Predicted mutation
evidence	seq id	position	mutation	annotation	gene	description
RA	NC_000913	2,877,914	C→G	intergenic (+296/+655)	iap → / ← cas2	alkaline phosphatase isozyme conversion protein/CRISPR‑associated endoribonuclease Cas2

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NC_000913	2,877,914	0	C	G	95.7%	62.8 / ‑2.5	24	intergenic (+296/+655)	iap/cas2	alkaline phosphatase isozyme conversion protein/CRISPR‑associated endoribonuclease Cas2
Reads supporting (aligned to +/- strand):  ref base C (0/1);  new base G (7/15);  total (8/16)
Fisher's exact test for biased strand distribution p-value = 1.00e+00
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 2.40e-01

GCATCCAGTGCGCCCGGTTTATCCCCGCTGATGCGGGGAACACCAGCGTCAGGCGTGAAATCTCACCGTCGTTGCCGGTTTATCCCTGCTGGCGCGGGGAACTCTCGGTTCAGGCGTTGCAAACCTGGCTACCGGGCGGTTTATCCCCGCTAACGCGGGGAACTCGTAGTCCATCATTCCACCTATGTCTGAACTCCCGGTTTATCCCCGCTGGCGCGGGGAACTCCCGGGGGATA‑ATGTTTACGGTCATGCGCCCCCCGGTTTATCCCCGCTGGCGCGGGGAACTCTGGGCGGCTTGCCTTGCAGCCAGCTCCAGCAGCGGTTTATCCCCGCTGGCGCGGGGAACTCAAGCTGGCTGGCAATCTCTTTCGGGGTGAGTCCGGTTTATCCCCGCTGGCGCGGGGAACTCTAGTTTCCGTATCTCCGGATTTATAAAGCTGACGGTTTATCCCCGCTGGCGCGGGGAACTCG  >  NC_000913/2877687‑2878157                                                                                                                                                                                                                                    |                                                                                                                                                                                                                                                     gCATCCAGTGCGCCCGGTTTAGCCCCGCTGATGCGGGGAACACCCGCGTCAGGCGTGAAATCTCACCGTCGTTGCCGGTTCATCCCTGCTGGCGCGGGGAACTCTCGGTTCAGGCGTTGCAAACCTGGCTACCGGGCGGTTTATCCCCGCTAACGCGGGGAACTCGTAGTCCATCATTCCACCTATGTCTGAACTCCCGGTTTATCCCCGCTGGCGCGGGGAACTCCCGGGGGATA‑ATGTTTACGGTCATg                                                                                                                                                                                                                              <  2:228662/251‑1 (MQ=255)                 gTTTATCCCCGCTGATGCGGGGAACACCAGAGTCAGGCGTGAAATCTCACCGTCGTTCCTGGTTTGTCCCTGCTGGCGTGGGGACCTCTCGCTTCCTGCGTTACAACCCTGGCTCCCGGGCGGTTTATCCCCGCTAACTCGGGGAACTCGTAGTCCATCATTCCCCCTATGTCTGAACTCCCGGTTTATCCTCGCTGTCGCGGGGAACTCC‑GGGGGATTTATCTTTACGGTCATTGGCCCCCCGGTTTATc                                                                                                                                                                                                              >  1:134969/1‑251 (MQ=255)                     aTCCCTGCTGATGCGGGGAACACCAGCGTCAGGCGTGAAATCTCACCGTCGTTGCCGGTTTATCCCTGCTGGCGCGGGGAACTCTCGGTTCATGCGTTGCAAACCTGGCTACCGGGCGGTTTATCCCCGCTAACGCGGGGAACTCGTAGTCCATCATTCCCCCTATGTCTTAACTCCCGGTGTAGCCCCGCGGGCGCGGGGAACTTCGTGGGGATA‑ATGTTTACGGTCATGCGCCCCCCGGTTTATCCCCg                                                                                                                                                                                                          <  1:293431/251‑1 (MQ=255)                                 gCGGGGAACACCAGCGTCAGGCGTGAAATCTCACCGTCGTTGCCGGTTTATCCCTGCTGGCGCGGGGAACTCTCGGTTCAGGCGTTGCAAACCTGGCTACCGGGCGGTTTATCCCCGCTAACGCGGGGAACTCGTAGTCCATCATTCCACCTATGTCTGAACTCCCGGTTTATCCCCGCTGGCGCGGGGAACTCCGGGGGGATA‑ATGTTTACGGTCATGCGCCCCCCGGTTTATCCCCGCTGGCGCgggg                                                                                                                                                                                               <  1:36094/250‑1 (MQ=255)                                     ggAACACCAGCGTCAGGCGTGAAATCTCACCGTCGTTGCCGGTTTATCCCTGCTGGCGCGGGGAACTCTCGGTTCAGGCGTTGCAAACCTGGCTACCGGGCGGTTTATCCCCGCTAACGCGGGGAACTCGTAGTCCATCATTCCACCTATGTCTGAACTCCCGGTTTATCCCCGCTGGCGCGGGGAACTCCGGGGGGATA‑ATGTTTACGGTCATGCGCCCCCCGGTTTATCCCCGCTGGCGCGGGGAActc                                                                                                                                                                                          >  2:62630/1‑251 (MQ=255)                                                  cAGGCGTGAAATCTCACCGTCGTTGCCGGTTTATCCCTGCTGGCGCGGGGAACTCTCGGTTCAGGCGTTGCAAACCTGGCTACCGGGCGGTTTATCCCCGCTAACGCGGGGAACTCGTAGTCCATCATTCCACCTATGTCTGAACTCCCGGTTTATCCCCGCTGGCGCGGGGAACTCCGGGGGGATA‑ATGTTTACGGTCATGCGCCCCCCGGTTTATCCCCGCTGGCGCGGGGAACTCTGGGCGGcttgcc                                                                                                                                                                             >  1:164408/1‑251 (MQ=255)                                                      cGTGAAATCTCACCGTCGTTGCCGGTTTATCCCTGCTGGCGCGGGGAACTCTCGGTTCAGGCGTTGCAAACCTGGCTACCGGGCGGTTTATCCCCGCGAACGCGGGGAACTCGTAGTCCATCATTCCACCTATTTCTGAACTCCCGGTTTATCCCCGCTGGCGCGGGGAACTCCGGGGGGATA‑ATGGTTACGGTCATGCGCCCCCCGGTTTATCCCCGCTGGCGCGGGGAAc                                                                                                                                                                                            <  1:147711/232‑1 (MQ=255)                                                      cGTGAAATCTCAACGTCGTTGCCGGTTTCTACCTGCTGGCGCGGGGAACTCTACGTTCAGGCGTTGAAAACCAGGCTACCGGGCGGTTTCTCCCGGCTAACGCGGGGAACTCGTAGTCCATCATTCCACCTATGTCTGAACTCCCGGTTTATCCCCGCTGGCGCGGGGAACTCCGGGGGGATA‑ATGTTTACGGTCATGCGCCGCCCGGTTTATCCCCGCTGGCGCGGGGAAc                                                                                                                                                                                            >  2:147711/1‑232 (MQ=255)                                                       