Predicted mutation
evidence	seq id	position	mutation	freq	annotation	gene	description
RA	NC_002947	4,826,283	A→C	8.7%	I1636S (ATC→AGC) ‡	pvdL ←	non‑ribosomal peptide synthetase

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NC_002947	4,826,283	0	A	C	8.7%	158.3 / 3.0	53	I1636S (ATC→AGC) ‡	pvdL	non‑ribosomal peptide synthetase
Reads supporting (aligned to +/- strand):  ref base A (23/25);  new base C (3/2);  total (26/27)
Fisher's exact test for biased strand distribution p-value = 6.69e-01
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 1.00e+00

TTCGAACAGGGCCTTGAGCGGCAGCTCGACATCGCAGGCCTGGCGGGTGCGCGAAACGATCTGGGTAGCCAGCAACGAGTGACCACCGAGGGCGAAGAAGTCGTCCTGCAGGCCAATGCGCGGCAGATTCAACACGTCGC‑GCCAGATGGCCGCGACCTGTTGTTGCAGCTCGGTTCGTGGCTCGACATGCTCACGCTG‑CTGCCACACTGGGGCAGGCAGTGCCTTGCGGTCGACCTTGCCGCTGGGGCCCAATGGCATCTGTGCCAAAGGGATGAGTTGCGCCGGCACCA  >  NC_002947/4826138‑4826427                                                                                                                                                   |                                                                                                                                                  ttCGAACAGGGCCTTGAGCGGCAGCTCGACATCGCAGGCCTGGCGGGTGCGCGAAACGATCTGGGTAGCCAGCAACGAGTGACCACCGAGGGCGAAGAAGTCGTCCTGCAGGCCAATGCGCGGCAGATTCAACACGTCGC‑GCCAGATgg                                                                                                                                                >  4:250689/1‑149 (MQ=255)        aGGGCCTTGAGCGGCAGCTCGACATCGCAGGCCTGGCGGGTGCGCGAAACGATCTGGGTAGCCAGCAACGAGTGACCACCGAGGGCGAAGAAGTCGTCCTGCAGGCCAATGCGCGGCAGATTCAACACGTCGC‑GCCAGATGGCCGCGAc                                                                                                                                         >  6:254109/1‑149 (MQ=255)             cTTGAGCGGCAGCTCGACATCGCAGGCCTGGCGGGTGCGCGAAACGATCTGGGTAGCCAGCAACGAGTGACCACCGAGGGCGAAGAAGTCGTCCTGCAGGCCAATGCGCGGCAGATTCAACACGTCGC‑GCCAGATGGCCGCGACCtgtt                                                                                                                                    >  8:91881/1‑149 (MQ=255)                    ggCAGCTCGACATCGCAGGCCTGGCGGGTGCGCGAAACGATCTGGGTAGCCAGCAACGAGTGACCACCGAGGGCGAAGAAGTCGTCCTGCAGGCCAATGCGCGGCAGATTCAACACGTCGC‑GCCAGATGGCAGCGACCTGTTGTTGCAg                                                                                                                             >  4:100448/1‑149 (MQ=255)                     gCAGCTCGACATCGCAGGCCTGGCGGGTGCGCGAAACGATCTGGGTAGCCAGCAACGAGTGACCACCGAGGGCGAAGAAGTCGTCCTGCAGGCCAATGCGCGGCAGATTCAACACGTCGC‑GCCAGATGGCCGCGAc                                                                                                                                         >  6:247079/1‑136 (MQ=255)                     gCAGCTCGACATCGCAGGCCTGGCGGGTGCGCGAAACGATCTGGGTAGCCAGCAACGAGTGACCACCGAGGGCGAAGAAGTCGTCCTGCAGGCCAATGCGCGGCAGATTCAACACGTCGC‑GCCAGATGGCCGCGAc                                                                                                                                         <  5:247079/136‑1 (MQ=255)                        gCTCGACATCGCAGGCCTGGCGGGTGCGCGAAACGAGCTGGGTAGCCAGCAACGAGTGACCACCGAGGGCGAAGAAGTCGTCCTGCAGGCCAATGCGCGGCAGATTCAACACGTCGC‑GCCAGATGGCCGCGACCTGTTGTTGCAGCTCg                                                                                                                         <  7:98190/149‑1 (MQ=255)                               aTCGCAGGCCTGGCGGGTGCGCGAAACGATCTGGGTAGCCAGCAACGAGTGACCACCGAGGGCGAAGAAGTCGTCCTGCAGGCCAATGCGCGGCAGATTCAACACGTCGC‑GCCAGATGGCCGCGACCTGTTGTTGCGGCTCGGTTCGTg                                                                                                                  >  6:54277/1‑149 (MQ=255)                               