Predicted mutation
evidence	seq id	position	mutation	freq	annotation	gene	description
RA	NC_002947	1,705,329	G→A	7.7%	A232T (GCC→ACC)	PP_1499 →	hypothetical protein

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NC_002947	1,705,329	0	G	A	7.7%	150.1 / 2.1	52	A232T (GCC→ACC)	PP_1499	hypothetical protein
Reads supporting (aligned to +/- strand):  ref base G (22/26);  new base A (2/2);  total (24/28)
Fisher's exact test for biased strand distribution p-value = 1.00e+00
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 8.55e-01

TGGAGATCCTCCAGCACCGGCTGAACAACGTGTTCGGCGAGGCCGAAGGTACCATTCGCGTGTTCGAGTCCGACGGTATCGTCGCCGACGCCGCAGCCGGTGCCGACTACATCAAGGTGCGTGCCGATGCCATGTTCAACGCCCGCGATGTGCGCGCCCTG‑GAGGTGCACGAAGGGTTGGTGCAC‑GTCGGTACCACGCTCAATGGCCTGAACCAGCCGATCTGTACCTTCCTGGCCAAGGGCCCGCCCTCGTCGACGGTAACCCAGGAGGGCCTGGCGATTCTCAT  >  NC_002947/1705189‑1705474                                                                                                                                             |                                                                                                                                                    tGGAGATCCTCCAGCACCGGCTTAACACCGTGTTCGGCGAGGCCGAAGGTACCATTCGCGTGTTCGAGTCCGACGGTATCGTCGCCGACGCCGCAGCCGGTGCCGACTACATCAAGGTGCGTGCCGATGCCATGTTCAACGCCCGCGAt                                                                                                                                             <  6:112857/149‑1 (MQ=255)   gagaTCCTCCAGCACCGGCTGAACAACGTGTTCGGCGAGGCCGAAGGTACCATTCGCGTGTTCGAGTCCGACGGTATCGTCGCCGACGCCGCAGCCGGTGCCGACTACATCAAGGTGCGTGCCGATGCCATGTTCAACGCCCGCGAtg                                                                                                                                            <  7:110507/148‑1 (MQ=255)        cctccAGCACCGGCTGAACAACGTGTTCGGCGAGGCCGAAGGTACCATTCGCTTGTTCGAGTCCGACGGTATCGTCGCCGACGCCGCAGCCGGTGCCGACTACATCAAGGTGCGTGCCGATGCCATGTTCAACACCCGCGATGTgcgcg                                                                                                                                      >  1:288940/1‑149 (MQ=255)         ctccAGCACCGGCTGAACAACGTGTTCGGCGAGGCCGAAGGTACCATTCGCGTGTTCGAGTCCGACGGTATCGTCGCCGACGCCGCAGCCGGTGCCGACTACATCAAGGTGCGTGCCGATGCCATGTTCAACGCCCGCGATGTgcgcgc                                                                                                                                     >  5:369050/1‑149 (MQ=255)          tccAGCACCGGCTGAACAACGTGTTCGGCGAGGCCGAAGGTACCATTCGCGTGTTCGAGTCCGACGGTATCGTCGCCGACGCCGCAGCCGGTGCCGACTACATCAAGGTGCGTGCCGATGCCATGTTCAACGCCCGCGATGTGCGCGcc                                                                                                                                    >  6:331637/1‑149 (MQ=255)          tccAGCACCGGCTGAACAACGTGTTCGGCGAGGCCGAAGGTACCATTCGCGTGTTCGAGTCCGACGGTATCGTCGCCGACGCCGCAGCCGGTGCCGACTACATCAAGGTGCGTGCCGATGCCATGTTCAACACCCGCGATGTGCGCGcc                                                                                                                                    >  7:345764/1‑149 (MQ=255)                          caacGTGTTCGGCGAGGCCGAAGGTACCATTCGCGTGTTCGAGTCCGACGGTATCGTCGCCGACGCCGCAGCCGGTGCCGACTACATCAAGGTGCGTGCCGATGCCATGTTCAACGCCCGCGATGTGCGCGCCCTG‑GAGGTGCACGAAg                                                                                                                   <  2:35467/149‑1 (MQ=255)                           aacGTGTTCGGCGAGGCCGAAGGTACCATTCGCGTGTTCGAGTCCGACGGTATCGTCGCCGACGCCGCAGCCGGTGCCGACTACATCAAGGTGCGTGCCGATGCCATGTTCAACGCCCGCGATGTGCGCGCCCTG‑GAGGTGCACGAAgg                                                                                                                  >  5:308178/1‑149 (MQ=255)                           aacGTGTTCGGCGAGGCCGAAGGTACCATTCGCGTGTTCGAGTCCGACGGTATCGTCGCCGACGCCGCAGCCGGTGCCGACTACATCAAGGTGCGTGCCGATGCCATGTTCAACGCCCGCGATGTGCGCGCCCTG‑GAGGTGCACGAAgg                                                                                                                  <  3:206030/149‑1 (MQ=255)                             cGTGTTCGGCGAGGCCGAAGGTACCATTCGCGTGTTCGAGTCCGACGGTATCGTCGCCGACGCCGCAGCCGGTGCCGACTACATCAAGGTGCGTGCCGATGCCATGTTCAACGCCCGCGATGTGCGCGCCCTG‑GAGGTGCACGAAGGGt                                                                                                                <  6:369050/149‑1 (MQ=255)                              gtgtTCGGCGAGGCCGAAGGTACCATTCGCGTGTTCGAGTCCGACGGTATCGTCGCCGACGCCGCAGCCGGTGCCGACTACATCAAGGTGCGTGCCGATGCCATGTTCAACGCCCGCGATGTGCGCGCCCTG‑GAGGTGCACGAAGGGtt                                                                                                               <  7:85563/149‑1 (MQ=255)                               tgtTCGGCGAGGCCGAAGGTACCATTCGCGTGTTCGAGTCCGACGGTATCGTCGCCGACGCCGCAGCCGGTGCCGACTACATCAAGGTGCGTGCCGATGCCATGTTCAACGCCCGCGATGTGCGCGCCCTG‑GAGGTGCACGAAGGGTTg                                                                                                              <  2:99605/149‑1 (MQ=255)                                gtTCGGCGAGGCCGAAGGTACCATTCGCGTGTTCGAGTCCGACGGTATCGTCGCCGACGCCGCAGCCGGTGCCGACTACATCAAGGTGCGTGCCGATGCCATGTTCAACGCCCGCGATGTGCGCGCCCTG‑GAGGTGCACGAAGGGTTgg                                                                                                             <  1:135539/149‑1 (MQ=255)                                    ggCGAGGCCGAAGGTACCATTCGCGTGTTCGAGTCCGACGGTATCGTCGCAGACGCCGCAGCCGGTGCCGACTACATCAAGGTGCGTGCCGATGCCATGTTCAACGCCCGCGATGTGCGCGCCCTG‑GAGGTGCACGAAGGGTTGGTGc                                                                                                          <  7:28630/148‑1 (MQ=255)                                         ggCCGAAGGTACCATTCGCGTGTTCGAGTCCGACGGTATCGTCGCCGACGCCGCAGCCGGTGCCGACTACATCAAGGTGCGTGCCGATGCCATGTTCAACACCCGCGATGTGCGCGCCCTG‑GAGGTGCACGAAGGGTTGGTGCAC‑GTCg                                                                                                   <  8:345764/149‑1 (MQ=255)                                          gCCGAAGGTACCATTCGCGTGTTCGAGTCCGACGGTATCGTCGCCGACGCCGCAGCCGGTGCCGACTACATCAAGGTGCGTGCCGATGCCATGTTCAACGCCCGCGATGTGCGCGCCCTG‑GAGGTGCACGAAGGGTTGGTGCAC‑GTCgg                                                                                                  >  4:157100/1‑149 (MQ=255)                                            cGAAGGTACCATTCGCGTGTTCGAGTCCGACGGTATCGTCGCCGACGCCGCAGCCGGTGCCGACTACATCAAGGTGCGTGCCGATGCCATGTTCAACGCCCGCGATGTGCGCGCCCTG‑GAGGTGCACCAACCCTTCGTGCAC‑CTccagg                                                                                                <  7:104994/149‑5 (MQ=255)                                            cGAAGGTACCATTCGCGTGTTCGAGTCCGACGGTATCGTCGCCGACGCCGCAGCCGGTGCCGACTACATCAAGGTGCGTGCCGATGCCATGTTCAACACCCGCGATGTGCGCGCCCTG‑GAGGTGCACGAAGGGTTGGTGCAC‑GTCGGTa                                                                                                <  2:288940/149‑1 (MQ=255)                                                  tACCATTCGCGTGTTCGAGTCCGACGGTATCGTCGCCGACGCCGCAGCCGGTGCCGACTACATCAAGGTGCGTGCCGATGCCATGTTCAACGCCCGCGATGTGCGCGCCCTG‑GAGGTGCACGAAGGGTTGGTGCAC‑GTCGGTACCACGc                                                                                          <  5:331637/149‑1 (MQ=255)                                                   aCCATTCGCGTGTTCGAGTCCGACGGTATCGTCGCCGACGCCGCAGCCGGTGCCGACTACATCAAGGTGCGTGCCGATGCCATGTTCAACGCCCGCGATGTGCGCGCCCTG‑GAGGTGCACGAAGGGTTGGTGCAC‑GTCGGTACCACGCt                                                                                         >  2:30536/1‑149 (MQ=255)                                                    ccATTCGCGTGTTCGAGTCCGACGGTATCGTCGCCGACGCCGCAGCCGGTGCCGACTACATCAAGGTGCGTGCCGATGCCATGTTCAACGCCCGCGATGTGCGCGCCCTG‑GAGGTGCACGAAGGGTTGGTGCAC‑GTCGGTACCACGCt                                                                                         <  6:308178/148‑1 (MQ=255)                                                      aTTCGCGTGTTCGAGTCCGACGGTATCGTCGCCGACGCCGCAGCCGGTGCCGACTACATCAAGGTGCGTGCCGATGCCATGTTCAACGCCCGCGATGTGCGCGCCCTG‑GAGGTGCACGTAGGGTTGGTGCAC‑GTCGGTACCACGCTCaa                                                                                      <  1:30536/149‑1 (MQ=255)                                                           cgTGTTCGAGTCCGACGGTATCGTCGCCGACGCCGCAGCCGGTGCCGACTACATCAAGGTGCGTGCCGATGCCATGTTCAACGCCCGCGATGTGCGCGCCCTG‑GAGGTGCACGAAGGGTTGGTGCAC‑GTCGGTACCACGCTCAATGGcc                                                                                 >  5:263392/1‑149 (MQ=255)                                                           cgTGTTCGAGTCCGACGGTATCGTCGCCGACGCCGCAGCCGGTGCCGACTACATCAAGGTGCGTGCCGATGCCATGTTCAACGCCCGCGATGTGCGCGCCCTG‑GAGGTGCACGAAGGGTTGGTGCAC‑GTCGGTACCACGCTCAATGGcc                                                                                 <  6:263392/149‑1 (MQ=255)                                                                      ccGACGGTATCGTCGCCGACGCCGCAGCCGGTGCCGACTACATCAAGGTGCGTGCCGATGCCATGTTCAACGCCCGCGATGTGCGCGCCCTG‑GAGGTGCACGAAGGGTTGGTGCAC‑GTCGGTACCACGCTCAATGGCCTGAACCAGcc                                                                       >  7:25741/1‑148 (MQ=255)                                                                           