Predicted mutation
evidence	seq id	position	mutation	freq	annotation	gene	description
RA	NC_002947	5,430,406	C→T	9.1%	intergenic (‑88/+73)	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	5,430,406	0	C	T	9.1%	121.7 / 2.6	44	intergenic (‑88/+73)	PP_4769/PP_4770	hypothetical protein/hypothetical protein
Reads supporting (aligned to +/- strand):  ref base C (17/23);  new base T (2/2);  total (19/25)
Fisher's exact test for biased strand distribution p-value = 1.00e+00
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 2.69e-01

CCTGGCGCACGGTGTAGTAGAGGTTCTGCACATCGGCGAACAGCGCGATCTTTTTCACCTGGGAACCTCATTTTTGGCCTGGAGTGCCGGGGGGC‑TGCTGCGCAG‑ACCTTCGCGGACACGCCCGCTCCCACAGGTAT‑CGCGCGTACACCCGTGGGAGCGGGCGTGCCCGCGAAGGGGCGCAAAGCGCCCCCGGAAATGCCAGCAGTATGCCAGACCTGTCAGACGTAAGAATCGTCGTCCGAGAAGAACCCACCGTCATCGCTGCCAAAACCACCGTCGGCGTATCCGCCCTG  >  NC_002947/5430261‑5430553                                                                                                                                                     |                                                                                                                                                    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)                                         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                                                                                                >  8:42091/1‑149 (MQ=255)                                                   tttttCACCTGGGAACCTCATTTTTGGCCTGGAGTGCCGGGGGGC‑TGCTGCGCAG‑ACCTTCGCGGACACGCCCGCTCCCACAGGTAT‑CGCGCGTACACCCGTGGGAGCGGGCGTGCCCGCGAAGGGGCGCAAAGCGCCCCCGGAAATGc                                                                                                >  1:17157/1‑149 (MQ=255)                                                   tttttCACCTGGGAACCTCATTTTTGGCCTGGAGTGCCGGGGGGC‑TGCTGCGCAG‑ACCTTCGCGGACACGCCCGCTCCCACAGGTAT‑CGCGCGTACACCCGTGGGAGCGGGCGTGCCCGCGAAGGGGCGCAAAGCGCCCCCGGAAATGc                                                                                                >  3:121089/1‑149 (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                                                           <  4:121089/149‑1 (MQ=255)                                                                                        cGGGGGGC‑TGCTGCGCAG‑ACCTTCGCGGACACGCCCGCTCCCACAGGTAT‑CGCGCGTACACCCGTGGGAGCGGGCGTGCCCGCGAAGGGGCGCAAAGCGCCCCCGGAAATGCCAGCAGTATGCCAGACCTGTCAGACGTAAGAAtcgtc                                                           <  7:42091/149‑1 (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                                                               >  6:36430/1‑107 (MQ=21)                                                                                                                                tCCCACGGGTGTACGCGCG‑ATACCTGTGGGAGCGGGCGTGCCCGCGAAGGGGCGCAAAGCGCCCCCGGAAATGCCAGCAGTATGCCAGACCTGTCAGACGTAAGAAt                                                               <  5:36430/107‑1 (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)                                                                                                                                                 cgTACACCCGTGGGAGCGGGCGTGCCCGCGAAGGGGCGCAAAGCGCCCCCGGAAATGCCAGCAGTATGCCAGACCTGTCAGACGTAAGAATCGTCGTCCGAGAAGAACCCACCGTCATCGCTGCCAAAACCACCGTCGGCGTATCCGcc     <  8:251165/149‑1 (MQ=255)                                                                                                                                                   tACACCCGTGGGAGCGGGCGTGCCCGCGAAGGGGCGCAAAGCGCCCCCGGAAATGCCAGCAGTATGCCAGACCTGTCAGACGTAAGAATCGTCGTCCGAGAAGAACCCACCGTCATCGCTGCCAAAACCACCGTCGGCGTATCCGCCCt   <  2:225937/149‑1 (MQ=255)                                                                                                                                                    acacCCGTGGGAGCGGGCGTGCCCGCGAAGGGGCGCAAAGCGCCCCCGGAAATGCCAGCAGTATGCCAGACCTGTCAGACGTAAGAATCGTCGTCCGAGAAGAACCCACCGTCATCGCTGCCAAAACCACCGTCGGCGTATCCGCCCTg  >  8:238038/1‑149 (MQ=255)                                                                                                                                                     |                                                                                                                                                    CCTGGCGCACGGTGTAGTAGAGGTTCTGCACATCGGCGAACAGCGCGATCTTTTTCACCTGGGAACCTCATTTTTGGCCTGGAGTGCCGGGGGGC‑TGCTGCGCAG‑ACCTTCGCGGACACGCCCGCTCCCACAGGTAT‑CGCGCGTACACCCGTGGGAGCGGGCGTGCCCGCGAAGGGGCGCAAAGCGCCCCCGGAAATGCCAGCAGTATGCCAGACCTGTCAGACGTAAGAATCGTCGTCCGAGAAGAACCCACCGTCATCGCTGCCAAAACCACCGTCGGCGTATCCGCCCTG  >  NC_002947/5430261‑5430553

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: ‑