Predicted mutation
evidence	seq id	position	mutation	freq	annotation	gene	description
RA	NC_002947	4,613,261	C→T	9.7%	R39R (CGC→CGT)	PP_4084 →	hypothetical protein

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NC_002947	4,613,261	0	C	T	9.7%	110.4 / 2.7	41	R39R (CGC→CGT)	PP_4084	hypothetical protein
Reads supporting (aligned to +/- strand):  ref base C (14/23);  new base T (2/2);  total (16/25)
Fisher's exact test for biased strand distribution p-value = 6.37e-01
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 4.10e-01

CACTGAACTCAAAAAGGACTTACCCAAGATGACCCGATACCTGACGCACGATGTAATCCTCAATCTGGGTGATGAAGCCCACGAGGACTCGACGCTGAACATGCTGCGCTTTCCCGACAGGCAAACCACGTTGGTGATCGCTCGCAGCCCTGTTGCAACCACCAAGACCCTGGATGAGGCCTTGGAGGAGCAACTGAACGTATTACGGAAGAAGTCAAAGGCGCTGACCATTACGCCCGCGAAAGTGACCCGCCTTGGAAGCAATGAGCATCCCGTCGACAGTCGGGAAA  >  NC_002947/4613117‑4613406                                                                                                                                                 |                                                                                                                                                  cACTGAACTCAAAAAGGACTTACCCAAGATGACCCGATACCTGACGCACGATGTAATCCTCAATCTGGGTGATGAAGCCCACGAGGACTCGACGCTGAACATGCTGCGCTTTCCCGACAGGCAAACCACGTTGGTGATCGCTCGCAGcc                                                                                                                                               <  6:149443/149‑1 (MQ=255)      aaCTCAAAAAGGACTTACCCAAGATGACCCGATACCTGACGCACGACGTAATCCTCAATCTGGGTGATGAAGCCCACGAGGACTCGACGCTGAACATGCTGCGCTTTCCCGACAGGCAAACCACGTTGGTGATCGCTCGCAGCCCTGtt                                                                                                                                          <  5:155421/149‑1 (MQ=255)         tCAAAAAGGACTTACCCAAGATGACCCGATACCTGACGCACGATGTAATCCTCAATCTGGGTGATGAAGCCCACGAGGACTCGACGCTGAACATGCTGCGCTTTCCCGACAGGCAAACCACGTTGGTGATCGCTCGCAGCCCTGTTGc                                                                                                                                        >  8:200635/1‑148 (MQ=255)              aaGGACTTACCCAAGATGACCCGATACCTGACGCACGATGTAATCCTCAATCTGGGTGATGAAGCCCACGAGGACTCGACGCTGAACATGCTGCGCTTTCCCGACAGGCAAACCACGTTGGTGATCGCTCGCAGCCCTGTTGCAaccac                                                                                                                                  <  6:245511/149‑1 (MQ=255)              aaGGACTTACCCAAGATGACCCGATACCTGACGCACGATGTAATCCTCAATCTGGGTGATGAAGCCCACGAGGACTCGACGCTGAACATGCTGCGCTTTCCCGACAGGCAAACCACGTTGGTGATCGCTCGCAGCCCTGTTGCAaccac                                                                                                                                  <  5:10577/149‑1 (MQ=255)                   cTTACCCAAGATGACCCGATACCTGACGCACGATGTAATCCTCAATCTGGGTGATGAAGCCCACGAGGACTCGACGCTGAACATGCTGCGCTTTCCCGACAGGCAAACCACGTTGGTGATCGCTCGCAGCCCTGTTGCAACCACCAAGa                                                                                                                             <  3:300236/149‑1 (MQ=255)                         cAAGATGACCCGATACCTGACGCACGATGTAATCCTCAATCTGGGTGATGAAGCCCACGAGGACTCGACGCTGAACATGCTGCGCTTTCCCGACAGGCAAACCACGTTGGTGATCGCTCGCAGCCCTGTTGCAACCACCAAGACCCTgg                                                                                                                       <  7:189321/149‑1 (MQ=255)                         cAAGATGACCCGATACCTGACGCACGATGTAATCCTCAATCTGGGTGATGAAGCCCACGAGGACTCGACGCTGAACATGCTGCGCTTTCCCGACAGGCAAACCACGTTGGTGATCGCTCGCAGCCCTGTTGCAACCACCAAGACCCTg                                                                                                                        >  3:291778/1‑148 (MQ=255)                          