Predicted mutation
evidence	seq id	position	mutation	freq	annotation	gene	description
RA	NC_002947	2,063,220	G→T	9.1%	intergenic (+77/‑130)	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	2,063,220	0	G	T	9.1%	168.0 / 6.9	55	intergenic (+77/‑130)	PP_1838/PP_1839	membrane protein/hypothetical protein
Reads supporting (aligned to +/- strand):  ref base G (24/26);  new base T (3/2);  total (27/28)
Fisher's exact test for biased strand distribution p-value = 6.69e-01
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 6.95e-01

ATCCAGACCGCGACCAAGAGCCTGCTGGATAACACCGCCGGCGTGGTGCACGGCACACCGAAGTAAACCGGGGCCGCGTTGCGGCCCATTCGCGGGCTTGCCCGCTCCCACAGGCATTGCACAGGGTTCGGACCTTGTGCAGGTCCTGTGCGAGC‑GGGCAAGCCCGCGAATGGGCCCCGCACAATTTTCCCGGACTGAACATTATCCCCGCCCCAAGGTCAGTTATTCAGGCATCACACACCTGGTGTTCGTTGACTGAGAGGGTCCGTTCAATGAAAGAGTGGGAAGTCA  >  NC_002947/2063078‑2063368                                                                                                                                               |                                                                                                                                                      atCCAGACCGCGACCAAGAGCCTGCTGGATAACACCGCCGGCGTGGTGCACGGCACACCGAAGTAAACCGGGGCCGCGTTGCGGCCCATTCGCGGGCTTGCCCGCTCCCACAGGCATTGCACAGGGTTCGGACCTTGTGCAGGTCCtgt                                                                                                                                                 >  1:257664/1‑149 (MQ=255) atCCAGACCGCGACCAAGAGCCTGCTGGATAACACCGCCGGCGTGGTGCACGGCACACCGAAGTAAACCGGGGCCGCGTTGCGGCCCATTCGCGGGCTTGCCCGCTCCCACAGGCATTGCACAGGGTTCGGACCTTGTGCAGGTCCtgt                                                                                                                                                 >  1:269086/1‑149 (MQ=255)    cAGACCGCGACCAAGAGCCTGCTGGATAACACCGCCGGCGTGGTGCACGGCACACCGAAGTAAACCGGGGCCGCGTTGCGGCCCATTCGCGGGCTTGCCCGCTCCCACAGGCATTGCACAGGGTTCGGACCTTGTGCAGGTCCTGTGc                                                                                                                                               <  3:317187/148‑1 (MQ=255)    cAGACCGCGACCAAGAGCCTGCTGGATAACACCGCCGGCGTGGTGCACGGCACACCGAAGTAAACCGGGGCCGCGTTGCGGCCCATTCGCGGGCTTGCCCGCTCCCACAGGCATTGCACAGGGTTCGGACCTTGTGCAGGTCCTGTGc                                                                                                                                               >  7:375721/1‑148 (MQ=255)    cAGACCGCGACCAAGAGCCTGCTGGATAACACCGCCGGCGTGGTGCACGGCACACCGAAGTAAACCGGGGCCGCGTTGCGGCCCATTCGCGGGCATGCCCCCGACCCCAGGCATTGCACAGGGTTCGGAAGATGTGGAGGTCCtgtggg                                                                                                                                              >  4:32047/1‑147 (MQ=255)         cgcgACCAAGAGCCTGCTGGATAACACCGCCGGCGTGGTGCACGGCACACCGAAGTAAACCGGGGCCGCGTTGCGGCCCATTCGCGGGCTTGCCCGCTCCCACAGGCATTGCACAGGGTTCGGACCTTGTGCAGGTCCTGTGCGAGC‑gg                                                                                                                                        <  8:341630/149‑1 (MQ=255)          gcgACCAAGAGCCTGCTGGATAACACCGCCGGCGTGGTGCACGGCACACCGAAGTAAACCGGGGCCGCGTTGCGGCCCATTCGCGGGCTTGCCCGCTCCCACAGGCATTGCACAGGGTTCGGACCTTGTGCAGGTCCTGTGCGAGC‑ggg                                                                                                                                       <  5:127239/149‑1 (MQ=255)                