Predicted mutation
evidence	seq id	position	mutation	freq	annotation	gene	description
RA	NC_002947	6,108,391	G→C	10.9%	W23C (TGG→TGC)	PP_5358 →	hypothetical protein

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NC_002947	6,108,391	0	G	C	10.9%	134.0 / 8.5	46	W23C (TGG→TGC)	PP_5358	hypothetical protein
Reads supporting (aligned to +/- strand):  ref base G (19/22);  new base C (2/3);  total (21/25)
Fisher's exact test for biased strand distribution p-value = 1.00e+00
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 5.26e-01

GCAGCGCAGTATGAACTTGATTGCTACCTGTACGACAGGCCAGGAACGCAGTTAAGCTGGATCTACCTGTTTGGAGCATATGCAAATGTTGACCCTGGAGAACCTCTTCGTCCTGATGCTGGTAGCCACGGCAGGCGCCTGGTTGTGGCACAACCATGGGTTGCGTGAAAAG‑GCCCTGGAACGGGTCAAACAGCAT‑TGCGCCAAACTCGACCTGGAGTTGCTTGACGATGCCGTAGCGCTCAAGCGTATCGCCTTTGTCCGGGATGCCAATGGCCGCAAGCGCCTGGCACGC  >  NC_002947/6108244‑6108535                                                                                                                                                    |                                                                                                                                                   gcagcgcagTATGAACTTGATTGCTACCTGTACGACAGGCCAGGAACGCAGTTAAGCTGGATCTACCTGTTTGGAGCATATGCAAATGTTGACCCTGGAGAACCTCTTCGTCCTGATGCTGGTAGCCACGGCAGGCGCCTGGTTGTGGca                                                                                                                                                  >  2:7446/1‑150 (MQ=255)   agcgcagTATGAACTTGATTGCTACCTGTACGACAGGCCAGGAACGCAGTTAAGCTGGATCTACCTGTTTGGAGCATATGCAAATGTTGACCCTGGAGAACCTCTTCGTCCTGATGCTGGTAGCCACGGCAGGCGCCTGGTTGTgg                                                                                                                                                    <  1:766449/146‑1 (MQ=255)   agcgcagTATGAACTTGATTGCTACCTGTACGACAGGCCAGGAACGCAGTTAAGCTGGATCTACCTGTTTGGAGCATATGCAAATGTTGACCCTGGAGAACCTCTTCGTCCTGATGCTGGTAGCCACGGCAGGCGCCTGGTTGTgg                                                                                                                                                    >  2:766449/1‑146 (MQ=255)         gTATGAACTTGATTGCTACCTGTACGACAGGCCAGGAACGCAGTTAAGCTGGATCTACCTGTTTGGAGCATATGCAAATGTTGACCCTGGAGAACCTCTTCGTCCTGATGCTGGTAGCCACGGCAGGCGCCTGGTTGTGGCACAACCATg                                                                                                                                          <  1:870477/150‑1 (MQ=255)          tATGAACTTGATTGCTACCTGTACGACAGGCCAGGAACGCAGTTAAGCTGGATCTACCTGTTTGGAGCATATGCAAATGTTGACCCTGGAGAACCTCTTCGTCCTGATGCTGGTAGCCACGGCAGGCGCCTGGTTGTGCCACAACCaggc                                                                                                                                         <  2:679707/150‑4 (MQ=255)               aCTTGATTGCTACCTGTACGACAGGCCAGGAACGCAGTTAAGCTGGATCTACCTGTTTGGAGCATATGCAAATGTTGACCCTGGAGAACCTCTTCGTCCTGATGCTGGTAGCCACGGCAGGCGCCTGGTTGTGGCACAACCATGGGTTGc                                                                                                                                    <  2:190674/150‑1 (MQ=255)                cTTGATTGCTACCTGTACGACAGGCCAGGAACGCAGTTAAGCTGGATCTACCTGTTTGGAGCATATGCAAATGTTGACCCTGGAGAACCTCTTCGTCCTGATGCTGGTAGCCACGGCAGGCGCGTGGTTGTGGCACAACCATGGGTTgag                                                                                                                                   >  1:56572/1‑148 (MQ=255)                         tACCTGTACGACAGGCCAGGAACGCAGTTAAGCTGGATCTACCTGTTTGGAGCATATGCAAATGTTGACCCTGGAGAACCTCTTCGTCCTGATGCTGGTAGCCACGGCAGGCGCCTGGTTGTGGCACAACCATGGGTTGCGTGAAAAG‑Gc                                                                                                                         >  2:884496/1‑150 (MQ=255)                          aCCTGTACGACAGGCCAGGAACGCAGTTAAGCTGGATCTACCTGTTTGGAGCATATGCAAATGTTGACCCTGGAGAACCTCTTCGTCCTGATGCTGGTAGCCACGGCAGGCGCCTGGTTGTGGCACAACCATGGGTTGCGTGAAAAG‑Gcc                                                                                                                        >  1:400900/1‑150 (MQ=255)                            cTGTACGACAGGCCAGGAACGCAGTTAAGCTGGATCTACCTGTTTGGAGCATATGCAAATGTTGACCCTGGAGAACCTCTTCGTCCTGATGCTGGTAGCCACGGCAGGCGCCTGGTTGTGGCACAACCATGGGTTGCGTGAAAAG‑GCCCt                                                                                                                      <  2:598117/150‑1 (MQ=255)                                   aCAGGCCAGGAACGCAGTTAAGCTGGATCTACCTGTTTGGAGCATATGCAAATGTTGACCCTGGAGAACCTCTTCGTCCTGATGCTGGTAGCCACGGCAGGCGCCTGGTTGTGGCACAACCATGGGTTGCGTGAAAAG‑GCCCTGGAACgg                                                                                                               <  1:491593/150‑1 (MQ=255)                                     aGGCCAGGAACGCAGTTAAGCTGGATCTACCTGTTTGGAGCATATGCAAATGTTGACCCTGGAGAACCTCTTCGTCCTGATGCTGGTAGCCACGGCAGGCGCCTGGTTGTGGCACAAc                                                                                                                                              >  2:1305195/1‑118 (MQ=255)                                     aGGCCAGGAACGCAGTTAAGCTGGATCTACCTGTTTGGAGCATATGCAAATGTTGACCCTGGAGAACCTCTTCGTCCTGATGCTGGTAGCCACGGCAGGCGCCTGGTTGTGGCACAAc                                                                                                                                              <  1:1305195/118‑1 (MQ=255)                                        ccAGGAACGCAGTTAAGCTGGATCTACCTGTTTGGAGCATATGCAAATGTTGACCCTGGAGAACCTCTTCGTCCTGATGCTGGTAGCCACGGCAGGCGCCTGGTTGTGGCACAACCATGGGTTGCGTGAAAAG‑GCCCTGGAACGGGTCaa                                                                                                          >  2:716211/1‑150 (MQ=255)                                          aGGAACGCAGTTAAGCTGGATCTACCTGTTTGGAGCATATGCAAATGTTGACCCTGGAGAACCTCTTCGTCCTGATGCTGGTAGCCACGGCAGGCGCCTGGTTGTGCCACAACCaggc                                                                                                                                         >  2:966909/1‑115 (MQ=255)                                          aGGAACGCAGTTAAGCTGGATCTACCTGTTTGGAGCATATGCAAATGTTGACCCTGGAGAACCTCTTCGTCCTGATGCTGGTAGCCACGGCAGGCGCCTGGTTGTGCCACAACCaggc                                                                                                                                         <  1:966909/118‑4 (MQ=255)                                              aCGCAGTTAAGCTGGATCTACCTGTTTGGAGCATATGCAAATGTTGACCCTGGAGAACCTCTTCGTCCTGATGCTGGTAGCCACGGCAGGCGCCTGGTTGTGGCACAACCATGGGTTGCGTGAAAAG‑GCCCTGGAACGGGTCAAACAGCa                                                                                                    <  1:716211/150‑1 (MQ=255)                                                          tGGATCTACCTGTTTGGAGCATATGCAAATGTTGACCCTGGAGAACCTCTTCGTCCTGATGCTGGTAGCCACGGCAGGCGCCTGGTTGTGGCACAACCATGGGTTGCg                                                                                                                                   <  2:1302884/108‑1 (MQ=255)                                                          tGGATCTACCTGTTTGGAGCATATGCAAATGTTGACCCTGGAGAACCTCTTCGTCCTGATGCTGGTAGCCACGGCAGGCGCCTGGTTGTGGCACAACCATGGGTTGCg                                                                                                                                   >  1:1302884/1‑108 (MQ=255)                                                                   cTGTTTGGAGCATATGCAAATGTTGACCCTGGAGAACCTCTTCGTCCTGATGCTGGTAGCCACGGCAGGCGCCTGGTTGTGGCACAACCATGGGTTGCGTGAAAAG‑GCCCTGGAACGAGAAAACTAGCAT‑TGCGCCAAACTCGACCTGGa                                                                              >  1:714119/1‑150 (MQ=255)                                                                     gTTTGGAGCATATGCAAATGTTGACCCTGGAGAACCTCTTCGTCCTGATGCTGGTAGCCACGGCAGGCGCCTGGTTGTGGCACAACCATGGGTTGCGTGAAAAG‑GCCCTGGAACGGGTCAAACAGCAT‑TGCGCCAAACTCGACCTGGAGt                                                                            >  1:548542/1‑150 (MQ=255)                                                                        tGGAGCATATGCAAATGTTGACCCTGGAGAACCTCTTCGTCCTGATGCTGGTAGCCACGGCAGGCGCCTGGTTGTGGCACAACCATGGGTTGCGTGAAAAG‑GCCCTGGAACGGGTCAAACAGCAT‑TGCGCCAAACTCGACCTGGAGTTGc                                                                         <  1:7446/150‑1 (MQ=255)                                                                            gCATATGCAAATGTTGACCCTGGAGAACCTCTTCGTCCTGATGCTGGTAGCCACGGCAGGCGCCTGGTTGTGGCACAACCATGGGTTGCGTGAAAAG‑GCCCTGGAACGGGTCAAACAGCAT‑TGCGCCAAACTCGACCTGGAGTTGCTTGa                                                                     <  2:212247/150‑1 (MQ=255)                                                                              atatGCAAATGTTGACCCTGGAGAACCTCTTCGTCCTGATGCTGGTAGCCACGGCAGGCGCCTGGTTGTGGCACAACCATgg                                                                                                                                         <  2:621884/82‑1 (MQ=255)                                                                              atatGCAAATGTTGACCCTGGAGAACCTCTTCGTCCTGATGCTGGTAGCCACGGCAGGCGCCTGGTTGTGGCACAACCATgg                                                                                                                                         >  1:621884/1‑82 (MQ=255)                                                                              atatGCAAATGTTGACCCTGGAGAACCTCTTCGTCCTGATGCTGGTAGCCACGGCAGGCGCCTGGTTGTGGCACAACCATGGGTTGCGTGAAAAG‑GCCCTGGAACGGGTCAAACAGCAT‑TGCGCCAAACTCGACCTGGAGTTGCTTGACg                                                                   >  2:558521/1‑150 (MQ=255)                                                                                 tGCAAATGTTGACCCTGGAGAACCTCTTCGTCCTGATGCTGGTAGCCACGGCAGGCGCCTGGTTGTGGCACAACCATGGGTTGCGTGAAAAG‑GCCCTGGAACGGGTCAAACAGCAT‑TGCGCCAAACTCGACCTGGAGTTGCTTGACGATg                                                                <  1:1099281/150‑1 (MQ=255)                                                                                  gCAAATGTTGACCCTGGAGAACCTCTTCGTCCTGATGCTGGTAGCCACGGCAGGCGCCTGGTTGTGGCACAACCATGGGTTGCGTGAAAAG‑Gccc                                                                                                                       >  2:792700/1‑95 (MQ=255)                                                                                  gCAAATGTTGACCCTGGAGAACCTCTTCGTCCTGATGCTGGTAGCCACGGCAGGCGCCTGGTTGTGGCACAACCATGGGTTGCGTGAAAAG‑Gccc                                                                                                                       <  1:792700/95‑1 (MQ=255)                                                                                              ccTGGAGAACCTCTTCGTCCTGATGCTGGTAGCCACGGCAGGCGCCTGGTTGTGGCACAACCATGGGTTGCGTGAAAAG‑GCCCt                                                                                                                      <  1:66461/84‑1 (MQ=255)                                                                                              ccTGGAGAACCTCTTCGTCCTGATGCTGGTAGCCACGGCAGGCGCCTGGTTGTGGCACAACCATGGGTTGCGTGAAAAG‑GCCCt                                                                                                                      >  2:66461/1‑84 (MQ=255)                                                                                                  gagaACCTCTTCGTCCTGATGCTGGTAGCCACGGCAGGCGCCTGGTTGTGGCACAACCATGGGTTGCGTGAAAAG‑GCCCTGGAACGGGTCAAACAGCAT‑Tgc                                                                                               <  2:684676/102‑1 (MQ=255)                                                                                                  gagaACCTCTTCGTCCTGATGCTGGTAGCCACGGCAGGCGCCTGGTTGTGGCACAACCATGGGTTGCGTGAAAAG‑GCCCTGGAACGGGTCAAACAGCAT‑Tgc                                                                                               >  1:684676/1‑102 (MQ=255)                                                                                                     aaCCTCTTCGTCCTGATGCTGGTAGCCACGGCAGGCGCCTGGTTGTGGCACAACCATGGGTTGAGTGACATGTGCTCT‑TCCCGGGTCAAA‑AGTGTGTTCGCCAGACTCGACCTGGAGTTGCTTGACGATGCCGTAGCGCTCAAGCGTATc                                            <  1:884496/150‑1 (MQ=255)                                                                                                         tctTCGTCCTGATGCTGGTAGCCACGGCAGGCGCCTGGCTTTGGCACAACCATGGGTTGCGTGAAAAG‑GCCCTGGAACGGGTCAAACAGCAT‑TGCGCCAAACTCGACCTGGAGTTGCTTGACGATGCCGTAGCGCTCAAGCGTATCGCCt                                        <  1:435128/150‑1 (MQ=255)                                                                                                                 cTGATGCTGGTAGCCACGGCAGGCGCCTGGTTGTGGCACAACCATGGGTTGCGTGAAAAG‑GCCCTGGAACGGGTCAAACAGCAT‑TGCGCCAAACTCGACCTGGAGTTGCTTGACGATGCCGTAGCGCTCAAGCGTATCGCCTTTGTCCgg                                <  2:400900/150‑1 (MQ=255)                                                                                                                  tGATGCTGGTAGCCACGGCAGGCGCCTGGTTGTGGCACAACCATGGGTTGCGTGAAAAG‑GCCCTGGAACGGGTCAAACAGCAT‑TGCGCCAAACTCGACCTGGAGTTGCTTGACGATGCCGTAGCGCTCAAGCGTATCGCCTTTGTCCggg                               >  1:1118142/1‑150 (MQ=255)                                                                                                                   gATGCTGGTAGCCACGGCAGGCGCCTGGTTGTGGCACAACCATGGGTTGCGTGAAAAG‑GCCCTGGAACGGGTCAAACAGCAT‑TGCGCCAAACTCGACCTGGAGTTGCTTGACGATGCCGTAGCGCTCAAGCGTATCGCCTTTGTCCGGGa                              <  2:548542/150‑1 (MQ=255)                                                                                                                          gTAGCCACGGAAGGCGCCTGGTTGTGGCACAACCATGGGTTGCGTGAAAAG‑GCCCTGGAACGGGTCAAACAGCAT‑TGCGCCAAACTCGACCTGGAGTTGCTTGACGATGCCGTAGCGCTCAAGCGTATCGCCTTTGTCCGGGATGCCAAt                       >  2:99333/1‑150 (MQ=255)                                                                                                                               cACGGCAGGCGCCTGGTTGTGGCACAACCATGGGTTGCGTGAAAAG‑GCCCTGGAACGGGTCAAACAGCAT‑TGCGCTAAACTCGACCTGGAGTTGCTTGACGATGCCGTAGCGCTCAAGCGTATCGCCTTTGTCCGGGATGCCAATGGccc                  >  1:1163266/1‑149 (MQ=255)                                                                                                                                aCGGCAGGCGCCTGGTTGTGGCACAACCATGGGTTGCGTGAAAAG‑GCCCTGGAACGGGTCAAACAGCAT‑TGCGCCAAACTCGACCTGGa                                                                              >  2:1226701/1‑89 (MQ=255)                                                                                                                                aCGGCAGGCGCCTGGTTGTGGCACAACCATGGGTTGCGTGAAAAG‑GCCCTGGAACGGGTCAAACAGCAT‑TGCGCCAAACTCGACCTGGa                                                                              <  1:1226701/89‑1 (MQ=255)                                                                                                                                        cgcCTGGTTGTGGCACAACCATGGGTTGCGTGAAAAG‑GCCCTGGAACGGGTCAAACAGCAT‑TGCGCCAAACTCGACCTGGAGTTGCTTGACGATGCCGTAGCGCGCAAGCGTATCGCCTTTGTCCGGGATGCCAATGGCCGCAAGCGCCt         <  1:558521/150‑1 (MQ=255)                                                                                                                                         ccatGGTTGTGGCACAACCATGGGTTGCGTGAAAAG‑GCCCTGGAACGGGTCAAACAGCAT‑TGCGCCAAACTCGACCTGGAGTTGCtt                                                                       >  2:613475/4‑87 (MQ=255)                                                                                                                                         ccatGGTTGTGGCACAACCATGGGTTGCGTGAAAAG‑GCCCTGGAACGGGTCAAACAGCAT‑TGCGCCAAACTCGACCTGGAGTTGCtt                                                                       <  1:613475/84‑1 (MQ=255)                                                                                                                                          catGGTTGTGCCACAACCATGGGTTGCGTGAAAAG‑GCCCTGGAACGGGTCAAACAGCAT‑TGCGCCAAACTCGACCTGGAGTTGCtt                                                                       >  2:474473/3‑86 (MQ=255)                                                                                                                                          catGGTTGTGCCACAACCATGGGTTGCGTGAAAAG‑GCCCTGGAACGGGTCAAACAGCAT‑TGCGCCAAACTCGACCTGGAGTTGCtt                                                                       <  1:474473/84‑1 (MQ=255)                                                                                                                                               ttGTGGCACAACCATGGGTTGCGTGAAAAG‑GCCCTGGAACGGGTCAAACAGCAT‑TGCGCCAAACTCGACCTGGAGTTGCTTGACGATGCCGTAGCGCTCAAGCGTATCGCCTTTGTCCGGGATGCCAATGGCCGCAAGCGCCTGGCAcgc  <  1:99333/150‑1 (MQ=255)                                                                                                                                                    gCACAACCATGGGTTGCGTGAAAAG‑GCCCTGGAACGGGTCAAACAGCAT‑TGCGCCAAACTCGACCTGGAGTTGCTTGACGATGCCGTAGCGCTCAAGCGTATCGCCTTTGTCCGGGATGCCAATGGCCGCaa               <  2:563311/132‑1 (MQ=255)                                                                                                                                                    gCACAACCATGGGTTGCGTGAAAAG‑GCCCTGGAACGGGTCAAACAGCAT‑TGCGCCAAACTCGACCTGGAGTTGCTTGACGATGCCGTAGCGCTCAAGCGTATCGCCTTTGTCCGGGATGCCAATGGCCGCaa               >  1:563311/1‑132 (MQ=255)                                                                                                                                                    |                                                                                                                                                   GCAGCGCAGTATGAACTTGATTGCTACCTGTACGACAGGCCAGGAACGCAGTTAAGCTGGATCTACCTGTTTGGAGCATATGCAAATGTTGACCCTGGAGAACCTCTTCGTCCTGATGCTGGTAGCCACGGCAGGCGCCTGGTTGTGGCACAACCATGGGTTGCGTGAAAAG‑GCCCTGGAACGGGTCAAACAGCAT‑TGCGCCAAACTCGACCTGGAGTTGCTTGACGATGCCGTAGCGCTCAAGCGTATCGCCTTTGTCCGGGATGCCAATGGCCGCAAGCGCCTGGCACGC  >  NC_002947/6108244‑6108535

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 22 ≤ ATCG/ATCG < 32 ≤ ATCG/ATCG < 41 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