Predicted mutation
evidence	seq id	position	mutation	freq	annotation	gene	description
RA	NC_002947	4,595,180	T→G	7.9%	intergenic (+96/‑23)	PP_4069 → / → PP_mr45	hypothetical protein/PrrF ncRNA

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NC_002947	4,595,180	0	T	G	7.9%	164.3 / 2.6	58	intergenic (+96/‑23)	PP_4069/PP_mr45	hypothetical protein/PrrF ncRNA
Reads supporting (aligned to +/- strand):  ref base T (26/27);  new base G (3/2);  total (29/29)
Fisher's exact test for biased strand distribution p-value = 1.00e+00
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 1.00e+00

GACATGGCTCGCGCACTGCTGGAGCACAAACACACCGAGTGACCGGGTTTATAGACAAGAAAGGAGGGAGAGTACGTGATGGCCGCGTAACGGCAAAAGCCCCGATTGCCGGGACAAGGAAGCGCGCCGGTAAAACTTTTTTACCG‑GATTAGCGAAAATTCATTTGAC‑TGCCAAATGATAACGATTATTATTGCACTCAGCTGATCGCGAGATCCGCTGGATAA‑CCTGAAAGCTTAGGTCGCTCTCAGATTATCTCCTCATCAGGCTAATCACGGTTTTT  >  NC_002947/4595043‑4595322                                                                                                                                          |                                                                                                                                                  gACATGGCTCGCGCACTGCTGGAGCACAAACACACCGAGTGACCGGGTTTATAGACAAGAAAGGAGGGAGAGTACGTGATGGCCGCGTAACGGCAAAAGCCCCGATTGCCGGGACAAGGAAGCGCGTCGGTAAAACTTTTTTACCG‑Ga                                                                                                                                        <  3:71053/148‑1 (MQ=255) gACATGGCTCGCGCACTGCTGGAGCACAAACACACCGAGTGACCGGGTTTATAGACAAGAAAGGAGGGAGAGTACGTGATGGCCGCGTAACGGCAAAAGCCCCGATTGCCGGGACAAGGAAGCGCGCCGGTAAAACTTTTTTACCG‑GAt                                                                                                                                       >  4:112764/1‑149 (MQ=255) gACATGGCTCGCGCACTGCTGGAGCACAAACACACCGAGTGACCGGGTTTATAGACAAGAAAGGAGGGAGAGTACGTGATGGCCGCGTAACGGCAAAAGCCCCGATTGCCGGGACAAGGAAGCGCGCCGGTAAAACTTTTTTACCG‑GAt                                                                                                                                       >  7:316699/1‑149 (MQ=255) gACATGGCTCGCGCACTGCTGGAGCACAAACACACCGAGTGACCGGGTTTATAGACAAGAAAGGAGGGAGAGTACGTGATGGCCGCGTAACGGCAAAAGCCCCGATTGCCGGGACAAGGAAGCGCGCCGGTAAAAAAGTTTTACCg‑gc                                                                                                                                        <  5:314009/148‑2 (MQ=255)        cTCGCGCACTGCTGGAGCACAAACACACCGAGTGACCGGGTTTATAGACAAGAAAGGAGGGAGAGTACGTGATGGCCGCGTAACGGCAAAAGCCCCGATTGCCGGGACAAGGAAGCGCGCCGGTAAAACTTTTTTACCG‑GATTAGCGa                                                                                                                                 >  1:232232/1‑148 (MQ=255)         tCGCGCACTGCTGGAGCACAAACACACCGAGAGACCGGGTTTATAGACAAGAAAGGAGGGAGAGTACGTGATGCCCGCGTAACGGCAAAAGCCCCGATAGCCGGGACAAGGAAGCGCGCCGGTAAAACTTTTTTACCG‑GATTAGCGaa                                                                                                                                >  5:42533/1‑148 (MQ=255)               aCTGCTGGAGCACAAACACACCGAGTGACCGGGTTTATAGACAAGAAAGGAGGGAGAGTACGTGATGGCCGCGTAACGGCAAAAGCCCCGATTGCCGGGACAAGGAAGCGCGCCGGTAAAACTTTTTTACCG‑GATTAGCGAAAATTCAt                                                                                                                         <  4:356075/149‑1 (MQ=255)               aCTGCTGGAGCACAAACACACCGACTGAACGTGTTTATAGACAAGAAAGGAGGGAGAGTACGTGATGGCCGCGTAACGGCAAAAGCCCCGATTGCCGGGACAAGGAAGCGCGCCGGTAAAACTTTTTTACCG‑GATTAGCGAAAATTCAt                                                                                                                         <  5:311232/149‑1 (MQ=255)                ctgctgGAGCACAAACACACCGAGTGACCGGGTTTATAGACAAGAAAGGAGGGAGAGTACGTGATGGCCGCGTAACGGCAAAAGCCCCGATTGCCGGGACAAGGAAGCGCGCCGGTAAAACTTTTTTACCG‑GATTAGCGAAAATTCAtt                                                                                                                        <  6:60168/149‑1 (MQ=255)                   ctgGAGCACAAACACACCGAGTGACCGGGTTTATAGACAAGAAAGGAGGGAGAGTACGTGATGGCCGCGTAACGGCAAAAGCCCCGATTGCCGGGACAAGGAAGCGCGCCGGTAAAACTTTTTTACCG‑GATTAGCGAAAATTCATTTGa                                                                                                                     <  1:328226/149‑1 (MQ=255)                    tgGAGCACAAACACACCGAGTGACCGGGTTTATAGACAAGAAAGGAGGGAGAGTACGTGATGGCCGCGTAACGGCAAAAGCCCCGATTGCCGGGACAAGGAAGCGCGCCGGTAAAACTTTTTTACCG‑GATTAGCGAAAATTCATTTGAc                                                                                                                    >  2:62778/1‑149 (MQ=255)                     ggAGCACAAACACACCGAGTGACCGGGTTTATAGACAAGAAAGGAGGGAGAGTACGTGATGGCCGCGTAACGGCAAAAGCCCCGATTGCCGGGACAAGGAAGCGCGCCGGGAAAACTTTTTTACCG‑GATTAGCGAAAATTCATTTGCC‑t                                                                                                                  >  8:256477/1‑149 (MQ=255)                      gAGCACAAACACACCGAGTGACCGGGTTTATAGACAAGAAAGGAGGGAGAGTACGTGATGGCCGCGTAACGGCAAAAGCCCCGAGTGCCGGGACAAGGACGCGCGCCGATAAAACTTTTTTACCG‑GATTAGCGAAAATTCATTTGAC‑Tg                                                                                                                 >  1:317158/1‑149 (MQ=255)                          acaAACACACCGAGTGACCGGGTTTATAGACAAGAAAGGAGGGAGAGTACGTGATGGCCGCGTAACGGCAAAAGCCCCGATTGCCGGGACAAGGAAGCGCGCCGGTAAAACTTTTTTACCG‑GATTAGCGAAAATTCATTTGAC‑TGCCa                                                                                                              >  6:362138/1‑148 (MQ=255)                          acaAACACACCGAGTGACCGGGTTTATAGACAAGAAAGGAGGGAGAGTACGTGATGGCCGCGTAACGGCAAAAGCCCCGATTGCCGGGACAAGGAAGCGCGCCGGTAAAACTTTTTTACCG‑GATTAGCGAAAATTCATTTGAC‑TGCCa                                                                                                              >  2:94159/1‑148 (MQ=255)                              acacacCGAGTGACCGGGTTTATAGACAAGAAAGGAGGGAGAGTACGTGATGGCCGCGTAACGGCAAAAGCCCCGATTGCCGGGACAAGGAAGCGCGCCGGTAAAACTTTTTTACCG‑GATTAGc                                                                                                                                   >  4:315787/1‑124 (MQ=255)                              acacacCGAGTGACCGGGTTTATAGACAAGAAAGGAGGGAGAGTACGTGATGGCCGCGTAACGGCAAAAGCCCCGATTGCCGGGACAAGGAAGCGCGCCGGTAAAACTTTTTTACCG‑GATTAGc                                                                                                                                   <  3:315787/124‑1 (MQ=255)                                  