aaGAGCCTGCTGGATAACACCGCCGGCGTGGTGCACGGCACACCGAAGTAAACCGGGGCCGCGTTGCGGCCCATTCGCGGGCTTGCCCGCTCCCACAGGCATTGCACAGGGTTCGGACCTTGTGCAGGTCCTGTGCGAGC‑GGGCAAGcc                                                                                                                                 <  3:32047/149‑1 (MQ=255)                   agCCTGCTGGATAACACCGCCGGCGTGGTGCACGGCACACCGAAGTAAACCGGGGCCGCGTTGCGGCCCATTCGCGGGCTTGCCCGCTCCCACAGGCATTGCACAGGGTTCGGACCTTGTGCAGGTCCTGTGCGAGC‑gg                                                                                                                                        <  1:65120/139‑1 (MQ=255)                   agCCTGCTGGATAACACCGCCGGCGTGGTGCACGGCACACCGAAGTAAACCGGGGCCGCGTTGCGGCCCATTCGCGGGCTTGCCCGCTCCCACAGGCATTGCACAGGGTTCGGACCTTGTGCAGGTCCTGTGCGAGC‑gg                                                                                                                                        >  2:65120/1‑139 (MQ=255)                         ctgGATAACACCGCCGGCGTGGTGCACGGCACACCGAAGTAAACCGGGGCCGCGTTGCGGCCCATTCGCGGGCTTGCCCGCTCCCACAGGCATTGCACAGGGTTCGGACCTTGTGCAGGTCCTGTGCGAGC‑GGGCAAGCCCGCGAAt                                                                                                                          <  8:375721/147‑1 (MQ=255)                                    cgccgGCGTGGTGCACGGCACACCGAAGTAAACCGGGGCCGCGTTGCGGCCCATTCGCGGGCTTGCCCGCGCCCACAGGCATTGCCCAGGGGTCGGACCTTGTGCAGGTCCTGTGCGAGC‑GGGCCAGCCCGCGCATGGGCCCCGCCCaa                                                                                                             >  3:78841/1‑149 (MQ=38)                                            tggtgCACGGCACACCGAAGTAAACCGGGGCCGCGTTGCGGCCCATTCGCGGGCTTGCCCGCTCCCCCAGGCATTGCACAGGGGTCGGACCTTGTGCAGGTCGTGTGCGAGC‑GGGCAAGCCCGCGAATGGGCCCCGCACAATTTTCCCg                                                                                                     <  8:220912/149‑1 (MQ=255)                                                 cACGGCACACCGAAGTAAACCGGGGCCGCGTTGCGGCCCATTCGCGGGCTTGCCCGCTCCCACAGGCCTTGCCCAGGGTTAGGACCTTTTGCAGGTACTGTGCGAGC‑GGGCAAGCCCGCGAAAGGGCCCCGCACAATTTTGCCGGGCt                                                                                                 >  7:226444/1‑148 (MQ=37)                                                   cGGCACACCGAAGTAAACCGGGGCCGGGTTGCGGCCCATTCGCGGGCTTGCCCGCTCCCCCAGGCATTGCACAGGGTTGGGACCTTGTGCAGGTCCTGTGCGAGC‑GGGCAAGCCCGCGAATGGGCCCCGCACAATTTTCCCGGACTGaa                                                                                              <  2:137058/149‑1 (MQ=255)                                                   cGGCACACCGAAGTAAACCGGGGCCGCGTTGCGGCCCATTCGCGGGCTTGCCCGCTCCCACAGGCATTGCACAGGGTTCGGACCTTGTGCAGGTCCTGTGCGAGC‑GGGCAAGCCCGCGAATGGGcc                                                                                                                     <  6:83040/126‑1 (MQ=255)                                                   cGGCACACCGAAGTAAACCGGGGCCGCGTTGCGGCCCATTCGCGGGCTTGCCCGCTCCCACAGGCATTGCACAGGGTTCGGACCTTGTGCAGGTCCTGTGCGAGC‑GGGCAAGCCCGCGAATGGGcc                                                                                                                     >  5:83040/1‑126 (MQ=255)                                                     gCACACCGAAGTAAACCGGGGCCGCGTTGCGGCCCATTCGCCGGCTTGCCCGCTCCCACAGGCATTGCACAGGGTGCGGACCTTGTGCAGGTCCTGTGCGAGC‑GGGCAAGCCCGCGAATGGGCCCCGCACAATTTTCCCGGACTGAACa                                                                                            <  1:122867/149‑1 (MQ=255)                                                         acCGAAGTAAACCGGGGCCGCGTTGCGGCCCATTCGCGGGCTTGCCCGCTCCCACAGGCATTGCACAGGGTTCGGACCTTGTGCAGGTCCTGTGCGa                                                                                                                                             <  8:364721/97‑1 (MQ=255)                                                         acCGAAGTAAACCGGGGCCGCGTTGCGGCCCATTCGCGGGCTTGCCCGCTCCCACAGGCATTGCACAGGGTTCGGACCTTGTGCAGGTCCTGTGCGa                                                                                                                                             >  7:364721/1‑97 (MQ=255)                                                           cGAAGTAAACCGGGGCCGCGTTGCGGCCCATTCGCGGGCTTGCCCGCTCCCACAGGCATTGCACAGGGTTCGGACCTTGTGCAGGTCCt                                                                                                                                                   >  5:130064/1‑89 (MQ=255)                                                           cGAAGTAAACCGGGGCCGCGTTGCGGCCCATTCGCGGGCTTGCCCGCTCCCACAGGCATTGCACAGGGTTCGGACCTTGTGCAGGTCCt                                                                                                                                                   <  6:130064/89‑1 (MQ=255)                                                             aaGTAAACCGGGGCCGCGTTGCGGCCCATTCGCGGGCTTTCCCGCTCCCACAGGCATTGCACAGGGTTAGGACCATTTGGAGGTGCGGTGCGAGC‑CGGCAAGCCCGCGAATGGGCCCCGCACAATTTTACCGGACTGAAAATTATgccc                                                                                    >  4:361909/1‑149 (MQ=37)                                                                      ggggCCGCGTTGCGGCCCATTCGCGGGCTTGCCCGCTCCCACAGGCATTGCACAGGGTTCGGACCTTGTGCAGGTGCTGTGCGAGC‑GGGCAAGCCCGCGAATGGGGCCCGCGCCATTTTGCCGGCCTGCACATTATGCCCGCCCCAAgg                                                                           >  1:254057/1‑149 (MQ=37)                                                                           cgcgTTGCGGCCCATTCGCGGGCTTGCCCGCTCCCACAGGCATTGCACAGGGTTCGGACCTTGTGCAGGTCCTGTGCGAGC‑GGGCAAGCCCGCGAATGGGCCCCGCACAATTTTCCCGGACTGAACATTATCCCCGCCCCAAGGTCAGt                                                                      <  2:82698/149‑1 (MQ=255)                                                                                  cGGCCCATTCGCGGGCTTGCCCGCTCCCACAGGCATTGCACAGGGTTCGGACCTTGTGCAGGTCCTGTGCGAGC‑GGGCAAGCCCGCGAATGGGCCCCGCACAATTTTCCCGGACTGAACATTATCCCCGCCCCAAGGTCAGTTATTCa                                                                <  2:257664/148‑1 (MQ=255)                                                                                   ggCCCATTCGCGGGCTTGCCCGCTCCCACAGGCATTGCACAGGGTTCGGACCTTGTGCAGGTCCTGTGCGCGC‑GGGCAAGCCCGCGAATGGGTCCCGCACAATTTTCCCGGACTGAACATTATCCCCGCCCCAAGGTCAGTTATTCAgg                                                              <  2:269086/149‑1 (MQ=255)                                                                                      acATTCGCGGGCTTGCCCGCTCCCACAGGCTTTGCACAGGGTTCGGACCTTGTGCTGGTCCTGTGCGAGC‑GGGCAAGCCCGCGAATGGGCCCCGCACAATTTTCCCGGACTGAACATTATCCCCGCCCCAAGGTCAGTTATTCAGGCAt                                                           <  4:78841/148‑1 (MQ=255)                                                                                             