Predicted mutation
evidence	seq id	position	mutation	annotation	gene	description
RA	NC_000913	3,187,697	(A)6→7	pseudogene (266/2434 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	1	.	A	100.0%	68.9 / NA	20	pseudogene (260/2434 nt)	yqiG	putative outer membrane usher protein YqiG
Reads supporting (aligned to +/- strand):  ref base . (0/0);  new base A (7/13);  total (7/13)

GGTATTAATTGATAACCAAACTGCAGTTTGCGTGACACCAGAGCAATTAACATTATTAGGATTTACTGATGAATTTATTG‑AAAAAACTCAGCAAAACCTGATCGATGGTTGTTACCCTATCGAAAAAGAAAAACAAATTACAACTTATCTCG  >  NC_000913/3187612‑3187763                                                                                 |                                                                         ggTATTAATTGATAACCAAACTGCAGTTTGCGTGACACCAGAGCAATTAACATTATTAGGATTTACTGATGAATTTATTG‑a                                                                         <  1:592106/81‑1 (MQ=255)        aTTGATAACCAAACTGCAGTTTGCGTGACACCAGAGCAATTAACATTATTAGGATTTACTGATGAATTTATTG‑aaaaaaac                                                                  >  1:592151/1‑79 (MQ=255)          tGATAACCAAACTGCAGTTTGCGTGACACCAGAGCAATTAACATTATTAGGATTTACTGATGAATTTATTG‑aaaaaaact                                                                 >  1:592136/1‑77 (MQ=255)             tAACCAAACTGCAGTTTGCGTGACACCAGAGCAATTAACATTATTAGGATTTACTGATGAATTTATTGAAAAAAACTCAGc                                                              <  1:592107/81‑1 (MQ=255)                ccAAACTGCAGTTTGCGTGACACCAGAGCAATTAACATTATTAGGATTTACTGATGAATTTATTGAAAAAAACTCAGCaaa                                                           <  1:592108/81‑1 (MQ=255)                        cAGTTTGCGTGACACCAGAGCAATTAACATTATTAGGATTTACTGATGAATTTATTGAAAAAAACTCAGCAAAACCTGATc                                                   <  1:592109/81‑1 (MQ=255)                         aGTTTGCGTGACACCAGAGCAATTAACATTATTAGGATTTACTGATGAATTTATTGAAAAAAACTCAGCAAAACCTGATc                                                   >  1:592140/1‑80 (MQ=255)                         aGTTTGCGTGACACCAGAGCAATTAACATTATTAGGATTTACTGATGAATTTATTGAAAAAAACTCAGCAAAACCTGATCg                                                  <  1:592110/81‑1 (MQ=255)                            ttGCGTGACACCAGAGCAATTAACATTATTAGGATTTACTGATGAATTTATTGAAAAAAACTCAGCAAAACCTGATCGATg                                               >  2:592142/1‑81 (MQ=255)                             tGCGTGACACCAGAGCAATTAACATTATTAGGATTTACTGATGAATTTATTGAAAAAAACTCAGCAAAACCTGATCGATgg                                              >  2:592137/1‑81 (MQ=255)                             tGCGTGACACCAGAGCAATTAACATTATTAGGATTTACTGATGAATTTATTGAAAAAAACTCAGCAAAACCTGATCGATg                                               <  1:592111/80‑1 (MQ=255)                               cGTGACACCAGAGCAATTAACATTATTAGGATTTACTGATGAATTTATTGAAAAAAACTCAGCAAAACCTGATCGATGgtt                                            <  1:592112/81‑1 (MQ=255)                                gTGACACCAGAGCAATTAACATTATTAGGATTTACTGATGAATTTATTGAAAAAAACTCAGCAAAACCTGATCGATGgttg                                           >  2:592133/1‑81 (MQ=255)                                  gACACCAGAGCAATTAACATTATTAGGATTTACTGATGAATTTATTGAAAAAAACTCAGCAAAACCTGATCGATGgttgt                                          >  2:592139/1‑80 (MQ=255)                                   acacCAGAGCAATTAACATTATTAGGATTTACTGATGAATTTATTGAAAAAAACTCAGCAAAACCTGATCGATGgttgtt                                         <  1:592113/80‑1 (MQ=255)                                       cAGAGCAATTAACATTATTAGGATTTACTGATGAATTTATTGAAAAAAACTCAGCAAAACCTGATCGATGGTTGTTACCCt                                    <  2:592114/81‑1 (MQ=255)                                            cAATTAACATTATTAGGATTTACTGATGAATTTATTGAAAAAAACTCAGCAAAACCTGATCGATGGTTGTTACCCTATCga                               <  2:592115/81‑1 (MQ=255)                                              aTTAACATTATTAGGATTTACTGATGAATTTATTGAAAAAAACTCAGCAAAACCTGATCGATGGTTGTTACCCTATCgaaa                             <  2:592116/81‑1 (MQ=255)                                                tAACATTATTAGGATTTACTGATGAATTTATTGAAAAAAACTCAGCAAAACCTGATCGATGGTTGTTACCCTATCgaaa                             >  2:592171/1‑79 (MQ=255)                                                     ttattaGGATTTACTGATGAATTTATTGAAAAAAACTCAGCAAAACCTGATCGATGGTTGTTACCCTATCgaaaaagaaaa                      <  1:592117/81‑1 (MQ=255)                                                          aGGATTTACTGATGAATTTATTGAAAAAAACTCAGCAAAACCTGATCGATAGTTGTTACCCTATCGAAAAAGAAAAACaaa                 >  1:592141/1‑81 (MQ=255)                                                           ggATTTACTGATGAATTTATTGAAAAAAACTCAGCAAAACCTGATCGATGGTTGTTACCCTATCGAAAAAGAAAAACAAAt                <  2:592118/81‑1 (MQ=255)                                                                         aTTTATTGAAAAAAACTCAGCAAAACCTGATCGATGGTTGTTACCCTATCGAAAAAGAAAAACAAATTACAACTTATCTCg  <  1:592119/81‑1 (MQ=255)                                                                                 |                                                                         GGTATTAATTGATAACCAAACTGCAGTTTGCGTGACACCAGAGCAATTAACATTATTAGGATTTACTGATGAATTTATTG‑AAAAAACTCAGCAAAACCTGATCGATGGTTGTTACCCTATCGAAAAAGAAAAACAAATTACAACTTATCTCG  >  NC_000913/3187612‑3187763

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 33 ≤ ATCG/ATCG < 34 ≤ ATCG/ATCG < 38 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