Predicted mutation
evidence	seq id	position	mutation	freq	annotation	gene	description
RA	NC_002947	2,063,185	C→G	15.1%	intergenic (+42/‑165)	PP_1838 → / → PP_1839	membrane protein/hypothetical protein

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NC_002947	2,063,185	0	C	G	15.1%	134.7 / 16.5	53	intergenic (+42/‑165)	PP_1838/PP_1839	membrane protein/hypothetical protein
Reads supporting (aligned to +/- strand):  ref base C (16/29);  new base G (4/4);  total (20/33)
Fisher's exact test for biased strand distribution p-value = 4.57e-01
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 7.37e-01

CCGGAAATGCTCAAGAAGCTGGAAGCGTATATCCAGACCGCGACCAAGAGCCTGCTGGATAACACCGCCGGCGTGGTGCACGGCACACCGAAGTAAACCGGGGCCGCGTTGCGGCCCATTCGCGGGCTTGCCCG‑CTCCCACAGGCATTGCACAGGGTTCGGACCTTGTG‑CAGGTCCTGTGCGAGCGGGCAAGCCCGCGAATGGGCCCCGCACAATTTTCCCGGACTG‑AACATTATCCCCGCCCCAAGGTCAGTTATTCAGGCATCACACACCTGGTGTTCGT  >  NC_002947/2063048‑2063329                                                                                                                                           |                                                                                                                                                   ccGGAAATGCTCAAGAAGCTGGAAGCGTATATCCAGACCGCGACCAAGAGCCTGCTGGATAACACCGCCGGCGTGGTGCACGGCACACCGAAGTAAACCGGGGCCGCGTTGCGGCCCATTCGCGGGCTTGCCCG‑CTCCCACAGGCATTg                                                                                                                                         >  6:384026/1‑149 (MQ=255)      aaTGCTCAAGAAGCTGGAAGCGTATATCCAGACCGCGACCAAGAGCCTGCTGGATAACACCGCCGGCGTGGTGCACGGCACACCGAAGTAAACCGGGGCCGCGTTGCGGCCCATTCGCGGGCTTGCCCG‑CTCCCACAGGCATTGCACAg                                                                                                                                    <  3:35134/149‑1 (MQ=255)           tCAAGAAGCTGGAAGCGTATATCCAGACCGCGACCAAGAGCCTGCTGGATAACACCGCCGGCGTGGTGCACGGCACACCGAAGTAAACCGGGGCCGCGTTGCGGCCCATTCGCGGGCTTGCCCG‑CTCGCACAGGACCTGCACAAGGtcc                                                                                                                               >  6:211340/1‑147 (MQ=38)               gaagCTGGAAGCGTATATCCAGACCGCGACCAAGAGCCTGCTGGATAACACCGCCGGCGTGGTGCACGGCACACCGAAGTAAACCGGGGCCGCGTTGCGGCCCATTCGCGGGCTTGCCCG‑CTCCCACAGGCATTGCACAGGGTTCGGAc                                                                                                                           >  4:10975/1‑149 (MQ=255)                  gCTGGAAGCGTATATCCAGACCGCGACCAAGAGCCTGCTGGATAACACCGCCGGCGTGGTGCACGGCACACCGAAGTAAACCGGGGCCGCGTTGCGGCCCATTCGCGGGCTTGCCCG‑CTCCCACAGGCATTGCACAGGGTTCGGACCtt                                                                                                                        <  2:319805/149‑1 (MQ=255)                   cTGGAAGCGTATATCCAGACCGCGACCAAGAGCCTGCTGGATAACACCGCCGGCGTGGTGCACGGCACACCGAAGTAAACCGGGGCCGCGTTGCGGCCCATTCGCGGGCTTGCCCGCCTCCCACAGGCATTGCACAGGGTTCGGACCtt                                                                                                                        <  1:247118/149‑1 (MQ=255)                   cTGGAAGCGTATATCCAGACCGCGACCAAGAGCCTGCTGGATAACACCGCCGGCGTGGTGCACGGCACACCGAAGTAAACCGGGGCCGCGTTGCGGCCCATTCGCGGGCTTGCCCGACTCCCACAGGCATTGCACAGGGTTCGGACCtt                                                                                                                        <  1:241600/149‑1 (MQ=255)                   cTGGAAGCGTATATCCAGACCGCGACCAAGAGCCTGCTGGATAACACCGCCGGCGTGGTGCACGGCACACCGAAGTAAACCGGGGCCGCGTTGCGGCCCATTCGCGGGCTTGCCCG‑CTCCCACAGGCATTGCACAGGGTTCGGACCTtg                                                                                                                       <  7:142111/149‑1 (MQ=255)                    tGGAAGCGTATATCCAGACCGCGACCAAGAGCCTGCTGGATAACACCGCCGGCGTGGTGCACGGCACACCGAAGTAAACCGGGGCCGCGTTGCGGCCCATTCGCGGGCTTGCCCG‑CTCCCACAGGCATTGCACAGGGTTCGGACCTtgt                                                                                                                      >  3:85425/1‑149 (MQ=255)                       taGCGTATATCCAGACCGCGACCAAGAGCCTGCTGGATAACACCGCCGGCGTGGTGCACGGCACACCGAAGTAAACCGGGGCCGCGTTGGGGCCCATTCGCGGGCTTGCCCG‑CTCCCACAGGCATTGCACAGGGTTCGGACCTTGTG‑c                                                                                                                   <  6:314088/147‑1 (MQ=255)                        aGCGTATATCCAGACCGCGACCAAGAGCCTGCTGGATAACACCGCCGGCGTGGTGCACGGCACACCGAAGTAAACCGGGGCCGCGTTGCGGCCCATTCGCGGGCTTGCCCG‑CTCCCACAGGCATTGCACAGGGTTCGGACCTTGTG‑CAg                                                                                                                 <  3:10975/149‑1 (MQ=255)                         gCGTATATCCAGACCGCGACCAAGAGCCTGCTGGATAACACCGCCGGCGTGGTGCACGGCACACCGAAGTAAACCGGGGCCGCGTTGCGGCCCATTCGCGGGCTTGCCCG‑CTCGCACAGGACCTGCACAAGGTCCGAACCCTGTG‑Caat                                                                                                                >  6:359465/1‑147 (MQ=25)                                tCCAGACCGCGACCAAGAGCCTGCTGGATAACACCGCCGGCGTGGTGCACGGCACACCGAAGTAAACCGGGGCCGCGTTGCGGCCCATTCGCGGGCTTGCCCG‑CTCCCACAGGCATTGCACAGGGTTCGGACCTTGTG‑CAGGTCCtgtg                                                                                                         <  4:345335/149‑1 (MQ=255)                                  cAGACCGCGACCAAGAGCCTGCTGGATAACACCGCCGGCGTGGTGCACGGCACACCGAAGTAAACCGGGGCCGCGTTGCGGCCCATTCGCGGGCTTGCCCG‑CTCCCACAGGCATTGCACAGGGTTCGGACCTTGTG‑CAGGTCCTGTGc                                                                                                        <  3:174125/148‑1 (MQ=255)                                   aGACCGCGACCAAGAGCCTGCTGGATAACACCGCCGGCGTGGTGCACGGCACACCGAAGTAAACCGGGGCCGCGTTGCGGCCCATTCGCGGGCTTGCCCG‑CTCGCACAGGACCTGCACAAGGTCCGAACCCTGTG‑CAATGCCTGTGGGa                                                                                                      <  5:211340/149‑1 (MQ=18)                                    gACCGCGACCAAGAGCCTGCTGGATAACACCGCCGGCGTGGTGCACGGCACACCGAAGTAAACCGGGGCCGCGTTGCGGCCCATTCGCGGGCTTGCCCG‑CTCGCACAGGACCTGCACAAGGTCCGAACCCTGTG‑CAATGCCTGTGGGAg                                                                                                     <  5:359465/149‑1 (MQ=18)                                     aCCGCGACCAAGAGCCTGCTGGATAACACCGCCGGCGTGGTGCACGGCACACCGAAGTAAACCGGGGCCGCGTTGCGGCCCATTCGCGGGCTTGCCCG‑CTCCCACAGGCATTGCACAGGGTTCGGACCTTGTG‑CAGGTCCTGTGCGAGc                                                                                                    <  5:384026/149‑1 (MQ=255)                                     aCCGCGACCAAGAGCCTGCTGGATAACACCGCCGGCGTGGTGCACGGCACACCGAAGTAAACCGGGGCCGCGTTGCGGCCCATTCGCGGGCTTGCCCG‑CTCCCACAGGCATTGCACAGGGTTCGGACCTTGTG‑CAGGTCCTGTGCGAGc                                                                                                    >  1:274780/1‑149 (MQ=255)                                       cgcgACCAAGAGCCTGCTGGATAACACCGCCGGCGTGGTGCACGGCACACCGAAGTAAACCGGGGCCGCGTTGCGGCCCATTCGCGGGCTTGCCCG‑CTCGCACAGGACCTGCACAAGGTCCGAACCCTGTG‑CAATGCCTGTGGGAGCgg                                                                                                  <  2:386717/149‑1 (MQ=18)                                       cgcgACCAAGAGCCTGCTGGATAACACCGCCGGCGTGGTGCACGGCACACCGAAGTAAACCGGGGCCGCGTTGCGGCCCATTCGCGGGCTTGCCCG‑CTCCCACAGGCATTGCACAGGGTTCGGACCTTGTG‑CAGGTCCTGTGCGAGCgg                                                                                                  <  2:274780/149‑1 (MQ=255)                                       cgcgACCAAGAGCCTGCTGGATAACACCGCCGGCGTGGTGCACGGCACACCGAAGTAAACCGGGGCCGCGTTGCGGCCCATTCGCGGGCTTGCCCG‑CTCCCACAGGCATTGCACAGGGTTCGGACCTTGTG‑CAGGTCCTGTGCGAGCgg                                                                                                  <  3:202096/149‑1 (MQ=255)                                       cgcgACCAAGAGCCTGCTGGATAACACCGCCGGCGTGGTGCACGGCACACCGAAGTAAACCGGGGCCGCGTTGCGGCCCATTCGCGGGCTTGCCCG‑CGCCCACAGGCATTGCACAAGGTCCGAACCCTGTG‑CAATGCCTGTGGGAGCgg                                                                                                  <  8:123269/149‑1 (MQ=25)                                         cgACCAAGAGCCTGCTGGATAACACCGCCGGCGTGGTGCACGGCACACCGAAGTAAACCGGGGCCGCGTTGCGGCCCATTCGCGGGCTTTCCCG‑CTGCCACAGGGATTGCACAGGGTTCGGACCATGTT‑CACGTACTGTTCGAGCagg                                                                                                 >  4:116361/1‑148 (MQ=255)                                                 agCCTGCTGGATAACACCGCCGGCGTGGTGCACGGCACACCGAAGTAACCCGGGGCCGCGTTGCGGCCCATTCGCGGGCTTGCCCG‑CTCCCACAGGCATTGCACAGGGTTCGGACCTTGTG‑CAGGTCCTGTGCGAGCGGGCAAGCCcgc                                                                                        <  5:71112/149‑1 (MQ=255)                                                  gCCTGCTGGATAACACCGCCGGCGTGGTGCACGGCACACCGAAGTAAACCGGGGCCGCGTTGCGGCCCATTCGCGGGCTTGCCCG‑CTCCCACAGGCATTGCACAGGGTTCGGACCTTGTG‑CAGGTCCTGTGCGAGCGGGCAAGCCcgc                                                                                        >  6:127688/1‑148 (MQ=255)                                                   ccTGCTGGATAACACCGCCGGCGTGGTGCACGGCACACCGAAGTAAACCGGGGCCGCGTTGCGGCCCATTCGCGGGCTTGCCCG‑CTCCCACAGGCATTGCACAGGGTTCGGACCGTGTG‑CAGGTCCTGTGCGCGCGGGCCAGCCcgcg                                                                                       >  5:6204/1‑148 (MQ=255)                                                      gctgGATACCACCGCCGGCGTGGGGCACGGCACACCGAATTACACCGGCGCCGCGTTGCGGCCCATTCGCGGGCTTGCCCG‑CTCCCACAGCCAGTGCACAGGGTTCGGCCCTTGTG‑CAGGTCCTGTGCGAGCGGGCAAGCCCGCGAATg                                                                                   <  1:30098/149‑1 (MQ=37)                                                      gctgGATAACACCGCCGGCGTGGTGCACGGCACACCGAAGTAAACCGGGGCCGCGTTGCGGCCCATTCGCGGGCTTGCCCG‑CTGCCACAGGCATTTCACAGGGTTCGGACCTTGTG‑CAGGTCCTTTGCGAGCGGGCAAGCCCGCGAATg                                                                                   >  8:182584/1‑149 (MQ=255)                                                      gctgGATAACACCGCCGGCGTGGTGCACGGCACACCGAAGCAAACCGGGGCCGCGTGGCGGCCCATTCGCGGGCTTGCCCG‑CTCCCACCGCCATTGCACAGGGTTCGGACCTTGTG‑CAGGTCCTGTGCGAGCGGGCAAGCCCGCGAATg                                                                                   <  3:18942/149‑1 (MQ=255)                                                       ctgGATAACCCCGCCGGCGTGGTGCACGGAACACCGAAGTAACCCGGGGCCGCGTTGCGGCCCATTCGCGGGCTTGCCCG‑CTCCCACAGGCATTGCACCGGGTTCGGACCTTGTG‑CAGGTCCTGTGCTAGCGGGCAAGCCCGCGAATg                                                                                   <  6:6204/148‑1 (MQ=38)                                                       ctgGATAACACCGCCGGCGTGGTGCACGGCACACCGAAGTAAACCGGGGCCGCGTTGCGGCCCATTCGCGGGCTTGCCCG‑CTCCCCCAGGCATTGGACAGGGGTGGGCCCTTGTG‑CAGGGCCGGTGCGAGCGGGCTAGCCCGCGAATg                                                                                   >  2:30098/1‑148 (MQ=38)                                                       ctgGATAACACCGCCGGCGTGGTGCACGGCACACCGAAGTAAACCGGGGCCGCGTTGCGGCCCATTCGCGGGCTTGCCCG‑CTCCCACAGGCATTGCACAGGGTTCGGACCTTGTG‑CAGGTCCTGTGCGAGCGGGCAAGCCCGCGAATg                                                                                   <  5:127688/148‑1 (MQ=255)                                                          gATAACACCGCCGGCGTGGTGCACGGCACACCGAAGTAAACCGGGGCCGCGTTGCGGCCCATGCGCGGGCTTGCCCG‑CTCCCACAGGCATTGCACAGGGTTCGGACCTTGTGCCAGGTCCTGTGCGAGCGGGCAAGCCCGCGAATgg                                                                                  <  1:251588/147‑1 (MQ=255)                                                               cacCGCCGGCGTGGTGCACGGCACACCGAAGTAAACCGGGGCCGCGTTGCGGCCCATTCGCGGGCTTGACCG‑CTCCCACAGGCATTGCACAGGGTTAGGACCTTGTG‑GAGGTCCTGTGCGAGCCGGCAAGCCCGCCAAAGGGCCCCGcc                                                                          >  6:380169/1‑148 (MQ=255)                                                                acCGCCGGCGTGGTGCACGGCACACCGAAGTAAACCGGGGCCGCGTTGCGGCCCATTCGCGGGCTTTCCCG‑CTCCCCCAGGGCTTGGACAGGGTTCGGGCCTTGTG‑GAGGGGCGGTGGGCGCGGGCCAGCCCGCGGATGGGGCCCGcc                                                                          >  1:239375/1‑147 (MQ=255)                                                                       