Predicted mutation
evidence	seq id	position	mutation	freq	annotation	gene	description
RA	NC_002947	5,539,752	T→C	13.3%	I412V (ATC→GTC) ‡	PP_4872 ←	hypothetical protein

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NC_002947	5,539,752	0	T	C	13.3%	106.4 / 7.7	45	I412V (ATC→GTC) ‡	PP_4872	hypothetical protein
Reads supporting (aligned to +/- strand):  ref base T (18/21);  new base C (3/3);  total (21/24)
Fisher's exact test for biased strand distribution p-value = 1.00e+00
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 8.96e-01

AGGCGATGCGGTACATGTTGGCAGTCGGCCCGCCAAGGTCCGAGACCACGCCGGTGAAGCCCGGCACCTTGTCACGCATCTCTTCGATTTCGTGCAGGATCGACTCGTGCGAGCGGTTCTGGATGATGCGGCCTTCGTGCT‑CGGTGATCGAGCA‑GAAGGTACAGCCACCGAAGCAGCCACGCATGATGTTCACCGAGAAACGGATCATCTCGTAGGCCGGGATGCGCTCCTTGCCATAGGCCGGGTGCGGCACACGGGCGTATGGCATGCCGAACACGTAGTCCATTTCCTCG  >  NC_002947/5539605‑5539897                                                                                                                                                     |                                                                                                                                                   aGGCGATGCGGTACATGTTGGCAGTCGGCCCGCCAAGGTCCGAGACCACGCCGGTGAAGCCCGGCACCTTGTCACGCATCTCTTCGATTTCGTGCAGGATCGACTCGTGCGAGCGGTTCTGGATGATGCGGCCTTCGTGCT‑CGGTGATc                                                                                                                                                   >  2:263530/1‑149 (MQ=255) aGGCGATGCGGTACATGTTGGCAGTCGGCCCGCCAAGGTCCGAGACCACGCCGGTGAAGCCCGGCACCTTGTCACGCATCTCTTCGATTTCGTGCAGGATCGACTCGTGCGAGCGGTTCTGGATGATGCGGCCTTCGTGCT‑CGGTGATc                                                                                                                                                   <  6:173731/149‑1 (MQ=255)    cGATGCGGTACATGTTGGCATTCGGCACGACAAGGTCCGAGACCACGCCGGTGAAGCCCGGCAGCTTGTCACGCATCTCTTCGATTTCGTGCAGTATCTAATCGTGCGAGCGGTTCTGGATTATTCGGCCTTCGTGAT‑CGGTGATCGAg                                                                                                                                                <  6:173103/149‑1 (MQ=255)     gATGCGGTACATGTTGGCAGTCGGCCCGCCAAGGTCCGAGACCACGCCGGTGAAGCCCGGCACCTTGTCACGCATCTCTTCGATTTCGTGCAGGATCGACTCGTGCGAGCGGTTCTGGATGATGCGGCCTTCGTGCT‑CGGTGATCGAGc                                                                                                                                               <  2:277854/149‑1 (MQ=255)        gCGGTACATGTTGGCAGTCGGCCCGCCAAGGTCCGAGACCACGCCGGTGAAGCCCGGCACCTTGTCACGCATCTCTTCGATTTCGTGCAGGATCGACTCGTGCGAGCGGTTCTGGATGATGCGGCCTTCGTGCT‑CGGTGATCGAGCA‑g                                                                                                                                            >  3:15316/1‑148 (MQ=255)           gTACATGTTGGCAGTCGGCCCGCCAAGGTCCGAGACCACGCCGGTGAAGCCCGGCACCTTGTCACGCATCTCTTCGATTTCGTGCAGGATCGACTCGTGCGAGCGGTTCTGGATGATGCGGCCTTCGTGCT‑CGGTGATCGAGCA‑GAAgg                                                                                                                                        <  7:245963/149‑1 (MQ=255)                  ttGGCAGTCGGCCCGCCAAGGTCCGAGACCACGCCGGTGAAGCCCGGCACCTTGTCACGCATCTCTTCGATTTCGTGCAGGATCGACTCGTGCGAGCGGTTCTGGATGATGCGGCCTTCGTGCT‑CGGTGATCGAGCA‑GAAGGTACAGc                                                                                                                                  <  5:241549/148‑1 (MQ=255)                           ggCCCGCCAAGGTCCGAGACCACGCCGGTGAAGCCCGGCACCTTGTCACGCATCTCTTCGATTTCGTGCAGGATCGACTCGTGCGAGCGGTTCTGGATGATGCGGCCTTCGTGCT‑CGGTGATCGAGCA‑GAAGGTACAGCCACCGAag                                                                                                                          >  7:75271/1‑147 (MQ=255)                           ggCCCGCCAAGGTCCGAGACCACGCCGGTGAAGCCCGGCACCTTGTCACGCATCTCTTCGAGTTCGTGCAGGATCGACTCGTGCGAGCGGTTCTGGATGATGCGGCCTTCGTGCT‑CGGTGCTCGAGCA‑GAAGGTACAGCCACCGAag                                                                                                                          >  8:216171/1‑147 (MQ=255)                                  cAAGGTCCGAGACCACGCCGGTGAAGCCCGGCACCTTGTCACGAATCTCTTCGATTTCGTGCAGGATCGACTCGTGCGAGGGGTTATGGATGATGCGGCCTTCGTGCT‑CGGTGATCGAGCA‑GAAGGTACAGCCACCGAAGAAGCCACg                                                                                                                  >  7:301106/1‑148 (MQ=255)                                           agaCCACGCCGGTGAAGCCCGGCACCTTGTCACGCTTCTCTTCGATTTCGTGCAGGATCGACTCGTGCGAGAGGTTGTGGATGATGCGGCCTTCGTGCT‑CGGTGATCGAGCA‑GAAGGTACAGCCACCGAAGAAGCGACGCATGATGtt                                                                                                         >  7:151853/1‑148 (MQ=255)                                           agaCCACGCCGGTGAAGCCCGGCACCTTGTCACGCATCTCTTCGATTTCGTGCAGGATCGACTCGTGCGAGCGGTTCTGGATGATGCGGCCTTCGTGCT‑CGGTGATCGAGCA‑GAAGGTa                                                                                                                                      <  5:141546/119‑1 (MQ=255)                                           agaCCACGCCGGTGAAGCCCGGCACCTTGTCACGCATCTCTTCGATTTCGTGCAGGATCGACTCGTGCGAGCGGTTCTGGATGATGCGGCCTTCGTGCT‑CGGTGATCGAGCA‑GAAGGTa                                                                                                                                      >  6:141546/1‑119 (MQ=255)                                           agaCCACGCCGGTGAAGCCCGGCACCTTGTCACGCATCTCTTCGATTTCGTGCAGGATCGACTCGTGCGAGCGGTTCTGGATGATGCGGCCTTCGTGCT‑CGGTGATCGAGCA‑GAAGGTACAGCCACCGAAGCAGCCACGCATGATGtt                                                                                                         >  4:216881/1‑148 (MQ=255)                                               cACGCCGGTGAAGCCCGGCACCTTGTCACGCATCTCTTCGATTTCGTGCAGGATCGACTCGTGCGAGCGGTTCTGGATGATGCGGCCTTCGTGCT‑CGGTGATCGAGCA‑GAAGGTACAGCCACCGAAGCAGCCACGCATGATGTTc                                                                                                        >  6:68408/1‑145 (MQ=255)                                               cACGCCGGTGAAGCCCGGCACCTTGTCACGCATCTCTTCGATTTCGTGCAGGATCGACTCGTGCGAGCGGTTCTGGATGATGCGGCCTTCGTGCT‑CGGTGATCGAGCA‑GAAGGTACAGCCACCGAAGCAGCCACGCATGATGTTc                                                                                                        <  5:68408/145‑1 (MQ=255)                                                  gCCGGTGAAGCCCGGCACCTTGTCACGCATCTCTTCGATTTCGTGCAGGATCGACTCGTGCGAGCGGTTCTGGATGATGCGGCCTTCGTGCTCCGGTGATCGAGCA‑GAAGGTACAGCCACCGAAGCAGCCACGCATGATGTTCACCgag                                                                                                  <  1:263530/149‑1 (MQ=255)                                                      gTGAAGCCCGGCACCTTGTCACGCATCTCTTCGATTTCGTGCAGGATCGACTCGTGCGAGCGGTTCTGGATGATGCGGCCTTCGTGCT‑CGGTGATCGAGCA‑GAAGGTACAGCCACCGAAGCAGCCACGCATGATGTTCACCGAGAAACg                                                                                             <  6:45247/149‑1 (MQ=255)                                                       tGAAGCCCGGCACCTTGTCACGCATCTCTTCGATTTCGTGCAGGATCGACTCGTGCGAGCGGTTCTGGATGATGCGGCCTTCGTGCT‑CGGTGATCGAGCA‑GAAGGTACAGCCACCGAAGCAGCCACGCATGATGTTCACCGAGAAACgg                                                                                            <  8:75271/149‑1 (MQ=255)                                                        gAAGCCCGGCACCTTGTCACGCATCTCTTCGATTTCGTGCAGGATCGACTCGTGCGAGCGGTTCTGGATGATGCGGCCTTCGTGCT‑CGGTGATCGAGCA‑GAAGGTACAGCCACCGAAGCAGCCACGCATGATGTTCACCGAGAAACGGa                                                                                           >  2:92692/1‑149 (MQ=255)                                                         aaGCCCGGCACCTTGTCACGCATCTCTTCGATTTCGTGCAGGATCGACTCGTGCGAGCGGTTCTGGATGATGCGGCCTTCGTGCT‑CGGTGATCGAGCA‑GAAGGTACAGCCACCGAAGCAGCCACGCATGATGTTCACCGAGAAACGGa                                                                                           <  5:24133/148‑1 (MQ=255)                                                         aaGCCCGGCACCTTGTCACGCATCTCTTCGATTTCGTGCAGGATCGACTCGTGCGAGCGGTTCTGGATGATGCGGCCTTCGTGCT‑CGGTGATCGAGCA‑GAAGGTACAGCCACCGAAGCAGCCACGCATGATGTTCACCGAGAAACGGa                                                                                           <  3:216881/148‑1 (MQ=255)                                                           gCCCGGCACCTTGTCACGCATCTCTTCGATTTCGTGCAGGATCGACTCGTGCGAGCGGTTCTGGATGATGCGGCCTTCGTGCT‑CGGTGATCGAGCA‑GAAGGTACAGCCACCGAAGCAGCCACGCATGATGTTCACCGAGAAACGGatca                                                                                        >  3:181669/1‑149 (MQ=255)                                                            cccGGCACCTTGTCACGCATCTCTTCGATTTCGTGCAGGATCGACTCGTGCGAGCGGTTCTGGATGATGCGGCCTTCGTGCT‑CGGTGATCGAGCA‑GAAGGTACAGCCACCGAAGCAGCCACGCATGATGTTCACCgag                                                                                                  >  5:323083/1‑138 (MQ=255)                                                            cccGGCACCTTGTCACGCATCTCTTCGATTTCGTGCAGGATCGACTCGTGCGAGCGGTTCTGGATGATGCGGCCTTCGTGCT‑CGGTGATCGAGCA‑GAAGGTACAGCCACCGAAGCAGCCACGCATGATGTTCACCgag                                                                                                  <  6:323083/138‑1 (MQ=255)                                                                          aCGCATCTCTTCGATTTCGTGCAGGATCGACTCGTGCGAGCGGTTCTGGATGATGCGGCCTTCGTGCT‑CGGTGATCGAGCA‑GAAGGTACAGCCACCGAAGCAGCCACGCATGATGTTCACCGAGAAACGGATCATCTCGTAGGCCGGGa                                                                         >  2:127237/1‑149 (MQ=255)                                                                            gCATCTCTTCGATTTCGTGCAGGATCGACTCGTGCGAGCGGTTCTGGATGATGCGGCCTTCGTGCT‑CGGTGATCGAGCA‑GAAGGTACAGCCACCGAAGCAGCCACGCATGATGtt                                                                                                         <  5:80461/115‑1 (MQ=255)                                                                            gCATCTCTTCGATTTCGTGCAGGATCGACTCGTGCGAGCGGTTCTGGATGATGCGGCCTTCGTGCT‑CGGTGATCGAGCA‑GAAGGTACAGCCACCGAAGCAGCCACGCATGATGtt                                                                                                         >  6:80461/1‑115 (MQ=255)                                                                              aTCTCTTCGATTTCGTGCAGGATCGACTCGTGCGAGCGGTTCTGGATGATGCGGCCTTCGTGCT‑CGGTGATCGAGCA‑GAAGGTACAGCCACCGAAGCAGCCACGCATGATGTTCACCGAGAAACGGATCATCTCGTAGGCCGGGATgc                                                                      >  8:233498/1‑148 (MQ=255)                                                                                  ctTCGATTTCGTGCAGGATCGACTCGTGCGAGCGGTTCTGGATGATGCGGCCTTCGTGCT‑CGGTGATCGAGCA‑GAAGGTa                                                                                                                                      <  6:67515/80‑1 (MQ=255)                                                                                                agcaTCGACTCGAGCGAGCGGTGCTGCATCATGCGGCCTTCGTGCT‑CGGTGATCGAGCA‑GAAGGTACAGCCACCGAAGCAGCCACGCATGAGGTTCACCGAGAAACGGATCATCTCGTAGGCCGCGATGCGCTCCTTGCCATAGGCCgg                                                   <  4:181669/146‑1 (MQ=255)                                                                                                              cGAGCGGTTCTGGATGATGCGGCCTTCGTGCT‑CGGTGATCGAGCA‑GAAGGTACAGCCACCGAAGCAGCCACGCATGATGTTCACCGAGAAACGGATCATCTCGTAGGCCGGGATGCGCTCCTTGCCATAGGCCGGGTGCGGCACACgg                                      <  1:92692/148‑1 (MQ=255)                                                                                                              cGAGCGGTTCTGGATGATGCGGCCTTCGTGCT‑CGGTGATCGAGCA‑GAAGGTACAGCCACCGAAGCAGCCACGCATGATGTTCACCGAGAAACGGATCATCTCGTAGGCCGGGATGCGCTCCTTGCCATAGGCCGGGTGCGGCACACgg                                      <  7:233498/148‑1 (MQ=255)                                                                                                                aGCGGTTCTGTATGATGCGGCCTTCGTGCT‑CGGTGATCGAGCA‑GAAGGTACAGCCACCGAAGCAGCCACGCATGATGTTCACCGAGAAACGGATCATCTCGTAGGCCGGGATGCGCTCCTTGCCATAGGCCGGGTGCGGCACACGGGCg                                   >  2:228399/1‑149 (MQ=255)                                                                                                                aGCGGTTCTGGATGATGCGGCCTTCGTGCT‑CGGTGATCGAGCA‑GAAGGTACAGCCACCGAAGCAGCCACGCATGATGTTCACCGAGAAACGGATCATCTCGTAGGCCGGGATGCGCTCCTTGCCATAGGCCGGGTGCGGCACACGGGCg                                   >  4:50830/1‑149 (MQ=255)                                                                                                                   gggtCTGGAGGCTGCGGCCCTCGCGCC‑CGGTGATCCAGCA‑GAAGGTACAGCCACCGAAGCACCCACGCACCATGTTCACCCAGCACCGGCTCATCTCCCCGGCCGGGATGCGCTCCTCGCCATACGCCGGGTGCGGCACACGGGCGTAt                                <  4:15316/146‑1 (MQ=255)                                                                                                                            tgatgCGGCCTTCGTGCT‑CGGTGATCGAGCA‑GAAGGTACAGCCACCGAAGCAGCCACGCATGATGTTCACCGAGAAACGGATCATCTCGTAGGCCGGGATGCGCTCCTTGCCATAGGCCGGGTGCGGCACACGGGCGTATGGCATGcc                        >  4:320195/1‑148 (MQ=255)                                                                                                                                     