Predicted mutation
evidence	seq id	position	mutation	freq	annotation	gene	description
RA	NC_002947	3,997,970	T→G	26.1%	D31A (GAT→GCT)	PP_3518 ←	hypothetical protein

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NC_002947	3,997,970	0	T	G	26.1%	26.5 / 2.5	32	D31A (GAT→GCT)	PP_3518	hypothetical protein
Reads supporting (aligned to +/- strand):  ref base T (10/12);  new base G (4/4);  total (15/17)
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

TTGACGCCATCAGCACCTGAGCCAGCAACTGATCAGGGTACAAGGCAATGGGGGCCAGCATCTGGTCCAGTTGCTCCTGGGAGAACACCGGGTCCTTGGCTACGAGCGTGGCAGCGGAAGGCGCCGGATCCGGCGCGGGCACGTCTGCGGCCTGCACCAGGCCAGGGGCAGCGCTCAGGCAAAGCAGTGCCGACAGGAAAGCAAACAATGGCATGCGCATCGCTTATCCCCATGAGGTCAGACCGCGTGGGTT  >  NC_002947/3997842‑3998094                                                                                                                                 |                                                                                                                             ttGACGCCATCAGCACCTGAGCCAGCAACTGATCCGGGTACAAGGCAATGGGGGCCAGCATCTGGTCCAGTTGCTCCTTGGAGAACACCGGGTCCTTGGCTACGAGCGTGGCAGCGGAAGGCGCCGGATCCGgcgc                                                                                                                       <  1:162576/136‑1 (MQ=255) ttGACGCCATCAGCACCTGAGCCAGCAACTGATCAGGGTACAAGGCAATTGGGGCCAGCATCTGGTCCAGTTGCTCCTGGGAGAACACCGGGTCCTTGGCTACGAGCGTGGCAGCGGAAGGCGCCGGATCCGgcgc                                                                                                                       <  2:454095/136‑1 (MQ=255)             gCACCTGAGCCAGCAACTGATCAGGGTACAAGGCAATGGGGGCCAGCATCTGGTCCAGTTGCTCCTGGGAGAACACCGGGTCCTTGGCTACGAGCGTGGCAGCGGAAGGCGGCGGCTCCGGCGCGGGCCCGTCTGc                                                                                                           >  1:135546/1‑136 (MQ=255)             ccACCTGAGCCAGCAACTGATCAGGGTACACGGCACTGGGGGCCAGCATCTGGGCCAGTGGCTCCTGGGAGAACACCGGGGCCTTGGCTACGAGCGTGGCAGCGGACGGCGCCGGATCCGGCGCGGGCACGTCTGc                                                                                                           <  1:541760/135‑1 (MQ=255)                    aGCCAGCAACTGAGCCGGTTACAAGGCAATGGGGGCCAGCATCTGGTCCAGTTGCTCCTGGGAGAACACCGGGTCCTTGGCTACGCGCGTGGCAGCGTAAGGCGCCGGATCCGGCGCGGGCACGTCTGCGGCCTGc                                                                                                    <  2:298315/136‑1 (MQ=255)                         gCAACTGATCAGGGTACAAGGCAATGGGGGCCAGCATCTGGTCCAGATGCTCCTGGGAGAACACCGGGTCCTTGGCTACGAGCGTGGCAGCGGAAGGCGCCGGAACCGGCGCGGCCCCGACAGCGGCCAGCAcccg                                                                                               >  2:502107/1‑134 (MQ=255)                           aaCTGATCAGGGTACAAGGCAATGGGGGCCAGCATCTGGTCCAGTTGCTCCTGGGAGAACACCGGGTCCTTGGCTACGAGCGTGGCAGCGGAAGGCGGCGGGTCCGGCGCGGGCCCGGCTGCGGCCGGccccccgc                                                                                             >  2:379316/1‑132 (MQ=255)                                     ggTACAAGGCAATGGGGGCCAGCATCTGGTCCAGTTGCTCCTGGGAGAACACCGGGTCCTTGGCTACGAGCGTGGCAGCGGAAGGCGGCGGGGCCGGCGCCGGCCCGGCGGCGGCCGGCACCCGGCCCGCGGCAgc                                                                                   >  1:73225/1‑136 (MQ=255)                                         cAAGGCAATGGGGGCCAGCATCTGGTCCAGTTGCTCCTGGGAGAACACCGGGTCCTTGGCTACGCGCGTGGCAGCGGAAGGCGCCGGATCCGGCGCGGGCACGTCTGCGGCCTGCACCAGGCCAGGGGCAGCGCTc                                                                               <  1:484860/136‑1 (MQ=255)                                               