Predicted mutation
evidence	seq id	position	mutation	annotation	gene	description
RA	NC_000913	1,650,215	A→G	pseudogene (138/921 nt)	ydfE →	Qin prophage; protein YdfE

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NC_000913	1,650,215	0	A	G	100.0%	130.1 / NA	36	pseudogene (138/921 nt)	ydfE	Qin prophage; protein YdfE
Reads supporting (aligned to +/- strand):  ref base A (0/0);  new base G (17/19);  total (17/19)

AGTCTTTATTTGCGCCGCTATTCCTGACGAACTGGCAACAAGGGAAGAAGGCGCTGTGGCTGTAGCCACAGCCATTGAAGCTGGCGACGAACGCCGTGCTCGAGCAAAATTTCACTGGCAATTCCTGGAACATTATCCGGCTGCTCAGGACTGCGCTTATAAATTTATTGTCTGCGAGGATAAACCTGGCATACCCCGCCCTGCCCTCGATTCATGGGATGCTGAATATATGCAGGAAAACCGCTGGGATGAGGAGTC  >  NC_000913/1650086‑1650343                                                                                                                                  |                                                                                                                                 aGTCTTTATTTGCGCCGCTATTCCTGACGAACTGGCAACAAGGGAAGAAGGCGCTGTGGCTGTAGCCACAGCCATTGAAGCTGGCGACGAACGCCGTGCTCGAGCAAAATTTCACTGGCAATTCCTGGAGCATTATCCgg                                                                                                                        <  2:1013676/140‑1 (MQ=255) aGTCTTTATTTGCGCCGCTATTCCTGACGAACTGGCAACAAGGGAAGAAGGCGCTGTGGCTGTAGCCACAGCCATTGAAGCTGGCGACGAACGCCGTGCTCGAGCAAAATTTCACTGGCAATTCCTGGAGCATTATCCgg                                                                                                                        <  2:693172/140‑1 (MQ=255)      ttATTTGCGCCGCTATTCCTGACGAACTGGCAACAAGGGAAGAAGGCGCTGTGGCTGTAGCCACAGCCATTGAAGCTGGCGACGAACGCCGTGCTCGAGCAAAATTTCACTGGCAATTCCTGGAGCATTATCCGgctgct                                                                                                                   >  1:184714/1‑140 (MQ=255)             cgccgcTATTCCTGACGAACTGGCAACAAGGGAAGAAGGCGCTGTGGCTGTAGCCACAGCCATTGAAGCTGGCGACGAACGCCGTGCTCGAGCAAAATTTCACTGGCAATTCCTGGAGCATTATCCGGCTGCTCAGGACt                                                                                                            >  2:1004496/1‑140 (MQ=255)             cgccgcTATTCCTGACGAACTGGCAACAAGGGAAGAAGGCGCTGTGGCTGTAGCCACAGCCATTGAAGCTGGCGACGAACGCCGTGCTCGAGCAAAATTTCACTGGCAATTCCTGGAGCATTATCCGGCTGCTCAGGACt                                                                                                            >  2:896791/1‑140 (MQ=255)              gccgcTATTCCTGACGAACTGGCAACAAGGGAAGAAGGCGCTGTGGCTGTAGCCACAGCCATTGAAGCTGGCGACGAACGCCGTGCTCGAGCAAAATTTCACTGGCAATTCCTGGAGCATTATCCGGCTGCTCAGGACTg                                                                                                           <  2:935753/140‑1 (MQ=255)                          gACGAACTGGCAACAAGGGAAGAAGGCGCTGTGGCTGTAGCCACAGCCATTGAAGCTGGCGACGAACGCCGTGCTCGAGCAAAATTTCACTGGCAATTCCTGGAGCATTATCCGGCTGCTCAGGACTGCGCTTATAAAtt                                                                                               >  1:369169/1‑140 (MQ=255)                          