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%	99.2 / NA	28	pseudogene (2194/2434 nt)	yqiG	putative outer membrane usher protein YqiG
Reads supporting (aligned to +/- strand):  ref base C (0/0);  new base A (13/15);  total (13/15)

GTTATCACCACCACCTTAACCGAGGGTGCTATTGGCTACGCCAAACTTGATACCCGCAAGGGCTACCAAATCATAGGGGTTATTCGCCTGGCAGATGGTAGTCATCCACCACTGGGGATTAGCGTAAAAGATGAAACCAGCCACAAAG  >  NC_000913/3189554‑3189701                                                                        |                                                                             gTTATCACCACCACCTTAACCGAGGGTGCTATTGGCTACGCCAAACTTGATACCCGCAAGGGCTACCAAATAATAGGGGt                                                                      >  2:592525/1‑80 (MQ=255)  ttATCACCACCACCTTAACCGAGGGTGCTATTGGCTACGCCAAACTTGATACCCGCAAGGGCTACCAAATAATAGGGGTTa                                                                    <  1:592489/81‑1 (MQ=255)   tATCACCACCACCTTAACCGAGAGTGCTATTGGCTACGCCAAACTTGATACCCGCAAGGGCTACCAAATAATAGGGGTTAt                                                                   >  2:592543/1‑81 (MQ=255)    aTCACCACCACCTTAACCGAGGGTGCTATTGGCTACGCCAAACTTGATACCCGCAAGGGCTACCAAATAATAGGGGTTAtt                                                                  >  2:592534/1‑81 (MQ=255)       accaccaccTTAACCGAGGGTGCTATTGGCTACGCCAAACTTGATACCCGCAAGGGCTACCAAATAATAGGGGTTATTCGc                                                               >  2:592532/1‑81 (MQ=255)               cTTAACCGAGGGTGCTATTGGCTACGCCAAACTTGATACCCGCAAGGGCTACCAAATAATAGGGGTTATTCGCCTGGCAGa                                                       <  1:592490/81‑1 (MQ=255)                  aaCCGAGGGTGCTATTGGCTACGCCAAACTTGATACCCGCAAGGGCTACCAAATAATAGGGGTTATTCGCCTGGCAGATgg                                                    >  1:592544/1‑81 (MQ=255)                    ccGAGGGTGCTATTGGCTACGCCAAACTTGATACCCGCAAGGGCTACCAAATAATAGGGGTTATTCGCCTGGCAGATGGTa                                                  <  2:592491/81‑1 (MQ=255)                      gAGGGTGCTATTGGCTACGCCAAACTTGATACCCGCAAGGGCTACCAAATAATAGGGGTTATTCGCCTGGCAGATGGTAGt                                                >  1:592584/1‑81 (MQ=255)                       aGGGTGCTATTGGCTACGCCAAACTTGATACCCGCAAGGGCTACCAAATAATAGGGGTTATTCGCCTGGCAGATGGTAGTc                                               <  1:592492/81‑1 (MQ=255)                         ggTGCTATTGGCTACGCCAAACTTGATACCCGCAAGGGCTACCAAATAATAGGGGTTATTCGCCTGGCAGATGGTAGTCAt                                             >  2:592537/1‑81 (MQ=255)                                  ggCTACGCCAAACTTGATACCCGCAAGGGCTACCAAATAATGGGGGTTATTCGCCTGGCAGATGGTAGTCATCcaccaca                                     <  2:592493/80‑2 (MQ=255)                                  ggCTACGCCAAACTTGATACCCGCAAGGGCTACCAAATAATAGGGGTTATTCGCCTGGCAGATGGTAGTCATCCACCACTg                                    >  2:592549/1‑81 (MQ=255)                                    cTACGCCAAACTTGATACCCGCAAGGGCTACCAAATAATAGGGGTTATTCGCCTGGCAGATGGTAGTCATCCACCACTggg                                  >  1:592539/1‑81 (MQ=255)                                       cGCCAAACTTGATACCCGCAAGGGCTACCAAATAATAGGGGTTATTCGCCTGGCAGATGGTAGTCATCCACCACTgggg                                 <  1:592494/79‑1 (MQ=255)                                        gCCAAACTTGATACCCGCAAGGGCTACCAAATAATAGGGGTTATTCGCCTGGCAGATGGTAGTCATCCACCACTGGGGAtt                              <  2:592495/81‑1 (MQ=255)                                           aaaCTTGATACCCGCAAGGGCTACCAAATAATAGGGGTTATTCGCCTGGCAGATGGTAGTCATCCACCACTGGGGATTAGc                           <  2:592497/81‑1 (MQ=255)                                           aaaCTTGATACCCGCAAGGGCTACCAAATAATAGGGGTTATTCGCCTGGCAGATGGTAGTCATCCACCACTGGGGATTAGc                           <  1:592496/81‑1 (MQ=255)                                                 gATACCCGCAAGGGCTACCAAATAATAGGTGTTATTCGCCTGGCAGATGGTAGTCATCCACCACTGGGGATTAGCGTaa                       >  1:592564/1‑79 (MQ=255)                                                     cccGCAAGGGCTACCAAATAATAGGGGTTATTCGCCTGGCAGATGGTAGTCATCCACCACTGGGGATTAGCGTAAAAGATg                 <  1:592498/81‑1 (MQ=255)                                                      ccGCAAGGGCTACCAAATAATAGGGGTTATTCGCCTGGCAGATGGTAGTCATCCACCACTGGGGATTAGCGTAAAAGATg                 >  1:592500/1‑80 (MQ=255)                                                      ccGCAAGGGCTACCAAATAATAGGGGTTATTCGCCTGGCAGATGGTAGTCATCCACCACTGGGGATTAGCGTAAAAGATGa                <  1:592499/81‑1 (MQ=255)                                                       cGCAAGGGCTACCAAATAATAGGGGTTATTCGCCTGGCAGATGGTAGTCATCCACCACTGGGGATTAGCGTAAAAGATGaa               <  2:592501/81‑1 (MQ=255)                                                        gCAAGGGCTACCAAATAATAGGGGTTATTCGCCTGGCAGATGGTAGTCATCCACCACTGGGGATTAGCGTAAAAGATGaaa              >  1:592545/1‑81 (MQ=255)                                                             ggCTACCAAATAATAGGGGTTATTCGCCTGGCAGATGGTAGTCATCCACCACTGGGGATTAGCGTAAAAGATGAAACCAGc         <  2:592502/81‑1 (MQ=255)                                                                   cAAATAATAGGGGTTATTCGCCTGGCAGATGGTAGTCATCCACCACTGGGGATTAGCGTAAAAGATGAAACCAGCCACaaa   <  1:592503/81‑1 (MQ=255)                                                                    aaaTAATAGGGGTTATTCGCCTGGCAGATGGTAGTCATCCACCACTGGGGATTAGCGTAAAAGATGAAACCAGCcaca     >  1:592550/1‑78 (MQ=255)                                                                    aaaTAATAGGGGTTATTCGCCTGGCAGATGGTAGTCATCCACCACTGGGGATTAGCGTAAAAGATGAAACCAGCCACAAAg  <  1:592504/81‑1 (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 < 35 ≤ ATCG/ATCG < 38 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