Predicted mutation
evidence	seq id	position	mutation	freq	annotation	gene	description
RA	NC_002947	3,257,677	T→G	7.6%	A92A (GCA→GCC)	PP_2854 ←	hypothetical protein

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NC_002947	3,257,677	0	T	G	7.6%	159.7 / 4.0	53	A92A (GCA→GCC)	PP_2854	hypothetical protein
Reads supporting (aligned to +/- strand):  ref base T (25/24);  new base G (2/2);  total (27/26)
Fisher's exact test for biased strand distribution p-value = 1.00e+00
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 8.21e-01

GGTCACGTTGATATCGACGTTGTTGTAAGCGGCGTTGTTGTCACCGGCTGCACGGACCACCTGGGTTACACCTTCGGTGGTGGTCAGGCCGTTGCCGCCCGTTACCACGCCAGTCCCGGCAGCAGAAGCGTTGCT‑CGGCGCCGGACCTGCGCCTTTTTTGTCAATCATCGAGACATAGAACTGGGGTTTGATGGTCGATTGCTGAACCTGCAGCGTGGACGTTGCCCCGATCACATCCCCTTTTGTATTTTGCCAAGTACTGGACATGACGATGCCGAAGCTCACGATTCGTCCG  >  NC_002947/3257530‑3257824                                                                                                                                                     |                                                                                                                                                    ggTCACGTTGATATCGACGTTGTTGTAAGCGGCGTTGTTGTCACCGGCTGCACGGACCACCTGGGTTACACCTTCGGTGGTGGTCAGGCCGTTGCCGCCCGTTACCACGCCAGTCCCGGCAGCAGAAGCGTTGCT‑CGGCGCCGGACCt                                                                                                                                                     <  2:124142/148‑1 (MQ=255)          gATATCGACGTTGTTGTAAGCGGCGTTGTTGTCACCGGCTGCACGGACCACCTGGGTTACACCTTCGGTGGTGGTCAGGCCGTTGCCGCCCGTTACCACGCCAGTCCCGGCAGCAGAAGCGTTGCT‑CGGCGCCGGACCTGCGCCtttt                                                                                                                                            <  2:313652/148‑1 (MQ=255)            tatCGACGTTGTTGTAAGCGGCGTTGTTGTCACCGGCTGCACGGACCACCTGGGTTACACCTTCGGTGGTGGTCAGGCCGTTGCCGCCCGTTACCACGCCAGTCCCGGCAGCAGAAGCGTTGCT‑CGGCGCCGGACCTGCGCCtttttt                                                                                                                                          <  7:295086/148‑1 (MQ=255)              tCGACGTTGTTGTAAGCGGCGTTGTTGTCACCGGCTGCACGGACCACCTGGGTTACACCTTCGGTGGTGGTCAGGCCGTTGCCGCCCGTTACCACGCCAGTCCCGGCAGCAGAAGCGTTGCT‑CGGCGCCGGACCTGCGCCTTTTTTGt                                                                                                                                        >  5:178947/1‑148 (MQ=255)               cGACGTTGTTGTAAGCGGCGTTGTTGTCACCGGCTGCACGGACCACCTGGGTTACACCTTCGGTGGTGGTCAGGCCGTTGCCGCCCGTTACCACGCCAGTCCCGGCAGCAGAAGCGTTGCT‑CGGCGCCGGACCTGCGCCTTTTTTGTc                                                                                                                                       >  2:108630/1‑148 (MQ=255)                  cGTTGTTGTAAGCGGCGTTGTTGTCACCGGCTGCACGGACCACCTGGGTTACACCTTCGGTGGTGGTCAGGCCGTTGCCGCCCGTTACCACGCCAGTCCCGGCAGCAGAAGCGTTGCT‑CGGCGCCGGACCTGCGCCTTTTTTGTCAatc                                                                                                                                   <  3:335470/149‑1 (MQ=255)                  