Predicted mutation
evidence	seq id	position	mutation	freq	annotation	gene	description
RA	NC_002947	2,635,443	G→A	11.3%	intergenic (+33/+84)	PP_2304 → / ← PP_2305	peptidyl‑prolyl cis‑trans isomerase D/hypothetical protein

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NC_002947	2,635,443	0	G	A	11.3%	139.3 / 7.5	53	intergenic (+33/+84)	PP_2304/PP_2305	peptidyl‑prolyl cis‑trans isomerase D/hypothetical protein
Reads supporting (aligned to +/- strand):  ref base G (24/23);  new base A (3/3);  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 = 5.48e-01

CCACCGACGAAGAGAAGCAGCAGATTCGCCGCTACCTCGCGTCACGTGCTGGCCAGCAGGACTTTGCCGCTTACCGCAAGCAGCTGGAAGCCAATGCAGACATCACCCGTTACTAAGGTGTTCGTTGCATGAAGAAACAGGCCGCCTCGTGCGGCCTGT‑‑TTCGT‑TTTCGCCAGCCGCGAGCACGGTCATTGTCGAAGGTCACAGTGCCTTCAGGGGTGGCGCTAACCAGGTGCTACCGCTTCACCCCTTCATAACTGTCCAGCGTATCGCGTGCAATCTCTCGCCCCAGGGC  >  NC_002947/2635295‑2635586                                                                                                                                                     |                                                                                                                                                   ccACCGACGAAGAGAAGCAGCAGATTCGCCGCTACCTCGCGTCACGTGCTGGCCAGCAGGACTTAGCCGCTTACCGCAAGCAGCTGGAAGCCAATGCAGACATCACCCGTTACTAAGGTGTTCGTTGCATCAAGAAACAGGCCGCCTCg                                                                                                                                                    >  7:75397/1‑149 (MQ=255)  cACCGACGAAGAGAAGCAGCAGATTCGCCGCTACCTCGCGTCACGTGCTGGCCAGCAGGACTTTGCCGCTTACCGCAAGCAGCTGGAAGCCAATGCAGACATCACCCGTTACTAAGGTGTTCGTTGCATGAAGAAACAGGCCGCCTCGt                                                                                                                                                   <  6:132568/149‑1 (MQ=255)              gaAGCAGCAGATTCGCCGCTACCTCGCGTCACGTGCTGGCCAGCAGGACTTTGCCGCTTACCGCAAGCAGCTGGAAGCCAATGCAGACATCACCCGTTACTAAGGTGTTCGTTGCATGAAGAAACAGGCCGCACGAGGCGGCCTGT‑‑TTc                                                                                                                                     <  7:99138/149‑1 (MQ=255)               aaGCAGCAGATTCGCCGCTACCTCGCGTCACGTGCTGGCCAGCAGGACTTTGCCGCTTACCGCAAGCAGCTGGAAGCCAATGCAGACATCACCCGTTACTAAGGTGTTCGTTGCATGAAGAAACAGGCCGCCTCGTGCGGCCt                                                                                                                                            <  3:268180/143‑1 (MQ=255)               aaGCAGCAGATTCGCCGCTACCTCGCGTCACGTGCTGGCCAGCAGGACTTTGCCGCTTACCGCAAGCAGCTGGAAGCCAATGCAGACATCACCCGTTACTAAGGTGTTCGTTGCATGAAGAAACAGGCCGCCTCGTGCGGCCt                                                                                                                                            >  4:268180/1‑143 (MQ=255)               aaGCAGCAGATTCGCCGCTACCTCGCGTCACGTGCTGGCCAGCAGGACTTTGCCGCTTACCGCAAGCAGCTGGAAGCCAATGCAGACATCACCCGTTACTAAGGTGTTCGTTGCATGAAGAAACAGGCCGCCTCGTGCGGCCTGT‑‑TTCg                                                                                                                                    >  6:4500/1‑149 (MQ=255)                