gCGTGGTGCACGGCACACCGAAGTAAACCGGGGCCGCGTTGCGGCCCATTCGCGGGCTTGCCCG‑CTCCCACAGGCATTGCACAGGGTTCGGACCTTGTG‑CAGGTCCTGTGCGAGCGGGCAAGCCCGCGAATGGGCCCCGCACAATTTTc                                                                  <  4:85425/149‑1 (MQ=255)                                                                              gCACGGCACACCGAAGTAAACCGGGGCCGCGTTGCGGCCCATTCGCGGGCTTGCCCG‑CTCCCAAAGGCATTGCACAGGGTTCGGACCTTGTG‑CAGGTCCTGTGCGAGCGGGCAAGCCCGCGAATGGGCCCCGCACAATTTTCCCGGACt                                                           >  2:107453/1‑149 (MQ=255)                                                                               cACGGCACACCGAAGTAAACCGGGGCCGCGTTGCGGCCCATTCGCGGGCTTGCCCG‑CTCCCACAGGCATTCCACAGGGTTCGGACCTTGTG‑CAGGTCCTGTGCGAGCGGGCAAGCCCGCGAATGGGCCCCGCACAATTTTCCCGGACTg                                                          <  5:380169/149‑1 (MQ=255)                                                                               cACGGCACACCGAAGTAAACCGGGGCCGCGTTGCGGCCCATTCGCGGGCTTGCCCG‑CACCCACAGGCATTGCACAGGGTTCGGACCTTGTG‑CAGGTCCTGTGCGAGCGGGCAAGCCCGCGAATGGGCCCCGCACAATTTTCCCGGACt                                                           >  6:311707/1‑148 (MQ=255)                                                                                       acCGAAGTAAACCGGGGCCGCGTTGCGGCCCATTCGCGGGCTTGCCCG‑CTCCCACACGCAGTGCACAGGGGTCGGCCCTTGTG‑CCGGGCCTGGGCGAGCGGGCACGCCCGCGAATGGGGCCCGCCCAAGTTTCCCGGCCGG‑ACCAGTAt                                                 >  7:126387/1‑149 (MQ=25)                                                                                          gAAGTAACCGGGGGCCGCGTTGCGGCCCATTCGCGGGCTTGCCCG‑CGCCCACAGCCATTGCACCGGGTGCGCCCCTTGTG‑CAGGTCCTGGGCGAGCGGGCAAGCCCGCGAATGGGCCCCGCACAATTTTCCCGGACTG‑AACATTATccc                                              <  8:213814/149‑1 (MQ=37)                                                                                                     gggCCGCGTTGCGGCCCATTCGCGGGCTTGCCCG‑CTCCCACAGGCATTGCACAGGGTTCGGACCTTGTG‑CAGGTCCTGTGCGAGCGGGCAAGCCCGCGAATGGGCCCCGCACAATTTTCCCGGACTG‑AACATTATCCCCGCCCCAAGGt                                   <  5:311707/149‑1 (MQ=255)                                                                                                     gggCCGCGTTGCGGCCCATTCGCGGGCTTGCCCG‑CTCCCACAGGCATTGCACAGGGTTCGGACCTTGTG‑CAGGTCCTGTGCGAGCGGGCAAGCCCGCGAATGGGCCCCGCACAATTTTCCCGGACTG‑AACATTATCCCCGCCCCAAGGt                                   <  7:182584/149‑1 (MQ=255)                                                                                                       cccGCGTTGCGGCCCATTCGCGGGCGTGCCCG‑CTCCCACAGGCATGCCACAGGGTGCGCCCCTTGTG‑CAGGTCCTGTGCGAGCGGGCAAGCCCGCGAATGGGCCCCGCACAATTTTCCCGGACTG‑AACATTATTCCCGCCCCAAGGTCa                                 <  6:301386/148‑1 (MQ=38)                                                                                                       cccGCGTGGCGGCCCATTCGCGGGCTTGCCCG‑CTCCCACAGGCATTGCACAGGGTTCGCACCTTGTC‑CAGGTCCTGTGCGAGCGGGCAAGCCCGCGAATGGGCCCCGCACAATTTTCCCGGa                                                             <  7:120849/121‑1 (MQ=255)                                                                                                                       