Predicted mutation
evidence	seq id	position	mutation	freq	annotation	gene	description
RA	NC_002947	4,820,205	A→T	9.4%	L3662Q (CTG→CAG)	pvdL ←	non‑ribosomal peptide synthetase

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NC_002947	4,820,205	0	A	T	9.4%	148.9 / 5.7	53	L3662Q (CTG→CAG)	pvdL	non‑ribosomal peptide synthetase
Reads supporting (aligned to +/- strand):  ref base A (21/27);  new base T (2/3);  total (23/30)
Fisher's exact test for biased strand distribution p-value = 1.00e+00
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 4.63e-01

GCTTCGAACTGCGCGATGTAGCTCTGCTCCAGCGGATAAACCCGCTCGGTCCGGTTGCAGTCCTCCAGCAGGAAGCCTTGCTCCTGGGCGCTCA‑GCAGCGGTAGCTCGCTCACCTCCCCTTCAAAACCTTGTACCAGCGCCAGCAGCAGGCGCTTGAATTCGGCCAGCAGGCGCTCGACGGTCGGGTAGTCGAAGTAGCGCTGGTCGAACGACAGGTGCAGGCCCAGGTCATCACCCGGGTAACACACCGCCGTCAGCGGGAAGTTGGTGTGGGTACGGCCCGAGTCGGAGCTGG  >  NC_002947/4820058‑4820352                                                                                                                                                     |                                                                                                                                                    gcTTCGAACTGCGCGATGTAGCTCTGCTCCAGCGGATAAACCCGCTCGGTCCGGTTGCAGTCCTCCAGCAGGAAGCCTTGCTCCTGGGCGCTCA‑GCAGCGGTAGCTCGCTCACCTCCCCTTCAAAACCTTGTACCAGCGCcagcagcag                                                                                                                                                    <  7:15880/149‑1 (MQ=255)      gAACTGCGCGATGTAGCTCTGCTCCAGCGGATAAACCCGCACGGTCCGGTTGCAGTCCTCCAGCAGGAAGCCTTGCTCCTGGGCGCTCA‑GCAGCGGTAGCTCGCTCACCTCCCCTTCAAAACCTTGTACCAGCGCCAGCAGCAGgcgc                                                                                                                                                <  5:280282/148‑1 (MQ=255)       aaCTGCGCGATGTAGCTCTGCTCCAGCGGATAAACCCGCTCGGTCCGGTTGCAGTCCTCCAGCAGGAAGCCTTGCTCCTGGGCGCTCA‑GCAGCGGTAGCTCGCTCACCTCCCCTTCAAAACCTTGTACCAGCGCCTGCTGCTGGCGCtg                                                                                                                                              <  8:181783/149‑2 (MQ=255)       aaCTGCGCGATGTAGCTCTGCTCCAGCGGATAAACCCGCTCGGTCCGGTTGCAGTCCTCCAGCAGGAAGCCTTGCTCCTGGGCGCTCA‑GCAGCGGTAGCTCGCTCACCTCCCCTTCAAAACCTTGTACCAGCGCCAGCAGCAGGCGCtt                                                                                                                                              <  4:269696/149‑1 (MQ=255)        aCTGCGCGATGTAGCTCTGCTCCAGCGGATAAACCCGCTCGGTCCGGTTGCAGTCCTCCAGCAGGAAGCCTTGCTCCTGGGCGCTCA‑GCAGCGGTAGCTCGCTCACCTCCCCTTCAAAACCTTGTACCAGCGCCTGCTGCTGGCGCtgg                                                                                                                                             <  2:155033/149‑3 (MQ=255)        aCTGCGCGATGTAGCTCTGCTCCAGCGGATAAACCCGCTCGGTCCGGTTGCAGTCCTCCAGCAGGAAGCCTTGCTCCTGGGCGCTCA‑GCAGCGGTAGCTCGCTCACCTCCCCTTCAAAACCTTGTACCAGCGCCTGCTGCTGGCGCtg                                                                                                                                              >  6:61030/1‑147 (MQ=255)        aCTGCGCGATGTAGCTCTGCTCCAGCGGATAAACCCGCTCGGTCCGGTTGCAGTCCTCCAGCAGGAAGCCTTGCTCCTGGGCGCTCA‑GCAGCGGTAGCTCGCTCACCTCCCCTTCAAAACCTTGTACCAGCGCCTGCTGCTGGCGCtg                                                                                                                                              <  5:61030/148‑2 (MQ=255)         cTGCGCGATGTAGCTCTGCTCCAGCGGATAAACCCGCTCGGTCCGGTTGCAGTCCTCCAGCAGGAAGCCTTGCTCCTGGGCGCTCA‑GCAGCGGTAGCTCGCTCACCTCCCCTTCAAAACCTTGTACCAGCGCCAGCAGCAGGCGCTTg                                                                                                                                             >  6:143247/1‑148 (MQ=255)               gATGTAGCTCTGCTCCAGCGGATAAACCCGCTCGGTCCGGTTGCAGTCCTCCAGCAGGAAGCCTTGCTCCTGGGCGCTCA‑GCAGCGGTAGCTCGCTCACCTCCCCTTCAAAACCTTGTACCAGCGCCAGCAGCAGGCGCTTGAATTCgg                                                                                                                                      <  6:292916/149‑1 (MQ=255)               gATGTAGCTCTGCTCCAGCGGATAAACCCGCTCGGTCCGGTTGCAGTCCTCCAGCAGGAAGCCTTGCTCCTGGGCGCTCA‑GCAGCGGTAGCTCGCTCACCTCCCCTTCAAAACCTTGTACCAGCGCCAGCAGCAGGCGCTTGAATTCgg                                                                                                                                      <  5:143247/149‑1 (MQ=255)               gATGTAGCTCTGCTCCAGCGGATAAACCCGCTCGGTCCGGTTGCAGTCCTCCAGCAGGAAGCCTTGCTCCTGGGCGCTCA‑GCAGCGGTAGCTCGCTCACCTCCCCTTCAAAACCTTGTACCAGCGCCAGCAGCAGGCGCTTGAATTCgg                                                                                                                                      >  5:140710/1‑149 (MQ=255)                aTGTAGCTCTGCTCCAGCGGATAAACCCGCTCGGTCCGGTTGCAGTCCTCCAGCAGGAAGCCTTGCTCCTGGGCGCTCA‑GCAGCGGTAGCTCGCTCACCTCCCCTTCAAAACCTTGTACCAGCGCCAGCAGCAGGCGCTTGAATTCGGc                                                                                                                                     >  3:144646/1‑149 (MQ=255)                      ctctGCTCCAGCGGATAAACCCGCTCGGTCCGGTTGCAGTCCTCCAGCAGGAAGCCTTGCTCCTGGGCGCTCA‑GCAGCGGTAGCTCGCTCACCTCCCCTTCAAAACCTTGTACCAGCGCCAGCAGCAGGCGCTTGAATTCGGCcagcag                                                                                                                               <  1:218786/149‑1 (MQ=255)                      ctctGCTCCAGCGGATAAACCCGCTCGGTCCGGTTGCAGTCCTCCAGCAGGAAGCCTTGCTCCTGGGCGCTCA‑GCAGCGGTAGCTCGCTCACCTCCCCTTCAAAACCTTGTACCAGCGCCAGCAGCAGGCGCTTGAATTCGGCcagcag                                                                                                                               <  1:22309/149‑1 (MQ=255)                          gCTCCAGCGGATAAACCCGCTCGGTCCGGTTGCAGTCCTCCAGCAGGAAGCCTTGCTCCTGGGCGCTCA‑GCAGCGGTAGCTCGCTCACCTCCCCTTCAAAACCTTGTACCAGCGCCAGCAGCAGgcgc                                                                                                                                                <  3:126598/128‑1 (MQ=255)                          gCTCCAGCGGATAAACCCGCTCGGTCCGGTTGCAGTCCTCCAGCAGGAAGCCTTGCTCCTGGGCGCTCA‑GCAGCGGTAGCTCGCTCACCTCCCCTTCAAAACCTTGTACCAGCGCCAGCAGCAGgcgc                                                                                                                                                >  4:126598/1‑128 (MQ=255)                           cTCCAGCGGATAAACCCGCTCGGTCCGGTTGCAGTCCTCCAGCAGGAAGCCTTGCTCCTGGGCGCTCA‑GCAGCGGTAGCTCGCTCACCTCCCCTTCAAAACCTTGTACCAGCGCCAGCAGCAGGCGCTTGAATTCGGCCAGCAGGCGCt                                                                                                                          <  6:140710/149‑1 (MQ=255)                                      aaaCCCGCTCGGCCCGGTTGCCGTCCTCCACCAGGAAGCCTTGCTCCTGGGCGCTCA‑GCAGCGGTAGCTCGCTCACCTCCCCTTCAAAACCTTGTACCAGCGCCAGCAGCAGGCGCTTGAATTCGGCCAGCAGGCGCTCGACGGTCggg                                                                                                               <  4:61654/149‑1 (MQ=255)                                                  tCCGGTTTCAGTCCTCCAGCAGGAAGCCTTGATCCTGGTCGCTAA‑GCAGCTGTAGCTCGCTCACCTCCCCTTCAATACCTTGTACCAGCGCCTGCAGCAGTCTCTTTAATTCTGCCAGCAGTCGCTCTAATGTCGGGTAGTCGAAg                                                                                                      <  8:220595/146‑1 (MQ=255)                                                     ggTTGCAGTCCTCCAGCAGGAAGCCTTGCTCCTGGGCGCTCAGGCAGCGGTAGCTCGCTCACCTCCCCTTCAAAACCTTGTACCAGCGCCAGCAGCAGGCGCTTGAATTCGGCCAGCAGGCGCTCGACGGTCGGGTAGTCGaa                                                                                                       >  1:226718/1‑143 (MQ=255)                                                     ggTTGCAGTCCTCCAGCAGGAAGCCTTGCTCCTGGGCGCTCA‑GCAGCGGTAGCTCGCTCACCTCCCCTTCAAAACCTTGTACCAGCGCCAGCAGCAGGCGCTTGAATTCGGCCAGCAGGCGCTCGACGGTCGGGTAGTCGaa                                                                                                       <  2:226718/142‑1 (MQ=255)                                                        tGCAGTCCTCCAGCAGGAAGCCTTGCTCCTGGGCGCTCA‑GCAGCGGTAGCTCGCTCACCTCCCCTTCAAAACCTTGTACCAGCGCCAGCAGCAGGCGCTTGAATTCg                                                                                                                                       >  8:253942/1‑107 (MQ=255)                                                        tGCAGTCCTCCAGCAGGAAGCCTTGCTCCTGGGCGCTCA‑GCAGCGGTAGCTCGCTCACCTCCCCTTCAAAACCTTGTACCAGCGCCAGCAGCAGGCGCTTGAATTCg                                                                                                                                       <  7:253942/107‑1 (MQ=255)                                                                tccAGCAGGAAGCCTTGCTCCTGGGCGCTCA‑GCAGCGGTAGCTCGCTCACCTCCCCTTCAAAACCTTGTACCAGCGCCAGCAGCAGGCGCTTGAATTCGGCCAGCAGGCGCTCGACGGTCGGGTAGTCGAAGTAGCGCTGGTCGAACGa                                                                                     >  1:114666/1‑149 (MQ=255)                                                                tccAGCAGGAAGCCTTGCTCCTGGGCGCTCA‑GCAGCGGTAGCTCGCTCACCTCCCCTTCAAAACCTTGTACCAGCGCCAGCAGCAGGCGCTTGAATTCGGCCAGCAGGCGCTCGACGGTCGGGTAGTCGAAGTAGCGCTGGTCGAACGa                                                                                     >  3:100104/1‑149 (MQ=255)                                                                  cagcagGAAGCCTTGCTCCTGGGCGCTCA‑GCAGCGGTAGCTCGCTCACCTCCCCTTCAAAACCTTGTACCAGCGCCAGCAGCAGGCGCTTGAATTCGGCCAGCAGGCGCTCGACGGTCGGGTAGTCGAAGTAGCGCTGGTCGAACGAc                                                                                    <  6:41450/148‑1 (MQ=255)                                                                        gAAGCCTTGCTCCTGGGCGCTCA‑GCAGCGGTAGCTCGCTCACCTCCCCTTCAAAACCTTGTACCAGCGCCAGCAGCAGGCGCTTGAATTCGGCCAGCAGGCGCTCGACGGTCGGGTAGTCGAAGTAGCGCTGGTCGAACGACAGGTg                                                                               >  3:68906/1‑147 (MQ=255)                                                                             cTTGCTCCTGGGCGCTCA‑GCAGCGGTAGCTCGCTCACCTCCCCTTCAAAACCTTGTACCAGCGCCAGCAGCAGGCGCTTGAATTCGGCCAGCAGGCGCTCGACGGTCGGGTAGTCGAAGTAGCGCTGGTCGAACGACAGGTGCAGGccc                                                                        >  3:23398/1‑149 (MQ=255)                                                                             cTTGCTCCTGGGCGCTCA‑GCAGCGGTAGCTCGCTCACCTCCCCTTCAAAACCTTGTACCAGCGCCAGCAGCAGGCGCTTGAATTCGGCCAGCAGGCGCTCGACGGTCGGGTAGTCGAAGTAGCGCTGGTCGAACGACAGGTGCAGGcc                                                                         >  5:298924/1‑148 (MQ=255)                                                                               tGCTCCTGGGCGCTCA‑GCAGCGGTAGCTCGCTCACCTCCCCTTCAAAACCTTGTACCAGCGCCAGCAGCAGGCGCTTGAATTCGGCCAGCAGGCGCTCGACGGTCGGGTAGTCGAAGTAGCGCTGGTCGAACGACAGGAGCAGGCCCAg                                                                      >  5:73928/1‑149 (MQ=255)                                                                                    cTGGGCGCTCA‑GCAGCGGTAGCTCGCTCACCTCCCCTTCAAAACCTTGTACCAGCGCCAGCAGCAGGCGCTTGAATTCGGCCAGCAGGCGCTCGACGGTCGGGTAGTCGAAGTAGCGCTGGTCGAACGACAGGTGCAGGCCCAGGtcat                                                                 <  5:72678/149‑1 (MQ=255)                                                                                       ggCGCTCA‑GCAGCGGTAGCTCGCTCACCTCCCCTTCAAAACCTTGTACCAGCGCCAGCAGCAGGCGCTTGAATTCGGCCAGCAGGCGCTCGACGGTCGGGTAGTCGAAGTCGCGCTGGTCGAACGACAGGTGCAGGCCCAGGGCGTCAc                                                              >  6:5419/1‑149 (MQ=255)                                                                                            tCA‑GCAGCGGTAGCTCGCTCACCTCCCCTTCAAAACCTTGTACCAGCGCCAGCAGCAGGCGCTTGAATTCGGCCAGCAGGCGCTCGACGGTCGGGTAGTCGAAGTAGCGCTGGTCGAACGAc                                                                                    >  2:231930/1‑122 (MQ=255)                                                                                            tCA‑GCAGCGGTAGCTCGCTCACCTCCCCTTCAAAACCTTGTACCAGCGCCAGCAGCAGGCGCTTGAATTCGGCCAGAAGGCGCTCGACGGTCGGGTAGTCGAAGTAGCGCTGGTCGAACGAc                                                                                    <  1:231930/122‑1 (MQ=255)                                                                                                  agcGGGAGCTCGCTCACCTCCCCTTCACAACCTTGTACCAGCGCCAGCAGCAGGCGCTTGAATTCGGCCAGCAGGCGCTCGACGGTCGTGTAGTCGAAGTAGCGCTGGTCGAACGACAGGTGCAGGCCCAGGTCATCACCCGGGTAaca                                                    <  8:210274/149‑1 (MQ=255)                                                                                                            cgctcACCTCCCCTTCAAAACCTTGTACCAGCGCCAGCAGCAGGCGCTTGAATTCGGCCAGCAGGCGCTCGACGGTCGGGTAGTCGAAGTAGCGCTGGTCGAACGACAGGTGCAGGCCCAGGTCATCACCCGGGTAACACACCGCCGt                                           >  2:172920/1‑148 (MQ=255)                                                                                                                 aCCTCCCCTTCAAAACCTTGTACCAGCGCCAGCAGCAGGCGCTTGAATTCGGCCAGCAGGCGCTCGACGGTCGGGTAGTCGAAGTAGCGCTGGTCGAACGACAGGTGCAGGCCCAGGTCATCACCCGGGTAACACACCGCCGTCAGCgg                                     <  6:195705/149‑1 (MQ=255)                                                                                                                   cTCCCCTTCAAAACCTTGTACCAGCGCCAGCAGCAGGCGCTTGAATTCGGCCAGCAGGCGCTCGACGGTCGGGTAGTCGAAGTAGCGATGGTCGAACGACAGGTGCAGGCCCAGGTCATAACCCGTGTAACAAACCGCAGTCATCggg                                    >  4:237008/1‑148 (MQ=255)                                                                                                                      cccTTCAAAACCTTGTACCAGCGCCAGCAGCAGGCGCTTGAATTCGGCCAGCAGGCGCTCGACGGTCGGGTAGTCGAAGTAGCGCTGGTCGAACGACAGGTGCAGGCCCAGGTCATCACCCGGGTAACACACCGCCGTCAGCGGGAAg                                 <  6:73928/148‑1 (MQ=255)                                                                                                                      cccTTCAAAACCTTGTACCAGCGCCAGCAGCAGGCGCTTGAATTCGGCCAGCAGGCGCTCGACGGGCGGGTAGTCGAAGTAGCGCTGGTCGAACGACAGGTGCAGGCCCAGGTCATCACCCGGGTAACACACCGCCGTCAGCGGGAAGt                                <  8:174222/149‑1 (MQ=255)                                                                                                                         ttCAAAACCTTGTACCAGCGCCAGCAGCAGGCGCTTGAATTCGGCCAGCAGGCGCTCGACGGTCGGGTAGTCGAAGTAGCGCTGGTCGAACGACAGGTGCAGGCCCAGGTCATCACCCGGGTAACACACCGCCGTCAGCGGGAAGTTgg                             >  8:197415/1‑149 (MQ=255)                                                                                                                         ttCAAAACCTTGTACCAGCGCCAGCAGCAGGCGCTTGAATTCGGCCAGCAGGCGCTCGACGGTCGGGTAGTCGAAGTAGCGCTGGTCGAACGACAGGTGCAGGCCCAGGTCATCACCCGGGTAACACACCGCCGTCAGCGGGAAGTTgg                             >  8:195915/1‑149 (MQ=255)                                                                                                                           cAAAACCTTGTACCAGCGCCAGCAGCAGGCGCTTGAATTCGGCCAGCAGGCGCTCGACGGTCGGGTAGTCGAAGTAGCGCTGGTCGAACGACAGGTGCAGGCCCAGGTCATCACCCGGGTAACACACCGCCGTCAGCGGGAAGTTGgt                            <  5:172588/148‑1 (MQ=255)                                                                                                                           cAAAACCTTGTACCAGCGCCAGCAGCAGGCGCTTGAATTCGGCCAGCAGGCGCTCGACGGTCGGGTAGTCGAAGTAGCGCTGGTCGAACGACAGGTGCAGGCCCAGGTCATCACCCGGGTAACACACCGCCGTCAGCGGGAAGTTGgt                            <  7:195915/148‑1 (MQ=255)                                                                                                                            aaaaCCTTGTACCAGCGCCAGCAGCAGGCGCTTGAATTCGGCCAGCAGGCGCTCGACGGTCGGGTAGTCGAAGTAGCGCTGGTCGCACGACAGGTGCAGGCCCAGGTCATCACCCGGGTAACACAACGCCGTCAGCGGGAAGGTGgtgt                          >  4:211711/1‑149 (MQ=255)                                                                                                                              aaCCTTGTACCAGCGCCAGCAGCAGGCGCTTGAATTCGGCCAGCAGGCGCTCGACGGTCGGGTAGTCGAAGTAGCGCTGGTCGAACGACAGGTGCAGGCCCAGGTCATCACCCGGGTAACACACCGCCGTCAGCGGGAAGTTGGTGTgg                        <  4:23398/149‑1 (MQ=255)                                                                                                                              aaCCTTGTACCAGCGCCAGCAGCAGGCGCTTGAATTCGGCCAGCAGGCGCTCGACGGTCGGGTAGTCGAAGTAGCGCTGGTCGAACGACAGGTGCAGGCCCAGGTCATCACCCGGGTAACACACCGCCGTCAGCGGGAAGTTGGTGTgg                        <  2:114666/149‑1 (MQ=255)                                                                                                                                     