Predicted mutation
evidence	seq id	position	mutation	freq	annotation	gene	description
RA	NC_002947	3,491,245	G→T	11.1%	L140M (CTG→ATG)	PP_3092 ←	hypothetical protein

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NC_002947	3,491,245	0	G	T	11.1%	119.8 / 2.6	36	L140M (CTG→ATG)	PP_3092	hypothetical protein
Reads supporting (aligned to +/- strand):  ref base G (23/9);  new base T (2/2);  total (25/11)
Fisher's exact test for biased strand distribution p-value = 5.70e-01
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 9.93e-01

CAGGGCTTTGGGCGCCTTGCGGTAGCGGGCGATATCCTGGCCCAGTGTATTGGCCAGGTAACGCAGCTGGTCCTTTTGGCCGAGGCTGAACTTGCCCTCGAAGCCCAGTGCCAGGCACAGGTGGTAAACCTCGAGCACGTCGATGTTCTGCTTGACGTCGGCGCGCAGCGCATCGACCTTCTCGAAGAAGCCTTCGCCGGCCAGGTGCACGCCGAAATAGCGGAACTGCAACGGCTGCAGCTCAAAGTGCCGAC  >  NC_002947/3491126‑3491379                                                                                                                        |                                                                                                                                       cAGGGCTTTGGGCGCCTTGCGGTAGCGGGCGATATCCTGGCCCAGTGTATTGGCCAGGTAACGCAGCTGGTCCTTTTGGCCGAGGCTGAACTTGCCCTCGAAGCCCAGTGCCAGGCACAGGTGGTAAACCTCGAGc                                                                                                                        >  2:419801/1‑136 (MQ=255) cAGGGCTTTGGGCGCATTGCGGTAGCGGGCGATATCCTGGCCCAGTGTATTGCCCAGGTAACGCAGCTGGTCCTTTTGGCCGAGGCTGAACTTGCCCTCGAAGCCCAGTGCAAGGCACAGCTGGTAAACCTCGAGc                                                                                                                        >  1:93797/1‑136 (MQ=255)      cTTTGGGCGCCTTGCGGTAGCGGGCGATATCCTGGCCCAGTGTATTGGCCAGGTAACGCAGCTGGTCCTTTTGGCCGAGGCTGAACTTGCCCTCGAAGCCCAGTGCCAGGCACAGGTGGTAAACCTCGAGCACGTc                                                                                                                   >  1:400740/1‑136 (MQ=255)                  tGCGGTAGCGGGCGATATCCTGGCCCAGTGTATTGGCCAGGTAACGCAGCTGGTCCTTTTGGCCGAGGCTGAACTTGCCCTCGAAGCCCAGTGCCAGGCACAGGTGGTAAACCTCGAGCACGTCGATGTTCTGCtt                                                                                                       >  2:533475/1‑136 (MQ=255)                   gCGGTAGCGGGCGATATCCTGGCCCAGTGTATTGGCCAGGTAACGCAGCTGGTCCTTTTGGCCGAGGCTGAACTTGCCCTCGAAGCCCAGTGCCAGGCACAGGTGGTAAACCTCGAGCACGTCGATGTTCTGCTTg                                                                                                      >  2:263987/1‑136 (MQ=255)                         gCGGGCGATATCCTGGCCCAGTGTATTGGCCAGGTAACGAAGATGGTCCTATTGGCCGAGGCTGAACTTGCCCTCGAAGCCCAGAGCCAGGCACAGGTGGTAAACCACGAGCACGACGATGTTCTGCTTGACGTcc                                                                                                >  2:255643/1‑135 (MQ=255)                                       ggCCCAGTGTATTGGCCAGGTAACGCAGCTGGTCCTTTTGGCCGAGGCTGAACTTGCCCTCGAAGCCCAGTGCCAGGCACAGGTGGTAAACCTCGAGCACGTCGATGTTCTGCTTGACGTCGGCGCGCAGCGCATc                                                                                  <  1:336063/136‑1 (MQ=255)                                         cccAGTGTATTGGCCAGGTAACGCAGCTGGTCCTTTTGGCCGAGGCTGAACTTGCCCTCGAAGCCCAGTGCCAGGCACAGGTGGTAAACCTCGAGCACGTCGATGTTCTGCTTGACGTCGGCGCGCAGCGCAt                                                                                   >  1:129228/1‑133 (MQ=255)                                         cccAGTGTATTGGCCAGGTAACGCAGCTGGTCCTTTTGGCCGAGGCTGAACTTGCCCTCGAAGCCCAGTGCCAGGCACAGGTGGTAAACCTCGAGCACGTCGATGTTCTGCTTGACGTCGGCGCGCAGCGCAt                                                                                   <  2:129228/133‑1 (MQ=255)                                                tATTGGCCAGGTAACGCAGCTGGTCCTTTTGGCCGAGGCTGAACTTGCCCTCGAAGCCCAGTGCCAGGCACAGGTGGTAAACCTCGAGCACGTCGATGTTCTGCTTGACGTCGGCGCGCAGCGCATCGACCTtctc                                                                         >  1:17917/1‑136 (MQ=255)                                                tATTGGCCAGGTAACGCAGCTGGTCCTTTTGGCCGAGGCTGAACTTGCCCTCGAAGCCCAGTGCCAGGCACAGGTGGTAAACCTCGAGCACGTCGATGTTCTGCTTGACGTCGGCGCGCAGCGCATCGACCTtctc                                                                         >  1:366374/1‑136 (MQ=255)                                                tATTGGCCAGGTAACGCAGCTGGTCCTTTTGGCCGAGGCTGAACTTGCCCTCGAAGCCCAGTGCCAGGCACAGGTGGTAAACCTCGAGCACGTCGATGTTCTGCTTGACGTCGGCGCGCAGCGCATCGACCTtctc                                                                         >  1:431109/1‑136 (MQ=255)                                                 ataggCCAGGTAACGCAGCTGGTCCTTTTGGCCGAGGCTGAACTTGCCCTCGAAGCCCAGTGCCAGGCACATGTGGTAAACCTCGAGCACGTCGATGTTCTGCTTGACGTCGGCGCGCAGCGCATCGACCTTCTCg                                                                        >  2:170770/4‑136 (MQ=255)                                                 aTTGGCCAGGTAACGCAGCTGGTCCTTTTGGCCGAGGCTGAACTTGCCCTCGAAGCCCAGTGCCAGGCACATGTGGTAAACCTCGAGCACGTCGATGTTCTGCTTGACGTCGGCGCGCAGCGCATCGACCTTCTCg                                                                        >  2:313458/1‑136 (MQ=255)                                                 aTTGGCCAGGTAACGCAGCTGGTCCTTTTGGCCGAGGCTGAACTTGCCCTCGAAGCCCAGTGCCAGGCACAGGTGGTAAACCTCGAGCACGTCGATGTTCTGCTTGACGTCGGCGCGCAGCGCATCGACCTTCTCg                                                                        >  2:577467/1‑136 (MQ=255)                                                 aTTGGCCAGGTAACGCAGCTGGTCCTTTTGGCCGAGGCTGAACTTGCCCTCGAAGCCCAGTGCCAGGCACAGGTGGTAAACCTCGAGCACGTCGATGTTCTGCTTGACGTCGGCGCGCAGCGCATCGACCTTCTCg                                                                        >  2:20072/1‑136 (MQ=255)                                                          gTAACGCAGCTGGTCCTTTTGGCCGAGGCTGAACTTGCCCTCGAAGCCCAGTGCCAGGCACATGTGGTAAACCTCGAGCACGTCGATGTTCTGCTTGACGTCGGCGCGCAGCGCATCGACCTTCTCGAAGAAGCCt                                                               <  1:313458/136‑1 (MQ=255)                                                          