Predicted mutation
evidence	seq id	position	mutation	freq	annotation	gene	description
RA	NC_002947	3,490,029	G→A	8.3%	I454I (ATC→ATT)	clpV ←	protein ClpV1

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NC_002947	3,490,029	0	G	A	8.3%	135.1 / 2.3	48	I454I (ATC→ATT)	clpV	protein ClpV1
Reads supporting (aligned to +/- strand):  ref base G (20/24);  new base A (2/2);  total (22/26)
Fisher's exact test for biased strand distribution p-value = 1.00e+00
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 3.35e-01

CAGCTCCTGCTGCCACTGGGCATTGAGCTGCTGTTCCTGCTGCTGCTCGGCCTGCAGGGCAGCCTGCAGCGATTCCAGGCGGCGGGCATGGTCGTGCCCCTTGCCGGCTTCGTGGCCGAGC‑ACGTCGATTTCCGCCTG‑CAGGTTGTCGATCTGCCGGCGGCAG‑TCTTCCAGTGCGCCGGGCAGCGAAGATTGCGCCAGGGCAATGCGCGCGCAGGCCGTGTCGAGCACGCTGACCGCCTTGTCGGGCAGCTGGCGGCCGGTGATGTAGCGGTTGGACAGGCG  >  NC_002947/3489882‑3490163                                                                                                                                                      |                                                                                                                                        cAGCTCCTGCTGCCACTGGGCATTGAGCTGCTGTTCCTGCTGCTGCTCGGCCTGCAGGGCAGCCTGCAGCGATTCCAGGCGGCGGGCATGGTCGTGCCCCTTGCCGGCTTCGTGGCCGAGC‑ACGTCGATTTCCGCCTG‑CAGGTTGTCg                                                                                                                                         <  4:23361/148‑1 (MQ=255) cAGCTCCTGCTGCCACTGGGCATTGAGCTGCTGTTCCTGCTGCTGCTCGGCCTGCAGGGCAGCCTGCAGCGATTCCAGGCGGCGGGCATGGTCGTGCCCCTTGCCGGCTTCGTGGCCGAGC‑ACGTCGATTTCCGCCTG‑CAGGTTGTCGa                                                                                                                                        >  5:147548/1‑149 (MQ=255)  aGCTCCTGCTGCCACTGGGCATTGAGCTGCTGTTCCTGCTGCTGCTCGGCCTGCAGGGCAGCCTGCAGCGATTCCAGGCGGCGGGCATGGTCGTGCCCCTTGCCGGCTTCGTGGCCGAGC‑ACGTCGATTTCCGCCTG‑CAGGTTGTCGAt                                                                                                                                       >  5:200148/1‑149 (MQ=255)        tgctgcCACTGGGCATTGAGCTGCTGTTCCTGCTGCTGCTCGGCCTGCAGGGCAGCCTGCAGCGATTCCAGGCGGCGGGCATGGTCGTGCCCCTTGCCGGCTTCGTGGCCGAGC‑ACGTCGATTTCCGCCTG‑CAGGTTGTCGATCTGCcg                                                                                                                                 >  6:266025/1‑149 (MQ=255)           tgcCACTGGGCATTGAGCTGCCGTTCCTGCTGCTGCTCGGCCTGCAGGGCAGCCTGCAGCGATTCCAGGCGGCGGGCATGGTCGTGCCCCTTGCCGGCTTCGTGGCCGAGC‑ACGTCGATTTCCGCCTG‑CAGGTTGTCGATCTGCcggcg                                                                                                                              >  3:52480/1‑149 (MQ=255)              cACTGGGCATTGAGCTGCTGTTCCTGCTGCTGCTCGGCCTGCAGGGCAGCCTGCAGCGATTCCAGGCGGCGGGCATGGTCGTGCCCCTTGCCGGCTTCGTGGCCGAGC‑ACGTCGATTTCCGCCTG‑CAGGTTGTCGATCTGCCGGCGGCa                                                                                                                           <  4:40369/149‑1 (MQ=255)               aCTGGGCATTGAGCTGCTGTTCCTGCTGCTGCTCGGCCTGCAGGGCAGCCTGCAGCGATTCCAGGCGGCGGGCATGGTCGTGCCCCTTGCCGGCTTCGTGGCCGAGC‑ACGTCGATTTCCGCCTG‑CAGGTTGTCGATCTGCCGGCGGCAg                                                                                                                          <  2:242233/149‑1 (MQ=255)                   ggCATTGAGCTGCTGTTCCTGCTGCTGCTCGGCCTGCAGGGCAGCCTGCAGCGATTCCAGGCGGCGGGCATGGTCGTGCCCCTTGCCGGCTTCGTGGCCGAGC‑ACGTCGATTTCCGCCTG‑CAGGTTGTCGATCTGCCGGCGGCAG‑TCtt                                                                                                                     >  4:260583/1‑149 (MQ=255)                    gCATTGAGCTGCTGTTCCTGCTGCTGCTCGGCCTGCAGGGCAGCCTGCAGCGATTCCAGGCGGCGGGCATGGTCGTGCCCCTTGCCGGCTTCGTGGCCGAGC‑ACGTCGATTTCCGCCTG‑CAGGTTGTCGATCTGCCGGCGGCAG‑TCTTc                                                                                                                    <  6:60771/149‑1 (MQ=255)                    gCATTGAGCTGCTGTTCCTGCTGCTGCTCGGCCTGCAGGGCAGCCTGCAGCGATTCCAGGCGGCGGGCATGGTCGTGCCCCTTGCCGGCTTCGTGGCCGAGC‑ACGTCGATTTCCGCCTG‑CAGGTTGTCGATCTGCCGGCGGCAG‑TCTTc                                                                                                                    <  6:212572/149‑1 (MQ=255)                     cATTGAGCTGCTGTTCCTGCTGCTGCTCGGCCTGCAGGGCAGCCTGCAGCGATTCCAGGCGGCGGGCATGGTCGTGCCCCTTGCCGGCTTCGTGGCCGAGCTACGTCGATTTCCGCCGG‑CAGATCGACAACCTGCaggcggaaa                                                                                                                          <  1:214850/144‑4 (MQ=255)                     cATTGAGCTGCTGTTCCTGCTGCTGCTCGGCCTGCAGGGCAGCCTGCAGCGATTCCAGGCGGCGGGCATGGTCGTGCCCCTTGCCGGCTTCGTGGCCGAGC‑ACGTCGATTTCCGCCGG‑CAGATCGACAACCTGCaggcggaaa                                                                                                                          >  2:214850/1‑140 (MQ=255)                      aTTGAGCTGCTGTTCCTGCTGCTGCTCGGCCTGCAGGGCAGCCTGCAGCGATTCCAGGCGGCGGGCATGGTCGTGCCCCTTGCCGGCTTCGTGGCCGAGC‑ACGTCGATTTCCGCCTG‑CAGGTTGTCGATCTGCCGGCGGCAG‑TCTTCCa                                                                                                                  <  6:147548/149‑1 (MQ=255)                           gctgctGTTCCTGCTGCTGCTCGGCCTGCAGGGCAGCCTGCAGCGATTCCAGGCGGCGGGCATGGTCGTGCCCCTTGCCGGCTTCGTGGCCGAGC‑ACGTCGATTTCCGCCTG‑CAGGTTGTCGATCTGCCGGCGGCAG‑TCTTCCAGTgcg                                                                                                             >  4:279762/1‑149 (MQ=255)                           gctgctGTTCCTGCTGCTGCTCGGCCTGCAGGGCAGCCTGCAGCGATTCCAGGCGGCGGGCATGGTCGTGCCCCTTGCCGGCTTCGTGGCCGAGC‑ACGTCGATTTCCGCCTG‑CAGGTTGTCGATCTGCCGGCGGCAG‑TCTTCCAGTgcg                                                                                                             >  3:104897/1‑149 (MQ=255)                           gctgctGGTCCTGCTGCTGCTCGGGCTGGAGGGCAGCCTGCATGGATTCCATGCGGCGGGCATGGGCGTGCCCCTTGCCGGGTTCGTGGCCGAGC‑ACGTCGATTTGCGCCTGCCAGGTTGTCGATCTGCCGGCGGCAG‑TCTTCCAGTg                                                                                                               <  1:201195/148‑1 (MQ=255)                            ctgctgTTCCTGCTGCTGCTCGGCCTGCAGGGCAGCCTGCAGCGATTCCAGGCGGCGGGCATGGTCGTGCCCCTTGCCGGCTTCGTGGCCGAGC‑ACGTCGATTTCCGCCTG‑CAGGTTGTCGATCTGCCGGCGGCAG‑TCTTCCAGTgcgc                                                                                                            >  4:14580/1‑149 (MQ=255)                                 gTTCCTGCTGCTGCGCGGCCTGCAGGGCAGCCTGCAGCGATTCCAGGCGGCGGGCATGGTCGTGCCCCTTGCCGGCTTCGTGGCCGAGC‑ACGTCGATTTCCGCCTG‑CAGGTTGTCGATCTGCCGGCGGCAG‑TCTTCCAGTGCGCCggg                                                                                                        >  7:263697/1‑148 (MQ=255)                                  ttCCTGCTGCTGCTCGGCCTGCAGGGCAGCCTGCAGCGATTCCAGGCGGCGGGCATGGTCGTGCCCCTTGCCGGCTTCGTGGCCGAGC‑ACGTCGATTTCCGCCTG‑CAGGTTGTCGATCTGCCGGCGGCAG‑TCTTCCAGTGCGCCGGGCa                                                                                                      <  5:266025/149‑1 (MQ=255)                                      tgctgctgcTCGGCCTGCAGGGCAGCCTGCAGCGATTCCAGGCGGCGGGCATGGTCGTGCCCCTTGCCGGCTTCGTGGCCGAGC‑ACGTCGATTTCCGCCTG‑CAGGTTGTCGATCTGCCGGCGGCAG‑TCTTCCAGTGCGCCGGGCAGCg                                                                                                   >  6:290465/1‑148 (MQ=255)                                           ctgctCGGCCTGCAGGGCAGCCTGCAGCGATTCCAGGCGGCGGGCATGGTCGTGCCCCTTGCCGGCTTCGTGGCCGAGC‑ACGTCGATTTCCGCCTG‑CAGGTTGTCGATCTGCCGGCGGCAG‑TCTTCCAGTGCGCCGGGCAGCGAAGa                                                                                               <  3:279762/147‑1 (MQ=255)                                            tgctCGGCCTGCAGGGCAGCCTGCAGCGATTCCAGGCGGCGGGCATGGTCGTGCCCCTTGCCGGCTTCGTGGCCGAGC‑ACGTCGATTTCCGCCTG‑CAGGTTGTCAATCTGCCGGCGGCAG‑TCTTCCAGTGCGCCGGGCAGCGAAGATTg                                                                                            >  4:283953/1‑149 (MQ=255)                                             gctCGGCCTGCAGGGCAGCCTGCAGCGATTCCAGGCGTCGGGCATGGTCGTGCCCCTTGCCGGCTTCGTGGCCGAGC‑ACGTCGATTTCCGCCTG‑CAGGTTGTCGATCTGCCGGCGGCAT‑TCTTCCAGTGCGCCGGGCAGCGAAGATTgc                                                                                           <  8:67567/149‑1 (MQ=255)                                             gctCGGCCTGCAGGGCAGCCTGCAGCGATTCCAGGCGGCGGGCATGGTCGTGCCCCTTGCCGGCTTCGTGGCCGAGC‑ACGTCGATTTCCGCCTG‑CAGGTTGTCGATCTGCCGGCGGCAG‑TCTTCCAGTGCGCCGGGCAGCGAAGATTgc                                                                                           >  6:186351/1‑149 (MQ=255)                                                  gCCTGCAGGGCAGCCTGCAGCGATTCCAGGCGGCGGGCATGGTCGTGCCCCTTGCCGGCTTCGTGGCCGAGC‑ACGTCGATTTCCGCCTG‑CAGGTTGTCGATCTGCCGGCGGCAGATCTTCCAGTGCGCCGGGCAGCGAAGATTGCGCCa                                                                                       <  1:40463/149‑1 (MQ=255)                                                  gCCTGCAGGGCAGCCTGCAGCGATTCCAGGCGGCGGGCATGGTCGTGCCCCTTGCCGGCTTCGTGGCCGAGC‑ACGTCGATTTCCGCCTG‑CAGGTTGTCAATCTGCCGGCGGCAG‑TCTTCCAGTGCGCCGGGCAGCGAAGATTGCGCCAg                                                                                      <  3:283953/149‑1 (MQ=255)                                                   ccTGCAGGGCAGCCTGCAGCGATTCCAGGCGGCGGGCATGGTCGTGCCCCTTGCCGGCTTCGTGGCCGAGC‑ACGTCGATTTCCGCCTG‑CAGGTTGTCGATCTGCCGGCGGCAG‑TCTTCCAGTGCGCCGGGCAGCGAAGATTGCGCCAgg                                                                                     <  5:290465/149‑1 (MQ=255)                                                   ccTGCAGGGCAGCCTGCAGCGATTCCAGGCGGCGGGCATGGTCGTGCCCCTTGCCGGCTTCGTGGCCGAGC‑ACGTCGATTTCCGCCTG‑CAGGTTGTCGATCTGCCGGCGGCAG‑TCTTCCAGTGCGCCGGGCAGCGAAGATTGCGCCAgg                                                                                     <  7:96091/149‑1 (MQ=255)                                                    cTGCAGGGCAGCCTGCAGCGATTCCAGGCGGCGGGCATGGTCGTGCCCCTTGCCGGCTTCGTGGCCGAGC‑ACGTCGATTTCCGCCTG‑CAGGTTGTCGATCTGCCGGCGGCAG‑TCTTCCAGTGCGCCGGGCAGCGAAGATTGCGCCAggg                                                                                    <  4:52480/149‑1 (MQ=255)                                                     tGCAGGGCAGCCTGCAGCGATTCCAGGCGGCGGGCATGGTCGTGCCCCTTGCCGGCTTCGTGGCCGAGC‑ACGTCGATTTCCGCCTG‑CAGGTTGTCGATCTGCCGGCGGCAG‑TCTTCCAGTGCGCCGGGCAGCGAAGATTGCGCCAggg                                                                                    >  6:202705/1‑148 (MQ=255)                                                                   cAGCGATTCCAGGCGGCGGGCATGGTCGTGCCCCTTGCCGGCTTCGTGGCCGAGC‑ACGTCGATTTCCGCCTG‑CAGGTTGTCGATCTGCCGGCGGCAG‑TCTTCCAGTGCGCCGGGCAGCGAAGATTGCGCCAGGGCAATGCGCGCGCa                                                                       <  6:200148/147‑1 (MQ=255)                                                                     gCGATTCCAGGCGGCGGGCATGGTCGTGCCCCTTGCCGGCTTCGTGGCCGAGC‑ACGTCGATTTCCGCCTG‑CAGGTTGTCGATCTGCCGGCGGCAG‑TCTTCCAGTGCGCCGGGCAGCGAAGATTGCGCCAGGGCAATGCGCGCGCAGGcc                                                                   >  4:203381/1‑149 (MQ=255)                                                                       gATTCCAGGCGGCGGGCATGGTCGTGCCCCTTGCCGGCTTCGTGGCCGAGC‑ACGTCGATTTCCGCCTG‑CAGGTTGTCGATCTGCCGGCGGCAG‑TCTTCCAGTGCGCCGGGCAGCGAAGATTGCGCCAGGGCAATGCGCGCGCAGGCCgt                                                                 <  5:178415/149‑1 (MQ=255)                                                                             aGGCGGCGGGCATGGTCGTTCCCCTTGCCGGCTTCGTGGCCGAGC‑ACGTCGATTTCCGCCTG‑CAGGTTGTCGATCTGCCGGCGGCAG‑TCTTCCAGTGCGCCGGGCAGCGAAGATTGCGCCAGGGCAATGCGCGCGCAGGCCGTGTCGAg                                                           <  4:73593/149‑1 (MQ=255)                                                                                           gTCGTGCCCCTTGCCGGCTTCGTGGCCGAGC‑ACGTCGATTTCCGCCTG‑CAGGTTGTCGATCTGCCGGCGGCAG‑TCTTCCAGTGCGCCGGGCAGCGAAGATTGCGCCAGGGCAATGCGCGCGCAGGCCGTGTCGAGCACGCTGACCGcc                                              <  8:263697/148‑1 (MQ=255)                                                                                           gTCGTGCCCCTTGCCGGCTTCGTGGCCGAGC‑ACGTCGATTTCCGCCTG‑CAGGTTGTCGATCTGCCGGCGGCAG‑TCTTCCAGTGCGCCGGGCAGCGAAGATTGCGCCAGGGCAATGCGCGCGCAGGCCGTGTCGAGCACGCTGACCGcc                                              <  3:260583/148‑1 (MQ=255)                                                                                                 ccccTTGCCGGCTTCGTGGCCGAGC‑ACGTCGATTTCCGCCTG‑CAGGTTGTCGATCTGCCGGCGGCAG‑TCTTCCAGTGCGCCGGGCAGCGAAGATTGCGCCAGGGCAATGCGCGCGCAGGCCGTGTCGAGCACGCTGACCGCCTTGTCg                                        <  3:14580/148‑1 (MQ=255)                                                                                                  cccTTGCCGGCTTCGTGGCCGAGC‑ACGTCGATTTCCGCCTG‑CAGGTTGTCGATCTGCCGGCGGCAG‑TCTTCCAGTGCGCCGGGCAGCGAAGATTGCGCCAGGGCAATGCGCGCGCAGGCCGTGTCGAGCACGCTGACCGCCTTGTCggg                                      >  5:254204/1‑149 (MQ=255)                                                                                                  cccTTGCCGGCTTCGTGGCCGAGC‑ACGTCGATTTCCGCCTG‑CAGGTTGTCGATCTGCCGGCGGCAG‑TCTTCCAGTGCGCCGGGCAGCGAAGATTGCGCCAGGGCAATGCGCGCGCAGGCCGTGTCGAGCACGCTGACCGCCTTGTCggg                                      >  6:62741/1‑149 (MQ=255)                                                                                                                 tGGCCGAGC‑ACGTCGATTTCCGCCTG‑CAGGTTGTCGATCTGCCGGCGGCAG‑TCTTCCAGTGCGCCGGGCAGCGAAGATTGCGCCAGGGCAATGCGCGCGCAGGCCGTGTCGAGCACGCTGACCGCCTTGTCGGGCAGCTGGCGGCCGGt                       <  3:203381/149‑1 (MQ=255)                                                                                                                   gCCGAGC‑ACGTCGATTTCCGCCTG‑CAGGTTGTCGATCTGCCGGCGGCAG‑TCTTCCAGTGCGCCGGGCAGCGAAGATTGCGCCAGGGCAATGCGCGCGCAGGCCGTGTCGAGCACGCTGACCGCCTTGTCGGGCAGCTGGCGGCCGGTg                      <  6:254204/148‑1 (MQ=255)                                                                                                                             gTCGATTTCCGCCTG‑CAGGTTGTCGATCTGCCGGCGGCAG‑TCTTCCAGTGCGCCGGGCAGCGAAGATTGCGCCAGGGCAATGCGCGCGCAGGCCGTGTCGAGCACGCTGACCGCCTTGTCGGGCAGCTGGCGGCCGGTGa                     >  3:65230/1‑140 (MQ=255)                                                                                                                             gTCGATTTCCGCCTG‑CAGGTTGTCGATCTGCCGGCGGCAG‑TCTTCCAGTGCGCCGGGCAGCGAAGATTGCGCCAGGGCAATGCGCGCGCAGGCCGTGTCGAGCACGCTGACCGCCTTGTCGGGCAGCTGGCGGCCGGTGa                     <  4:65230/140‑1 (MQ=255)                                                                                                                             gTCGATTTCCGCCTG‑CAGGTTGTCGATCTGCCGGCGGCAG‑TCTTCCAGTGCGCCGGGCAGCGAAGATTGCGCCAGGGCAATGCGCGCGCAGGCCGTGTCGAGCACGCTGACCGCCTTGTCGGGCAGCTGGCGGCCGGTGATGTAGCGGt            >  7:138782/1‑149 (MQ=255)                                                                                                                             gTCGATTTCCGCCTG‑CAGGTTGTCGATCTGCCGGCGGCAG‑TCTTCCAGTGCGCCGGGCAGCGAAGATTGCGCCAGGGCAATGCGCGCGCAGGCCGTGTCGAGCACGCTGACCGCCTTGTCGGGCAGCTGGCGGCCGGTGATGTAGCGGt            >  8:173224/1‑149 (MQ=255)                                                                                                                                     ccGCCTG‑CAGGTTGTCGATCTGCCGGCGGCAG‑TCTTCCAGTGCGCCGGGCAGCGAAGATTGCGCCAGGGCAATGCGCGCGCAGGCCGTGTCGAGCACGCTGACCGCCTTGTCGGGCAGCTGGCGGCCGGTGATGTAg                >  7:123411/1‑137 (MQ=255)                                                                                                                                     ccGCCTG‑CAGGTTGTCGATCTGCCGGCGGCAG‑TCTTCCAGTGCGCCGGGCAGCGAAGATTGCGCCAGGGCAATGCGCGCGCAGGCCGTGTCGAGCACGCTGACCGCCTTGTCGGGCAGCTGGCGGCCGGTGATGTAg                <  8:123411/137‑1 (MQ=255)                                                                                                                                     ccGCCTG‑CAGGTTGTCGATCTGCCGGCGGCAG‑TCTTCCAGTGCGCCGGGCAGCGAAGATTGCGCCAGCGCAATGCGCGCGCAGGCCGTGTCGAGCACGCTGACCGCCTTGTCGGGCAGCTGGCGGCCGGTGATGTAGCGGTTGGACAg     <  7:7090/148‑1 (MQ=255)                                                                                                                                        ccTG‑CAGGTTGTCGATCTGCCGGCGGCAG‑TCTTCCAGTGCGCCGGGCAGCGAAGATTGCGCCAGGGCAATGCGCGCGCAGGCCGTGTCGAGCACGCTGACCGCCTTGTCGGGCAGCTGGCGGCCGGTGATGTAGCGGTTGGACAGGCg  >  5:105139/1‑148 (MQ=255)                                                                                                                                                      |                                                                                                                                        CAGCTCCTGCTGCCACTGGGCATTGAGCTGCTGTTCCTGCTGCTGCTCGGCCTGCAGGGCAGCCTGCAGCGATTCCAGGCGGCGGGCATGGTCGTGCCCCTTGCCGGCTTCGTGGCCGAGC‑ACGTCGATTTCCGCCTG‑CAGGTTGTCGATCTGCCGGCGGCAG‑TCTTCCAGTGCGCCGGGCAGCGAAGATTGCGCCAGGGCAATGCGCGCGCAGGCCGTGTCGAGCACGCTGACCGCCTTGTCGGGCAGCTGGCGGCCGGTGATGTAGCGGTTGGACAGGCG  >  NC_002947/3489882‑3490163

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: ‑