acCGAGTGACCGGGTTTATAGACAAGAAAGGAGGGAGAGTACGTGATGGCCGCGTAACGGCAAAAGCCCAGATTGCCGCGACAAGGAAGCGCGCCGGTAAAACTTTTTTACCG‑GATTAGCGAAAATTCATTTGAC‑TGCCAAATGATAAc                                                                                                     >  5:265021/1‑149 (MQ=255)                                     gAGTGAACGGGTTTATAGACAAGAAAGTAGGGAGAGTACGTGATGGCCGCGTAACCGCAAAAGCCCCGATTGCCTGGACAAGGAAGCGCGCCGGTAAAACTTTTTTACCG‑GATTAGCGAAAATTCATTTGAC‑TGCCAAATGATAACGat                                                                                                  <  7:254134/149‑1 (MQ=255)                                      aGTGACCGGGTTTATAGACAAGAAAGGAGGGAGAGTACGTGATGGCCGCGTAACGGCAAAAGCCCCGATTGCCGGGACAAGGAAGCGCGCCGGTAAAACTTTTTTACCG‑GATTAGCGAAAATTCATTTGAC‑TGCCAAATGATAACGat                                                                                                  >  7:65745/1‑148 (MQ=255)                                            cGGGTTTATAGACAAGAAAGGAGGGAGAGTACGTGATGGCCGCGTAACTGCAAAAGCCCCGATTGCCGGGACAAGGAAGCGCGACGTTAAAACTTTTTTACCG‑GATTAGCGAAAATTCATTTGAC‑TGCCAAATGATAACGattattatt                                                                                           <  7:256477/149‑1 (MQ=255)                                            cGGGTTTATAGACAAGAAAGGAGGGAGAGTACGTGATGGCCGCGTAACGGCAAAAGCCCCGATTGCCGGGACAAGGAAGCGCGCCGGTAAAACTTTTTTACCG‑GATTAGCGAAAATTCATTTGAC‑TGCCAAATGATAACGattattatt                                                                                           <  2:80076/149‑1 (MQ=255)                                              ggTTTATAGACAAGAAAGGAGGGAGAGTACGTGATGGCCGCGTAACGGCAAAAGCCCCGATTGCCGGGACAAGGAAGCGCGCCGGTAAAACTTTTTTACCG‑GATTAGCGAAAATTCATTTGAC‑TGCCAAATGATAACGATTATTATTGc                                                                                         <  6:15401/149‑1 (MQ=255)                                                tttATAGACAAGAAAGGAGGGAGAGTACGTGATGGCCGCGTAACGGCAAAAGCCCCGATTGCCGGGACAAGGAAGCGCGCCGGTAAAACTTTTTTACCG‑GATTAGCGAAAATTCATTTGAC‑TGCCAAATGATAACGATTATTATTGCAc                                                                                       <  6:42533/149‑1 (MQ=255)                                                      gACAAGAAAGGAGGGAGAGTACGTGATGGCCGCGTAACGGCAAAAGCCCCGATTGCCGGGACAAGGAAGCGCGCCGGTAAAACTTTTTTACCG‑GATTAGCGAAAATTCATTTGAC‑TGCCAAATGATAACGATTATTATTGCACTCAGCt                                                                                 <  2:232232/149‑1 (MQ=255)                                                       aCAAGAAAGGAGGGAGAGTACGTGATGGCCGCGTAACGGCAAAAGCCCCGATTGCCGGGACAAGGAAGCGCGCCGGTAAAACTTTTTTACCG‑GATTAGCGAAAATTCATTTGAC‑TGCCAAATGATAACGATTATTATTGCACTCAGCTg                                                                                >  6:285562/1‑149 (MQ=255)                                                              aggaggGAGAGTACGTGATGGCCGCGTAACGGCAAAAGCCCCGATTGCCGGGACAAGGAAGCGCGCCGGTAAAACTTTTTTACCG‑GATTAGCGAAAATTCATTTGAC‑TGCCAAATGATAACGATTATTATTGCACTCAGCTGATCGCga                                                                         <  5:362138/149‑1 (MQ=255)                                                              aggaggGAGAGTACGTGATGGCCGCGTAACGGCAAAAGCCCCGATTGCCGGGACAAGGAAGCGCGCCGGTAAAACTGTTTTACCG‑GATTAGCGAAATTTCATTTGAC‑TGCCAAATGATAACGATTATTATTGCACTCAGCTGATcgc                                                                           >  6:277540/1‑147 (MQ=255)                                                              