aaGATGACCCGATACCTGACGCACGATGTAATCCTCAATCTGGGTGATGAAGCCCACGAGGACTCGACGCTGAACATGCTGCGCTTTCCCGACAGGCAAACCACGTTGGTGATCGCTCGCAGCCCTGTTGCAACCACCAAGACCCTGGa                                                                                                                      <  7:305913/149‑1 (MQ=255)                           aGATGACCCGATACCTGACGCACGATGTAATCCTCAATCTGGGTGATGAAGCCCACGAGGACTCGACGCTGAACATGCTGCGCTTTCCCGACAGGCAAACCACGTTGGTGATCGCTCGCAGCCCTGTTGCAACCACCAAGACCCTGGAt                                                                                                                     <  6:130096/149‑1 (MQ=255)                              tGACCCGATACCTGACGCACGATGTAATCCTCAATCTGGGTGATGAAGCCCACGAGGACTCGACGCTGAACATGCTGCGCTTTCCCGACAGGCAAACCACGTTGGTGATCGCTCGCAGCCCTGTTGCAACCACCAAGACCCTGGATGAg                                                                                                                  <  7:200635/149‑1 (MQ=255)                                aCCCGATACCTGACGCACGATGTAATCCTCAATCTGGGTGATGAAGCCCACGAGGACTCGACGCTGAACATGCTGCGCTTTCCCGACAGGCAAACCACGTTGGTGATCGCTCGCAGCCCTGTTGCAACCACCAAGACCCTGGATGAGGc                                                                                                                >  7:307783/1‑149 (MQ=255)                                      tACCTGACGCACGATGTAATCCTCAATCTGGGTGATGAAGCCCACGAGGACTCGACGCTGAACATGCTGCGCTTTCCCGACAGGCAAACCACGTTGGTGATCGCTCGCAGCCCTGTTGCAACCACCAAGACCCTGGATGAGGCCTTgga                                                                                                          <  7:315334/149‑1 (MQ=255)                                         cTGACGCACGATGTAATCCTCAATCTGGGTGATGAAGCCCACGAGGACTCGACGCTGAACATGCTGCGCTTTCCCGACAGGCAAACCACGTTGGTGATCGCTCGCAGCCCTGTTGCAACCACCAAGACCCTGGATGAGGCCTTggag                                                                                                         >  3:4295/1‑147 (MQ=255)                                                aCGATGTAATCCTCAATCTGGGTGATGAAGCCCACGAGGACTCGACGCTGAACATGCTGCGCTTTCCCGACAGGCAAACCACGTTGGTGATCGCTCGCAGCCCTGTTGCAACCACCAAGACCCt                                                                                                                         >  2:323868/1‑124 (MQ=255)                                                       aaTCCTCAATCTGGGTGATGAAGCCCACGAGGACTCGACGCTGAACATGCTGCGCTTTCCCGACAGGCAAACCACGTTGGTGATCGCTCGCAGCCCTGTTGCAACCACCAAGACCCTGGATGAGGCCTTGGAGGAGCAACTGAACGTAt                                                                                         >  6:323870/1‑149 (MQ=255)                                                        aTCCTCAATCTGGGTGATGAAGCCCACGAGGACTCCACGCTGAACATGCTGCGCTTTCACGACAGGCAAACCACGTTGGTGATCGCTCGCAGCCCTGTTGCAACCACCAAGACACTGGATGAGGCCTTGCAGGAGCAACTGAACGTAt                                                                                         >  7:188788/1‑148 (MQ=255)                                                           cTCAATCTGGGTGATGAAGCCCACGAGGACTCGACGCTGAACATGCTGCGCTTTCCCGACAGGCAAACCACGTTGGTGATCGCTCGTAGCCCTGTTGCAACCACCAAGACCCTGGATGAGGCCTTGGAGGAGCAACTGAACGTATTACg                                                                                     >  6:188858/1‑149 (MQ=255)                                                           cTCAATCTGGGTGATGAAGCCCACGAGGACTCGACGCTGAACATGCTGCGCTTTCCCGACAGGCAAACCACGTTGGTGATCGCTCGTAGCCCTGTTGCAACCACCAAGACCCTGGATGAGGCCTTGGAGGAGCAACTGAACGTATTACg                                                                                     >  6:193441/1‑149 (MQ=255)                                                              aaTCTGGGTGATGAAGCCCACGAGGACTCGACGCTGAACATGCTGCGCTTTCCCGACAGGCAAACCACGTTGGTGATCGCTCGCAGCCCTGTTGCAACCACCAAGACCCTGGATGAGGCCTTGGAGGAGCAACTGAACGTATTACGga                                                                                   <  7:310526/148‑1 (MQ=255)                                                                