Predicted mutation
evidence	seq id	position	mutation	freq	annotation	gene	description
RA	NC_002947	1,114,869	T→C	9.4%	intergenic (‑63/+116)	rlmF ← / ← valS	ribosomal RNA large subunit methyltransferase F/valine‑‑tRNA ligase

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NC_002947	1,114,869	0	T	C	9.4%	142.3 / 4.6	53	intergenic (‑63/+116)	rlmF/valS	ribosomal RNA large subunit methyltransferase F/valine‑‑tRNA ligase
Reads supporting (aligned to +/- strand):  ref base T (25/23);  new base C (2/3);  total (27/26)
Fisher's exact test for biased strand distribution p-value = 6.69e-01
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 9.06e-01

CAGGGTGGGCCTTGATCAGGCTGGGGAAGTCGTAGCGACCCTGGTGGCGGTTGCGCGGGTGCAGGGTGGGTTTGTTCGGGGTCATGGCAGTGTCCAGCCCTATACGAGCGGTGGCTTGAAGACCCTGGGGCTGCTGCGCAGCCCTTTTGCGACACAAGGCCGCTCCCACAGGAGGGTGGC‑GCCTTGAAGGTTGGCGCCGTCCTGTGGGAGCGGCCTTGTGTCGCGAAAGGGCCGTACAGCGGCCCCAACGGTCTCTCTAGTGATTACAGCGCTGCAATCCGCGCATGCTGCT  >  NC_002947/1114722‑1115013                                                                                                                                                    |                                                                                                                                                  cAGGGTGGGCCTTGATCAGGCTGGGGAAGTCGTAGCGACCCTGGTGGCGGTTGCGCGGGTGCAGGGTGGGTTTGTTCGGGGTCATGGCAGTGTCCAGGCCTATACGAGCGGTGGCTTGAAGACCCTGGGGCTGCTGCGCAGCCCtttt                                                                                                                                                   <  1:102349/148‑1 (MQ=255)   gggTGGGCCTTGATCAGGCTGGGGAAGTCGTAGCGACCCTGGTGGCGGTTGCGCTGGTGCAGGGTGGGTTTGTTCGGGGTCATGGCAGTGTCCAGCCCTATACGAGCGGTGGCTTGAAGACCCTGGGGCTGCTGCGCAGCCCTTTTGc                                                                                                                                                 >  8:72061/1‑148 (MQ=255)        ggCCTTGATCAGGCTGGGGAAGTCGTAGCGACCCTGGTGGCGGTTGCGCGGGTGCAGGGTGGGTTTGTTCGGGGTCATGGCAGTGTCCAGCCCTATACGAGCGGTGGCTTGAAGACCCTGGGGCTGCTGCGCAGCCCTTTCGCGacac                                                                                                                                            <  6:84966/148‑1 (MQ=255)         gCCTTGATCAGGCTGGGGAAGTCGTAGCGACCCTGGTGGCGGTTGCGCGGGTGCAGGGTGGGTTTGTTCGGGGTCATGGCAGTGTCCAGCCCTATACGAGCGGTGGCTTGAAGACCCTGGGGCTGCTGCGCAGCCCTTTTGCGacac                                                                                                                                            >  2:28981/1‑147 (MQ=255)                tCAGGCTGGGGAAGTCGTAGCGACCCTGGTGGCGGTTGCGCGGGTGCAGGGTGGGTTTGTTCGGGGTCATGGCAGTGTCCAGCCCTATACGAGCGGTGGCTTGAAGACCCTGGGGCTGCTGCGCAGCCCTTTCGCGACACAAGGCCGCt                                                                                                                                   >  7:108596/1‑149 (MQ=255)                  aGGCTGGGGAAGTCGTAGCGACCCTGGTGGCGGTTGCGCGGGTGCAGGGTGGGTTTGTTCGGGGTCATGGCAGTGTCCAGCCCTATACGAGCGGTGGCTTGAAGACCCTGGGGCTGCTGCGCAGCCCTTTTGCGACACAAGGCCGCTcc                                                                                                                                 >  2:269321/1‑149 (MQ=255)                      