Predicted mutation
evidence	seq id	position	mutation	freq	annotation	gene	description
RA	NC_002947	3,727,133	Δ1 bp	7.8%	coding (346/645 nt)	PP_3292 →	membrane protein

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NC_002947	3,727,133	0	A	.	7.8%	148.2 / 7.7	51	coding (346/645 nt)	PP_3292	membrane protein
Reads supporting (aligned to +/- strand):  ref base A (23/22);  new base . (2/2);  total (25/26)
Fisher's exact test for biased strand distribution p-value = 1.00e+00
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 5.93e-01

AGCGGGGCGTGAAGCGCACCGTTGGCAAAGCCATTTTCAACGGCCAGGAGACAGGCTGGCAGGCCAGACTGGCGTTCCTTCGCTCAGTGGCTCGGGAATCGAACATCCTGCTGGTGGTGCTGTTGTGCCTG‑GCCCTGCTGGGCACAGGCACCTTTTGGCTGGCAGGGCGCTCAGTGACGCAGATCGTGGCGAACTGCGAGGCCAACCTGCAGGCTCAAGTGGATATACCCGAAGATGAAAAACTCACCGCGCTTCTCGGCAAACCGGTGTGCACGTGCCTGGCGCAGACCT  >  NC_002947/3726990‑3727280                                                                                                                                                 |                                                                                                                                                    aGCGGGGCGTGAAGCGCACCGTTGGCAAAGCCATTTTCAACGGCCAGGAGACAGGCTGGCAGGCCAGACTGGCGTTCCTTCGCTCAGTGGCTCGGGAATCGAACATCCTGCTGGTGGTGCTGTTGTGCCTG‑GCCCTGCTGGGCACAgg                                                                                                                                                 >  3:321310/1‑148 (MQ=255)   cGGGGCGTGAAGCGCACCGTTGGCAAAGCCATTTTCAACGGCCAGGAGACAGGCTGGCAGGCCAGACTGGCGTTCCTTCGCTCAGTGGCTCGGGAATCGAACATCCTGCTGGTGGTGCTGTTGTGCCTG‑GCCCTGCTGGGCACAGGCAc                                                                                                                                              <  5:120950/149‑1 (MQ=255)      ggCGTGAAGCGCACCGTTGGCAAAGCCATTTTCAACGGCCAGGAGACAGGCTGGCAGGCCAGACTGGCGTTCCTTCGCTCAGTGGCTCGGGAATCGAACATCCTGCTGGTGGTGCGGTTGTGCCTGTGCCCAGCAGGGC‑CAGGCAcaac                                                                                                                                           <  7:170540/149‑4 (MQ=255)         gTGAAGCGCACCGTTGGCAAAGCCATTTTCAACGGCCAGGAGACAGGCTGGCAGGCCAGACTGGCGTTCCTTCGCTCAGTGGCTCGGGAATCGAACATCCTGCTGGTGGTGCTGTTGTGCCTG‑GCCCTGCTGGGCACAGGCACCTTTtg                                                                                                                                        <  4:299130/149‑1 (MQ=255)          tGAAGCGCACCGTTGGCAAAGCCATTTTCAACGGCCAGGAGACAGGCTGGCAGGCCAGACTGGCGTTCCTTCGCTCAGTGGCTCGGGAATCGAACATCCTGCTGGTGGTGCTGTTGTGCCTG‑GCCCTGCTGGGCACAGGc                                                                                                                                                >  3:313151/1‑140 (MQ=255)          tGAAGCGCACCGTTGGCAAAGCCATTTTCAACGGCCAGGAGACAGGCTGGCAGGCCAGACTGGCGTTCCTTCGCTCAGTGGCTCGGGAATCGAACATCCTGCTGGTGGTGCTGTTGTGCCTG‑GCCCTGCTGGGCACAGGc                                                                                                                                                <  4:313151/140‑1 (MQ=255)                   