Predicted mutation
evidence	seq id	position	mutation	freq	annotation	gene	description
RA	NC_002947	479,499	A→T	10.8%	intergenic (‑31/+25)	cca ← / ← ycgB	multifunctional tRNA nucleotidyltransferase/2',3'‑cyclic phosphodiesterase/2' nucleotidase/phosphatase/type IV piliation protein

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NC_002947	479,499	0	A	T	10.8%	151.4 / 7.3	55	intergenic (‑31/+25)	cca/ycgB	multifunctional tRNA nucleotidyltransferase/2',3'‑cyclic phosphodiesterase/2' nucleotidase/phosphatase/type IV piliation protein
Reads supporting (aligned to +/- strand):  ref base A (26/23);  new base T (3/3);  total (29/26)
Fisher's exact test for biased strand distribution p-value = 1.00e+00
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 1.00e+00

GCTAGCATTTCTTCGACGGTGGCGCCCACCACCAGCCAGTCGATATCGCTGACAGGGCGGCCGAGCAAACGGTCGCGCACGGCGCCGCCAACTTTGTAGATGTGCATGTGCAGCTCTCCATAACTGCCGACAGGATAACCCGTCGGCGGTCATGGGGTTGCATCAGAGGTGGTGGATAACAGCCAGGTCCATGCGGCCATAG‑TCGGCGCTTTCGCTATGCTCGCCGCGCGGCGGCATGTGGTGAGTACTCATCACTTGCTCGCCTTGCACGGTCTC  >  NC_002947/479362‑479637                                                                                                                                          |                                                                                                                                            gCTAGCATTTCTTCGACGGTGGCGCCCACCACCAGCCAGTCGATATCGCTGACAGGGCGGCCGAGCAAACGGTCGCGCACGGCGCCGCCAACTTTGTAGATGTGCATGTGCAGCTCTCCATAACTGCCGACAGGATAACCCGTcggcg                                                                                                                                   <  6:10729/148‑1 (MQ=255)   tAGCATTTCTTCGACGGTGGCGCCCACCACCAGCCAGTCGATATCGCTGACAGGGCGGCCGAGCAAACGGTCGCGCACGGCGCCGCCAACTTTGTAGATGTGCATGTGCAGCTCTCCATAACTGCCGACAGGATAACCCGTCGGCGGt                                                                                                                                 >  3:76551/1‑148 (MQ=255)   tAGCATTTCTTCGACGGTGGCGCCCACCACCAGCCAGTCGATATCGCTGACAGGGCGGCCGAGCAAACGGTCGCGCACGGCGCCGCCAACTTTGTAGATGTGCATGTGCAGCTCTCCATAACTGCCGACAGGATAACCCGTCGGCGGt                                                                                                                                 >  2:313055/1‑148 (MQ=255)     gCATTTCTTCGACGGTGGCGCCCACCACCAGCCAGTCGATATCGCTGACAGGGCGGCCGAGCAAACGGTCGCGCACGGCGCCGCCAACTTTGTAGATGTGCATGTGCAGCTCTCCATAACTGCCGACAGGATAACCCGTCGGCGGTCAt                                                                                                                              >  7:188163/1‑149 (MQ=255)     gCATTTCTTCGACGGGGGCGCCCACCACCAGCCAGTCGATATCGCGGACAGGGCGGCCGAGCAAACGGGCGCGCACGGCGCCGCCAACTTTGTAGATGTGCATGTGCAGCTCTCCATAACTGCCGACAGGATAACCCGTCGGCGGTc                                                                                                                                <  6:326706/147‑1 (MQ=255)      cATTTCTTCGACGGTGGCGCCCACCACCAGCCAGTCGATATCGCTGACAGGGCGGCCGAGCAAACGGTCGCGCACGGCGCCGCCAACTTTGTAGATGTGCATGTGCAGCTCTCCATAACCGCCGACGGGTTATCCTGTCGGCAGTTATg                                                                                                                             <  4:119525/149‑1 (MQ=255)        tttCTTCGACGGTGGCGCCCACCACCAGCCAGTCGATATCGCTGACAGGGCGGCCGAGCAAACGGTCGCGCACGGCGCCGCCAACTTTGTAGATGTGCATGTGCAGCTCTCCATAACTGCCGACAGGATAACCCGTCGGCGGTCATggg                                                                                                                           >  6:209574/1‑149 (MQ=255)           cttcGACGGTGGCGCCCACCACCAGCCAGTCGATATCGCTGACAGGGCGGCCGAGCAAACGGTCGCGCACGGCGCCGCCAACTTTGTAGATGTGCATGTGCAGCTCTCCATGACCGCCGACGGGTTATCCTGTCGGCAGTTATggaga                                                                                                                         <  2:269384/148‑4 (MQ=38)            ttcGACGGTGGCGCCCACCACCAGCCAGTCGATATCGCTGACAGGGCGGCCGAGCAAACGGTCGCGCACGGCGCCGCCAACTTTGTAGATGTGCATGTGCAGCTCTCCATAACTGCCGACAGGATAACCCGTCGGCGGTCATGGGGTTg                                                                                                                       >  1:195644/1‑149 (MQ=255)              cGACGGTGGCGCCCACCACCAGCCAGTCGATATCGCTGACAGGGCGGCCGAGCAAACGGTCGCGCACGGCGCCGCCAACTTTGTAGATGTGCATGTGCAGCTCTCCATAACTGCCGACAGGATAACCCGTCGGCGGTCATGGGGTTGc                                                                                                                      <  3:66531/148‑1 (MQ=255)               gACGGTGGCGCCCACCACCAGCCAGTCGATATCGCTGACAGGGCGGCCGAGCAAACGGTCGCGCACGGCGCCGCCAACTTTGTAGATGTGCATGTGCAGCTCTCCATAACTGCCGACAGGATAACCCGTCGGCGGTCATGGGGTTGCAt                                                                                                                    >  4:236846/1‑149 (MQ=255)                 cGGTGGCGCCCACCACCAGCCAGTCGATATCGCTGACAGGGCGGCCGAGCAAACGGTCGCGCACGGCGCCGCCAACTTTGTAGATGTGCATGTGCAGCTCTCCATAACTGCCGACAGGATAACCCGTCGGCGGTCATGGGGTTGCATCa                                                                                                                  <  2:174471/149‑1 (MQ=255)                      gcgcCCACCACCAGCCAGTCGATATCGCTGACAGGGCGGCCGAGCAAACGGTCGCGCACGGCGCCGCCAACTTTGTAGATGTGCATGTGCAGCTCTCCATAACTGCCGACAGGATAACCCGTCGGCGGTCATGGGGTTGCATCAGAggt                                                                                                             <  4:276876/149‑1 (MQ=255)                        gcCCACCACCAGCCAGTCGATATCGCTGACAGGGCGGCCGAGCAAACGGTCGCGCACGGCGCCGCCAACTTTGTAGATGTGCATGTGCAGCTCTCCATAACTGCCGACAGGATAACCCGTCGGCGGTCATGGGGTTGCATCAGAggtgg                                                                                                           >  8:210821/1‑149 (MQ=255)                         cccACCACCAGCCAGTCGATATCGCTGACAGGGCGGCCGAGCAAACGGTCGCGCACGGCGCCGCCAACTTTGTAGATGTGCATGTGCAGCTCTCCATAACTGCCGACAGGATAACCCGTCGGCGGTCATGGGGTTGCATCAGAggtggt                                                                                                          <  4:76551/149‑1 (MQ=255)                           caccaccaGCCAGTCGATATCGCTGACAGGGCGGCCGAGCAAACGGTCGCGCACGGCGCCGCCAACTTTGTAGATGTGCATGTGCAGCTCTCCATAACTGCCGACAGGATAAc                                                                                                                                            >  8:143150/1‑113 (MQ=255)                           