gcttctGCT‑CGATCACCGAGCACGAATGTACAGCCACCGAAGCAGCCACGCATGATGTTCACCGAGAAACGGATCATCTCGTAGGCCGGGATGCGCTCCTTGCCATAGGCCGGGTGCGGCACACGGGCGTATGGCATGCCGAACACGTa               <  5:276376/144‑1 (MQ=255)                                                                                                                                       ttctGCT‑CGATCACCGAGCACGAAGGTACAGCCACCGAAGCGGCCACGCATGATGTTCACCGAGAAACGGATCATCTCGTAGGCCGGGATGCGCTCCTTGCCATAGGCCGGGTGCGGCACACGGGCGTATGGCATGCCGAACACGTa               >  2:323278/4‑147 (MQ=255)                                                                                                                                       ttctGCT‑CGATCACCGAGCACGAAGGTACAGCCACCGAAGCGGCCACGCATGATGTTCACCGAGAAACGGATCATCTCGTAGGCCGGGATGCGCTCCTTGCCATAGGCCGGGTGCGGCACACGGGCGTATGGCATGCCGAACACGTa               >  2:328292/4‑147 (MQ=255)                                                                                                                                       ttctGCT‑CGATCACCGAGCACGAAGGTACAGCCACCGAAGCGGCCACGCATGATGTTCACCGAGAAACGGATCATCTCGTAGGCCGGGATGCGCTCCTTGCCATAGGCCGGGTGCGGCACACGGGCGTATGGCATGCCGAACACGTa               <  1:328292/144‑1 (MQ=255)                                                                                                                                       ttctGCT‑CGATCACCGAGCACGAAGGTACAGCCACCGAAGCGGCCACGCATGATGTTCACCGAGAAACGGATCATCTCGTAGGCCGGGATGCGCTCCTTGCCATAGGCCGGGTGCGGCACACGGGCGTATGGCATGCCGAACACGTa               <  1:323278/144‑1 (MQ=255)                                                                                                                                       ttctGCT‑CGATCACCGAGCACGAAGGTACAGCCACCGAAGCAGCCACGCATGATGTTCACCGAGAAACGGATCATCTCGTAGGCCGGGATGCGCTCCTTGCCATAGGCCGGGTGCGGCACACGGGCGTATGGCATGCCGAACACGTa               >  6:276376/4‑147 (MQ=255)                                                                                                                                                ggTGATCGAGCA‑GAAGGTACAGCCACCGAAGCAGCCACGCATGATGTTCACCGAGAAACGGATCATCTCGTAGGCCGGGATGCGCTCCTTGCCATAGGCCGGGTGCGGCACACGGGCGTATGGCATGCCGAACACGTAGTCCATTTCCt    <  3:320195/149‑1 (MQ=255)                                                                                                                                                  tGATCGAGCA‑GAAGGTACAGCCACCGAAGCAGCCACGCATGATGTTCACCGAGAAACGGATCATCTCGTAGGCCGGGATGCGCTCCTTGCCATAGGCCGGGTGCGGCACACGGGCGTATGGCATGCCGAACACGTAGTCCATTTCCTCg  <  1:228399/149‑1 (MQ=255)                                                                                                                                                     |                                                                                                                                                   AGGCGATGCGGTACATGTTGGCAGTCGGCCCGCCAAGGTCCGAGACCACGCCGGTGAAGCCCGGCACCTTGTCACGCATCTCTTCGATTTCGTGCAGGATCGACTCGTGCGAGCGGTTCTGGATGATGCGGCCTTCGTGCT‑CGGTGATCGAGCA‑GAAGGTACAGCCACCGAAGCAGCCACGCATGATGTTCACCGAGAAACGGATCATCTCGTAGGCCGGGATGCGCTCCTTGCCATAGGCCGGGTGCGGCACACGGGCGTATGGCATGCCGAACACGTAGTCCATTTCCTCG  >  NC_002947/5539605‑5539897

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 14 ≤ ATCG/ATCG < 15 ≤ ATCG/ATCG < 32 ≤ ATCG/ATCG < 36 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