ccGTTGGCAAAGCCATTTTCAACGGCCAGGAGACAGGCTGGCAGGCCAGACTGGCGTTCCTTCGCTCAGTGGCTCGGGAATCGAACATCCTGCTGGTGGTGCTGTTGTGCCTG‑GCCCTGCTGGGCACAGGCACCTTTTGGCTGGCAggg                                                                                                                              >  5:153829/1‑149 (MQ=255)                    cGTTGGCAAAGCCATTTTCAACGGCCAGGAGACAGGCTGGCAGGCCAGACTGGCGTTCCTTCGCTCAGTGGCTCGGGAATCGAACATCCTGCTGGTGGTGCTGTTGTGCCTG‑GCCCTGCTGGGCACAGGCACCTTTTGGCTGGCAGGgc                                                                                                                             >  5:238249/1‑149 (MQ=255)                             aGCCATTTTCAACGGCCAGGAGACAGGCTGGCAGGCCAGACTGGCGTTCCTTCGCTCAGTGGCTCGGGAATCGAACATCCTGCTGGTGGTGCTGTTGTGCCTG‑GCCCTGCTGGGCACAGGCAc                                                                                                                                              <  1:80964/123‑1 (MQ=255)                             aGCCATTTTCAACGGCCAGGAGACAGGCTGGCAGGCCAGACTGGCGTTCCTTCGCTCAGTGGCTCGGGAATCGAACATCCTGCTGGTGGTGCTGTTGTGCCTG‑GCCCTGCTGGGCACAGGCAc                                                                                                                                              >  2:80964/1‑123 (MQ=255)                               ccATTTTCAACGGCCAGGAGACAGGCTGGCAGGCCAGACTGGCGTTCCTTCGCTCAGTGGCTCGGGAATCGAACATCCTGCTGGTGGTGCTGTTGTGCCTG‑GCCCTGCTGGGCACAGGCACCTTTTGGCTGGCAGGGCGCTCAGTGACg                                                                                                                  <  2:264648/149‑1 (MQ=255)                               ccATTTTCAACGGCCAGGAGACAGGCTGGCAGGCCAGACTGGCGTTCCTTCGCTCAGTGGCTCGGGAATCGAACATCCTGCGGGTGGTGCTGTTGTGCCTG‑GCCCTGCTGGGCACAGGCACCTTTTGGCTGGCAGGGCGCTCAGTGACg                                                                                                                  <  4:26702/149‑1 (MQ=255)                                            ccAGGAGACAGGCTGGCAGGCCAGACTGGCGTTCCTTCGCTCAGTGGCTCGGGAATCGAACATCCTGCTGGTGGTGCTGTTGTGCCTG‑GCCCTGCTGGGCACAGGCACCTTTTGGCTGGCAGGGCGCTCAGTGACGCAGATCGTGGc                                                                                                       <  6:347184/147‑1 (MQ=255)                                                   aCAGGCTGGCAGGCCAGACTGGCGTTCCTTCGCTCAGTGGCTCGGGAATCGAACATCCTGCTGGTGGTGCTGTTGTGCCTGTGCCCAGCAGGGC‑CAGGCAcaac                                                                                                                                           <  5:402941/104‑4 (MQ=37)                                                   aCAGGCTGGCAGGCCAGACTGGCGTTCCTTCGCTCAGTGGCTCGGGAATCGAACATCCTGCTGGTGGTGCTGTTGTGCCTGTGCCCAGCAGGGC‑CAGGCAcaac                                                                                                                                           >  6:402941/1‑101 (MQ=37)                                                     aGGCTGGCAGGCCAGACTGGCGTTCCTTCGCTCAGTGGCTCGGGAATCGAACATCCTGCTGGTGGTGCTGTTGTGCCTG‑GCCCTGCTGGGCACAGGCACCTTTTGGCTGGCAGGGCGCTCAGTGACGCAGATCGTGGCGAACTGCGAgg                                                                                            <  5:155827/149‑1 (MQ=255)                                                     aGGCTGGCAGGCCAGACTGGCGTTCCTTCGCTCAGTGGCTCGGGAATCGAACATCCTGCTGGTGGTGCTGTTGTGCCTG‑GCCCTGCTGGGCACAGGCACCTTTTGGCTGGCAGGGCGCTCAGTGACGCAGATCGTGGCGAACTGCGAgg                                                                                            >  4:164123/1‑149 (MQ=255)                                                       gCTGGCAGGCCAGACTGGCGTTCCTTCGCTCAGTGGCTCGGGAATCGAACATCCTGCTGGTGGTGCTGTTGTGCCTG‑GCCCTGCTGGGCACAGGCACCTTTTGGCTGGCAGGGCGCTCAGTGACGCAGATCGTGGCGAACTGCGAGGc                                                                                           >  5:2285/1‑148 (MQ=255)                                                          ggcctgCCAGCCTGGCGTTCCTTCGCTCAGTGGCTCGGGAATCGAACATCCTGCTGGTGGTGCTGTTGTGCCTG‑GCCCTGCTGGGCACAGGCACCTTTTGGCTGGCAGGGCGCTCAGTGACGCAGATCGTGGCGaa                                                                                                    <  3:95235/131‑1 (MQ=255)                                                          ggcctgCCAGCCTGGCGTTCCTTCGCTCAGTGGCTCGGGAATCGAACATCCTGCTGGTGGTGCTGTTGTGCCTG‑GCCCTGCTGGGCACAGGCACCTTTTGGCTGGCAGGGCGCTCAGTGACGCAGATCGTGGCGaa                                                                                                    >  4:95235/6‑136 (MQ=255)                                                          ggCAGGCCAGACTGGCGTTCGTTCGCTCTGTGGCTCGGTAATCGTACATCCTGCTGGTGGTGCTGTTGTGCCTG‑GCGGTGCTGGGCTCAGGCAGGTTTTGGGTGGCAGGGCGCTCAGTGACGAAGTTCGTGGCGATCTTCGAGGCCAAc                                                                                       <  6:47307/149‑1 (MQ=255)                                                             aGGCCAGACTGGCGTTCCTTCGCTCAGTGGCTCGGGAATCGAACATCCTGCTGGTGGTGCTGTTGTGCCTG‑GCCCTGCTGGGCACAGGCACCTTTTGGCTGGCAGGGCGCTCAGTg                                                                                                                     <  4:351458/116‑1 (MQ=255)                                                              ggcaccaCTGGCGTTCGTTCGCCCCGTGGCCCGGCAAGCCACCATCCTCCGGGTGGGGCTGTGGTGCCTG‑CCCCTGCTGGCCACTGGCACCTTTTGGCTGGCAGGGCGCTCAGTGACGCAGATCGTGGCGAACTGCGAGGCCAACCTGc                                                                                   <  1:121385/143‑1 (MQ=255)                                                                  aGACTGGCGTTCCTTCGCTCAGTGGCTCGGGAATCGAACATCCTGCTGGTGGTGCTGTTGTGCCTG‑GCCCTGCTGGGCTCAGGCACCTTTTGGCTGGCAGGGCGCTCAGTGACGCAGATCGTGGCGAACTGCGAGGCCAACCTGCAGGc                                                                               <  6:2285/149‑1 (MQ=255)                                                                    aCTGGCGTTCCTTCGCTCAGTGGCTCGGGAATCGAACATCCTGCTGGTGGTGCTGTTGTGCCTG‑GCCCTGCTGGGCACAGGCACCTTTTGGCTGGCAGGGCGCTCAGTGACGCAGATCGTGGCGAACTGCGAGGCCAACCTGCAGGCt                                                                              >  3:54313/1‑148 (MQ=255)                                                                      tGGCGTTCCTTCGCTCAGTGGCTCGGGAATCGAACATCCTGCTGGTGGTGCTGTTGTGCCTG‑GCCCTGCTGGGCACAGGCACCTTTTGGCTGGCAGGGCGCTCAGTGACGCAGATCGTGGCGAACTGCGAGGCCAACCTGCAGGCTCaa                                                                           >  5:157048/1‑149 (MQ=255)                                                                          gTTCCTTCGCTCAGTGGCTCGGGAATCGAACATCCTGCTGGTGGTGCTGTTGTGCCTG‑GCCCTGCTGGGCACAGGCACCTTTTGGCTGGCAGGGCGCTCAGTGACGCAGATCGTGGCGAACTGCGAGGCCAACCTGCAGGCTCAAGTgg                                                                       <  4:321310/149‑1 (MQ=255)                                                                          gTTCCTTCGCTCAGTGGCTCGGGAATCGAACATCCTGCTGGTGGTGCTGTTGTGCCTG‑GCCCTGCTGGGCACAGGCACCTTTTGGCTGGCAGGGCGCTCAGTGACGCAGATCGTGGCGAACTGCGAGGCCAACCTGCAGGCTCAAGTg                                                                        >  7:174489/1‑148 (MQ=255)                                                                               ttCGCTCAGTGGCTCGGGAATCGAACATCCTGCTGGTGGTGCTGTTGTGCCTG‑GCCCTGCTGGGCACAGGCACCTTTTGGCTGGCAGGGCGCTCAGTGACGCAGATCGTGGCGAACTGCGAGGCCAACCTg                                                                                    <  4:372254/131‑1 (MQ=255)                                                                               ttCGCTCAGTGGCTCGGGAATCGAACATCCTGCTGGTGGTGCTGTTGTGCCTG‑GCCCTGCTGGGCACAGGCACCTTTTGGCTGGCAGGGCGCTCAGTGACGCAGATCGTGGCGAACTGCGAGGCCAACCTg                                                                                    >  3:372254/1‑131 (MQ=255)                                                                                 cGCTCAGTGGCTCTGGAATGGAACATCCTGCTGGTGGTGCTGTTGTGGCTG‑GCCCTGCTGGGCACAGGCACCTTTTGGCTGGCAGGGCTCTCAGTGACGCAGATCGTGGCGAACTGCGAGGCCAACCTGCAGGCTCAAGTGGATATAc                                                                 <  7:385986/148‑1 (MQ=255)                                                                                          gCTCGGGAATCGAACATCCTGCTGGTGGTGCTGTTGTGCCTG‑GCCCTGCTGGGCACAGGCACCTTTTGGCTGGCAGGGCGCTCAGTGACGCAGATCGTGGCGAACTGCGAGGCCAACCTGCAGGCTCAAGTGGATATAccc                                                               <  7:272237/141‑1 (MQ=255)                                                                                          gCTCGGGAATCGAACATCCTGCTGGTGGTGCTGTTGTGCCTG‑GCCCTGCTGGGCACAGGCACCTTTTGGCTGGCAGGGCGCTCAGTGACGCAGATCGTGGCGAACTGCGAGGCCAACCTGCAGGCTCAAGTGGATATAccc                                                               >  8:272237/1‑141 (MQ=255)                                                                                            tCGGGAATCGAACATGCTGCTGGTGGTGCTGTTTTGCCTG‑GCCCTGATGGGCACAGGCACCTTTTGGCTGGCAGGGCGATAAGTGACGCAGATCGTGGCGAACTGAGAGGCCAACCTGCAGGCAAAATTGGATAAACACGAAGATGaa                                                      >  6:292418/1‑148 (MQ=255)                                                                                            tCGGGAATCGAACATCCTGCTGGTGGTGCTGTTGTGCCTG‑GCCCTGCTGGGCACAGGCACCTTTTGGCTGGCAGGGCGCTCAGTGACGCAGATCGTGGCGAACTGCGAGGCCAACCTGCAGGCTCAAGTGGATATACCCGAAGATGaa                                                      >  6:11238/1‑148 (MQ=255)                                                                                                           