agcagcAGATTCGCCGCTACCTCGCGTCACGTGCTGGCCAGCAGGACTTTGCCGCTTACCGCAAGCAGCTGGAAGCCAATGCAGACATCACCCGTTACTAAGGTGTTCGTTGCATGAAGAAACAGGCCGCCTCGTGCGGCCTGT‑‑TTCGt                                                                                                                                   <  6:167625/149‑1 (MQ=255)                    gcagATTCGCCGCTACCTCGCGTCACGTGCTGGCCAGCAGGACTTTGCCGCTTACCGCAAGCAGCTGGAAGCCAATGCAGACATCACCCGTTACTAAGGTGTTCGTTGCATGAAGAAACAGGCCGCCTCGTGCGGCCTGT‑‑TTCGT‑TTTc                                                                                                                              <  6:132591/149‑1 (MQ=255)                    gcagATTCGCCGCTACCTCGCGTCACGTGATGGCCAGCAGGACTTTGCCGCTTACCGCAAGCAGATGGAAGCCAATGCAGACATCACCCGTTACTAAGGTGTTCGTTGCATGAAGAAACAGGCCGCCTCGTGCGGCCTGT‑‑TTAGT‑TTTc                                                                                                                              >  4:249346/1‑149 (MQ=255)                       gATTCGCCGCTACCTCGCGTCACGTGCTGGCCAGCAGGACTTTGCCGCTTACCGCAAGCAGCTGGAAGCCTATGCAGACATCACCCGTTACTAAGGTGTTCGTTGCATGAAGAAACAGGCCGCCTCGTGCGGCCTGT‑‑TTCGT‑TTTCGc                                                                                                                            >  6:245180/1‑148 (MQ=255)                               gcTACCTCGCGTCACGTGCTGGCCAGCAGGACTTTGCCGCTTACCGCAAGCAGCTGGAAGCCAATGCAGACATCACCCGTTACTAAGGTGTTCGTTGCATGAAGAAACAGGCCGCCTCGTGCGGCCTGT‑‑TTCGT‑TTTCGCCAGCCGCGa                                                                                                                   <  7:119978/149‑1 (MQ=255)                                       gcgTCACGTGCTGGCCAGCAGGACTTTGCCGCTTACCGCAAGCAGCTGGAAGCCAATGCAGACATCACCCGTTACTAAGGTGTTCGTTGCATGAAGAAACAGGCCGCCTCGTGCGGCCTGT‑‑TTCGT‑TTTCGCCAGCCGCGAGCACGGTc                                                                                                           <  5:102941/149‑1 (MQ=255)                                         gTCACGTGCTGGCCAGCAGGACTTTGCCGCTTACCGCAAGCAGCTGGAAGCCAATGCAGACATCACCCGTTACTAAGGTGTTCGTTGCATGAAGAAACAGGCCGCCTCGTGCGGCCTGT‑‑TTCGT‑TTTCGCCAGCCGCGAGCACGGTCAt                                                                                                         >  2:100794/1‑149 (MQ=255)                                              gTGCTGGCCAGCAGGACTTTGCCGCTTACCGCAAGCAGCTGGAAGCCAATGCAGACATCACCCGTTACTAAGGTGTTCGTTGCATGAAGAAACAGGCCGCCTCGTGCGGCCTGT‑‑TTCGT‑TTTc                                                                                                                              >  6:58355/1‑123 (MQ=255)                                              gTGCTGGCCAGCAGGACTTTGCCGCTTACCGCAAGCAGCTGGAAGCCAATGCAGACATCACCCGTTACTAAGGTGTTCGTTGCATGAAGAAACAGGCCGCCTCGTGCGGCCTGT‑‑TTCGT‑TTTc                                                                                                                              <  5:58355/123‑1 (MQ=255)                                                   ggCCAGCAGGACTTTGCCGCTTACCGCAAGCAGCTGGAAGCCAATGCAGACATCACCCGTTACTAAGGTGTTCGTTGCATGAAGAAACAGGCCGCCTCGTGCGGCCTGT‑‑TTCGT‑TTTCGCCAGCCGCGAGCACGGTCATTGTCGAAGGt                                                                                               >  2:2978/1‑149 (MQ=255)                                                     