ttCGCGGGCTTGCCCG‑CTCGCACAGGACCTGCACAAGGTCCGAACCCTGTG‑CAATGCCTGTGGGAGCGGGCAAGCCCGCGAATGGGCCCCGCACAATTTTCCCGGCCTG‑AACATTATCCCCGCCCCAAGGTCAGTTATTCAGGCATcac                 >  5:140953/1‑149 (MQ=14)                                                                                                                          gcgGGCTTGCCCG‑CTCCCACAGGCATTGCACAGGGTTCGGACCTTGTG‑CAGGTCCTGTGCGAGCGGGCAAGCCCGCGAATGGGCCCCGCACAATTTTCCCGGACTG‑AACATTATCCCCGCCCCAAGGTCAGTTATTCAGGCATcacaca              >  1:354211/1‑149 (MQ=255)                                                                                                                                ttGCCCG‑CTCCCACAGGCTTTGCACTGGGTGCGGACGTTGTG‑CAGGTCGTGTGCGAGCGGGAAAGCCCGCGAATGGGCCCCGCACAATTTTCCCGGACTG‑AACATTATCCCCGCCCCAAGGTCAGTTATTCAGGCATCACACACCTGgt        <  5:206649/149‑1 (MQ=255)                                                                                                                                  gCCCG‑CTCCCACAGGCATTGCACAGGGTTCGGACCTTGTG‑CAGGTCCTGTGCGAGCGGGCAAGCCCGCGAATGGGCCCCGCACAATTTTCCCGGACTG‑AACATTATCCCCGCCCCAAGGTCAGTTATTCAGGCATCACACACCTGgtgt      >  8:206854/1‑149 (MQ=255)                                                                                                                                    ccG‑CTCGCACAGGACCTGCACAAGGTCCGAACCCTGTG‑CAATGCCTGTGGGAGCGGGCAAGCCCGCGAATGGGCCCCGCACAATTTTCCCGGACTG‑AACATTATCCCCGCCCCAAGGTCAGTTATTCa                         >  2:153087/1‑128 (MQ=14)                                                                                                                                    ccG‑CTCGCACAGGACCTGCACAAGGTCCGAACCCTGTG‑CAATGCCTGTGGGAGCGGGCAAGCCCGCGAATGGGCCCCGCACAATTTTCCCGGACTG‑AACATTATCCCCGCCCCAAGGTCAGTTATTCa                         <  1:153087/128‑1 (MQ=14)                                                                                                                                      g‑CTCCCACAGGCATTGCACAGGGTTCGGACCTTGTG‑CAGGTCCTGTGCGAGCGGGCAAGCCCGCGAATGGGCCCCGCACAATTTTCCCGGACTG‑AACATTATCCCCGCCCCAAGGTCAGTTATTCAGGCATCACACACCTGGTGTTCGt  <  2:239375/149‑1 (MQ=255)                                                                                                                                        cTCCCATAGGCATTGCACAGGGTTCGGACCTTGTG‑CAGGTCCTGTGCGAGCGGGCAAGCCCGCGAATGGGCCCCGCACAATTTTCCCGGACTGCAACATTATCCCCGCCCCAAGGTCAGTTATTCAGGCATCACACACCTGGTGTTCGt  <  1:107453/149‑1 (MQ=255)                                                                                                                                           |                                                                                                                                                   CCGGAAATGCTCAAGAAGCTGGAAGCGTATATCCAGACCGCGACCAAGAGCCTGCTGGATAACACCGCCGGCGTGGTGCACGGCACACCGAAGTAAACCGGGGCCGCGTTGCGGCCCATTCGCGGGCTTGCCCG‑CTCCCACAGGCATTGCACAGGGTTCGGACCTTGTG‑CAGGTCCTGTGCGAGCGGGCAAGCCCGCGAATGGGCCCCGCACAATTTTCCCGGACTG‑AACATTATCCCCGCCCCAAGGTCAGTTATTCAGGCATCACACACCTGGTGTTCGT  >  NC_002947/2063048‑2063329

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: ‑