Predicted mutation
evidence	seq id	position	mutation	annotation	gene	description
RA	NC_000913	1,657,767	G→A	C68Y (TGC→TAC)	ynfD →	DUF1161 family periplasmic protein

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NC_000913	1,657,767	0	G	A	100.0%	170.8 / NA	48	C68Y (TGC→TAC)	ynfD	DUF1161 family periplasmic protein
Reads supporting (aligned to +/- strand):  ref base G (0/0);  new base A (30/18);  total (30/18)

GTGAGCGCATACAGAGCGATATATCACAGCGCATTATCAATAATGGCGTACCCGAAAGCAGCTTCACGTTAAGTATTGTACCCAATGACCAGGTTGATCAGCCTGATTCCCAGGTCGTCGGCCATTGCGCTAATGATACGCATAAAATTCTCTATACCCGCACCACCAGCGGTAACGTCTCTGCTCCCGCGCAGTCTAGCCAGGATGGCGCGCCTGCCGAACCGCAGTAACACATTATCGACTGAACGCCGGATAT  >  NC_000913/1657641‑1657896                                                                                                                               |                                                                                                                                  gtgAGCGCATACAGAGCGATATATCACAGCGCATTATCAATAATGGCGTACCCGAAAGCAGCTTCACGTTAAGTATTGTACCCAATGACCAGGTTGATCAGCCTGATTCCCAGGTCGTCGGCCATTACGCTAATGATAc                                                                                                                       <  2:321790/139‑1 (MQ=255) gtgAGCGCATACAGAGCGATATATCACAGCGCATTATCAATAATGGCGTACCCGAAAGCAGCTTCACGTTAAGTATTGTACCCAATGACCAGGTTGATCAGCCTGATTCCCAGGTCGTCGGCCATTACGCTAATGATAc                                                                                                                       <  1:326977/139‑1 (MQ=255)             agagCGATATATCAAAGCGCATTATCAATAATGGCGTACCCGAAAGCAGCTTCACGTTAAGTATTGTACCCAATGACCAGGTTGATCAGCCTGATTCCCAGGTCGTCGGCCATTACGCTAATGATACGCATAAAAGtct                                                                                                           <  1:18285/139‑1 (MQ=255)               agCGATATATCACAGCGCATTATCAATAATGGCGTACCCGAAAGCAGCTTCACGTTAAGTATTGTACCCAATGACCAGGTTGATCAGCCTGATTCCCAGGTCGTCGGCCATTACGCTAATGATACGCATAAAATTctct                                                                                                         >  1:1061065/1‑139 (MQ=255)                              cgcATTATCAATAATGGCGTACCCGAAAGCAGCTTCACGTTAAGTATTGTACCCAATGACCAGGTTGATCAGCCTGATTCCCAGGTCGTCGGCCATTACGCTAATGATACGCATAAAATTCTCTATACCCGCAccacca                                                                                          >  2:274384/1‑139 (MQ=255)                              cgcATTATCAATAATGGCGTACCCGAAAGCAGCTTCACGTTAAGTATTGTACCCAATGACCAGGTTGATCAGCCTGATTCCCAGGTCGTCGGCCATTACGCTAATGATACGCATAAAATTCTCTATACCCGCAccacca                                                                                          >  1:691850/1‑139 (MQ=255)                                cATTATCAATAATGGCGTACCCGAAAGCAGCTTCACGTTAAGTATTGTACCCAATGACCAGGTTGATCAGCCTGATTCCCAGGTCGTCGGCCATTACGCTAATGATACGCATAAAATTCTCTATACCCGCACCACCAGc                                                                                        >  1:384627/1‑139 (MQ=255)                                             ggCGTACCCGAAAGCAGCTTCACGTTAAGAATTGTACCCAATGACCAGGTTGATCAGCCTGATTCCCAGGTCGTAGGCCATTACGCTAATGATACGCATAAAATTCTCTATACCCGCACCACCAGCGGTAACGTCTCTg                                                                           >  2:788124/1‑139 (MQ=255)                                               cGTACCCGAAAGCAGCTTCACGTTAAGTATTGTACCCAATGACCAGGTTGATCAGCCTGATTCCCAGGTCGTCGGCCATTACGCTAATGATACGCATAAAATTCTCTATACCCGc                                                                                                 <  2:1067321/115‑1 (MQ=255)                                               cGTACCCGAAAGCAGCTTCACGTTAAGTATTGTACCCAATGACCAGGTTGATCAGCCTGATTCCCAGGTCGTCGGCCATTACGCTAATGATACGCATAAAATTCTCTATACCCGc                                                                                                 >  1:1067321/1‑115 (MQ=255)                                               cGTACCCGAAAGCAGCTTCACGTTAAGTATTGTACCCAATGACCAGGTTGATCAGCCTGATTCCCAGGTCGTCGGCCATTACGCTAATGATACGCATAAAATTCTCTATACCCGCACCACCAGCgg                                                                                      >  2:449072/1‑126 (MQ=255)                                               cGTACCCGAAAGCAGCTTCACGTTAAGTATTGTACCCAATGACCAGGTTGATCAGCCTGATTCCCAGGTCGTCGGCCATTACGCTAATGATACGCATAAAATTCTCTATACCCGCACCACCAGCgg                                                                                      <  1:449072/126‑1 (MQ=255)                                               cGTACCCGAAAGCAGCTTCACGTTAAGTATTGTACCCAATGACCAGGTTGATCAGCCTGATTCCCAGGTCGTCGGCCATTACGCTAATGATACGCATAAAATTCTCTATACCCGCACCACCAGCGGTAACGTCTCTGCt                                                                         <  1:788124/139‑1 (MQ=255)                                               cGTACCCGAAAGCAGATTCACGTTAAGTATTGTACCCAATGACCAGGTTGATCAGCCTGATTCCCAGGTCGTCGGCCATTACGCTAATGATACGCATAAAATTCTCTATACCCGCACCACCAGCGGTAACGTCTCTGCt                                                                         >  1:786707/1‑139 (MQ=255)                                                 tACCCGAAAGCAGCTTCACGTTAAGTATTGTACCCAATGACCAGGTTGATCAGCCTGATTCCCAGGTCGTCGGCCATTACGCTAATGATACGCATAAAATTCTCTATACCGGCACCACCAGCGGTAACGTCTCTGCTcc                                                                       >  2:706697/1‑139 (MQ=255)                                                         agcagcTTCACGTTAAGTATTGTACCCAATGACCAGGTTGATCAGCCTGATTCCCAGGTCGTCGGCCATTACGCTAATGATACGCATAAAATTCTCTATACCCGCACCACCAGCGGTAACGTCTCTGCTCCCGCGCAGt                                                               <  1:1032753/139‑1 (MQ=255)                                                         agcagcTTCACGTTAAGTATTGTACCCAATGACCAGGTTGATCAGCCTGATTCCCAGGTCGTCGGCCATTACGCTAATGATACGCATAAAATTCTCTATACCCGCACCACCAGCGGTAACGTCTCTGCTCCCGCGCAGt                                                               <  1:869109/139‑1 (MQ=255)                                                              cTTCACGTTAAGTATTGTACCCAATGACCAGGTTGATCAGCCTGATTCCCAGGTCGTCGGCCATTACGCTa                                                                                                                              >  2:144379/1‑71 (MQ=255)                                                              cTTCACGTTAAGTATTGTACCCAATGACCAGGTTGATCAGCCTGATTCCCAGGTCGTCGGCCATTACGCTa                                                                                                                              <  1:144379/71‑1 (MQ=255)                                                              cTTCACGTTAAGTATTGTACCCAATGACCAGGTTGATCAGCCTGATTCCCAGGTCGTCGGCCATTACGCTAATGATACGCATAAAATTCTCTATACCCGCACCACCAGCGGTAACGTCTCTGCTCCCGCGCAGTCTAGc                                                          >  1:970637/1‑139 (MQ=255)                                                              cTTCACGTTAAGTATTGTACCCAATGACCAGGTTGATCAGCCTGATTCCCAGGTCGTCGGCCATTACGCTAATGATACGCATAAAATTCTCTATACCCGCACCACCAGCGGTAACGTCTCTGCTCCCGCGCAGTCTAGc                                                          >  2:908365/1‑139 (MQ=255)                                                                             tGTACCCAATGACCAGGTTGATCAGCCTGATTCCCAGGTCGTCGGCCATTACGCTAATGATACGCATAAAATTCTCTATACCCGCACCACCAGCGGTAACGTCTCTGCTCCCGCGCAGt                                                               <  1:847642/119‑1 (MQ=255)                                                                             tGTACCCAATGACCAGGTTGATCAGCCTGATTCCCAGGTCGTCGGCCATTACGCTAATGATACGCATAAAATTCTCTATACCCGCACCACCAGCGGTAACGTCTCTGCTCCCGCGCAGt                                                               >  2:847642/1‑119 (MQ=255)                                                                              