cgGGCTTGCCCGCTCCCACAGGCATTGCACAGGGTTCGGACCTTGTGCAGGTCCTGTGCGAGC‑GGGCAAGCCCGCGAATGGGCCCCGCACAATTTTCCCGGACTGAACATTATCCCCGCCCCAAGGTCAGTTATTCAGGCATCacacac                                                    <  3:361909/149‑1 (MQ=255)                                                                                                    gCCCGCTCCCACAGGCATTGCACAGGGTTCGGACCTTGTGCAGGTCCTGTGCGAGC‑GGGCAAGCCCGCGAATGGGCCCCGCACAATTTTCCCGGACTGAACa                                                                                            <  7:290349/102‑1 (MQ=255)                                                                                                    gCCCGCTCCCACAGGCATTGCACAGGGTTCGGACCTTGTGCAGGTCCTGTGCGAGC‑GGGCAAGCCCGCGAATGGGCCCCGCACAATTTTCCCGGACTGAACa                                                                                            >  8:290349/1‑102 (MQ=255)                                                                                                      ccGCTCGCACAGGACCTGCACAAGGTCCGAACCCTGTGCAATGCCTGTGGGAGC‑GGGCAAGCCCGCGAATGGGCCGCGCACAATTTTCCCGGACTGAACATTATCCCCGCCCCAAGGTCAGTTATTCAGGCATCACACACCTGGTGTTc                                           >  6:138023/1‑149 (MQ=17)                                                                                                      ccGCTCCCACAGGCATTGCACAGGGTTCGGACCTTGTGCAGGTCCTGTGCGTGC‑GGGAAAGCCCGCGAATGGGCCCCGCACAATTTTCCCGGACTGAACATTATCCCCGCCCCAAGGTCAGTTATTCAGGCATCACACACCTGGTGTTc                                           <  8:226444/149‑1 (MQ=255)                                                                                                      ccGCTCCCACAGGCATTGCACAGGGTTCGGACCTTGTGCAGGTCCTGTGCGAGC‑GGGCAAGCCCGCGAATGGGCCCCGCACAATTTTCCCGGACTGAACATTATCCCCGCCCCAAGGTCAGTTATTCAGGCATc                                                          <  1:56285/134‑1 (MQ=255)                                                                                                      ccGCTCCCACAGGCATTGCACAGGGTTCGGACCTTGTGCAGGTCCTGTGCGAGC‑GGGCAAGCCCGCGAATGGGCCCCGCACAATTTTCCCGGACTGAACATTATCCCCGCCCCAAGGTCAGTTATTCAGGCATc                                                          >  2:56285/1‑134 (MQ=255)                                                                                                      ccGCTCCCACAGGCATTGCACAGGGTTAGGACCTTGTGCAGGACCTGTGCAAGC‑GGGCAAACCCGCGAAAGGGCCCCGCACAATTTTACCGGACTGAACATTATCCCCGACCCAAGGTCAGTTATTCAGGCATAACAAAACTGGTGttg                                           >  7:61095/1‑148 (MQ=255)                                                                                                        gCTCGCACAGGACCTGCACAAGGTCCGAACCCTGTGCAATGCCTGTGGGAGC‑GGGCAAGCCCGCGAATGGGCCCCGCACAATTTTCCCGGACTGAACATTATCCCCGCCCCAAGGTCAGTTATTCAGGCATCACACACCTGGTGTTc                                           <  3:172627/147‑1 (MQ=18)                                                                                                        gCTCGCACAGGACCTGCACAAGGTCCGAACCCTGTGCAATGCCTGTGGGAGC‑GGGCAAGCCCGCGAATGGGCCCCGCACAATTTTCCCGGACTGAACATTATCCCCGCCCCAAGGTCAGTTATTCAGGCATCACACACCTGGTGTTc                                           >  4:172627/1‑147 (MQ=18)                                                                                                             cacaGGCATTGCACAGGGTTCGGACCTTGTGCAGGTCCTGTGCGAGC‑GGGCAAGCCCTCTAATGGGCCCCGTACAATTTTCCCGTACTGAACATTATCCCCGTTTCAAGGTTAGTTATTCATGCATCATACACTTGGTGTTCGTTGACt                                    <  8:61095/149‑1 (MQ=255)                                                                                                             cacaGGCATTGCACAGGGTTCGGACCTTGTGCAGGTCCTGTGCGAGC‑GGGCAAGCCCGCGAATGGGCCCCGCACAATTTTCCCGGACTGAACATTATCCCCGCCCCAAGGTCAGTTATTCAGGCATCACACACCTGGTGTTCGTTGACt                                    >  6:424110/1‑149 (MQ=255)                                                                                                              acaGGCATTGCACAGGGTTCGGACCTTGTGCAGGTCCTGTGCGAGC‑GGGCAAGCCCGCGAATGGGCCCCGCACAATTTTCCCGGACTGAACATTATCCCCGCCCCAAGGTCAGTTATTc                                                                 >  7:162137/1‑119 (MQ=255)                                                                                                              acaGGCATTGCACAGGGTTCGGACCTTGTGCAGGTCCTGTGCGAGC‑GGGCAAGCCCGCGAATGGGCCCCGCACAATTTTCCCGGACTGAACATTATCCCCGCCCCAAGGTCAGTTATTc                                                                 <  8:162137/119‑1 (MQ=255)                                                                                                                 ggCATTGCACAGGGTTCGGACCTTGTGCAGGTCCTGTGCGAGC‑GGGCAAGCCCGCGAATGGGCCCCGCACAATTTTCCCGGACTGAACATTATCCCCGCCCCAAGGTCAGTTATTCAGGCATCACACACCTGGTGTTCGTTGACTga                                  >  4:215799/1‑147 (MQ=255)                                                                                                                   cATTGCACAGGGTTCGGACCTTGTGCAGGTCCTGTGCGAGC‑GGGCAAGCCCGCGAATGGGCCCCGCACAATTTTCCCGGACTGAACATTATCCCCGCCCCAAGGTCAGTTATTCAGGCATCACACACCTGGTGTTCGTTGACTGAGAgg                              >  4:218255/1‑149 (MQ=255)                                                                                                                     ttGCACAGGGTTCGGACCTTGTGCAGGTCCTGTGCGTGC‑GGGAAAGCCCGCGAATGGGCCCCGCTCAATTTTCCCGGACTGAACATTATCCCCGCCCCAAGGTCAGTTATTCAGGCATCACACACCTGGTGTTCGTTGACTGAGAGGGt                            <  2:254057/149‑1 (MQ=255)                                                                                                                         acaGGGTTCGGACCTTGTGCAGGTCCTGTGCGAGC‑GGGCAAGCCCGCGAATGGGCCCCGCACAATTTTCCCGGACTGAACATTATCCCCGCCCCAAGGTCAGTTATTCAGGCATCACACACCTGGTGTTCGTTGACTGAGAGGGTCCGt                        >  6:71852/1‑149 (MQ=255)                                                                                                                         acaGGGTTCGGACCTTGTGCAGGTCCTGTGCGAGC‑GGGCAAGCCCGCGAATGGGCCCCGCACAATTTTCCCGGACTGAACATTATCCCCGCCCCAAGGTCAGTTATTCAGGCATCACACACCTGGTGTTCGTTGACTGAGAGGGTCCGt                        >  8:260801/1‑149 (MQ=255)                                                                                                                         acaGGGTTCGGACCTTGTGCAGGTCCTGTGCGAGC‑GGGCAAACCCGCGAATGGGCCCCGCACAATTTTCCCGGACTGAACATTAACCCCGCCCCAAGGTAAGTTATTCAGGCATCAAACACCTGGTGTTCGATGACTTAGAGGGTCCGt                        >  8:253288/1‑149 (MQ=255)                                                                                                                           aaggTCCGAACCCTGTGCAATGCCTGTGGGAGCGGGGCAAGCCCGCGAATGGGCCCCGCACAATTTTCCCGGACTGAACATTATCCCCGCCCCAAGGTCAGTTATTCAGGCATCACACACCTGGTGTTCGTTGACTGAGAGGGTCCGtt                       >  1:274085/3‑149 (MQ=37)                                                                                                                           