Predicted mutation
evidence	seq id	position	mutation	freq	annotation	gene	description
RA	NC_002947	3,432,765	G→A	14.3%	R33R (CGG→CGA)	PP_3049 →	hypothetical protein

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NC_002947	3,432,765	0	G	A	14.3%	117.2 / 10.6	49	R33R (CGG→CGA)	PP_3049	hypothetical protein
Reads supporting (aligned to +/- strand):  ref base G (22/20);  new base A (4/3);  total (26/23)
Fisher's exact test for biased strand distribution p-value = 1.00e+00
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 9.93e-01

GTGAGCCTGGAGGCGATGGCCTTGTAACGCTGATCTTGAGGAAGGCGGTATGAGTGTTGGTAGCTATCACAAGCAGTCGGCCAGCAGCGGGTTGATCTCGCTGCAGGTGGACCCGC‑AGGCCCCCAAAGGTTTTCAGGACTTCACGCGGCT‑GGTCCCCAAAGCGGCGCATGCCGCGCAGCGACGGGCAGTCAACAAGACGCTGCGCTGGCTTCGAACCCACATCGCCCGGGAGGTAGGCCGCCAGGAGCGCATCGCTATTGCGGCTGTGCGGCAGCGGCTGAGGGCGTTCCCGGT  >  NC_002947/3432618‑3432911                                                                                                                                                     |                                                                                                                                                    gTGAGCCTGGAGGCGATGGCCTTGTAACGCTGATCTTGAGGAAGGCTGTATGAGTGTTGGTAGCTATCACAAGCAGTCGGCCAGCAGCGGGTTGATCTCGCTGCAGGTGGACCCGC‑AGGCCCCCAAAGTTTTTCAGGACTTCACGCGGc                                                                                                                                                    <  1:363626/149‑1 (MQ=255)     gCCTGGAGGCGATGGCCTTGTAACGCTGATCTTGAGGAAGGCGGTATGAGTGTTGGTAGCTATCACAAGCAGTCTGCCAGCAGCGGGTTGATCTCGCTGCAGGTGGACACGC‑AGGCCCCCAAAGGTTTTCGGGACTTCACGCGACT‑GGt                                                                                                                                               >  3:24189/1‑149 (MQ=255)      ccTGGAGGCGATGGCCTTGTAACGCTGATCTTGAGGAAGGCGGTATGAGTGTTGGTAGCTATCACAAGCAGTCGGCCAGCAGCGGGTTGATCTCGCTGCAGGTGGACCCGC‑AGGCCCCCAAAGGTTTTCAGGACTTCACGCGGCT‑GGTc                                                                                                                                              <  1:44502/149‑1 (MQ=255)           aGGCGATGGCCTTGTAACGCTGATCTTGAGGAAGGCGGTATGAGTGTTGGTAGCTATCACAAGCAGTCGGCCAGCAGCGGGTTGATCTCGCTGCAGGTGGACCCGC‑AGGCCCCCAAAGGTTTTCAGGACTTCACGCGGCT‑GGTCCCCaa                                                                                                                                         <  6:126818/149‑1 (MQ=255)                aTGGCCTTGTAACGCTGATCTTGAGGAAGGCGGTATGAGTGTTGGTAGCTATCACAAGCGGTCGGCCAGCAGCGGGTTGATCTCGCTGCAGGTGGACCCGC‑AGGCCCCCAAAGGTTTTCAGGACTTCACGCGGCT‑GGTCCCCAAAgcgg                                                                                                                                    <  4:332478/149‑1 (MQ=255)                     cTTGTAACGCTGATCTTGAGGAAGGCGGTATGAGTGTTGGTAGCTATCACAAGCAGTCGGCCAGCAGCGGGTTGATCTCGCTGCAGGTGGACCCGC‑AGGCCCCCAAAGGTTTTCAGGACTTCACGCGGCT‑GGTCCCCAAAGCGGCGCAt                                                                                                                               >  5:33409/1‑149 (MQ=255)                           aCGCTGATCTTGAGGAAGGCGGTATGAGTGTTGGTAGCTATCACAAGCAGTCGGCCAGCAGCGGGTTGATCTCGCTGCAGGTGGACCCGC‑AGGCCCCCAAAGGTTTTCAGGACTTCACGCGGCT‑GGTCCCCAAAGCGGCGCATGCcgcg                                                                                                                         <  4:77100/149‑1 (MQ=255)                                 