cGTTGTTGTAAGCGGCGTTGTTGTCACCGGCTGCACGGACCACCTGGGTTACACCTTCGGTGGTGGTCAGGCCGTTGCCGCCCGTTACCACGCCAGTCCCGGCAGCAGAAGCGTTGCT‑CGGCGCCGGACCTGCGCCTTTTTTGTCAatc                                                                                                                                   <  5:158473/149‑1 (MQ=255)                       ttgtAAGCGGCGTTGTTGTCACCGGCTGCACGGACCACCTGGGTTACACCTTCGGTGGTGGTCAGGCCGTTGCCGCCCGTTACCACGCCAGTCCCGGCAGCAGAAGCGTTGCT‑CGGCGCCGGACCTGCGCCTTTTTTGTCAATCATCga                                                                                                                              <  4:210389/149‑1 (MQ=255)                         gtAAGCGGCGTTGTTGTCACCGGCTGCACGGACCACCTGGGTTACACCTTCGGTGGTGGTCAGGCCGTTGCCGCCCGTTACCACGCCAGTCCCGGCAGCAGAAGCGTTGCT‑CGGCGCCGGACCTGCGCCTTTTTTGTCAATCATCgag                                                                                                                             >  7:328221/1‑148 (MQ=255)                                           aCCGGCTGCACGGACCACCTGGGTTACACCTTCGGTGGTGGTCAGCCCGTTGCCGCCCGTTACCACGCCAGTCCCGGCAGCAGAAGCGTTGCT‑CGGCGCCGGACCTGCGCCTTTTTTGTCAATCATCGAGACATAGAACTGGGGTTTGa                                                                                                          >  8:221520/1‑149 (MQ=255)                                           aCCGGCTGCACGGACCACCTGGGGTACACCTTCGGTGGTGGTCAGGCCGTTGCCGCCCGTTACCACGCCAGTCCCGGCAGCAGAAGCGTTGCT‑CGGCGCCGGACCTGCGCCTTTTTTGTCAATCATCGAGACATAGAACTGGGGTTTGa                                                                                                          <  8:148460/149‑1 (MQ=255)                                                cTGCACGGACCACCTGGGTTACACCTTCGGTGGTGGTCAGGCCGTTGCCGCCCGTTACCACGCCAGTCCCGGCAGCAGAAGCGTTGCT‑CGGCGCCGGACCTGCGCCTTTTTTGTCAATCATCGAGACATAGAACTGGGGTTTGATGGTc                                                                                                     <  2:315656/149‑1 (MQ=255)                                                    aCGGACCAGCTGGTTTTCACCTTCGGTGGTGGTGAGGCCGTTGCCGCCCGTTACCACGCCATTCCCGGAAGCAGAAGCGTTGCT‑CGGCGCCGGACCTGCGCCTTTTTTGTCAATCATCGAGACATAGAACTGGGGTTTGATGGTCGAtt                                                                                                 <  7:19872/149‑1 (MQ=255)                                                    aCGGACCACCTGGGTTACACCTTCGGTGGTGGTCAGGCCGTTGCCGCCCGTTACCACGCCAGTCCCGGCAGCAGAAGCGTTGCT‑CGGCGCCGGACCTGCGCCTTTTTTGTCAATCATCGAGACATAGAACTGGGGTTTGATGGTCGAtt                                                                                                 <  6:178947/149‑1 (MQ=255)                                                    aCGGACCACCTGGGTTACACCTTCGGTGGTGGTCAGGCCGTTGCCGCCCGTTACCACGCCAGTCCCGGCAGCAGAAGCGTTGCT‑CGGCGCCGGACCTGCGCCTTTTTTGTCAATCATCGAGACATAGAACTGGGGTTTGATGGTCGAtt                                                                                                 >  8:87467/1‑149 (MQ=255)                                                             cTGGGGTACACCTTCGGTGGTGGTCAGGCCGTTGCCGCCCGTTACCACGCCAGTCCCGGCAGCAGAAGCGTTGCT‑CGGCGCCGGACCTGCGCCTTTTTTGTCAATCATCGAGACATAGAACTGGGGTTTGATGGTCGATTGCTGAACCt                                                                                        <  6:275021/149‑1 (MQ=255)                                                                