Predicted mutation
evidence	seq id	position	mutation	annotation	gene	description
RA	NC_000913	1,650,406	C→T	pseudogene (329/921 nt)	ydfE →	Qin prophage; protein YdfE

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NC_000913	1,650,406	0	C	T	100.0%	87.3 / NA	24	pseudogene (329/921 nt)	ydfE	Qin prophage; protein YdfE
Reads supporting (aligned to +/- strand):  ref base C (0/0);  new base T (10/14);  total (10/14)

CTGGGATGAGGAGTCTGCTTCTTTTGTCCCGGTTGAGACTGAATCCGATCCGATGAACGTCACTTTTGACAAGCTGGCCCCTGAAGTACAGAACGCTGTCATGGTTAAGTTCGACACATGTGAAAACATCACCGTTGATATGGTTATTAGCGC  >  NC_000913/1650329‑1650481                                                                              |                                                                            cTGGGATGAGGAGTCTGCTTCTTTTGTCCCGGTTGAGACTGAATCCGATCCGATGAACGTCACTTTTGACAAGCTGGtccc                                                                          >  2:280776/1‑81 (MQ=255)      aTGAGGAGTCTGCTTCTTTTGTCCCGGTTGAGACTGAATCCGATCCGATGAACGTCACTTTTGACAAGCTGGTCCCTGAAg                                                                     <  1:280745/81‑1 (MQ=255)       tGAGGAGTCTGCTTCTTTTGTCCCGGTTGAGACTGAATCCGATCCGATGAACGTCACTTTTGACAAGCTGGTCCCTGAAGt                                                                    <  2:280746/81‑1 (MQ=255)        gaggagTCTGCTTCTTTTGTCCCGGTTGAGACTGAATCCGATCCGATGAACGTCACTTTTGACAAGCTGGTCCCTGAAGTa                                                                   >  2:280782/1‑81 (MQ=255)             gTCTGCTTCTTTTGTCCCGGTTGAGACTGAATCCGATCCGATGAACGTCACTTTTGACAAGCTGGTCCCTGAAGTACAGaa                                                              >  2:280783/1‑81 (MQ=255)                  cttcttTTGTCCCGGTTGAGACTGAATCCGATCCGATGAACGTCACTTTTGACAAGCTGGTCCCTGAAGTACAGAACGc                                                           <  1:280747/79‑1 (MQ=255)                    tcttTTGTCCCGGTTGAGACTGAATCCGATCCGATGAACGTCACTTTTGACAAGCTGGTCCCTGAAGTACAGAACGCTGt                                                        >  2:280780/1‑80 (MQ=255)                     cttTTGTCCCGGTTGAGACTGAATCCGATCCGATGAACGTCACTTTTGACAAGCTGGTCCCTGAAGTACAGAACGCTGt                                                        <  1:280748/79‑1 (MQ=255)                      ttttGTCCCGGTTGAGACTGAATCCGATCCGATGAACGTCACTTTTGACAAGCTGGTCCCTGAAGTACAGAACGCTGTCAt                                                     >  2:280774/1‑81 (MQ=255)                       tttGTCCCGGTTGAGACTGAATCCGATCCGATGAACGTCACTTTTGACAAGCTGGTCCCTGAAGTACAGAACGCTGTCATg                                                    >  2:280775/1‑81 (MQ=255)                           tCCCGGTTGAGACTGAATCCGATCCGATGAACGTCACTTTTGACAAGCTGGTCCCTGAAGTACAGAACGCTGTCATGGtt                                                 <  2:280750/80‑1 (MQ=255)                           tCCCGGTTGAGACTGAATCCGATCCGATGAACGTCACTTTTGACAAGCTGGTCCCTGAAGTACAGAACGCTGTCATGGTTa                                                <  2:280749/81‑1 (MQ=255)                                    agaCTGAATCCGATCCGATGAACGTCACTTTTGACAAGCTGGTCCCTGAAGTACAGAACGCTGTCATGGTTAAGTTCGaca                                       <  2:280751/81‑1 (MQ=255)                                     gaCTGAATCCGATCCGATGAACGTCACTTTTGACAAGCTGGTCCCTGAAGTACAGAACGCTGTCATGGTTAAGTTCGaca                                       >  1:280784/1‑80 (MQ=255)                                      aCTGAATCCGATCCGATGAACGTCACTTTTGACAAGCTGGTCCCTGAAGTACAGAACGCTGTCATGGTTAAGTTCGAcaca                                     >  1:280781/1‑81 (MQ=255)                                          aaTCCGATCCGATGAACGTCACTTTTGACAAGCTGGTCCCTGAAGTACAGAACGCTGTCATGGTTAAGTTCGACACAtgt                                  <  2:280752/80‑1 (MQ=255)                                                       gAACGTCACTTTTGACAAGCTGGTCCCTGAAGTACAGAACGCTGTCATGGTTAAGTTCGACACATGTGAAAACATCACCGt                    >  1:280787/1‑81 (MQ=255)                                                        aaCGTCACTTTTGACAAGCTGGTCCCTGAAGTACAGAACGCTGTCATGGTTAAGTTCGACACATGTGAAAACATCACCGt                    <  2:280753/80‑1 (MQ=255)                                                         aCGTCACTTTTGACAAGCTGGTCCCTGAAGTACAGAACGCTGTCATGGTTAAGTTCGACACATGTGAAAACATCACCGTTg                  <  2:280754/81‑1 (MQ=255)                                                                 tttGACAAGCTGGTCCCTGAAGTACAGAACGCTGTCATGGTTAAGTTCGACACATGTGAAAACATCACCGTTGATATGGt           >  2:280785/1‑80 (MQ=255)                                                                  ttGACAAGCTGGTCCCTGAAGTACAGAACGCTGTCATGGTTAAGTTCGACACATGTGAAAACATCACCGTTGATATGGtt          <  2:280755/80‑1 (MQ=255)                                                                    gACAAGCTGGTCCCTGAAGTACAGAACGCTGTCATGGTTAAGTTCGACACATGTGAAAACATCACCGTTGATATGGttat        <  2:280756/80‑1 (MQ=255)                                                                        aGCTGGTCCCTGAAGTACAGAACGCTGTCATGGTTAAGTTCGACACATGTGAAAACATCACCGTTGATATGGTTATTAgcg   <  2:280757/81‑1 (MQ=255)                                                                         gCTGGTCCCTGAAGTACAGAACGCTGTCATGGTTAAGTTCGACACATGTGAAAACATCACCGTTGATATGGTTATTAgcgc  <  1:280758/81‑1 (MQ=255)                                                                         gCTGGTCCCTGAAGTACAGAACGCTGTCATGGTTAAGTTCGACACATGTGAAAACATCACCGTTGATATGGTTATTAgcg   >  1:280786/1‑80 (MQ=255)                                                                              |                                                                            CTGGGATGAGGAGTCTGCTTCTTTTGTCCCGGTTGAGACTGAATCCGATCCGATGAACGTCACTTTTGACAAGCTGGCCCCTGAAGTACAGAACGCTGTCATGGTTAAGTTCGACACATGTGAAAACATCACCGTTGATATGGTTATTAGCGC  >  NC_000913/1650329‑1650481

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: ‑