Predicted mutation
evidence	seq id	position	mutation	annotation	gene	description
RA	1	225,225	2 bp→AA	coding (99‑100/375 nt)	unknown ←	hypothetical protein

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	1	225,225	0	C	A	100.0%	11.6 / NA	8	A34S (GCG→TCG)	unknown	hypothetical protein
Reads supporting (aligned to +/- strand):  ref base C (0/0);  new base A (5/3);  total (5/3)
*	1	225,226	0	G	A	100.0%	11.6 / NA	8	H33H (CAC→CAT)	unknown	hypothetical protein
Reads supporting (aligned to +/- strand):  ref base G (0/0);  new base A (5/3);  total (5/3)

CCAACTCCTTTAGGTAAGCAATCTGTGCACGTGCTAATGCCAGCTCTCGTTGCAGCTTTTTAAACGCTTTTGGGGAAAAGTCTGTTTGTTCCGGGATTTCAATCGCTTTCTTTTTCATCTTTGGCTTCACTATTTTAGGGCGTTGAGGGTTTATATAAGGGGATTTTACGCCATTAAGCCCTCTTTCACGAAATGCTTTTAGCCAATAAATGACGAGCGCGTGGGAGATTTTATGAAGTTTCGCCACCTCACGGATACCAAAATCCTGCTCGGTGACCTGTTTGATAGTTTTTAAACGAAATTGATAAGAGTAAGACATAATCTGCACCTCAAATTAGGTGTCCGGGTTTTGGGGTGCAGATCACTTTTTTGTTTCGGAAAGCGGATTATTTAATTACACCACACGCCATACGCGGACCGCCGC  >  1/225006‑225429                                                                                                                                                                                                                            ||                                                                                                                                                                                                            ccAACTCCTTTAGGTAAGCAATCTGTGCACGTGCTAATGCCAGCTCTCGTTGCAGCTTTTTAAACGCTTTTGGGGAAAAGTCTGTTTGTTCCGGGATTTCAATCGCTTTCTTTTTCATCTTTGGCTTCACTATTTTAGGGCGTTGAGGGTTTATATAAGGGGATTTTACGCCATTAAGCCCTCTTTCACGAAATGCTTTTAGCCAATAAATGACGAGCGAATGGGAGATTTTATGAAGTTTCGcc                                                                                                                                                                                     >  1:477617/1‑245 (MQ=255)                                      tGCCAGCTCTCGTTGCAGCTTTTTAAACGCTTTTGGGGAAAAGTCTGTTTGTTCCGGGATTTCAATCGCTTTCTTTTTCATCTTTGGCTTCACTATTTTAGGGCGTTGAGGGTTTATATAAGGGGATTTTACGCCATTAAGCCCTCTTTCACGAAAGGCTTTT‑‑CCAATAAATGACGAGCGAATGGGAGATTTTATg                                                                                                                                                                                               >  1:822717/1‑196 (MQ=11)                                                                   cTTTTGGGGAAAAGTCTGTTTGTTCCGGGATTTCAATCGCTTTCTTTTTCATCTTTGGCTTCACTATTTTAGGGCGTTGAGGGTTTATATAAGGGGATTTTACGCCATTAAGCCCTCTTTCACGAAATGCTTTTAGCCAATAAATGACGAGCGAATGGGAGATTTTATGAAGTTTCGCCACCTCACGGATACCAAAATCCTGCTCGGTGACCTGTTTGATAGTTTTTAAACGAAATTGGTAAGAGTAAGAc                                                                                                             <  1:897128/251‑1 (MQ=18)                                                                                                                                                                  