Predicted mutation
evidence	seq id	position	mutation	annotation	gene	description
RA	NC_000913	3,059,395	C→T	pseudogene (217/231 nt)	yqfE ←	conserved protein YqfE

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NC_000913	3,059,395	0	C	T	100.0%	56.3 / NA	17	pseudogene (217/231 nt)	yqfE	conserved protein YqfE
Reads supporting (aligned to +/- strand):  ref base C (0/0);  new base T (9/8);  total (9/8)

GCCGGGCTGAACATACTGAAGTGCCGCCCATCCTACTGCTTTTTTCAATTCATCCTGCGTCATGATCGTTTCGCCTGTGGTATGAAATTTCACACGCATTATATACAAAAAAAGCGATTCAGACCCCGTTGGCAAGCCGCGTGGTTAACTCATCCATAAAATATCGCGCAATGGCAGGCATCCCCTTTCGCCCCGCAAATAAAGCATACAACGGTCTGGGTATGCCGCTCCACGGTGCAAACAGGCGCACCAGTT  >  NC_000913/3059263‑3059517                                                                                                                                     |                                                                                                                           gCCGGGCTGAACATACTGAAGTGCCGCCCATCCTACTGCTTTTTTCAATTCATCCTGCGTCATGATCGTTTCGCCTGTGGTATGAAATTTCACACGCATTATATACAAAAAAAGCGATTCAGACCCCGTTGGTAAGCcgc                                                                                                                     <  1:87557/140‑1 (MQ=255)    gggCTGAACATACTGAAGTGCCGCCCATCCTACTTCTTTTTTCAATTTATCCTGCGTCATGATCGTTTCGCCTGTGGTATGAAATTTCACACGCATTATATACAAAAAAAGCGATTCAGACCCCGTTGGTAAGCCGCGTg                                                                                                                  >  2:19075/1‑140 (MQ=255)          aaCATACTGAAGTGCCGCCCATCCTACTGCTTTTTTCAATTCATCCTGCGTCATGATCGTTTCGCCTGTGGTATGAAATTTCACACGCATTATATACAAAAAAAGCGATTCAGACCCCGTTGGTAAGCcgc                                                                                                                     >  1:364873/1‑131 (MQ=255)          aaCATACTGAAGTGCCGCCCATCCTACTGCTTTTTTCAATTCATCCTGCGTCATGATCGTTTCGCCTGTGGTATGAAATTTCACACGCATTATATACAAAAAAAGCGATTCAGACCCCGTTGGTAAGCcgc                                                                                                                     <  2:364873/131‑1 (MQ=255)            cATACTGAAGTGCCGCCCATCCTACTGCTTTTTTCAATTCATCCTGCGTCATGATCGTTTCGCCTGTGGTATGAAATTTCACACGCATTATATACAAAAAAAGCGATTCAGACCCCGTTGGTAAGCCGCGTGGTTAACTc                                                                                                          <  2:72709/140‑1 (MQ=255)                        ccgccCATCCTACTGCTTTTTTCAATTCATCCTGCGTCATGATCGTTTCGCCTGTGGTATGAAATTTCACACGCATTATATACAAAAAAAGCGATTCAGACCCCGTTGGTAAGCCGCGTGGTTAACTCATCCATAAAata                                                                                              >  1:109201/1‑140 (MQ=255)                                   aCTGCTTTTTTCAATTCATCCTGCGTCATGATCGTTTCGCCTGTGGTATGAAATTTCACACGCATTATATACAAAAAAAGCGATTCAGACCCCGTTGGTAAGCCGCGTGGTTAACTCATCCATAAAATATCGCGCAATgg                                                                                   <  2:109201/140‑1 (MQ=255)                                                                       tCGCCTGTGGTATGAAATTTCACACGCATTATATACAAAAAAAGCGATTCAGACCCCGTTGGTAAGCCGCGTGGTTAACTCATCCATAAAATATCGCGCAATGGCAGGCATCCCCTTTCGCCCCGCAAATAAAGCATACa                                               <  1:252641/140‑1 (MQ=255)                                                                       tCGCCTGTGGTATGAAATTTCACACGCATTATATACAAAAAAAGCGATTCAGACCCCGTTGGTAAGCCGCGTGGTTAACTCATCCATAAAATATCGCGCAATGGCAGGCATCCCCTTTCGCCCCGCAAATAAAGCATACa                                               >  2:45618/1‑140 (MQ=255)                                                                          ccTGTGGTATGAAATTTCACACGCATTATATACAAAAAAAGCGATTCAGACCCCGTTGGTAAGCCGCGTGGTTAACTCATCCATAAAATATCGCGCAATGGCAGGCATCCCCTTTCGCCCCGCAAATAAAGCATACAACg                                            >  2:218944/1‑140 (MQ=255)                                                                            tgtgGTATGAAATTTCACACGCATTATATACAAAAAAAGCGATTCAGACCCCGTTGGTAAGCCGCGTGGTTAACTCATCCATAAAATATCGCGCAATGGCAGGCATCCCCTTTCGCCCCGCAAATAAAGCATACAACGGt                                          <  1:338452/140‑1 (MQ=255)                                                                                                            aaaaaaGCGATTCAGACCCCGTTGGTAAGCCGCGTGGTTAACTCATCCATAAAATATCGCGCAATGGCAGGCATCCCCTTTCGCCCCGCAAATAAAGCATACAACGGTCTGGGTATGCCGCTCCACGGTGCAAACAGgcg          >  2:89385/1‑140 (MQ=255)                                                                                                            aaaaaaGCGATTCAGACCCCGTTGGTAAGCCGCGTGGTTAACTCATCCATAAAATATCGCGCAATGGCAGGCATCCCCTTTCGCCCCGCAAATAAAGCATACAACGGTCTGGGTATGCCGCTCCACGGTGCAAACAGgcg          <  2:190945/140‑1 (MQ=255)                                                                                                            aaaaaaGCGATTCAGACCCCGTTGGTAAGCCGCGTGGTTAACTCATCCATAAAATATCGCGCAATGGCAGGCATCCCCTTTCGCCCCGCAAATAAAGCATACAACGGTCTGGGTATGCCGCTCCACGGTGCAAACAGgcg          >  1:150843/1‑140 (MQ=255)                                                                                                                aaGCGATTCAGACCCCGTTGGTAAGCCGCGTGGTTAACTCATCCATAAAATATCGCGCAATGGCAGGCATCCCCTTTCGCCCCGCAAATAAAGCATACAACGGTCTGGGTATGCCGCTCCACGGTGCAAACAGGCGCAcc      >  1:66526/1‑140 (MQ=255)                                                                                                                aaGCGATTCAGACCCCGTTGGTAAGCCGCGTGGTTAACTCATCCATAAAATATCGCGCAATGGCAGGCATCCCCTTTCGCCCCGCAAATAAAGCATACAACGGTCTGGGTATGCCGCTCCACGGTGCAAACAGGCGCAcc      >  1:329045/1‑140 (MQ=255)                                                                                                                    gATTCAGACCCCGTTGGTAAGCCGCGTGGTTAACTCATCCATAAAATATCGCGCAATGGCAGGCATCCCCTTTCGCCCCGCAAATAAAGCATACAACGGTCTGGGTATGCCGCTCCACGGTGCAAACAGGCGCACCAGtt  <  1:218944/140‑1 (MQ=255)                                                                                                                                     |                                                                                                                           GCCGGGCTGAACATACTGAAGTGCCGCCCATCCTACTGCTTTTTTCAATTCATCCTGCGTCATGATCGTTTCGCCTGTGGTATGAAATTTCACACGCATTATATACAAAAAAAGCGATTCAGACCCCGTTGGCAAGCCGCGTGGTTAACTCATCCATAAAATATCGCGCAATGGCAGGCATCCCCTTTCGCCCCGCAAATAAAGCATACAACGGTCTGGGTATGCCGCTCCACGGTGCAAACAGGCGCACCAGTT  >  NC_000913/3059263‑3059517

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 33 ≤ ATCG/ATCG < 34 ≤ ATCG/ATCG < 37 ≤ ATCG/ATCG < 40 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