gACGAACTGGCAACAAGGGAAGAAGGCGCTGTGGCTGTAGCCACAGCCATTGAAGCTGGCGACGAACGCCGTGCTCGAGCAAAATTTCACTGGCAATTCCTGGAGCATTATCCGGCTGCTCAGGACTGCGCTTATAAAtt                                                                                               >  1:924133/1‑140 (MQ=255)                           aCGAACTGGCAACAAGGGAAGAAGGCGCTGTGGCTGTAGCCACAGCCATTGAAGCTGGCGACGAACGCCGTGCTCGAGCAAAATTTCACTGGCAATTCCTGGAGCATTATCCGGCTGCTCAGGACTGCGCTTATAAAttt                                                                                              >  2:147784/1‑140 (MQ=255)                               aCTGGCAACAAGGGAAGAAGGCGCTGTGGCTGTAGCCACAGCCATTGAAGCTGGCGACGAACGCCGTGCTCGAGCAAAATTTCACTGGCAATTCCTGGAGCATTATCCGGCTGCTCAGGACTGCGCTta                                                                                                     <  2:844728/129‑1 (MQ=255)                               aCTGGCAACAAGGGAAGAAGGCGCTGTGGCTGTAGCCACAGCCATTGAAGCTGGCGACGAACGCCGTGCTCGAGCAAAATTTCACTGGCAATTCCTGGAGCATTATCCGGCTGCTCAGGACTGCGCTta                                                                                                     >  1:844728/1‑129 (MQ=255)                               aCTGGCAACAAGGGAAGAAGGCGCTGTGGCTGTAGCCACAGCCATTGAAGCTGGCGACGAACGCCGTGCTCGAGCAAAATTTCACTGGCAATTCCTGGAGCATTATCCGGCTGCTCAGGACTGCGCTTATAAATTTATTg                                                                                          >  1:133600/1‑140 (MQ=255)                                    caacaaGGGAAGAAGGCGCTGTGGCTGTAGCCACAGCCATTGAAGCTGGCGACGAACGCCGTGCTCGAGCAAAATTTCACTGGCAATTCCTGGAGCATTATCCGGCTGCTCAGGACTGCGCTTATAAATTTATTGTCTGc                                                                                     <  1:896791/140‑1 (MQ=255)                                     aacaaGGGAAGAAGGCGCTGTGGCTGTAGCCACAGCCATTGAAGCTGGCGACGAACGCCGTGCTCGAGCAAAATTTCACTGGCAATTCCTGGAGCATTATCCGGCTGCTCAGGACTGCGCTTATAAATTTATTGTCTGCg                                                                                    <  1:460979/140‑1 (MQ=255)                                        aaGGGAAGAAGGCGCTGTGGCTGTAGCCACAGCCATTGAAGCTGGCGACGAACGCCGTGCTCGAGCAAAATTTCACTGGCAATTCCTGGAGCATTATCCGGCTGCTCAGGACTGCGCTTATAAATTTATTGTCTGCGAgg                                                                                 <  1:609757/140‑1 (MQ=255)                                         aGGGAAGAAGGCGCTGTGGCTGTAGCCACAGCCATTGAAGCTGGCGACGAACGCCGTGCTCGAGCAAAATTTCACTGGCAATTCCTGGAGCATTATCCGGCTGCTCAGGACTGCGCTTATAAATTTATTGTCTGCGAGGa                                                                                <  1:32448/140‑1 (MQ=255)                                             aagaagGCGCTGTGGCTGTAGCCACAGCCATTGAAGCTGGCGACGAACGCCGTGCTCGAGCAAAATTTCACTGGCAATTCCTGGAGCATTATCCGGCTGCTCAGGACTGCGCTTATAAATTTATTGTCTGCGAGGATaaa                                                                            >  2:183540/1‑140 (MQ=255)                                               gaagGCGCTGTGGCTGTAGCCACAGCCATTGAAGCTGGCGACGAACGCCGTGCTCGAGCAAAATTTCACTGGCAATTCCTGGAGCATTATCCGGCTGCTCAGGACTGCGCTTATAAATTTATTGTCTGCGAGGATAAAcc                                                                          >  1:663062/1‑140 (MQ=255)                                                   gcgcTGTGGCTGTAGCCACAGCCATTGAAGCTGGCGACGAACGCCGTGCTCGAGCAAAATTTCACTGGCAATTCCTGGAGCATTATCCGGCTGCTCAGGACTGCGCTTATAAATTTATTGTCTGCGAGGATAAACCTGGc                                                                      <  2:924133/140‑1 (MQ=255)                                                     gcTGTGGCTGTAGCCACAGCCATTGAAGCTGGCGACGAACGCCGTGCTCGAGCAAAATTTCACTGGCAATTCCTGGAGCATTATCCGGCTGCTCAGGACTGCGCTTATAAATTTATTGTCTGCGAGGATAAACCTGGCAt                                                                    >  2:1008151/1‑140 (MQ=255)                                                     gcTGTGGCTGTAGCCACAGCCATTGAAGCTGGCGACGAACGCCGTGCTCGAGCAAAATTTCACTGGCAATTCCTGGAGCATTATCCGGCTGCTCAGGACTGCGCTTATAAATTTATTGTCTGCGAGGATAAACCTGGCAt                                                                    >  1:395858/1‑140 (MQ=255)                                                      cTGTGGCTGTAGCCACAGCCATTGAAGCTGGCGACGAACGCCGTGCTCGAGCAAAATTTCACTGGCAATTCCTGGAGCATTATCCGGCTGCTCAGGACTGCGCTTATAAATTTATTGTCTGCGAGGATAAACCTGGCact                                                                   >  2:586962/1‑138 (MQ=255)                                                      cTGTGGCTGTAGCCACAGCCATTGAAGCTGGCGACGAACGCCGTGCTCGAGCAAAATTTCACTGGCAATTCCTGGAGCATTATCCGGCTGCTCAGGACTGCGCTTATAAATTTATTGTCTGCGAGGATAAACCTGGCATa                                                                   >  2:901592/1‑140 (MQ=255)                                                             tGTAGCCACAGCCATTGAAGCTGGCGACGAACGCCGTGCTCGAGCAAAATTTCACTGGCAATTCCTGGAGCATTATCCGGCTGCTCAGGACTGCGCTTATAAATTTATTGTCTGCGAGGATAAACCTGGCATACCCCgcc                                                            <  2:833676/140‑1 (MQ=255)                                                                aGCCACAGCCATTGAAGCTGGCGACGAACGCCGTGCTCGAGCAAAATTTCACTGGCAATTCCTGGAGCATTATCCGGCTGCTCAGGACTGCGCTTATAAATTTATTGTCTGCGAGGATAAACCTGGCATACCCCgccctg                                                         <  1:173105/140‑1 (MQ=255)                                                                    acaGCCATTGAAGCTGGCGACGAACGCCGTGCTCGAGCAAAATTTCACTGGCAATTCCTGGAGCATTATCCGGCTGCTCAGGACTGCGCTTATAAATTTATTGTCTGCGAGGATAAACCTGGCATACCCCgccctgccct                                                     <  2:133600/140‑1 (MQ=255)                                                                    acaGCCATTGAAGCTGGCGACGAACGCCGTGCTCGAGCAAAATTTCACTGGCAATTCCTGGAGCATTATCCGGCTGCTCAGGACTGCGCTTATAAATTTATTGTCTGCGAGGATAAACCTGGCATACCCCgccctgccct                                                     <  1:901592/140‑1 (MQ=255)                                                                    acaGCCATTGAAGCTGGCGACGAACGCCGTGCTCGAGCAAAATTTCACTGGCAATTCCTGGAGCATTATCCGGCTGCTCAGGACTGCGCTTATAAATTTATTGTCTGCGAGGATAAACCTGGCATACCCCgccctgccct                                                     <  2:929245/140‑1 (MQ=255)                                                                           ttGAAGCTGGCGACGAACGCCGTGCTCGAGCAAAATTTCACTGGCAATTCCTGGAGCATTATCCGGCTGCTCAGGACTGCGCTTATAAATTTATTGTCTGCGAGGATAAACCTGGCATACCCCGCCCTGCCCTCGATTCa                                              >  1:875145/1‑140 (MQ=255)                                                                                  tGGCGACGAACGCCGTGCTCGAGCAAAATTTCACTGGCAATTCCTGGAGCATTATCCGGCTGCTCAGGACTGCGCTTATAAATTTATTGTCTGCGAGGATAAACCTGGCATACCCCGCCCTGCCCTCGATTCATGGGATg                                       <  2:639223/140‑1 (MQ=255)                                                                                       acgaACGCCGTGCTCGAGCAAAATTTCACTGGCAATTCCTGGAGCATTATCCGGCTGCTCAGGACTGCGCTTATAAATTTATTGTCTGCGAGGATAAACCTGGCATACCCCGCCCTGCCCTCGATTCATGGGATGCTGaa                                  <  1:1008151/140‑1 (MQ=255)                                                                                        cgaACGCCGTGCTCGAGCAAAATTTCACTGGCAATTCCTGGAGCATTATCCGGCTGCTCAGGACTGCGCTTATAAATTTATTGTCTGCGAGGATAAACCTGGCATACCCCGCCCTGCCCTCGATTCATGGGATGCTGAat                                 <  2:191860/140‑1 (MQ=255)                                                                                        cgaACGCCGTGCTCGAGCAAAATTTCACTGGCAATTCCTGGAGCATTATCCGGCTGCTCAGGACTGCGCTTATAAATTTATTGTCTGCGAGGATAAACCTGGCATACCCCGCCCTGCCCTCGATTCATGGGATGCTGAat                                 <  1:1053538/140‑1 (MQ=255)                                                                                                 tGCTCGAGCAAAATTTCACTGGCAATTCCTGGAGCATTATCCGGCTGCTCAGGACTGCGCTTATAAATTTATTGTCTGCGAGGATAAACCTGGCATACCCCGCCCTGCCCTCGATTCATGGGATGCTGAATATATGCAgg                        >  2:779947/1‑140 (MQ=255)                                                                                                           aaaTTTCACTGGCAATTCCTGGAGCATTATCCGGCTGCTCAGGACTGCGCTTATAAATTTATTGTCTGCGAGGATAAACCTGGCATACCCCGCCCTGCCCTCGATTCATGGGATGCTGAATATATGCAGGAAAACCGCTg              >  1:330771/1‑140 (MQ=255)                                                                                                                       cAATTCCTGGAGCATTATCCGGCTGCTCAGGACTGCGCTTATAAATTTATTGTCTGCGAGGATAAACCTGGCATACCCCGCCCTGCCCTCGATTCATGGGATGCTGAATATATGCAGGAAAACCGCTGGGATGAGGAGTc  <  2:875145/140‑1 (MQ=255)                                                                                                                                  |                                                                                                                                 AGTCTTTATTTGCGCCGCTATTCCTGACGAACTGGCAACAAGGGAAGAAGGCGCTGTGGCTGTAGCCACAGCCATTGAAGCTGGCGACGAACGCCGTGCTCGAGCAAAATTTCACTGGCAATTCCTGGAACATTATCCGGCTGCTCAGGACTGCGCTTATAAATTTATTGTCTGCGAGGATAAACCTGGCATACCCCGCCCTGCCCTCGATTCATGGGATGCTGAATATATGCAGGAAAACCGCTGGGATGAGGAGTC  >  NC_000913/1650086‑1650343

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 27 ≤ ATCG/ATCG < 33 ≤ ATCG/ATCG < 37 ≤ ATCG/ATCG < 40 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