gATTTTACGCCATTAAGCCCTCTTTCACGAAAGGCTTTT‑‑CCAATAAATGACTTGAGAACGAGAAATCTGATGAAGTTCAGCCACCTCACGGATACCAAAATCCTGCTCGGTGACCTGTTTGATAATTTCTAAACGAAATTGATAAGAGTAAGACATAATCTGCACCTCAAATTAGGTGTCCAGGTTTTGGGGTGCAGATCACTTTTTTGTTTCGGAAAGCGGATTATTTAATTACACCACACGCCATAcg             <  1:624914/250‑1 (MQ=255)                                                                                                                                                                   aTTTTACGCCATTAAGCCCTCTTTCACGAAAGGCTTTT‑‑CCAATAAATGACTTGAGAACGAGAAATCTGATGAAGTTCAGCCACCTCACGGATACCAAAATCCTGCTCGGTGACCTGTTTGATAATTTCTAAACGAAATTGATAAGAGTAAGACATAATCTGCACCTCAAATTAGGTGTCCAGGTTTTGGGGTGCAGATCACTTTTTTGTTTCGGAAAGCGGATTATTTAATTACACCACACGCCATAcgcg           >  1:661990/1‑251 (MQ=11)                                                                                                                                                                    ttttACGCCATTAAGCCCTCTTTCACGAAAGGCTTTT‑‑CCAATAAATGACTTGAGAACGAGAAATCTGATGAAGTTCAGCCACCTCACGGATACCAAAATCCTGCTCGGTGACCTGTTTGATAATTTCTAAACGAAATTGATAAGAGTAAGACATAATCTGCACCTCAAATTAGGTGTCCAGGTTTTGGGGTGCAGATCACTTTTTTGTTTCGGAAAGCGGATTATTTAATTACACCACACGCCATAcg             <  1:226559/248‑1 (MQ=255)                                                                                                                                                                             aTTAAGCCCTCTTTCACGAAAGGCTTTT‑‑CCAATAAATGACTTGAGAACGAGAAATCTGATGAAGTTCAGCCACCTCACGGATACCAAAATCCTGCTCGGTGACCTGTTTGATAATTTCTAAACGAAATTGATAAGAGTAAGACATAATCTGCACCTCAAATTAGGTGTCCAGGTTTTGGGGTGCAGATCACTTTTTTGTTTCGGAAAGCGGATTATTTAATTACACCACACGCCATAcgc            >  1:303672/1‑240 (MQ=11)                                                                                                                                                                             aTTAAGCCCTCTTTCACGAAAGGCTTTT‑‑CCAATAAATGACTTGAGAACGAGAAATCTGATGAAGTTCAGCCACCTCACGGATACCAAAATCCTGCTCGGTGACCTGTTTGATAATTTCTAAACGAAATTGATAAGAGTAAGACATAATCTGCACCTCAAATTAGGTGTCCAGGTTTTGGGGTGCAGATCACTTTTTTGTTTCGGAAAGCGGATTATTTAATTACACCACACGCCATACGCGGAccgccgc  >  1:675978/1‑250 (MQ=11)                                                                                                                                                                                                                            ||                                                                                                                                                                                                            CCAACTCCTTTAGGTAAGCAATCTGTGCACGTGCTAATGCCAGCTCTCGTTGCAGCTTTTTAAACGCTTTTGGGGAAAAGTCTGTTTGTTCCGGGATTTCAATCGCTTTCTTTTTCATCTTTGGCTTCACTATTTTAGGGCGTTGAGGGTTTATATAAGGGGATTTTACGCCATTAAGCCCTCTTTCACGAAATGCTTTTAGCCAATAAATGACGAGCGCGTGGGAGATTTTATGAAGTTTCGCCACCTCACGGATACCAAAATCCTGCTCGGTGACCTGTTTGATAGTTTTTAAACGAAATTGATAAGAGTAAGACATAATCTGCACCTCAAATTAGGTGTCCGGGTTTTGGGGTGCAGATCACTTTTTTGTTTCGGAAAGCGGATTATTTAATTACACCACACGCCATACGCGGACCGCCGC  >  1/225006‑225429

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 32 ≤ ATCG/ATCG < 37 ≤ ATCG/ATCG < 38 ≤ ATCG/ATCG < 39 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