agcTTGAGGAAGGCGGTATGAGTGTTGGTAGCTATCACAAGCAGTCGGCCAGCAGCGGGTTGATCTCGCTGCAGGTGGACCCGC‑AGGCCCCCAAAGGTTTTCAGGACTTCACGCGGCT‑GGTCCCCAAAGCGGCGCATGCCGCGCAGc                                                                                                                     <  2:227594/145‑1 (MQ=255)                                          aaGGCGGTATGAGTGTTGGTAGCTATCACAAGCAGTCGGCCAGCAGCGGGTTGATCTCGCTGCAGGTGGACCCGC‑AGGCCCCCAAAGGTTTTCAGGACTTCACGCGGCT‑GGTCCCCAAAGCGGCGCATGCCGCGCAGCGACGGGCAGTc                                                                                                          <  4:357167/149‑1 (MQ=255)                                           aGGCGGTATGAGTGTTGGTAGCTATCACAAGCAGTCGGCCAGCAGCGGGTTGATCTCGCTGCAGGTGGACCCGC‑AGGCCCCCAAAGGTTTTCAGGACTTCACGCGACT‑GGTCCCCAAAGCGGCGCATGCCGCGCAGCGACGGGCAGTc                                                                                                          >  3:197344/1‑148 (MQ=255)                                            ggCGGAATGAGTGTTGCTAGCTATCACAAGCAGTCGGCCAGCAGCGGGTTGATCTCGCTGCAGGTGGACCCGC‑ACCCCCCCAAAGGTTTTCAGGACTTCACGCGGCT‑GGTCCCCAAAGCGGCGCATGCCGCGCAGCGACGGGCAGTcaa                                                                                                        >  4:144787/1‑149 (MQ=255)                                                 tATGAGTGTTGGTAGCTATCACAAGCAGTCGGCCAGCAGCGGGTTGATCTCGCTGCAGGTGGACCCGC‑AGGCCCCCAAAGGTTTTCAGGACTTCACGCGGCT‑GGTCCCCAAAGCGGCGCATGCCGCGCAGCGACGGGCAGTCAACAAGa                                                                                                   <  2:246032/149‑1 (MQ=255)                                                 tATGAGTGTTGGTAGCTATCACAAGCAGTCGGCCAGCAGCGGGTTGATCTCGCTGCAGGTGGACCCGC‑AGGCCCCCAAAGGTTTTCAGGACTTCACGCGACT‑GGTCCCCAAAGCGGCGCATGCCGCGCAGCGACGGGCAGTCAACAAGa                                                                                                   >  3:290807/1‑149 (MQ=255)                                                        gtTGGTAGCTATCACAAGCAGTCGGCCAGCAGCGGGTTGATCTCGCTGCAGGTGGACCCGC‑AGGCCCCCAAAGGTTTTCAGGACTTCACGCGGCT‑GGTCCCCAAAGCGGCGCATGCCGCGCAGCGACGGGCAGTCAACAAGAcgctgcg                                                                                            >  8:123456/1‑149 (MQ=255)                                                            gTAGCTATCACAAGCAGTCGGCCAGCAGCGTGTTGATCTCGCTGCAGGTGGACACGA‑AGTCCACCAAAGGTTTTCAGGACTTCACGAGGCT‑GGTCCCCAAAGCGGCGCATGCCGCGCAGCGACGGGCAGTCAACAAGACGCTGCGCTgg                                                                                        >  4:193118/1‑149 (MQ=255)                                                                 tATCACAAGCAGTCGGCCAGCAGCGGGTTGATCTCGCTGCAGGTGGACCCGC‑AGGCCCCCAAAGGTTTTCAGGACTTCACGCGACT‑GGTCCCCAAAGCGGCGCATGCCGCGCAGCGACGGGCAGTCAACAAGACGCTGCGCTGGCTTc                                                                                    >  4:345633/1‑148 (MQ=255)                                                                   tCACAAGCAGTGGGCCAGCTGCGGTTTGATCTCTCTGCAGGTGGACCCGC‑AGGCCCCCAAAGGTTTTCGGGACTTCACGCGACT‑GGTCCCCAAAGCGGCGCATGCCGCGCAGCGACGGGCAGTCAACAAGACGCTGCGCTGGCTTc                                                                                    <  4:24189/146‑1 (MQ=255)                                                                   tCACAAGCAGTCGGCCAGCAGCGGGTTGATCTCGCTGCAGGTGGACCCGC‑AGGCCCCCAAAGGTTTTCAGGACTTCACGCGGCT‑GGTCCCCAAAGCGGCGCATGCCGCGCAGCGACGGGCAGTCAACAAGACGCTGCGCTGGCTTCGaa                                                                                 >  4:122173/1‑149 (MQ=255)                                                                   