ggTATCGTCGCCGACGCCGCAGCCGGTGCCGACTACATCAAGGTGCGTGCCGATGCCATGTTCAACGCCCGCGATGTGCGCGCCCTGTCAGGTGCACGAAGGGTTGGTGCAC‑GTCGGTACCACGCTCAATGGCCTGAACCAGCCGATCt                                                                  <  1:298943/149‑1 (MQ=255)                                                                               tcgtcgCCGACGCCGCAGCCGGTGCCGACTACATCAAGGTGCGTGCCGATGCCATGTTCAACGCCCGCGATGTGCGCGCCCTG‑GAGGTGCACGAAGGGTTGGTGCAC‑GTCGGTACCACGCTCAATGGCCTGAACCAGCCGATCTGTAc                                                              <  1:758/148‑1 (MQ=255)                                                                                          gccgcAGCCGGTGCCGACTACATCAAGGTGCGTGCCGATGCCATGTTCAACGCCCGCGATGTGCGCGCCCTG‑GAGGTGCACGAAGGGTTGGTGCAC‑GTCGGTACCACGCTCAATGGCCTGAACCAGCCGATCTGTACCTTCCTGGCCaa                                                  <  3:157100/149‑1 (MQ=255)                                                                                            cgcAGCCGGTGCCGACTACATCAAGGTGCGTGCCGATGCCATGTTCAACGCCCGCGATGTGCGCGCCCTG‑GAGGTGCACGAAGGGTTGGTGCAC‑GTCGGTACCACGCTCAATGGCCTGAACCAGCCGATCTGTACCTTCCTGGCCAAgg                                                >  1:180057/1‑149 (MQ=255)                                                                                            cgcAGCCGGTGCCGACTACATCAAGGTGCGTGCCGATGCCATGTTCAACGCCCGCGATGTGCGCGCCCTG‑GAGGTGCACGAAGGGTTGGTGCAC‑GTCGGTACCACGCTCAATGGCCTGAACCAGCCGATCTGTACCTTCCTGGCCAAgg                                                <  7:106867/149‑1 (MQ=255)                                                                                                gCCGGTGCCGACTACATCAAGGTGCGTGCCGATGCCATGTTCAACGCCCGCGATGTGCGCGCCCTG‑GAGGTGCACGAAGGGTTGGTGCAC‑GTCGGTACCACGCTCAATGGCCTGAACCAGCCGAt                                                                    <  5:391287/125‑1 (MQ=255)                                                                                                gCCGGTGCCGACTACATCAAGGTGCGTGCCGATGCCATGTTCAACGCCCGCGATGTGCGCGCCCTG‑GAGGTGCACGAAGGGTTGGTGCAC‑GTCGGTACCACGCTCAATGGCCTGAACCAGCCGAt                                                                    >  6:391287/1‑125 (MQ=255)                                                                                                 ccGGTGCCGACTACATCAAGGTGCGTGCCGATGCCATGTTCAACGCCCGCGATGTGCGCGCCCTG‑GAGGTGCACGAAGGGTTGGTGCAC‑GTCGGTACCACGCTCAATGGCCTGAACCAGCCGATCTGTACCTTCCTGGCCAAGGgcccg                                           <  8:25741/149‑1 (MQ=255)                                                                                                        cGACTACATCAAGGTGCGTGCCGATGCCATGTTCAACGCCCGCGATGTGCGCGCCCTG‑GAGGTGCACGAAGGGTTGGTGCAc                                                                                                        <  8:168357/82‑1 (MQ=255)                                                                                                        cGACTACATCAAGGTGCGTGCCGATGCCATGTTCAACGCCCGCGATGTGCGCGCCCTG‑GAGGTGCACGAAGGGTTGGTGCAc                                                                                                        >  7:168357/1‑82 (MQ=255)                                                                                                        cGACTACATCAAGGTGCGTGCCGATGCCATGTTCAACGCCCGCGATGTGCGCGCCCTG‑GAGGTGCACGAAGGGTTGGTGCAC‑GTCGGTACCACGCTCAATGGCCTGAACCAGCCGATCTGTACCTTCCTGGCCAAGGGCCCGCCCtcgt                                    >  8:342116/1‑149 (MQ=255)                                                                                                        cGACTACATCAAGGTGCGTGCCGATGCCATGTTCAACGCCCGCGATGTGCGCGCCCTG‑GAGGTGCACGAAGGGTTGGTGCAC‑GTCGGTACCACGCTCAATGGCCTGAACCAGCCGATCTGTACCTTCCTGGCAAAGGGCCCGCCCtcgt                                    >  6:1589/1‑149 (MQ=255)                                                                                                        cGACTACATCAAGGTGCGTGCCGATGCCATGTTCAACGCCCGCAATGTGCGCGCCCTG‑GAGGTGCACGAAGGGTTGGTGCAC‑GTCGGTACCACGCTCAATGGCCTGAACCAGCCGATCTGTACCTTCCTGGCCAAGGGCCCGCCCtcgt                                    >  6:7001/1‑149 (MQ=255)                                                                                                        cGACTACATCAACGTGCGTGCCGATGCCATGTTCAACGCCCGCGATGTGCGCGCCCTG‑GAGGTGCACGAAGGGTTGGTGCAC‑GTCGGTACCACGCTCAATGGCCTGAACCAGCCGATCTGTACCTTCCTGGCCAAGGGCCCGCCCtcgt                                    <  2:180057/149‑1 (MQ=255)                                                                                                         gACTACATCAAGGTGCGTGCCGATGCCATGTTCAACGCCCGCGATGTGCGCGCCCTG‑GAGGTGCACGAAGGGTTGGTGCAC‑GTCGGTACCACGCTCAATGGCCTGAACCAGCCGATCTGTACCTTCCTGGCCAAGGGCCCGCCCtcgtc                                   >  8:41048/1‑149 (MQ=255)                                                                                                              cATCAAGGTGCGTGCCGATGCCATGTTCAACGCCCGCGATGTGCGCGCCCTG‑GAGGTGCACGAAGGGTTGGTGCAC‑GTCGGTACCACGCTCAATGGCCTGAACCAGCCGATCTGTACCTTCCTGGCCAAGGGCCCGCCCTCGTCGACgg                              >  7:252379/1‑149 (MQ=255)                                                                                                              cATCAAGGTGCGTGCCGATGCCATGTTCAACGCCCGCGATGTGCGCGCCCTG‑GAGGTGCACGAAGGGTTGGTGCAC‑GTCGGTACCACGCTCAATGGCCTGAACCAGCCGATCTGTACCTTCCTGGCCAAGGGCCCGCCCTCGTCGACg                               <  6:108796/148‑1 (MQ=255)                                                                                                               aTCAAGGTGCGTGCCGATGCCATGTTCAACGCCCGCGATGTGCGCGCCCTG‑GAGGTGCACGAAGGGTTGGTGCAC‑GTCGGTACCACGCTCAATGGCCTGAACCAGCCGATCt                                                                  >  4:192529/1‑112 (MQ=255)                                                                                                               aTCAAGGTGCGTGCCGATGCCATGTTCAACGCCCGCGATGTGCGCGCCCTG‑GAGGTGCACGAAGGGTTGGTGCAC‑GTCGGTACCACGCTCAATGGCCTGAACCAGCCGATCt                                                                  <  3:192529/112‑1 (MQ=255)                                                                                                                