caccaccaGCCAGTCGATATCGCTGACAGGGCGGCCGAGCAAACGGTCGCGCACGGCGCCGCCAACTTTGTAGATGTGCATGTGCAGCTCTCCATAACTGCCGACAGGATAAc                                                                                                                                            <  7:143150/113‑1 (MQ=255)                           caccaccaGCCAGTCGATATCGCTGACAGGGCGGCCGAGCAAACGGTCGCGCACGGCGCCGCCAACTTTGTAGATGTGCATGTGCAGCTCTCCATAACTGCCGACAGGATAACCCGTCGGCGGTCATGGGGTTGCATCAGAGgtggtg                                                                                                         >  5:167643/1‑148 (MQ=255)                           caccaccaGCCAGTCGATATCGCTGACAGGGCGGCCGAGCAAACGGTCGCGCACGGCGCCGCCAACTTTGTAGATGTGCATGTGCAGCTCTCCATAACTGCCGACAGGATAACCCGTCGGCGGTCATGGGGTTGCATCAGAGgtggtg                                                                                                         >  8:150220/1‑148 (MQ=255)                             ccaccaGCCAGTCGATATCGCTGACAGGGCGGCCGAGCAAACGGTCGCGCACGGCGCCGCCAACTTTGTAGATGTGCATGTGCAGCTCTCCATAACTGCCGACAGGATAACCCGTCGGCGGTCATGGGGTTGCATCAGAGGTGGTGGAt                                                                                                      <  6:225785/149‑1 (MQ=255)                             ccaccaGCCAGTCGATATCGCTGACAGGGCGGCCGAGCAAACGGTCGCGCACGGCGCCGCCAACTTTGTAGATGTGCATGTGCAGCTCTCCATAACTGCCGACAGGATAACCCGTCGGCGGTCATGGGGTTGCATCAGAGGTGGTGGAt                                                                                                      <  7:210821/149‑1 (MQ=255)                              caccaGCCAGTCGATATCGCTGACAGGGCGGCCGAGCAAACGGTCGCGCACGGCGCCGCCAACTTTGTAGATGTGCATGTGCAGCTCTCCATAACTGCCGACAGGATAACCCGTCGGCGGTCATGGGGTTGCATCAGAGGTGGTGGAt                                                                                                      >  8:102950/1‑148 (MQ=255)                              caccaGCCAGTCGATATCGCTGACAGGGCGGCCGAGCAAACGGTCGCGCACGGCGCCGCCAACTTTGTAGATGTGCATGTGCAGCTCTCCATAACTGCCGACAGGATAACCCGTCGGCGGTCATGGGGTTGCATAAGAGGTGGTGGAt                                                                                                      >  8:72343/1‑148 (MQ=255)                                 cagccagTCGATATCGCTGACAGGGCGGCCGAGCAAACGGTCGCGCACGGCGCCGCCAACTTTGTAGATGTGCATGTGCAGCTCTCCATAACTGCCGACAGGATAACCCGTCGGCGGTCATGGGGTTGCATCAGAGGtggtgg                                                                                                        >  4:257786/1‑143 (MQ=255)                                 cagccagTCGATATCGCTGACAGGGCGGCCGAGCAAACGGTCGCGCACGGCGCCGCCAACTTTGTAGATGTGCATGTGCAGCTCTCCATAACTGCCGACAGGATAACCCGTCGGCGGTCATGGGGTTGCATCAGAGGtggtgg                                                                                                        <  3:257786/143‑1 (MQ=255)                                 cagccagTCGATATCGCTGACAGGGCGGCCGAGCAAACGGTCGCGCACGGCGCCGCCAACTTTGTAGATGTGCATGTGCAGCTCTCCATAACTGCCGACAGGATAACCCGTCGGCGGTCATGGGGTTGCATCAGAGGTGGTGGATAACa                                                                                                  <  8:188163/149‑1 (MQ=255)                                 