ggTTACACCTTCGGTGGTGGTCAGGCCGTTGCCGCCCGTTACCACGCCAGTCCCGGCAGCAGAAGCGTTGCT‑CGGCGCCGGACCTGCGCCTTTTTTGTCAATCATCGAGACATAGAACTGGGGTTTGATGGTCGATTGCTGAACCTGCa                                                                                     <  1:217138/149‑1 (MQ=255)                                                                  ttACACCTTCGGTGGTGGTCAGGCCGTTGCCGCCCGTTACCACGCCAGTCCCGGCAGCAGAAGCGTTGCT‑CGGCGCCGGACCTGCGCCTTTTTTGTCAATCATCGAGACATAGAACTGGGGTTTGATGGTCGATTGCTGAACCTGCAGc                                                                                   >  3:174730/1‑149 (MQ=255)                                                                    acacCTTCGGTGGTGGTCAGGCCGTTGCCGCCCGTTACCACGCCAGTCCCGGCAGCAGAAGCGTTGCT‑CGGCGCCGGACCTGCGCCTTTTTTGTCAATCATCGAGACATAGAACTGGGGTTTGATGGTCGATTGCTGAACCTGCAGCGt                                                                                 >  6:61166/1‑149 (MQ=255)                                                                      acCTTCGGTGGTGGTCAGGCCGTTGCCGCCCGTTACCACGCCAGTCCCGGCAGCAGAAGCGATGCT‑CCGCGCCGGACCTGCGCCTTTTTTGTCAATACTCGAGACATAGAACTGGGCTTAGATGGTCGATTGGTGAAACTGCAGCGTgg                                                                               >  4:296302/1‑149 (MQ=255)                                                                              tggtggtCAGGCCGTTGCCGCCCGTTACCACGCCAGTCCCGGCAGCAGAAGCGTTGCT‑CGGCGCCGGACCTGCGCCTTTTTTGTCAATCATCGAGACATAGAACTGGGGTTTGATGGTCGATTGCTGAACCTGCAGCGTGGACGTTGcc                                                                       >  1:367198/1‑149 (MQ=255)                                                                               ggtggtCAGGCCGTTGCCGCCCGTTACCACGCCAGTCCCGGCAGCAGAAGCGTTGCT‑CGGCGCCGGACCTGCGCCTTTTTTGTCAATCATCGAGACATAGAACTGGGGTTTGATGGTCGATTGCTGAACCTGCAGCGTGGACGTTGccc                                                                      <  8:328221/149‑1 (MQ=255)                                                                                  ggtCAGGCCGTTGCCGCCCGTTACCACGCCAGTCCCGGCAGCAGAAGCGTTGCT‑CGGCGCCGGACCTGCGCCTTTTTTGTCAATCATCGAGACATAGAACTGGGGTTTGATGGTCGATTGCTGAAACTGCAGCGTGGACGTTGCCCCGa                                                                   >  4:151887/1‑149 (MQ=255)                                                                                   gtCAGGCCGTTGCCGCCCGTTACCACGCCAGTCCCGGCAGCAGAAGCGTTGCT‑CGGCGCCGGACCTGCGCCTTTTTTGTCAATCATCGAGACATAGAACTGGGGTTTGATGGTCGATTGCTGAACCTGCAGCGTGGACGTTGCCCCGAt                                                                  >  4:259204/1‑149 (MQ=255)                                                                                   gtCAGGCCGTTGCCGCCCGTTACCACGCCAGTCCCGGCAGCAGAAGCGTTGCT‑CGGCGCCGGACCTGCGCCTTTTTTGTCAATCATCGAGACATAGAACTGGGGTTTGATGGTCGATTGCTGAACCTGCAGCGTGGACGTTGCCCCGAt                                                                  <  5:61166/149‑1 (MQ=255)                                                                                    tCAGGCCGTTGCCGCCCGTTACCACGCCAGTCCCGGCAGCAGAAGCGTTGCT‑CGGCGCCGGACCTGCGCCTTTTTTGTCAATCATCGAGACATAGAACTGGGGTTTGATGGTCGATTGCTGAACCTGCAGCGTGGACGTTGCCCCGATc                                                                 <  3:259204/149‑1 (MQ=255)                                                                                       