tCACAAGCAGTCGGCCAGCAGCGGGTTGATCTCGCTGCAGGTGGACCCGC‑AGGCCCCCAAAGGTTTTCAGGACTTCACGCGGCT‑GGTCCCCAAAGCGGCGCATGCCGCGCAGCGACGGGCAGTCAACAAGACGCTGCGCTGGCTTCGaa                                                                                 >  1:80227/1‑149 (MQ=255)                                                                    cacaAGCAGTCGGCCAGCAGCGGGTTGATCTCGCTGCAGGTGGACCCGC‑AGGCCCCCAAAGGTTTTCAGGACTTCACGCGGCT‑GGTCCCCAAAGCGGCGCATGCCGCGCAGCGACGGGCAGTCAACAAGACGCTGCGCTGGCTTCGAAc                                                                                >  3:356328/1‑149 (MQ=255)                                                                      caAGCAGTCGGCCAGCAGCGGGTTGATCTCGCTGCAGGTGGACCCGC‑AGGCCCCCAAAGGTTTTCAGGACTTCACGCGGCT‑GGTCCCCAACGCGGCGCATGCCGCGCAGCGACGGGCAGTCAACAAGACGCTGCGCTGGCTTCGAAcc                                                                               >  4:118270/1‑148 (MQ=255)                                                                      caAGCAGTCGGCCAGCAGCGGGTTGATCTCGCTGCAGGTGGACCCGC‑AGGCCCCCAAAGGTTTTCAGGACTTCACGCGGCT‑GGTCCCCAAAGCGGCGCATGCCGCGCAGCGACGGGCAGTCAACAAGACGCTGCGCTGGCTTCGAAcc                                                                               >  6:320250/1‑148 (MQ=255)                                                                           aGTCGGCCAGCAGCGGGTTGATCTCGCTGCAGGTGGACCCGC‑AGGCCCCCAAAGGTTTTCAGGACTTCACGCGGCT‑GGTCCCCAAAGCGGCGCATGCCGCGCAGCGACGGGCAGTCAACAAGACGCTGCGCTGGCTTCGAACCCACATc                                                                         >  5:116353/1‑149 (MQ=255)                                                                             tCGGCCAACAGCCGGTTGATCTCGCTGCAGGTGGACCCGC‑AGGCCCCCAAAGGATTTCAGGACTTCACGCGGCA‑GGTCCCCAAAGCGGCGCATGCCGAGCAGCGACGGGCAGTCAACAAGACGCTGCGCTGGCAACGAACCCACATCGc                                                                       >  4:214947/1‑149 (MQ=255)                                                                               ggCCAGCAGCGGGTTGATCTCGCTGCAGGTGGACCCGC‑AGGCCCCCAAAGGTTTTCAGGACTTCACGCGGCT‑GGTCCCCAAAGCGGCGCATGCCGCGCAGCGACGGGCAGTcaac                                                                                                       >  7:271712/1‑115 (MQ=255)                                                                               ggCCAGCAGCGGGTTGATCTCGCTGCAGGTGGACCCGC‑AGGCCCCCAAAGGTTTTCAGGACTTCACGCGGCT‑GGTCCCCAAAGCGGCGCATGCCGCGCAGCGACGGGCAGTcaac                                                                                                       <  8:271712/115‑1 (MQ=255)                                                                                gCCAGCAGCGGGTTGATCTCGCTGCAGGTGGACCCGC‑AGGCCCCCAAAGGTTTTCAGGACTTCACGCGGCT‑GGTCCCCAAAGCGGCGCATGCCGCGCAGCGACGGGCAGTCAACAAGACGCTGCGCTGGCTTCGAACCCACATCGccag                                                                    >  8:242576/1‑147 (MQ=255)                                                                                 ccAGCAGCGGGTTGATCTCGCTGCAGGTGGACCCGC‑AGGCCCCCAAAGGTTTTCAGTACTTCACGCGGCT‑GGTCCCCAAAGCGGCGCATGCCGCGCAGCGACGGGCAGTCAACAAGACGCTGCGCTGGCTTCGAACCCACATCGCCCgg                                                                   <  6:33409/149‑1 (MQ=255)                                                                                 ccAGCAGCGGGTTGATCTCGCTGCAGGTGGACCCGC‑AGGCCCCCAAAGGTTTTCAGGACTTCACGCGGCT‑GGTCCCCAAAGCGGCGCATGCCGCGCAGCGACGGGCACTCAACAAGACGCTGCGCTGGCTTCGAACCCACATCGCCCgg                                                                   >  5:313177/1‑149 (MQ=255)                                                                                  