Predicted mutation
evidence	seq id	position	mutation	freq	annotation	gene	description
RA	NC_002947	2,288,819	T→C	26.7%	F80L (TTC→CTC)	PP_2015 →	hypothetical protein

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NC_002947	2,288,819	0	T	C	26.7%	17.8 / 6.1	15	F80L (TTC→CTC)	PP_2015	hypothetical protein
Reads supporting (aligned to +/- strand):  ref base T (4/7);  new base C (2/2);  total (6/9)
Fisher's exact test for biased strand distribution p-value = 1.00e+00
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 9.53e-01

GCCGAGCAGAAAGAGCTGTCGCTGCAGGCGGTCATCGCCTGGGAGATGAAGAACCTGCCCGAAGACCAGCGCACCGGCTACATGGGCCCACAGGAATGTGCGTCGAAGTCCGCGCCCATCGCCAACATTCTGTTCAAGTCGGACTCGGTACATTGATCGAACTCGCACGTGGCTCGTTGAGCAAGATGGCCGTAAGCCTGCAGGCACCGGTGGTGCAGTACAGCTTCCGCCTGGATGACACCCAGGTGCCGGTCAACCCCATGATCGG  >  NC_002947/2288687‑2288954                                                                                                                                     |                                                                                                                                        gccgAGCAGAAAGAGCTGTCGCTGCAGGCGGTCATCGCCTGGGAGATGAAGAACCTGCCCGAAGACCAGCGCACCGGCTACATGGGCCCACAGGAATGTGCGTCGAAGTCCGCGCCCATCGCCAACATTCTGTTCa                                                                                                                                      >  1:2007/1‑136 (MQ=255)              agCTGTCGCTGCAGGCGGTCATCGCCTGGGAGATGAAGAACCTGCCCGAAGACCAGCGCACCGGCTACATGGGCCCACAGGAATGTGCGTCGAAGTCCGCGCCCATCGCCAACATTCTGTTCAAGTCGGACTCGGt                                                                                                                         <  1:388559/136‑1 (MQ=255)              agCTGTCGCTGCAGGCGGTCATCGCCTGGGAGATGAAGAACCTGCCCGAAGACCAGCGCACCGGCTACATGGGCCCACAGGAATGTGCGTCGAAGTCCGCGCCCATCGCCAACATTCTGTTCAAGTCGGACTCGGt                                                                                                                         <  1:415509/136‑1 (MQ=255)                                                  agaaCCTGCCCGAAGACCAGCGCACCGGCTACATGGGCCCACAGGAATGTGCGTCGAAGTCCGCGCCCAACGCCAACATTCTGTTCAAGTCGGACTCGGTACATTGATCGAACTCGCACGTGGCTCGTTGAGCAAg                                                                                     >  1:98079/1‑136 (MQ=255)                                                            cGAAGACCAGCGCACCGGCTACATGGGCCCACAGGAATGTGCGTCGAAGTCCGCGCCCATCGCCAACATTCTGTTCAAGTCGGACTCGGTACATTGATCGAACTCGCACGTGGCTCGTTGAGCAAGATGGCCGTaa                                                                           >  2:238549/1‑136 (MQ=255)                                                                   cAGCGCACCGGCTACATGGGCCCACAGGAATGTGCGTCGAAGTCCGCGCCCATCGCCAACATTCTGTTCAAGTCGGACTCGGTACATTGATCGAACTCGCACGTGGCTCGTTGAGCAAGATGGCCGTAAGCCTGCa                                                                    <  2:229616/136‑1 (MQ=255)                                                                        cACCGGCTACATGGGCCCACAGGAATGTGCGTCGAAGTCCGCGCCCATCGCCAACATTCTGTTCAAGTCGGACTCGGTACATTGATCGAACTCGCACGTGGCTCGTTGAGCAAGATGGCCGTAAGCCTGCAGGCAc                                                               <  1:80289/136‑1 (MQ=255)                                                                             