ccAGCAGGACTTTGCCGCTTACCGCAAGCAGCTGGGAGCCAATGCAGACATCACCCGTTACTAAGGTGTTCGTTGCATGAAGAAACAGGCCGCCTCGTGCGGCCTGT‑‑TTCGT‑TTTCGCCAGCCGCGAGCACGGTCATTGTCGAAGGTca                                                                                             <  6:299059/149‑1 (MQ=255)                                                     ccAGCAGGACTTTGCCGCTTACCGCAAGCAGCTGGAAGCCAATGCAGACATCACCCGTTACTAAGGTGTTCGTTGCATGAAGAAACAGGCCGCCTCGTGCGGCCTGT‑‑TTCGT‑TTTCGCCAGCCGCGAGCACGGTCATTGTCGAAGGTca                                                                                             >  3:148796/1‑149 (MQ=255)                                                           ggACTTTGCCGCTTACCGCAAGCAGCTGGAAGCCAATGCAGACATCACCCGTTACTAAGGTGTTCGTTGCATGAAGAAACAGGCCGCCTCGTGCGGCCTGT‑‑TTCGT‑TTTCGCCAGCCGCGAGCACgg                                                                                                             <  7:94502/127‑1 (MQ=255)                                                           ggACTTTGCCGCTTACCGCAAGCAGCTGGAAGCCAATGCAGACATCACCCGTTACTAAGGTGTTCGTTGCATGAAGAAACAGGCCGCCTCGTGCGGCCTGT‑‑TTCGT‑TTTCGCCAGCCGCGAGCACgg                                                                                                             >  8:94502/1‑127 (MQ=255)                                                           ggACTTTGCCGCTTACCGCAAGCAGCTGGAAGCCAATGCAGACATCACCCGTTACTAAGGTGTTCGTTGCATGAAGAAACAGGCCGCCTCGTGCGGCCTGT‑‑TTCGT‑TTTCGCCAGCCGCGAGCACGGTCATTGTCGAAGGTCACAGTGc                                                                                       <  1:287429/149‑1 (MQ=255)                                                            gACTTTGCCGCTTACCGCAAGCAGCTGGAAGCCAATGCAGACATCAACCGTTACTTAGGTGTTCGTTGCATGAAGAAACAGGCCGCCTCGTGCGGCCTGA‑‑CACCTGTTTCTCCAGCCGCTAGCACGGTCATTGTCTAAGTTCAAAGTga                                                                                       >  1:108390/1‑148 (MQ=255)                                                            gACTTTGCAGCTTACCTCAAGCAGCTGGAAGCCAATGCAGACATCACCCGTTACTAAGGTGTTCGTTGCATGAAGAAACAGGCCGCCTCGTGCGGCCTGT‑‑TTCGT‑TTTCGCCAGCCGCGAGCACGGTCATTGTCGAAGGTCACAGt                                                                                         <  2:108390/146‑1 (MQ=255)                                                                         aCCGCAAGCAGCTGGAAGCCTATGCAGACATCACCCGTTACTAAGGTGTTCGTTGCATGAAGAAACAGGCCGCCTCGTGCGGCCTGT‑‑TTCGT‑TTTCGCCAGCCGCGAGCACGGTCATTGTCGAAGGTCACAGTGCCTTCAGGGGTgg                                                                           <  5:245180/147‑1 (MQ=255)                                                                                     tGGAAGCCAATGCAGACATCACGCGTTACTAAGGTGTTCGTTGAATGAAGAAACAGGCCGCCTCGTGCGGCCTGT‑‑TTCGT‑TTTCGGCAGCCGAGAGCACGGTCATTGTCGATGGTCAAAGAGCCTTCAGCGGTGGGGCTAACCAGGTGc                                                             >  8:61568/1‑149 (MQ=255)                                                                                     tGGAAGCCAATGCAGACATCACCCGTTACTAAGGTGTTCGTTGCATGAAGAAACAGGCCGTCTCGTGCGGCCTGT‑‑TTCGT‑TTTCGCCAGCCGCGAGCACGGTCATTGTCGAAGGTCACAGTGCCTTCAGGGGTGGCGCTAACCAGGTGc                                                             >  1:256117/1‑149 (MQ=255)                                                                                       