tACCAGCGCCAGCAGCAGGCGCTTGAATTCGGCCAGCAGGCGCTCGACGGTCGGGTAGTCGAAGTAGCGCTGGTCGAACGACAGGTGCAGGCCCAGGTCATCACCCGGGTAACACACCGCCGTCAGCGGGAAGTTGGTGTGGGTACgg                  <  4:144646/148‑1 (MQ=255)                                                                                                                                       ccAGCGCCAGCAGCAGGCGCTTGAATTCGGCCAGCAGGCGCTCGACGGTCGGGTAGTCGAAGTAGCGCTGGTCGAACGACAGGTGCAGGccc                                                                        <  3:216632/92‑1 (MQ=255)                                                                                                                                       ccAGCGCCAGCAGCAGGCGCTTGAATTCGGCCAGCAGGCGCTCGACGGTCGGGTAGTCGAAGTAGCGCTGGTCGAACGACAGGTGCAGGccc                                                                        >  4:216632/1‑92 (MQ=255)                                                                                                                                       ccAGCGCCAGCAGCAGGCGCTTGAATTCGGCCAGCAGGCGCTCGACGGTCGGGTAGTCGAAGTAGCGCTGGTCGAACGACAGGTGCAGGCCCAGGTCATCACCCGGGTAACACACCGCCGTCAGCGGGAAGTTGGTGTGGGTACGGccc               <  4:100104/149‑1 (MQ=255)                                                                                                                                       caaGCGCCTGCTGCTGGCGCTTGAATTCGGCCAGCAGGCGCTCGACGGTCGGGTAGTCGAAGTAGCGCTGGTCGAACGACAGGTGCAGGCCCAGGTCATCACCCGGGTAACACACCGCCGTCAGCGGGAAGTTGGTGTGGGTACGGccc               >  1:223707/3‑149 (MQ=255)                                                                                                                                         aGCGCCAGCAGCAGGCGCTTGAATTCGGCCAGCAGGCGCTCGACGGGCGGGTAGTCGAAGTAGCGCTGGTCGAACGACAGGTGCAGGCCCAGGTCATCACCCGGGTAACACACCGCCGTCAGCGGGAAGTTGGTGTGGGTACGGCCCGa             <  4:16918/149‑1 (MQ=255)                                                                                                                                          gcgcCAGCAGCAGGCGCTTGAATTCGGCCAGCAGGCGCTCGACGGTCGGGTAGTCGAAGTAGCGCTGGTCGAACGACAGGTGCAGGCCCAGGTCATCACCCGGGTAACACACCGCCGTCAGCGGGAAGTTGGTGTGGGTACGGCCCGAg            >  6:93785/1‑149 (MQ=255)                                                                                                                                                    cagGCGCTTGAATTCGGCCAGCAGGCGCTCGACGGTCGGGTAGTCGAAGTAGCGCTGGTCGAACGACAGGTGCAGGCCCAGGTCATCACCCGGGTAACACACCGCCGTCAGCGGGAAGTTGGTGTGGGTACGGCCCGAGTCGGAGCTgg  >  5:56143/1‑149 (MQ=255)                                                                                                                                                     |                                                                                                                                                    GCTTCGAACTGCGCGATGTAGCTCTGCTCCAGCGGATAAACCCGCTCGGTCCGGTTGCAGTCCTCCAGCAGGAAGCCTTGCTCCTGGGCGCTCA‑GCAGCGGTAGCTCGCTCACCTCCCCTTCAAAACCTTGTACCAGCGCCAGCAGCAGGCGCTTGAATTCGGCCAGCAGGCGCTCGACGGTCGGGTAGTCGAAGTAGCGCTGGTCGAACGACAGGTGCAGGCCCAGGTCATCACCCGGGTAACACACCGCCGTCAGCGGGAAGTTGGTGTGGGTACGGCCCGAGTCGGAGCTGG  >  NC_002947/4820058‑4820352

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 14 ≤ ATCG/ATCG < 27 ≤ ATCG/ATCG < 32 ≤ ATCG/ATCG < 36 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