Predicted mutation
evidence	seq id	position	mutation	annotation	gene	description
RA	NC_000913	1,630,986	A→G	intergenic (‑73/+16)	ydfI ← / ← ydfJ	putative NAD‑dependent D‑mannonate oxidoreductase/pseudogene, MFS transporter family, interrupted by Qin prophage,Phage or Prophage Related, putative transport protein

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NC_000913	1,630,986	0	A	G	100.0%	111.1 / NA	31	intergenic (‑73/+16)	ydfI/ydfJ	putative NAD‑dependent D‑mannonate oxidoreductase/pseudogene, MFS transporter family, interrupted by Qin prophage,Phage or Prophage Related, putative transport protein
Reads supporting (aligned to +/- strand):  ref base A (0/0);  new base G (17/14);  total (17/14)

GTTATTAAGATCATAAACAGGGAGTGTCGCTTTTGCTGATAACAAATTATTTCCCATAACAATTCCTTAAATATAAATATGGCAAGCTATATGTTTTGTTATATGAATAAAAATCCCCTCTCCGGTAAGAGAA‑GGGATTAAGGGTTTACAGACTTCTGGAAGGTTGCGCAGCTCTTACAACACGCGGTTGATCTTCCGCAGCGTCTTCCAGCGCACTTAAATCACGGTCTTTCACCTCTGGCATTTTCAGCGCAGAGATTAAACC  >  NC_000913/1630857‑1631121                                                                                                                                  |                                                                                                                                         gTTATTAAGATCATAAACAGGGAGTGTCGCTTTTGCTGATAACAAATTATTTCCCATAACAATTCCTTAAATATAAATATGGCAAGCTATATGTTTTGTTATATGAATAAAAATCCCCTCTCCGGTAAGGGAA‑GGGAtt                                                                                                                                <  1:254031/139‑1 (MQ=255)            cATAAACAGGGAGTGTCGCTTTTGCTGATAACAAATTATTTCCCATAACAATTCCTTAAATATAAATATGGCAAGCTATATGTTTTGTTATATGAATAAAAATCCCCTCTCCGGTAAGGGAA‑GGGATTAAGGGTTTACa                                                                                                                     >  1:844138/1‑139 (MQ=255)                    gggAGTGTCGCTTTTGCTGATAACAAATTATTTCCCATAACAATTCCTTAAATATAAATATGGCAAGCTATATGTTTTGTTATATGAATAAAAATCCCCTCTCCGGTAAGGGAA‑GGGATTAAGGGTTTACAGACTTCTg                                                                                                             >  1:55912/1‑139 (MQ=255)                       aGTGTCGCTTTTGCTGATAACAAATTATTTCCCATAACAATTCCTTAAATATAAATATGGCAAGCTATATGTTTTGTTATATGAATAAAAATCCCCTCTCCGGTAAGGGAAGGGGATTAAGGGTTTACAGACTTCTGGa                                                                                                           >  2:855807/1‑139 (MQ=255)                             gCTTTTGCTGATAACAAATTATTTCCCATAACAATTCCTTAAATATAAATATGGCAAGCTATATGTTTTGTTATATGAATAAAAATCCCCTCTCCGGTAAGGGAA‑GGGATTAAGGGTTTACAGACTTCTGGAAGGTTgc                                                                                                    <  1:577049/139‑1 (MQ=255)                              cTTTTGCTGATAACAAATTATTTCCCATAACAATTCCTTAAATATAAATATGGCAAGCTATATGTTTTGTTATATGAATAAAAATCCCCTCTCCGGTAAGGGAA‑GGGATTAAGGGTTTACAGACTTCTGGAAGGTTgcg                                                                                                   <  2:950774/139‑1 (MQ=255)                               ttttGCTGATAACAAATTATTTCCCATAACAATTCCTTAAATATAAATATGGCAAGCTATATGTTTTGTTATATGAATAAAAATCCCCTCTCCGGTAAGGGAA‑GGGATTAAGGGTTTACAGACTTCTGGAAGGTTgcgc                                                                                                  <  2:844138/139‑1 (MQ=255)                                         aaCAAATTATTTCCCATAACAATTCCTTAAATATAAATATGGCAAGCTATATGTTTTGTTATATGAATAAAAATCCCCTCTCCGGTAAGGGAA‑GGGATTAAGGGTTTACAGACTTCTGGAAGGTTGCGCAGCTCTTaca                                                                                        >  2:616717/1‑139 (MQ=255)                                                       cATAACAATTCCTTAAATATAAATATGGCAAGCTATATGTTTTGTTATATGAATAAAAATCCCCTCTCCGGTAAGGGAA‑GGGATTAAGGGTTTACAGACTTCTGGAAGGTTGCGCAGCTCTTACAACACGCGGTTGATc                                                                          <  2:279459/139‑1 (MQ=255)                                                                    taaatataaataTGGCAAGCTATATGTTTTGTTATATGAATAAAAATCCCCTCTCCGGTAAGGGAA‑GGGATTAAGGGTTTACAGACTTCTGGAAGGTTGCGCAGCTCTTACAACACGCGGTTGATCTTCCg                                                                     <  2:1009322/131‑1 (MQ=255)                                                                    taaatataaataTGGCAAGCTATATGTTTTGTTATATGAATAAAAATCCCCTCTCCGGTAAGGGAA‑GGGATTAAGGGTTTACAGACTTCTGGAAGGTTGCGCAGCTCTTACAACACGCGGTTGATCTTCCg                                                                     >  1:1009322/1‑131 (MQ=255)                                                                                 ggCAAGCTATATGTTTTGTTATATGAATAAAAATCCCCTCTCCGGTAAGGGAA‑GGGATTAAGGGTTTACAGACTTCTGGAAGGTTGCGCAGCTCTTACAACACGCGGTTGATCTTCCGCAGCGTCTTCCAgc                                                       >  1:5029/1‑132 (MQ=255)                                                                                 ggCAAGCTATATGTTTTGTTATATGAATAAAAATCCCCTCTCCGGTAAGGGAA‑GGGATTAAGGGTTTACAGACTTCTGGAAGGTTGCGCAGCTCTTACAACACGCGGTTGATCTTCCGCAGCGTCTTCCAgc                                                       <  2:5029/132‑1 (MQ=255)                                                                                           atGTTTTGTTATATGAATAAAAATCCCCTCTCCGGTAAGGGaa                                                                                                                                       >  1:480263/1‑43 (MQ=255)                                                                                           atGTTTTGTTATATGAATAAAAATCCCCTCTCCGGTAAGGGaa                                                                                                                                       <  2:480263/43‑1 (MQ=255)                                                                                            tGTTTTGTTATATGAATAAAAATCCCCTCTCCGGTAAGGGAA‑GGGATTAAGGGTTTACAGACTTCTGGAAGGTTGCGCAGCTCTTACAACACGCGGTTGATCTTCCGCAGCGTCTTCCAGCGCACTTAAATCACGGTCt                                     >  2:840123/1‑139 (MQ=255)                                                                                                 tGTTATATGAATAAAAATCCCCTCTCCGGTAAGGGAA‑GGGATTAAGGGTTTACAGACTTCTg                                                                                                             <  1:18107/62‑1 (MQ=255)                                                                                                 tGTTATATGAATAAAAATCCCCTCTCCGGTAAGGGAA‑GGGATTAAGGGTTTACAGACTTCTg                                                                                                             >  2:18107/1‑62 (MQ=255)                                                                                                 tGTTATATGAATAAAAATCCCCTCTCCGGTAAGGGAA‑GGGATTAAGGGTTTACAGACTTCTGGAAGGTTGCGCa                                                                                                 >  2:143312/1‑74 (MQ=255)                                                                                                 tGTTATATGAATAAAAATCCCCTCTCCGGTAAGGGAA‑GGGATTAAGGGTTTACAGACTTCTGGAAGGTTGCGCa                                                                                                 <  1:143312/74‑1 (MQ=255)                                                                                                 tGTTATATGAATAAAAATCCCCTCTCCGGTAAGGGAA‑GGGATTAAGGGTTTACAGACTTCTGGAAGGTTGCGCAGCTCTTACAACACGCGGTTGATCTTCCGCAGCGTCTTCCAGCGCACTTAAATCACGGTCTTTCAc                                >  1:414885/1‑139 (MQ=255)                                                                                                  