Predicted mutation
evidence	seq id	position	mutation	freq	annotation	gene	description
RA	AE015451	3,151,990	A→C	27.3%	T49P (ACC→CCC)	PP_2768 →	putative Branched‑chain amino acid ABC transporter, permease protein

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	AE015451	3,151,990	0	A	C	27.3%	34.3 / 2.9	20	T49P (ACC→CCC)	PP_2768	putative Branched‑chain amino acid ABC transporter, permease protein
Reads supporting (aligned to +/- strand):  ref base A (7/7);  new base C (4/2);  total (11/9)
Fisher's exact test for biased strand distribution p-value = 6.42e-01
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 1.00e+00

CCGACGTGATCGCGGCCTATCTGGGTGTACGCCCGGCGGCGGCTTCGGGGCTGTTCCCACACAGGAGCGCGACATGGCATTCTTTTTCGAAGTGCTGATCGGTGGCCTGCTGGCCGGGGTGATGTACTCCCTGGTGGCCATCGGTTTCGTACTGATCTACAAAGCCAGCGGTGTGTTCAACTTCGCCCAGGGGGCGATGGTACTGTTCGCCGCGCTGACCTTCGTCAGCCTGCTG‑GAGCGCGGCGTGCCGTTCTGGCTGTCCTTTCTCGTCACCCTGGCGACGATGATCGCCCTGGCGCTGCTGATCGAACGGGCGGTACTGCGGCCATTGGTCGGGCGTTCGCCGATAACCCTGTTCATGGCCACGCTCGGCCTGGCCTACATCATCGAGGGCGCCGCCCAGGC  >  AE015451/3151773‑3152177                                                                                                                                                                                                                          |                                                                                                                                                                                             ccGACGTGATCGCGGCCTATCTGGGTGTACGCCCGGCGGCGGCTTCGGGGCTGTTCCCACACAGGAGCGCGACATGGCATTCTTTTTCGAAGTGCTGATCGGTGGCCTGCTGGCCGGGGTGATGTACTCCCTGGTGGCCATCGGTTTCGTACTGATCTACAAAGCCAGCGGTGTGTTCAACTTCGCCCAGGGGGCGATGGTACTGTTCGCCGCGCTGACCtt                                                                                                                                                                                          >  2:350416/1‑222 (MQ=255)                    tCTGGGTGTACGCCCGGCGGCGGCTTCGGGGCTGTTCCCACACAGGAGCGCGACATGGCATTCTTTTTCGAAGTGCTGATCGGTGGCCTGCTGGCCGGGGTGATGTACTCCCTGGTGGCCATCGGTTTCGTACTGATCTACAAAGCCAGCGGTGTGTTCAACTTCGCCCAGGGGGCGATGGTACTGTTCGCCGCGCTGACCTTCGTCAGCctgct                                                                                                                                                                              <  1:164842/215‑1 (MQ=255)                       gggTGTACGCCCGGCGGCGGCTTCGGGGCTGTTCCCACACAGGAGCGCGACATGGCATTCTTTTTCGAAGTGCTGATCGGTGGCCTGCTGGCCGGGGTGATGTACTCCCTGGTGGCCATCGGTTTCGTACTGATCTACAAAGCCAGCGGTGTGTTCAACTTCGCCCAGGGGGCGATGGTACTGTTCGCCGCGCTGCCCTTCGTCAGCCTGCTG‑GAGCGCGGCGTGCCGtt                                                                                                                                                           >  2:418875/1‑230 (MQ=255)                                 ccGGCGGCGGCTTCGGGGCTGTTCCCACACAGGAGCGCGACATGGCATTCTTTTTCGAAGTGCTGATCGGTGGCCTGCTGGCCGGGGTGATGTACTCCCTGGTGGCCATCGGTTTCGTACTGATCTACAAAGCCAGCGGTGTGTTCAACTTCGCCCAGGGGGCGATGGTACTGTTCGCCGCGCTGACCTTCGTCAGCCTGCTG‑GAGCGCGGCGTGCCGTTCTGGCTGTCCttt                                                                                                                                              >  2:192581/1‑233 (MQ=255)                                                                        aCATGGCATTCTTTTTCGAAGTGCTGATCGGTGGCCTGCTGGCCGGGGTGATGTACTCCCTGGTGGCCATCGGTTTCGTACTGATCTACAAAGCCAGCGGTGTGTTCAACTTCGCCCAGGGGGCGATGGTACTGTTCGCCGCGCTGACCTTCGTCAGCCTGCTG‑GAGCGCGGCGTGCCGTTCTGGCTGTCCTTTCTCGTCACCCTGGCGACGATGATCGCCCTGGCGCTGCTGAt                                                                                                     <  1:350420/235‑1 (MQ=255)                                                                                                        