Predicted mutation
evidence	seq id	position	mutation	annotation	gene	description
RA	NC_000913	1,220,871	G→A	pseudogene (1271/2648 nt)	ycgH →	putative transporter component, N‑terminal fragment

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NC_000913	1,220,871	0	G	A	100.0%	45.3 / NA	14	pseudogene (1271/2648 nt)	ycgH	putative transporter component, N‑terminal fragment
Reads supporting (aligned to +/- strand):  ref base G (0/0);  new base A (10/4);  total (10/4)

GAATATGAAAGATGACTCCGTTGTTACCCATCTGACTAATTCAGACAGTATTATCAATCTTTCGTATGATGATGGTCAAACATTTACCCAAGGAAAAACATTAACCGTAAAAGGTAATTATGTCGGTAATAATGGTCAGCTTAATATCCGCA  >  NC_000913/1220797‑1220948                                                                           |                                                                              gAATATGAAAGATGACTCCGTTGTTACCCATCTGACTAATTCAGACAGTATTATCAATCTTTCGTATGATGATGATCAAAc                                                                         <  2:240962/81‑1 (MQ=255)     atGAAAGATGACTCCGTTGTTACCCATCTGACTAATTCAGACAGTATTATCAATCTTTCGTATGATGATGATCAAACAtt                                                                      >  2:240973/1‑80 (MQ=255)       gAAAGATGACTCCGTTGTTACCCATCTGACTAATTCAGACAGTATTATCAATCTTTCGTATGATGATGATCAAACATTTAc                                                                   >  2:240984/1‑81 (MQ=255)        aaaGATGACTCCGTTGTTACCCATCTGACTAATTCAGACAGTATTATCAATCTTTCGTATGATGATGATCAAACATTTAcc                                                                  <  2:240963/81‑1 (MQ=255)           gATGACTCCGTTGTTACCCATCTGACTAATTCAGACAGTATTATCAATCCTTCGTATGATGATGATCAAACATTTAccc                                                                 >  2:240983/1‑79 (MQ=255)               aCTCCGTTGTTACCCATCTGACTAATTCAGACAGTATTATCAATCTTTCGTATGATGATGATCAAACATTTACCCAAGGa                                                            >  1:240981/1‑80 (MQ=255)                 tCCGTTGTTACCCATCTGACTAATTCAGACAGTATTATCAATCTTTCGTATGATGATGATCAAACATTTACCCAAGGaaa                                                          >  2:240991/1‑80 (MQ=255)                 tCCGTTGTTACCCATCTGACTAATTCAGACAGTATTATCAATCTTTCGTATGATGATGATCAAACATTTACCCAAGGaaa                                                          >  2:240993/1‑80 (MQ=255)                          aCCCATCTGACTAATTCAGACAGTATTATCAATCTTTCGTATGATGATGATCAAACATTTACCCAAGGAAAAACATTAAcc                                                >  1:241006/1‑81 (MQ=255)                                 tGACTAATTCAGACAGTATTATCAATCTTTCGTATGATGACGATCTAACATTTACCCAAGGAAAAACATTAACCGTAAAAg                                         >  2:240994/1‑81 (MQ=255)                                               aGTATTATCAATCTTTCGTATGATGATGATCAAACATTTACCCAAGGAAAAACATTAACCGTAAAAGGTAATTATGTCgg                            >  2:240985/1‑80 (MQ=255)                                                   ttatCAATCTTTCGTATGATGATGATCAAACATTTACCCAAGGAAAAACATTAACCGTAAAAGGTAATTATGTCGGtaat                        <  1:240964/80‑1 (MQ=255)                                                      tCAATCTTTCGTATGATGATGATCAAACATTTACCCAAGGAAAAACATTAACCGTAAAAGGTAATTATGTCGGTAATAATg                    <  1:240965/81‑1 (MQ=255)                                                                        atgATCAAACATTTACCCAAGGAAAAACATTAACCGTAAAAGGTAATTATGTCGGTAACAATGGTCAGCTTAATATCCGCa  >  1:241005/1‑81 (MQ=255)                                                                           |                                                                              GAATATGAAAGATGACTCCGTTGTTACCCATCTGACTAATTCAGACAGTATTATCAATCTTTCGTATGATGATGGTCAAACATTTACCCAAGGAAAAACATTAACCGTAAAAGGTAATTATGTCGGTAATAATGGTCAGCTTAATATCCGCA  >  NC_000913/1220797‑1220948

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 23 ≤ ATCG/ATCG < 34 ≤ ATCG/ATCG < 38 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