Predicted mutation
evidence	seq id	position	mutation	freq	annotation	gene	description
RA	NC_002947	2,166,644	T→A	9.3%	intergenic (‑488/‑293)	PP_5483 ← / → PP_1921	hypothetical protein/hypothetical protein

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NC_002947	2,166,644	0	T	A	9.3%	121.1 / 3.5	43	intergenic (‑488/‑293)	PP_5483/PP_1921	hypothetical protein/hypothetical protein
Reads supporting (aligned to +/- strand):  ref base T (19/20);  new base A (2/2);  total (21/22)
Fisher's exact test for biased strand distribution p-value = 1.00e+00
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 9.27e-01

TTTTTTCCCCGGGTGAGCATTCAGTGATTAGCTGGCAATGGCGGGTGAGTTGACGTCATCTCCCTCGATCAGAAAGTTACTCTCAGCAACCTATTGCAGAGGGTTTAAGGATCGCC‑GTTGGCCATTATGTGAAACGACCCGCTCCTGGAGCGGGATGATCCGAGGGCTGTT‑GGGGTGTCGCTGGTTGAGTGAAGCTCAATCAACCTGGCTTCCAGGTTGCAGGTCGTAGGGAGTAGGGAGTAGGGAGTAGGGAGTAGGGGCAGGGAGAGTCGGCGCGGGTGCAGATTCT  >  NC_002947/2166499‑2166787                                                                                                                                                   |                                                                                                                                                 ttttttCCCCGGGTGAGCATTCAGTGATTAGCTGGCAATGGCGGGTGAGTTGACGTCATCTCCCTCGATCAGAAAGTTACTCTCAGCAACCTATTGCAGAGGGTTTAAGGATCGCC‑GTTGGCCATTATGTGAAACGACCCGCTCCTGGa                                                                                                                                               <  6:246966/149‑1 (MQ=255)       ccccGGGTGAGCATTCAGTGATTAGCTGGCAATGGCGGGTGAGTTGACGTCATCTCCCTCGATCAGAAAGTTACTCTCAGCAACCTATTGCAGAGGGTTTAAGGATCGCC‑GTTGGCCATTATGTGAAACGACCCGCTCCTGGAGCggg                                                                                                                                          <  2:263552/148‑1 (MQ=255)        cccGGGTGAGCATTCAGTGATTAGCTGGCAATGGCGGGTGAGTTGACGTCATCTCCCTCGATCAGAAAGTTACTCTCAGCAACCTATTGCAGAGGGTTTAAGGATCGCC‑GTTGGCCATTATGTGAAACGACCCGCTCCTGGAGCGGga                                                                                                                                         <  4:280891/148‑1 (MQ=255)        cccGGGTGAGCATTCAGTGATTAGCTGGCAATGGCGGGTGAGTTGACGTCATCTCCCTCGATCAGAAAGTTACTCTCAGCAACCTATTGCAGAGGGTTTAAGGATCGCC‑GTTGGCCATTATGTGAAACGACCCGCTCCAGGAGCgggtc                                                                                                                                        <  5:155512/149‑3 (MQ=255)                aGCATTCAGTGATTAGCTGGCAATGGCGGGTGAGTTGACGTCATCTCCCTCGATCAGAAAGTTACTCTCAGCAACCTATTGCAGAGGGTTTAAGGATCGCC‑GTTGGCCATTATGTGAAACGACCCGCTCCTGGAGCGGGATGATCCGAg                                                                                                                                <  2:280416/149‑1 (MQ=255)                aGCATTCAGTGATTAGCTGGCAATGGCGGGTGAGTTGACGTCATCTCCCTCGATCAGAAAGTTACTCTCAGCAACCTATTGCAGAGGGTTTAAGGATCGCC‑GTTGGCCATTATGTGAAACGACCCGCTCCTGGAGCGGGATGATCCGAg                                                                                                                                >  7:256788/1‑149 (MQ=255)                           aTTAGCTGGCAATGGCGGGTGAGGTGACGTCATCTCCCTCGATCAGAAAGTTACTCTCAGCAACCTATTGCAGAGGGTTTAAGGATCGCC‑GTTGGCCATTATGTGAAACGACCCGCTCCTGGAGCGGGATGATCCGAGGGCTGTT‑ggg                                                                                                                     <  5:326894/148‑1 (MQ=255)                               gCTGGCAATGGCGGGTGAGTTGACGTCATCTCCCTCGATCAGAAAGTTACTCTCAGCAACCTATTGCAGAGGGTTTAAGGATCGCC‑GTTGGCCATTATGTGAAACGACCCGCTCCTGGAGCGGGATGATCCGAgg                                                                                                                               <  5:311204/135‑1 (MQ=255)                               gCTGGCAATGGCGGGTGAGTTGACGTCATCTCCCTCGATCAGAAAGTTACTCTCAGCAACCTATTGCAGAGGGTTTAAGGATCGCC‑GTTGGCCATTATGTGAAACGACCCGCTCCTGGAGCGGGATGATCCGAgg                                                                                                                               >  6:311204/1‑135 (MQ=255)                                 tGGCAATGGCGGGTGAGTTGACGTCATCTCCCTCGATCAGAAAGTTACTCTCAGCAACCTATTGCAGAGGGTTTAAGGATCGCC‑GTTGGCCATTATGTGAAACGACCCGCTCCTGGAGCGGGATGATCCGAGGGCTGtt                                                                                                                         <  6:45571/139‑1 (MQ=255)                                 tGGCAATGGCGGGTGAGTTGACGTCATCTCCCTCGATCAGAAAGTTACTCTCAGCAACCTATTGCAGAGGGTTTAAGGATCGCC‑GTTGGCCATTATGTGAAACGACCCGCTCCTGGAGCGGGATGATCCGAGGGCTGtt                                                                                                                         >  5:45571/1‑139 (MQ=255)                                 tGGCAATGGCGGGTGAGTTGACGTCATCTCCCTCGATCAGAAAGTTACTCTCAGCAACCTATTGCAGAGGGTTTAAGGATCGCC‑GTTGGCCATTATGTGAAACGACCCGCTCCTGGAGCGGGATGATCCGAGGGCTGTT‑GGGGTGTCGc                                                                                                              >  5:329359/1‑149 (MQ=255)                                         gCGGGTGAGTTGACGTCATCTCCCTCGATCAGAAAGTTACTCTCAGCAACCTATTGCAGAGGGTTTAAGGATCGCC‑GTTGGCCATTATGTGAAACGACCCGCTCCTGGAGCGGGATGATCCGAGGGCTGTT‑GGGGTGTCGCTGGTTGa                                                                                                       <  2:100311/148‑1 (MQ=255)                                                 gTTGACGTCATCTCCCTCGATCAGAAAGTTACTCTCAGCAACCTATTGCAGAGGGTTTAAGGATCGCC‑GTTGGCCATTATGTGAAACGACCCGCTCCTGGAGCGGGATGATCCGAGGGCTGTT‑GGGGTGTCGCTGGTTGAGTGAAGCt                                                                                               >  3:265678/1‑148 (MQ=255)                                                 gTTGACGTCATCTCCCTCGATCAGAAAGTTACTCTCAGCAACCTATTGCAGAGGGTTTAAGGATCGCC‑GTTGGCCATTATGTGAAACGACCCGCTCCTGGAGCGGGATGATCCGAGGGCTGTT‑GGGGTGTCGCTGGTTGAGTGAAGCt                                                                                               >  7:109346/1‑148 (MQ=255)                                                     aCGTCATCTCCCTCGATCAGAAAGTTACTCTCAGCAACCTATTGCAGAGGGTTTAAGGATCGCC‑GTTGGCCATTATGTGAAACGACCCGCTCCTGGAGCGGGATGATCCGAGGGCTGTT‑GGGGTGTCGCTGGTTGAGTGAAGCtcaat                                                                                           <  4:265678/148‑1 (MQ=255)                                                       gTCATCTCCCTCGATCAGAAAGTTACTCTCAGCAACCTATTGCAGAGGGTTTAAGGATCGCC‑GTTGGCCATTATGTGAAACGACCCGCTCCTGGAGCgg                                                                                                                                           >  3:77399/1‑99 (MQ=255)                                                       gTCATCTCCCTCGATCAGAAAGTTACTCTCAGCAACCTATTGCAGAGGGTTTAAGGATCGCC‑GTTGGCCATTATGTGAAACGACCCGCTCCTGGAGCgg                                                                                                                                           <  4:77399/99‑1 (MQ=255)                                                       gTCATCTCCCTCGATCAGAAAGTTACTCTCAGCAACCTATTGCAGAGGGTTTAAGGATCGCC‑GTTGGCCATTATGTGAAACGACCCGCTCCTGGAGCGGGATGATCCGAGGGCTGTT‑GGGGTGTCGCTGGTTGa                                                                                                       <  8:153339/134‑1 (MQ=255)                                                       gTCATCTCCCTCGATCAGAAAGTTACTCTCAGCAACCTATTGCAGAGGGTTTAAGGATCGCC‑GTTGGCCATTATGTGAAACGACCCGCTCCTGGAGCGGGATGATCCGAGGGCTGTT‑GGGGTGTCGCTGGTTGa                                                                                                       >  7:153339/1‑134 (MQ=255)                                                             tcCCTCGATCAGAAAGTTACTCTCAGCAACCTATTGCAGAGGGTTTAAGGATCGCC‑GTTGGCCATTATGTGAAACGACCCGCTCCTGGAGCGGGATGATCCGAGGGCTGTT‑g                                                                                                                       <  4:264094/112‑1 (MQ=255)                                                             tcCCTCGATCAGAAAGTTACTCTCAGCAACCTATTGCAGAGGGTTTAAGGATCGCC‑GTTGGCCATTATGTGAAACGACCCGCTCCTGGAGCGGGATGATCCGAGGGCTGTT‑g                                                                                                                       >  3:264094/1‑112 (MQ=255)                                                              cccTCGATCAGAAAGTTACTCTCAGCAACCTATTGCAGAGGGTTTAAGGATCGCC‑GTTGGCCATTATGTGAAACGACCCGCTCCTGGAGCGGGATGATCCGAGGGCTGTT‑GGGGTGTCGCTGGTTGAGTGAAGCTCAATCAACCTGGCt                                                                                 >  5:37187/1‑149 (MQ=255)                                                                cTCGATCAGAAAGTTACTCTCAGCAACCTATTGCAGAGGGTTTAAGGATCGCCGGTTGGCCATTATGTGAAACGACCCGCTCCTGGAGCGGGATGATCCGAGGGCTGTT‑GGGGTGTCGCTGGTTGAGTGAAGCTCAATCAACCTGGCta                                                                                >  1:84199/1‑148 (MQ=255)                                                                 tCGATCAGAAAGTTACTCTCAGCAACCTATTGCAGAGGGTTTAAGGATCGCC‑GTTGGCCATTATGTGAAACGACCCGCTCCTGGAGCGGGATGATCCGAGGGCTGTT‑GGGGTGTCGATGGTTGAGTGAAGCTCAATCAACCTGGCTTc                                                                               >  7:267093/1‑148 (MQ=255)                                                                     tCAGAAAGTTACTCTCAGCAACCTATTGCAGAGGGTTTAAGGATCGCC‑GTTGGCCATTATGTGAAACGACCCGCTCCTGGAGCGGGATGATCCGAGGGCTGTT‑GGGGTGTCGCTGGTTGAGTGAAGCTCAATCAACCTGGCTTCCa                                                                             <  6:329359/146‑1 (MQ=255)                                                                     tCAGAAAGTTACTCTCAGCAACCTATTGCAGAGGGTTTAAGGATCGCC‑GTTGGCCATTATGTGAAACGACCCGCTCCTGGAGCGGGATGATCCGAGGGCTGTT‑GGGGTGTCGCTGGTTGAGTGAAGCTCAATCAACCTGGCTTCCAGGt                                                                          >  7:147252/1‑149 (MQ=255)                                                                          aaGTTACTCTCAGCAACCTATTGCAGAGGGTTTAAGGATCGCC‑GTTGGCCATTATGTGAAACGACCCGCTCCTGGAGCGGGATGATCCGAGGGCTGTT‑GGGGTGTCGCTGGTTGAGTGAAGCTCAATCAACCTGGCTTCCAGGTTGCAg                                                                     <  6:37187/149‑1 (MQ=255)                                                                                   tcAGCAACCTATTGCAGAGGGTTTAAGGATCGCC‑GTTGGCCATTATGTGAAACGACCCGCTCCTGGAGCGGGATGATCCGAGGGCTGTT‑GGGGTGTCGCTGGTTGAGTGAAGCTCAATCAACCTGGCTTCCAGGTTg                                                                        >  4:302969/1‑137 (MQ=255)                                                                                   tcAGCAACCTATTGCAGAGGGTTTAAGGATCGCC‑GTTGGCCATTATGTGAAACGACCCGCTCCTGGAGCGGGATGATCCGAGGGCTGTT‑GGGGTGTCGCTGGTTGAGTGAAGCTCAATCAACCTGGCTTCCAGGTTg                                                                        <  3:302969/137‑1 (MQ=255)                                                                                     aGCAACCTATTGCAGAGGGTTTAAGGATCGCC‑GTTGGCCATTATGTGAAACGACCCGCTCCTGGAGCGGGATGATCCGAGGGCTGTT‑GGGGTGTCGCTGGTTGAGTGAAGCTCAATCAACCTGGCTTCCAGGTTGCAGGTCgtagggag                                                          >  1:277050/1‑149 (MQ=255)                                                                                         aCCTATTGCAGAGGGTTTAAGGATCGCC‑GTTGGCCATTATGTGAAACGACCCGCTCCTGGAGCGGGATGATCCGAGGGCTGTT‑GGGGTGTCGCTGGTTGAGTGAAGCTCAATCAACCTGGCTTCCAGGTTGCAGGTCgtagggagtagg                                                      >  6:150426/1‑149 (MQ=255)                                                                                            tATTGCAGAGGGTTTAAGGATCGCC‑GTTGGCCATTATGTGAAACGACCCGCTCCTGGAGCGGGATGATCCGAGGGCTGTT‑GGGGTGTCGCTGGTTGAGTGAAGCTCAATCAACCTGGCTTCCAGGTTGCAGGTCgtagggagtagggag                                                   <  8:109346/149‑1 (MQ=255)                                                                                                                       ttGGCCATTATGTGAAACGACCCGCTCCTGGAGCGGGATGATCCGAGGGCTGTT‑GGGGTGTCGCTGGTTGAGTGAAGCTCAATCAACCTGGCTTCCAGGTTGCAGGTCGTAGGGAGTAGGGAGTAGGGAGTAGGGAGTAGGGGCAGGga                         <  8:147252/149‑1 (MQ=255)                                                                                                                        tGGCCATTATGTGAAACGACCCGCTCCTGGAGCGGGATGATCCGAGGGCTGTT‑GGGGTGTCGCTGGTTGAGTGAAGCTCAATCAACCTGGCTTCCAGGTTGCAGGTCGTAGGGAGTAGGGAGTAGGGAGTAGGGAGTAGGGGCAGGga                         <  8:256788/148‑1 (MQ=255)                                                                                                                                  