ggCCGTTGCCGCCCGTTACCACGCCAGTCCCGGCAGCAGAAGCGTTGCT‑CGGCGCCGGACCTGCGCCTTTTTTGTCAATCATCGAGACATAGAACTGGGGTTTGATGGTCGATTGCTGAACCTGCAGCGTGGACGTTGCCCCGATcaca                                                              >  3:289040/1‑149 (MQ=255)                                                                                                cgccCGTTACCACGCCAGTCCCGGCAGCAGAAGCGTTGCT‑CGGCGCCGGACCTGCGCCTTTTTTGTCAATCATCGAGACATAGAACTGGGGTTTGATGGTCGATTGCTGAACCTGCAGCGTGGACGTTGCCCCGATCACATCCCCtttt                                                     <  3:151887/149‑1 (MQ=255)                                                                                                cgccCGTTACCACGCCAGTCCCGGCAGCAGAAGCGTTGCT‑CGGCGCCGGACCTGCGCCTTTTTTGTCAATCATCGAGACATAGAACTGGGGTTTGATGGTCGATTGCTGAACCTGCAGCGTGGACGTTGCCCCGATCACATCCCCttt                                                      <  7:221520/148‑1 (MQ=255)                                                                                                     gTTACCACGCCAGTCCCGGCAGCAGAAGCGTTGCT‑CGGCGCCGGACCTGCGCCTTTTTTGTCAATCATCGAGACATAGAACTGGGGTTTGATGGTCGATTGCTGAACCTGCAGCGTGGACGTTGCCCCGATCACATCCCCTTTTGTAtt                                                >  7:116383/1‑149 (MQ=255)                                                                                                         ccACGCCAGTCCCGGCAGCAGAAGCGTTGCT‑CGGCGCCGGACCTGCGCCTTTTTTGTCAATCATCGAGACATAGAACTGGGGTTTGATGGTCGATTGCTGAACCTGCAGCGTGGACGTTGCCCCGATCACATCCCCTTTTGTATTTTGc                                            >  4:344768/1‑149 (MQ=255)                                                                                                          cACGCCAGTCCCGGCAGCAGAAGCGTTGCTACGGCGCCGGACGTGCGCCTTTTTTGTCAATCATCGAGACATAGAACTGGGGTTTGATGGTCGATTGCTGAACCTGCAGCGTGGACGTTGCCCCGATCACAGCCCCTTTTGTATTTTg                                             >  1:222517/1‑148 (MQ=255)                                                                                                          cACGCCAGTCCCGGCAGCAGAAGCGTTGCT‑CGGCGCCGGACCTGCGCCTTTTTTGTCAATCATCGAGACATAGAACTGGGGTTTGATGGTCGATTGCTGAACCTGCAGCGTGGACGTTGCCCCGATCACATCCCCTTTTGTATTTTGc                                            >  5:321301/1‑148 (MQ=255)                                                                                                           aCGCCAGTCCCGGCAGCAGAAGCGTTGCT‑CGGCGCCGGACCTGCGCCTTTTTTGTCAATCATCGAGACATAGAACTGGGGTTTGATGGTCGATTGCTGAACCTGCAGCGTGGACGTTGCCCCGATCACATCCCCTTTTGTATTTTGcc                                           >  5:343954/1‑148 (MQ=255)                                                                                                            cGCCAGTCCCGGCAGCAGAAGCGTTGCT‑CGGCGCCGGACCTGCGCCTTTTTTGTCAATCATCGAGACATAGAACTGGGGTTTGATGGTCGATTGCTGAACCTGCAGCGTGGACGTTGCCCCGATCACATCCCCTTTTGTATTTTGCCaa                                         <  1:108630/149‑1 (MQ=255)                                                                                                                  tCCCGGCAGCAGAAGCGTTGCT‑CGGCGCCGGACCTGCGCCTTTTTTGTCAATCATCGAGACATAGAACTGGGGTTTGATGGTCGATTGCTGAACCTGCAGCGTGGACGTTGCCCCGATCACATCCCCTTTTGTATTTTGCCAAGTACTg                                   <  8:116383/149‑1 (MQ=255)                                                                                                                  