cagcagCGGGTTGATCTCGCTGCAGGTGGACGCGC‑AGGCCCCCAAAGGTTTTCAGGACTTCACGCGGCT‑GGTCCCCAAAGCGGCGCATGCCGCGCAGCGACGGGCAGTCAACAAGACGCTGCGCTGGCTTCGAAcc                                                                               <  2:236789/136‑1 (MQ=255)                                                                                  cagcagCGGGTTGATCTCGCTGCAGGTGGACCCGCGAGGCCCCCAAAGGTTTTCAGGACTTCACGCGGCT‑GGTCCCCAAAGCGGCGCATGCCGCGCAGCGAAGGGCAGTCAACAAGACGCTGCGCTGGCTTCGAAcc                                                                               >  1:236789/1‑137 (MQ=255)                                                                                          ggTTGATCTCGCTGCAGGTGGACCCGC‑AGGCCCCCAAAGGTTTTCAGGACTTCACGCGACT‑GGTCCCCAAAGCGGCGCATGCCGCGCAGCGACGGGCAGTCAACAAGACGCTGCGCTGGCTTCGAACCCACATCGCCCGGGAGGTAGgc                                                          <  4:290807/149‑1 (MQ=255)                                                                                              gATCTCGCTGCAGGTGGACCCGC‑AGGCCCCCAAAGGTTTTCAGGACTTCACGCGGCT‑GGTCCCCAAAGCGGCGCATGCCGCGCAGCGACGGGCAGTCAACAAGACGCTGCGCTGGCTTCGAACCCACATCGCCCGGGAGGTAGgccgc                                                       >  5:69074/1‑148 (MQ=255)                                                                                               aTCTCGCTGCAGGTGGACCCGC‑AGGCCCCCAAAGGTTTTCAGGACTTCACGCGGCT‑GGTCCCCAAAGCGGCGCATGCCGCGCAGCGACGGGCAGTCAACAAGACGCTGCGCTGGCTTCGAACCCACATCGCCCGGGAGGTAGgccgc                                                       >  8:83523/1‑147 (MQ=255)                                                                                                tctcGCTGCAGGTGGACCCGC‑AGGCCCCCAAAGGTTTTCAGGACTTCACGCGGCT‑GGTCCCCAAAGCGGCGCATGCCGCGCAGCGACGGGCAGTCAACAAGACGCTGCGCTGGCTTCGAACCCACATCGCCCGGGAGGTAGGCCGCCAg                                                    >  7:41941/1‑149 (MQ=255)                                                                                                    gCTGCAGGTGGACCCGC‑AGGCCCCCAAAGGTTTTCAGGACTTCACGCGGCT‑GGTCCCCAAAGCGGCGCATGCCGCGCAGCGACGGGCAGTCAACAAGACGCTGCGCTGGCTTCGAACCCACATCGCCCGGGAGGTAGGCCGCCAGGAgc                                                <  7:123456/149‑1 (MQ=255)                                                                                                    gCTGCAGGTGGACCCGC‑AGGCCCCCAAAGGTTTTCAGGACTTCACGCGACT‑GGTCCCCAAAGCGGCGCATGCCGCGCAGCGACGGGCAGTCAACAAGACGCTGCGCTGGCTTCGAACCCACATCGCCCGGGAGGTAGGCCGCCAGGa                                                  <  3:345633/147‑1 (MQ=255)                                                                                                           gTGGACCCGC‑AGGCCCCCAAAGGTTTTCAGGACTTCACGCGGCT‑GGTCCCCAAAGCGGCGCATGCCGCGCAGCGACGGGCAGTCAACAAGACGCTGCGCTGGCTTCGAACCCACATCGCCCGGGAGGTAGGCCGCCAGGAGCGCATCGc                                         <  2:80227/149‑1 (MQ=255)                                                                                                                cccGC‑AGGCCCCCAAAGGTTTTCAGGACTTCACGCGGCT‑GGTCCCCAAAGCGGCGCATGCCGCGCAGCGACGGGCAGTCAACAAGACGCTGCGCTGGCTTCGAACCCACATCGCCCGGGAGGTAGGCCGCCAGGAGCGCATCGCTATTg                                    >  8:236393/1‑149 (MQ=255)                                                                                                                        gCCCCCAAAGGTTTTCAGGACTTCACGCGGCT‑GGTCCCCAAAGCGGCGCATGCCGCGCAGCGACGGGCAGTCAACAAGACGCTGCGCTGGCTTCGAACCCACATCGCCCGGGAGGTAGGCCGCCAGGAGCGCATCGCTATTGCGGCtgt                             <  3:122173/149‑1 (MQ=255)                                                                                                                          ccccAAAGGTTTTCAGGACTTCACGCGGCTGGGTCCCCAAAGCGGCGCATGCCGCGCAGCGACGGGCAGTCAACAAGACGCTGCGCTGGCTTCGAACCCACATCGCCCGGGAGGTAGGCCGCCAGGAGCGCATCGCTATTGCGGCtgtg                            >  1:37103/1‑149 (MQ=255)                                                                                                                                       cAGGACTTCACGCGGCT‑GGTCCCCAAAGCGGCGCATGCCGCGCAGCGACGGGCAGTCAACAAGACGCTGCGCTGGCTTCGAACCCACATCGCCCGGGAGGTAGGCCGCCAGGAGCGCATCGCTATTGCGGCTGTGCGGCAGCGGCTGa               <  6:313177/148‑1 (MQ=255)                                                                                                                                       cAGGACTTCACGCGGCT‑GGTCCCCAAAGCGGCGCATGCCGCGCAGCGACGGGCAGTCAACAAGACGCTGCGCTGGCTTCGAACCCACATCGCCCGGGAGGTAGGCCGCCAGGAGCGCATCGCTATTGCGGCTGTGCGGCAGCGGCTGa               <  4:356328/148‑1 (MQ=255)                                                                                                                                          gACTTCACGCGGCT‑GGTCCCCAAAGCGGCGCATGCCGCGCAGCGACGGGCAGTCAACAAGACGCTGCGCTGGCTTCGAACCCACATCGCCCGGGAGGTAGGCCGCCAGGAGCGCATCGCTATAGCGGCTGTGCGGCAGCGTCTGAGGGc           <  7:236393/149‑1 (MQ=255)                                                                                                                                             ttCACGCGGCT‑GGTCCCCAAAGCGGCGTATGCCGCGCAGCGACGGGCAGTCAACAAGACGCTGCGCTGGCTTCGAACCCACATCGCCCGGGAGGTAGGCCGCCAGGAGCGCATCGCTATTGCGGCTGTGCGGCAGCGGCTGAGGGCGtt        >  1:286839/1‑149 (MQ=255)                                                                                                                                               cACGCGGCT‑GGTCCCCAAAGCGGCGCATGCCGCGCAGCGACGGGCAGTCAACAAGACGCTGCGCTGGCTTCGAACCCACATCGCCCGGGAGGTAGGCCGCCAGGAGCGCATCGCTATTGCGGCTGTGCGGCAGCGGCTGAGGGCGtt        <  6:116353/147‑1 (MQ=255)                                                                                                                                                aCGCGGCT‑GGTCCCCAAAGCGGCGCATGCCGCGCAGCGACGGGCAGTCAACAAGACGCTGCGCTGGCTTCGAACCCACATCGCCCGGGAGGTAGGCCGCCAGGAGCGCATCGCTATTGCgg                                 <  7:219/121‑1 (MQ=255)                                                                                                                                                aCGCGGCT‑GGTCCCCAAAGCGGCGCATGCCGCGCAGCGACGGGCAGTCAACAAGACGCTGCGCTGGCTTCGAACCCACATCGCCCGGGAGGTAGGCCGCCAGGAGCGCATCGCTATTGCgg                                 >  8:219/1‑121 (MQ=255)                                                                                                                                                   cgGCT‑GGTCCCCAAAGCGGCGCATGCCGCGCAGCGACGGGCAGTCAACAAGACGCTGCGCTGGCTTCGAACCCACATCGCCCGGGAGGTAGGCCGCCAGGAGCGCATCGCTATTGCGGCTGTGCGGCAGCGGCTGAGGGCGTTCCCGGt  <  7:242576/149‑1 (MQ=255)                                                                                                                                                     |                                                                                                                                                    GTGAGCCTGGAGGCGATGGCCTTGTAACGCTGATCTTGAGGAAGGCGGTATGAGTGTTGGTAGCTATCACAAGCAGTCGGCCAGCAGCGGGTTGATCTCGCTGCAGGTGGACCCGC‑AGGCCCCCAAAGGTTTTCAGGACTTCACGCGGCT‑GGTCCCCAAAGCGGCGCATGCCGCGCAGCGACGGGCAGTCAACAAGACGCTGCGCTGGCTTCGAACCCACATCGCCCGGGAGGTAGGCCGCCAGGAGCGCATCGCTATTGCGGCTGTGCGGCAGCGGCTGAGGGCGTTCCCGGT  >  NC_002947/3432618‑3432911

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: ‑