aggaggGAGAGTACGTGATGGCCGCGTAACGGCAAAAGCCCCGATTGCCGGGACAAGGAAGCGCGCCGGTAAAACGTTTTTACCG‑GAGTAGCGAAAATTCATTTGAC‑TGCCAAATGATAAAGATTATTATTGCACTCAGCTGATcgc                                                                           >  6:277536/1‑147 (MQ=255)                                                                           cGTGATGGCCGCGTAACGGCAAAAGCCCCGATTGCCGGGACAAGGAAGCGCGCCGGTAAAACTTTTTTACCG‑GATTAGCGAAAATTCATTTGAC‑TGTCAAATGATAACGATTATTATTGCACTCAGCTGATCGCGAGATCCGCTGGAt                                                             >  6:263387/1‑148 (MQ=255)                                                                             tGATGGCCGCGTAACGGCAAAAGCCCCGATTGCCGGGACAAGGAAGCGCGCCTGTAATACTTTTTTACCG‑GATTAGCGAAAATTCATTTGAC‑TGCCAAATGATAACGATTATTATTGCACTGAGCTGATCGCGAGATCCGCTGGATAA‑c                                                         <  4:152462/149‑1 (MQ=255)                                                                             tGATGGCCGCGTAACGGCAAAAGCCCCGATTGCCGGGACAAGGAAGCGCGCCGGTAAAACTTTTTTACCG‑GATTAGCGAAAATTCATTTGAC‑TGCCAAATGATAACGATTATTATTGCACTCAGCTGATCGCGAGATCCGCTGGATAA‑c                                                         <  4:146675/149‑1 (MQ=255)                                                                                tGGCCGCGTAACGGCAAAATCCCTGATTGCCGGGACAAGGAAGCGCGCCGGTAAAACTTTTTTACCG‑GATTAGCGAAAATTCATTTGAC‑TGCCAAATGATAACGATTATTATTGCACTCAGCTGATCGCGAGATCCGCTGGATAA‑CCt                                                       <  6:265021/148‑1 (MQ=255)                                                                                   ccGCGTAACGGCAAAAGCCCCGATTGCCGGGACAAGGAAGCGCGCCGGTAAAACTTTTTTACCG‑GATTAGCGAAAATTCATTTGAC‑TGCCAAATGATAACGATTATTATTGCACTCAGCTGATCGCGAGATCCGCTGGATAA‑CCTGaaa                                                   <  8:316699/149‑1 (MQ=255)                                                                                   ccGCGTAACGGCAAAAGCCCCGATTGCCGGGACAAGGAAGCGCGCCGGTAAAACTTTTTTACCG‑GATTAGCGAAAATTCATTTGAC‑TGCCAAATGATAACGATTATTATTGCACTCAGCTGATCGCGAGATCCGCTGGATAA‑CCTGaaa                                                   <  3:112764/149‑1 (MQ=255)                                                                                     gcgTAACGGCAAAAGCCCCGATTGCCGGGACAAGGAAGCGCGCCGGTAAAACTTTTTTACCG‑GATTAGCGAAAATTCATTTGAC‑TGCCAAATGATAACGatt                                                                                                 >  7:74787/1‑102 (MQ=255)                                                                                     gcgTAACGGCAAAAGCCCCGATTGCCGGGACAAGGAAGCGCGCCGGTAAAACTTTTTTACCG‑GATTAGCGAAAATTCATTTGAC‑TGCCAAATGATAACGatt                                                                                                 <  8:74787/102‑1 (MQ=255)                                                                                     gcgTAACGGCAAAAGCCCCGATTGCCGGGACAAGGAAGCGCGCCGGTAAAACTTTTTTACCG‑GATTAGCGAAAATTCATTTGAC‑TGCCAAATGATAACGatt                                                                                                 <  4:16518/102‑1 (MQ=255)                                                                                     gcgTAACGGCAAAAGCCCCGATTGCCGGGACAAGGAAGCGCGCCGGTAAAACTTTTTTACCG‑GATTAGCGAAAATTCATTTGAC‑TGCCAAATGATAACGatt                                                                                                 >  3:16518/1‑102 (MQ=255)                                                                                        tAACGGCAAAAGCCCCGATTGCCGGGACAAGGAAGCGCGCCGGTAAAACTTTTTTACCG‑GATTAGCGAAAATTCATTTGAC‑TGTCAAATGATAACGATTATTATTGCACTCAGCTGATCGCGAGATCCGCTGGATAA‑CCTGAAAGCTTa                                              <  5:263387/149‑1 (MQ=255)                                                                                                 aaGCCCCGATTGCCGGGACAAGGAAGCGCGCCGGTAAAACTTTTTTACCG‑GATTAGCGAAAATTCATTTGAC‑TGCCAAATGATAACGATTATTATTGCACTCAGCTGATCGCGAGATCCGCTGGATAA‑CCTGAAAGCTTAGGTCGctc                                      >  1:186398/1‑148 (MQ=255)                                                                                                     cccGATTGCCGGGACAAGGAAGCGCGCCGGTAAAACTTTTTTACCG‑GATTAGCGAAAATTCATTTGAC‑TGCCAAATGATAACGATTATTATTGCACTCAGCTGATCGCGAGATCCGCTGGATAA‑CCTGAAAGCTTAGGTCGCTCTCAGa                                 <  5:165518/149‑1 (MQ=255)                                                                                                      ccGATTGCCGGGACAAGGAAGCGCGCCGGTAAAACTTTTTTACCG‑GATTAGCGAAAATTCATTTGAC‑TGCCAAATGATAACGATTATTATTGCACTCAGCTGATCGCGAGATCCGCTGGATAA‑CCTGAAAGCTTAGGTCGCTCTCAGAt                                >  3:185127/1‑149 (MQ=255)                                                                                                       cGATTGCCGTGACAAGGAAGCGCGCCGGTAAAACTTTTTTACCG‑GATTAGCGAAAATTCATTTGAC‑TGCCAAATGATAACGATTATTATTGCACTCAGCTGATCGCGAGATCCGCTGGATAA‑CCTGAAAGCTTAGGTCGCTCTCAGAtt                               <  5:117586/149‑1 (MQ=255)                                                                                                            gCCGGGACAAGGAAGCGCGCCGGTAAAACTTTTTTACCG‑GATTAGCGAAAATTCATTTGAC‑TGCCAAATGATAACGATTATTATTGCACTCAGCTGATCGCGAGATCCGCTGGATAA‑CCTGAAAGCTTAGGTCGCTCTCAGATTAtctc                          >  3:272538/1‑149 (MQ=255)                                                                                                              cGGGACAAGGAAGCGCGCCGGTAAAACTTTTATACCG‑GATTAGCGAAAATTCATTTGAC‑TGCCAAATGATAACGATTATTATTGCACTCAGCTGATCGCGAGATCCGCTGGATAA‑CCTGAAAGCTTAGGTCGCTCTCAGATTATctcc                         >  2:366426/1‑148 (MQ=255)                                                                                                                 gACAAGGAAGCGCGCCGGTAAAACTTTTTTACCG‑GATTAGCGAAAATTCATTTGAC‑TGCCa                                                                                                              >  4:214285/1‑61 (MQ=255)                                                                                                                 gACAAGGAAGCGCGCCGGTAAAACTTTTTTACCG‑GATTAGCGAAAATTCATTTGAC‑TGCCa                                                                                                              <  3:214285/61‑1 (MQ=255)                                                                                                                  aCAAGGAAGCGCGCCGGTAAAACTTTTTTACCG‑GATTAGCGAAAATTCATTTGAC‑TGCCAAATGATAACGATTATTATTGCACTCAGCTGATCGCGAGATCCGCTGGATAA‑CCTGAAAGCTTAGGTCGCTCTCAGATTATCTCCtcat                     >  7:245394/1‑148 (MQ=255)                                                                                                                  