tCTGGGTGATGAAGCCCACGAGGACTCAACGCTGAACATGCTGCGCTTTCCCGACAGGCAAACCACGTTGGTGATCGCTCGCAGCCCTGTTGCAACCACCAAGACCCTGGATGAGGCCTTGGAGGAGCAACTGAACGTATTACGgaag                                                                                 >  7:209844/1‑148 (MQ=255)                                                                        atgaAGCCCACGAGGACTCGACGCTGAACATGCTGCGCTTTCCCGACAGGCAAACCACGTTTGTGATCGCTCGCAGCCCTGTTGCAACCACCAAGACCCTGGATGAGGCCTTGGAGGAGCAACTGAACGTATTACGGAAGAAGTCaaa                                                                         <  1:214385/148‑1 (MQ=255)                                                                          gaAGCCCACGAGGACTCGACGCTGAACATGCTGCGCTTTCCCGACAGGCAAACCACGTTGGTGATCGCTCGCAGCCCTGTTGCAACCACCAAGACCCTGGATGAGGCCTTGGAGGAGCAACTGAACGTATTACGGAAGAAGTCAAAgtc                                                                      >  3:14817/1‑147 (MQ=255)                                                                           aaGCCCACGAGGACTCGACGCTGAACATGCTGCGCTTTCCCGACAGGCAAACCACGTTGGTGATCGCTCGCAGCCCTGTTGCAACCACCAAGACCCTGGATGAGGCCTTGGAGGAGCAACTGAACGTATTACGGAAGAAGTCAAAGgcg                                                                     <  8:99217/149‑1 (MQ=255)                                                                           aaGCCCACGAGGACTCGACGCTGAACATGCTGCGCTTTCCCGACAGGCAAACCACGTTGGTGATCGCTCGCAGCCCTGTTGCAACCACCAAGACCCTGGATGAGGCCTTGGAGGAGCAACTGAACGTATTACGGAAGAAGTCAAAGgcg                                                                     <  4:291778/149‑1 (MQ=255)                                                                                cACGAGGACTCGACGCTGAACATGCTGCGCTTTCCCGACAGGCAAACCACGTTGGTGATCGCTCGCAGCCCTGTTGCAACCACCAAGACCCTGGATGAGGCCTTGGAGGAGCAACTGAACGTATTACg                                                                                     <  5:49029/128‑1 (MQ=255)                                                                                cACGAGGACTCGACGCTGAACATGCTGCGCTTTCCCGACAGGCAAACCACGTTGGTGATCGCTCGCAGCCCTGTTGCAACCACCAAGACCCTGGATGAGGCCTTGGAGGAGCAACTGAACGTATTACg                                                                                     >  6:49029/1‑128 (MQ=255)                                                                                       aCTCGACGCTGAACATGCTGCGCTTTCCCGACAGGCAAACCACGTTGGTGATCGCTCGTAGCCCTGTTGCAACCACCAAGACCCTGGATGAGGCCTTGGAGGAGCAACTGAACGTATTACGGAAGAAGTCAAAGGCGCTGACCATTACg                                                         <  5:193441/149‑1 (MQ=255)                                                                                       aCTCGACGCTGAACATGCTGCGCTTTCCCGACAGGCAAACCACGTTGGTGATCGCTCGTAGCCCTGTTGCAACCACCAAGACCCTGGATGAGGCCTTGGAGGAGCAACTGAACGTATTACGGAAGAAGTCAAAGGCGCTGACCATTACg                                                         <  5:188858/149‑1 (MQ=255)                                                                                         tCGACGCTGAACATGCTGCGCTTTCCCGACAGGCAAACCACGTTGGTGATCGCTCGCAGCCCTGTTGCAACCACCAAGACCCTGGATGAGGCCTTGGAGGAGCAACTGAACGTATTACGGAAGAAGTCAAAGGCGCTGACCATTACGcc                                                       >  6:23698/1‑149 (MQ=255)                                                                                                  aaCATGCTGCGCTTTCCCGACAGGCAAACCACGTTGGTGATCGCTCGCAGCCCTGTTGCAACCACCAAGACCCTGGATGAGGCCTTGGAGGAGCAACTGAACGTATTACGGAAGAAGTCAAAGGCGCTGACCATTACGCCCGCGaaa                                                <  8:307783/147‑1 (MQ=255)                                                                                                   aCATGCTGCGCTTTCCCGACAGGCAAACCACGTTGGTGATCGCTCGCAGCCCTGTTGCAACCACCAAGACCCTGGATGAGGCCTTGGAGGAGCAACTGAACGTATTACGGAAGAAGTCAAAGGCGCTGACCATTACGCCCGCGAAAGTg                                             <  4:4295/149‑1 (MQ=255)                                                                                                            