taaGCCAATGCAGACATCACCGGTTAATAAGGTGTTCGTTGCATGAATAAACAGGCCGCCTCGTGCGGCCTGTTCTTCGT‑TTTCGCCAGCCGCGAGCACGGTCATTGTCGAAGGTCACAGTGCCTTCAGGGGTGGCGCTAACCAGGTg                                                              <  1:100794/147‑1 (MQ=255)                                                                                             aaTGGAGACATCACCCGTTACTAAGGTGTTCGTTGCATGAAGAAACAGGCCGCCTCGTGCGGCCTGT‑‑TTCGT‑TTTCGGCAGCCGCGAGCACGGTCATTGTCGCAGGTCACAGTGCCTTCAGGGGTGGCGCTACCCAGGTGCTACCGCtt                                                     >  8:81777/1‑149 (MQ=255)                                                                                             aaTGCAGACATCACCCGTTACTAAGGTGTTCGTTGCATGAAGAAACAGGCCGCCTCGTGCGGCCTGT‑‑TTCGT‑TTTCGCCAGCCGCGAGCACGGTCATTGTCGAAGGTCACAGTGCCTTCAGGGGTGGCGCTAACCAGGTGCTACCGCtt                                                     <  4:148796/149‑1 (MQ=255)                                                                                                  aGACATCACCCGTTACTAAGGTGTTCGTTGCATGAAGAAACAGGCCGCCTCGTGCGGCCTGT‑‑TTCGT‑TTTCGCCAGCCGCGAGCACGGTCATTGTCGAAGGTCACAGTGCCTTCAGGGGTGGCGCTAACCAGGTGCTACCGCTTCAccc                                                >  3:268721/1‑149 (MQ=255)                                                                                                   gACATCACCCGTTACTAAGGTGTTCGTTGCATGAAGAAACAGGCCGCCTCGTGCGGCCTGT‑‑TTCGT‑TTTCGCCAGCCGCGAGCACGGTCATTGTCGAAGGTCACAGTGCCTTCAGGGGTGGCGCTAACCAGGTGCTACCGCTTCAcccc                                               >  5:323839/1‑149 (MQ=255)                                                                                                      aTCACCCGTTACTAAGGTGTTCGTTGCATGAAGAAACAGGCCGCCTCGTGCGGCCTGT‑‑TTCGT‑TTTCGCCAGCCGCGAGCACGGTCATTGTCGAAGGTCACAGTGCCTTCAGGGGTGGCGCTAACCAGGTGCTACCGCTTCACCCCtt                                             >  2:138869/1‑148 (MQ=255)                                                                                                         aCCCGTTTCTAAGGTGTTCGTTGCATGAAGAAACAGGCCGCCTCGTGCGGCCTGT‑‑TTCGT‑TTTCGCCAGCGGCGAGCACGGTGATTGTCGAAGGTCACAGTGCCTTCAGGTGTGGCGCTAACCAGGTGCTACCGCTTCACCCCTTCAt                                          <  8:252350/148‑1 (MQ=255)                                                                                                            cGTTACTAAGGTGTTCGTTGCATGAAGAAACAGGCCGCCTCGTGCGGCCTGT‑‑TTCGT‑TTTCGCCAGCCGCGAGCACGGTCATTGTCGAAGGTCACAGTGCCTTCAGGGGTGGCGCTAACCAGGTGCTACCGCTTCACCCCTTCATAACt                                      <  3:249346/149‑1 (MQ=255)                                                                                                            cGTTACTAAGGTGTTCGTTGCATGAAGAAACAGGCCGCCTCGTGCGGCCTGT‑‑TTCGT‑TTTCGCCAGCCGCGAGCACGGTCATTGTCGAAGGTCACAGTGCCTTCAGGGGTGGCGCTAACCAGGTGCTACCGCTTCACCCCTTCATAACt                                      <  1:138869/149‑1 (MQ=255)                                                                                                                            gTTGCATGAAGAAACAGGCCGCCTCGTGCGGCCTGT‑‑TTCGT‑TTTCGCCAGCCGCGAGCACGGTCATTGTCGAAGGTCACAGTGCCTTCAGGGGTGGCGCTAACCAGGTGCTACCGCTTCACCCCTTCATAACTGTCCAGCGTATCGCGt                      >  7:98972/1‑149 (MQ=255)                                                                                                                                cATGAAGAAACAGGCCGCCTCGTGCGGCCTGT‑‑TTCGT‑TTTCGCCAGCCGCGAGCACGGTCATTGTCGAAGGTCACAGTGCCTTCAGGGGTGGCGCTAACCAGGTGCTACCGCTTCACCCCTTCATa                                         <  8:56171/126‑1 (MQ=255)                                                                                                                                cATGAAGAAACAGGCCGCCTCGTGCGGCCTGT‑‑TTCGT‑TTTCGCCAGCCGCGAGCACGGTCATTGTCGAAGGTCACAGTGCCTTCAGGGGTGGCGCTAACCAGGTGCTACCGCTTCACCCCTTCATa                                         >  7:56171/1‑126 (MQ=255)                                                                                                                                 aTGAAGAAACAGGCCGCCTCGTGCGGCCTGT‑‑TTCGT‑TTTCGCCAGCCGCGAGCACGGTCATTGTCGAAGGTCACAGTGCCTTCAGGGGTGGCGCTAACCAGGTGATACCGCTTCACCCATTCATAACTGTCCAGCGTATCGCGTGCaa                  >  2:134399/1‑148 (MQ=255)                                                                                                                                     cgaaACAGGCCGCACGAGGCGGCCTGT‑‑TTCGT‑TTTCGCCAGCCGCGAGCACGGTCATTGTCGACGGTCACAGTGCCTTCAGGGGTGGCGCTAAGCAGGTGCTACCGCTTCACCCCTTCATAACTGTCCAGCGTATCGCGt                      <  7:57819/139‑1 (MQ=255)                                                                                                                                     cgaaACAGGCCGCACGAGGCGGCCTGT‑‑TTCGT‑TTTCGCCAGCCGCGAGCACGGTCATTGTCGAAGGTCACAGTGCCTTCAGGGGTGGCGCTAACCAGGTGCTACCGCTTCACCCCTTCATAACTGTCAATCGTATCGCGt                      >  8:57819/2‑140 (MQ=255)                                                                                                                                     agaaACAGGCCGGCTCGTGCGGCCTGT‑‑TTCGT‑TTTCGCCAGCCGCGAGCACGGTCATTGTCGAAGGTCACAGTGCCTTCAGGGGTGGCGCTAACCAGGTGCTACCGCTTCACCCCTTCATAACTGTCCAGCGTATCGCGTGCAAtctct             <  2:256117/149‑1 (MQ=255)                                                                                                                                      gaaACAGGCCGCCTCGTGCGGCCTGT‑‑TTCGT‑TTTCGCCAGCCGCGAGCACGGTCATTGTCGAAGGTCACAGTGCCTTCAGGGGTGGCGCTAACCAGGTGCTACCGCTTCACCCCTTCATAACTGTCCAGCGTATCGCGTGCAAtctctc            >  7:195967/1‑149 (MQ=255)                                                                                                                                      gaaACAGGCCGCACGAGGCGGCCTGT‑‑TTCGT‑TTTCGCCAGCCGCGAGCACGGTCATTGTCGAAGGTCACAGTGCCTTCAGGGGTGGCGCTAACCAGGTGCTACCGCTTCACCCCTTCATaa                                        <  6:321821/121‑1 (MQ=255)                                                                                                                                      gaaACAGGCCGCACGAGGCGGCCTGT‑‑TTCGT‑TTTCGCCAGCCGCGAGCACGGTCATTGTCGAAGGTCACAGTGCCTTCAGGGGTGGCGCTAACCAGGTGCTACCGCTTCACCCCTTCATaa                                        >  5:321821/1‑121 (MQ=255)                                                                                                                                      gaaACAGGCCGCACGAGGCGGCCTGT‑‑TTCGT‑TTTCGCCAGCCGCGAGCACGGTCATTGTCGAAGGTCACAGTGCCTTCAGGGGTGGCGCTAACCAGGTGCTACCGCTTCACCCCTTCATAACTGTCCAGCGTATCGCGTGCAAtctctc            >  7:175268/1‑149 (MQ=255)                                                                                                                                          cAGGCCGCCTCGTGCGGCCTGT‑‑TTCGT‑TTTCGCCAGCCGCGAGCACGGTCATTGTCGAAGGTCACAGTGCCTTCAGGGGTGGCGCTAACCAGGTGCTACCGCTTCACCCCTTCATAACTGTCCAGCGTATCGCGTGCAATCTCTCGccc        <  4:268721/149‑1 (MQ=255)                                                                                                                                              ccgccTCGTGCGGCCTGT‑‑TTCGT‑TTTCGCCAGCCGCGAGCACGGTCATTGTCGAAGGTCACAGTGCCTTCAGGGGTGGCGCTAACCAGGTGCTACCGCTTCACCCCTTCATAACTGTCCAGCGTATCGCGTGCAATCTCTCGCCCCAgg    >  5:265903/1‑149 (MQ=255)                                                                                                                                               cgccTCGTGCGGCCTGT‑‑TTCGT‑TTTCGCCAGCCGCGAGCACGGTCATTGTCGAAGGTGACAGTGCCTTCAGGGGTGGCGCTAACCAGGTGCTACCGCTTCACCCCTTCATAACTGTCCAGCGTATCGCGTGCAATCTCTCGCCCCAggg   <  8:75397/149‑1 (MQ=255)                                                                                                                                               cgccTCGTGCGGCCTGT‑‑TTCGT‑TTTCGCCAGCCGCGAGCACGGTCATTGTCGAAGGTCACAGTGCCTTCAGGGGTGGCGCTAACCAGGTGCTACCGCTTCACCCCTTCATAACt                                      >  3:246929/1‑114 (MQ=255)                                                                                                                                               cgccTCGTGCGGCCTGT‑‑TTCGT‑TTTCGCCAGCCGCGAGCACGGTCATTGTCGAAGGTCACAGTGCCTTCAGGGGTGGCGCTAACCAGGTGCTACCGCTTCACCCCTTCATAACt                                      <  4:246929/114‑1 (MQ=255)                                                                                                                                               cgccTCGTGCGGCCTGT‑‑TTCGT‑TTTCGCCAGCCGCGAGCACGGTCATTGTCGAAGGTCACAGTGCCTTCAGGGGTGGCGCTAACCAGGTGCTACCGCTTCACCCCTTCATAACTGTCCAGCGTATCGCGTGCAATCTCTCGCCCCAggg   <  6:265903/149‑1 (MQ=255)                                                                                                                                                gccTCGTGCGGCCTGT‑‑TTCGT‑TTTCGCCAGCCGCGAGCACGGTCATTGTCGAAGGTCACAGTGCCTTCAGGGGTGGCGCTAACCAGGTGCTACCGCTTCACCCCTTCATAACTGTCCAGCGTATCGCGTGCAATCTCTCGCCCCAGGGc  >  5:207550/1‑149 (MQ=255)                                                                                                                                                 ccTCGTGCGGCCTGT‑‑TTCGT‑TTTCGCCAGCCGCGAGCACGGTCATTGTCGAAGGTCACAGTGCCTTCAGGGGTGGCGCTAACCAGGTGCTACCGCTTCACCCCTTCATAACTGTCCAGCGTATCGCGTGCAATCTCTCGCCCCAGGGc  >  4:82149/1‑148 (MQ=255)                                                                                                                                                     |                                                                                                                                                   CCACCGACGAAGAGAAGCAGCAGATTCGCCGCTACCTCGCGTCACGTGCTGGCCAGCAGGACTTTGCCGCTTACCGCAAGCAGCTGGAAGCCAATGCAGACATCACCCGTTACTAAGGTGTTCGTTGCATGAAGAAACAGGCCGCCTCGTGCGGCCTGT‑‑TTCGT‑TTTCGCCAGCCGCGAGCACGGTCATTGTCGAAGGTCACAGTGCCTTCAGGGGTGGCGCTAACCAGGTGCTACCGCTTCACCCCTTCATAACTGTCCAGCGTATCGCGTGCAATCTCTCGCCCCAGGGC  >  NC_002947/2635295‑2635586

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: ‑