Predicted mutation
evidence	seq id	position	mutation	annotation	gene	description
RA	NC_000913	3,189,625	C→A	pseudogene (2194/2434 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	3,189,625	0	C	A	100.0%	68.3 / NA	20	pseudogene (2194/2434 nt)	yqiG	putative outer membrane usher protein YqiG
Reads supporting (aligned to +/- strand):  ref base C (0/0);  new base A (4/16);  total (4/16)

GTTATCACCACCACCTTAACCGAGGGTGCTATTGGCTACGCCAAACTTGATACCCGCAAGGGCTACCAAATCATAGGGGTTATTCGCCTGGCAGATGGTAGTCATCCACCACTGGGGATTAGCGTAAAAGATGAAACCAGCCACAAAG  >  NC_000913/3189554‑3189701                                                                        |                                                                             gTTATCACCACCACCTTAACCGAGGGTGCTATTGGCTACGCCAAACTTGATACCCGCAAGGGCTACCAAATAATAGGGGtt                                                                     <  1:588562/81‑1 (MQ=255)    aTCACCACCACCTTAACCGAGGGTGCTATTGGCTACGCCAAACTTGATACCCGCAAGGGCTACCAAATAATAGGGGTTAt                                                                   <  2:588563/80‑1 (MQ=255)     tCACCACCACCTTAACCGAGGGTGCTATTGGCTACGCCAAACTTGATACCCGCAAGGGCTACCAAATAATAGGGGTTATTc                                                                 <  2:588564/81‑1 (MQ=255)       accaccaccTTAACCGAGGGTGCTATTGGCTACGCCAAACTTGATACCCGCAAGGGCTACCAAATAATAGGGGTTATTCg                                                                <  1:588565/80‑1 (MQ=255)         caccaccTTAACCGAGGGTGCTATTGGCTACGCCAAACTTGATACCCGCAAGGGCTACCAAATAATAGGGGTTATTCGCCt                                                             >  1:588596/1‑81 (MQ=255)            caccTTAACCGAGGGTGCTATTGGCTACGCCAAACTTGATACCCGCAAGGGCTACCAAATAATAGGGGTTATTCGCCTgg                                                           >  1:588606/1‑80 (MQ=255)                  aaCCGAGGGTGCTATTGGCTACGCCAAACTTGATACCCGCAAGGGCTACCAAATAATAGGGGTTATTCGCCTGGCAGATg                                                     <  2:588566/80‑1 (MQ=255)                   aCCGAGGGTGCTATTGGCTACGCCAAACTTGATACCCGCAAGGGCTACCAAATAATAGGGGTTATTCGCCTGGCAGATgg                                                    <  2:588567/80‑1 (MQ=255)                          gTGCTATTGGCTACGCCAAACTTGATACCCGCAAGGGCTACCAAATAATAGGGGTTATTCGCCTGGCAGATGGTAGTCATc                                            >  1:588605/1‑81 (MQ=255)                                ttGGCTACGCCAAACTTGATACCCGCAAGGGCTACCAAATAATAGGGGTTATTCGCCTGGCAGATGGTAGTCATCcaccac                                      <  2:588568/81‑1 (MQ=255)                                  ggCTACGCCAAACTTGATACCCGCAAGGGCTACCAAATAATAGGGGTTATTCGCCTGGCAGATGGTAGTCATCCACCACt                                     <  1:588569/80‑1 (MQ=255)                                   gCTACGCCAAACTTGATACCCGCAAGGGCTACCAAATAATAGGGGTTATTCGCCTGGCAGATGGTAGTCATCCACCACTgg                                   <  2:588570/81‑1 (MQ=255)                                         ccAAACTTGATACCCGCAAGGGCTACCAAATAATAGGGGTTATTCGCCTGGCAGATGGTAGTCATCCACCACTGGGGATTa                             <  2:588571/81‑1 (MQ=255)                                              cTTGATACCCGCAAGGGCTACCAAATAATAGGGGTTATTCGCCTGGCAGATGGTAGTCATCCACCACTGGGGATTAGCGTa                        <  2:588572/81‑1 (MQ=255)                                                     cccGCAAGGGCTACCAAATAATAGGGGTTATTCGCCTGGCAGATGGTAGTCATCCACCACTGGGGATTAGCGTAAAAGAt                  <  1:588574/80‑1 (MQ=255)                                                     cccGCAAGGGCTACCAAATAATAGGGGTTATTCGCCTGGCAGATGGTAGTCATCCACCACTGGGGATTAGCGTAAAAGAt                  <  1:588573/80‑1 (MQ=255)                                                       cGCAAGGGCTACCAAATAATAGGGGTTATTCGCCTGGCAGATGGTAGTCATCCACCACTGGGGATTAGCGTAAAAGATGaa               <  2:588575/81‑1 (MQ=255)                                                                  ccAAATAATAGGGGTTATTCGCCTGGCAGATGGTAGTCATCCACCACTGGGGATTAGCGTAAAAGATGAAACCAGCcaca     >  1:588602/1‑80 (MQ=255)                                                                    aaaTAATAGGGGTTATTCGCCTGGCAGATGGTAGTCATCCACCACTGGGGATTAGCGTAAAAGATGAAACCAGCCACAAAg  <  2:588576/81‑1 (MQ=255)                                                                    aaaTAATAGGGGTTATTCGCCTGGCAGATGGTAGTCATCCACCACTGGGGATTAGCGTAAAAGATGAAACCAGCCACAAAg  <  2:588577/81‑1 (MQ=255)                                                                        |                                                                             GTTATCACCACCACCTTAACCGAGGGTGCTATTGGCTACGCCAAACTTGATACCCGCAAGGGCTACCAAATCATAGGGGTTATTCGCCTGGCAGATGGTAGTCATCCACCACTGGGGATTAGCGTAAAAGATGAAACCAGCCACAAAG  >  NC_000913/3189554‑3189701

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: ‑