aTCGCAGGCCTGGCGGGTGCGCGAAACGATCTGGGTAGCCAGCAACGAGTGACCACCGAGGGCGAAGAAGTCGTCCTGCAGGCCAATGCGCGGCAGATTCAACACGTCGC‑GCCAGATGGCCGCGACCTGTTGTTGCAGCTCGGTTCGTg                                                                                                                  <  3:250689/149‑1 (MQ=255)                                      gCCTGGCGGGTGCGCGAAACGATCTGGGTAGCCAGCAACGAGTGACCACCGAGGGCGAAGAAGTCGTCCTGCAGGCCAATGCGCGGCAGATTCAACACGTCGC‑GCCAGATGGCCGCGACCTGTTGTTGCAGCTCGGTTCGTGGCTCGa                                                                                                            >  2:126350/1‑148 (MQ=255)                                      gCCTGGCGGGTGCGCGAAACGATCTGGGTAGCCAGCAACGAGTGACCACCGAGGGCGAAGAAGTCGTCCTGCAGGCCAATGCGCGGCAGATTCAACACGTCGC‑GCCAGATGGCCGCGACCTGTTGTTGCAGCTCGGTTCGTGGCTCGAc                                                                                                           <  6:28819/149‑1 (MQ=255)                                           gCGGGTGCGCGAAACGATCTGGGTAGCCAGCAACGAGTGACCACCGAGGGCGAAGAAGTCGTCCTGCAGGCCAATGCGCGGCAGATTCAACACGTCGC‑GCCAGATGGCCGCGACCTGTTGTTGCAGCTCGGTTCGTGGCTCGACATGc                                                                                                       <  3:25170/148‑1 (MQ=255)                                                tGCGCGAAACGATCTGGGTAGCCAGCAACGAGTGACCACCGAGGGCGAAGAAGTCGTCCTGCAGGCCAATGCGCGGCAGATTCAACACGTCGC‑GCCAGATGGCCGCGACCTGTTGTTGCAGCTCGGTTCGTGGCTCGACATGCTCACgc                                                                                                 <  2:212323/149‑1 (MQ=255)                                                tGCGCGAAACGATCTGGGTAGCCAGCAACGAGTGACCACCGAGGGCGAAGAAGTCGTCCTGCAGGCCAATGCGCGGCAGATTCAACACGTCGC‑GCCAGATGGCCGCGACCTGTTGTTGCAGCTCGGTTCGTGGCTCGACATGCTCACgc                                                                                                 <  5:254109/149‑1 (MQ=255)                                                   gcgAAACGATCTGGGTAGCCAGCAACGAGTGACCACCGAGGGCGAAGAAGTCGTCCTGCAGGCCAATGCGCGGCAGATTCAACACGTCGC‑GCCAGATGGCCGCGACCTGttgttg                                                                                                                                <  3:222574/115‑1 (MQ=255)                                                   gcgAAACGATCTGGGTAGCCAGCAACGAGTGACCACCGAGGGCGAAGAAGTCGTCCTGCAGGCCAATGCGCGGCAGATTCAACACGTCGC‑GCCAGATGGCCGCGACCTGTTGTTGCAGCTCGGTTCGTGGCTCGACATGCTCACgctg‑c                                                                                             >  4:4703/1‑149 (MQ=255)                                                    cgAAACGATCTGGGTAGCCAGCAACGAGTGACCACCGAGGGCGAAGAAGTCGTCCTGCAGGCCAATGCGCGGCAGATTCAACACGTCGC‑GCCAGATGGCCGCGACCTGTTGTTGCAGCTCGGTTCGTGGCTCGACATGCTCACgctg‑ct                                                                                            <  5:191098/149‑1 (MQ=255)                                                       aaCGATCTGGGTAGCCAGCAACGAGTGACCACCGAGGGCGAAGAAGTCGTCCTGCAGGCCAATGCGCGGCAGATTCAACAGGTCGCGGCCATCTGG‑CGCGACGtgttgaa                                                                                                                                 >  1:119157/1‑108 (MQ=37)                                                       aaCGATCTGGGTAGCCAGCAACGAGTGACCACCGAGGGCGAAGAAGTCGTCCTGCAGGCCAATGCGCGGCAGATTCAACAGGTCGCGGCCATCTGG‑CGCGACGtgttgaa                                                                                                                                 <  2:119157/110‑3 (MQ=37)                                                            tCTGGGTAGCCAGCAACGAGTGACCACCGAGGGCGAAGAAGTCGTCCTGCAGGCCAATGCGCGGCAGATTCAACACGTCGC‑GCCAGATGGCCGCGACCTGTTGTTGCAGCTCGGTTCGTGGCTCGACATGCTCACGCTG‑CTGCCACACt                                                                                    >  