Predicted mutation
evidence	seq id	position	mutation	freq	annotation	gene	description
RA	NC_002947	5,539,537	A→C	21.4%	R499R (CGT→CGG)	PP_4872 ←	hypothetical protein

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NC_002947	5,539,537	0	A	C	21.4%	44.8 / 11.0	28	R499R (CGT→CGG)	PP_4872	hypothetical protein
Reads supporting (aligned to +/- strand):  ref base A (8/14);  new base C (2/4);  total (10/18)
Fisher's exact test for biased strand distribution p-value = 1.00e+00
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 9.66e-01

GGGCCACGCTCGGTGTGCTCCGGGGCAATCTTCAGGTAGCCGCCAACGTGGTGGGTGACCAGTTCCTTGACGTACTCCGGCGATTCCACCGCCAGGTCGTAGCGCAGGCCGGAAGCAATCAGGATCTTTTTCACACCCGGCAAGGCACGGGCCTTGCGGTAAAGCTCGATCAACGAGCTGTGGTCGGTATTGAGGTTTTCGCAGATACCCGGGAATACGCACGACGGCTTGCGGCAGTACTTCTCGATTTCGGGGCTTTTGCAGGCGATGCGGTACATGTTGGCAGTCGGCCCGCC  >  NC_002947/5539391‑5539686                                                                                                                                                   |                                                                                                                                                      gggCCACGCTCGGTGTGCTCCGGGGCAATCTTCAGGTAGCCGCCAACGTGGTGGGTGACCAGTTCCTTGACGTACTCCGGCGATTCCACCGCCAGGTCGTAGCGCAGGCCGGAAGCAATCAGGATCTTTTTCACACCCGGCAAGGCACgg                                                                                                                                                    <  2:129262/150‑1 (MQ=255)   gCCACGCTCGGTGTGCTCCGGGGCAATCTTCAGGTAGCCGCCAACGTGGTGGGTGACCAGTTCCTTGACGTACTCCGGCGATTCCACCGCCAGGTCGTAGCGCAGGCCGGAAGCAATCAGGATCTTTTTCACACCCGGCAAGGCACGGGc                                                                                                                                                  <  1:679824/150‑1 (MQ=255)    ccACGCTCGGTGTGCTCCGGGGCAATCTTCAGGTAGCCGCCAACGTGGTGGGTGACCAGTTCCTTGACGTACTCCGGCGATTCCACCGCCAGGTCGTAGCGCAGGCCGGAAGCAATCAGGATCTTTTTCACACCCGGCAAGGCACgggtg                                                                                                                                                 <  1:256200/150‑3 (MQ=255)        gCTCGGTGTGCTCCGGGGCAATCTTCAGGTAGCCGCCAACGTGGTGGGTGACCAGTTCCTTGACGTACTCCGGCGATTCCACCGCCAGGTCGTAGCGCAGGCCGGAAGCAATCAGGATCTTTTTCACACCCGGCAAGGCACGGGCCTTGc                                                                                                                                             >  2:223980/1‑150 (MQ=255)             gtgtGCTCCGGGGCAATCTTCAGGTAGCCGCCAACGTGGTGGGTGACCAGTTCCTTGACGTACTCCGGCGATTCCACCGCCAGGTCGTAGCGCAGGCCGGAAGCAATCAGGATCTTTTTCACACCCGGCAAGGCCCGTGCCTTGccgggt                                                                                                                                        <  1:772031/150‑6 (MQ=255)             gtgtGCTCCGGGGCAATCTTCAGGTAGCCGCCAACGTGGTGGGTGACCAGTTCCTTGACGTACTCCGGCGATTCCACCGCCAGGTCGTAGCGCAGGCCGGAAGCAATCAGGATCTTTTTCACACCCCGCAAGGCCCGTGCCTTGccgggt                                                                                                                                        <  1:247788/150‑6 (MQ=255)             gtgtGCTCCGGGGCAATCTTCAGGTAGCCGCCAACGTGGTGGGTGACCAGTTCCTTGACGTACTCCGGCGATTCCACCGCCAGGTCGTAGCGCAGGCCGGAAGCAATCAGGATCTTTTTCACACCCCGCAAGGCCCGTGCCTTGccgggt                                                                                                                                        <  1:247798/150‑6 (MQ=255)              tgtgCTCCGGGGCAATCTTCAGGTAGCCGCCAACGTGGTGGGTGACCAGTTCCTTGACGTACTCCGGCGATTCCACCGCCAGGTCGTAGCGCAGGCCGGAAGCAATCAGGATCTTTTTCACACCCGGCAAGGCACGGGCCTTGCGGTaaa                                                                                                                                       <  2:603112/150‑1 (MQ=255)                   tCCGGGGCAATCTTCAGGTAGCCGCCAACGTGGTGGGTGACCAGTTCCTTGACGTACTCCGGCGATTCCACCGCCAGGTCGTAGCGCAGGCCGGAAGCAATCAGGATCTTTTTCACACCCGGCAAGGCCCGTGCCTTGccgggt                                                                                                                                        <  1:709966/144‑6 (MQ=255)                   tCCGGGGCAATCTTCAGGTAGCCGCCAACGTGGTGGGTGACCAGTTCCTTGACGTACTCCGGCGATTCCACCGCCAGGTCGTAGCGCAGGCCGGAAGCAATCAGGATCTTTTTCACACCCGGCAAGGCCCGTGCCTTGccgggt                                                                                                                                        >  2:709966/1‑139 (MQ=255)                   tCCGGGGCAATCTTCAGGTAGCCGCCAACGTGGTGGGTGACCAGTTCCTTGACGTACTCCGGCGATTCCACCGCCAGGTCGTAGCGCAGGCCGGAAGCAATCAGGATCTTTTTCACACCCGGCAAGGCACGGGCCTTGCGGTAAAGCTCg                                                                                                                                  >  1:766621/1‑150 (MQ=255)                            aTCTTCAGGTAGCCGCCAACGTGGTGGGTGACCAGTTCCTTGATGTTCTCCGGCGATTCCACCGCCAGGTCGTAGCGCAGGCCGGAAGCAATCAGGATCTTTTTCCCACCCGGCAAGGCACGGGCCTTGCGGTAAAGCTCGATCAACGAg                                                                                                                         <  1:766798/150‑1 (MQ=255)                                tCAGGTAGCCGCCAACGTGGTGGGTGACCAGTTCCTTGACGTACTCCGGCGATTCCACCGCCAGGTCGTAGCGCAGGCCGGAAGCAATCAGGATCTTTTTCACACCCGGCAAGGCACGGGCCTTGCGGTAAAGCTCGATCAACGAGCtgt                                                                                                                     <  1:5524/150‑1 (MQ=255)                                    gTAGCCGCCAACGTGGTGGGTGACCAGTTCCTTGACGTACTCCGGCGATTCCACCGCCAGGTCGTAGCGCAGGCCGGAAGCAATCAGGATCTTTTTCACACCCGGCAAGGCACGGGCCTTGCGGTAAAGCTCGATCAACGAGCTGTGGTc                                                                                                                 >  2:175779/1‑150 (MQ=255)                                         cgccAACGTGGTGGGTGACCAGTTCCTTGACGTACTCCGGCGATTCCACCGCCAGGTCGTAGCGCAGGCCGGAAGCTATCAGGATCTTTTTCACACCCGGCAAGGCACGGGCCTTGCGGTAAAGCTCGATCAACGAGCTGTGGTCGGTAt                                                                                                            <  2:64229/150‑1 (MQ=255)                                             aaCGTGGTGGGTGACCAGTTCCTTGACGTACTCCGGCGATTCCACCGCCAGGTCGTAGCGCAGGCCGGAAGCAATCAGGATCTTTTTCACACCCGGCAAGGCACGGGCCTTGCGGTAAAGCTCGATCAACGAGCTGTGGTCGGTATTGAg                                                                                                        <  1:223980/150‑1 (MQ=255)                                                          aCCAGTTCCTTGACGTACTCCGGCGATTCCACCGCCAGGTCGTAGCGCAGGCCGGAAGCAATCAGGATCTTTTTCACACCCGGCAAGGCACGGGCCTTGCGGTAAAGCTCGATCAACGAGCTGTGGTCGGTATTGAGGTTTTCGCAGATa                                                                                           >  1:774306/1‑150 (MQ=255)                                                                  cTTGACGTACTCCGGCGATTCCACCGCCAGGTCGTAGCGCAGGCCGGAAGCAATCAGGATCTTTTTCACACCCGGCAAGGCACGGGCCTTGCGGTAAAGCTCGATCAACGAGCTGTGGTCGGTATTGAGGTTTTCGCAGATACCCGGGaa                                                                                   <  2:790101/150‑1 (MQ=255)                                                                           cTCCGGCGATTCCACCGCCAGGTCGTAGCGCAGGCCGGAAGCAATCAGGATCTTTTTCACACCCGGCAAGGCACGGGCCTTGCGGTAAAGCTCGATCAACGAGCTGTGGTCGGTATTGAGGTTTTCGCAGATACCCGGGAATACGCacga                                                                          >  2:175652/1‑150 (MQ=255)                                                                                      