Predicted mutation
evidence	seq id	position	mutation	freq	annotation	gene	description
RA	NC_002947	2,063,205	T→C	12.5%	intergenic (+62/‑145)	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	2,063,205	0	T	C	12.5%	93.7 / 4.7	40	intergenic (+62/‑145)	PP_1838/PP_1839	membrane protein/hypothetical protein
Reads supporting (aligned to +/- strand):  ref base T (14/21);  new base C (2/3);  total (16/24)
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

AGAAGCTGGAAGCGTATATCCAGACCGCGACCAAGAGCCTGCTGGATAACACCGCCGGCGTGGTGCACGGCACACCGAAGTAAACCGGGGCCGCGTTGCGGCCCATTCGCGGGCTTGCCCGCTCCCACAGGCATTGCACAGGGTTC‑GGACCTTGTGCAGGTCCTGTGCGAGCGGGCAAGCCCGCGAATGGGCCCCGCACAATTTTCCCGGACTGAACATTATCCCCGCCCCAAGGTCAGTTATTCAGGCATCACACACCTGGTGTTCGTTGACTGAGAGGGTCCGTTCAAT  >  NC_002947/2063061‑2063351                                                                                                                                                 |                                                                                                                                                    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)                                                                                                                                               gTTC‑GGACCTTGTGCAGGTCCTGTGCGAGCGGGCAAGCCCGCGAATGGGCCCCGCACAATTTTCCCGGACTGAACATTATCCCCGCCCCAAGGTCAGTTATTCAGGCATCACACACCTGGTGTTCGTTGACTGAGAGGGTCCGTTCAAt  <  6:329609/149‑1 (MQ=255)                                                                                                                                                 |                                                                                                                                                    AGAAGCTGGAAGCGTATATCCAGACCGCGACCAAGAGCCTGCTGGATAACACCGCCGGCGTGGTGCACGGCACACCGAAGTAAACCGGGGCCGCGTTGCGGCCCATTCGCGGGCTTGCCCGCTCCCACAGGCATTGCACAGGGTTC‑GGACCTTGTGCAGGTCCTGTGCGAGCGGGCAAGCCCGCGAATGGGCCCCGCACAATTTTCCCGGACTGAACATTATCCCCGCCCCAAGGTCAGTTATTCAGGCATCACACACCTGGTGTTCGTTGACTGAGAGGGTCCGTTCAAT  >  NC_002947/2063061‑2063351

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: ‑