Predicted mutation
evidence	seq id	position	mutation	freq	annotation	gene	description
RA	NC_002947	5,539,748	G→A	13.9%	T413I (ACC→ATC)	PP_4872 ←	hypothetical protein

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NC_002947	5,539,748	0	G	A	13.9%	103.5 / 8.5	43	T413I (ACC→ATC)	PP_4872	hypothetical protein
Reads supporting (aligned to +/- strand):  ref base G (18/19);  new base A (3/3);  total (21/22)
Fisher's exact test for biased strand distribution p-value = 1.00e+00
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 6.91e-01

AGGCGATGCGGTACATGTTGGCAGTCGGCCCGCCAAGGTCCGAGACCACGCCGGTGAAGCCCGGCACCTTGTCACGCATCTCTTCGATTTCGTGCAGGATCGACTCGTGCGAGCGGTTCTGGATGATGCGGCCTTCGTGCT‑CGGTGATCGAGCA‑GAAGGTACAGCCACCGAAGCAGCCACGCATGATGTTCACCGAGAAACGGATCATCTCGTAGGCCGGGATGCGCTCCTTGCCATAGGCCGGGTGCGGCACACGGGCGTATGGCATGCCGAACACGTAGTCCATTTCCT  >  NC_002947/5539605‑5539895                                                                                                                                                 |                                                                                                                                                     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                                                                                                       >  6:80461/1‑115 (MQ=255)                                                                            gCATCTCTTCGATTTCGTGCAGGATCGACTCGTGCGAGCGGTTCTGGATGATGCGGCCTTCGTGCT‑CGGTGATCGAGCA‑GAAGGTACAGCCACCGAAGCAGCCACGCATGATGtt                                                                                                       <  5:80461/115‑1 (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                                    <  7:233498/148‑1 (MQ=255)                                                                                                              cGAGCGGTTCTGGATGATGCGGCCTTCGTGCT‑CGGTGATCGAGCA‑GAAGGTACAGCCACCGAAGCAGCCACGCATGATGTTCACCGAGAAACGGATCATCTCGTAGGCCGGGATGCGCTCCTTGCCATAGGCCGGGTGCGGCACACgg                                    <  1:92692/148‑1 (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)                                                                                                                                                 |                                                                                                                                                     AGGCGATGCGGTACATGTTGGCAGTCGGCCCGCCAAGGTCCGAGACCACGCCGGTGAAGCCCGGCACCTTGTCACGCATCTCTTCGATTTCGTGCAGGATCGACTCGTGCGAGCGGTTCTGGATGATGCGGCCTTCGTGCT‑CGGTGATCGAGCA‑GAAGGTACAGCCACCGAAGCAGCCACGCATGATGTTCACCGAGAAACGGATCATCTCGTAGGCCGGGATGCGCTCCTTGCCATAGGCCGGGTGCGGCACACGGGCGTATGGCATGCCGAACACGTAGTCCATTTCCT  >  NC_002947/5539605‑5539895

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: ‑