Predicted mutation
evidence	seq id	position	mutation	freq	annotation	gene	description
RA	NC_002947	2,063,201	G→A	12.5%	intergenic (+58/‑149)	PP_1838 → / → PP_1839	membrane protein/hypothetical protein

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NC_002947	2,063,201	0	G	A	12.5%	95.0 / 5.9	40	intergenic (+58/‑149)	PP_1838/PP_1839	membrane protein/hypothetical protein
Reads supporting (aligned to +/- strand):  ref base G (15/20);  new base A (2/3);  total (17/23)
Fisher's exact test for biased strand distribution p-value = 1.00e+00
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 2.00e-01

TGCTCAAGAAGCTGGAAGCGTATATCCAGACCGCGACCAAGAGCCTGCTGGATAACACCGCCGGCGTGGTGCACGGCACACCGAAGTAAACCGGGGCCGCGTTGCGGCCCATTCGCGGGCTTGCCCGCTCCCACAGGCATTGCACAGGGTTC‑GGACCTTGTGCAGGTCCTGTGCGAGCGGGCAAGCCCGCGAATGGGCCCCGCACAATTTTCCCGGACTGAACATTATCCCCGCCCCAAGGTCAGTTATTCAGGCATCACACACCTGGTGTTCGTTGACTGAGAG  >  NC_002947/2063055‑2063339                                                                                                                                                   |                                                                                                                                            tGCTCAAGAAGCTGGAAGCGTATATCCAGACCGCGACCAAGAGCCTGCTGGATAACACCGCCGGCGTGGTGCACGGCACACCGAAGTAAACCGGGGCCGCGTTGCGGCCCATTCGCGGGCTTGCCCGCTCCCACAGGCATTGCACAggg                                                                                                                                           <  8:110336/149‑1 (MQ=255)  gCTCAAGAAGCTGGAAGCGTATATCCAGACCGCGACCAAGAGCCTGCTGGATAACACCGCCGGCGTGGTGCACGGCACACCGAAGTAAACCGGGGCCGCGTTGCGGCCCATTCGCGGGCTTGCCCGCTCCCACAGGCATTGCACAGGGt                                                                                                                                          >  8:274036/1‑149 (MQ=255)       agaagCTGGAAGCGTATATCCAGACCGCGACCAAGAGCCTGCTGGATAACACCGCCGGCGTGGTGCACGGCACACCGAAGTAAACCGGGGCCGCGTTGCGGCCCATTCGCGGGCTTGCCCGCTCCCACAGGCATTGCACAGGGTTC‑GGa                                                                                                                                    >  4:311305/1‑149 (MQ=255)           gCTGGAAGCGTATATCCAGACCGCGACCAAGAGCCTGCTGGATAACACCGCCGGCGTGGTGCACGGCACACCGAAGTAAACCGGGGCCGCGTTGCGGCCCATTCGCGGGCTTGCCCGCTCGCACAGGACCTGCACAAGGTCC‑GAAccct                                                                                                                                <  8:50695/149‑3 (MQ=37)           gCTGGAAGCGTATATCCAGACCGCGACCAAGAGCCTGCTGGATAACACCGCCGGCGTGGTGCACGGCACACCGAAGTAAACCGGGGCCGCGTTGCGGCCCATTCGCGGGCTTGCCCGCTCCCACAGGCATTGCACAGGGTTC‑GGACCtt                                                                                                                                <  8:316122/149‑1 (MQ=255)           gCTGGAAGCGTATATCCAGACCGCGACCAAGAGCCTGCTGGATAACACCGCCGGCGTGGTGCACGGCACACCGAAGTAAACCGGGGCCGCGTTGCGGCCCATTCGCGGGCTTGCCCGCTCCCACAGGCATTGCACAGGGTTC‑GGACCtt                                                                                                                                <  2:49642/149‑1 (MQ=255)            cTGGAAGCGTATATCCAGACCGCGACCAAGAGCCTGCTGGATAACACCGCCGGCGTGGTGCACGGCACACCGAAGTAAACCGGGGCCGCGTTGCGGCCCATTCGCGGGCTTGCCCGCTCCCACAGGCATTGCACAGGGTTC‑GGACCTtg                                                                                                                               <  7:145854/149‑1 (MQ=255)               gAAGCGTATATCGAGACCGCGACCAAGAGCCTGCTGGATAACACCGCCGGCGTGGTGCACGGCACACCGAAGTAAACCGGGGCCGCGTTGCGGCCCATTCGGGGGCTTGCCCGCTCCCACAGGCATTGCACAAGGTCC‑GAACCCtgtg                                                                                                                             <  1:148449/148‑1 (MQ=38)                    gTATATCCAGACCGCGACCAAGAGCCTGCTGGATAACACCGCCGGCGTGGTGCACGGCACACCGAAGTAAACCGGGGCCGCGTTGCGGCCCATTCGCGGGCTTGCCCGCTCCCACAGGCATTGCACAGGGTTC‑GGACCTTGTGCAGGTc                                                                                                                       <  3:31944/149‑1 (MQ=255)                         tCCAGACCGCGACCAAGAGCCTGCTGGATAACACCGCCGGCGTGGTGCACGGCACACCGAAGTAAACCGGGGCCGCGTTGCGGCCCATTCGCGGGCTTGCCCGCTCCCACAGGCATTGCACAGGGTTC‑GGACCTTGTGCAGGTCCtgtg                                                                                                                  <  7:91199/149‑1 (MQ=255)                         tCCAGACCGCGACCAAGAGCCTGCTGGATAACACCGCCGGCGTGGTGCACGGCACACCGAAGTAAACCGGGGCCGCGTTGCGGCCCATTCGCGGGCTTGCCCGCTCCCACAGGCATTGCACAGGGTTC‑GGACCTTGTGCAGGTCCtgtg                                                                                                                  <  5:112049/149‑1 (MQ=255)                         tCCAGACCGCGACCAAGAGCCTGCTGGATAACACCGCCGGCGTGGTGCACGGCACACCGAAGTAAACCGGGGCCGCGTTGCGGCCCATTCGCGGGCTTGCCCGCTCCCACAGGCATTGCACAGGGTTC‑GGACCTTGTGCAGGTCCtgt                                                                                                                   <  5:92568/148‑1 (MQ=255)                              aCCGCGACCAAGAGCCTGCTGGATAACACCGCCGGCGTGGTGCACGGCACACCGAAGTAAACCGGGGCCGCGTTGCGGCCCATTCGCGGGCTTGCCCGCTCCCACAGGCATTGCACAGGGTTC‑GGACCTTGTGCAGGTCCTGTGCGAGc                                                                                                             <  8:55391/149‑1 (MQ=255)                                 gcgACCAAGAGCCTGCTGGATAACACCGCCGGCGTGGTGCACGGCACACCGAAGTAAACCGGGGCCGCGTTGCGGCCCATTCGCGGGCTTGCCCGCTCCCACAGGCATTGCACAGGGTTC‑GGACCTTGTGCAGGTCCTGTGCGAGCggg                                                                                                          <  2:248532/149‑1 (MQ=255)                                    aCCAAGAGCCTGCTGGATAACACCGCCGGCGTGGTGCACGGCACACCGAAGTAAACCGGGGCCGCGTTGCGGCCCATTCGCGGGCTTGCCCGCTCCCACAGCCATTTCACAGGGTTC‑GGACCTTGTGCAGTTCCTGTGCGAGCGGGCaa                                                                                                       <  5:130367/149‑1 (MQ=255)                                          agCCTGCTGGATAACACCGCCGGCGTGGTGCACGGCACACCGAAGTAAACCGGGGCCGCGTTGCGGCCCATTCGCGGGCTTGCCCGCTCCCACAGGCATTGCACAGGGTTC‑GGACCTTGTGCAGGTCCTGTGCGAGCGGGCAAGCCcgc                                                                                                 <  3:311305/149‑1 (MQ=255)                                                 tgGATAACACCGCCGGCGTGGTGCACGGCACACCGAAGTAAACCGGGGCCGCGTTGCGGCCCATTCGCGGGCTTGCCCGCTCCCACAGGCATTGCACAGGGTTC‑GGACCTTGTGCAGGTCCTGTGCGAGCGGGCAAGCCCGCGAATggg                                                                                          >  5:329609/1‑149 (MQ=255)                                                   gATAACACCGCCGGCGTGGTGCACGGCACACCGAAGTAAACCGGGGCCGCGTTGCGGCCCAATCGCGGGCTTGCCCGCTCCCAGAGGCATTGCACAGGGTTC‑GGTCCTTGTGCAGGTGCTGTGCGAGCGGGCAAGCCCGCGAATggggc                                                                                        >  1:283802/1‑147 (MQ=255)                                                    aTAACACCGCCGGCGTGGTGCACGGCACACCGAAGTAAACCGGGGCCGCGTTGCGGCCCATTCGCGGGCTTTCCCGCTCCCACAGGCATTGCACAGGGTTC‑GGACCTTGTGCAGGTCCTGTGCGAGCGGGCAAGCCCCCGAATCGGccc                                                                                       >  6:113363/1‑149 (MQ=255)                                                      aaCACCGCCGGCGTGGTGCACGGCACACCGAAGTAAACCGGGGCCGCGTTGCGGCCCATTCGCGGGCTTGCCCGCTCCCACAGGCATTGCACAGGGTTC‑GGACCTTGTGCAGGTCCTGTGCGAGCGGGCAAGCCCGCGAATGGGCCCCg                                                                                     >  1:82222/1‑149 (MQ=255)                                                          ccgccgGCGTGGTGCACGGCACACCGAAGTAAACCGGGGCCGCGTTGCGGCCCATTCGCGGGCTTGCCCGCTCCCACAGGCATTGCCCAGGGGTC‑GGACCTTGTGCAGGTCCTGTGCGAGCGGGCCAGCCCGCGCATGGGCCCCGcac                                                                                  >  7:327321/1‑148 (MQ=255)                                                                         ccGGAACACCTAAGTAACCGGGGGCCGCTTGGGGGCCCTTGCGGGGGCTTGCCCGCTCCCACTGGCTTTCCACTGGGTTC‑GCACCTTGTGCTGTCCCTGTGCTCGCGGGAATGCCCGCGAATGGGCCCCGCACAATTTTCCCGGACTGa                                                                  <  4:133039/148‑1 (MQ=255)                                                                                 ccGAAGTAAACCGGGGCCGCGTTGCGGCCCATTCGCGGGCTTGCCCGCTCCCACAGGCATTGCACAGGGTTC‑GGACCTTGTGCAGGTCCTGTGCGAGCGGGCAAGCCCGGGAATGGGCCCCGCACAATTTTCCCGGACTGAACATTATc                                                          <  1:50686/149‑1 (MQ=255)                                                                                     aGTACACCGGGGCCGCGTTGCGGCCCATGCGCGGGCGTGCCCGCGCCCCCAGGCATTGCACCGGGTTC‑GGCCCTTGTGCAGGGCCTGTGCGAGCGGGCAAGCCCGCGAATGGGCCCCGCACAATTTTCCCGGACTGAACATTATCCCCg                                                      <  8:327321/149‑1 (MQ=38)                                                                                      gTAAACCGGGGCCGCGTTGCGGCCCATTCGCGGGCTTGCCCGCTCCCACAGGCATTGCACAGGGTTC‑GGACCTTGTGCAGGTCCTGTGCGCGCGGGCAAGCCCGCGAATGGGCCCCGCACAATTTTCCCGGACTGAACATTATCCCCGc                                                     >  5:330297/1‑149 (MQ=255)                                                                                         aaCCGGGGCCGCGTTGCGGCCCATTCGCGGGCATTCCCCCGCCCCCAGGCCATGGACAGGGGTA‑GGCCCATTTTGAGGTACAGTTCGCGCCGGCCAGCCCGCCCATTGGCCCCCCACAAATTTAACCGACGGAAAATTTTAACCGccc                                                   >  4:101156/1‑148 (MQ=255)                                                                                                 ccGCGTTGCGGCCCATTCGCGGGCTTGCCCGCTCCCACAGGCATTGCACAGGGTTC‑GGACCTTGTGCAGGTCCTTTGCGAGCGGGCAAGCCCGCGAATGGGCCCCGCACAATTTTCCCGGACTGAACATTATCCCCGCCCCAAGGTCAg                                          <  5:113363/149‑1 (MQ=255)                                                                                                   gcgTTGCGGCCCATTCGCGGGCTTGCCCGCGCCCACAGGCATTGCACAGGGTTCGGGGCCTTGTGCAGGGCCTGTGCGAGCGGGCAAGCCCGCGAATGGGCCCCGCACAATTTTGCCGGACTGAACATTATGCCCGCCCCAAgggccgg                                         >  1:98742/1‑144 (MQ=37)                                                                                                      ttGCGGCCCATTCGCGGGCTTGCCCGCTCCCACAGGCATTGCACAGGGTTC‑GGACCTTGTGCAGGTCCTGTGCGAGCGGGCAAGCCCGCGAATGGGCCCCGCACAATTTTCCCGGACTGAACATTATCCCCGCCCCAAGGTCAGTTAtt                                     <  8:72986/149‑1 (MQ=255)                                                                                                      ttGCGGCCCATTCGCGGGCTTGCCCGCTCCCACAGGCATTGCACAGGGTTC‑GGACCTTGTGCAGGTCCTGTGCGAGCGGGCAAGCCCGCGAATGGGCCCCGCACAATTTTCCCGGACTGAACATTATCCCCGCCCCAAGGTCAGTTAtt                                     <  2:82222/149‑1 (MQ=255)                                                                                                      ttGCGGCCCATTCGCGGGCTTGCCCGCTCCCACAGGCATTGCACAGGGTTC‑GGACCTTGTGCAGGTCCTGTGCGAGCGGGCAAGCCCGCGAATGGGCCCCGCACAATTTTCCCGGACTGAACATTATCCCCGCCCCAAGGTCAGTTAtt                                     <  7:274036/149‑1 (MQ=255)                                                                                                             