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%	84.9 / NA	24	pseudogene (2194/2434 nt)	yqiG	putative outer membrane usher protein YqiG
Reads supporting (aligned to +/- strand):  ref base C (0/0);  new base A (9/15);  total (9/15)

AAACTCGGTTATCACCACCACCTTAACCGAGGGTGCTATTGGCTACGCCAAACTTGATACCCGCAAGGGCTACCAAATCATAGGGGTTATTCGCCTGGCAGATGGTAGTCATCCACCACTGGGGATTAGCGTAAAAGATGAAACCAGCC  >  NC_000913/3189547‑3189695                                                                               |                                                                       aaaCTCGGTTATCACCACCACCTTAACCGAGGGTGCTATTGGCTACGCCAAACTTGATACCCGCAAGGGCTACCAaataat                                                                      <  1:546685/81‑1 (MQ=255) aaaCTCGGTTATCACCACCACCTTAACCGAGGGTGCTATTGGCTACGCCAAACTTGATACCCGCAAGGGCTACCAaataat                                                                      <  2:546686/81‑1 (MQ=255)       ggTTATCACCACCACCTTAACCGAGGGTGCTATTGGCTACGCCAAACTTGATACCCGCAAGGGCTACCAAATAATAgggg                                                                 <  2:546687/80‑1 (MQ=255)         ttATCACCACCACCTTAACCGAGGGTGCTATTGGCTACGCCAAACTTGATACCCGCAAGGGCTACCAAATAATAGGGGTTa                                                              >  1:546720/1‑81 (MQ=255)                   caccTTAACCGAGGGTGCTATTGGCTACGCCAAACTTGATACCCGCAAGGGCTACCAAATAATAGGGGTTATTCGCCTgg                                                     >  1:546717/1‑80 (MQ=255)                   caccTTAACCGAGGGTGCTATTGGCTACGCCAAACTTGATACCCGCAAGGGCTACCAAATAATAGGGGTTATTCGCCTGGc                                                    <  1:546688/81‑1 (MQ=255)                     ccTTAACCGAGGGTGCTATTGGCTACGCCAAACTTGATACCCGCAAGGGCTACCAAATAATAGGGGTTATTCGCCTGGCAg                                                  <  1:546689/81‑1 (MQ=255)                         aaCCGAGGGTGCTATTGGCTACGCCAAACTTGATACCCGCAAGGGCTACCAAATAATAGGGGTTATTCGCCTGGCAGAt                                                <  1:546690/79‑1 (MQ=255)                            cGAGGGTGCTATTGGCTACGCCAAACTTGATACCCGCAAGGGCTACCAAATAATAGGGGTTATTCGCCTGGCAGATGGTAg                                           >  1:546719/1‑81 (MQ=255)                            cGAGGGTGCTATTGGCTACGCCAAACTTGATACCCGCAAGGGCTACCAAATAATAGGGGTTATTCGCCTGGCAGATGGTAg                                           <  2:546691/81‑1 (MQ=255)                                  tGCTATTGGCTACGCCAAACTTGATACCCGCAAGGGCTACCAAATAATAGGGGTTATTCGCCTGGCAGATGGTAGTCATcc                                     <  2:546692/81‑1 (MQ=255)                                    cTATTGGCTACGCCAAACTTGATACCCGCAAGGGCTACCAAATAATAGGGGTTATTCGCCTGGCAGATGGTAGTCATccac                                   <  2:546693/81‑1 (MQ=255)                                      aTTGGCTACGCCAAACTTGATACCCGCAAGGGCTACCAAATAATAGGGGTTATTCGCCTGGCAGATGGTAGTCATccacca                                 >  1:546722/1‑81 (MQ=255)                                         ggCTACGCCAAACTTGATACCCGCAAGGGCTACCAAATAATAGGGGTTATTCGCCTGGCAGATGGTAGTCATCCACCACt                               <  1:546694/80‑1 (MQ=255)                                          gCTACGCCAAACTTGATACCCGCAAGGGCTACCAAATAATAGGGGTTATTCGCCTGGCAGATGGTAGTCATCCACCACTg                              <  1:546696/80‑1 (MQ=255)                                          gCTACGCCAAACTTGATACCCGCAAGGGCTACCAAATAATAGGGGTTATTCGCCTGGCAGATGGTAGTCATCCACCACTg                              <  2:546695/80‑1 (MQ=255)                                             aCGCCAAACTTGATACCCGCAAGGGCTACCAAATAATAGGGGTTATTCGTCTGGCAGATGGTAGTCATCCACCACTGGGGa                          >  2:546729/1‑81 (MQ=255)                                                    aCTTGATACCCGCAAGGGCTACCAAATAATAGGGGTTATTCGCCTGGCAGATGGTAGTCATCCACCACTGGGGATTAGCGt                   <  2:546697/81‑1 (MQ=255)                                                     cTTGATACCCGCAAGGGCTACCAAATAATAGGGGTTATTCGCCTGGCAGATGGTAGTCATCCACCACTGGGGATTAGCGTa                  <  2:546698/81‑1 (MQ=255)                                                        gATACCCGCAAGGGCTACCAAATAATAGGGGTTATTCGCCTGGCAGATGGTAGTCATCCACCACTGGGGATTAGCGTaa                 <  1:546699/79‑1 (MQ=255)                                                        gATACCCGCAAGGGCTACCAAATAATAGGGGTTATTCGCCTGGCAGATGGTAGTCATCCACCACTGGGGATTAGCGTaa                 >  2:546726/1‑79 (MQ=255)                                                             ccGCAAGGGCTACCAAATAATAGGGGTTATTCGCCTGGCAGATGGTAGTCATCCACCACTGGGGATTAGCGTAAAAGATGa          <  2:546700/81‑1 (MQ=255)                                                               gCAAGGGCTACCAAATAATAGGGGTTATTCGCCTGGCAGATGGTAGTCATCCACCACTGGGGATTAGCGTAAAAGATGaaa        >  1:546725/1‑81 (MQ=255)                                                                 aaGGGCTACCAAATAATAGGGGTTATTCGCCTGGCAGATGGTAGTCATCCACCACTGGGGATTAGCGTAAAAGATGAAAc       >  2:546723/1‑80 (MQ=255)                                                                 aaGGGCTACCAAATAATAGGGGTTATTCGCCTGGCAGATGGTAGTCATCCACCACTGGGGATTAGCGTAAAAGATGAAAc       >  2:546727/1‑80 (MQ=255)                                                                     gCTACCAAATAATAGGGGTTATTCGCCTGGCAGATGGTAGTCATCCACCACTGGGGATTAGCGTAAAAGATGAAACCAGcc  <  2:546701/81‑1 (MQ=255)                                                                               |                                                                       AAACTCGGTTATCACCACCACCTTAACCGAGGGTGCTATTGGCTACGCCAAACTTGATACCCGCAAGGGCTACCAAATCATAGGGGTTATTCGCCTGGCAGATGGTAGTCATCCACCACTGGGGATTAGCGTAAAAGATGAAACCAGCC  >  NC_000913/3189547‑3189695

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 34 ≤ ATCG/ATCG < 35 ≤ ATCG/ATCG < 38 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