ccTGCTGGTGGTGCTGTTGTGCCTG‑GCCCTGCTGGGCACAGGCACCTTTTGGCTGGCAGGGCGCTCAGTGACGCAGATCGTGGCGAACTGCGAGGCCAACCTGCAGGCTCAAg                                                                          >  4:229082/1‑113 (MQ=255)                                                                                                           ccTGCTGGTGGTGCTGTTGTGCCTG‑GCCCTGCTGGGCACAGGCACCTTTTGGCTGGCAGGGCGCTCAGTGACGCAGATCGTGGCGAACTGCGAGGCCAACCTGCAGGCTCAAg                                                                          <  3:229082/113‑1 (MQ=255)                                                                                                              gctgGTGGTGCTGTTGTGCCTG‑GCCCTGCTGGGCACAGGCACCTTTTGGCTGGCAGGGCGCTCAGTGACGCAGATCGTGGCGAACTGCGAGGCCAACCTGCAGGCTCAAGTGGATATAc                                                                 >  8:185560/1‑119 (MQ=255)                                                                                                              gctgGTGGTGCTGTTGTGCCTG‑GCCCTGCTGGGCACAGGCACCTTTTGGCTGGCAGGGCGCTCAGTGACGCAGATCGTGGCGAACTGCGAGGCCAACCTGCAGGCTCAAGTGGATATAc                                                                 <  7:185560/119‑1 (MQ=255)                                                                                                                           ttgtGCCTG‑GCCCTGCTTGGCACAGGCACCTTTTGGCTGGCAGGGCGCTCAGTGACGCAGATCGTGGCGAACTGCGAGGCCAACCTGCAGGCTCAAGTGGATATACCCGAAGATGAAAAACTCACCGCGCTTCTCGGCAAACCGgtgt                       <  6:238249/148‑1 (MQ=255)                                                                                                                           ttgtGCCTG‑GCCCTGCTGGGCACAGGCACCTTTTGGCTGGCAGGGCGCTCAGTGACGCAGATCGTGGCGAACTGCGAGGCCAACCTGCAGGCTCAAGTGGATATACCCGAAGATGAAAAACTCACCGCGCTTCTCGGCAAACCGGtgtg                      <  6:157048/149‑1 (MQ=255)                                                                                                                           ttgtGCCTG‑GCCCTGCTGGGCACAGGCACCTTTTGGCTGGCAGGGCGCTCAAGGACGCAGATCGTGGCGAACTGCGAGGGCCACCGGGAGGGTGAAGTGGATATACCCGAAGCTGAAAAACTCACCGCGCTTCTGGGCAAACCGGtgtg                      >  1:101190/1‑149 (MQ=255)                                                                                                                             gtgCCTG‑GGCCTGCTGGGCACAGGCACCTTTTGGCTGGCAGGGCGCTCAGTGACGCAGATCGTGGCGAACTGCGAGGCCAACATGCATGCTCATGTGGATATACCCGAAGATGAAAAACTCACCGCGCTTCTCGGCAAACCGGTGTGc                     <  5:292418/148‑1 (MQ=255)                                                                                                                                cctgtgCCCAGCAGGGC‑CAGGCACCTTTTGGCTGGCAGGGCGCTCAGTGACGCAGATCGTGGCGAACCGCGAGGCCAACCTGCAGGCTCAAGTGGATATACCCGAAGATGAAAAACTCACCGCGCTTCTCGGCAAACCGGTGTGCACGt                 >  8:317104/6‑149 (MQ=255)                                                                                                                                ccTG‑GCCCTGCTGGGCACAGGCACCTTTTGGCTGGCAGGGCGCTCAGTGACGCAGATCGTGGCGAACTGCGAGGCCAACCTGCAGGCTCAAGTGGATATACCCGAAGATGAAAAACTCACCGCGCTTCTCGGCAAACCGGTGTGCACGt                 <  7:376951/149‑1 (MQ=255)                                                                                                                                 