Predicted mutation
evidence	seq id	position	mutation	freq	annotation	gene	description
RA	CP009273	3,664,009	C→T	16.1%	A353V (GCC→GTC)	treF →	cytoplasmic trehalase

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	CP009273	3,664,009	0	C	T	16.1%	46.8 / 4.9	25	A353V (GCC→GTC)	treF	cytoplasmic trehalase
Reads supporting (aligned to +/- strand):  ref base C (10/11);  new base T (2/2);  total (12/13)
Fisher's exact test for biased strand distribution p-value = 1.00e+00
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 3.77e-01

TGGTCGCCCGCCCAACGAGGTGTACCGCGATTTACGCGCGGGGGCGGCCTCCGGTTGGGATTACTCTTCCCGTTGGCTGCGTGATACTGGTCGTCTGGCGAGCATTCGTACCACCCAGTTCATCCCCATCGATCTGAATGCCTTCCTGTTTAAACTGGAGAGCGCCATCGCCAACATCTCGGCGCTGAAAGGCGAGAAAGAGACAGAAGCACTGTTCCGCCAGAAAGCCAGTGCCCGTCGCGATGCGGTAAACCGTTACCTCTGGGATGATGAAAACGGCATCT  >  CP009273/3663869‑3664152                                                                                                                                             |                                                                                                                                                tGGTCGCCCGCCCAACGAGGTGTACCGCGATTTACGCGCGGGGGCGGCCTCCGGTTGGGATTACTCTTCCCGTTGGCTGCGTGATACTGGTCGTCTGGCGAGCATTCGTACCACCCAGTTCATCCCCATCGATCTGAATGCCTTCCTGt                                                                                                                                         <  1:375037/149‑1 (MQ=255) tGGTCGCCCGCCCAACGAGGTGTACCGCGATGTACGCGCGGGGGCGGCCTCCGGTTGGGATTACTCTTCCCGTTGGCTGCGTGATACTGGTCGTCTGGCGAGCATTCGTACCACCCAGTTCATCCCCATCGATCTGAATGCCTTCCTGt                                                                                                                                         <  1:16304/149‑1 (MQ=255)  ggTCGCCCGCCCAACGAGGTGTACCGCGATTTACGCGCGGGGGCGGCCTCCGGTTGGGATTACTCTTCCCGTTGGCTGCGTGATACTGGTCGTCTGGCGAGCATTCGTACCACCCAGTTCATCCCCATCGATCTGAATGCCTTc                                                                                                                                             >  2:82651/1‑144 (MQ=255)     cgcccgccCCACGAGGTGTACCGCGATTTACGCGCGGGGGCGGCCTCCGGTTGGGATTACTCTTCCCGTTGGCTGCGTGATACTGGTCGTCTGGCGAGCATTCGTACCACCCAGTTCATCCCAATCGATCTGAATGCCTTCCTg                                                                                                                                          <  2:239498/144‑1 (MQ=255)                          cgcgATTTACGCGCGGGGGCGGCCTCCGGTTGGGAATAATCTTCCCGTTGGCTGCGTGATACTGGTCGTCTGGCGAGCATTCGTACCACCCAGTTCATCCCCATCGATCTGAATGCCTTCCTGTTTAAACTGGAGAGCGCCATc                                                                                                                     >  2:251587/1‑144 (MQ=255)                                            gcggcCTCCGGTTGGGATTACTCTTCCCGTTGGCTGCGTGATACTGGTCGTCTGGCGAGCATTCGTACCACCCAGTTCATCCCCATCGATCTGAATGCCTTCCTGTTTAAACTGGAGAGCGCCCTCGCCCACATCTCGgcgccg                                                                                                   >  2:154093/1‑142 (MQ=255)                                                    cGGTTGGGATTACTCTTCCCGTTGGCTGCGTGATACTGGTCGTCTGGCGAGCATTCGTACCACCCAGTTCATCCCCATCGATCTGAATGCCTTCCTGTTTAAACTGGAGAGCGCCATCGCCAACATCTCGGCGCTGAAAGGCga                                                                                           <  2:87753/144‑1 (MQ=255)                                                      gTTGGGATTACTCTTCCCGTTGGCTGCGTGATACTGGTCGTCTGGCGAGCATTCGTACCACCCAGTTCATCCCCATCGATCTGAATGCCTTCCTGTTTAAACTGGAGAGCGCCATCGCCAACATCTCGGCGCTGAAAGGCgaga                                                                                         <  2:142853/144‑1 (MQ=255)                                                       ttGGGATTACTCTTCCCGTTGGCTGCGTGATACTGGTCGTCTGGCGAGCATTCGTACCACCCAGTTCATCCCCATCGATCTGGATGCCTTCCTGTTTAAACTGGAGCGCGCCATCGCCAACATCTCGGCGCTGAAAGGCGAGAAAgaga                                                                                   <  1:174845/149‑1 (MQ=255)                                                          ggATTACTCTTCCCGTTGGCTGCGTGATACTGGTCGTCTGGCGAGCGTTCGTACCACCCAGTTCATCCCCATCGATCTGAATGCCTTCCTGTTTAAACTGGAGAGCGCCATCGCCAACATCTCGGCGCTGAAAGGAGAGAAaga                                                                                     >  2:144502/1‑144 (MQ=255)                                                            agtACCCTTCCCGTTGGCTGCGTGATACTGGTCGTCTGGCGAGCATTCGTACCACCCAGTTCATCCCCACCGATCTGAATGCCTTCCTGTTTAAACTGGAGAGCGCCATCGCCAACATCTCGGCGCTGAAAGGCGAGAAAGAGACAGaa                                                                              <  1:110683/147‑1 (MQ=255)                                                               aCTCTTCCCGTTGGCTGCGTGATACTGGTCGTCTGGCGAGCATTCGTACCACCCAGTTCATCCCCATCGATCTGAATGCCTTCCTGTTTAAACTGGAGAGCGCCATCGCCAACATCCCGGCGCTGAAAGGCGGGAAAGAGAccg                                                                                >  2:141312/1‑142 (MQ=255)                                                                   ttCCCGTTGGCTGCGTGATACTGGTCGTCTGGCGAGCATTCGTACCACCCAGTTCATCCCCATCGATCTGAATGTCTTCCTGTTTAAACTGGAGAGCGCCATCGCCAACATCTCGGCGCTGAAAGGCGGGAAAGAGACAGAAGCACTGt                                                                       >  1:13147/1‑149 (MQ=255)                                                                   ttCCCGTTGGCTGCGTGATACTGGTCGTCTGGCGAGCATTCGTACCACCCAGTTCATACAAATCGATCTGAATGTCTTCCTGTTTAAACTGGAGAGCGCCATCGCCTACATCTCGGCGCTGAAAGGCGAGAAAGAGACAGAAGCACTGt                                                                       >  1:231508/1‑149 (MQ=255)                                                                       cGTTGGCTGCGTGATACTGGTCGTCTGGCGAGCATTCGTACCACCCAGTTCATCCCCATCGATCTGAATGCCTTCCTGTTTAAACTGGAGAGCGCCATCGCCAACATCTCGGCGCTGAAAGGCGAGAAAGAGGCAGAAGCACTGTTCCg                                                                   >  1:105400/1‑149 (MQ=255)                                                                       cGTTGGCTGCGTGATACTGGTCGTCTGGCGAGCATTCGTACCACCCAGTTCATCCCCATCGATCTGAATGCCTTCCTGTTTAAACTGGAGAGCGCCATCGCCAACATCTCGGCGCTGAAAGGCGAGAAAGAGACAGAAGCACTg                                                                        >  2:308722/1‑144 (MQ=255)                                                                                cGTGATACTGGTCGTCTGGCGAGCATTCGTCCCACCCAGTTCATCCCCATCGATCTGAAGGCCTTCCTGTTGAAACTGGAGAGCGCCATCGCCAACATCTCGGCGCTGAAAGGCGAGAAAGAGACAGAAGCCCTGTTCCGCCAAAAAGc                                                          >  1:60115/1‑149 (MQ=255)                                                                                                   cgggCATTCGTACCACCCAGTTCATCCCCTTCGATCTGAATGCCTTCCTGTTTAAACTGGAGAGCGCCATCGCCAACATCTCGGCGCTGAAAGGCGAGAAAGAGACAGAAGCACTGTTCCGCCAGAAAGCCAGTGCCCGTCGCGATGCg                                       <  1:68260/146‑1 (MQ=255)                                                                                                    gAGCATTCGTACCACCCAGTTCATCCCCATCGATCTGAATGCCTTCCTGTTTAAACTGGAGAGCGCCATCGCCAACATCTCGGCGCTGAAAGGCGAGAAAGAGACAGAAGCACTGTTCCGCCAGAAAGCCAGTGCCCGTCGCGATGCgg                                      <  1:149338/149‑1 (MQ=255)                                                                                                        aTTCGTACCACCCAGTTCATCCCCATCGATCTGAATGCCTTCCTGTTTAAACTGGAGAGCGCCATCGCCAACATCTCGGCGCTGAAAGGCGAGAAAGAGACAGAAGCACTGTTCCGCCAGAAAGCCAGTGCCCGTCGCGATGCg                                       >  2:279084/1‑144 (MQ=255)                                                                                                         ttCGTACCCCCCAGTTCATCCCCATCGATCTGAATGTCTTCCTGTTTAAACTGGAGAGCGCCATCGCCAACATCTCGGCGCTGAAAGGCGAGAAAGAGACAGAAGCACTGTTCCGCCAGAAAGCCAGTGCCCGTCGCGATGCgg                                      <  2:11518/144‑1 (MQ=255)                                                                                                         ttCGTACCACCCAGTTCATCCCCATCGATCTGAATGTCTTCCTGTTTAAACTGGAGAGCGCCATCGCCTACATCTCGGCGCTGAAAGGCGAGAAAGAGACAGAAGCACTGTTCCGCCAGAAAGCCAGTGCCCGTCGCGATGCgg                                      <  2:204894/144‑1 (MQ=255)                                                                                                             tACCACCCAGTTCATCCCCATCGATCTGAATGCCTTCCTGTTTAAACTGGAGAGCGCCATCGCCAACATCTCGGCGCTGAAAGGCGAGAAAGAGACAGAAGCACTGTTCCGCCAGAAAGCCAGTGCCCGTCGCGATGCGGTAAACCGtt                             <  1:282103/149‑1 (MQ=255)                                                                                                                               cATCGATCTGAATGCCTTCCTGTTTAAACTGGAGAGCGCCATCGCCAACATCTCGGCGCTGAAGGGCGAGAAAGAGACAGAAGCACTGTTCCGCCAGAAAGCCAGTGCCCGTCGCGATGCGGTAAACCGGTGCCTCGGGgagaa                >  2:199084/1‑141 (MQ=255)                                                                                                                                        gAATGCCTTCCTGTTTAAACTGGAGAGCGCCATCGCCAACATCTCGGCGCTGAAAGGCGAGAAAGAGACAGAAGCACTGTTCCGCCAGAAAGCCAGTGCCCGTCGCGATGCGGTAAACCGTTACCTCTGGGATGATGAAAACGGCATCt  <  1:365483/149‑1 (MQ=255)                                                                                                                                             |                                                                                                                                                TGGTCGCCCGCCCAACGAGGTGTACCGCGATTTACGCGCGGGGGCGGCCTCCGGTTGGGATTACTCTTCCCGTTGGCTGCGTGATACTGGTCGTCTGGCGAGCATTCGTACCACCCAGTTCATCCCCATCGATCTGAATGCCTTCCTGTTTAAACTGGAGAGCGCCATCGCCAACATCTCGGCGCTGAAAGGCGAGAAAGAGACAGAAGCACTGTTCCGCCAGAAAGCCAGTGCCCGTCGCGATGCGGTAAACCGTTACCTCTGGGATGATGAAAACGGCATCT  >  CP009273/3663869‑3664152

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 12 ≤ ATCG/ATCG < 22 ≤ ATCG/ATCG < 32 ≤ ATCG/ATCG < 41 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