gTGAAGTCTCACCGTCGTTGCCGGTTTATCCCTGCTGGCGCGGGGAACTCTCGGTTCAGGCGTTGCAAACCTGGCTACCGGGCGGTTTATCCCCGCTAACGCGGGGAACTCGTAGTCCATCATTCCACCTATGTCTGAACTCCCGGTTTATCCCCGCTGGCGCGGGGAACTCCGGGGGGATA‑ATGTTTACGGTCATGCGCCCCCCGGTTTATCCCCGCTGGCGCGGGGAACTCTGGGCGGCTTGCCTTGca                                                                                                                                                                        <  1:62630/251‑1 (MQ=255)                                                                cACCGTCGTTGCCGGTTTATCCCTGCTGGCGCGGGGAACTCTCGGTTCAGGCGTTGCAAACCTGGCTACCGGGCGGTTTATCCCCGCTAACGCGGGGAACTCGTAGTCCATCATTCCACCTATGTCTGAACTCCCGGTTTATCCCCGCTGGCGCGGGGAACTCCGGGGGGATA‑ATGTTTACGGTCATGCGCCCCCCGGTTTATCCCCGCTGGCGCGGGGAACTCTGGGCGGCTTGCCTTGcagccag                                                                                                                                                                   <  1:143900/247‑1 (MQ=255)                                                                           ccGGTTTATCCCTGCTGGCGCGGGGAACTCTCGGTTCAGGCGTTGCAAACCTGGCTACCGGGCGGTTTATCCCCGCTAACGCGGGGAACTCGTAGTCCATCATTCCACCTATGTCTGAACTCCCGGTTTATCCCCGCTGGCGCGGGGAACTCCGGGGGGATA‑ATGTTTACGGTCATGCGCCCCCCGGTTTATCCCCGCTGGCGCGGGGAACTCTGGGCGGCTTGCCTTGCAGCCAGCTCCAGCAGCGGttt                                                                                                                                                    >  1:292154/1‑251 (MQ=255)                                                                           ccGGTTTATCCCTGCTGGCGCGGGGAACTCTCGGTTCAGGCGGTGCAAACCTGGCTACCGGGCGGTTTATCCCCGCTAACGCGGGGAAATCGTAGTCCATCATTCCACCTATGTCTGAACTCCCGGTTTATCCCCGCTGGCGCGGGGAACTCCGGGGGGATA‑ATGTTTACGGTCATGCGCCCCCCGGTTTATCCCCGCTGGCGCGGGGAACTCTGGGCGGCTGGCCTTGCAGCCAGCTCCAGCAGCGGttt                                                                                                                                                    <  2:267704/251‑1 (MQ=255)                                                                                     ccTGCGGGCGGGGGGAACTCGCGGTTCAGGCGTTGCAAACCTGGCTACCGGGCGGTTTATCCCCGCTAACGCGGGGAACTCGTAGTCCATCATTCCACCTATGTCTGAACTCCCGGTTTATCCCCGCTGGCGCGGGGAACTCCGGGGGGATA‑ATGTTTACGGTCATGCGCCCCCCGGTTTATCCCCGCTGGCGCGGGGAACTCTGGGCGGCTTGCCTTGCAGCCAGCTCCAGCAGCGGTTTATCCCCGCTg                                                                                                                                          <  2:182172/251‑1 (MQ=255)                                                                                                          cGGTTCAGGCGTTGCAAACCTGGCTTCCGGGCGGTTTATCCCCGCTAACGCGGGGAACTCGGAGTCCATCATTCCACCTATGTCTGAACTCCCGGTTTATCCCCGCTGGCGCGGGGAACTCCGGGGGGATA‑ATGTTTACGGTCATGCGCCCCCCGGTTTATCCCCGCTGGCGCGGGGAACTCTGGGCGGCTTGCCTTGCAGCCAGCTCCAGCAGCGGTTTATCCCCGCTGGCGCGGGGAACTCAAgctggc                                                                                                                     <  2:292154/251‑1 (MQ=255)                                                                                                                    