGGAGCGGGCGTGCCCGCGAAGGGGCGCAAAGCGCCCCCGGAAATGCCAGCAGTATGCCAGACCt                                                                      <  6:124229/148‑1 (MQ=255)                                                                                   tttttGGCCTGGAGTGCCGGGGGGC‑TGCTGCGCAG‑ACCTTCGCGGACACGCCCGCTCCCACAGGTAT‑CGCGCGTACACCCGTGGGAGCGGGCGTGCCCGCGAAGGGGCGCAAAGCGCCCCCGGAAATGCCAGCAGTATGCCAGACCTGt                                                                    <  6:215460/149‑1 (MQ=255)                                                                                         gCCTGGAGTGCCGGGGGGC‑TGCTGCGCAG‑ACCTTCGCGGACACGCCCGCTCCCACAGGTAT‑CGCGCGTACACCCGTGGGAGCGGGCGTGCCCGCGAAGGGGCGCAAAGCGCCCCCGGAAATGCCAGCAGTATGCCAGACCTGTCAGAc                                                               <  2:54655/148‑1 (MQ=255)                                                                                           cTGGAGTGCCGGGGGGC‑TGCTGCGCAG‑ACCTTCGCGGACACGCCCGCTCCCACAGGTAT‑CGCGCGTACACCCGTGGGAGCGGGCGTGCCCGCGAAGGGGCGCAAAGCGCCCCCGGAAATGCCAGCAGTATGCCAGACCTGTCAGACGt                                                             >  6:140924/1‑148 (MQ=255)                                                                                               aGTGCCGAGGGGC‑TGCTGCGCAG‑ACCTTCGCGGACACGCCCGCTCCCACAGGTAT‑CGCGCGTACACCCGTGGGAGCGGGCGTGCCCGCGAAGGGGCGCAAAGCGCCCCCGGAAATGCCAGCAGTATGCCAGACCTGTCAGACGTAAGaa                                                        <  4:131566/149‑1 (MQ=255)                                                                                                    cGGGGGGC‑TGCTGCGCAG‑ACCTTCGCGGACACGCCCGCTCCCACAGGTAT‑CGCGCGTACACCCGTGGGAGCGGGCGTGCCCGCGAAGGGGCGCAAAGCGCCCCCGGAAATGCCAGCAGTATGCCAGACCTGTCAGACGTAAGAAtcgtc                                                   <  7:42091/149‑1 (MQ=255)                                                                                                    cGGGGGGC‑TGCTGCGCAG‑ACCTTCGCGGACACGCCCGCTCCCACAGGTAT‑CGCGCGTACACCCGTGGGAGCGGGCGTGCCCGCGAAGGGGCGCAAAGCGCCCCCGGAAATGCCAGCAGTATGCCAGACCTGTCAGACGTAAGAAtcgtc                                                   <  4:121089/149‑1 (MQ=255)                                                                                                                                  acacGCCCGCTCCCACAGGTAT‑CGCGCGTACACCCGTTGGAGCGGGCGTGCCCGCGAAGGGGCGCAAAGCGCCCCCGGAAATGCCAGCAGTATGCCAGACCTGTCAGACGTAAGAATCGTCGTCCGAGAAGAACCCACCGTCATCGCTg                       <  3:260531/149‑1 (MQ=255)                                                                                                                                  acacGCCCGCTCCCACAGGTAT‑CGCGCGTACACCCGTGGGAGCGGGCGTGCCCGCGAAGGGGCGCAAAGCGCCCCCGGAAATGCCAGCAGTATGCCAGACCTGTCAGACGTAAGAATCGTCGTCCGAGAAGAACCCACCGTCATCGCTg                       <  1:102600/149‑1 (MQ=255)                                                                                                                                  acacGCCCGCTCCCACAGGTAT‑CGCGAGTACACCCGTGGGAGCGGGCGTGCCCGCGAAGGGGCGCAAAGCGCCCCCGGAAATGCCAGCAGTATGCCAGACCTGTCAGACGTAAGAATCGTCGTCCGAGAAGAACCCACCGTCATCGCTg                       <  7:74470/149‑1 (MQ=255)                                                                                                                                   