Predicted mutation
evidence	seq id	position	mutation	freq	annotation	gene	description
RA	KT2440	3,626,117	A→C	50.3%	T178P (ACC→CCC)	hcf136_3 →	Ycf48‑like protein

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	KT2440	3,626,117	0	A	C	50.3%	‑1.2 / 11.9	25	T178P (ACC→CCC)	hcf136_3	Ycf48‑like protein
Reads supporting (aligned to +/- strand):  ref base A (3/9);  new base C (5/8);  total (8/17)
Fisher's exact test for biased strand distribution p-value = 6.73e-01
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 6.88e-01

CAGACGAGCGTCGCCTGGCGGCGGCGCAACGGCTGCTGGCCGACGGCGCGGACAAGCCGTTGTTGGCCCTGAATTTCACCGATGCCCGCAACGGCCTGGTCGTCGGTGCCTACGGGGTGGCC‑ATGCGCACCGACGACGGCGGGCGCAGCTGGCAGTCGGAGATCGGCCGACTGCCGAACGGGCGTGGACTGCACCTGTATGCCCTGGCGCGCCAAGGCAACCAGGTGTACATCGCCGGCGAGCAGGGCCTGCTGCT  >  KT2440/3625989‑3626244                                                                                                                                  |                                                                                                                                cAGACGAGCGTCGCCTGGCGGCGGCGCAACGGCTGCTGGCCGACGGCGCGGACAAGCCGTTGTTGGCCCTGAATTTCCCCGATGCCCGCAACGGCCTGGTCCTCGGTGCCGACGGGGTGGCC‑ATGCGCCCccacg                                                                                                                           >  5:175763/1‑135 (MQ=255)  aGACGAGCGTCGCCTGGCGGCGGCGCAACGGCTGCTGGCCGACGGCGCGGACAAGCCGTTGTTGGCCCTGAATTTCACCGATGCCCGCAACGGCCTGGTCGTCGGTGGCTACGGGGTGGCC‑ATGCGCCccgccgc                                                                                                                          >  2:155119/1‑134 (MQ=255)  aGACGAGCGTCGCCTGGCGGCGGCGCAACGGCTGCTGGCCGACGGCGCGGACAAGCCGTTGTTGGCCCTGAATTTCACCGATGCCCGCAACGGCCTGGTCGTCGGTGCCGTCGGGGTGGCC‑CAGCGCACcgacga                                                                                                                          >  2:317559/1‑135 (MQ=255)         cGTCGCCTGGCGGCGGCGCAACGGCTGCTGGCCGACGGCGCGGACAAGCCGTTGTTGGCCCTGAATTTCACCGATGCCCGCAACGGCCTGGTACTAGGTGCCTACGGGGTGGCC‑ATTCGCACCGACGACggcggg                                                                                                                   >  4:439609/1‑135 (MQ=255)              cggggcggggccCCAAGGGCGGCGGGCCGACGGCGCGGACACGCCGTTGTGGCCCCTTAATTTCCCCGATCCCCCCACCGGCCTGGGCGGCGGGGCCTCCGGGGGGGCC‑ATGCGCCCCGACGACGGCGGGCGCAGc                                                                                                             <  8:441046/133‑1 (MQ=255)                                        ccGAGGGCGCGCACAAGCGGTTGTGGGCCCTCAATTGCCCCGAGGCCCGAACCGGCGGGGGGGGGGGGGCCT‑CGGGGGGGCCAATGCGCACCTACGACGGCGGGCGCAGCTGGCAGTCGGAGATCGGCCGACTGcc                                                                                   <  8:249667/136‑1 (MQ=255)                                         ggccGGCGCGGACACGCGGTTGTGGGCCCTGAATTGCCCCGAGGCCCGCACCGGCCTGGGCGGCGGGGCCTCGGGGGGGGCC‑AGGCGCCCCGACGACGGCGGGCGCAGCTGGCAGTCGGAGATCGGCCGACTGcc                                                                                   <  2:44635/132‑1 (MQ=255)                                         cgccGGCGCGCACACGCGGTTGTGGGCCCTTAATTCCCCCGAGCCCCGCACCGGCGGGGCGGGGGGTGCCTCGGGGGGGGCC‑AGGCCCACCGACGACGGCGGGCGCAGCTGGCAGTCGGAGATCGGCCGACTGcc                                                                                   <  4:395579/132‑1 (MQ=255)                                         cGAGGGCGCGCACAAGCCGTTGTTGCCCCTCAATTTCCCCCAGCCCCCCACCGGCCTGGGCGGCGGGGCCTCCGGGGGGCCC‑AGGCCCACCGACGACGGCGGGCGCAGCTGGCAGTCGGAGATCGGCCGACTGcc                                                                                   <  3:184274/135‑1 (MQ=255)                                               ggcgGACACGGGGTTGTTGCCCCTCAATTCCCCCGATCCCCGCACCGGCGGGGTGGGGGGTGCCTCGGGGGGGGCC‑AGCCGCCCGGACGACGGCGGGCGCAGCTGGCAGTCGGAGATCGGCCGACTGCCGAACgg                                                                             <  1:72596/134‑1 (MQ=255)                                                gcgGACACGCGGTTGTGGGCCCTGAATTCCACCGAGGCCCCCAACGGCCGGGGGGGGGGTGCCTCCGGGGGGGCC‑TGGCGCCCCGCCGACGGCGGGCGCAGCTGGCAGTCGGAGATCGGCCGACTGCCGAACGGGc                                                                           <  8:351514/136‑1 (MQ=255)                                                    aCAAGCCGTTGTTGGCCCTGAATTTCACCGATGCCCGCAACGGCCTGGTCGTCGGTGCCGACGGGGTGGCC‑ATGCGCCCCGCCGCCGGCGGGCGCAGCTGGCAGTCGGAGCTCGGCCGCCTGCCGCCCGGGCGTg                                                                        >  5:146012/1‑135 (MQ=255)                                                     cAAGCGTTTGTTGGCCCTTAATTACCCCCAGGCCCGCACGGGGGGGGGCGTGGGTGCTTCGGGGGTGGCC‑ATGCCCACCGTGGACGGCGGGCGCAGCTGGCAGTCGGAGATCGGCCGACTGCCGAACGGGCGTGGa                                                                      <  7:256152/136‑1 (MQ=255)                                                       cgcggttgttGGCCTTTATTAGCACCTAGGCCCCAAAGGGCCTGTTCGTCGGGGCATACGGGGGGGCA‑AGCCTAACCGACGACGGCGGGCGCAGCTGGCAGTCGGAGATCGGCCGACTGCCGAACGGGCGTGGAc                                                                     <  6:433049/131‑1 (MQ=255)                                                        gcggttgtgGGCCTTTATTTTCACCGTTCCCCGCACCGGGCGGGGGGGGGGTGCCTCGGGGGGGCCC‑ATGCGCCCCGAGGACGGCGGGCGCAGCTGGCAGTCGGAGATCGGCCGACTGCCGAACGGGCGTGGACt                                                                    <  4:310879/132‑1 (MQ=255)                                                                     cTGATTTTCCCCCAGCCCCGCACCGGCGGGGTCGGGGGTGCCTAGGGGGGGCCC‑ATGCCCACCGCCGACGGCGGGCGCAGCTGGCAGTCGGAGATCGGCCGACTGCCGAACGGGCGTGGACTGCACCTGTATGccc                                                      <  7:139457/136‑1 (MQ=255)                                                                       gAATTTCACCGATGCCCGCAACGGCCTGGTCGTCGGTGCCTACGGGGTGGCC‑ATGCGCCACGCAGACGGCCGGCGCCGCTGGCAGTCGGAGATCGGCCGCCTGCCGAACGGGCGTGGACAGCACCAGTATGcccag                                                    >  8:56308/1‑134 (MQ=255)                                                                                    gCCCGCAACGGCCTGGGGGTCGGTGCCTACGGGGTGCCC‑ATGCGCACCGACGACGGCGGGCGCAGCTGGCAGTCGGAGATCGGCCGACTGCCGAACGGGCGTGGACTGCACCTGTATGCCCTGGCGCGCCAAGGc                                        <  4:308224/135‑1 (MQ=255)                                                                                    ccccGCACCGGCCGGGGCGGCGGGGCCTCGGGGGGGGCC‑AGCCGCCCCGACGACGGCGGGCGCAGCTGGCAGTCGGAGATCGGCCGACTGCCGAACGGGCGTGGACTGCACCTGTATGCCCTGGCGCGCCAAGGc                                        <  1:155119/134‑1 (MQ=255)                                                                                        gCAACGGCCTGGTCGTCGGTGCCTACGGGGTGGCC‑ATGCGCCCCGACGACGGCGGGCGCAGCTGGCAGTCGGAGATCGGCCGACTGCCGAACGGGCGTGGACTGCACCTGTATGCCCTGGCGCGCCAAGGCAACCa                                   >  8:41220/1‑136 (MQ=255)                                                                                               cggggTCGGCGGGGCCTACGGGGGGGCC‑ATGCGCACCGACGACGGCGGGCGCAGCTGGCAGTCGGAGATCGGCCGACTGCCGAACGGGCGTGGACTGCACCTGTATGCCCTGGCGCGCCAAGGCAACCAGGTGTa                             <  3:426025/132‑1 (MQ=255)                                                                                                       gcgGGGCCTCCGGGTGGGCC‑CGCCGCCCCGACGACGGCGGGCGCAGCTGGCAGTCGGAGATCGGCCGACTGCCGAACGGGCGTGGACTGCACCTGTATGCCCTGGCGCGCCAAGGCAACCAGGTGTACATCGCCg                     <  6:175763/134‑1 (MQ=255)                                                                                                                     ggggCC‑AGGCGCCCGGAGGACGGCGGGCGCAGCTGGCAGTCGGAGAGCGGCCGACTGCCGAACGGGCGTGGACTGCACCTGTATGCCCTGGCGCGCCAAGGCAACCAGGTGTACATCGCCGGCGAGCAGGGCctg       <  3:198723/133‑1 (MQ=255)                                                                                                                       ggCC‑CTGCCCACCGACGACGGCGGGCGCAGCTGGCAGTCGGAGATCGGCCGACTGCCGAACGGGCGGGGACTGCACCTGTATGCCCTGGCGCGCCAAGGCAACCAGGTGTACATCGCCGGCGAGCAGGGCctgct     <  3:116278/135‑1 (MQ=255)                                                                                                                          c‑ATGCGCACCGACGACGGCGGGCGCAGCTGGCAGTCGGAGATCGGCCGACTGCCGAACGGGCGTGGACTGCACCTGTATGCCCTGGCGCGCCAAGGCAACCAGGTGTACATCGCCGGCGAGCAGGGCCTgctgct  >  2:156356/1‑135 (MQ=255)                                                                                                                                  |                                                                                                                                CAGACGAGCGTCGCCTGGCGGCGGCGCAACGGCTGCTGGCCGACGGCGCGGACAAGCCGTTGTTGGCCCTGAATTTCACCGATGCCCGCAACGGCCTGGTCGTCGGTGCCTACGGGGTGGCC‑ATGCGCACCGACGACGGCGGGCGCAGCTGGCAGTCGGAGATCGGCCGACTGCCGAACGGGCGTGGACTGCACCTGTATGCCCTGGCGCGCCAAGGCAACCAGGTGTACATCGCCGGCGAGCAGGGCCTGCTGCT  >  KT2440/3625989‑3626244

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 14 ≤ ATCG/ATCG < 15 ≤ ATCG/ATCG < 16 ≤ ATCG/ATCG < 36 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