gCTACATGGGCCCACAGGAATGTGCGTCGAAGTCCGCGCCCATCGCCAACATTCTGTTCAAGTCGGACTCGGTACATTGATCGAACTCGCACGTGGCTCGTTGAGCAAGATGGCCGTAAGCCTGCAGGCACCggtg                                                          <  2:360541/136‑1 (MQ=255)                                                                                    gggCCCACAGGAATGTGCGTCGAAGTCCGCGCCCATCGCCAACATTCTGTTCAAGTCGGACTCGGTACATTGATCGAACTCGCACGTGGCTCGTTGAGCAAGATGGCCGTAAGCCTGCAGGCACCGGTGGTGCAGt                                                   >  2:432715/1‑136 (MQ=255)                                                                                              gAATGTGCGTCGAAGTCCGCGCCCATCGCCAACATTCTGCTCAAGTCGGACTCGGTACATTGATCGAACTCGCACGTGGCTCGTTGAGCAAGATGGCCGTAAGCCTGCAGGCAc                                                               <  1:246119/114‑1 (MQ=255)                                                                                              gAATGTGCGTCGAAGTCCGCGCCCATCGCCAACATTCTGCTCAAGTCGGACTCGGTACATTGATCGAACTCGCACGTGGCTCGTTGAGCAAGATGGCCGTAAGCCTGCAGGCAc                                                               <  1:248628/114‑1 (MQ=255)                                                                                              gAATGTGCGTCGAAGTCCGCGCCCATCGCCAACATTCTGCTCAAGTCGGACTCGGTACATTGATCGAACTCGCACGTGGCTCGTTGAGCAAGATGGCCGTAAGCCTGCAGGCAc                                                               >  2:246119/1‑114 (MQ=255)                                                                                              gAATGTGCGTCGAAGTCCGCGCCCATCGCCAACATTCTGCTCAAGTCGGACTCGGTACATTGATCGAACTCGCACGTGGCTCGTTGAGCAAGATGGCCGTAAGCCTGCAGGCAc                                                               >  2:248628/1‑114 (MQ=255)                                                                                                                   cccATCGCCAACATTCTGTTCAAGTCGGACTCGGTACATTGATCGAACTCGCACGTGGCTCGTTGAGCAAGATGGCCGTAAGCCTGCAGGCACCGGTGGTGCAGTAGAGCTTCCGCCTGGATGACACCCAGGTGcc                    <  1:388291/136‑1 (MQ=255)                                                                                                                           cAACATTCTGTTCAAGTCGGACTCGGTACATTGATCGAACTCGCACGTGGCTCGTTGAGCAAGATGGCCGTAAGCCTGCAGGCACCGGTGGTGCAGTACAGCTTCCGCCTGGATGACACCCAGGTGCCGGTCAAcc            <  1:72258/136‑1 (MQ=255)                                                                                                                                     ttCAAGTCGGACTCGGTACATTGATCGAACTCGCACGTGGCTCGTTGAGCAAGATGGCCGTAAGCCTGCAGGCACCGGTGGTGCAGTACAGCTTCCGCCTGGATGACACCCAGGTGCCGGTCAACCCCATGATCgg  >  2:457536/1‑136 (MQ=255)                                                                                                                                     |                                                                                                                                        GCCGAGCAGAAAGAGCTGTCGCTGCAGGCGGTCATCGCCTGGGAGATGAAGAACCTGCCCGAAGACCAGCGCACCGGCTACATGGGCCCACAGGAATGTGCGTCGAAGTCCGCGCCCATCGCCAACATTCTGTTCAAGTCGGACTCGGTACATTGATCGAACTCGCACGTGGCTCGTTGAGCAAGATGGCCGTAAGCCTGCAGGCACCGGTGGTGCAGTACAGCTTCCGCCTGGATGACACCCAGGTGCCGGTCAACCCCATGATCGG  >  NC_002947/2288687‑2288954

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: ‑