gTACCCAATGACCAGGTTGATCAGCCTGATTCCCAGGTCGTCGGCCATTACGCTAATGAt                                                                                                                         <  1:884646/60‑1 (MQ=255)                                                                              gTACCCAATGACCAGGTTGATCAGCCTGATTCCCAGGTCGTCGGCCATTACGCTAATGAt                                                                                                                         >  2:884646/1‑60 (MQ=255)                                                                               tACCCAATGACCAGGTTGATCAGCCTGATTCCCAGGTCGTCGGCCATTACGCTAATGATACGCATAAAATTCTCTATACCCGCACCACCAGCGGTAACGTCTCTGCTCCCGCGCAGTCTAGCCAGGATGGCGCGCCTGc                                         >  1:878240/1‑139 (MQ=255)                                                                                 cccAATGACCAGGTTGATCAGCCTGATTCCCAGGTCGTCGGCCATTACGCTAATGATACGCATAAAATTCTCTATACCCGCACCACCAGCGGTAACGTCTCTGCTCCCGCGCAGTCTAGCCAGGATGGCGCGCCTGCCg                                       >  2:350926/1‑139 (MQ=255)                                                                                  ccAATGACCAGGTTGATCAGCCTGATTCCCAGGTCGTCGGCCATTACGCTAATGATACGCATAAAATTCTCTATACCCGCAccacca                                                                                          >  2:140792/1‑87 (MQ=255)                                                                                  ccAATGACCAGGTTGATCAGCCTGATTCCCAGGTCGTCGGCCATTACGCTAATGATACGCATAAAATTCTCTATACCCGCAccacca                                                                                          <  1:140792/87‑1 (MQ=255)                                                                                    aaTGACCAGGTTGATCAGCCTGATTCCCAGGTCGTCGGCCATTACGCTAATGATACGCATAAAATTCTCTATACCCGCACCACCAGCGGTAACGTCTCTGCTCCCGCGCCGTCTAGCCAGGATGGCGCGCCTGCCGAAc                                    <  2:786707/139‑1 (MQ=255)                                                                                      tGACCAGGTTGATCAGCCTGATTCCCAGGTCGTCGGCCATTACGCTAATGATACGCATAAAATTCTCTATACCCGCACCACCAGCGGTAACGTCTCTGCTCCCGCGCAGTCTAGCCAGGATGGCGCGCCTGCCGAACCg                                  >  2:1151814/1‑139 (MQ=255)                                                                                      tGACCAGGTTGATCAGCCTGATTCCCAGGTCGTCGGCCATTACGCTAATGATACGCATAAAATTCTCTATACCCGCACCACCAGCGGTAACGTCTCTGCTCCCGCGCAGTCTAGCCAGGATGGCGCGCCTGCCGAACCg                                  <  2:878240/139‑1 (MQ=255)                                                                                             gTTGATCAGCCTGATTCCCAGGTCGTCGGCCATTACGCTAATGATACGCATAAAATTCTCTATACCCGCACCACCAGCGGTAACGTCTCTGCTCCCGCGCAGTCTAGCCAGGATGGCGCGCCTGCCGAACCGCAGTAac                           >  1:1098214/1‑139 (MQ=255)                                                                                                 aTCAGCCTGATTCCCAGGTCGTCGGCCATTACGCTAATGATAc                                                                                                                       <  2:982928/43‑1 (MQ=255)                                                                                                 aTCAGCCTGATTCCCAGGTCGTCGGCCATTACGCTAATGATAc                                                                                                                       >  1:982928/1‑43 (MQ=255)                                                                                                 aTCAGCCTGATTCCCAGGTCGTCGGCCATTACGCTAATGATACGCATAAAATTCTCTATACCCGCACCACCAGCGGTAACGTCTCTGCTCCcgcg                                                                   <  2:1082061/95‑1 (MQ=255)                                                                                                 aTCAGCCTGATTCCCAGGTCGTCGGCCATTACGCTAATGATACGCATAAAATTCTCTATACCCGCACCACCAGCGGTAACGTCTCTGCTCCcgcg                                                                   >  1:1082061/1‑95 (MQ=255)                                                                                                  tCAGCCTGATTCCCAGGTCGTCGGCCATTACGCTAATGATACGCATAAAATTCTCTATACCCGCACCACCAGCGGTAACGTCTCTGCTCCCGCGCAGTCTAGCCAGGATGGCGCGCCTGCCGAACCGCAGTAACACAtt                      >  2:272077/1‑139 (MQ=255)                                                                                                  tCAGCCTGATTCCCAGGTCGTCGGCCATTACGCTAATGATACGCATAAAATTCTCTATACCCGCACCACCAGCGGTAACGTCTCTGCTCCCGCGCAGTCTAGCCAGGATGGCGCGCCTGCCGAACCGCAGTAACACAtt                      >  1:557563/1‑139 (MQ=255)                                                                                                      ccTGATTCCCAGGTCGTCGGCCATTACGCTAATGATACGCATAAAATTCTCTATACCCGCACCACCAGCGGTAACGTCTCTGCTCCCGCGCAGTCTAGCCAGGATGGCGCGCCTGCCGAACCGCAGTAACACATTATCg                  >  1:243269/1‑139 (MQ=255)                                                                                                           ttCCCAGGTCGTCGGCCATTACGCTAATGATACGCATAAAATTCTCTATACCCGCACCACCAGCGGTAACGTCTCTGCTCCCGCGCAGTCTAGCCAGGATGGCGCGCCTGCCGAACCGCAGTAACACATTATCGACTGa             >  2:70200/1‑139 (MQ=255)                                                                                                                     gtcgGCCATTACGCTAATGATACGCATAAAATTCTCTATACCCGCACCACCAGCGGTAACGTCTCTGCTCCCGCGCAGTCTAGCCAGGATGGCGCGCCTGCCg                                       <  2:431327/103‑1 (MQ=255)                                                                                                                     gtcgGCCATTACGCTAATGATACGCATAAAATTCTCTATACCCGCACCACCAGCGGTAACGTCTCTGCTCCCGCGCAGTCTAGCCAGGATGGCGCGCCTGCCg                                       >  1:431327/1‑103 (MQ=255)                                                                                                                      tcgGCCATTACGCTAATGGTACGCATAAAATTCTCTATACCCGCACCACCAGCGGTAACGTCTCTGCTCCCGCGCAGTCTAGCCAGGATGGCGCGCCTGCCGAACCGCAGTAACACATTATCGACTGAACGCCGGatat  >  2:1135787/1‑139 (MQ=255)                                                                                                                      tcgGCCATTACGCTAATGATACGCATAAAATTCTCTATACCCGCACCACCAGCGGTAACGt                                                                                <  1:944156/61‑1 (MQ=255)                                                                                                                      tcgGCCATTACGCTAATGATACGCATAAAATTCTCTATACCCGCACCACCAGCGGTAACGt                                                                                >  2:944156/1‑61 (MQ=255)                                                                                                                      tcgGCCATTACGCTAATGATACGCATAAAATTCTCTATACCCGCACCACCAGCGGTAACGTCTCTGCTCCCGCGCAGTCTAGCCAGGATGGCGCGCCTGCCGAACCGCAGTAACACATTATCGACTGAACGCCGGatat  >  2:230407/1‑139 (MQ=255)                                                                                                                      tcgGCCATTACGCTAATGATACGCATAAAATTCTCTATACCCGCACCACCAGCGGTAACGTCTCTGCTCCCGCGCAGTCTAGCCAGGATGGCGCGCCTGCCGAACCGCAGTAACACATTATCGACTGAACGCCGGatat  >  2:190184/1‑139 (MQ=255)                                                                                                                               |                                                                                                                                  GTGAGCGCATACAGAGCGATATATCACAGCGCATTATCAATAATGGCGTACCCGAAAGCAGCTTCACGTTAAGTATTGTACCCAATGACCAGGTTGATCAGCCTGATTCCCAGGTCGTCGGCCATTGCGCTAATGATACGCATAAAATTCTCTATACCCGCACCACCAGCGGTAACGTCTCTGCTCCCGCGCAGTCTAGCCAGGATGGCGCGCCTGCCGAACCGCAGTAACACATTATCGACTGAACGCCGGATAT  >  NC_000913/1657641‑1657896

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: ‑