tCCCGGCAGCAGAAGCGTTGCT‑CGGCGCCGGACCTGCGCCTTTTTTGTCAATCATCGAGACATAGAACTGGGGTTTGATGGTCGATTGCTGAACCTGCAGCGTGGACGTTGCCCCGATCACATCCCCTTTTGTATTTTGCCAAGTACTg                                   >  5:181721/1‑149 (MQ=255)                                                                                                                         agcagAAGCGTTGCT‑CGGCGCCGGACCTGCGCCTTTTTTGTCAATCATCGAGACATAGAACTGGGGTTTGATGGTCGATTGCTGAACCTGCAGCGTGGACGTTGCCCCGATCACATCCCCTTTTGTATTTTGCCAAGTACTGGACATGa                            <  4:289040/149‑1 (MQ=255)                                                                                                                          gcagAAGCGTTGCT‑CGGCGCCGGACCTGCGCCTTTTTTGTCAATCATCGAGACATAGAACTGGGGTTTGATGGTCGATTGCTGAACCTGCAGCGTGGACGTTGCCCCGATCACATCCCCTTTTGTATTTTGCCAAGTACTGGACATGAc                           <  2:222517/149‑1 (MQ=255)                                                                                                                          gcagAAGCGTTGCT‑CGGCGCCGGACCTGCGCCTTTTTTGTCAATCATCGAGACATAGAACTGGGGTTTGATGGTCGATTGCTGAACCTGCAGCGTGGACGTTGCCCCGATCACATCCCCTTTTGTATTTTGCCAAGTACTGGACATGAc                           <  7:87467/149‑1 (MQ=255)                                                                                                                            agAAGCGTTGCT‑CGGCGCCGGACCTGCGCCTTTTTTGTCAATCATCGAGACATAGAACTGGGGTTTGATGGTCGATTGCTGAACCTGCAGCGTGGACGTTGCCCCGATCACATCCCCTTTTGTATTTTGCCAAGTACTGGACATGACGa                         >  7:320513/1‑149 (MQ=255)                                                                                                                                   ttGCT‑CGGCGCCGGACCTGCGCCTTTTTTGTCAATCATCGAGACATAGAACTGGGGTTTGATGGTCGATTGCTGAACCTGCAGCGTGGACGTTGCCCCGATCACATCCCCTTTTGTATTTTGCCAAGTACTGGACATGACGATGCCg                    >  5:286173/1‑147 (MQ=255)                                                                                                                                     gCT‑CGGCGCCGGACCTGCGCCTTTTTTGTCAATCATCGAGACATAGAACTGGGGGTTGATGGTCGATTGCTGAACCTGCAGCGTGGACGTTGCCCCGATCACATCCCCTTTTGTATTTTGCCAAGTACTGGACATGACGATGCCGAAg                 <  2:367198/148‑1 (MQ=255)                                                                                                                                     aaaaaggCGCAGGTCCGGCGCCTTTTTTGTCAATCATCGAGACATAGAACTGGGGTTTGATGGTCGATTGCTGAACCTGCAGCGTGGACGTTGCCCCGATCACATCCCCTTTTGTATTTTGCCAAGTACTGGACATGACGATGCCGAAg                 >  3:115883/6‑149 (MQ=255)                                                                                                                                      aaaaggCGCAGGTCCGGCGCCTTTTTTGTCAATCATCGAGACATAGAACTGGGGTTTGATGGTCGATTGCTGAACCTGCAGCGTGGAc                                                                             >  7:128546/5‑88 (MQ=255)                                                                                                                                      aaaaggCGCAGGTCCGGCGCCTTTTTTGTCAATCATCGAGACATAGAACTGGGGTTTGATGGTCGATTGCTGAACCTGCAGCGTGGAc                                                                             <  8:128546/84‑1 (MQ=255)                                                                                                                                        