Predicted mutation
evidence	seq id	position	mutation	annotation	gene	description
RA	NC_000913	3,187,691	G→A	pseudogene (260/2434 nt)	yqiG →	putative outer membrane usher protein YqiG

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NC_000913	3,187,691	0	G	A	100.0%	59.6 / NA	18	pseudogene (260/2434 nt)	yqiG	putative outer membrane usher protein YqiG
Reads supporting (aligned to +/- strand):  ref base G (0/0);  new base A (5/13);  total (5/13)

ATTGATAACCAAACTGCAGTTTGCGTGACACCAGAGCAATTAACATTATTAGGATTTACTGATGAATTTATTGAAAAAACTCAGCAAAACCTGATCGATGGTTGTTACCCTATCGAAAAAGAAAAACAAATTACAACTT  >  NC_000913/3187619‑3187757                                                                         |                                                                   aTTGATAACCAAACTGCAGTTTGCGTGACACCAGAGCAATTAACATTATTAGGATTTACTGATGAATTTATTAAAAAAACt                                                            <  1:556680/81‑1 (MQ=255) aTTGATAACCAAACTGCAGTTTGCGTGACACCAGAGCAATTAACATTATTAGGATTTACTGATGAATTTATTAAAAAAACt                                                            >  2:556704/1‑81 (MQ=255)       aaCCAAACTGCAGTTTGCGTGACACCAGAGCAATTAACATTATTAGGATTTACTGATGAATTTATTAAAAAAACTCAGCa                                                       >  1:556703/1‑80 (MQ=255)            aaCTGCAGTTTGCGTGACACCAGAGCAATTAACATTATTAGGATTTACTGATGAATTTATTAAAAAAACTCAGCAAAACCt                                                 <  1:556681/81‑1 (MQ=255)                 cAGTTTGCGTGACACCAGAGCAATTAACATTATTAGGATTTACTGATGAATTTATTAAAAAAACTCAGCAAAACCTGATc                                             <  1:556682/80‑1 (MQ=255)                       gCGTGACACCAGAGCAATTAACATTATTAGGATTTACTGATGAATTTATTAAAAAAACTCAGCAAAACCTGATCGATGgt                                       <  1:556683/80‑1 (MQ=255)                          tGACACCAGAGCAATTAACATTATTAGGATTTACTGATGAATTTATTAAAAAAACTCAGCAAAACCTGATCGATGgttgtt                                   <  1:556684/81‑1 (MQ=255)                            acacCAGAGCAATTAACATTATTAGGATTTACTGATGAATTTATTAAAAAAACTCAGCAAAACCTGATCGATGGTTGTTa                                  <  1:556685/80‑1 (MQ=255)                              acCAGAGCAATTAACATTATTAGGATTTACTGATGAATTTATTAAAAAAACTCAGCAAAACCTGATCGATGGTTGTTAccc                               >  2:556706/1‑81 (MQ=255)                                 agagCAATTAACATTATTAGGATTTACTGATGAATTTATTAAAAAAACTCAGCAAAACCTGATCGATGGTTGTTACCCTAt                            <  1:556686/81‑1 (MQ=255)                                     cAATTAACATTATTAGGATTTACTGATGAATTTATTAAAAAAACTCAGCAAAACCTGATCGATGGTTGTTACCCTATCgaa                        <  2:556687/81‑1 (MQ=255)                                         tAACATTATTAGGATTTACTGATGAATTTATTAAAAAAACTCAGCAAAACCTGATCGATGGTTGTTACCCTATCgaaa                       >  1:556708/1‑78 (MQ=255)                                          aaCATTATTAGGATTTACTGATGAATTTATTAAAAAAACTCAGCAAAACCTGATCGATGGTTGTTACCCTATCgaaaaag                    >  1:556707/1‑80 (MQ=255)                                            cATTATTAGGATTTACTGATGAATTTATTAAAAAAACTCAGCAAAACCTGATCGATGGTTGTTACCCTATCgaaaaagaaa                 <  2:556688/81‑1 (MQ=255)                                                      aTTTACTGATGAATTTATTAAAAAAACTCAGCAAAACCTGATCGATGGTTGTTACCCTATCGAAAAAGAAAAACAAATTAc       <  2:556689/81‑1 (MQ=255)                                                      aTTTACTGATGAATTTATTAAAAAAACTCAGCAAAACCTGATCGATGGTTGTTACCCTATCGAAAAAGAAAAACAAATTAc       <  1:556690/81‑1 (MQ=255)                                                           cTGATGAATTTATTAAAAAAACTCAGCAAAACCTGATCGATGGTTGTTACCCTATCGAAAAAGAAAAACAAATTACAACtt  <  2:556691/81‑1 (MQ=255)                                                           cTGATGAATTTATTAAAAAAACTCAGCAAAACCTGATCGATGGTTGTTACCCTATCGAAAAAGAAAAACAAATTACAACtt  <  2:556692/81‑1 (MQ=255)                                                                         |                                                                   ATTGATAACCAAACTGCAGTTTGCGTGACACCAGAGCAATTAACATTATTAGGATTTACTGATGAATTTATTGAAAAAACTCAGCAAAACCTGATCGATGGTTGTTACCCTATCGAAAAAGAAAAACAAATTACAACTT  >  NC_000913/3187619‑3187757

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 27 ≤ ATCG/ATCG < 34 ≤ ATCG/ATCG < 37 ≤ ATCG/ATCG < 38 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