gtgAAACGACCCGCTCCTGGAGCGGGATGATCCGAGGGCTGTT‑GGGGTGTCGCTGGTTGAGTGAAGCTCAATCAACCTGGCTTCCAGGTTGCAGGTCGTAGGGAGTAGGGAGTAGGGAGTAGGGAGTAGGGGCAGGga                         >  7:288797/1‑138 (MQ=255)                                                                                                                                  gtgAAACGACCCGCTCCTGGAGCGGGATGATCCGAGGGCTGTT‑GGGGTGTCGCTGGTTGAGTGAAGCTCAATCAACCTGGCTTCCAGGTTGCAGGTCGTAGGGAGTAGGGAGTAGGGAGTAGGGAGTAGGGGCAGGga                         <  8:288797/138‑1 (MQ=255)                                                                                                                                  gtgAAACGACCCGCTCCTGGAGCGGGATGATCCGAGGGCTGTT‑GGGGTGTCGCTGGTTGAGTGAAGCTCAATCAACCTGGCTTCCAGGTTGCAGGTCGTAGGGAGTAGGGAGTAGGGAGTAGGGAGTAGGGGCAGGGAGAGTCGGcgcg              >  3:175913/1‑149 (MQ=255)                                                                                                                                     aaaCGACCCGCTCCTGGAGCGGGATGATCCGAGGGCTGTT‑GGGGTGTCGCTGGTTGAGTGAAGCTCAATCAACCTGGCTTCCAGGTTGCAGGTCGTAGGGAGTAGGGAGTAGGGAGTAGGGAGTAGGGGCAGGGAGAGTCGGCGCggg            <  5:150426/148‑1 (MQ=255)                                                                                                                                          tcccGCTCCAGGAGCGGGATGATCCGAGGGCTGTT‑GGGGTGTCGCTGGTTGAGTGAAGCTCAATCAACCTGGCTTCCAGGTTGCAGGTCGTAGGGAGTAGGGAGTAGGGAGTAGGGAGTAGGGGCAGGGAGAGTCGGCGCGGGTg          >  7:231259/2‑145 (MQ=255)                                                                                                                                           cccGCTCCTGGAGCGGGATGATCCGAGGGCTGTT‑GGGGTGTCGCTGGTTGAGTGAAGCTCAATCAACCTGGCTTCCAGGTTGCAGGTCGTAGGGAGTAGGGAGTAGGGAGTAGGGAGTAGGGGCAGGGAGAGTCGGCGCGGGTGCAGAt     >  6:42856/1‑149 (MQ=255)                                                                                                                                             cGCTCCAGGAGCGGGATGATCCGAGGGCTGTTGGGGGTGTCGCTGGTTGAGTGAAGCTCAATCAACCTGGCTTCCAGGTTGCAGGTCGTAGGGAGTAGGGAGTAGGGAGTAGGGAGTAGGGGCAGGGAGAGTCGGCGCGGGTGCAGAtt    >  1:214677/1‑149 (MQ=255)                                                                                                                                              gCTCCAGGAGCGGGATGATCCGAGGGCTGTT‑GGGGTGTCGCTGGTTGAGTGAAGCTCAATCAACCTGGCTTCCAGGTTGCAGGTCGTAGGGAGTAGGGAGTAGGGAGTAGGGAGTAGGGGCAGGGAGAGTCGGCGCGGGTGCAGATTCt  <  2:214677/149‑1 (MQ=255)                                                                                                                                                   |                                                                                                                                                 TTTTTTCCCCGGGTGAGCATTCAGTGATTAGCTGGCAATGGCGGGTGAGTTGACGTCATCTCCCTCGATCAGAAAGTTACTCTCAGCAACCTATTGCAGAGGGTTTAAGGATCGCC‑GTTGGCCATTATGTGAAACGACCCGCTCCTGGAGCGGGATGATCCGAGGGCTGTT‑GGGGTGTCGCTGGTTGAGTGAAGCTCAATCAACCTGGCTTCCAGGTTGCAGGTCGTAGGGAGTAGGGAGTAGGGAGTAGGGAGTAGGGGCAGGGAGAGTCGGCGCGGGTGCAGATTCT  >  NC_002947/2166499‑2166787

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 14 ≤ ATCG/ATCG < 27 ≤ ATCG/ATCG < 32 ≤ ATCG/ATCG < 36 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