cagccagTCGATATCGCTGACAGGGCGGCCGAGCAAACGGTCGCGCACGGCGCCGCCAACTTTGTAGATGTGCATGTGCAGCTCTCCATAACTGCCGACAGGATAACCCGTCGGCGGTCATGGGGTTGCATCAGAGGTGGTGGATAACa                                                                                                  <  1:313055/149‑1 (MQ=255)                                     cagTCGATATCGCTGACAGGGCGGCCGAGCAAACGGTCGCGCACGGCGCCGCCAACTTTGTAGATGTGCATGTGCAGCTCTCCATAACTGCCGACAGGATAACCCGTCGGCGGTCATGGGGTTGCATCAGAGGTGGTGGATAACAGc                                                                                                >  7:97350/1‑147 (MQ=255)                                      agTCGATATCGCTGACAGGGCGGCCGAGCAAACGGTCGCGCACGGCGCCGCCAACTTTGTAGATGTGCATGTGCAGCTCTCCATAACTGCCGACAGGATAACCCGTCGGCGGTCATggg                                                                                                                           >  5:266248/1‑119 (MQ=255)                                      agTCGATATCGCTGACAGGGCGGCCGAGCAAACGGTCGCGCACGGCGCCGCCAACTTTGTAGATGTGCATGTGCAGCTCTCCATAACTGCCGACAGGATAACCCGTCGGCGGTCATggg                                                                                                                           <  6:266248/119‑1 (MQ=255)                                              tCGCTGACAGGGCGGCCGAGCAAACGGTCGCGCACGGCGCCGCCAACTTTGTAGATGTGCATGTGCAGCTCTCCATAACTGCCGACAGGATAACCCGTCGGCGGTCATGGGGTTGCATCAGAGGTGGTGGATAACAGCCAGGTCCATGc                                                                                     >  1:53403/1‑149 (MQ=255)                                                       gggCGGCCGAGCAAACGGTCGCGCACGGCGCCGCCAACTTTGTAGATGTGCATGTGCAGCTCTCCATAACTGCCGACAGGATAACCCGTCGGCGGTCATGGGGTTGCATCAGAGGTGGTGGATAACAGCCAGGTCCATGCGGCCATAG‑t                                                                           >  8:293416/1‑149 (MQ=255)                                                         gcggcCGAGCAAACGGTCGCGCACGGCGCCGCCAACTTTGTAGATGTGCATGTGCAGCTCTCCATAACTGCCGACAGGATAACCCGTCGGCGGTCATGGGGTTGCATCAGAGGTGGTGGATAACAGCCAGGTCCATGCGGCCATAG‑TCg                                                                         <  2:195644/149‑1 (MQ=255)                                                            gcCGAGCAAACGGTCGCGCACGGCGCCGCCAACTTTGTAGATGTGCATGTGCAGCTCTCCATAACTGCCGACAGGATAACCCGTCGGCGGTCATGGGGTTGCATCAGAGGTGGTGGATAACAGCCAGGTCCATGCGGCCATAG‑TCGgcg                                                                      >  6:6184/1‑149 (MQ=255)                                                             ccGAGCAAACGGTCGCGCACGGCGCCGCCAACTTTGTAGATGTGCATGTGCAGCTCTCCATAACTGCCGACAGGATAACCCGTCGGCGGTCATGGGGTTGCATCAGAGGTGGTGGATAACAGCCAGGTCCATGCGGCCATAG‑TCGgcgc                                                                     >  5:11405/1‑149 (MQ=255)                                                                aGCAAACGGTCGCGCACGGCGCCGCCAACTTTGTAGATGTGCATGTGCAGCTCTCCATAACTGCCGACAGGATAACCCGTCGGCGGTCATGGGGTTGCATCAGAGGTGGTGGATAACAGCCAGGTCCATGCGGCCATAG‑TCGGCGCttt                                                                  <  7:29472/149‑1 (MQ=255)                                                                  cAAACGGTCGCGCACGGCGCCGCCAACTTTGTAGATGTGCATGTGCAGCTCTCCATAACTGCCGACAGGATAACCCGTCGGCGGTCATGGGGTTGCATCAGAGGTGGTGGATAACAGCCAGGTCCATGCGGCCATAG‑TCGGCGCTTTCg                                                                <  3:236846/149‑1 (MQ=255)                                                                                 ggCACCGCCAACTTTGTAGATGTGCATGTGCAGCTCTCCATAACTGCCGACAGGATAACCCGTCGGCGGTCATGGGGTTGCATCAGAGGTGGTGGATAACAGCCAGGTCCATGCGGCCATAG‑TCGGCGCtt                                                                   <  4:255486/131‑1 (MQ=255)                                                                                 ggCACCGCCAACTTTGTAGATGTGCATGTGCAGCTCTCCATAACTGCCGACAGGATAACCCGTCGGCGGTCATGGGGTTGCATCAGAGGTGGTGGATAACAGCCAGGTCCATGCGGCCATAG‑TCGGCGCtt                                                                   >  3:255486/1‑131 (MQ=255)                                                                                              ttGTAGATGTGCATGTGCAGCTCTCCATAACTGCCGACAGGATAACCCGTCGGCGGTCATGGGGTTGCATCAGAGGTGGTGGATAACAGCCAGGTCCATGCGGCCATAG‑TCGGCGCTTTCGCTATGCTCGCCGCGCGGCGGCATgtggt                                    >  2:146039/1‑149 (MQ=255)                                                                                               tGTAGATGTGCATGTGCAGCTCTCCATAACTGCCGACAGGATAACCCGTCGGCGGTCATGGGGTTGCATCAGAGGTGGTGGATAACAGCCAGGTCCATGCGGCCATAG‑TCGGCGCTTTCGCTATGCTCGCCGCGCGGCGGCATgtggt                                    <  7:72343/148‑1 (MQ=255)                                                                                               tGTAGATGTGCATGTGCAGCTCTCCATAACTGCCGACAGGATAACCCGTCGGCGGTCATGGGGTTGCATCAGAGGTGGGGGATAACAGCCAGGTGCATGCGGCCATAG‑TCGGCGCTTTCGCTATGCTCGCCGCGCGGCGGCATgtgg                                     <  5:209574/147‑1 (MQ=255)                                                                                                gTAGATGTGCATGTGCAGCTCTCCATAACTGCCGACAGGATAACCCGTCGGCGGTCATGGGGTTGCATCAGAGGTGGTGGATAACAGCCAGGTCCATGCGGCCATAG‑TCGGCGCTTTCGCTATGCTCGCCGCGCGGCGGCATgtggt                                    >  7:9211/1‑147 (MQ=255)                                                                                                 tAGATGTGCATGTGCAGCTCTCCATAACTGCCGACAGGATAACCCGTCGGCGGTCATGGGGTTGCATCAGAGGTGGTGGATAACAGCCAGGTCCATGCGGCCATAA‑TCGGCGCTTTCGCTATGCTCGCCGCGCGGCGGCATGTGGTGa                                  <  8:97350/148‑1 (MQ=255)                                                                                                        gcatgtgcaGCTCTCCATAACTGCCGACAGGATAACCCGTCGGCGGTCATGGGGTTGCATCAGAGGTGGTGGATAACAGCCAGGTCCATGCGGCCATAG‑TCGGCGCTTTCGCTATGCTCGCCGCGCGGCGGCATGTGGTGAGTACtcat                          >  2:212731/1‑149 (MQ=255)                                                                                                                    ccccATGACCGCCGACGGGTTATCCTGTCGGCAGTTATGGGGTTGCATCAGAGGTGGTGGATAACAGCCAGGTCCATGCGGCCATAG‑TCGGCGCTTTCGCTATGCTCGCCGCGCGGCGGCATGTGGTGAGTACTCATCACTTGCTCGcc              >  5:294024/3‑149 (MQ=38)                                                                                                                       cATAACTGCCGACAGGATAACCCGTCGGCGGTCATGGGGTTGCATCAGAGGTGGTGGATAACAGCCAGGTCCATGCGGCCATAG‑TCGGCGCTTTCGCTATGCTCGCCGCGCGGCGGCATGTGGTGa                                  >  6:273714/1‑126 (MQ=255)                                                                                                                           aCTGCCGACAGGATAACCCGTCGGCGGTCATGGGGTTGCATCAGAGGTGGTGGATAACAGCCAGGTCCATGCGGCCATAG‑TCGGCGCTTTCGCTATGCTCGCCGCGCGGCGGCATGTGGTGAGTACTCATCACTTGCTCGCCTTGCACg       <  1:212731/149‑1 (MQ=255)                                                                                                                            cTGCCGACAGGATAACCCGTCGGCGGTCATGGGGTTGCATCAGAGGTGGTGGATAACAGCCAGGTCCATGCGGCCATAGCTAGGCGCTTTCGCTATGCTCGCCGCGCGGCGGCATGTGGTGAGTACTCATCACTTGCTCGCCTTGCACg       <  1:106076/149‑1 (MQ=255)                                                                                                                             tGCCGACAGGATAACCCGTCGGCGGTCATGGGGTTGCATCAGAGGTGGTGGATAACAGCCAGGTCCATGCGGCCATAG‑TCGGCGCTTTCGCTATGCTCGCCGCGCGGCGGCATGTGGTGAGTACTCATCACTTGCTCGCCTTGCACgg      >  4:216251/1‑148 (MQ=255)                                                                                                                              gCCGACGGGTTATCCTGTCGGCGGTCATGGGGTTGCATCAGAGGTGGTGGATAACAGCCAGGTCCATGCGGCCATAG‑TCGGCGCTTTCGCTATGCTCGCCGCGCGGCGGCATGTGGTGAGTACTCATCACTTGCTCGCCtt            <  4:320423/141‑1 (MQ=255)                                                                                                                              gCCGACGGGTTATCCTGTCGGCGGTCATGGGGTTGCATCAGAGGTGGTGGATAACAGCCAGGTCCATGCGGCCATAG‑TCGGCGCTTTCGCTATGCTCGCCGCGCGGCGGCATGTGGTGAGTACTCATCACTTGCTCGCCtt            >  3:320423/1‑141 (MQ=255)                                                                                                                              gCCGACGGGTTATCCTGTCGGCGGTCATGGGGTTGCATCAGAGGTGGTGGATAACAGCCAGGTCCATGCGGCCATAG‑TCGGCGCTTTCGCTATGCTCGCCGCGCGGCGGCATGTGGTGAGTACTCATCACTTGCTCGCCTTGCACGGtc    >  8:295547/1‑149 (MQ=255)                                                                                                                                      gATAACCCGTCGGCGGTCATGGGGTTGCATCAGAGGTGGTGGATAACAGCCAGGTCCATGCGGCCATAG‑TCGGCGCTTTCGCTATGCTCGCCGCGCGGCGGCATGTGGTGAGTACTCATCACTTGCTCGCCTTGCACGGtctc  <  6:323793/143‑1 (MQ=255)                                                                                                                                      gATAACCCGTCGGCGGTCATGGGGTTGCATCAGAGGTGGTGGATAACAGCCAGGTCCATGCGGCCATAG‑TCGGCGCTTTCGCTATGCTCGCCGCGCGGCGGCATGTGGTGAGTACTCATCACTTGCTCGCCTTGCACGGtctc  >  5:323793/1‑143 (MQ=255)                                                                                                                                          |                                                                                                                                            GCTAGCATTTCTTCGACGGTGGCGCCCACCACCAGCCAGTCGATATCGCTGACAGGGCGGCCGAGCAAACGGTCGCGCACGGCGCCGCCAACTTTGTAGATGTGCATGTGCAGCTCTCCATAACTGCCGACAGGATAACCCGTCGGCGGTCATGGGGTTGCATCAGAGGTGGTGGATAACAGCCAGGTCCATGCGGCCATAG‑TCGGCGCTTTCGCTATGCTCGCCGCGCGGCGGCATGTGGTGAGTACTCATCACTTGCTCGCCTTGCACGGTCTC  >  NC_002947/479362‑479637

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: ‑