gcTTTCCCGACAGGCAAACCACGTTGGTGATCGCTCGCAGCCCTGTTGCAACCACCAAGACCCTGGATGAGGCCTTGGAGGAGCAACTGAACGTATTACGGAAGAAGTCAAAGGCGCTGACCATTACGCCCGCGAAAGTGACCCGCCtt                                    <  8:209844/149‑1 (MQ=255)                                                                                                                 cccGACATGCAAACCACGTTTGTGATCGCTCGCAGCCCTGTTGCAACCACCAAGACCCTGGATGAGGCCTTGGAGGAGCAACTGAACGTATTACGGAAGAAGTCAAAGGCGCTGACCATTACGCCCGCGAAAGTGACCCGCCTTGGaa                                <  2:287181/148‑1 (MQ=255)                                                                                                                  ccGACAGGCAAACCACGTTGGTGATCGCTCGCAGCCCTGTTGCAACCACCAAGACCCTGGATGAGGCCTTGGAGGAGCAACTGAACGTATTACGGAAGAAGTCAAAGGCGCTGACCATTACGCCCGCGAAAGTGACCCGCCTTGGAAg                               <  6:340167/148‑1 (MQ=255)                                                                                                                      cAGTCAAACCACGTTGGTGATAGCTCGCAGTCCTGTTGCAACCACCAAGAGCCTGGATGAGGCCTTGGAGGAGCAACTGAACGTATTACGTAAGAAGTCAAAGGCGCTGACCATTACGCCCGCGAAAGTGACCCGCCTTGGAAGCAAt                           <  4:14817/148‑1 (MQ=255)                                                                                                                       aGGCAAACCACGTTGGTGATCGCTCGCAGCCCTGTTGCAACCACCAAGACCCTGGATGAGGCCTTGGAGGAGCAACTGAACGTATTACGGAAGAAGTCAAAGGCGCTGACCATTACGCCCGCGAAAGTGACCCGCCTTGGAAGCAATGa                         <  5:323870/149‑1 (MQ=255)                                                                                                                         gCAAACCACGTTGGTGATCGCTCGCAGCCCTGTTGCAACCACCAAGACCCTGGATGAGGCCTGGGAGGAGCAACTGAACGTATTACGGAAGAAGTCAAAGGCGCTGACCATTACGCCCGCGAAAGTGACCCGCCTTGGAAGCAATGAg                        >  4:273264/1‑148 (MQ=255)                                                                                                                                      gTGATCGCTCGCAGCCCTGTTGCAACCACCAAGACCCTGGATGAGGCCTTGGAGGAGCAACTGAACGTATTACGGATGAAGTCAAAGGCGCTGACCATTACGCCCGCGAAAGTGACCCGCCTTGGAAGCAATGAGCATCCCGTCGACAg          >  1:318864/1‑149 (MQ=255)                                                                                                                                        gATCGCTCGCAGCCCTGTTGCAACCACCAAGACCCTGGATGAGGCCTTGGAGGAGCAACTGAACGTATTACGGAAGAAGTCAAAGGCGCTGACCATTACGCCCGCGAAAGTGACCCGCCTTGGAAGCAATGAGCATCCCGTCGACAGTc        >  6:117531/1‑149 (MQ=255)                                                                                                                                         aTCGCTCGCAGCCCTGTTGCAACCACAAAGACCCTGGATGAGGCCTTGGAGGAGCAACTGAACGTATTACGGAAGAAGTCAAAGGCGCTGACCATTACGCCCGCGAAAGTGACCCGCCTTGGAAGCAATGAGCATCCCGTCGACAGTc        <  8:188788/148‑1 (MQ=255)                                                                                                                                              tcgcAGCCCTGTTGCAACCACCAAGACCCTGGATGAGGGCTTGGAGGAGCAACTGAACGTTTTACGGAAGAAGTCAAAGGCGCTGACCATTACGCCCGCGAAAGTGACCCGCCTTGGAAGCAATGAGCATCCCGTCGACAGTCGGGaaa  >  3:232435/1‑149 (MQ=255)                                                                                                                                                 |                                                                                                                                                  CACTGAACTCAAAAAGGACTTACCCAAGATGACCCGATACCTGACGCACGATGTAATCCTCAATCTGGGTGATGAAGCCCACGAGGACTCGACGCTGAACATGCTGCGCTTTCCCGACAGGCAAACCACGTTGGTGATCGCTCGCAGCCCTGTTGCAACCACCAAGACCCTGGATGAGGCCTTGGAGGAGCAACTGAACGTATTACGGAAGAAGTCAAAGGCGCTGACCATTACGCCCGCGAAAGTGACCCGCCTTGGAAGCAATGAGCATCCCGTCGACAGTCGGGAAA  >  NC_002947/4613117‑4613406

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: ‑