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%	77.5 / NA	21	pseudogene (2194/2434 nt)	yqiG	putative outer membrane usher protein YqiG
Reads supporting (aligned to +/- strand):  ref base C (0/0);  new base A (10/11);  total (10/11)

CGGTTATCACCACCACCTTAACCGAGGGTGCTATTGGCTACGCCAAACTTGATACCCGCAAGGGCTACCAAATCATAGGGGTTATTCGCCTGGCAGATGGTAGTCATCCACCACTGGGGATTAGCGTAAAAGATGAAACCAGCCACAA  >  NC_000913/3189552‑3189699                                                                          |                                                                           cGGTTATCACCACCACCTTAACC‑AGGGTGCTATTGGCTACGCCAAACTTGATACCCGCAAGGGCTACCAAATAATAGGGGt                                                                    >  1:578530/1‑81 (MQ=255)   gTTATCACCACCACCTTAACCGAGGGTGCTATTGGCTACGCCAAACTTGATACCCGCAAGGGCTACCAAATAATAGGGGtt                                                                   <  2:578527/81‑1 (MQ=255)                      ccGAGGGTGCTATTGGCTACGCCAAACTTGATACCCGCAAGGGCTACCAAATAATAGGGGTTATTCGCCTGGCAGATgg                                                  >  2:578555/1‑79 (MQ=255)                          gggTGCTATTGGCTACGCCAAACTTGATACCCGCAAGGGCTACCAAATAATAGGGGTTATTCGCCTGGCAGATGGTAGTCa                                            >  1:578543/1‑81 (MQ=255)                              gCTATTGGCTACGCCAAACTTGATACCCGCAAGGGCTACCAAATAATAGGGGTTATTCGCCTGGCAGATGGTAGTCATcca                                        >  2:578560/1‑81 (MQ=255)                              gCTATTGGCTACGCCAAACTTGATACCCGCAAGGGCTACCAAATAATAGGGGTTATTCGCCTGGCAGATGGTAGTCATcca                                        >  1:578573/1‑81 (MQ=255)                               cTATTGGCTACGCCAAACTTGATACCCGCAAGGGCTACCAAATAATAGGGGTTATTCGCCTGGCAGATGGTAGTCATccac                                       <  2:578528/81‑1 (MQ=255)                                 aTTGGCTACGCCAAACTTGATACCCGCAAGGGCTACCAAATAATAGGGGTTATTCGCCTGGCAGATGGTAGTCATccacca                                     >  2:578559/1‑81 (MQ=255)                                    ggCTACGCCAAACTTGATACCCGCAAGGGCTACCAAATAATAGGGGTTATTCGCCTGGCAGATGGTAGTCATCCACCACt                                   <  2:578530/80‑1 (MQ=255)                                    ggCTACGCCAAACTTGATACCCGCAAGGGCTACCAAATAATAGGGGTTATTCGCCTGGCAGATGGTAGTCATCCACCACt                                   <  2:578529/80‑1 (MQ=255)                                         cGCCAAACTTGATACCCGCAAGGGCTACCAAATAATAGGGGTTATTCGCCTGGCAGATGGTAGTCATCCACCACTGGGGa                              <  2:578531/80‑1 (MQ=255)                                             aaaCTTGATACCCGCAAGGGCTACCAAATAATAGGGGTTATTCGCCTGGCAGATGGTAGTCATCCACCACTGGGGATTAGc                         >  1:578563/1‑81 (MQ=255)                                                    aTACCCGCAAGGGCTACCAAATAATAGGGGTTATTCGCCTGGCAGATGGTAGTCATCCACCACTGGGGATTAGCGTaaaa                   <  1:578533/80‑1 (MQ=255)                                                    aTACCCGCAAGGGCTACCAAATAATAGGGGTTATTCGCCTGGCAGATGGTAGTCATCCACCACTGGGGATTAGCGTAAAAg                  <  2:578532/81‑1 (MQ=255)                                                       cccGCAAGGGCTACCAAATAATAGGGGTTATTCGCCTGGCAGATGGTAGTCATCCACCACTGGGGATTAGCGTAAAAGATg               <  1:578534/81‑1 (MQ=255)                                                           cAAGGGCTACCAAATAATAGGGGTTATTCGCCTGGCAGATGGTAGTCATCCACCACTGGGGATTAGCGTAAAAGATGAAAc           >  2:578565/1‑81 (MQ=255)                                                            aaGGGCTACCAAATAATAGGGGTTATTCGCCTGGCAGATGGTAGTCATCCACCACTGGGGATTAGCGTAAAAGATGAAAc           >  1:578561/1‑80 (MQ=255)                                                              gggCTACCAAATAATAGGGGTTATTCGCCTGGCAGATGGTAGTCATCCACCACTGGGGATTAGCGTAAAAGATGAAACCAg        <  2:578535/81‑1 (MQ=255)                                                                gCTACCAAATAATAGGGGTTATTCGCCTGGCAGATGGTAGTCATCCACCACTGGGGATTAGCGTAAAAGATGAAACCAGcc      <  1:578536/81‑1 (MQ=255)                                                                    ccAAATAATAGGGGTTATTCGCCTGGCAGATGGTAGTCATCCACCACTGGGGATTAGCGTAAAAGATGAAACCAGCCACaa  <  1:578537/81‑1 (MQ=255)                                                                     cAAATAATAGGGGTTATTCGCCTGGCAGATGGTAGTCATCCACCACTGGGGATTAGCGTAAAAGATGAAACCAGCcaca   >  1:578557/1‑79 (MQ=255)                                                                          |                                                                           CGGTTATCACCACCACCTTAACCGAGGGTGCTATTGGCTACGCCAAACTTGATACCCGCAAGGGCTACCAAATCATAGGGGTTATTCGCCTGGCAGATGGTAGTCATCCACCACTGGGGATTAGCGTAAAAGATGAAACCAGCCACAA  >  NC_000913/3189552‑3189699

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 34 ≤ ATCG/ATCG < 36 ≤ ATCG/ATCG < 38 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