Predicted mutation
evidence	seq id	position	mutation	freq	annotation	gene	description
RA	NC_002947	873,428	T→C	20.6%	L20P (CTT→CCT)	PP_5457 →	hypothetical protein

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NC_002947	873,428	0	T	C	20.6%	57.9 / 8.6	29	L20P (CTT→CCT)	PP_5457	hypothetical protein
Reads supporting (aligned to +/- strand):  ref base T (10/13);  new base C (3/3);  total (13/16)
Fisher's exact test for biased strand distribution p-value = 1.00e+00
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 1.00e+00

GCCAGGTGTGCTGTCAGCCTGTGGTGTGCATTCTGCAGGTGCATGGTGACGAATGGATGCTTGAAGTCCGCCGCGAGGACGACACCTGATGCAGCGTATCTACGAACCGGAAAGCCTGCTTGAGGCGCAAATGCTGGCAGGCATGCTTGCCAGCGAGGGGATCGATGTACACGTGGTCGGCCGTGACCTTGTCGGTGCCGCCGGCGAGCTGCCCTTGCAGGGCCTGCTGGGGCTCGTCGTGGCTGATGAGCAGGCCGAATGCGCACGGCAGCTGATCGATGCGTACAATGATG  >  NC_002947/873282‑873574                                                                                                                                                   |                                                                                                                                                   gCCAGGTGTGCTGTCAGCCTGTGGTGTGCATTCTGCAGGTGCATGGTGACGAATGGATGCTTGAAGTCCGCCGCGAGGACGACACCTGATGCAGCGTATCTACGAACCGGAAAGCCTGCTTGAGGCGCAAATGCTGGCAAGCATGCCTGc                                                                                                                                                 <  2:361895/150‑1 (MQ=255)        gtgCTGTCAGCCTGTGGTGTGCATTCTGCAGGTGCATGGTGACGAATGGATGCTTGAAGTCCGCCGCGAGGACGACACCTGATGCAGCGTATCTACGAACCGGAAAGCCTGCTTGAGGCGCAAATGCTGGCAAGCATGCCTGCCAGcatt                                                                                                                                          >  1:185718/1‑147 (MQ=255)         tgCTGTCAGCCTGTGGTGTGCATTCTGCAGGTGCATGGTGACGAATGGATGCTTGAAGTCCGCCGCGAGGACGACACCTGATGCAGCGTATCTACGAACCGGAAAGCCTGCTTGAGGCGCAAATGCTGGCAAGCATGCCTGCCAGcattt                                                                                                                                         <  2:185718/150‑5 (MQ=255)                        gtgtGCATTCTGCAGGTGCATGGTGACGAATGGATGCTTGAAGTCCGCCGCGAGGACGACACCTGATGCAGCGTATCTACGAACCGGAAAGCCTGCTTGAGGCGCAAATGCTGGCAGGCATGCTTGCCAGCGAGGGGATc                                                                                                                                    >  1:334117/1‑140 (MQ=255)                        gtgtGCATTCTGCAGGTGCATGGTGACGAATGGATGCTTGAAGTCCGCCGCGAGGACGACACCTGATGCAGCGTATCTACGAACCGGAAAGCCTGCTTGAGGCGCAAATGCTGGCAGGCATGCTTGCCAGCGAGGGGATc                                                                                                                                    <  2:334117/140‑1 (MQ=255)                              aTTCTGCAGGTGCATGGTGACGAATGGATGCTTGAAGTCCGCCGCGAGGACGACACCTGATGCAGCGTATCTACGAACCGGAAAGCCTGCTTGAGGCGCAAATGCTGGCAGGCATGCTTGCCAGCGAGGGGATCGAt                                                                                                                                 >  2:408393/1‑137 (MQ=255)                              aTTCTGCAGGTGCATGGTGACGAATGGATGCTTGAAGTCCGCCGCGAGGACGACACCTGATGCAGCGTATCTACGAACCGGAAAGCCTGCTTGAGGCGCAAATGCTGGCAGGCATGCTTGCCAGCGAGGGGATCGAt                                                                                                                                 <  1:408393/137‑1 (MQ=255)                                                   gAATGGATACTTGAAGTCCGCCGCGAGGACGACACCGGAGTCAGCGTATCTACGAACCGGAAAGCCTGCTTGAGGCGCAACTGCTGACAAGAATAACACGAACACAAGGCTCCGGGTTACACGTGGTCGGCCGTTACCTTGTCGGTgccg                                                                                               >  2:439417/1‑150 (MQ=255)                                                          tGCTTGAAGTCCGCCGCGAGGACGACACCTGATGCAGCGTATCTACGAACCGGAAAGCCTGCTTGAGGCGCAAATGCTGGCAGGCATGCTTGCCAGCGAGGGGATCGATGTACACGTGGTCGGCCGTGACCTTGTCGGTGCCGCCGGCGa                                                                                        <  2:515229/150‑1 (MQ=255)                                                                      gccgcGAGGACGACACCTGATGCAGCGTATCTACGAACCGGAAAGCCTGCTTGAGGCGCAAATGCTGGCAGGCATGCTTGCCAGCGAGGGGATCGATGTACACGTGGTCGGCCGTGACCTTGTCGGTGCCGCCGGCGAGCTGCCCTTGCa                                                                            >  2:151231/1‑150 (MQ=255)                                                                         gcgAGGACGACACCTGATGCAGCGTATCTACGAACCGGAAAGCCTGCTTGAGGCGCAAATGCTGGCAGGCATGCTTGCCAGCGAGGGGATCGATGTACACGTGGTCGGCCGTGACCTTGTCGGTGCCGCCGGCGAGCTGCCCTTGCAggg                                                                         >  1:435387/1‑150 (MQ=255)                                                                          cgAGGACGACACCTGATGCAGCGTATCTACGAACCGGAAAGCCTGCTTGAGGCGCAAATGCTGGCAGGCATGCTTGCCAGCGAGGGGATCGATGTACACGTGGTCGGCCGTGACCTTGTCGGTGCCGCCGGCGAGCTGCCCTTGCAGGGc                                                                        <  1:439417/150‑1 (MQ=255)                                                                                 gacACCTGATGCAGCGTATCTACGAACCGGAAAGCCTGCTTGAGGCGCAAATGCTGGCAGGCATGCTTGCCAGCGAGGGGATCGATGTACACGTGGTCGGCCGTGACCTTGTCGGTGCCGCCGGCGAGCTGCCCTTGCAGGGCCTGCTgg                                                                 <  1:151231/150‑1 (MQ=255)                                                                                      cTGATGCAGCGTATCTACGAACCGGAAAGCCTGCTTGAGGCGCAAATGCTGGCAGGCATGCTTGCCAGCGAGGGGATCGATGTACACGTGGTCGGCCGTGACCTTGTCGGTGCCGCCGGCGAGCTGCCCTTGCAGGGCCTGCTGGGGCtc                                                            >  1:482941/1‑150 (MQ=255)                                                                                       tGATGCAGCGTATCTACGAACCGGAAAGCCTGCTTGAGGCGCAAATGCTGGCAGGCATGCTTGCCAGCGAGGGGATCGATGTACACGTGGTCGGCCGTGACCTTGTCGGTGCCGCCGGCGAGCTGCCCTTGCAGGGCCTGCTGGGGCtcg                                                           >  1:534987/1‑150 (MQ=255)                                                                                                   tCTACGAACCGGAAAGCCTGCTTGAGGCGCAAATGCTGGCAGGCATGCTTGCCAGCGAGGGGATCGATGTACACGTGGTCGGCCGTGACCTTGTCGGTGCCGCCGGCGAGCTGCCCtt                                                                               <  2:343946/118‑1 (MQ=255)                                                                                                   tCTACGAACCGGAAAGCCTGCTTGAGGCGCAAATGCTGGCAGGCATGCTTGCCAGCGAGGGGATCGATGTACACGTGGTCGGCCGTGACCTTGTCGGTGCCGCCGGCGAGCTGCCCtt                                                                               >  1:343946/1‑118 (MQ=255)                                                                                                    cTACGAACCGGAAAGCCTGCTTGAGGCGCAAATGCTGGCAGGCATGCTTGCCAGCGAGGGGATCGATGTACACGTGGTCGGCCGTGACCTTGTCGGTGCCGCCGGCGAGCTGCCCTTGCAGGGCCTGCTGGGGCTCGTCGTGGCtgatga                                              <  2:435387/150‑1 (MQ=255)                                                                                                                    cTGCTTGAGGCGCAAATGCTGGCAGGCATGCTTGCCAGCGAGGGGATCGATGTACACGTGGTCGGCCGTGACCTTGTCGGTGCCGCCGGCGAGCTGCCCTTGCAGGGCCTGCTGGGGCTCGTCGTGGCTGATGAGCAGGCCGAATGCGCa                              <  2:534987/150‑1 (MQ=255)                                                                                                                         tGAGGCGCAAATGCTGGCAGGCATGCTTGCCAGCGAGGGGATCGATGTACACGTGGTCGGCCGTGACCTTGTCGGTGCCGCCGGCGAGCTGCCCTTGCAGGGCCTGCTGGGGCTCGTCGTGGCTGATGCGCAGGCCGATTGCGCACGGCa                         <  2:482941/150‑1 (MQ=255)                                                                                                                                   aTGCTGGCAGGCATGCTTGCCAGCGAGGGGATCGATGTACACGTGGTCGGCCGTGACCTTGTCGGTGCCGCCGGCGAGCTGCCCTTGCAGGGCCTGCTGGGGCTCGTCGTGGCTGCTGAGCAGGCCGAATGCGCACGGCAGCTGATCGAt               <  2:31104/150‑1 (MQ=255)                                                                                                                                           aggcaTGCTTGCCAGCGAGGGGATCGATGTACACGTGGTCGGCCGTGACCTTGTCGGTGCCGCCGGCGAGCTGCCCTTGCAGGGCCTGCTGGGGCTCGTCGTGGCTGATGAGCAGGCCGAATGCGCACGGCAGCTGATCGATGCGTACaa       >  1:325914/1‑150 (MQ=255)                                                                                                                                           aagcaTGCCTGCCAGCGAGGGGATCGATGTACACGTGGTCGGCCGTGACCTTGTCGGTGCCGCCGGCGAGCTGCCCTTGCa                                                                            >  2:90286/3‑81 (MQ=255)                                                                                                                                           aagcaTGCCTGCCAGCGAGGGGATCGATGTACACGTGGTCGGCCGTGACCTTGTCGGTGCCGCCGGCGAGCTGCCCTTGCa                                                                            <  1:90286/79‑1 (MQ=255)                                                                                                                                             gcaTGCTTGCCAGCGAGGGGATCGATGTACACGTGGTCGGCCGTGACCTTGTCGGTGCCGCCGGCGAGCTGCCCTTGCAGGGCCTGCTgggg                                                               <  2:559737/92‑1 (MQ=255)                                                                                                                                             gcaTGCTTGCCAGCGAGGGGATCGATGTACACGTGGTCGGCCGTGACCTTGTCGGTGCCGCCGGCGAGCTGCCCTTGCAGGGCCTGCTgggg                                                               >  1:559737/1‑92 (MQ=255)                                                                                                                                             gcaTGCTTGCCAGCGAGGGGATCGATGTACACGTGGTCGGCCGTGACCTTGTCGGTGCCGCCGGCGAGCTGCCCTTGCAGGGCCTGCTGGGGCTCGTCGTGGCTGATGAGCAGGCCGAATGCGCACGGCAGCTGATCGATGCGTACAatg     >  2:467117/1‑150 (MQ=255)                                                                                                                                               aTGCTTGCCAGCGAGGGGATCGATGTACCCGTGGTCCGTCGGGACCTGGTCGGTGCCGCCGGCGAGCTGCCCTTTCAGGGCCTGCTGGGGCTCGTCGTGGCTGATGAGCAGGCCGAATGCGCACGGCAGCTGATCGATGCGTACAatgat   <  1:290735/150‑1 (MQ=255)                                                                                                                                                tGCTTGCCAGCGAGGGGATCGATGTACACGTGGTCGGCCGTGACCTTGTCGGTGCCGCCGGCGAGCTGCCCTTGCAGGGCCTGCTGGGGCTCGTCGTGGCTGATGAGCAGGCCGAATGCGCACGGCAGCTGATCGATGCGTACAatgatg  <  1:355258/150‑1 (MQ=255)                                                                                                                                                   |                                                                                                                                                   GCCAGGTGTGCTGTCAGCCTGTGGTGTGCATTCTGCAGGTGCATGGTGACGAATGGATGCTTGAAGTCCGCCGCGAGGACGACACCTGATGCAGCGTATCTACGAACCGGAAAGCCTGCTTGAGGCGCAAATGCTGGCAGGCATGCTTGCCAGCGAGGGGATCGATGTACACGTGGTCGGCCGTGACCTTGTCGGTGCCGCCGGCGAGCTGCCCTTGCAGGGCCTGCTGGGGCTCGTCGTGGCTGATGAGCAGGCCGAATGCGCACGGCAGCTGATCGATGCGTACAATGATG  >  NC_002947/873282‑873574

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 12 ≤ ATCG/ATCG < 32 ≤ ATCG/ATCG < 41 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