tGGGGAAGTCGTAGCGACCCTGGTGGCGGTTGCGCGGGTGCAGGGTGGGTTTGTTCGGGGTCATGGCAGTGTCCAGCCCTATACGAGCGGTGGCTTGAAGACCCTGGGGCTGCTGCGCAGCCCTTTTGCGACACAAGGCCGCTCCca                                                                                                                               >  6:311854/1‑147 (MQ=255)                       ggggAAGTCGTAGCGACCCTGGTGGCGGTTGCGCGGGTGCAGGGTGGGTTTGTTCGGGGTCATGGCAGTGTCCAGCCCTATACGAGCGGTGGCTTGAAGACCCTGGGGCTGCTGCGCAGCCCTTTTGCGACACAAGGCCGCTCCCACag                                                                                                                            >  6:184476/1‑149 (MQ=255)                         ggAAGTCGTAGCGACCCTGGTGGCGGTTGCGCGGGTGCAGGGTGGGTTTGTTCGGGGTCATGGCAGTGTCCAGCCCTATACGAGCGGTGGCTTGAAGACCCTGGGGCTGCTGCGCAGCCCTTTTGCGACACAAGGCCGCTCCCACagga                                                                                                                          <  1:28981/149‑1 (MQ=255)                         ggAAGTCGTAGCGACCCTGGTGGCGGTTGCGCGGGTGCAGGGTGGGTTTGTTCGGGGTCATGGCAGTGTCCAGCCCTATACGAGCGGTGGCTTGAAGACCCTGGGGCTGCTGCGCAGCCCTTTTGCGACACAAGGCCGCTCCCACagga                                                                                                                          <  7:72061/149‑1 (MQ=255)                                gTAGCGACCCTGGTGGCGGTTGCGCGGGTGCAGGGTGGGTTTGTTCGGGGTCATGGTAGTGTCCAGCCCTATACGAGCGGTGGCTTGAAGACCCTGGGGCTGCTGCGCAGCCCTTTTGCGACACAAGGCCGCTCCCACAGGAGCGTGgc                                                                                                                   >  5:223589/1‑149 (MQ=255)                                gTAGCGACCCTGGTGGCGGTTGCGCGGGTGCAGGGTGGGTTTGTTCGGGGTCATGGCAGTGTCCAGCCCTATACGAGCGGTGGCTTGAAGACCCTGGGGCTGCTGCGCAGCCCTTTTGCGACACAAGGCCGCTCCCACAGGAGGGTGgc                                                                                                                   >  7:103713/1‑149 (MQ=255)                                   gCGACCCTGGTGGCGGTTGCGCGGGTGCAGGGTGGGTTTGTTCGGGGTCATGGCAGTGTCCAGCCCTATACGAGCGGTGGCTTGAAGACCCTGGGGCTGCTGCGCAGCCCTTTTGCGACACAAGGCCGCTCCCACAGGAGGGTGGC‑Gcc                                                                                                               >  4:342203/1‑149 (MQ=255)                                      aCCCTGGTGGCGGTTGCGCGGGTGCAGGGTGGGTTTGTTCGGGGTCATGGCAGTGTCCAGCCCTATACGAGCGGTGGCTTGAAGACCCTGGGGCTGCTGCGCAGCCCTTTTGCGACACAAGGCCGCTCCCACAGGAGGGTGGC‑GCCTTg                                                                                                            <  5:323502/149‑1 (MQ=255)                                         cTGGTGGCGGTTGCGCGGGTGCAGGGTGGGTTTGTTCGGGGTCATGGCAGTGTCCAGCCCTATACGAGCGGTGGCTTGAAGACCCTGGGGCTGCTGCGCAGCCCTTTTGCGACACAAGGCCGCTCCCACAGGAGGGTGGC‑GCCTTGAAg                                                                                                         <  2:303225/149‑1 (MQ=255)                                           ggtggCGGTTGCGCGGGTGCAGGGTGGGTTTGTTCGGGGTCATGGCAGTGTCCAGCCCTATACGAGCGGTGGCTTGAAGACCCTGGGGCTGCTGCGCAGCCCTTTTGCGACACAAGGCCGCTCCCACAGGAGGGTGGC‑GCCTTGAAGGt                                                                                                       >  5:65593/1‑149 (MQ=255)                                            gtggCGGTTGCGCGGGTGCAGGGTGGGTTTGTTCGGGGTCATGGCAGTGTCCAGCCCTATACGAGCGGTGGCTTGAAGACCCTGGGGCTGCTGCGCAGCCCTTTTGCGACACAAGGCCGCTCCCACAGGAGGGTGGC‑GCCTTGAAGGtt                                                                                                      <  3:335393/149‑1 (MQ=255)                                                   ttGCGCGGGTGCAGGGTGGGTTTGTTCGGGGTCATGGCAGTGTCCAGCCCTATACGAGCGGTGGCTTGAAGACCCTGGGGCTGCTGCGCAGCCCTTTTGCGACACAAGGCCGCTCCCACAGGAGGGTGGC‑GCCTTGAAGGTTGGCGCCg                                                                                               >  2:2893/1‑149 (MQ=255)                                                      cgcgGGTGCAGGGTGGGTTTGTTCGGGGTCATGGCAGTGTCCAGCCCTATACGAGCGGTGGCTTGAAGACCCTGGGGCTGCTGCGCAGCCCTTTTGCGACACAAGGCCGCTCCCACAGGAGGGTGGC‑GCCtt                                                                                                             >  7:58126/1‑132 (MQ=255)                                                      cgcgGGTGCAGGGTGGGTTTGTTCGGGGTCATGGCAGTGTCCAGCCCTATACGAGCGGTGGCTTGAAGACCCTGGGGCTGCTGCGCAGCCCTTTTGCGACACAAGGCCGCTCCCACAGGAGGGTGGC‑GCCtt                                                                                                             <  8:58126/132‑1 (MQ=255)                                                       gcgGGTGCAGGGTGGGTTTGTTCGGGGTCATGGCAGTGTCCAGCCCTATACGAGCGGTGGCTTGAAGACCCTGGGGCTGCTGCGCAGCCCTTTTGCGACACAAGGCCGCTCCCACAGGAGGGTGGC‑GCCTTGAAGGTTg                                                                                                     >  7:220261/1‑139 (MQ=255)                                                       gcgGGTGCAGGGTGGGTTTGTTCGGGGTCATGGCAGTGTCCAGCCCTATACGAGCGGTGGCTTGAAGACCCTGGGGCTGCTGCGCAGCCCTTTTGCGACACAAGGCCGCTCCCACAGGAGGGTGGC‑GCCTTGAAGGTTg                                                                                                     <  8:220261/139‑1 (MQ=255)                                                       gcgGGTGCAGGGTGGGTTTGTTCGGGGTCATGGCAGTGTCCAGCCCTATACGAGCGGTGGCTTGAAGACCCTGGGGCTGCTGCGCAGCCCTTTTGCGACACAAGGCCGCTCCCACAGGAGGGTGGC‑GCCTTGAAGGTTGGCGCCGTCCt                                                                                           >  3:16810/1‑149 (MQ=255)                                                          ggTGCAGGGTGGGTTTGTTCGGGGTCATGGCAGTGTCCAGCCCTATACGAGCGGTGGCTTGAAGACCCTGGGGCTGCTGCGCAGCCCTTTTGCGACACAAGGCCGCTCCCACAGGAGGGTGGC‑GCCTTGAAGGTTGGCGCCGTCCtgtg                                                                                        <  1:2893/149‑1 (MQ=255)                                                             gCAGGGTGGGTTTGTTCGGGGTCATGGCAGTGTCCAGCCCTTTACGAGCGGTGGCTTGAAGACCCTGGGGCTGCTGCGCAGCCCTTTTGCGACACAAGGCCGCTCCCACAGGAGGGTGGC‑GCCTTGAAGGTTGGCGCCGTCCTGTGGGa                                                                                     <  5:311854/149‑1 (MQ=255)                                                              cAGGGTGGGTTTGTTCGGGGTCATGGCAGTGTCCAGCCCTATACGAGCGGTGGCTTGAAGACCCTGGGGCTGCTGCGCAGCCCTTTTGCGACACAAGGCCGCTCCCACAGGAGGGTGGC‑GCCTTGAAGGTTGGCGCCGTCCTGTGGGa                                                                                     <  6:65593/148‑1 (MQ=255)                                                               atggtgggtTTGGTCGGGGTCATGGCAGTGTCCATGCCTATACGATCGGTGGCTTGAAGACCCTGGGGCTGCTGCGCAGCCCTTTTGCGACACAAGGCCGCTCCCACAGGAGGGTGGC‑GCCTTGAAGGTTGGCGCCGTCCTGTGGGAGc                                                                                   <  8:103713/147‑1 (MQ=255)                                                                gggtgggtTTGTTCGGGGTCATGGCAGTGTCCAGCCCTATACGAGCGGTGGCTTGAAGACCCTGGGGCTGCTGCGCAGCCCTTTTTCGACACAAGGCCGCTCCCACAGGAGGGTGGC‑GCCTTGAAGGTTGGCGCCGTCCTGTGGGAGCg                                                                                  >  3:139365/1‑149 (MQ=255)                                                                gggtgggtTTGTTCGGGGTCATGGCAGTGTCCAGCCCTATACGAGCGGTGGCTTGAAGACCCTGGGGCTGCTGCGCAGCCCTTTCGCGACACAAGGCCGCTCCCACAGGACGGCGCCAACCTTCAAGG‑CGCCACCCTCCTGTGGGAGc                                                                                   >  7:258747/1‑148 (MQ=17)                                                                gggtgggtTTGTTCGGGGTCATGGCAGTGTCCAGCCCTATACGAGCGGTGGCTTGAAGACCCTGGGGCTGCTGCGCAGCCCTTTCGCGACACAAGGCCGCTCCCACAGGACGGCGCCAACCTTCAAGG‑CGCCACCCTCCTGTGGGAGc                                                                                   <  8:258747/148‑1 (MQ=17)                                                                 ggtgggtTTGTTCGGGGTCATGGCAGTGTCCAGCCCTATACGAGCGGTGGCTTGAAGACCCTGGGGCTGCTGCGCAGCCCTTTTGCGACACAAGGCCGCTCCCACAGGAGGGTGGC‑GCCTTGAAGGTTGGCGCCGTCCTGTGGGAGCgg                                                                                 <  5:184476/149‑1 (MQ=255)                                                                  gtgggtTTGTTCGGGGTCATGGCAGTGTCCAGCCCTATACGAGCGGTGGCTTGAAGACCCTGGGGCTGCTGCGCAGCCCTTTTGCGACACAAGGCCGCTCCCACAGGAGGGTGGC‑GCCTTGAAGGTTGGCGCCGTCCtg                                                                                          <  5:327199/139‑1 (MQ=255)                                                                  gtgggtTTGTTCGGGGTCATGGCAGTGTCCAGCCCTATACGAGCGGTGGCTTGAAGACCCTGGGGCTGCTGCGCAGCCCTTTTGCGACACAAGGCCGCTCCCACAGGAGGGTGGC‑GCCTTGAAGGTTGGCGCCGTCCtg                                                                                          >  6:327199/1‑139 (MQ=255)                                                                  gtgggtTTGTTCGGGGTCATGGCAGTGTCCAGCCCTATACGAGCGGTGGCTTGAAGACCCTGGGGCTGCTGCGCAGCCCTTTTGCGACACAAGGCCGCTCCCACAGGAGGGTGGC‑GCCTTGAAGGTTGGCGCCGTCCTGTGGGAGCGGc                                                                                <  4:16810/149‑1 (MQ=255)                                                                       tttGTTCGGGGTCATGGCAGTGTCCAGCCCTATACGAGCGGTGGCTTGAAGACCCTGGGGCTGCTGCGCAGCCCTTTCGCGACACAAGGCCGCTCCCACAGGACGGCGCCAACCTTCAAGG‑CGCCACCCTCCTGTGGGAGCGGCCTtgt                                                                           <  8:108596/149‑1 (MQ=17)                                                                           ttCGGGGTCATGGCAGTGTCCAGCCCTATACGAGCGGTGGCTTGAAGACCCTGGGGCTGCTGCGCAGCCCTTTTGCGACACAAGGCCGCTCCCACAGGAGGGTGGC‑GCCTTGAAGGTTGGCGCCGTCCTGTGGGAGCGGCCTTGTGTcg                                                                       >  3:51560/1‑149 (MQ=255)                                                                           ttCGGGGTCATGGCAGTGTCCAGCCCTATACGAGCGGTGGCTTGAAGACCCTGGGGCTGCTGCGCAGCCCTTTTGCGACACAAGGCCGCTCCCACAGGAGGGTGGC‑GCCTTGAAGGTTGGCGCCGTCCTGTGGGAGCGGCCTTGTGTc                                                                        <  1:196960/148‑1 (MQ=255)                                                                              ggggTCATGTTAGTGTCCATCCCTATAGTTGCGGTGGATTTAATAGCCTGGGGCTGTTGCGCAGCCCTTTTGCGACACAAGGCGGCTCACATAGTTGGGTGGC‑GCCTTTATGGTTGGCGCCTTCCTGTGGTAGCGGCCTTGTGTcgcg                                                                     <  4:139365/148‑1 (MQ=255)                                                                                    ttGGCAGTGTCCAGCCCTATACGAGCGGTGGCTTGAAGACCCTGGGGCTGCTGCGCAGCCCTTTTGCGACACAAGGCCGCTCCCACAGGAGGGTGGC‑GCCTTGAAGGTTGGCGCCGTCCTGTGGGAGCGGCCTtgt                                                                           >  3:121807/2‑136 (MQ=255)                                                                                    ttGGCAGTGTCCAGCCCTATACGAGCGGTGGCTTGAAGACCCTGGGGCTGCTGCGCAGCCCTTTTGCGACACAAGGCCGCTCCCACAGGAGGGTGGC‑GCCTTGAAGGTTGGCGCCGTCCTGTGGGAGCGGCCTtgt                                                                           <  4:121807/135‑1 (MQ=255)                                                                                        cAGTGTCCAGGCCTATACGAGCGGTGGCTTGAAGACCCTGGGGCTGCTGCGCAGCCCTTTTGCGACACAAGGCCGCTCCCACAGGAGGGTGGC‑GCCTTGAAGGTTGGCGCCGTCCTGTGGGAGCGGCCTTGTGTCGCGAAAGGGCCGTa                                                          >  8:33188/1‑149 (MQ=255)                                                                                               cAGCCCTATACGAGCGGTGGCTTGAAGACCCTGGGGCTGCTGCGCAGCCCTTTTGCGACACAAGGCCGCTCCCACAGGAGGGTGGC‑GCCTTGAAGGTTGGCGCCGTCCTGTGGGAGCGGCCTtgt                                                                           >  4:275080/1‑125 (MQ=255)                                                                                               cAGCCCTATACGAGCGGTGGCTTGAAGACCCTGGGGCTGCTGCGCAGCCCTTTTGCGACACAAGGCCGCTCCCACAGGAGGGTGGC‑GCCTTGAAGGTTGGCGCCGTCCTGTGGGAGCGGCCTtgt                                                                           <  3:275080/125‑1 (MQ=255)                                                                                                     tataCGAGCGGTGGCTTGAAGACCCTGGGGCTGCTGCGCAGCCCTTTTGCGACACAAGGCCGCTCCCACAGGAGGGTGGC‑GCCTTGAAGGTTGGCGCCGTCCTGTGGGAGCGGCCTTGTGTCGCGAAAGGGcc                                                             >  2:9011/1‑133 (MQ=255)                                                                                                     tataCGAGCGGTGGCTTGAAGACCCTGGGGCTGCTGCGCAGCCCTTTTGCGACACAAGGCCGCTCCCACAGGAGGGTGGC‑GCCTTGAAGGTTGGCGCCGTCCTGTGGGAGCGGCCTTGTGTCGCGAAAGGGcc                                                             <  1:9011/133‑1 (MQ=255)                                                                                                      ataCGAGCGGTGGCTTGAAGACCCTGGGGCTGCTGCGCAGCCCTTTTGCGACACAAGGCCGCTCCCACAGGAGGGTGGC‑GCCTTGAAGGTTGGCGCCGTCCTGTGGGAGCGGCCTTGTGTCGCGAAAGGGCCGTACAGCGGCCCCAACg                                            <  3:342203/149‑1 (MQ=255)                                                                                                                 ggCTTGAAGACCCTGGGGCTGCTGCGCAGCCCTTTTGCGACACAAGGCCGCTCCCACAGGAGGGTGGC‑GCCTTGAAGGTTGGCGCCGTCCTGTGGGAGCGGCCTTGTGTCGCGAAAGGGCCGTACAGCGGCCCCAACGGTCTCTCTAGt                                 <  4:51560/149‑1 (MQ=255)                                                                                                                   cTTGAAGACCCTGGGGCTGCTGCGCAGCCCTTTTGCGACACAAGGCCGCTCCCACAGGAGGGTGGC‑GCCTTGAAGGTTGGCGCCGTCCGGTGGGAGCGGCCTTGTGTCGCGAAAGGGCCGTACAGCGGCCCCAACGGTGTCTGTAGTgg                               >  2:339058/1‑148 (MQ=255)                                                                                                                            ccTGGGGCTGCTGCGCAGCCCTTTTGCGACACAAGGCCGCTCCCACAGGAGGGTGGC‑GCCTTGAAGGTTGGCGCCGTCCTGTGGGAGCg                                                                                  <  3:258601/89‑1 (MQ=255)                                                                                                                            ccTGGGGCTGCTGCGCAGCCCTTTTGCGACACAAGGCCGCTCCCACAGGAGGGTGGC‑GCCTTGAAGGTTGGCGCCGTCCTGTGGGAGCg                                                                                  >  4:258601/1‑89 (MQ=255)                                                                                                                                    tgctgcGCAGCCCTTTTGCGACACAAGGCCGCTCCCACAGGAGGGTGGC‑GCCTTGAAGGTTGGCGCCGTCCTGTGGGAGCGGCCTTGTGTCGCGAAAgg                                                                >  3:146735/1‑99 (MQ=255)                                                                                                                                           cAGCTCTTTTGCGACCATTGGCCGCTCCCCCTGGAGTGTGGG‑GCCTTGTTGGTGGGCGCGGTCCTGTGGGAGCGGCCTTTTGTCGCGAAAGGGCCGTACAGCGGCCCCAACGGTCTCTCTAGTGATTACAGCGCTGCAATCCGCGCAtg       <  8:304194/149‑1 (MQ=255)                                                                                                                                              cccTTTTGCGACACAAGGCCGCTCCCACAGGAGGGTGGC‑GCCTTGAAGGTTGGCGCCGTCCTGTGGGAGCGGCCTTGTGTCGCGAAAGGGCCGTACAGCGGCCCCAACGGTCTCTCTAGTGATTACAGCGCTGCAATCCGCGCAtgctg    >  7:166853/1‑149 (MQ=255)                                                                                                                                                cTTTTGCGACACAAGGCCGCTCCCACAGGAGGGTGGC‑GCCTTGAAGGTTGGCGCCGTCCTGTGGGAGCGGCCTTGTGTCGCGAAAGGGCCGTACAGCGGCCCCAACGGTCTCTCTAGTGATTACAGCGCTGCAATCCGCGCATgctgct  >  4:134595/1‑149 (MQ=255)                                                                                                                                                    |                                                                                                                                                  CAGGGTGGGCCTTGATCAGGCTGGGGAAGTCGTAGCGACCCTGGTGGCGGTTGCGCGGGTGCAGGGTGGGTTTGTTCGGGGTCATGGCAGTGTCCAGCCCTATACGAGCGGTGGCTTGAAGACCCTGGGGCTGCTGCGCAGCCCTTTTGCGACACAAGGCCGCTCCCACAGGAGGGTGGC‑GCCTTGAAGGTTGGCGCCGTCCTGTGGGAGCGGCCTTGTGTCGCGAAAGGGCCGTACAGCGGCCCCAACGGTCTCTCTAGTGATTACAGCGCTGCAATCCGCGCATGCTGCT  >  NC_002947/1114722‑1115013

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: ‑