aCAAGGAAGCGCGCCGGTAAAACTTTTTTACCG‑GATTAGCGAAAATTCATTTGAC‑TGCCAAATGATAACGATTATTATTGCACTCAGCTGATCGCGAGATCCGCTGGATAA‑CCTGAAAGCTTAGGTCGCTCTCAGATTATCTCCtcat                     >  1:60182/1‑148 (MQ=255)                                                                                                                         gctaatccGGTAAAAAAGTTTTACCGAGATTAGCGAAAATTCATTTGAC‑TGCCAAATGATAACGATTATTATTGCACTCAGCTGATCGCGAGATCCGCTGGATAA‑CCTGAAAGCTTAGGTCGCTCTCAGATTATCTCCTCATCAGGCt               >  1:4780/7‑148 (MQ=255)                                                                                                                         gctaatccGGTAAAAAAGTTTTACCG‑GATTAGCGAAAATTCATTTGAC‑TGCCAAATGATAACGATTATTATTGCACTCAGCTGATCGCGAGATCCGCTGGATAA‑CCTGAAAGCTTAGGTCGCTCTCAGATTATCTCCTCATCAGGCTaa             >  6:226989/7‑149 (MQ=255)                                                                                                                                cGGTAAAAAAGTTTTACCG‑GATTAGCGAAAATTCATTTGAC‑TGCCAAATGATAACGATTATTATTGCACTCAGCTGATCGCGAGATCCGCTGGATAA‑CCTGAAAGCTTAGGTCGCTCTCAGATTATCTCCTCATCAGGCTAATCACGGt      <  5:226989/149‑1 (MQ=255)                                                                                                                                 ggTAAAACTTTTTTACCG‑GATTAGCGAAAATTCATTTGAC‑TGCCAAATGATAACGATTATTATTGCACTCAGCTGATCGCGAGATCCGCTGGATAACCCTGAAAGCTTAGGTCGCTCTCAGATTATCTCCTCATCAGGCTAATCACGGt      <  1:94159/149‑1 (MQ=255)                                                                                                                                  gTAAAACTTTTTTACCG‑GATTAGCGAAAATTCATTTGAC‑TGCCAAATGATAACGATTATTATTGCACTCAGCTGATCGCGAGATCCGCTGGATAA‑CCTGAAAGCTTAGGTCGCTCTCAGATTATCTCCTCATCAGGCTAATCACGGttt    <  5:285562/149‑1 (MQ=255)                                                                                                                                    aaaaCTTTTTTACCG‑GATTAGCGAAAATTCATTTGACTTGCCAAATGATAACGATTATTATTGCACTCAGCTGATCGCGAGATCCGCTGGATAA‑CCTGAAAGCTTAGGTCGCTCTCAGATTATCTCCTCATCAGGCTAATCACGGtttt   >  1:257216/1‑149 (MQ=255)                                                                                                                                    aaaaCTTTTTTACCG‑GATTAGCGAAAATTCATTTGAC‑TGCCAAATGATAACGATTATTATTGCACTCAGCTGATCGCGAGATCCGCTGGATAA‑CCTGAAAGCTTAGGTCGCTCTCAGATTATCTCCTCATCAGGCTAATCACGGttttt  >  8:177028/1‑149 (MQ=255)                                                                                                                                     aaaCTTTTTTACCG‑GATTAGCGAAAATTCATTTGAC‑TGCCAAATGATAACGATTATTATTGCACTCAGCTGATCGCGAGATCCGCTGGATAA‑CCTGAAAGCTTAGGTCGCTCTCAGATTATCTCCTCATCAGGCTAATCACGGttttt  <  8:245394/148‑1 (MQ=255)                                                                                                                                          |                                                                                                                                                  GACATGGCTCGCGCACTGCTGGAGCACAAACACACCGAGTGACCGGGTTTATAGACAAGAAAGGAGGGAGAGTACGTGATGGCCGCGTAACGGCAAAAGCCCCGATTGCCGGGACAAGGAAGCGCGCCGGTAAAACTTTTTTACCG‑GATTAGCGAAAATTCATTTGAC‑TGCCAAATGATAACGATTATTATTGCACTCAGCTGATCGCGAGATCCGCTGGATAA‑CCTGAAAGCTTAGGTCGCTCTCAGATTATCTCCTCATCAGGCTAATCACGGTTTTT  >  NC_002947/4595043‑4595322

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: ‑