Predicted mutation
evidence	seq id	position	mutation	annotation	gene	description
RA	NC_000913	2,166,682	C→T	L339L (CTG→TTG)	trhP →	tRNA wobble base hydroxylation protein TrhP

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NC_000913	2,166,682	0	C	T	100.0%	29.6 / NA	12	L339L (CTG→TTG)	trhP	tRNA wobble base hydroxylation protein TrhP
Reads supporting (aligned to +/- strand):  ref base C (0/0);  new base T (7/5);  total (7/5)

CCATCGCCCATGTAGAACGCCTGACCAAAATGGGCGTGCATTCGCTGAAAATCGAAGGTCGTACCAAATCTTTCTACTATTGTGCACGCACCGCACAGGTTTACCGCAAAGCTATCGATGACGCCGCTGCGGGAAAACCGTTCGATACCAGCCTGCTGGAAACTCTGGAAGGTCTGGCGCATCGTGGCTATACCGAAGGTTTCCTGCGTCGTCATACTCACGACGATTATCAGAACTACGAATACGGTTATTCAGTTTCTGACCGCCAGCAGTTTGTTGGTGAGTTTACCGGTGAGCGCAAGGGGGACCTCGCGGCGGTAGCGGTGAAAAATAAATTCTCCGTTGGCGACAGCCTTGAGCTGATGACGCCGCAAGGCAACATTAATTTTACCCTTGAGCACATGGAAAACGCCAAAGGCGAAGCTATGCCGATAGCACC  >  NC_000913/2166479‑2166917                                                                                                                                                                                                            |                                                                                                                                                                                                                                            ncATCGCCCATGTAGAACGCCTGACCAAAATGGGCGTGCATTCGCTGAAAATCGAAGGTCGTACCAAATCTTTCTACTATTGTGCACGCACCGCACAGGTTTACCGCAAAGCTATCGATGACGCCGCTGCGGGAAAACCGTTCGATACCAGCCTGCTGGAAACTCTGGAAGGACTGGCGCATCGTGGCTATACCGAAGGTTTCTTGCGTCGTCATACTCACGACGATTATCAGAACTACGAATACGGTTAt                                                                                                                                                                                              >  1:99812/2‑251 (MQ=255)                                  gcgggCATTCGCTGAAAATCGAAGGTCGTACCAAATCTTTCTACTATTGTGCACGCACCGCACAGGTTTACCGCAAAGCTAGCGAGGACGCCGCTGCGGGAAAACCGTTCGATACCAGCCTGCGGGAAACTCTGGAAGGTCTGGCGCATCGTGGCTATACCGAAGGTTTCTTGCGTCGTCATACTCACGACGATTATCAGAACTACGAATACGGTGATTCAGTTTCGGACCGCCAGCAGTTTGTTGGTGAg                                                                                                                                                             <  1:53542/247‑1 (MQ=255)                                  gCGTGCATTCGCTGAAAATCGAAGGTCGTACCAAATCTTTCTACTATTGTGCACGCACCGCACAGGTTTACCGCACAGCTATCGATGACGCCGCTGCGGGAAAACCGTTCGATACCCGCCTGCTGGAAACTCTGGCAGGTCTGGCGCATCGTGGCTATACCGAAGGTTTCTTGCGTCGTCATACTCACGACGATTATCAGAACTACGAATACGGTTATTCAGTTTCTGACCGCCAGCAGTTTGTTGGTg                                                                                                                                                               >  1:52473/1‑249 (MQ=255)                                                                                                                     gATGACGCCGCGGCGGGAAAACCGTTCGATACCAGCCTGCTGGAAACTCTGGAAGGTCTGGCGCATCGTGGCTATACCGAAGGTTTCTTGCGTCGTCATACGCACGACGATTATCAGAACGACGAATTCGGTTATTCAGTTTCTGACCGCCAGCAGTTTGTTGGTGATTTTACCGGTGAGCTCAAGGGGGACCGCGCGGCGGTAGCGGTGAAAAATAAATTCTCCGTTGGCGACAGCCTTGAGCTGATGAc                                                                          <  1:149291/251‑1 (MQ=255)                                                                                                                                 nnggnNNNNCCGNTCGATACCAGCCTGCTGGAAACTCTGGAAGGTCTGGCGCATCGTGGCTATACCGAAGGTTTCTTGCGTCTTCATACTCACGACGATTATCAGAACTACGAATACGGTTATTCAGTTTCTGACCGCCAGCAGtt                                                                                                                                                                       <  2:99812/144‑1 (MQ=255)                                                                                                                                   gtgAAAACCGTTCGATACCAGCCTGCTGGAAACTCTGAACCGTCTGGCGCATCGTACCTCTACCGCAGGTTTCTTGCGTCGTCATACTCACGACGATTATCAGAACTACGACTACGGTTCTTCAGTTTCTGCCCGCCAGCACTTTGTTGGTGAGTTTACCGGTGAGAGCAAGGGGGACCTCGCGGCGGTATCGGTGAAAAATAAATTCTCCGTTTGCGACAGCCTTGAGCTGATGACGCCGCAAGGccac                                                             >  1:110572/3‑247 (MQ=255)                                                                                                                                     gAAAACCGTTCGATACCAGCCTGCTGGAAACTCTGGAAGGTCTGGCGCATCGTGGCTATACCGAAGGTTTCTTGCGTCGTCATACTCACGACGATTATCAGAACTACGAATACGGTTATTCAGTTTCTGACCGCCAGCAGTTTGTTGGTGAGTTTACCGGGGAGCGCAAGGGGGACCTCGCGGCGGTAGCGGTGAAAAATAAATTCTCCGTTGGCGACAGCCTTg                                                                                    >  1:87163/1‑225 (MQ=255)                                                                                                                                          ccGTTNNATNNNAGNNTGCTGGAAACTCTGGAAGGTCTGNCGCATCGTGGCTATACCGAAGGTTTCTTGNGNCNTAATNNTCANGACGATTATCNGAACTACGAATACGGTTATTCAGTTTCTGACCGCCAGCAGTTTGTTGGNGNGTTTACCGGTGAGCGCAAGGGGGACCTCGCGNCGGTAGCGGTGAAAAATAAATTTTNCGttnnggncnnnnnnnn                                                                                   >  2:122110/1‑207 (MQ=255)                                                                                                                                                            ctgGAAACTCTGGAAGGTCTGGCGCATCGTGGCTATACCGAAGGTTTCTTGCGTCGTCATACTCACGACGATTATCAGAACTACGAATACGGTTATTCAGTTTCTGACCGCCAGCAGTTTGTTGGTGAGTTTACCGGTGAGCGCAAGGGGGACCTCGCGGCGGTAGCGGTGAAAAATAAATTCTCCGTTGGCGACAGCCTTGAGCTGATGACGCCGCAAGGCAACATTAATTTTACCCTTGAGCACATgg                                    >  1:89617/1‑250 (MQ=255)                                                                                                                                                                                ggCGCATCGTGGCTATACCGAAGGTTTCTTGCGTNGTCATACTCANGACNNTTATNANANCTACGAATACGGTTATTCAGTTTCTGACCNCCAGCAGTTTGTTGGTGAGTTTANNGGNNNGCNNAAggg                                                                                                                                         <  2:127248/129‑1 (MQ=255)                                                                                                                                                                                ggCGCATCGTGGCTATACCGAAGGTTTCTTGCGTCGTCAGACTCACGACGATTATCAGAACTACGAATACGGTTATTCAGTTTCTGACCGCAAGCAGTTTGTTGGTGAGTTTACCGGTGAGCGCAAggg                                                                                                                                         >  1:127248/1‑129 (MQ=255)                                                                                                                                                                                              ataCCGAAGGTTTCTTGCGTCGTCATACTCACGACGATTATCAGAACTACGAATACGGTTATTCAGTTTCTGACCGCCAGCAGTTTGTTGGTGAGTTTACCGGTGAGCGCAAGGGGGACCTCGCGGCGGTAGCGGTGAAAAATAAATTCTCCTTTGGCGACAGCCTTGAGCTGATGACGCCGCAAGGCAACATTAATTTTACCCTTGAGCACATGGAAAACGCCAAAGGCGAAGCTATGCCGATAGCAcc  <  1:122110/250‑1 (MQ=255)                                                                                                                                                                                                            |                                                                                                                                                                                                                                            CCATCGCCCATGTAGAACGCCTGACCAAAATGGGCGTGCATTCGCTGAAAATCGAAGGTCGTACCAAATCTTTCTACTATTGTGCACGCACCGCACAGGTTTACCGCAAAGCTATCGATGACGCCGCTGCGGGAAAACCGTTCGATACCAGCCTGCTGGAAACTCTGGAAGGTCTGGCGCATCGTGGCTATACCGAAGGTTTCCTGCGTCGTCATACTCACGACGATTATCAGAACTACGAATACGGTTATTCAGTTTCTGACCGCCAGCAGTTTGTTGGTGAGTTTACCGGTGAGCGCAAGGGGGACCTCGCGGCGGTAGCGGTGAAAAATAAATTCTCCGTTGGCGACAGCCTTGAGCTGATGACGCCGCAAGGCAACATTAATTTTACCCTTGAGCACATGGAAAACGCCAAAGGCGAAGCTATGCCGATAGCACC  >  NC_000913/2166479‑2166917

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 13 ≤ ATCG/ATCG < 14 ≤ ATCG/ATCG < 31 ≤ ATCG/ATCG < 38 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