cctccGCCAGGTCGTAGCGCAGGCCGGAAGCAATCAGGATCTTTTTCACACCCGGCAAGGCACGGGCCTTGCg                                                                                                                                            <  2:550582/70‑1 (MQ=255)                                                                                      ccACCGCCAGGTCGTAGCGCAGGCCGGAAGCAATCAGGATCTTTTTCACACCCGGCAAGGCACGGGCCTTGCg                                                                                                                                            >  1:550582/1‑73 (MQ=255)                                                                                                        gcAGGCCGGAAGCAATCAGGATCTTTTTCACACCCGGCAAGGCACGGGCCTTGCGGTAAAGCTCGATCAACGAGCTGTGGTCGGTATTGAGGTTTTCGCAGATACCCGGGAATACGCACGACGGCTTGCGGCAGTACTTCTCGATTTCgg                                             <  1:633287/150‑1 (MQ=255)                                                                                                               ggAAGCAATCAGGATCTTTTTCACACCCGGCAAGGCACGGGCCTTGCGGTAAAGCTCGATCAACGAGCTGTGGTCGGTATTGAGGTTTTCGCAGATACCCGGGAATACGCACGACGGCTTGCGGCAGTACTTCTCGATTTCGGGGCtttt                                      <  1:625882/150‑1 (MQ=255)                                                                                                                           gATCTTTTTCACACCCGGCAAGGCACGGGCCTTGCGATAAAGCTCGATCAACGAGCTGTGGTCGGTATTGAGGTTTTCGCAGATACCCGGGAATACGCACGACGGCTTGCGGCAGTACTTCTCGATTTCGGGGCTTTTGCAGGCGATGCg                          >  2:81444/1‑150 (MQ=255)                                                                                                                                    cacaCCCGGCAAGGCACGGGCCTTGCGGTAAAGCTCGATCAACGAGCTGTGGTCGGTATTGAGGTTTTCGCAGATACCCGGGAATACGCACGACGGCTTGCGGCAGTACTTCTCGATTTCGGGGCTTTTGCAGGCGATGCGGTACATGtt                 >  2:586935/1‑150 (MQ=255)                                                                                                                                           cgCAAGGCCCGTGCCTTGCGGTAAAGCTCGATCAACGAGCTGTGGTCGGTATTGAGGTTTTCGCAGATACCCGGGAATACGCACGACGGCTTGCGGCAGTACTTCTCGATTTCGGGGCTTTTGCAGGCGATGCGGTACATGTTGGCAGTc          >  2:411047/2‑150 (MQ=255)                                                                                                                                                ggCACGGGCCTTGCGGTAAAGCTCGATCAACGAGCTGTGGTCGGTATTGAGGTTTTCGCAGATACCCGGGAATACGCACGACGGCTTGCGGCAGTACTTCTCGATTTCGGGGCTTTTGCAGGCGATGCGGTACATGTTGGCAGTCGGccc     <  2:774306/150‑1 (MQ=255)                                                                                                                                                ggCACGGGCCTTGCGGTAAAGCTCGATCAACGAGCTGTGGTCGGTATCGAGGTTTTCGCAGATACCCGGGAATACGCACGACGGCTTGCGGCAGTACTTCTCGATTTCGGGGCTTTTGCAGGCGATGCGGTACATGTTGGCAGTCGGccc     <  2:766621/150‑1 (MQ=255)                                                                                                                                                   aCGGGCCTTGCGGTAAAGCTCGATCAACGAGCTGTGGTCGGTATTGAGGTTTTCGCAGATACCCGGGAATACGCACGACGGCTTGCGGCAGTACTTCTCGATTTCGGGGCTTTTGCAGGCGATGCGGTACATGTTGGCAGTCGGCCCGcc  >  2:671909/1‑150 (MQ=255)                                                                                                                                                   |                                                                                                                                                      GGGCCACGCTCGGTGTGCTCCGGGGCAATCTTCAGGTAGCCGCCAACGTGGTGGGTGACCAGTTCCTTGACGTACTCCGGCGATTCCACCGCCAGGTCGTAGCGCAGGCCGGAAGCAATCAGGATCTTTTTCACACCCGGCAAGGCACGGGCCTTGCGGTAAAGCTCGATCAACGAGCTGTGGTCGGTATTGAGGTTTTCGCAGATACCCGGGAATACGCACGACGGCTTGCGGCAGTACTTCTCGATTTCGGGGCTTTTGCAGGCGATGCGGTACATGTTGGCAGTCGGCCCGCC  >  NC_002947/5539391‑5539686

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