1:232374/1‑149 (MQ=255)                                                                ggTAGCCAGCAACGAGTGACCACCGAGGGCGAAGAAGTCGTCCTGCAGGCCAATGCGCGGCAGATTCAACACGTCGC‑GCCAGATGGCCGCGACCTGTTGTTGCAGCTCGGTTCGTGGCTCGACATGCTCACg                                                                                                  <  3:133438/132‑1 (MQ=255)                                                                ggTAGCCAGCAACGAGTGACCACCGAGGGCGAAGAAGTCGTCCTGCAGGCCAATGCGCGGCAGATTCAACACGTCGC‑GCCAGATGGCCGCGACCTGTTGTTGCAGCTCGGTTCGTGGCTCGACATGCTCACg                                                                                                  >  4:133438/1‑132 (MQ=255)                                                                ggTAGCCAGCAACGAGTGACCACCGAGGGCGAAGAAGTCGTCCTGCAGGCCAATGCGCGGCAGATTCAACACGTCGC‑GCCAGATGGCCGCGACCTGTTGTTGCAGCTCGGTTCGTGGCTCGACATGCTCACGCTG‑CTGCCACACTgggg                                                                                <  1:126350/149‑1 (MQ=255)                                                                ggTAGCCAGCAACGAGTGACCACCGAGGGCGAAGAAGTCGTCCTGCAGGCCAATGCGCGGCAGATTCAACACGTCGC‑GCCAGATGGCCGCGACCTGTTGTTGCAGCTCGGTTCGTGGCTCGACATGCTCACGCTG‑CTGCCACACTgggg                                                                                <  4:64812/149‑1 (MQ=255)                                                                        gCAACGAGTGACCACCGAGGGCGAAGAAGTCGTCCTGCAGGCCAATGCGCGGCAGATTCAACACGTCGC‑GCCAGATGGCCGCGACCTGTTGTTGCAGCTCGGTTCGTGGCTCGACATGCTCACGCTGCCTGCCCCAGTGTggcagcagc                                                                         <  7:211060/149‑5 (MQ=255)                                                                        gCAACGAGTGACCACCGAGGGCGAAGAAGTCGTCCTGCAGGCCAATGCGCGGCAGATTCAACACGTCGC‑GCCAGATGGCCGCGACCTGTTGTTGCAGCTCGGTTCGTGGCTCGACATGCTCACGCTG‑CTGCCACACTGGGGCAGGCAGt                                                                        <  6:250498/149‑1 (MQ=255)                                                                                      ccGAGGGCGAAGAAGTCGTCCTGCAGGCCAATGCGCGGCAGATTCAACACGTCGC‑GCCAGATGGCCGCGACCTGTTGTTGCAGCTCGGTTCGTGGc                                                                                                                <  6:210383/96‑1 (MQ=255)                                                                                      ccGAGGGCGAAGAAGTCGTCCTGCAGGCCAATGCGCGGCAGATTCAACACGTCGC‑GCCAGATGGCCGCGACCTGTTGTTGCAGCTCGGTTCGTGGc                                                                                                                >  5:210383/1‑96 (MQ=255)                                                                                       cGAGGGCGAAGAAGTCGTCCTGCAGGCCAATGCGCGGCAGATTCAACACGTCGC‑GCCAGATGGCCGCGACCTGTTGTTGCAGCTCGGTTCGTGGCTCGACATGCTCACGCTG‑CTGCCACACTGGGGCAGGCAGTGCCTTGCGGTCGAcc                                                         <  2:232374/149‑1 (MQ=255)                                                                                          gggCGAAGAAGTCGTCCTGCAGGCCAATGCGCGGCAGATTCAACACGTCGC‑GCCAGATGGCCGCGACCTGTTGTTGCAGCTCGGTTCGTGGCTCGACATGCTCACGCTG‑CTGCCACACTGGGGCAGGCAGTGCCTTGCGGTCGACCTTg                                                      <  3:15765/149‑1 (MQ=255)                                                                                            gCGAAGAAGTCGTCCTGCAGGCCAATGCGCGGCAGATTCAACACGTCGC‑GCCAGATGGCCGCGACCTGTTGTTGCAGCTCGGTTCGTGGCTCGACATGCTCACGCTG‑CTGCCACACTGGGGCAGGCAGTGCCTTGCGGTCGACCTTGcc                                                    >  7:131717/1‑149 (MQ=255)                                                                                                    gtcgtcCTGCAGGCCAATGCGCGGCAGATTCAACACGTCGC‑GCCAGATGGCCGCGCCCTGTTGTTGCAGCTCGGTTCGTGGCTCGACATGCTCAGGCTG‑CTGCCACACTGGGGCAGGCAGTGCCTTGCGGTCGACCTTGCCGCTGGGGc                                            >  7:111314/1‑149 (MQ=255)                                                                                                    gtcgtcCTGCAGGCCAATGCGCGGCAGATTCAACACGTCGC‑GCCAGATGGCCGCGACCTGTTGTTGCAGCTCGGTTCGTGGCTCGACATGc                                                                                                       <  5:191506/91‑1 (MQ=255)                                                                                                    gtcgtcCTGCAGGCCAATGCGCGGCAGATTCAACACGTCGC‑GCCAGATGGCCGCGACCTGTTGTTGCAGCTCGGTTCGTGGCTCGACATGc                                                                                                       >  6:191506/1‑91 (MQ=255)                                                                                                       gtcCTGCAGGCCAATGCGCGGCAGATTCAACACGTCGC‑GCCAGATGGCCGCGACCTGTTGTTGCAGCTCGGTTCGTGGCTCGACATGCTCACGctg‑ctg                                                                                           >  3:148883/1‑99 (MQ=255)                                                                                                       gtcCTGCAGGCCAATGCGCGGCAGATTCAACACGTCGC‑GCCAGATGGCCGCGACCTGTTGTTGCAGCTCGGTTCGTGGCTCGACATGCTCACGctg‑ctg                                                                                           <  4:148883/99‑1 (MQ=255)                                                                                                             cAGGCCAATGCGCGGCAGATTCAACACGTCGC‑GCCAGATGGCCGCGACCTGTTGTTGCAGCTCGGTTCGTGGCTCGACATGCTCACGCTG‑CTGCCACACTGGGGCAGGCAGTGCCTTg                                                                  >  2:76149/1‑118 (MQ=255)                                                                                                                  cAATGCGCGGCAGATTCAACACGTCGC‑GCCAGATGGCCGCGACCTGTTGTTGCAGCTCGGTTCGTGGCTCGACATGCTCACGCTG‑CTGCCACACTGGGGCAGGCAGTGCCTTGCGGTCGACCTTGCCGCTGGGGCCCAATGGCATCtgt                              >  8:63836/1‑149 (MQ=255)                                                                                                                  cAATGCGCGGCAGATTCAACACGTCGC‑GCCAGATGGCCGCGACCTGTTGTTGCAGCTCGGTTCGTGGCTCGACATGCTCACGCTG‑CTGCCACACTGGGGCAGGCAGTGCCTTGCGGTCGACCTTGCCGCTGGGGCCCAATGGCATCtgt                              >  7:147473/1‑149 (MQ=255)                                                                                                                  cAATGCGCGGCAGATTCAACACGTCGC‑GCCAGATGGCCGCGACCTGTTGTTGCAGCTCGGTTCGTGGCTCGACATGCTAACgc                                                                                                 >  4:149499/1‑83 (MQ=255)                                                                                                                   aaTGCGCGGCAGATTCAACACGTCGC‑GCCAGATGGCCGCGACCTGTTGTTGCAGCTCGGTTCGTGGCTCGACATGCTCACGCTG‑CTGCCACACTGGGGCAGGCAGTGCCTTGCGGTCGACCTTGCCGCTGGGGCCCAATGGCATCtgtg                             >  1:108247/1‑149 (MQ=255)                                                                                                                     tGCGCGGCAGATTCAACACGTCGC‑GCCAGATGGCCGCGACCTGTTGTTGCAGCTCGGTTCGTGGCTCGACATGCTCACGCTG‑CTGCCACACTGGGGCAGGCAGTGCCTTGCGGTCGACCTTGCCGCTGGGGCCCAATGGCATCTGTGcc                           <  3:100448/149‑1 (MQ=255)                                                                                                                           gCAGATTCAACACGTCGC‑GCCAGATGGCCGCGACCTGTTGTTGCGGCTCGGTTCGTGGCTCGACATGCTCACGCTG‑CTGCCACACTGGGGCAGGCAGTGCCTTGCGGTCGACCTTGCCGCTGGGGCCCAATGGCATCTGTGCCAAAggg                     <  5:54277/149‑1 (MQ=255)                                                                                                                             