gTTGCAAGCCTGGCTACCGTGCGGTTTCTCCCCGCTAACGCGGGGAACTCGGCGTCCATCATTCCACCTATGTCGGAACTCCCGGGTTATCCCCGCTGGCGCGGGGAACTCCGGGGGGATA‑ATGTTTACGGTCATGCGCCCCCCGGTTTATCCCCGCTGGCGCGGGGAACTCTGGGCGGCTTGCCTTGCAGCCAGCTCCAGCAGCGGTTTATCCCCGCTGGCGCGGGGAACTCAAGCTGGCTGGCAAtctc                                                                                                           <  2:239834/251‑1 (MQ=255)                                                                                                                      tGCAAACCTGGCTACCGGGCGGTTTATCCCCGCTAACGCGGGGAACTCGTAGTCCATCATTCCACCTATGTCTGAACTCCCGGTTTATCCCCGCTGGCGCGGGGAACTCCGGGGGGATA‑ATGTTTACGGTCATGCGCCCCCCGGTTTATCCCCGCTGGCGCGGGGAACTCTGGGCGGCTTGCCTTGCAGCCAGCTCCAGCAGCGGTTTATCCCCGCTGGCGCGGGGAACTCAAGCTGGCTGGCAATCTCtt                                                                                                         >  1:98795/1‑251 (MQ=255)                                                                                                                        cAAACCTGGCTACCGGGCGGTTTATCCCCGCTAACGCGGGGAACTCGTAGTCCATCATTCCACCTATGTCTGAACTCCCGGTTTATCCCCGCTGGCGCGGGGAACTCCGGGGGGATA‑ATGTTTACGGTCATGCGCCCCCCGGTTTATCCCCGCTGGCGCGGGGAACTCTGGGCGGCTTGCCTTGCAGCCAGCTCCAGCAGCGGTTTATCCCCGCTGGCGCGGGGAACTCAAGCTGGCTGGCAATCTCTTTc                                                                                                       <  1:176784/251‑1 (MQ=255)                                                                                                                               ggCTACCGGTCGGTTTATCCCCGCGAACGCGGGGAACGCGTAGGCCATCATTCCACCTAGGTCTGAACTCCCGGTTTATCCCCGCTGGCGCGGGGAACGCCGGGGGGATA‑ATGTTTACGGTCATGCGCCCCCCGGTTTATCCCCGCTGGCGCGGGGAACTCTGGGCGGCTTGCCTTGCAGCCAGCTCCAGCAGCGGTTTATCCCCGCTGGCGCGGGGAACTCAAGCTGGCTGGCAATCTCTTTCGGGGTGa                                                                                                <  2:50204/251‑1 (MQ=255)                                                                                                                                  tACCGGGCGGTTTATCCCCGCTAACGCGGGGAACTCGTAGTCCATCATTCCACCTATGTCTGAACTCCCGGTTTATCCCCGCTGGCGCGGGGAACTCCGGGGGGATA‑ATGTTTACGGTCATGCGCCCCCCGGTTTATCCCCGCTGGCGCGGGGAACTCTGGGCGGCTTGCCTTGCAGCCAGCTCCAGCAGCGGTTTATCCCCGCTGGCGCGGGGAACTCAAGCTGGCTGGCAATCTCTTTCGGGGTGAGTc                                                                                             >  1:177575/1‑251 (MQ=255)                                                                                                                                                    cGCTAACGCGGGGAACCCGTAGGCCATCGTTCCACCGATGTCAGACCTCCCGGTTTATCCCCGCGGGCGCGGGGAACTCCGGGGGGATA‑ATGTTTACGGTCATGCGCCCCCCGGTTTATCCCCGCTGGCGCGGGGAACTCTGGGCGGCTTGCCTTGCAGCCAGCTCCAGCAGCGGTTTATCCCCGCTGGCGCGGGGAACTCAAGCTGGCTGGCAATCTCTTTCGGGGTGAGTCCGGTTTATCCCCGCTGgc                                                                           <  2:121281/251‑1 (MQ=255)                                                                                                                                                                                         