cacGCCCGCTCCCACAGGTAT‑CGCGCGTACACCCGTGGGAGCGGGCGTGCCCGCGAAGGGGCGCAAAGCGCCCCCGGAAATGCCAGCAGTATGCCAGACCTGTCAGACGTAAGAATCGTCGTCCGAGAAGAACCCACCGTCATCGCTGc                      <  1:262537/149‑1 (MQ=255)                                                                                                                                      gCCCGCTCCCACAGGTAT‑CGCGCGTACACCCGTGGGAGCGGGCGTGCCCGCGAAGGGGCGCAAAGCGCCCCCGGAAATGCCAGCAGTATGCCAGACCTGTCAGACGTAAGAATCGTCGTCCGAGAAGAACCCACCGTCATCGCTGCCa                    >  1:193350/1‑148 (MQ=255)                                                                                                                                        ccGCTCCCACGGGTGTACGCGCG‑ATACCTGTGGGAGCGGGCGTGCCCGCGAAGGGGCGCAAAGCGCCCCCGGAAATGCCAGCAGTATGCCAGACCTGTCAGACGTAAGAATCGTCGTCCGAGAAGAACCCACCGTCATCGCTGCCaaaa                 >  6:299372/1‑149 (MQ=37)                                                                                                                                            tCCCACGGGTGTACGCGCG‑ATACCTGTGGGAGCGGGCGTGCCCGCGAAGGGGCGCAAAGCGCCCCCGGAAATGCCAGCAGTATGCCAGACCTGTCAGACGTAAGAAt                                                       <  5:36430/107‑1 (MQ=21)                                                                                                                                            tCCCACGGGTGTACGCGCG‑ATACCTGTGGGAGCGGGCGTGCCCGCGAAGGGGCGCAAAGCGCCCCCGGAAATGCCAGCAGTATGCCAGACCTGTCAGACGTAAGAAt                                                       >  6:36430/1‑107 (MQ=21)                                                                                                                                              ccACAGGTAT‑CGCGCGTACACCCGTGGGAGCGGGCGTGCCCGCGAAGGGGCGCAAAGCGCCCCCGGAAATGCCAGCAGTATGCCAGACCTGTCAGACGTAAGAATCGTCGTCCGAGAAGAACCCACCGTCATCGCTGCCAAAACCACCg           >  7:294305/1‑149 (MQ=255)                                                                                                                                              ccACAGGTAT‑CGCGCGTACACCCGTCGGAGCGGGCGTGCCCGCGAAGGGGCGCAAAGCGCCCCCGGAAATGCCAGCAGTATGCCAGACCTGTCAGACGTAAGAATCGTCGTCCGAGAAGAACCCACCGTCATCGCTGCCAAAACCACCg           >  4:110137/1‑149 (MQ=255)                                                                                                                                                       t‑CGCGCGTACACCCGTGGGAGCGGGCGTGCCCGCGAAGGGGCGCAAAGCGCCCCCGGAAATGCCAGCAGTATGCCAGACCTGTCAGACGAAAGAATCGTCGTCCGAGAAGAACCCACCGTCATCGCTGCCAAAACCACCGTCGGCGTAt  <  4:287943/149‑1 (MQ=255)                                                                                                                                                        |                                                                                                                                                     GGCAGCCGTGGGCCTGGCGCACGGTGTAGTAGAGGTTCTGCACATCGGCGAACAGCGCGATCTTTTTCACCTGGGAACCTCATTTTTGGCCTGGAGTGCCGGGGGGC‑TGCTGCGCAG‑ACCTTCGCGGACACGCCCGCTCCCACAGGTAT‑CGCGCGTACACCCGTGGGAGCGGGCGTGCCCGCGAAGGGGCGCAAAGCGCCCCCGGAAATGCCAGCAGTATGCCAGACCTGTCAGACGTAAGAATCGTCGTCCGAGAAGAACCCACCGTCATCGCTGCCAAAACCACCGTCGGCGTAT  >  NC_002947/5430249‑5430545

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: ‑