Predicted mutation
evidence	seq id	position	mutation	freq	annotation	gene	description
RA	NC_000913	3,769,672	(A)8→7	100%	pseudogene (1/111 nt)	yibV →	pseudogene, putative cryptic Rhs immunity protein

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NC_000913	3,769,665	0	A	.	100.0%	34.5 / NA	9	pseudogene (322/327 nt)	yibV	pseudogene, putative cryptic Rhs immunity protein
Reads supporting (aligned to +/- strand):  ref base A (0/0);  new base . (4/5);  total (4/5)
Rejected as polymorphism: Frequency below/above cutoff threshold.
Rejected as polymorphism: Variant not supported by required number of reads on each strand.

GGACGAAAAGCGTGTTCACTAAGCTATTTTGCCTGTAAGGCCGCAGAGGCTGAACTCGGACTGGCATATATGGCTGCGAATGATAACAAGGAATTTCTCACATCCTTATCTAATATAATGAGGTACAAAATAGATGCTGGACTTTCCGAATCCTATACATGCTATTTATTAAGTAAGGGAAAGATCATAAGACCATATCTGAAAAATCTAAATCCACTCCAACTTGCCGCTGATTGCATTGAAACAGTAAATAAAATAAAAGATAAGAATAAAAAAAATCATTGATATAAATTCAGTTAATATTTGTAGTGATGATAAAAATATAAAATTGAGAGTTAATAGTACTATTATGGCCATTGATGATTCTATAAAGTGCATCGATGAATGATAACTTAATTTTATTTAAAAATATATTAATAACTCACTCTCCAGGAGTTTTTTTAACT  >  NC_000913/3769395‑3769840                                                                                                                                                                                                                                                                               |                                                                                                                                                                                ggACGAAAAGCGTGTTCACTAAGCTATTTTGCCTGTAAGGCCGCAGAGGCTGAACTCGGACTGGCATATATGGCTGCGAATGATAACAAGGAATTTCTCACATCCTTATCTAATATAATGAGGTACAAAATAGATGCTGGACTTTCCGAATCCTATACATGCTATTTATTAAGTAAGGGAAAGATCATAAGACCATATCTGAAAAATCTAAATCCACTCCAACTTGCCGCTGATTGCATTGAAACAGTAAATAAAATAAAAGATAAGAAT‑AAAAAAATCATTGATATaa                                                                                                                                                              >  1:591989/1‑289 (MQ=255)         aGCGTGTTCACTAAGCTATTTTGCCTGTAAGGCCGCAGAGGCTGAACTCGGACTGGCATATATGGCTGCGAATGATAACAAGGAATTTCTCACATCCTTATCTAATATAATGAGGTACAAAATAGATGCTGGACTTTCCGAATCCTATACATGCTATTTATTAAGTAAGGGAAAGATCATAAGACCATATCTGAAAAATCTAAATCCACTCCAACTTGCCGCTGATTGCATTGAAACAGTAAATAAAATAAAAGATAAGAAT‑AAAAAAATCATTGATATAAATTCAGtt                                                                                                                                                      <  1:492676/289‑1 (MQ=255)                                                   tGAACTCGGACTGGCATATATGGCTGCGAATGATAACAAGGAATTTCTCACATCCTTATCTAATATAATGAGGTACAAAATAGATGCTGGACTTTCCGAATCCTATACATGCTATTTATTAAGTAAGGGAAAGATCATAAGACCATATCTGAAAAATCTAAATCCACTCCAACTTGCCGCTGATTGCATTGAAACAGTAAATAAAATAAAAGATAAGAAT‑AAAAAAATCATTGATATAAATTCAGTTAATATTTGTAGTGATGATAAAAATATAAAATTGAGAGTTaa                                                                                                             <  1:675967/288‑1 (MQ=255)                                                                                                                                                 tCCGAATCCTATACATGCTATTTATTAAGTAAGGGAAAGATCATAAGACCATATCTGAAAAATCTAAATCCACTCCAACTTGCCGCTGATTGCATTGAAACAGTAAATAAAATAAAAGATAAGAAT‑AAAAAAATCATTGATATAAATTCAGTTAATATTTGTAGTGATGATAAAAATATAAAATTgaga                                                                                                                  <  1:41543/189‑1 (MQ=255)                                                                                                                                                 tCCGAATCCTATACATGCTATTTATTAAGTAAGGGAAAGATCATAAGACCATATCTGAAAAATCTAAATCCACTCCAACTTGCCGCTGATTGCATTGAAACAGTAAATAAAATAAAAGATAAGAAT‑AAAAAAATCATTGATATAAATTCAGTTAATATTTGTAGTGATGATAAAAATATAAAATTgaga                                                                                                                  >  2:41543/1‑189 (MQ=255)                                                                                                                                                                      ttattaAGTAAGGGAAAGATCATAAGACCATATCTGAAAAATCTAAATCCACTCCAACTTGCCGCTGATTGCATTGAAACAGTAAATAAAATAAAAGATAAGAAT‑AAAAAAATCATTGATATAAATTCAGTTAATATTTGTAGTGATGATAAAAATATAAAATTga                                                                                                                    <  1:222697/166‑1 (MQ=255)                                                                                                                                                                      ttattaAGTAAGGGAAAGATCATAAGACCATATCTGAAAAATCTAAATCCACTCCAACTTGCCGCTGATTGCATTGAAACAGTAAATAAAATAAAAGATAAGAAT‑AAAAAAATCATTGATATAAATTCAGTTAATATTTGTAGTGATGATAAAAATATAAAATTga                                                                                                                    >  2:222697/1‑166 (MQ=255)                                                                                                                                                                                                          aaaaaTCTAAATCCACTCCAACTTGCCGCTGATTGCATTGAAACAGTAAATAAAATAAAAGATAAGAAT‑AAAAAAATCATTGATATAAATTCAGTTAATATTTGTAGTGATGATAAAAATATAAAATTGAGAGTTAATAGTACTATTATGGCCATTGATGATTCTATAAAGTGCATCGATGAATGATAACTTAATTTTATTTAAAAATATATTAATAACTCACTCTCCAGGAGTTTTTTTAACt  <  1:687565/244‑1 (MQ=255)                                                                                                                                                                                                          aaaaaTCTAAATCCACTCCAACTTGCCGCTGATTGCATTGAAACAGTAAATAAAATAAAAGATAAGAAT‑AAAAAAATCATTGATATAAATTCAGTTAATATTTGTAGTGATGATAAAAATATAAAATTGAGAGTTAATAGTACTATTATGGCCATTGATGATTCTATAAAGTGCATCGATGAATGATAACTTAATTTTATTTAAAAATATATTAATAACTCACTCTCCAGGAGTTTTTTTAACt  >  2:687565/1‑244 (MQ=255)                                                                                                                                                                                                                                                                               |                                                                                                                                                                                GGACGAAAAGCGTGTTCACTAAGCTATTTTGCCTGTAAGGCCGCAGAGGCTGAACTCGGACTGGCATATATGGCTGCGAATGATAACAAGGAATTTCTCACATCCTTATCTAATATAATGAGGTACAAAATAGATGCTGGACTTTCCGAATCCTATACATGCTATTTATTAAGTAAGGGAAAGATCATAAGACCATATCTGAAAAATCTAAATCCACTCCAACTTGCCGCTGATTGCATTGAAACAGTAAATAAAATAAAAGATAAGAATAAAAAAAATCATTGATATAAATTCAGTTAATATTTGTAGTGATGATAAAAATATAAAATTGAGAGTTAATAGTACTATTATGGCCATTGATGATTCTATAAAGTGCATCGATGAATGATAACTTAATTTTATTTAAAAATATATTAATAACTCACTCTCCAGGAGTTTTTTTAACT  >  NC_000913/3769395‑3769840

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 34 ≤ ATCG/ATCG < 37 ≤ ATCG/ATCG < 38 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