gTTATATGAATAAAAATCCCCTCTCCGGTAAGGGAA‑GGGATTAAGGGTTTACAGACTTCTGGAAGGTTGCGCAGCTCTTACAACACGCGGTTGATCTTCCGCAGCGTCTTCCAGCGCACTTAAATCACGGTCTTTCAcc                               >  2:391214/1‑139 (MQ=255)                                                                                                  gTTATATGAATAAAAATCCCCTCTCCGGTAAGGGAA‑GGGATTAAGGGTTTACAGACTTCTGGAAGGTTGCGCAGCTCTTACAACACGCGGTTGATCTTCCGCAGCGTCTTCCAGCGCACTTAAATCACGGTCTTTCAcc                               >  2:404057/1‑139 (MQ=255)                                                                                                   ttATATGAATAAAAATCCCCTCTCCGGTAAGGGAA‑GGGATTAAGGGTTTACAGACTTCTGGAAGGTTGCGCAGCTCTTACAACACGCGGTTGATCTTCCGCAGCGTCTTCCAGCGCACTTAAATCACGGTCTTTCACct                              <  2:84696/139‑1 (MQ=255)                                                                                                      tatGAATAAAAATCCCCTCTCCGGTAAGGGAA‑GGGATTAAGGGTTTACAGACTTCTGGAAGGTTGCGCAGCTCTTACAACACGCGGTTGATCTTCCGCAGCGTCTTCCAGCGCACTTAAATCACGGTCTTTCACCTCTg                           >  1:430198/1‑139 (MQ=255)                                                                                                        tGAATAAAAATCCCCTCTCCGGTAAGGGAA‑GGGATTAAGGGTTTACAGACTTCTGGAAGGTTGCGCAGCTCTTACAACACGCGGTTGATCTTCCGCAGCGTCTTCCAg                                                        >  1:695724/1‑108 (MQ=255)                                                                                                        tGAATAAAAATCCCCTCTCCGGTAAGGGAA‑GGGATTAAGGGTTTACAGACTTCTGGAAGGTTGCGCAGCTCTTACAACACGCGGTTGATCTTCCGCAGCGTCTTCCAg                                                        <  2:695724/108‑1 (MQ=255)                                                                                                           aTAAAAATCCCCTCTCCGGTAAGGGAA‑GGGATTAAGGGTTTACAGACTTCTGGAAGGTTGCGCAGCTCTTACAACACGCGGTTGATCTTCCGCAGCGTCTTCCAGCGCACTTAAATCACGGTCTTTCACCTCTGGCAtt                      >  2:854592/1‑139 (MQ=255)                                                                                                               aaaTCCCCTCTCCGGTAAGGGAA‑GGGATTAAGGGTTTACAGACTTCTGGAAGGTTGCGCAGCTCTTACAACACGCGGTTGATCTTCCGCAGCGTCTTCCAGCGCACTTAAATCACGGTCTTTCACCTCTGGCATTTTCa                  <  2:731657/139‑1 (MQ=255)                                                                                                                   ccccTCTCCGGTAAGGGAA‑GGGATTAAGGGTTTACAGACTTCTGGAAGGTTGCGCAGCTCTTACAACACGCGGTTGATCTTCCGCAGCGTCTTCCAGCGCACTTAAATCACGGTCTTTCACCTCTGGCATTTTCAgcgc              <  1:854592/139‑1 (MQ=255)                                                                                                                             gTAAGGGAA‑GGGATTAAGGGTTTACAGACTTCTGGAAGGTTGCGCAGCTCTTACAACACGCGGTTGATCTTCCGCAGCGTCTTCCAGCGCACTTAAATCACGGTCTTTCACCTCTGGCATTTTCAGCGCAGAGATTaaa    >  1:86653/1‑139 (MQ=255)                                                                                                                               aagggaa‑gggATTAAGGGTTTACAGACTTCTGGAAGGTTGCGCAGCTCTTACAACACGCGGTTGATCTTCCGCAGCGTCTTCCAGCGCACTTAAATCACGGTCTTTCACCTCTGGCATTTTCAGCGCAGAGATTAAAcc  <  1:404057/139‑1 (MQ=255)                                                                                                                                  |                                                                                                                                         GTTATTAAGATCATAAACAGGGAGTGTCGCTTTTGCTGATAACAAATTATTTCCCATAACAATTCCTTAAATATAAATATGGCAAGCTATATGTTTTGTTATATGAATAAAAATCCCCTCTCCGGTAAGAGAA‑GGGATTAAGGGTTTACAGACTTCTGGAAGGTTGCGCAGCTCTTACAACACGCGGTTGATCTTCCGCAGCGTCTTCCAGCGCACTTAAATCACGGTCTTTCACCTCTGGCATTTTCAGCGCAGAGATTAAACC  >  NC_000913/1630857‑1631121

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 30 ≤ ATCG/ATCG < 36 ≤ ATCG/ATCG < 39 ≤ ATCG/ATCG < 40 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