Predicted mutation
evidence	seq id	position	mutation	freq	annotation	gene	description
RA	NC_002947	5,539,800	T→C	18.2%	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	5,539,800	0	T	C	18.2%	36.8 / 3.8	22	I412V (ATC→GTC) ‡	PP_4872	hypothetical protein
Reads supporting (aligned to +/- strand):  ref base T (9/9);  new base C (2/2);  total (11/11)
Fisher's exact test for biased strand distribution p-value = 1.00e+00
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 7.24e-01

GCGGTACATGTTGGCAGTCGGCCCGCCAAGGTCCGAGACCACGCCGGTGAAGCCCGGCACCTTGTCACGCATCTCTTCGATTTCGTGCAGGATCGACTCGTGCGAGCGGTTCTGGATGATGCGGCCTTCGTGCTCGGTGATCGAGCA‑GAAGGTACAGCCACCGAAGCAGCCACGCATGATGTTCACCGAGAAACGGATCATCTCGTAGGCCGGGATGCGCTCCTTGCCATAGGCCGGGTGCGGCACACGG  >  NC_002947/5539660‑5539909                                                                                                                                             |                                                                                                               ggagTACATGTTGGCAGTCGGCCCGCCAAGGTCCGAGACCACGCCGGTGAAGCCCGGCACCTTGTCACGCATCTCTTCGATTTCGTGCAGGATCGACTCGTGCGAGCGGTTCTGGATGATGCGGCCTTCGTGCTCGGTGATCGAGCA‑Gaa                                                                                                      >  1:329823/4‑150 (MQ=255)   ggTACATGTTGGCAGTCGGCCCGCCAAGGTCCGAGACCACGCCGGTGAAGCCCGGCACCTTGTCACGCATCTCTTCGATTTCGTGCAGGATCGACTCGTGCGAGCGGTTCTGGATGATGCGGCCTTCGTGCTCGATCACCGAGCacgaag                                                                                                     <  2:56237/150‑6 (MQ=255)     tACATGTTGGCAGTCGGCCCGCCAAGGTCCGAGACCACGCCGGTGAAGCCCGGCACCTTGTCACGCATCTCTTCGATTTCGTGCAGGATCGACTCGTGCGAGCGGTTCTGGATGATGCGGCCTTCGTTCTCGGTGATCGAGCA‑GAAGGTa                                                                                                  >  2:552046/1‑150 (MQ=255)        aTGTTGGCAGTCGGCCCGCCAAGGTCCGAGACCACGCCGGTGAAGCCCGGCACCTTGTCACGCATCTCTTCGATTTCGTGCAGGATCGACTCGTGCGAGCGGTTCTGGATGATGCGGCCTTCGTGCTCGATCACCGAGCACGAAggccgc                                                                                                <  2:361669/150‑5 (MQ=255)                aGTCGGCCCGCCAAGGTCCGAGACCACGCCGGTGAAGCCCGGCACCTTGTCACGCATCTCTTCGATTTCGTGCAGGATCGACTCGTGCTAGCGGTTCTGGATGATGCGGCCTTCGTGCTCGGTGATCGAGCA‑GAAGGTACAGCCACCGaa                                                                                       >  1:174944/1‑150 (MQ=255)                     gCCCGCCAAGGTCCGAGACCACGCCGGTGAAGCCCGGCACCTTGTCACGCATCTCTTCGATTTCGTGCAGGATCGACTCGTGCGAGCGGTTCTGGATGATGCGGCCTTCGTGCTCGGTGATCGAGCA‑GAAGGTACAGCCACCGAagcagc                                                                                  >  2:588945/1‑150 (MQ=255)                        cGCCAAGGTCCGAGACCACGCCGGTGAAGCCCGGCACCTTGTCACGCATCTCTTCGATTTCGTGCAGGATCGACTCGTGCGAGCGGTTCTGGATGATGCGGCCTTCGTGCTCGGTGATCGAGCA‑GAAGGTACAGCCACCGAagtagttaa                                                                               >  1:412422/1‑146 (MQ=255)                                        cACGCCGGTGAAGCCCGGCACCTTGTCACGCATCTCTTCGATTTCGTGCAGGATCGACTCGTGCGAGCGGTTCTGGATGATGCGGCCTTCGTGCTCGGTGATCGAGCA‑GAAGGTACAGCCACCGAAGCAGCCACGCATGATGTTCACCga                                                               >  1:250999/1‑150 (MQ=255)                                             cGGTGAAGCCCGGCACCTTGTCACGCATCTCTTCGATTTCGTGCAGGATCGACTCGTGCGAGCGGTTCTGGATGATGCGGCCTTCGTGCTCGGTGATCGAGCA‑GAAGGTACAGCCACCGAAGCAGCCACGCATGATGTTCACCGAGAAAc                                                          <  2:250999/150‑1 (MQ=255)                                                                   aCGCATCTCTTCGTTTTCGTGCAGGATCGCCTCGTGCGAGCGGTTCTGGATGATGCGGCCTTCGTGCTCGGTGATCGAGCA‑GAAGGTACAGCCACCGAAGCAGCCACGCATGATGTTCACCGAGAAACGGATCATCTCGTAGGCCGGGAt                                    <  1:524415/150‑1 (MQ=255)                                                                     