gTAACGCAGCTGGTCCTTTTGGCCGAGGCTGAACTTGCCCTCGAAGCCCAGTGCCAGGCACATGTGGTAAACCTCGAGCACGTCGATGTTCTGCTTGACGTCGGCGCGCAGCGCATCGACCTTCTCGAAGAAGCCt                                                               <  1:170770/136‑1 (MQ=255)                                                           tAACGCAGCTGGTCCTTTTGGCCGAGGCTGAACTTGCCCTCGAAGCCCAGTGCCAGGCACAGGTGGTAAACCTCGAGCACGTCGATGTTCTGCTTGACGTCGGCGCGCAGCGCATCGACCTTCTCGAAGAAGCCtt                                                              >  2:539732/1‑136 (MQ=255)                                                           tAACGCAGCTGGTCCTTTTGGCCGAGGCTGAACTTGCCCTCGAAGCCCAGTGCCAGGCACAGGTGGTAAACCTCGAGCACGTCGATGTTCTGCTTGACGTCGGCGCGCAGCGCATCGACCTTCTCGAAGAAGCCtt                                                              >  1:173490/1‑136 (MQ=255)                                                                  gCTGGTCCTTTTGGCCGAGGCTGAACTTGCCCTCGAAGCCCAGTGCCAGGCACAGGTGGTAAACCTCGAGCACGTCGATGTTCTGCTTGACGTCGGCGCGCAGCGCATCGACCTTCTCGAAGAAGCCTTCGCCGGc                                                       >  2:432092/1‑136 (MQ=255)                                                                      gTCCTTTTGGCCGAGGCTGAACTTGCCCTCGAAGCCCAGTGCCAGGCACAGGTGGTAAACCTCGAGCACGTCGATGTTCTGCTTg                                                                                                      >  1:518940/1‑85 (MQ=255)                                                                      gTCCTTTTGGCCGAGGCTGAACTTGCCCTCGAAGCCCAGTGCCAGGCACAGGTGGTAAACCTCGAGCACGTCGATGTTCTGCTTg                                                                                                      <  2:518940/85‑1 (MQ=255)                                                                      gTCCTTTTGGCCGAGGCTGAACTTGCCCTCGAAGCCCAGTGCCAGGCACAGGTGGTAAACCTCGAGCACGTCGATGTTCTGCTTGACGTCGGCGCGCAGCGCATCGACCTTCTCGAAGAAGCCTTCGCCGGCCAgg                                                   >  1:101466/1‑136 (MQ=255)                                                                      gTCCTTTTGGCCGAGGCAGAACTTGCCCTCGAAGCCCAGTGCCAGGCACAGGTGGTAAACCTCGAGCACGTCGATGTTCTGCTTGACGTCGGCGCGCAGCGCATCGACCTTCTCGAAGAAGCCTTCGCCGGCCAgg                                                   >  1:368800/1‑136 (MQ=255)                                                                       tCCTTTTGGCCGAGGCTGAACTTGCCCTCGAAGCCCAGTGACAGGCACAGGTGGTAAACCTCGAGCACGTCGATGTTCTGCTTGACGTCGGCGCGCAGCGCATCGACCTACTCGAAGAAGCCTTCGCCGCCCAGGt                                                  >  1:273237/1‑136 (MQ=255)                                                                                  gAGGCTGAACTTGCCCTCGAAGCCCAGTGCCAGGCACAGGTGGTAAACCTCGAGCACGTCGATGTTCTGCTTGACGTCGGCGCGCAGCGCATCGACCTTCTCGAAGAAGCCTTCGCCGGCCAGGTGCACGCCGaaa                                       <  2:479909/136‑1 (MQ=255)                                                                                                 cTCGAAGCCCAGTGCCAGGCACAGGTGGTAAACCTCGAGCACGTCGATGTTCTGCTTGACGTCGGCGCGCAGCGCATCGACCTTCTCGAAGAAGCCTTCGCCGGCCAGGTGCACGCCGAAATAGCGGAACTGCAAc                        >  1:486646/1‑136 (MQ=255)                                                                                                  tCGAAGCCCAGTGCCAGGCACAGGTGGTAAACCTCGAGCACGTCGATGTTCTGCTTGACGTCGGCGCGCAGCGCATCGACCTTCTCGAAGAAGCCTTCGCCGGCCAGGTGCACGCCGAAATAGCGGAACTGCAACg                       >  1:137987/1‑136 (MQ=255)                                                                                                      aGCCCAGTGCCAGGCACAGGTGGTAAACCTCGAGCACGTCGATGTTCTGCTTGACGTCGGCGCGCAGCGCATCGACCTTCTCGAAGAAGCCTTCGCCGGCCAGGTGCACGCCGAAATAGCGGAACTGCAACGGCTg                   <  1:194016/136‑1 (MQ=255)                                                                                                               ccAGGCACAGGTGGTAAACCTCGAGCACGTCGATGTTCTGCTTGACGTCGGCGCGCAGCGCATCGACCTTCTCGAAGAAGCCTTCGCCGGCCAGGTGCACGCCGAAATAGCGGAACTGCAACGGCTGCAGCTCaaa          >  2:129405/1‑136 (MQ=255)                                                                                                                cAGGCACAGGTGGTAAACCTCGAGCACGGCGATGTTCTGCTTGACGTCGGCGCGCAGCGCATCGACCTTCTCGAAGAAGCCTTCGCCGGCCAGGTGCACGCCGAAATAGCGGAACTGCAACGGCTGCAGCTCAAAg         <  1:214830/136‑1 (MQ=255)                                                                                                                     acaGGTGGTAAACCTCGAGCACGTCGATGTTCTGCTTGCCGTCGGCGCGCAGCGCATCGACCTTCTCGAAGAAGCCTTCGCCGGCCAGGTGCACGCCGAAATAGCGGAACTGCAACGGCTGCCGCTCAAAGTGCCg    >  1:311741/1‑136 (MQ=255)                                                                                                                     acaGGTGGTAAACCTCGAGCACGTCGATGTTCTGCTTGACGTCGGCGCGCAGCGCATCGACCTTCTCGAAGAAGCCTTCGCCGGCCAGGTGCACGCCGAAATAGCGGAACTGCAACGGCTGCAGCTCAAAGTGCCg    <  2:400740/136‑1 (MQ=255)                                                                                                                     acaGGTGGTAAACCTCGAGCACGTCGATGTTCTGCTTGACGTCGGCGCGCAGCGCATCGACCTTCTCGAAGAAGCCTTCGCCGGCCAGGTGCACGCCGAAATAGCGGAACTGCAACGGCTGCAGCTCAAAGTGCCg    <  2:17917/136‑1 (MQ=255)                                                                                                                       aGGTGGTAAACCTCGAGCACGTCGATGTTCTGCTTGACGTCGGCGCGCAGCGCATCGACCTTCTCGAAGAAGCCTTCGCCGGCCAGGTGCACGCCGAAATAGCGGAACTGCAACGGCTGCAGCTCAAAGTGCCGAc  <  1:476543/136‑1 (MQ=255)                                                                                                                        |                                                                                                                                       CAGGGCTTTGGGCGCCTTGCGGTAGCGGGCGATATCCTGGCCCAGTGTATTGGCCAGGTAACGCAGCTGGTCCTTTTGGCCGAGGCTGAACTTGCCCTCGAAGCCCAGTGCCAGGCACAGGTGGTAAACCTCGAGCACGTCGATGTTCTGCTTGACGTCGGCGCGCAGCGCATCGACCTTCTCGAAGAAGCCTTCGCCGGCCAGGTGCACGCCGAAATAGCGGAACTGCAACGGCTGCAGCTCAAAGTGCCGAC  >  NC_002947/3491126‑3491379

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: ‑