ggCCTGCTGGCCGGGGTGATGTACTCCCTGGTGGCCATCGGTTTCGTACTGATCTACAAAGCCAGCGGTGTGTTCAACTTCGCCCAGGGGGCGATGGTACTGTTCGCCGCGCTGACCTTCGTCAGCCTGCTG‑GAGCGCGGCGTGCCGTTCTGGCTGTCCTTTCTCGTCACCCTGGCGACGATGATCGCCCTGGCGCTGCTGATCGAACGGGCGGTACTGCGGCCATTGGTCGGGc                                                                     <  1:192585/235‑1 (MQ=255)                                                                                                          ccTGCTGGCCGGGGTGATGTACTCCCTGGGGGCCATCGGTTTCGTACTGATCTACAAAGCCAGCGGTGTGTTCAACTTCGCCCAGGGGGCGATGGTACTGTTCGCCGCGCT‑CCAGCAGGCTGACGAAGGTCAGCGCGGCGTGCCGTTCTGGCTGTCCTTTCTCGTCACCCTGGCGACGATGATCGCCCTGGCGctgctgct                                                                                                     >  1:65724/1‑199 (MQ=255)                                                                                                                         gATGTACTCCCTGGTGGCCATCGGTTTCGTACTGATCTACAAAGCCAGCGGTGTGTTCAACTTCGCCCAGGGGGCGATGGTACTGTTCGCCGCGCTGACCTTCGTCAGCCTGCTG‑GAGCGCGGCGTGCCGTTCTGGCTGTCCTTTCTCGTCACCCTGGCGACGATGATCGCCCTGGCGCTGCTGATCGAACGGGCGGTACTGCGGCCATTGGTCGGGCGTTCGCCGATAACCCTGt                                                   >  1:221096/1‑236 (MQ=255)                                                                                                                                    tggtggCCATCGGTTTCGGAATGATCTACAAAGCCAGCGGTGTGTTCAACTTCACCCAGGGGGCGATGGTACTGTTCGCCGCGCTGCCCTTCGTCAGCCTGCTG‑GAgc                                                                                                                                                                        <  2:110147/108‑1 (MQ=255)                                                                                                                                          ccATCGGTTTCGTACTGATCTACAAAGCCAGCGGTGTGTTCAACTTCGCCCAGGGGGCGATGGTACTGTTCGCCGCGCT‑CCAGCAGGCTGACGAAGGTCAGCGCGGCGTGCCGTTCTGGCTGTCCTTTCTCGTCACCCTGGCGACGATGATCGCCCTGgcg                                                                                                             >  1:62251/1‑161 (MQ=25)                                                                                                                                                   tCGTACTGATCTACAAAGCCAGCGGTGTGTTCAACTTCGCCCAGGGGGCGATGGTACTGTTCGCCGCGCTGACCTTCGTCAGCCTGCTG‑GAGCGCGGCGTGCCGTTCTGGCTGTCCTTTCTCGTCACCCTGGCGACGATGATCGCCCTGGCGCTGCTGATCGAACGGGCGGTACTGCGGCCATTGGTCGGGCGTTCGcc                                                              <  1:88629/199‑1 (MQ=255)                                                                                                                                                    cGTACTGATCTACAAAGCCAGCGGTGTGTTCATCTTCGCCCAGGGGGCGATGGTACTGTTCGCCGCGCTGACCTTCGTCAGCCTGCTG‑GAGCGCGGCGTGCCGTTCTGGCTGTCCTTTCTCGTCACCCTGGCGACGATGATCGCCCTGGCGCTGCTGATCGAACGGGCGGTACTGCGGCCATTGGTCGGGCGTTCGCCGATa                                                          <  1:66069/202‑1 (MQ=255)                                                                                                                                                            tCTACAAAGCCAGCGGTGTGTTCAACTTCGCCCAGGGGGCGATGGTACTGTTCGCCGCGCTGACCTGCGTCAGCCTGCTG‑GAGCGCGGCGTGCCGTTCTGGCTGTCCTTTCTCGTCACCCTGGCGACGATGATCGCCCTGGCGCTGCTGATCGAACGGGCGGTACTGCGGCCATTGGTCGGGCGTTCGCCGATAACCCTGTTCATGGCCACGCTCGGCCTGGCCTACATCATCGAg                <  1:152242/236‑1 (MQ=255)                                                                                                                                                                ccaaGCCAGCGGTGTGTTCAACTTCGCCCAGGGGGCGATGGTACTGTTCGCCGCGCT‑CCAGCAGGCTGACGAAGGTCAGCGCGGCGTGCCGTTCTGGCTGTCCTTTCTCGTCACCCTGGCGACGATGATCGCCCTGGCGCTGCTGATCGAACGGGCGGTACTGCGGCCATTGGTCGGGCGTTCGCCGATAACCCTGTTCAt                                               <  1:347685/199‑1 (MQ=255)                                                                                                                                                                     ccAGCGGTGTGTTCGACTTCGCCCAGGGGGCGATGGTACTGTTCGCCGCGCTGACCTTCGTCAGCCTGCTG‑GAGCGCGGCGTGCCGTTCTGGCTGTCCTTTCTCGTCACCCTGGCGACGATGATCGCCCTGGCGCTGCTGATCGAACGGGCGGTACTGCGGCCATTGGTCGGGCg                                                                    <  2:356426/175‑1 (MQ=255)                                                                                                                                                                        gCGGTGTGTTCAACTTCGCCCAGGGGGCGATGGTACTGTTCGCCGCGCTGCCCTTCGTCAGCCTGCTG‑GAGCGCGGCGTGCCGTTCTGGCTGTCCTTTCTCGTCACCCTGGCGACGATGATCGCCCTGGCGCTGCTGATCGaa                                                                                                 >  2:481080/1‑143 (MQ=255)                                                                                                                                                                        gCGGTGTGTTCAACTTCGCCCAGGGGGCGATGGTACTGTTCGCCGCGCTGACCTTCGTCAGCCTGCTG‑GAGCGCGGCGTGCCGtt                                                                                                                                                           >  2:110756/1‑85 (MQ=255)                                                                                                                                                                        gCGGTGTGTTCAACTTCGCCCAGGGGGCGATGGTACTGTTCGCCGCGCTGACCTTCGTCAGCCTGCTG‑GAGCGCGGCGTGCCGTTCTGGCTGTCCTTTCTCGTCACCCTGGCGACGATGATCGCCCTGGCGCTGCTGATCGAACGGGCGGTACTGCGGCCATTGGTCGGGCGTTCGCCGATACCCCTGTTCATGGCCACGCTCGGCCTGGCCTAcgt                       >  1:312033/1‑215 (MQ=255)                                                                                                                                                                           gtgtgtTCAACTTCGCCCAGGGGGCGATGGTACTGTTCGCCGCGCTGACCTTCGTCAGCCTGCTG‑GAGCGCGGCGTGCCGTTCTGGCTGTCCTTTCTCGTCACCCTGGCGACGATGATCGCCCTGGCGCTGCTGATCGAACGGGCGGTACTGCGGCCATTGGTCGGGCGTTCGCCGATAACCGTGTTCATGGCCACGCTCGGCCTGGCCTACATCATCGAGCGCGCCGCCCAGGc  >  1:153383/1‑235 (MQ=255)                                                                                                                                                                                           ccAGGGGGCGATGGTACTGTTCGCCGCGCTGACCTTCGTCAGCCTGCTG‑GAGCGCGGCGTGCCGTTCTGGCTGTCCTTTCTCGTCACCCTGGCGACGATGATCGCCCTGGCGCTGCTGATCGAACGGGCGGTACTGCGGCGTTTGGTCGGGCGTTCGCCGa                                                            >  1:319134/1‑161 (MQ=255)                                                                                                                                                                                                                          |                                                                                                                                                                                             CCGACGTGATCGCGGCCTATCTGGGTGTACGCCCGGCGGCGGCTTCGGGGCTGTTCCCACACAGGAGCGCGACATGGCATTCTTTTTCGAAGTGCTGATCGGTGGCCTGCTGGCCGGGGTGATGTACTCCCTGGTGGCCATCGGTTTCGTACTGATCTACAAAGCCAGCGGTGTGTTCAACTTCGCCCAGGGGGCGATGGTACTGTTCGCCGCGCTGACCTTCGTCAGCCTGCTG‑GAGCGCGGCGTGCCGTTCTGGCTGTCCTTTCTCGTCACCCTGGCGACGATGATCGCCCTGGCGCTGCTGATCGAACGGGCGGTACTGCGGCCATTGGTCGGGCGTTCGCCGATAACCCTGTTCATGGCCACGCTCGGCCTGGCCTACATCATCGAGGGCGCCGCCCAGGC  >  AE015451/3151773‑3152177

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 12 ≤ ATCG/ATCG < 25 ≤ ATCG/ATCG < 35 ≤ ATCG/ATCG < 40 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