ccATCTCTTCGATTTCGTGGAGGATCGACTCGTGCGAGCGGTTCTGGATGATGCGGCCTTCGTGCTCGGTGATCGAGCA‑GAAGGTACAGCCACCGAAGCAGCCACGCATGATGTTCACCGAGAAACGGATCATCTCGTAGGCCGGGATgc                                  <  2:141054/149‑1 (MQ=255)                                                                              cGATTTCGTGCAGGATCGACTCGTGCGAGCGGTTCCGGATGATGCGGCCTTCGTGCTCGGTGATCGAGCA‑GAAGGTACAGCCACCGAAGCAGGCACGCATGATGTTCACCGAGAAACGGATCATCTCGTAGGCCGGGATGCGCTCCTTGc                         <  2:329823/150‑1 (MQ=255)                                                                                aTTTCGTGCAGGATCGACTCGTGCGAGCGGTTCTGGATGATGCGGCCTTCGTGCTCGGTGATCGAGCA‑GAAGGTACAGCCACCGAAGCAGCCACGCATGATGTTCACCGAGAAACGGATCATCTCGTAGGCCGGGATGCGCTCCTTGCCa                       <  2:420267/150‑1 (MQ=255)                                                                                           gATCGACTCGTGCGAGCGGTTCTGGATGATGCGGCCTTCGTGCTCGGTGATCGAGCA‑GAAGGTACAGCCACCGAAGCAGCCACGCATGATGTTCACCGAGAAACGGATCATCTCGTAGGCCGGGATGCGCTCCTTGCCATAGGCCGGGTg            >  2:363731/1‑150 (MQ=255)                                                                                               gccTCGTGCGAGCGGTTCTGGATGATGCGGCCTTCGTGCTCGGTGATCGAGCA‑GAAGGTACAGCCACGGAAGCAGCAGCGGGTGATGGTGACCGAGAAACGGATCATCTCGTAGGCCGGGATGCGCTCCTTGCCATAGGCCGGGTGCGGc        <  2:149796/148‑1 (MQ=255)                                                                                                     ggcgcgcGGTTCTTGATCATGCGTCCCTCGGGTTCGGTGATCGAGCA‑GAAGGTTCAGCCGCCGAAGCAGCCACGCATGATGTTCACCGAGAAACGGATCATCTCGTAGGGCGGGATGCGCTCCTTGCCATAGGCCGGGTGCGGCACACgg  <  1:588945/149‑1 (MQ=255)                                                                                                                   gatgatGCGGCCTTCGTGCTCGGTGATCGAGCA‑GAAGGTACAGCCACCGAAGCAGCCACGCATGATGTTCACCg                                                                >  2:352762/1‑74 (MQ=255)                                                                                                                   gatgatGCGGCCTTCGTGCTCGGTGATCGAGCA‑GAAGGTACAGCCACCGAAGCAGCCACGCATGATGTTCACCg                                                                <  1:352762/74‑1 (MQ=255)                                                                                                                           ggCCTTCGTGCTCGGTGATCGAGCA‑GAAGGTACAGCCACCGAAGCAGCCACGCATGATGTTCACCga                                                               <  2:18386/67‑1 (MQ=255)                                                                                                                           ggCCTTCGTGCTCGGTGATCGAGCA‑GAAGGTACAGCCACCGAAGCAGCCACGCATGATGTTCACCga                                                               >  1:18386/1‑67 (MQ=255)                                                                                                                               cttctGCTCGATCACCGAGCA‑GAAGGTACAGCCACCGAAGCAGCCACGCATGATGTTCACCGAGAAACGGATCATCTCGTAGGCCGGGATGCGCTCCTTGCCATAGGCCg                >  1:496870/5‑110 (MQ=255)                                                                                                                                ttctGCTCGATCACCGAGCACGAAGGTACAGCCACCGAAGCAGCCACGCATGATGTTCACCGAGAAACGGATCATCTCGTAGGCCGGGATGCGCTCCTTGCCATAg                    >  1:327690/4‑106 (MQ=255)                                                                                                                                             |                                                                                                               GCGGTACATGTTGGCAGTCGGCCCGCCAAGGTCCGAGACCACGCCGGTGAAGCCCGGCACCTTGTCACGCATCTCTTCGATTTCGTGCAGGATCGACTCGTGCGAGCGGTTCTGGATGATGCGGCCTTCGTGCTCGGTGATCGAGCA‑GAAGGTACAGCCACCGAAGCAGCCACGCATGATGTTCACCGAGAAACGGATCATCTCGTAGGCCGGGATGCGCTCCTTGCCATAGGCCGGGTGCGGCACACGG  >  NC_002947/5539660‑5539909

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 12 ≤ ATCG/ATCG < 22 ≤ ATCG/ATCG < 37 ≤ ATCG/ATCG < 41 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