caggCGCAGGCCCGGCGCCTTTTTTGTCAATCATCGAGACATAGAACTGGGGTTTGATGGTCGATTGCTGAACCTGCAGCGTGGACGTTGCCCCGATCACATCCCCTTTTGTATTTTGCCAAGTACTGGACATGACGATGCCGAAGCTc              <  4:7358/147‑1 (MQ=255)                                                                                                                                         cGGCGCCGGACCTGCGCCTTTTTTGTCAATCATCGAGACATAGAACTGGGGTTTGATGGTCGATTGCTGAACCTGCAGCGTGGACGTTGCCCCGATCACATCCCCTTTTGTATTTTGCCAAGTACTGGACATGACGATGCCGAAGCTCa             >  5:335977/1‑149 (MQ=255)                                                                                                                                            cgcCGGACCTGCGCCTTTTTTGTCAATCATCGAGACATAGAACTGGGGTTTGATGGTCGATTGCTGAACCTGCAGCGTGGACGTTGCCCCGATCACATCCCCTTTTGTATTTTGCCAAGTACTGGACATGATGATGCCGAAGCTCACGa          <  6:321301/149‑1 (MQ=255)                                                                                                                                             gcCGGACCTGCGCCTTTTTTGTCAATCATCGAGACATAGAACTGGGGTTTGATGGTCGATTGCTGAACCTGCAGCGTGGACGTTGCCCCGATCACATCCCCTTTTGTATTTTGCCAAGTACTGGACATGACGATGCCGCAGCTCACGAt         >  8:102734/1‑149 (MQ=255)                                                                                                                                             gcCGGACCTGCGCCTTTTTTGTCAATCATCGAGACATAGAACTGGGGTTTGATGGTCGATTGCTGAACCTGCAGCGTGGACGTTGCCCCGATCACATCCCCTTTTGTATTTTGCCAAGTACTGGACATGACGATGCCGAAGCTCACGAt         <  6:343954/149‑1 (MQ=255)                                                                                                                                                  aCCTGCGCCTTTTTTCTCAATAATAGAGACATAGAACTGGCGATTGATGGTCGATTGCTGAACCTCCAGCGTGGACGTTGCCCCGATCACATCCCCTTTTGTATTTTGACAAGTACTGGACATGACGATGCCGAAGCTCACGATTCgac    >  2:118524/1‑147 (MQ=255)                                                                                                                                                    cTGCGCCTTTTTTGTCAATCATCGAGACATAGAACTGGGGTTTGATGGTCGATTGCTGAACCTGCAGCGTGGACGTTGCCCCGATCACATCCCCTTTTGTATTTTGCCAAGTACTGGACATGACGATGCCGAAGCTCACGATTCGTCCg  >  8:233224/1‑149 (MQ=255)                                                                                                                                                    cTGCGCCTTTTTTGTCAATCATCGAGACATAGAACTGGGGTTTGATGGTCGATTGCTGAACCTGCAGCGTGGACGTTGCCCCGATCACATCCCCTTTTGTATTTTGCCAAGTACTGGACATGACGATGCCGAAGCTCACGATTCGTCCg  >  5:147201/1‑149 (MQ=255)                                                                                                                                                     |                                                                                                                                                    GGTCACGTTGATATCGACGTTGTTGTAAGCGGCGTTGTTGTCACCGGCTGCACGGACCACCTGGGTTACACCTTCGGTGGTGGTCAGGCCGTTGCCGCCCGTTACCACGCCAGTCCCGGCAGCAGAAGCGTTGCT‑CGGCGCCGGACCTGCGCCTTTTTTGTCAATCATCGAGACATAGAACTGGGGTTTGATGGTCGATTGCTGAACCTGCAGCGTGGACGTTGCCCCGATCACATCCCCTTTTGTATTTTGCCAAGTACTGGACATGACGATGCCGAAGCTCACGATTCGTCCG  >  NC_002947/3257530‑3257824

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 14 ≤ ATCG/ATCG < 21 ≤ ATCG/ATCG < 32 ≤ ATCG/ATCG < 36 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