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%	81.3 / NA	23	pseudogene (2194/2434 nt)	yqiG	putative outer membrane usher protein YqiG
Reads supporting (aligned to +/- strand):  ref base C (0/0);  new base A (11/12);  total (11/12)

CGGTTATCACCACCACCTTAACCGAGGGTGCTATTGGCTACGCCAAACTTGATACCCGCAAGGGCTACCAAATCATAGGGGTTATTCGCCTGGCAGATGGTAGTCATCCACCACTGGGGATTAGCGTAAAAGATGAAACCAGCCACA  >  NC_000913/3189552‑3189698                                                                          |                                                                          cGGTTATCACCACCACCTTAACCGAGGGTGCTATTGGCTACGCCAAACTTGATACCCGCAAGGGCTACCAAATAATAgggg                                                                    >  1:531793/1‑81 (MQ=255)   gTTATCACCACCACCTTAACCGAGGGTGCTATTGGCTACGCCAAACTTGATACCCGCAAGGGCTACCAAATAATAGGGGtt                                                                  <  2:531765/81‑1 (MQ=255)      aTCACCACCACCTTAACCGAGGGTGCTATTGGCTACGCCAAACTTGATACCCGCAAGGGCTACCAAATAATAGGGGTTAt                                                                <  1:531767/80‑1 (MQ=255)           caccaccTTAACCGAGGGTGCTATTGGCTACGCCAAACTTGATACCCGCAAGGGCTACCAAATAATAGGGGTTATTCGCCt                                                          >  2:531811/1‑81 (MQ=255)           caccaccTTAACCGAGGGTGCTATTGGCTACGCCAAACTTGATACCCGCAAGGGCTACCAAATAATAGGGGTTATTCGCCt                                                          <  2:531767/81‑1 (MQ=255)            accaccTTAACCGAGGGTGCTATTGGCTACGCCAAACTTGATACCCGCAAGGGCTACCAAATAATAGGGGTTATTCGCCTg                                                         <  1:531769/81‑1 (MQ=255)             ccaccTTAACCGAGGGTGCTATTGGCTACGCCAAACTTGATACCCGCAAGGGCTACCAAATAATAGGGGTTATTCGCCTgg                                                        <  2:531769/81‑1 (MQ=255)               accTTAACCGAGGGTGCTATTGGCTACGCCAAACTTGATACCCGCAAGGGCTACCAAATAATAGGGGTTATTCGCCTgg                                                        >  2:531796/1‑79 (MQ=255)                         aGGGTGCTATTGGCTACGCCAAACTTGATACCCGCAAGGGCTACCAAATAATAGGGGTTATTCGCCTGGCAGATGGTAGt                                             >  2:531799/1‑80 (MQ=255)                            gTGCTATTGGCTACGCCAAACTTGATACCCGCAAGGGCTACCAAATAATAGGGGTTATTCGCCTGGCAGATGGTAGTCATc                                         >  1:531809/1‑81 (MQ=255)                               cTATTGGCTACGCCAAACTTGATACCCGCAAGGGCTACCAAATAATAGGGGTTATTCGCCTGGCAGATGGTAGTCATccac                                      >  2:531806/1‑81 (MQ=255)                                    ggCTACGCCAAACTTGATACCCGCAAGGGCTACCAAATAATAGGGGTTATTCGCCTGGCAGATGGTAGTCATCCACCACt                                  <  1:531771/80‑1 (MQ=255)                                        aCGCCAAACTTGATACCCGCAAGGGCTACCAAATAATAGGGGTTATTCGCCTGGCAGATGGTAGTCATCCACCACTGGGGa                             >  2:531803/1‑81 (MQ=255)                                             aaaCTTGATACCCGCAAGGGCTACCAAATAATAGGGGTTATTCGCCTGGCAGATGGTAGTCATCCACCACTGGGGATTAGc                        <  1:531772/81‑1 (MQ=255)                                              aaCTTGATACCCGCAAGGGCTACCAAATAATAGGGGTTATTCGCCTGGCAGATGGTAGTCATCCACCACTGGGGATTAGCg                       >  2:531772/1‑81 (MQ=255)                                                    aTACCCGCAAGGGCTACCAAATAATAGGGGTTATTCGCCTGGCAGATGGTAGTCATCCACCACTGGGGATTAGCGTaaaa                  <  1:531774/80‑1 (MQ=255)                                                      aCCCGCAAGGGCTACCAAATAATAGGGGTTATTCGCCTGGCAGATGGTAGTCATCCACCACTGGGGATTAGCGTAAAAGAt               >  1:531806/1‑81 (MQ=255)                                                       cccGCAAGGGCTACCAAATAATAGGGGTTATTCGCCTGGCAGATGGTAGTCATCCACCACTGGGGATTAGCGTAAAAGAt               >  1:531803/1‑80 (MQ=255)                                                       cccGCAAGGGCTACCAAATAATAGGGGTTATTCGCCTGGCAGATGGTAGTCATCCACCACTGGGGATTAGCGTAAAAGAt               <  2:531774/80‑1 (MQ=255)                                                        ccGCAAGGGCTACCAAATAATAGGGGTTATTCGCCTGGCAGATGGTAGTCATCCACCACTGGGGATTAGCGTAAAAGATGa             <  1:531776/81‑1 (MQ=255)                                                              gggCTACCAAATAATAGGGGTTATTCGCCTGGCAGATGGTAGTCATCCACCACTGGGGATTAGCGTAAAAGATGAAACCAg       <  2:531776/81‑1 (MQ=255)                                                                    ccAAATAATAGGGGTTATTCGCCTGGCAGATGGTAGTCATCCACCACTGGGGATTAGCGTAAAAGATGAAACCAGCcac   <  2:531777/79‑1 (MQ=255)                                                                     cAAATAATAGGGGTTATTCGCCTGGCAGATGGTAGTCATCCACCACTGGGGATTAGCGTAAAAGATGAAACCAGCcaca  >  2:531812/1‑79 (MQ=255)                                                                          |                                                                          CGGTTATCACCACCACCTTAACCGAGGGTGCTATTGGCTACGCCAAACTTGATACCCGCAAGGGCTACCAAATCATAGGGGTTATTCGCCTGGCAGATGGTAGTCATCCACCACTGGGGATTAGCGTAAAAGATGAAACCAGCCACA  >  NC_000913/3189552‑3189698

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: ‑