Predicted mutation
evidence	seq id	position	mutation	freq	annotation	gene	description
RA	NC_002947	5,032,844	C→A	14.8%	S105R (AGC→AGA)	PP_4435 →	hypothetical protein

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NC_002947	5,032,844	0	C	A	14.8%	65.3 / 2.0	27	S105R (AGC→AGA)	PP_4435	hypothetical protein
Reads supporting (aligned to +/- strand):  ref base C (11/12);  new base A (2/2);  total (13/14)
Fisher's exact test for biased strand distribution p-value = 1.00e+00
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 8.91e-01

GAAAATCCTCACAGTGACTATCTATCTGAACGACATCACCACCGACTTCGCTGCCATGAACGAGGTTTGGGAAGAGTGGGTCGCGGAAGGTCAGGCTCCTGCGCGAGCCTGTGTTGAGGCGGCTATGTTCAAGCCAAGCCTGCTCGTTGAGATGTCCGTAGTAGCAGCAATCGCCTGACGCTTAAAAGCGCACCCGGCAGGCGCCTATCCAGCCTGGTAACAGGTCAGAGGCGCTCGCCGGGCACCGCTAAATCGATCCAGGAACAAACTCATGAACCACGT  >  NC_002947/5032706‑5032987                                                                                                                                           |                                                                                                                                                gAAAATCCTCACAGTGACTATCTATCTGAACGACATCACCACCGACTTCGCTGCCATGAACGAGGTTTGGGAAGAGTGGGTCGCGCAAGGTCAGGCTCCTGCGCGAGCCTGTGTTGAGGCGGCTATGTTCAAGCCAAGCCTGCTCGTTga                                                                                                                                      <  1:533865/150‑1 (MQ=255)  aaaaTCCTCACAGTGACTATCTATCTGAACGACATCACCACCGACTTCGCTGCCATGAACGAGGTTTGGGAAGAGTGGGTCGCGGAAGGTCAGGCTCCTGCGCGAGCCTGTGTTGAGGCGGCTATGTTCAAGCCAAGACTGCTCGTTgag                                                                                                                                     >  1:404319/1‑150 (MQ=255)  aaaaTCCTCACAGTGACTATCTATCTGAACGACATCACCACCGACTTCGCTGCCATGAACGAGGTTTGGGAAGAGTGGGTCGCGGAAGGTCAGGCTCCTGCGCGAGCCTGTGTTGAGGCGGCTATGTTCAAGCCAAGACTGCTCGTTgag                                                                                                                                     >  1:404352/1‑150 (MQ=255)     aTCCTCACAGTGACTATCTATCTGAACGACATCACCACCGACTTCGCTGCCATGAACGAGGTTTGGGAAGAGTGGGTCGCGGAAGGTCAGGCTCCTGCGCGAGCCTGTGTTGAGGCGGCTATGTTCAAGCCAAGCCTGCTCGTTGAGATg                                                                                                                                  <  1:36191/150‑1 (MQ=255)         tCACAGTGACTATCTATCTGAACGACATCACCACCGACTTCGCTGCCATGAACGAGGTTTGGGAAGAGTGGGTCGCGGAAGGTCAGGCTCCTGCGCGAGCCTGTGTTGAGGCGGCTATGTTCAAGCCAAGCCTGCACGTTGAGATGTCCg                                                                                                                              >  1:293211/1‑150 (MQ=255)                 aCTATCTATCTGAACGACATCACCACCGACTTCGCTGCCATGAACGAGGTTTGGGAAGAGTGGGTCGCGGAAGGTCAGGCTCCTGCGCGAGCCTGTGTTGAGGCGGCTATGTTCAAGCCAAGACTGCTCGTTGAGATGTCCGCAGTagca                                                                                                                      <  2:404352/150‑1 (MQ=255)                 aCTATCTATCTGAACGACATCACCACCGACTTCGCTGCCATGAACGAGGTTTGGGAAGAGTGGGTCGCGGAAGGTCAGGCTCCTGCGCGAGCCTGTGTTGAGGCGGCTATGTTCAAGCCAAGACTGCTCGTTGAGATGCCCGcagtagta                                                                                                                      <  2:404319/150‑3 (MQ=255)                         tctGAACGACATCACCACCGACTTCGCTGCCATGAACGAGGTTTGGGAAGAGTGGGTCGCGGAAGGTCAGGCTCCTGCGCGAGCCTGTGTTGAGGCGGCTATGTTCAAGCCAAGCCTGCTCGTTGAGATGTCCGTAGTAGCAGCAATCGc                                                                                                              <  2:311336/150‑1 (MQ=255)                           tGAACGACATCACCACCGACTTCGCTGCCATGAACGAGGTTTGGGAAGAGTGGGTCGCGGAAGGTCAGGCTCCTGCGCGAGCCTGTGTTGAGGCGGCTATGTTCAAGCCAAGCCTGCTCGTTGAGATGTCCGTAGTAGCAGCAATCGCCt                                                                                                            >  2:37931/1‑150 (MQ=255)                                      accaccGACTTCGCTGCCATGAACGAGGTTTGGGAAGAGTGGGTCGCGGAAGGTCAGGCTCCTGCGCGAGCCTGTGTTGAGGCGGCTATGTTCAAGCCAAGCCTGCTCGTTGAGATGTCCGTAGTAGCAGCAATCGCCTGACGCTTaaaa                                                                                                 <  2:96489/150‑1 (MQ=255)                                              cTTCGCTGCCATGAACGAGGATTGGGAAGAGTGGGTAGCGGACGGTCAGGCTCCTGCGCGAGCGTGTGTTGGGGCGGCTAGGTTCAAGACAAGCCTGCTCGTTGAGATGTCCGTAGTGGCAGCCATCGACTGACGCTTAAAAGCGCAccc                                                                                         >  2:1687/1‑150 (MQ=255)                                                 cGCTGCCATGAACGAGGTTTGGGAAGAGTGGGTCGCGGAAGGTCAGGCTCCTGCGCGAGCCTGTGTTGAGGCGGCTATGTTCAAGCCAAGCCTGCTCGTTGAGATGTCCGTAGTAGCAGCAATCGCCTGACGCTTAAAAGCGCACCCGGc                                                                                      <  1:1687/150‑1 (MQ=255)                                                          gAACGAGGTTTGGGAAGAGTGGGTCGCGGAAGGTCAGGCTCCTGCGCGAGCCTGTGTTGAGGCGGCTATGTTCAAGCCAAGCCTGCTCGTTGAGATGTCCGTAGTAGCAGCAATCGCCTGACGCTTAAAAGCGCACCCGGCAGGCGCCTa                                                                             >  2:421297/1‑150 (MQ=255)                                                             cGAGGTTTGGGAAGAGTGGGTCGCGGAAGGTCAGGCTCCTGCGCGAGCCTGTGTTGAGGCGGCTATGTTCAAGCCAAGCCTGCTCGTTGAGATGTCCGTAGTAGCAGCAATCGCCTGACGCTTAAAAGCGCACCCGGCAGGCGCCTATcc                                                                          >  1:676603/1‑150 (MQ=255)                                                                    tGGGAAGAGTGGGTCGCGGAAGGTCAGGCTCCTGCGCGAGCCTGTGTTGAGGCGGCTATGTTGAAGCAAAGCCGGCGCGTTGAGATGTCCGTAGTAGCAGCAATCGCCTGACGCTTAAAAGCGCACCCGGCAGGCGCCTATCCAGCCTgg                                                                   <  2:250124/150‑1 (MQ=255)                                                                       gAAGAGTGGGTCGCGGAAGGTCAGGCTCCTGCGCGAGCCTGTGTTGAGGCGGCTATGTTCAAGCCAAGCCTGCTCGTTGAGATGTCCGTAGTAGCAGCAATCGCCTGACGCTTAAAAGCGCACCCGGCAGGCGCCTATCCAGCCTGGTaa                                                                >  1:627867/1‑150 (MQ=255)                                                                               gcgagcgAAAGCTCAGGCTCCTACGCGAGCCTGTGTTGAGGCGGCTATGTTCAAGCCAAGCCTGCTCGTTGAGATGTCCGTAGTAGCAGCAATCACCTGATGCTTAATAGCGCACCCGGCAGGCGCCTATCTAGCCTCGTAACTGGTCag                                                        <  2:293211/146‑1 (MQ=255)                                                                                           tCAGGCTCCTGCGCGAGCCTGTGTTGAGGCGGCTATGTTCAAGCCCAGCCTGCTCGTTGAGATGTCCGTAGTAGCAGCAATCGCCTGACGCt                                                                                                      <  1:173060/92‑1 (MQ=255)                                                                                           tCAGGCTCCTGCGCGAGCCTGTGTTGAGGCGGCTATGTTCAAGCCAAGCCTGCTCGTTGAGATGTCCGTAGTAGCAGCAATCGCCTGACGCt                                                                                                      >  2:173060/1‑92 (MQ=255)                                                                                             aGGCTCCTGCGCGAGCCTGTGTTGAGGCGGCTATGTTcaagccaagc                                                                                                                                                 >  1:688299/1‑47 (MQ=255)                                                                                             aGGCTCCTGCGCGAGCCTGTGTTGAGGCGGCTATGTTcaagccaagc                                                                                                                                                 <  2:688299/47‑1 (MQ=255)                                                                                                         gAGCCTGTGTTGAGGCGGCTATGTTCAAGCCAAGCCTGCTCGTTGAGATGTCCGTAGTAGCAGCAATCGCCTGACGCTTAAAAGCGCACCCGGCAGGCGCCTATCCAGCCTGGTAACAGGTCAGAGGCGCTCGCCGGGCACCGCTAAATc                              >  1:172052/1‑150 (MQ=255)                                                                                                            ccTGTGTTGAGGCGGCTATGTTCAAGCCAAGCCTGCTCGTTGAGATGTCCGGAGTAGCAGCAATCGCCTGACGCTTAAAAGCGCACCCGGCAGGCGCCTATCCAGCCTGGTAACAGGTCAGAGGCGCTCGCCGGGCACCGCTAAATCGAt                           <  1:421297/150‑1 (MQ=255)                                                                                                                       gcggcTATGTTCAAGCCAAGCCTGCTCGTTGAGATGTCCGTAGTAGCAGCAATCGCCTGACGCTTAAAAGCGCACCCGGCAGGCGCCTATCCAGCCTGGTAACAGGTCAGAGGCGCTCGCCGGGCACCGCTAAATCGATCCAGGAACaaa                >  1:347345/1‑150 (MQ=255)                                                                                                                           cTATGTTCAAGCCAAGCCTGCTCGTTGAGATGTCCGTAGTAGCAGCAATCGCCTGACGCTTAAAAGCGCACCCGGCAGGCGCCTATCCAGCCTGGTAACAGGTCAGAGGCGCTCGCCGGGCACCGCTAAATCGATCCAGGAACAAACTCa            <  2:347345/150‑1 (MQ=255)                                                                                                                            tATGTTCAAGCCAAGCCTGCTCGTTGAGATGTCCGTAGTAGCAGCAATCGCCTGACGCTTAAAAGCGCACCCGGCAGGCGCCTATCCAGCCTGGTAACAGGTCAGAGGCGCTCGCCGGGCACCGCTAAATCGATCCAGGAACAAACTCAt           >  1:720895/1‑150 (MQ=255)                                                                                                                             aTGTTCAAGCCAAGCCTGCTCGTTGAGATGTCCGTAGTAGCAGCAATCGCCTGACGCTTAAAAGCGCACCCGGCAGGCGCCTATCCAGCCTGGTAACAGGTCAGAGGCGCTCGCCGGGCACCGCTAAATCGATCCAGGAACAAACTCATg          <  2:627867/150‑1 (MQ=255)                                                                                                                                ttCAAGCCAAGCCTGCTCGTTGAGATGTCCGTAGTAGCAGCAATCGCCTGACGCTTAAAAGCGCACCCGGCAGGCGCCTATCCAGCCTGGTAACAGGTCAGAGGCGCTCGCCgg                                           <  1:411905/114‑1 (MQ=255)                                                                                                                                ttCAAGCCAAGCCTGCTCGTTGAGATGTCCGTAGTAGCAGCAATCGCCTGACGCTTAAAAGCGCACCCGGCAGGCGCCTATCCAGCCTGGTAACAGGTCAGAGGCGCTCGCCgg                                           >  2:411905/1‑114 (MQ=255)                                                                                                                                     gccaagccTGCTCGTTGAGATGTCCGTAGTAGCAGCAATCGCCTGACGCTTAAAAGCGCACCCGGCAGGCGCCTATCCAGCCTAGTAACAGGTCAGAGGCGCTCGCCGGGCACCGCTAAATCGATCCAGGAACAAACTCATGAACCACGt  <  2:350891/150‑1 (MQ=255)                                                                                                                                        aagccTGCTCGTTGAGATGTCCGTAGTAGCAGCAATCGCCTGACGCTTAAAAGCGCACCCGGCAGGCGCCTATc                                                                           >  2:564038/1‑74 (MQ=255)                                                                                                                                        aagccTGCTCGTTGAGATGTCCGTAGTAGCAGCAATCGCCTGACGCTTAAAAGCGCACCCGGCAGGCGCCTATc                                                                           <  1:564038/74‑1 (MQ=255)                                                                                                                                           |                                                                                                                                                GAAAATCCTCACAGTGACTATCTATCTGAACGACATCACCACCGACTTCGCTGCCATGAACGAGGTTTGGGAAGAGTGGGTCGCGGAAGGTCAGGCTCCTGCGCGAGCCTGTGTTGAGGCGGCTATGTTCAAGCCAAGCCTGCTCGTTGAGATGTCCGTAGTAGCAGCAATCGCCTGACGCTTAAAAGCGCACCCGGCAGGCGCCTATCCAGCCTGGTAACAGGTCAGAGGCGCTCGCCGGGCACCGCTAAATCGATCCAGGAACAAACTCATGAACCACGT  >  NC_002947/5032706‑5032987

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 12 ≤ ATCG/ATCG < 27 ≤ ATCG/ATCG < 37 ≤ ATCG/ATCG < 41 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