aaTGGGGGCCAGCATCTGGTCCAGTTGCTCCTGGGAGAACACCGGGTCCTTGGCTACGAGCGTGGCAGCGGAAGGCGCCGGCTACGGCGCCGGCCCCTCTGCGGCCTGCCCCAGGCCCGGGGCCGCGCTCACGcca                                                                         >  2:430204/1‑134 (MQ=255)                                                  gggggCCAGCATCTGGTCCAGTTGCTCCTGGGAGAACACCGGGTCCTTGGCTACGAGCGTGGCAGCGGAAGGCGGCGGGGCCGGCGCGGGCCCGGCGGCGGCCGGCCCCCGGCCCGCGGCCGCGCGCACGccaccc                                                                      >  1:120419/1‑131 (MQ=255)                                                  gggggCCAGCATCTGGTCCAGTTGCTCCTGGGAGAACACCGGGTCCTTGGCTACGAGCGTGGCAGCGGAAGGCGCCGGGGCCGGCGCGGGCCCGGCTGCGGCCGGCCCCAGGCCCGGGGCGGCGCGCCGGCGAAGc                                                                      >  1:299043/1‑136 (MQ=255)                                                  gggggCCAGCATCTGGTCCAGTTGCTCCTGGGAGAACACCGGGTCCTTGGCTACGAGCGTGGCAGCGGAAGGCCCCGGATCCGGCGCGGGCACGGCTGCGGCCGGCACCAGGCCAGGGGCAGCGCTCAGGCAAAGc                                                                      >  2:551699/1‑136 (MQ=255)                                                        cAGCATCTGGTCCAGTTGCTCCTGGGACAACACCGGGGCCTTGGCTACGCGCGTGGCAGCGGAAGGCGCCGGACCCGGCGCGGGCACGTCTGCGGCCTGCACCAGGCCATGGGCAGCGCTCAGGCAAAGCAGTGcc                                                                <  2:387079/136‑1 (MQ=255)                                                         aGCATCTGGTCCAGTTGCTCCTGGGAGAACACCGGGTCCTTGGCTACGAGCGTGGCAGCGGAAGGCGCCGGATCCGGCGCGGGTACGTCTGCGGCCTGCACCAGGCCAGGGGCAGCGCTCAGGCAAAGCAGTGCCg                                                               <  2:551270/136‑1 (MQ=255)                                                           cATCTGGTCCAGTTGCTCCTGGGAGAACACCGGGTCCTTGGCTACGAGCGTGGCAGCGGAAGGCGGCGGCGCCGGCGCGGGCGCGGCTGCGGCCGGCACCACGCCCCGGGCCGCGCGCAGGCCAAGCACTGCCgcc                                                             >  1:148191/1‑134 (MQ=255)                                                           cATCTGGTCCAGTTGCTCCTGGGAGAACACCGGGTCCTTGGCTACGAGCGTGGCAGCGGAAGGCGCCGGGTCCCGCGCGGGCACGACTGCGGCCAGCACCCCCCCACGGGCACCGCGACCGCCAACCAGTGCCGAc                                                             >  2:302394/1‑136 (MQ=255)                                                                          tttcTGGGATAACCCCGGGTCTTTGGTTACGAGCGTGGTAGCGTATGGCGCCGGATCCGGCGCGGGCACGTCTGCGGCCTGCACCAGGCCAGGGGCAGCGCTCAGGCAAAGCAGTGCCGACAGGAAAGCAAACAAt                                              <  2:290921/133‑1 (MQ=255)                                                                          cTCCTGGGAGAACACCGGGTCCTTGGCTACGAGCGTGGCAGCGTAAGGCGCCGGATCCGGCGCGGGCACGTCTGCGGCCTGCACCAGGCCAGGGGCAGCGCTCAGGCAAAGCAGTGCCGACAGGAAAGCAAACAAt                                              <  2:323569/136‑1 (MQ=255)                                                                             cTGGGAGAACACCGGGTCCTTGGCTACGAGCGTGGCAGCGGAAGGCGCCGGATCCGGCGCGGGCACGTCTGCGGCCTGCACCAGGCCAGGGGCAGCGCTCAGGCAAAGCAGTGCCGACAGGAAAGCAAACAATGGc                                           <  2:181186/136‑1 (MQ=255)                                                                                      ccccGGGGCCTTGGCTACGAGCGGGGCAGCGGACGGCGCCGGATCCGGCGCGGGCACGTCTGCGGCCTGCACCAGGCCAGGGGCAGCGCTCAGGCAAAGCAGTGCCGACAGGAAAGCAAACAATGGCATGCGCATc                                  <  2:476639/134‑1 (MQ=255)                                                                                                   gCTACGAGCGTGGCAGCGGAAGGCGCCGGATCCGGCGCGGGCACGTCTGCGGCCTGCACCAGGCCAGGGGCAGCGCTCAGGCAAAGCAGTGCCGACAGGAAAGCAAACAATGGCATGCGCATCGCTTATCCCCATg                     >  2:463682/1‑136 (MQ=255)                                                                                                      ccGAGGGTGGCTGGGGAAGGCGCCGGAGGGGGGGCGGGCACGTCTGCGGCCTGCACCAGGCCAGGGGCAGCGCTCAGGCAAAGCAGTGCCGACAGGAAAGCAAACAATGGCATGCGCATCGCTTATCCCCATGAgg                  <  2:474914/135‑1 (MQ=255)                                                                                                          gCGTGGCAGCGGAAGGCGCCGGCTCCGGCGCGGGCCCGTCTGCGGCCGGCACCCGGCCCGGGGCCGCGCGCAGGCAAAGCAGTGCCGCCAGGAAAGCAAACAAAGGCATGCGCATCGCTTATCCCCCAGAGGTCAg              >  1:227043/1‑136 (MQ=255)                                                                                                          gCGTGGCAGCGGAAGGCGCCGGCTCCGGCGCGGGCCCGTCTGCGGCCGGCACCCGGCCAGGGGCAGCGCGCAGGCCAAGCAGTGCCGACAGGAAAGCAAACAAAGGCATGCGCATCGCTTATACCCATGAGGTCaa              >  1:481215/1‑135 (MQ=255)                                                                                                            gTGGCAGCGGAAGGCGCCGGATCCGGCGCGGGCACGTCTGCGGCCTGCACCAGGCCAGGGGCAGCGCTCAGGCAAAGCAGTGCCGACAGGAAAGCAAACAATGGCATGCGCCTCGCATATACCCATGAGGTCAGAc            >  2:188203/1‑136 (MQ=255)                                                                                                             gggCTGCGGCCGGCGCCGGAGCCGGCGCGGGCACGTCTGCGGCCTGCACCAGGCCAGGGGCAGCGCTCAGGCAAAGCAGTGCCGACAGGAAAGCAAACAATGGCATGCGCATCGCTTATCCCCATGAGGTCAGAcc           <  1:379316/135‑1 (MQ=255)                                                                                                             gggCTGCGGATGGCGCCTGAGCCGGCGCGGGCACGTCTGCGGCCTGCACCAGGCCAGGGGCAGCGCTCAGGCAAAGCAGTGCCGACAGGAAAGCAAACAATGGCATGCGCATCGCTTATCCCCATGAGGTCAGAcc           <  1:232888/135‑1 (MQ=255)                                                                                                             gggCAGGGGATGGCGCCGGATCGGGCGCGGGCACGTCTGCGGCCTGCACCAGGCCAGGGGCAGCGCTCAGGCAAAGCAGTGCCGACAGGAAAGCAAACAATGGCATGCGCATCGCTTATCCCCATGAGGTCAGAcc           <  2:298546/135‑1 (MQ=255)                                                                                                             gggCAGCGGAAGGCGCCGGATCCGGCGCGGGCACGTCTGCGGCCTGCACCAGGCCAGGGGCAGCGCTCAGGCAAAGCAGTGCCGACAGGAAAGCAAACAATGGCATGCGCATCGCTTATCCCCATGAGGTCAGAcc           <  2:135546/135‑1 (MQ=255)                                                                                                                   gggccggCGCCGGAGCCGGCGCGGGCACGTCTGCGGCCTGCACCAGGCCAGGGGCAGCGCTCAGGCAAAGCAGTGCCGACAGGAAAGCAAACAATGGCATGCGCATCGCTTATCCCCATGAGGTCAGACCGCGTgg     <  1:5913/131‑1 (MQ=255)                                                                                                                      aaGGCGCCGGATCCGGCGCGGGCACGTCTGCGGCCTGCACCAGGCCAGGGGCAGCGCTCAGGCAAAGCAGTGCCGACACGAAAGCAAACAATGGCATGCGCCTCGCTTATCCCCATGAGGTCAGACCGCGTGGGtt  >  1:142123/1‑136 (MQ=255)                                                                                                                                 |                                                                                                                             TTGACGCCATCAGCACCTGAGCCAGCAACTGATCAGGGTACAAGGCAATGGGGGCCAGCATCTGGTCCAGTTGCTCCTGGGAGAACACCGGGTCCTTGGCTACGAGCGTGGCAGCGGAAGGCGCCGGATCCGGCGCGGGCACGTCTGCGGCCTGCACCAGGCCAGGGGCAGCGCTCAGGCAAAGCAGTGCCGACAGGAAAGCAAACAATGGCATGCGCATCGCTTATCCCCATGAGGTCAGACCGCGTGGGTT  >  NC_002947/3997842‑3998094

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 14 ≤ ATCG/ATCG < 15 ≤ ATCG/ATCG < 27 ≤ ATCG/ATCG < 36 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