aTGTCTGAACTCCCGGTTTATCCCCGCTGGCGCGGGGAACTCCGGGGGGATA‑ATGTTTACGGTCATGCGCCCCCCGGTTTATCCCCGCTGGCGCGGGGAACTCTGGGCGGCTTGCCTTGCAGCCAGCTCCAGCAGCGGTTTATCCCCGCTGGCGCGGGGAACTCAAGCTGGCTGGCAATCTCTTTCGGGGTGAGTCCGGTTTATCCCCGCTGGCGCGGGGAACTCTAGTTTCCGTATCTCCGGATTtat                                        <  1:51371/249‑1 (MQ=255)                                                                                                                                                                                         aTGTCTGAACTCCCGGTTTATCCCCGCTGGCGCGGGGAACTCCGGGGGGATA‑ATGTTTACGGTCATGCGCCCCCCGGTTTATCCCCGCTGGCGCGGGGAACTCTGGGCGGCTTGCCTTGCAGCCAGCTCCAGCAGCGGTTTATCCCCGCTGGCGCGGGGAACTCAAGCTGGCTGGCAATCTCTTTCGGGGTGAGTCCGGTTTATCCCCGCTGGCGCGGGGAACTCTAGTTTCCGTATCTCCGGATTTATaa                                      <  1:227246/251‑1 (MQ=255)                                                                                                                                                                                                               cccGCTGGCGCGGGGAACTCCGGGGGGATA‑ATGTTTACGGTCATGCGCCCCCCGGTTTATCCCCGCTGGCGCGGGGAACTCTGGGCGGCTTGCCTTGCAGCCAGCTCCAGCAGCGGTTTATCCCCGCTGGCGCGGGGAACTCAAGCTGGCTGGCAATCTCTTTCGGGGTGAGTCCGGTTTATCCCCGCTGGCGCGGGGAACTCTAGTTTCCGTATCTCCGGATTTATAAAGCTGACGGTTTATCCCCGCTg                >  1:126811/1‑251 (MQ=255)                                                                                                                                                                                                                             gAACTCCGGGGGGATA‑ATGTTTACGGTCATGCGCCCCCCGGTTTATCCCCGCTGGCGCGGGGAACTCTGGGCGGCTTGCCTTGCAGCCAGCTCCAGCAGCGGTTTATCCCCGCTGGCGCGGGGAACTCAAGCTGGCTGGCAATCTCTTTCGGGGTGAGTCCGGTTTATCCCCGCTGGCGCGGGGAACTCTAGTTTCCGTATCTCCGGATTTATAAAGCTGACGGTTTATCCCCGCTGGCGCGGGGAACTCg  <  1:47905/251‑1 (MQ=255)                                                                                                                                                                                                                                    |                                                                                                                                                                                                                                                     GCATCCAGTGCGCCCGGTTTATCCCCGCTGATGCGGGGAACACCAGCGTCAGGCGTGAAATCTCACCGTCGTTGCCGGTTTATCCCTGCTGGCGCGGGGAACTCTCGGTTCAGGCGTTGCAAACCTGGCTACCGGGCGGTTTATCCCCGCTAACGCGGGGAACTCGTAGTCCATCATTCCACCTATGTCTGAACTCCCGGTTTATCCCCGCTGGCGCGGGGAACTCCCGGGGGATA‑ATGTTTACGGTCATGCGCCCCCCGGTTTATCCCCGCTGGCGCGGGGAACTCTGGGCGGCTTGCCTTGCAGCCAGCTCCAGCAGCGGTTTATCCCCGCTGGCGCGGGGAACTCAAGCTGGCTGGCAATCTCTTTCGGGGTGAGTCCGGTTTATCCCCGCTGGCGCGGGGAACTCTAGTTTCCGTATCTCCGGATTTATAAAGCTGACGGTTTATCCCCGCTGGCGCGGGGAACTCG  >  NC_000913/2877687‑2878157

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 12 ≤ ATCG/ATCG < 14 ≤ ATCG/ATCG < 32 ≤ ATCG/ATCG < 38 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