aGATTCAACACGTCGC‑GCCAGATGGCCGCGACCTGTTGTTGCAGCTCGGTTCGTGGCTCGACATGCTCACGCTG‑CTGCCACACTGGGGCAGGCAGTGCCTTGCGGTCGACCTTGCCGCTGGGGCCCAATGGCATCTGTGCCGAAGGGAt                   <  7:63836/149‑1 (MQ=255)                                                                                                                               caacAACAGGTCGCGGCCATCTGG‑CGCGACGTGTTGTTGCAGCTCGGTTCGTGGCTCGACATGCTCACGCTG‑CTGCCACACTGGGGCAGGCAGTGCCTTGCGGTCGACCTTGCCGCTGGGGCCCAATGGCCTCTGTGCCAAAGGGAt                   >  5:255298/4‑147 (MQ=38)                                                                                                                                aacAACAGGTCGCGGCCATCTGG‑CGCGACGTGTTGTTGCAGCTCGGTTCGTGGCTCGACATGCTCACGCTG‑CTGCCACACTGGGGCAGGCAGTGCCTTGCGGTCGACCTTGCCGCTGGGGCCCAATg                                      >  7:11027/3‑127 (MQ=37)                                                                                                                                aacAACAGGTCGCGGCCATCTGG‑CGCGACGTGTTGTTGCAGCTCGGTTCGTGGCTCGACATGCTCACGCTG‑CTGCCACACTGGGGCAGGCAGTGCCTTGCGGTCGACCTTGCCGCTGGGGCCCAATg                                      <  8:11027/125‑1 (MQ=37)                                                                                                                                  cAACACGTCGC‑GCCAGATGGCCGCGACCTGTTGTTGCAGCTCGGTTCGTGGCTCGACATGCTCACGCTG‑CTGCCACACTGGGGCAGGCAGTGCCTTGCGGTCGACCTTGCCGCTGGGGCCCAATGGCAt                                  <  4:142866/129‑1 (MQ=255)                                                                                                                                  cAACACGTCGC‑GCCAGATGGCCGCGACCTGTTGTTGCAGCTCGGTTCGTGGCTCGACATGCTCACGCTG‑CTGCCACACTGGGGCAGGCAGTGCCTTGCGGTCGACCTTGCCGCTGGGGCCCAATGGCAt                                  >  3:142866/1‑129 (MQ=255)                                                                                                                                   aaCACGTCGC‑GCCAGATGGCCGCGACCTGTTGTTGCAGCTCGGTTCGTGGCTCGACATGCTCACGCTG‑CTGCCACACTGGGGCAGGCAGTGCCTTGCGGTCGACCTTGCCGCTGGGGCCCAATGGCATCTGTGCCAAAGGGATGAGTTg             >  1:237381/1‑149 (MQ=255)                                                                                                                                        gTCGC‑GCCAGATGGCCGCGACCTGTTGTTGCAGCTCGGTTCGTGGCTCGACATGCTCACGCTG‑CTGCCACACTGGGGCAGGCAGTGCCTTGCGGTCGACCTTGCCGCTGGGGCCCAATGGCATCt                                <  7:167089/125‑1 (MQ=255)                                                                                                                                              gcCAGATGGCCGCGACCTGTTGTTGCAGGTCGGTTCGTGGCTCGACATGCTCACGCTG‑CTGCCACACTGGGGCAGGCAGTGCCTTGCGGTCGACCTTGCCGCTGGGGCCCAATGGCATCTGTGCCAAAGGGATGAGTTGCGCCGGCAc    >  1:151510/1‑148 (MQ=255)                                                                                                                                               ccAGATGGCCGCGACCTGTTGTTGCAGCTCGGTTCGTGGCTCGACATGCTCACGCTG‑CTGCCACACTGGGGCAGGCAGTGCCTTGCGGTCGACCTTGCCGCTGGGGCCCAATGGCATCTGTGCCAAAGGGATGAGTTGCGCCGGCACCa  <  3:4703/149‑1 (MQ=255)                                                                                                                                                   |                                                                                                                                                  TTCGAACAGGGCCTTGAGCGGCAGCTCGACATCGCAGGCCTGGCGGGTGCGCGAAACGATCTGGGTAGCCAGCAACGAGTGACCACCGAGGGCGAAGAAGTCGTCCTGCAGGCCAATGCGCGGCAGATTCAACACGTCGC‑GCCAGATGGCCGCGACCTGTTGTTGCAGCTCGGTTCGTGGCTCGACATGCTCACGCTG‑CTGCCACACTGGGGCAGGCAGTGCCTTGCGGTCGACCTTGCCGCTGGGGCCCAATGGCATCTGTGCCAAAGGGATGAGTTGCGCCGGCACCA  >  NC_002947/4826138‑4826427

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 14 ≤ ATCG/ATCG < 27 ≤ ATCG/ATCG < 36 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