cTG‑GCCCTGCTGGGCACAGGCACCTTTTGGCTGGCAGGGCGCTCAGTGACGCAGATCGTGGCGAACTGCGAGGCCAACCTGCAGGCTCAAGTGGATATACCCGAAGATGAAAAACTCACCGCGCTTCTCGGCAAACCGGTGTGCACGTg                >  4:67761/1‑149 (MQ=255)                                                                                                                                   g‑gCCCTGCTGGGCACAGGCACCTTTTGGCTGGCAGGGCGCTCAGTGACGCAGATCGTGGCGAACTGCGAGGCCAACCTGCAGGCTCAAGTGGATATACCCGAAGATGAAAACCTCACCGCGCTTCTCGGCAAACCGGTGTGCACGTGcc              >  8:263007/1‑149 (MQ=255)                                                                                                                                     gCCCTGCTGGGCACAGGCACCTTTTGGCTGGCAGGGCGCTCAGTGACGCAGATCGTGGCGAACTGCGAGGCCAACCTGCAGGCTCAAGTGGATATACCCGAAGATGAAAAACTCACCGCGCTTCTCGGCAAACCGGTGTGCACGTGCCt             >  1:268060/1‑149 (MQ=255)                                                                                                                                       ccTGCTGGGCACAGGCACCTTTTGGCTGGCAGGGCGCTCAGTGACGCAGATCGTGGCGAACTGCGAGGCCAACCTGCAGGCTCAAGTGGATATACCCGAAGATGAAAAACTCACCGCGCTTCTCGGCAAACCGGTGTGCACGTGCCTgg           >  4:354340/1‑149 (MQ=255)                                                                                                                                           ctgGGCACAGGCACCTTTTGGCTGGCAGGGCGCTCAGTGACGCAGATCGTGGCGAACTGCGAGGCCAACCTGCAGGCTCAAGTGGATATACCCGAAGATGAAAAACTCACCGCGCTTCTCGGCAAACCGGTGTGCACGTGCCTGGCGCa       <  3:164123/149‑1 (MQ=255)                                                                                                                                            tgGGCACAGGCACCTTTTGGCTGGCAGGGCGCTCAGTGACGCAGATCGTGGCGAACTGCGAGGCCAACCTGCAGGCTCAAGTGGATATACCCGAAGATGAAAAACTCACCGCGCTTCTCGGCAAACCGGTGTGCACGTGCCTGGCGCAg      >  1:402782/1‑149 (MQ=255)                                                                                                                                                cacaGGCACCTTTTGGCTGGCAGGGCGCTCAGTGACGCAGATCGTGGCGAACTGCGAGGCCAACCTGCAGGCTCAAGTGGATATACCCGAAGATGAAAAACTCACCGCGCTTCTCGGCAAACCGGTGTGCACGTGCCTGGCGCAGACCt  <  3:67761/149‑1 (MQ=255)                                                                                                                                                cacaGGCACCTTTTGGCTGGCAGGGCGCTCAGTGACGCAGATCGTGGCGAACTAAGAGGCCAACCTGCAGGCTCAAGTGGATATACCAGAAGATGAAAAACTCACCGCGCTTCTCGGCAAACAGGTGTGCACGTGCCAGGCGCAGAcc   >  1:314293/1‑148 (MQ=255)                                                                                                                                                 |                                                                                                                                                    AGCGGGGCGTGAAGCGCACCGTTGGCAAAGCCATTTTCAACGGCCAGGAGACAGGCTGGCAGGCCAGACTGGCGTTCCTTCGCTCAGTGGCTCGGGAATCGAACATCCTGCTGGTGGTGCTGTTGTGCCTG‑GCCCTGCTGGGCACAGGCACCTTTTGGCTGGCAGGGCGCTCAGTGACGCAGATCGTGGCGAACTGCGAGGCCAACCTGCAGGCTCAAGTGGATATACCCGAAGATGAAAAACTCACCGCGCTTCTCGGCAAACCGGTGTGCACGTGCCTGGCGCAGACCT  >  NC_002947/3726990‑3727280

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: ‑