Predicted mutation
evidence	seq id	position	mutation	freq	annotation	gene	description
RA	NC_002947	2,984,778	T→A	8.3%	N209I (AAC→ATC)	PP_2611 ←	membrane protein

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NC_002947	2,984,778	0	T	A	8.3%	124.2 / 3.6	48	N209I (AAC→ATC)	PP_2611	membrane protein
Reads supporting (aligned to +/- strand):  ref base T (20/24);  new base A (2/2);  total (22/26)
Fisher's exact test for biased strand distribution p-value = 1.00e+00
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 8.73e-01

TTGTAGGGAAACAGCACGGCCCAGAACGGCAATTGCCAGTTCTTTTTACCCTGCATTTCACCGGGCTCGCCGGTTCGCCAAGGTGCATAGTGGCGCCAGGCTTCTGCCGGGGTCAGGCAGATGGCGTGCAGTGGCTTGTGCCACCAGTTGGGTT‑CACCGGGCGGAGGGAGTTTGTCCGGGCCGTGATCCATGAAGTGGCGGAGGTATTCCCATACCTCGGCGACATGCTTGACGCCGGGTTCGGTGGGTTCGTTACTGTCGACCCAGAGGCAGTCTTTTTGGTGCAGGCTGCCGTC  >  NC_002947/2984631‑2984926                                                                                                                                                    |                                                                                                                                                      ttGTAGGGAAACAGCACGGCCCAGAACGGCAATTGCCAGTTCTTTTTACCCTGCATTTCACCGGGCTCGCCGGTTCGCCAAGGTGCATAGTGGCGCCAGGCTTCTGCCGGGGTCAGGCAGATGGCGTGCAGTGGCTTGTGCCACCAGtt                                                                                                                                                      <  2:73293/149‑1 (MQ=37)    tAGGGAAACAGCACGGCCCAGAACGGCAATTGCCAGTTCTTTTTACCCTGCATTTCACCGGGCTCGCCGGTTCGCCAAGGTGCATAGTGGCGCCAGGCTTCTGCCGGGGTCAGGCAGATGGCGTGCAGTGGCTTGTGCCACCAGTTggg                                                                                                                                                   <  2:203532/149‑1 (MQ=37)       ggAAACAGCACGGCCCAGAACGGCAATTGCCAGTTCTTTTTACCCTGCATTTCACCGGGCTCGCCGGTTCGCCAAGGTGCATAGTGGCGCCAGGCTTCTGCCGGGGTCAGGCAGATGGCGTGCAGTGGCTTGTGCCACCAGTTGGGtt                                                                                                                                                 >  8:156611/1‑148 (MQ=37)           aCAGCAAGGCCCAGAACGGCAATAGACAGTAATATTTACCCTGCATTTCACCGGGCTCGACGCATCGCCAAGGTGCATACTGGCGCCACGCATCTGCCGGGGTCAGGAAGATGGAGTGCAGAGGCTAGTGCCACCAGTTGCGTT‑CACCg                                                                                                                                           >  4:184223/1‑149 (MQ=11)               cACGGCCCAGAACGGCAATTGCCAGTTCTTTTTACCCTGCATTTCACCGGGCTCGCCGGTTCGCCAAGGTGCATAGTGGCGCCAGGCTTCTGCCGGGGTCAGGCAGATGGCGTGCAGTGGCTTGTGCCACCAGTTGGGTT‑CACCGGGCg                                                                                                                                       >  6:101598/1‑149 (MQ=37)                 cGGCCCAGAACGGCAATTGCCAGTTCTTTTTACCCTGCATTTCACCGGGCTCGCCGGTTCGCCAAGGTGCATAGTGGCGCCAGGCTTCTGCCGGGGTCAGGCAGATGGCGTGCAGTGGCTTGTGCCACCAGTTGGGTT‑CACCGGGCgga                                                                                                                                     <  1:199388/149‑1 (MQ=38)                     ccAGAACGGCAATTGCCAGTTCTTTTTACCCTGCATTTCACCGGGCTCGCCGGTTCGCCAAGGTGCATAGTGGCGCCAGGCTTCTGCCGGGGTCAGGCAGATGGCGTGCAGTGGCTTGTGCCACCAGTTGGGTT‑CACCGGGCggagg                                                                                                                                   >  1:353843/1‑147 (MQ=39)                     ccAGAACGGCAATTGCCAGTTCTTTTTACCCTGCATTAAACCGGGCACGCCGGTTCGCCAACGTGCAAAATGGCGCCAGGCTTCTGTAGGGGTGAGGCAGATGGCGTGCAGTTGCTTGTGGCACCAGTTGGGTT‑CACCGGGCggaggga                                                                                                                                 >  1:279134/1‑149 (MQ=14)                            ggCAATTGCCAGTTCTTTTTACCCTGCATTTCACCGGGCTCGCCGGTTCGCCAAGGTGCATAGTGGCGCCAGGCTTCTGCCGGGGTCAGGCAGATGGCGTGCAGTGGCTTGTGCCACCAGTTGGGTT‑CACCGGGCGGAGGGAGTTTGTc                                                                                                                          <  5:101598/149‑1 (MQ=39)                              cAATTGCCAGCTCTTTTTACCCTGCATTTCACCGGGCTCGCCGGTTCGCCAAGGTGCATAGTGGCGCCAGGCTTCTGCCGGGGTCAGGCAGATGGCGTGCAGTGGCTTGTGCCACCAGTTGGGTT‑CACCGGGCGGAGGGAGTTTGTCCg                                                                                                                        <  6:352882/149‑1 (MQ=255)                                           tttttACCCTGCATTTCACCGGGCTCGCCGGTTCGCCAAGGTGCATAGTGGCGCCAGGCTTCTGCCGGGGTCAGGCAGATGGCGTGCAGTGGCTTGTGCCACCAGTTGGGTT‑CACCGGGCGGAGGGAGTTTGTCCGGGCCGTGAt                                                                                                               <  6:383520/145‑1 (MQ=40)                                           tttttACCCTGCATTTCACCGGGCTCGCCGGTTCGCCAAGGTGCATAGTGGCGCCAGGCTTCTGCCGGGGTCAGGCAGATGGCGTGCAGTGGCTTGTGCCACCAGTTGGGTT‑CACCGGGCGGAGGGAGTTTGTCCGGGCCGTGAt                                                                                                               >  5:383520/1‑145 (MQ=40)                                                aCCCTGCATTTCACCGGGCTCGCCGGTTCGCCAAGGTGCATAGTGGCGCCAGGCTTCTGCCGGGGTCAGGCAGATGGCGTGCAGTGGCTTGTGCCAACAGTTGGGTT‑CACCGGGCGGAGGGAGTTTGTCCGGGCCGTGATCCATGAAGt                                                                                                      >  6:102077/1‑149 (MQ=255)                                                   cTGCATTTCACCGGGCTCGCCGGTTCGCCAAGGTGCATAGTGGCGCCAGGCTTCTGCCGGGGTCAGGCAGATGGCGTGCAGTGGCTTGTGCCACCAGTTGGGTT‑CACCGGGCGGAGGGAGTTTGTCCGGGc                                                                                                                     >  8:89604/1‑131 (MQ=37)                                                    tGCATTTCACCGGGCTCGCCGGTTCGCCAAGGTGCATAGTGGCGCCAGGCTTCTGCCGGGGTCAGGCAGATGGCGTGCAGTGGCTTGTGCCACCAGTTGGGTT‑CACCGGGCGGAGGGAGTTTGTCCGGGCCGTGATGCATGAAGTg                                                                                                     <  2:59653/146‑1 (MQ=255)                                                    tGCATTTCACCGGGCTCGCCGGTTCGCCAAGGTGCATAGTGGCGCCAGGCTTCTGCCGGGGTCAGGCAGATGGCGTGCAGTGGCTTGTGCCACCAGTTGGGTT‑CACCGGGCGGAGGGAGTTTGTCCGGGCCGTGATCCATGAAGTg                                                                                                     >  1:59653/1‑146 (MQ=39)                                                       ttttCACCGGGCTCGCCGGTTCGCCAAGGTGCATAGTGGCGCCAGGTTTCTGCCGGGGTCAGGCAGATGGCGTGCAGTGGCTTGTGCCACCAGTTGGGTT‑CACCGGGCGGAGGGAGTTTGTCCGGGCCGTGATCCATGAAGTGGCGGAg                                                                                               <  7:77755/148‑1 (MQ=255)                                                         ttCACCGGGCTCGCCGGTTCGCCAAGGTGCATAGTGGCGCCAGGTTTCTGCCGGGGTCAGGCAGATGGCGTGCAGTGGCTTGTGCCACCAGTTGGGTT‑CACCGGGCGGAGGGAGTTTGTCCGGGCCGTGATCCATGAAGTGGCGGAg                                                                                               >  8:77755/1‑147 (MQ=255)                                                            aCCGGGCTCGCCGGTTCGCCAAGGTGCATAGTGGCGCCAGGCTTCTGCCGGGGTCAGGCAGATGGCGTGCAGTGGCTTGTGCCACCAGTTGGGTT‑CACCGGGCGGAGGGAGTTTGTCCGGGCCGTGATCCATGAAGTGGCGGAGGTAt                                                                                           <  2:353843/148‑1 (MQ=255)                                                              cGGGCTCGCCGGTTCGCCAAGGTGCATAGTGGCGCCAGGCTTCTGCCGGGGTCAGGCAGATGGCGTGCAGTGGCTTGTGCCACCAGTTGGGTT‑CACCGGGCGGAGGGAGTTTGTCCGGGCCGTGATCCATGAAGTGGCGGAGGTATTcc                                                                                        >  1:99226/1‑149 (MQ=255)                                                                 gCTCGCCGGTTCGCCAAGGTGCATAGTGGCGCCAGGCTTCTGCCGGGGTCAGGCAGATGGCGTGCAGTGGCTTGTGCCACCAGTTGGGTT‑CACCGGGCGGAGGGAGTTTGTCCGGGCCGTGATCCATGAAGTGGCGGAGGTATTCCCAt                                                                                     <  2:99226/149‑1 (MQ=255)                                                                 gCTCGCCGGTTCGCCAAGGTGCATAGTGGCGCCAGGCTTCTGCCGGGGTCAGGCAGATGGCGTGCAGTGGCTTGTGCCACCAGTTGGGTT‑CACCGGGCGGAGGGAGTTTGTCCGGGCCGTGATCCATGAAGTGGCGGAGGTATTCCCAt                                                                                     <  1:403404/149‑1 (MQ=255)                                                                   tCGCCGGTTCGCCAAGGTGCATAGTGGCGCCAGGCTTCTGCCGGGGTCAGGCAGATGGCGTGCAGTGGCTTGTGCCACCAGTTGGGTT‑CACCGGGCGGAGGGAGTTTGTCCGGGCCGTGATCCATGAAGTGGCGGAGGTATTCCCATAc                                                                                   >  4:164324/1‑149 (MQ=255)                                                                   gcGCCTGTTCTCCAAGGGGCATACTGGCGCCAGGCTTCTGCCGGGGTCAGGCAGATGGCGTGCAGTGGCTTGTTCCACCAGTTGGGTT‑CACCGGGCGGAGGGAGTTTGTCCGGGCCGTGATCCATGAAGTGGCGGAGGTATTCCCATAc                                                                                   <  6:288884/148‑1 (MQ=11)                                                                     gCCGGTTCGCCAAGGTGCATAGTGGCGCCAGGCTTCTGCCGGGGTCAGGCAGATGGCGTGCAGTGGCTTGTGCCACCAGTTGGGTT‑CACCGGGCGGAGGGAGTTTGTCCGGGCCGTGATCCATGAAGTGGCGGAGGTATTCCCATACCt                                                                                 >  5:389888/1‑149 (MQ=255)                                                                        ggTTCGCCAAGGTGCATAGTGGCGCCAGGCTTCTGCCGGGGTCAGGCAGATGGCGTGCAGTGGCTTGTGCCACCAGTTGGGTT‑CACCGGGCGGAGGGAGTTTGTCCGGGCCGTGATCCATGAAGTGGCGGAGGTATTCCCATACCTCgg                                                                              <  3:164324/149‑1 (MQ=255)                                                                             gCCAAGGTGCATAGTGGCGCCAGGCTTCTGCCGGGGTCAGGCAGATGGCGTGCAGTGGCTTGTGCCACCAGATGGGTT‑CACCGGGCGGAGGGAGTTTGTCCGGGCCGTGATCCATGAAGTGGCGGAGGTATTCCCATACCTCGGCGACa                                                                         >  8:268270/1‑149 (MQ=255)                                                                             gCCAAGGTGCATAGTGGCGCCAGGCTTCTGCCGGGGTCAGGCAGATGGCGTGCAGTGGCTTGTGCCACCAGATGGGTT‑CACCGGGCGGAGGGAGTTTGTCCGGGCCGTGATCCATGAAGTGGCGGAGGTATTCCCATACCTCGGCGACa                                                                         >  8:263488/1‑149 (MQ=255)                                                                                             gcgcCAGGCTTCTGTCGGGGTCAGGCAGATGGCGTGCAGTGGCTTGTGCCACCAGTTGGGTT‑CACCGGGCGGAGGGAGTTTGTCCCGGCCGTGATCCATGAAGTGGCGGAGGTATTCCCATACCTCGGCGACATGCTTGACGCCGGGt                                                          <  2:279134/148‑1 (MQ=21)                                                                                              cgcCAGGCTTCTGCCGGGGTCAGGCAGATGGCGTGCAGTGGCTTGTGCCACCAGTTGGGTT‑CACCGGGCGGAGGGAGTTTGTCCGGGCCGTGATCCATGAAGTGGCGGAGGTATTCCCATACCTCGGCGTCAAGCATGTCGCCgaggta                                                        <  4:342964/149‑6 (MQ=11)                                                                                                   ggCTTCTGCCGGGGTCAGGCAGATGGCGTGCAGTGGCTTGTGCCACCAGTTGGGTT‑CACCGGGCGGAGGGAGTTTGTCCGGGCCGTGATCCATGAAGTGGCGGAGGTATTCCCATACCTCGGCGACATGCTTGACGCCGGGTTCGGTgg                                                   <  7:156611/149‑1 (MQ=34)                                                                                                        cTGCCGGGGTCAGGCAGATGGCGTGCAGTGGCTTGTGCCACCAGTTGGGTT‑CACCGGGCGGAGGGAGTTTGTCCGGGCCGTGATCCATGAAGTGGCGGAGGTATTCCCATACCTCGGCGACATGCTTGACGCCGGGTTCGGTGGGtt                                                <  4:243155/147‑1 (MQ=34)                                                                                                           ccGGGGTCAGGCAGATGGCGTGCAGTGGCTTGTGCCACCAGTTGGGTT‑CACCGGGCGGAGGGAGTTTGTCCGGGCCGTGATCCATGAAGTGGCGGAGGTATTCCCATAcc                                                                                  <  4:94574/110‑1 (MQ=35)                                                                                                           ccGGGGTCAGGCAGATGGCGTGCAGTGGCTTGTGCCACCAGTTGGGTT‑CACCGGGCGGAGGGAGTTTGTCCGGGCCGTGATCCATGAAGTGGCGGAGGTATTCCCATAcc                                                                                  >  3:94574/1‑110 (MQ=35)                                                                                                           ccGGGGTCAGGCAGATGGCGTGCAGTGGCTTGTGCCACCAGTTGGGTT‑CACCGGGCGGAGGGAGTTTGTCCGGGCCGTGATCCATGAAGTGGCGGAGGTATTCCCATACCTCGGCGACATGCTTGACGCCGGGTTCGGTGGGTTCGTTa                                           <  6:389888/149‑1 (MQ=34)                                                                                                                   aGGCAGATGGCGTGCAGTGGCTTGTGCCACCAGTTGGGTT‑CACCGGGCGGAGGGAGTTTGTCCGGGCCGTGATCCATGAAGTGGCGGAGGTATTCCCATACCTCGGCGACATGCTTGACGCCGGGATCGGTGGGTTCGTTACTGTCGAc                                   >  5:417238/1‑149 (MQ=21)                                                                                                                        gATGGCGTGCAGTGGCTTGTGCCACCAGTTGGGTTGCACCGGGCGGAGGGAGTTTGTCCGGGCCGTGATCCATGAAGTGGCGGAGGTATTCCCATACCTCGGCGACATGCTTGACGCCGGGTTCGGTGGGTTCGTTACTGTCGAcc                                  >  1:61015/1‑146 (MQ=21)                                                                                                                                gCAGTGGCTTGTGCCACCAGTTGGGTT‑CACCGGGCGGAGGGAGTTTGTCCGGGCCGTGATCCATGAAGTGGCGGAGGTATTCCCATACCTCGGCGACATGCTTGACGCCGGGTTCGGTGGGTTCGTTACTGTCGACCCAGAGGCAGTCt                      >  4:232655/1‑149 (MQ=34)                                                                                                                                  aGTGGCTTGTGCCACCAGATGGGTT‑CACCGGGCGGAGGGAGTTTGTCCGGGCCGTGATCCATGAAGTGTCGGAGGTATTCCCATACCTCGGCGACATGCTTGACGCCGGGTTCGGTGGGTTCGTTACTGTCGACCCAGAGGCAGTCttt                    <  7:268270/149‑1 (MQ=21)                                                                                                                                  aGTGGCTTGTGCCACCAGATGGGTT‑CACCGGGCGGAGGGAGTTTGTCCGGGCCGTGATCCATGAAGTGGCGGAGGTATTCCCATACCTCGGCGACATGCTTGACGCCGGGTTCGGTGGGTTCGTTACTGTCGACCCAGAGGCAGTCttt                    <  7:263488/149‑1 (MQ=21)                                                                                                                                    tGGCTTGTGCCACCAGTTGGGTT‑CACCGGGCGGAGGGAGTTTGTCCGGGCCGTGATCCATGAAGTGGCGGAGGTATTCCCATACCTCGGCGACATGCTTGACGCCGGGTTCGGTGGGTTCGTTACt                                         <  1:356107/126‑1 (MQ=35)                                                                                                                                    tGGCTTGTGCCACCAGTTGGGTT‑CACCGGGCGGAGGGAGTTTGTCCGGGCCGTGATCCATGAAGTGGCGGAGGTATTCCCATACCTCGGCGACATGCTTGACGCCGGGTTCGGTGGGTTCGTTACt                                         >  2:356107/1‑126 (MQ=35)                                                                                                                                     ggCTTGTGCCACCAGTTGGGTT‑CACCGGGCGGAGGGAGTTTGTCCGGGCCGTGATCCATGAAGTGGCGGAGGTATTCCCATACCTCGGCGACATGCTTGACGCCGGGTTCGGTGGGTTCGTTACTGTCGACCCAGAGGCAGTCTTTTTg                 <  5:195924/149‑1 (MQ=34)                                                                                                                                     ggCTTGTGCCACCAGTTGGGTT‑CACCGGGCGGAGGGAGTTTGTCCGGGCCGTGATCCATGAAGTGGCGGAGGTATTCCCATACCTCGGCGACATGCTTGACGCCGGGTTCGGTGGGTTCGTTACTGTCGACCCAGAGGCAGTCTTTTTg                 <  5:102077/149‑1 (MQ=34)                                                                                                                                      gattGTGCCTCCTTTTGGGTT‑CACCGGGCGGAGGGAGTTTGTCCGGGCCGTGATCCATGAAGTGGCTGAGGTATTCCCATACCTCGGCTTCATGCTTGTCGCCGGGTTCGGTGGGTTCGTTTCTGTCGTCCCAGAGGCAGTCTTTTTg                 <  3:184223/146‑1 (MQ=11)                                                                                                                                      gCTTGTGCCACCAGTTGGGTT‑CACCGGGCGGAGGAAGTTTGTCCGGGCCGTGATCCATGAAGTGGCGGAGGTATTCCCATACCTCGGCGACATGCTTGACGCCGGGTTCGGTGGGTTCGTTACTGTCGACCCAGAGGCAGCCtgcacc                 >  1:53363/1‑143 (MQ=255)                                                                                                                                                 caGTTGGGTT‑CACCGGGCGGAGGGAGTTTGTCCGGGCCGTGATCCATGAAGTGGCGGAGGTATTCCCATACCTCGGCGACATGCTTGACGCCGGGTTCGGTGGGTTCGTTACTGTCGACCCAGAGGCAGTCttttt                  >  4:101436/1‑136 (MQ=34)                                                                                                                                                 caGTTGGGTT‑CACCGGGCGGAGGGAGTTTGTCCGGGCCGTGATCCATGAAGTGGCGGAGGTATTCCCATACCTCGGCGACATGCTTGACGCCGGGTTCGGTGGGTTCGTTACTGTCGACCCAGAGGCAGTCttttt                  <  3:101436/136‑1 (MQ=34)                                                                                                                                                 caGTTGGGTT‑CACCGGGCGGAGGGAGTTTGTCCGGGCCGTGATCCATGAAGTGGCGGAGGTATTCCCATACCTCGGCGACATGCTTGACGCCGGGTTCGGTGGGTTCGTTACTGTCGACCCAGAGGCAGTCtttt                   <  1:164175/135‑1 (MQ=34)                                                                                                                                                    ttGGGTT‑CACCGGGCGGAGGGAGTTTGTCCGGGCCGTGATCCATGAAGTGGCGGAGGTATTCCCATACCTCGGCGACATGCTTGACGCCGGGTTCGGTGGGTTCGTTACTGTCGACCCAGAGGCAGTCTTTTTGGTGCAGGCTGCCGTc  >  8:18106/1‑149 (MQ=37)                                                                                                                                                    |                                                                                                                                                      TTGTAGGGAAACAGCACGGCCCAGAACGGCAATTGCCAGTTCTTTTTACCCTGCATTTCACCGGGCTCGCCGGTTCGCCAAGGTGCATAGTGGCGCCAGGCTTCTGCCGGGGTCAGGCAGATGGCGTGCAGTGGCTTGTGCCACCAGTTGGGTT‑CACCGGGCGGAGGGAGTTTGTCCGGGCCGTGATCCATGAAGTGGCGGAGGTATTCCCATACCTCGGCGACATGCTTGACGCCGGGTTCGGTGGGTTCGTTACTGTCGACCCAGAGGCAGTCTTTTTGGTGCAGGCTGCCGTC  >  NC_002947/2984631‑2984926

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: ‑