ccATTCGCGGGCTTGCCCGCTCCCACAGGCATTGCACAGGGTTC‑GGACCTTGTGCAGGTCCTGTGCGAGCGGGCAAGCCCGCGAATGGGCCCGCCACAATTTTACCGGACTGAACATTATAACCCCCCCAAGGTCAGTTATTCAGGCa                               >  6:292081/1‑148 (MQ=37)                                                                                                               aTTCGCGGGCTTGCCCGCTCCCACAGGCATTGCACAGGGTTC‑GGACCTTGTGCAGGTCCTGTGCGAGCGGGCAAGCCCGCGAATGGGCCCCGCACAATTTTCCCGGACTGAACATTATCCCCGCCCCAAGGTCAGTTATTCAGGCATca                            >  7:19313/1‑149 (MQ=255)                                                                                                                       gCTTGCCCGCTCCCACAGGCATTGCACAGGGTTC‑GGACCTTGTGCAGGTCCTGTGCGAGCGGGCAAGCCCGCGAATGGGCCCCGCACAATTTTCCCGGACTGAACATTATCCCCGCCCCAAGGTCAGTTATTCAGGCATCACACACCTg                    <  8:19313/149‑1 (MQ=255)                                                                                                                             ccGCTCGCACAGGACCTGCACAAGGTCC‑GAACCCTGTGCAATGCCTGTGGGAGCGGGCAAGCCCGCGAATGGGCCCCGCACAATTTTCCCGGACTGAACATTATCCCCGCCCCAAGGTCAGTTATTCAGGCATCACACACCTGGTGTTc              >  2:338255/1‑149 (MQ=18)                                                                                                                             ccGCTCCCACAGGCATTGCACAGGGTTC‑GGACCTTGTGCAGGTCCTGTGCGAGCGGGCAAGCCCGCGAATGGGCCCCGCACAATTTTCCCGGACTGAACATTATCCCCGCCCCAAGGTCAGTTATTCAGGCATCACACACCTGGTGTTc              >  5:160940/1‑149 (MQ=255)                                                                                                                                cccccACCGGCATTGCACCGGTCTC‑GCCCTTCGTGCCGGTCCTGGGCGCGCGGGCATGCCCGCGAATGGGCCCCGCACAATTTTCCCGGACTGAACATTATCCCCGCCCCAAGGTCAGTTATTCAGGCATCACACACCTGGTGTTCGtt           <  2:283802/147‑1 (MQ=255)                                                                                                                                   ccACAGGCATTGCACAGGGTTC‑GGACCTTGTGCAGGTCCTGTGCGAGCGGGCAAGCCCGCGAATGGGCCCCGCACAATTTTCCCGGACTGAACATTATCCCCGCCCCAAGGTCAGTTATTCAGGCATCACACACCTGGTGTTCGTTGAc        >  3:334420/1‑149 (MQ=255)                                                                                                                                    cacaGGCATTGCACAGGGTTC‑GGACCTTGTGCAGGTCCTGTGCGAGCGGGCAAGCCCGCGAATGGGCACCGCACAATTTTCACGGAATGAACATTATCCCCGACCCAAGGTCAGTTATTAAGGCATCACACACCTGGTGTTAGTTGaat       >  5:613/1‑147 (MQ=255)                                                                                                                                         gacctGCACAAGGTCC‑GAACCCTGTGCAATGCCTGTGCGAGCGGGCAAGCCCGCGAATGGGCCCCGCACAATTTTCCAGGACTGAACATTATCCCCGCCCCAAGTTCAGTTATTCAGGCATCACACACCTGGTTTTCGTTTACAgatcg  >  4:10275/5‑146 (MQ=21)                                                                                                                                         gaactGCACAAGGTCC‑GAACCCTGTGCAATGCCTGTGCGAGCTGGCAAGCCCGCGAATGGGCCCCGCACAATTTTCCCGGACTGAACATTATCCCCGCCCCAAGGTCAGTTATTCAGGCATCACACACCTGGTGTTCGTTGa         <  3:10275/138‑1 (MQ=25)                                                                                                                                                   |                                                                                                                                            TGCTCAAGAAGCTGGAAGCGTATATCCAGACCGCGACCAAGAGCCTGCTGGATAACACCGCCGGCGTGGTGCACGGCACACCGAAGTAAACCGGGGCCGCGTTGCGGCCCATTCGCGGGCTTGCCCGCTCCCACAGGCATTGCACAGGGTTC‑GGACCTTGTGCAGGTCCTGTGCGAGCGGGCAAGCCCGCGAATGGGCCCCGCACAATTTTCCCGGACTGAACATTATCCCCGCCCCAAGGTCAGTTATTCAGGCATCACACACCTGGTGTTCGTTGACTGAGAG  >  NC_002947/2063055‑2063339

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 14 ≤ ATCG/ATCG < 15 ≤ ATCG/ATCG < 32 ≤ ATCG/ATCG < 36 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