Predicted mutation
evidence	seq id	position	mutation	freq	annotation	gene	description
RA	CP009273	3,365,908	G→A	100%	P9L (CCG→CTG)	nanT ←	sialic acid transporter

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	CP009273	3,365,908	0	G	A	100.0%	28.8 / NA	11	P9L (CCG→CTG)	nanT	sialic acid transporter
Reads supporting (aligned to +/- strand):  ref base G (0/0);  new base A (5/6);  total (5/6)
Rejected as polymorphism: Frequency below/above cutoff threshold.
Rejected as polymorphism: Variant not supported by required number of reads on each strand.

GAGAAGAGAACGATGCTGGTGACCATTGCCAGACGACGCCCGTAGCGGTCACCCATAGCGCCGAGCATCAGGCCGCCGAACCAGCGAGAGATAAAGGCTGCAGAGATCAGACTTGCCGCCTGCACCGTCGTCAGCCCGAATTCACCTTGTACTTCGGTGAGTACCAGGGCGATTAAAACGAAATCAAAACCGTCAAGCAGATATCCCAACCAGGCAGCGGAAAATGCGCGCCATTGTGCACGGTTGAGATGGCGATACCACGGGATATTCTGGGTTGTAGTACTCATTGTGAGTCTCCCGCGGTGGGCGATGCCCACACGCTTTGGTATGAAAATTGTAGGGTACAGATGCGTTTATTTCCCCTCACCCGGTAGGGGCGAGCGAGGGGAAACAACTCACCCGCGCTCTTGCATCAACTGCTGGGCCAGCGCCTTCAGTTCTGGCA  >  CP009273/3365647‑3366091                                                                                                                                                                                                                                                                      |                                                                                                                                                                                        gagaagagaaCGATGCTGGTGACCATTGCCAAAGGACGCCCGTAGCGGTCACCCATAGCGCCGAGCATCCGGCCGCCGAACCAGCGAGAGATAAAGGCTGCAGAGATCAGACTTGCCGCCTGCACCGTCGTCAGCCCGAATTCACCTTGTACTTCGGTGAGTACCAGTGCGATTAAAACGAAATCAAAACCGTCAAGCAGATATCCCAACCAGGCAGCGGAAAATGCGCGCCATTGTGCACGGTTGAGATGGCGATACCACAGGATATTCTggg                                                                                                                                                                             <  1:70631/274‑1 (MQ=255) gagaagagaaAAAACATGGTGACACTTGCCACACGCGGCCCGTAGAGGTCACCCATAGCGCCGAGCATCAGGCCGCCGAACAAGCGAGAGATAAAGGCTGCAGAGATCAGACTTGCAGCCTGCACCGTCGTCAGCCCGAATTCACCTTGTACTTCGGTGAGTACCAGGGCGATTAAAACGAAATCAAAACCGTCAAGCAGATATCCCAACCAGGCAGCGGAAAATGCGCGCCATTGTGCACGGTTGAGATGGCGATACCACAGGATATTCTggg                                                                                                                                                                             <  2:400902/274‑1 (MQ=255)                        cATTGCCAGACGACGCCCGTAGCGGTCACCCATAGCGCCGAGCATCAGGCCGCCGAACCAGCGAGAGATAAAGGCTGCAGAGATCAGACTTGCCGCCTGCACCGTCGTCAGCCCGAATTCACCTTGTACTTCGGTGAGTACCAGGGCGATTAAAACGAAATCAAAACCGTCAAGCAGATATCCCAACCAGGCAGCGGAAAATGCGCGCAATTGTGCACGGATGAGATGGCGATACCACAGGACATTCTGGGTTGAAGTACTAATGGTGAGTcccc                                                                                                                                                     >  1:123354/1‑275 (MQ=255)                                                gccACCCCTGGCGCCGACCCACAGTCCGCCGAACCAGCGCCGGAGCAAGGCTGCAGAGATCAGCCTTGCCGCCTGCACCGTCGTCAGCCCGAATTCACCTGGTACTTCGGTAAGTACCAGGGCGCTTAAAACGAAATCCAAACCGTCAAGCAGATATCCCAACCAGGCCGCGGAAAATGCGCGCCATTGTGCACGGTTGAGATGGCGATACCACAGGCTATTCTGGGTTGTAGTACTCATTGTGAGTCTCCCGCGGTGGGCGATGCCCACACGCt                                                                                                                             <  2:210140/273‑1 (MQ=255)                                                                                                                                                     gTACTTCGGTGAGTACCAGGGCGATTAAAACGAAATCAAAACCGTCAAGCAGATATCCCAACCAGGCAGCGGAAAATGCGCGCCATTGTGCACGGTTGAGATGGCGATACCACAGGATATTCTGGGTTGTAGTACTCATTGTGAGTCTCCCGCGGTg                                                                                                                                              >  1:157333/1‑157 (MQ=255)                                                                                                                                                         ttCGGTGAGTACCAGGGCGATTAAAACGAAATCAAAACCGTCAAGCAGATATCCCAACCAGGCAGCGGAAAATGCGCGCCATTGTGCACGGTTGAGATGGCGATACCACAGGATATTCTGGGTTGTAGTACTCATTGTGAGTCTCCCGCGGTGGGCg                                                                                                                                          <  2:157332/157‑1 (MQ=255)                                                                                                                                                                            aTTAAAACGAAATCAAAACCGTCAAGCAGATATCCCAACCAGGCAGCGGAAAATGCGCGCCATTGTGCACGGTTGAGATGGCGATACCACAGGATATTCTGGGTTGTAGTACTCATTGTGAGTCTCCCGCGGTGGGCGATGCCCACACGCTTTGGTATGAAAATTGTAGGGTACAGATGCGTTTATTTCCCCTCACCCGGTAGGGGCGAGCGAGGGGAAACAACTCACTCGCGCTCTTGCATCAACTGCTGGGCCCGCGCCTTCAGTTCTGGCa  >  1:28466/1‑274 (MQ=255)                                                                                                                                                                                                             cccAACCAGGCAGCGGAAAATGCGCGCCATTGTGCACGGTTGAGATGGCGATACCACagg                                                                                                                                                                                       <  1:238282/60‑1 (MQ=255)                                                                                                                                                                                                                          cGGAAAATGCGCGCCATTGTGCACGGTTGAGATGGCGATACCACagg                                                                                                                                                                                       <  2:138767/47‑1 (MQ=255)                                                                                                                                                                                                                                           tgtgCACGGTTGAGATGGCGATACCACAGGATATTc                                                                                                                                                                                 >  1:48870/1‑36 (MQ=255)                                                                                                                                                                                                                                               cACGGTTGAGATGGCGATACCACAGGATATTCTggg                                                                                                                                                                             <  2:48870/36‑1 (MQ=255)                                                                                                                                                                                                                                                              gATACCACAGGATATTCTGGGTTGTAGTACTCATtgt                                                                                                                                                             >  2:148690/1‑37 (MQ=255)                                                                                                                                                                                                                                                                  ccACAGGATATTCTGGGTTGTAGTACTCATTGTGAGt                                                                                                                                                         <  1:148691/37‑1 (MQ=255)                                                                                                                                                                                                                                                                      |                                                                                                                                                                                        GAGAAGAGAACGATGCTGGTGACCATTGCCAGACGACGCCCGTAGCGGTCACCCATAGCGCCGAGCATCAGGCCGCCGAACCAGCGAGAGATAAAGGCTGCAGAGATCAGACTTGCCGCCTGCACCGTCGTCAGCCCGAATTCACCTTGTACTTCGGTGAGTACCAGGGCGATTAAAACGAAATCAAAACCGTCAAGCAGATATCCCAACCAGGCAGCGGAAAATGCGCGCCATTGTGCACGGTTGAGATGGCGATACCACGGGATATTCTGGGTTGTAGTACTCATTGTGAGTCTCCCGCGGTGGGCGATGCCCACACGCTTTGGTATGAAAATTGTAGGGTACAGATGCGTTTATTTCCCCTCACCCGGTAGGGGCGAGCGAGGGGAAACAACTCACCCGCGCTCTTGCATCAACTGCTGGGCCAGCGCCTTCAGTTCTGGCA  >  CP009273/3365647‑3366091

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 9 ≤ ATCG/ATCG < 14 ≤ ATCG/ATCG < 34 ≤ ATCG/ATCG < 38 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