aGGGTTCGGACCTTGTGCAGGTCCTGTGCGAGC‑GGGCAAGCCCGCGAATGGGCCCCGCACAATTTTCCCGGACTGAACATTATCCCCGCCCCAAGGTCAGTTATTCAGGCGTCACACACCTGGTGTTc                                           <  6:337490/128‑1 (MQ=255)                                                                                                                           aGGGTTCGGACCTTGTGCAGGTCCTGTGCGAGC‑GGGCAAGCCCGCGAATGGGCCCCGCACAATTTTCCCGGACTGAACATTATCCCCGCCCCAAGGTCAGTTATTCAGGCGTCACACACCTGGTGTTc                                           >  5:337490/1‑128 (MQ=255)                                                                                                                              gTTCGGACCTTGTGCAGGTCCTGTGCGAGC‑GGGCAAGCCCGCGAATGGGCCCCGCACAATTTTCCCGGACTGAACATTATCCCCGCCCCAAGGTCAGTTATTCAGGCATCACACACCTGGTGTTCGTTGACTGAGAGGGTCCGTTCAAt                   <  5:424110/149‑1 (MQ=255)                                                                                                                                  gaaCCCTGTGCAATGCCTGTGGGAGC‑GGGCAAGCCCGCGAATGGGCCCCGCACAATTTTCCCGGACTGAACATTATCCCCGCCCCAAGGTCAGTTATTCAGGCATCACACACCTGGTGTTCGTTGACTGAGAGGGTCCGTTCAATGaaa               <  2:274085/147‑1 (MQ=38)                                                                                                                                         gtgCAGGTCCTGTGCGAGC‑GGGCAAGCGCGCGAATGGGCCCCGCACAATTTTCCCGGACTGAACATTATCCCCGCCCCAAGGTCAGTTATTCAGGCATCACACACCTGGTGTTCGTTGACTGAGAGGGTCCGTTCAATGAAAGAGTg          <  7:253288/147‑1 (MQ=255)                                                                                                                                            cAGGTCCTGTGCGAGC‑GGGCAAGCCCGCGAATGGGCCCCGCACAATTTTCCCGGACTGAACATTATCCCCGCCCCAAGGTCAGTTATGCAGACATCACACACCTGGTGTTCGTTGACTGAGAGGGTCCGTTCAATGAAAGAGTGGGAAg     >  7:84665/1‑149 (MQ=255)                                                                                                                                               gTCCTGTGCGAGC‑GGGCAAGCCCGCGAATGGGCCCCGCACAATTTTCCCGGACTGAACATTATCCCCGCCCCAAGGTCAGTTATTCAGGCATCACACACCTGGTGTTCGTTGACTGAGAGGGTCCGTTCAAt                   <  6:184462/132‑1 (MQ=255)                                                                                                                                               gTCCTGTGCGAGC‑GGGCAAGCCCGCGAATGGGCCCCGCACAATTTTCCCGGACTGAACATTATCCCCGCCCCAAGGTCAGTTATTCAGGCATCACACACCTGGTGTTCGTTGACTGAGAGGGTCCGTTCAAt                   >  5:184462/1‑132 (MQ=255)                                                                                                                                               gTCCTGTGCGAGC‑GGGCAAGCCCGCGAATGGGCCCCGCACAATTTTCCCGGACTGAACATTATCCCCGCCCCAAGGTCAGTTATTCAGGCATCACACACCTGGTGTTCGTTGACTGAGAGGGTCCGTTCAATGAAAGAGTGGGAAGTCa  >  6:199079/1‑149 (MQ=255)                                                                                                                                               |                                                                                                                                                      ATCCAGACCGCGACCAAGAGCCTGCTGGATAACACCGCCGGCGTGGTGCACGGCACACCGAAGTAAACCGGGGCCGCGTTGCGGCCCATTCGCGGGCTTGCCCGCTCCCACAGGCATTGCACAGGGTTCGGACCTTGTGCAGGTCCTGTGCGAGC‑GGGCAAGCCCGCGAATGGGCCCCGCACAATTTTCCCGGACTGAACATTATCCCCGCCCCAAGGTCAGTTATTCAGGCATCACACACCTGGTGTTCGTTGACTGAGAGGGTCCGTTCAATGAAAGAGTGGGAAGTCA  >  NC_002947/2063078‑2063368

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: ‑