tCAAGGTGCGTGCCGATGCCATGTTCAACGCCCGCGATGTGCGCGCCCTG‑GAGGTGCACGAAGGGTTGGTGCAC‑GTCGGTACCACGCTCAATGGCCTGAACCAGCCGATCTGTACCTTCCTGGCCAAGCGCCCGCCCTCGTCGACGGt                             >  3:335018/1‑148 (MQ=255)                                                                                                                              gATGCCATGTTCAACGCCCGCGATGTGCGCGCCCTG‑GAGGTGCACGAAGGGTTGGTGCAC‑GTCGGTACCACGCTCAATGGCCTGAACCAGCCGATCTGTACCTTCCTCGCCAAGGGCCCGCCCTCGTCGACCGTAACCCACGAGGGc                >  6:210903/1‑147 (MQ=255)                                                                                                                               aTGCCATGTTCACCGCCCGCGATGTGCGCGCCCTG‑GAGGTGCACGAAGGGTTGGTGCAC‑GTCGGTACCACGCTCAATCGCCTGAACCAGCCGATCTGTACCTTCCTCGCCAAGGGCCCGCCCTCGTCGACGGTAACCCAGGAGGGCCTg             <  8:18508/149‑1 (MQ=255)                                                                                                                               aTGCCATGTTCAACGCCCGCGATGTGCGCGCCCTG‑GAGGTGCACGAAGGGTTGGTGCACAGGAGGTACCACGCTGCATGGCCTTCACCAGCCGATCAGTTCCTTACATGCCCAGGGCCCGCCCTAGTCGACGGTTACCCACGAAGGCCt              >  1:299022/1‑149 (MQ=255)                                                                                                                               aTGCCATGTTCAACGCCCGCGATGTGCGCGCCCTG‑GAGGTGCACGAAGGGTTGGTGCAC‑GTCGGTACCACGCTCAATGGCCTGAACCAGCCGATCTGTACCTTCCTGGCCAAGGGCCCGCCCTCGTCGACGGTAACCCAGGAGGGCCTg             >  5:272278/1‑149 (MQ=255)                                                                                                                                   cATGTTCAACGCCCGCGATGTGCGCGCCCTG‑GAGGTGCACGAAGGGTTGGTGCAC‑GTCGGTACCACGCTCAATGGCCTGAACCAGCCGATCTGTACCTTCCTGGCCAAGGGCCCGCCCTCGTCGACGGTAACCCAGGAGGGCCTGGCGa         >  3:271031/1‑149 (MQ=255)                                                                                                                                          aaCGCCCGCGATGTGCGCGCCCTG‑GAGGTGCACGAAGGGTTGGTGCAC‑GTCGGTACCACGCTCAATGGCCTGAACCAGCCGATCTGTACCTTCCTGGCCAAGGGCCCGCCCTCGTCGACGGTAACCCAGGAGGGCCTGGCGATTCTCa   <  4:271031/148‑1 (MQ=255)                                                                                                                                          aaCGCCCGCGATGTGCGCGCCCTG‑GAGGTGCACGAAGGGTTGGTGCAC‑GTCGGTACCACGCTCAATGGCCTGAACCAGCCGATCTGTACCTTCCTGGCCAAGGGCCCGCCCTCGTCGACGGTAACCCAGGAGGGCCTGGCGATTCTCAt  >  8:27574/1‑149 (MQ=255)                                                                                                                                             |                                                                                                                                                    TGGAGATCCTCCAGCACCGGCTGAACAACGTGTTCGGCGAGGCCGAAGGTACCATTCGCGTGTTCGAGTCCGACGGTATCGTCGCCGACGCCGCAGCCGGTGCCGACTACATCAAGGTGCGTGCCGATGCCATGTTCAACGCCCGCGATGTGCGCGCCCTG‑GAGGTGCACGAAGGGTTGGTGCAC‑GTCGGTACCACGCTCAATGGCCTGAACCAGCCGATCTGTACCTTCCTGGCCAAGGGCCCGCCCTCGTCGACGGTAACCCAGGAGGGCCTGGCGATTCTCAT  >  NC_002947/1705189‑1705474

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: ‑