Predicted mutation
evidence	seq id	position	mutation	annotation	gene	description
RA	NC_000913	2,562,984	G→A	G154D (GGC→GAC)	yffP →	CPZ‑55 prophage, uncharacterized protein

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NC_000913	2,562,984	0	G	A	100.0%	95.2 / NA	29	G154D (GGC→GAC)	yffP	CPZ‑55 prophage, uncharacterized protein
Reads supporting (aligned to +/- strand):  ref base G (0/0);  new base A (13/16);  total (13/16)

AGCAAGGTGCTTGCCTGGGTGAGCTTATCGCACAAAGACACCTTCACGGGTGCGAAACGGTTTCAATACTTCCAAACGATGTACGACATGGAACGGCAAATCAACGCAAACCTGCCGGTTGGCGGCCTTCCCAACGTTGACACAGAGCGAACTGGCAAACTGTTCCAACGCGATGACTTTTCTGAGGATAGCCATGCCAACGATCCGAAGTTGGTTGGTGATGATTACGTCCCCCAGGCAC  >  NC_000913/2562860‑2563100                                                                                                                             |                                                                                                                     aGCAAGGTGCTTGCCTGGGTGAGCTTATCGCACAAAGACACCTTCACGGGTGCGAAACGGTTTCAATACTTCCAAACGATGTACGACATGGAACGGCAAATCAACGCAAACCTGCCGGTTGGCGACCTTCCCAACGTTg                                                                                                        >  1:578052/1‑139 (MQ=255)    aaGGTGCTTGCCTGGGTGAGCTTATCGCACAAAGACACCTTCACGGGTGCGAAACGGTTTCAATACTTCCAAACGATGTACGACATGGAACGGCAAATCAACGCAAACCTGCCGGTTGGCGACCTTCCCAACGTTGaca                                                                                                     <  2:492224/139‑1 (MQ=255)      ggTGCTTGCCTGGGTGAGCTTATCGCACAAAGACACCTTCACGGGTGCGAAACGGTTTCAATACTTCCAAACGATGTACGACATGGAACGGCAAATCAACGCAAACCTGCCGGTTGGCGACCTTCCCAACGTTGaca                                                                                                     <  1:221968/137‑1 (MQ=255)      ggTGCTTGCCTGGGTGAGCTTATCGCACAAAGACACCTTCACGGGTGCGAAACGGTTTCAATACTTCCAAACGATGTACGACATGGAACGGCAAATCAACGCAAACCTGCCGGTTGGCGACCTTCCCAACGTTGaca                                                                                                     >  2:221968/1‑137 (MQ=255)        tGCTTGCCTGGGTGAGCTTATCGCACAAAGACACCTTCACGGGTGCGAAACGGTTTCAATACTTCCAAACGATGTACGACATGGAACGGCAAATCAACGCAAACCTGCCGGTTGGCGACCTTCCCAACGTTGACACaga                                                                                                 >  2:399100/1‑139 (MQ=255)                 gggTGAGCTTATCGCACAAAGACACCTTCACGGGTGCGAAACGGTTTCAATACTTCCAAACGATGTACGACATGGAACGGCAAATCAACGCAAACCTGCCGGTTGGCGACCTTccc                                                                                                               <  1:263685/116‑1 (MQ=255)                 gggTGAGCTTATCGCACAAAGACACCTTCACGGGTGCGAAACGGTTTCAATACTTCCAAACGATGTACGACATGGAACGGCAAATCAACGCAAACCTGCCGGTTGGCGACCTTccc                                                                                                               >  2:263685/1‑116 (MQ=255)                                          cTTCACGGGTGCGAAACGGTTTCAATACTTCCAAACGATGTACGACATGGAACGGCAAATCAACGCAAACCTGCCAGTTGGCGACCTTCCCAACGTTGACACAGAGCGAACTGGCAAACTGTTCCAACGCGATGACttt                                                               >  1:391802/1‑139 (MQ=255)                                             cACGGGTGCGAAACGGTTTCAATACTTCCAAACGATGTACGACATGGAACGGCAAATCAACGCAAACCTGCCGGTTGGCGACCTTCCCAACGTTGACACAGAGCGAACTGGCAAACTGTTCCAACGCGATGACTTTTCt                                                            <  2:391802/139‑1 (MQ=255)                                                        aaCGGTTTCAATACTTCCAAACGATGTACGACATGGAACGGCAAATCAACGCAAACCTGCCGGTTGGCGACCTTCCCAACGTTGACACAGAGCGAACTGGCAAACTGTTCCAACGCGATGACTTTTCTGAGGATAGCCa                                                 <  1:556812/139‑1 (MQ=255)                                                                   tACTTCCAAACGATGTACGACATGGAACGGCAAATCAACGCAAACCTGCCGGTTGGCGACCTTCCCAACGTTGACACAGAGCGAACTGGCAAACTGTTCCAACGCGATGACTTTTCTGAGGATAGCCATGCCAACGATc                                      <  1:85511/139‑1 (MQ=255)                                                                      ttCCAAACGATGTACGACATGGAACGGCAAATCAACGCAAACCTGCCGGTTGGCGACCTTCCCAACGTTGACACAGAGCGAACTGGCAAACTGTTCCAACGCGATGACTTTTCTGAGGATAGCCATGCCAACGATCCGa                                   >  2:402982/1‑139 (MQ=255)                                                                      ttCCAAACGATGTACGACATGGAACGGCAAATCAACGCAAACCTGCCGGTTGGCGACCTTCCCAACGTTGACACAGAGCGAACTGGCAAACTGTTCCAACGCGATGACTTTTCTGAGGATAGCCATGCCAACGATCCGa                                   >  2:226434/1‑139 (MQ=255)                                                                             cGATGTACGACATGGAACGGCAAATCAACGCAAACCTGCCGGTTGGCGACCTTCCCAACGTTGACACAGAGCGAACTGGCAAACTGTTCCAACGCGATGACTTTTCTGAGGATAGCCATGCCAACGATCCGAAgttggt                            <  2:14227/139‑1 (MQ=255)                                                                                tGTACGACATGGAACGGCAAATCAACGCAAACCTGCCGGTTGGCGACCTTCCCAACGTTGACACAGAGCGAACTGGCAAACTGTTCCAACGCGATGACTTTTCTGAGGATAGCCATGCCAACGATCCGAAGttggttgg                         >  2:236468/1‑139 (MQ=255)                                                                                          ggAACGGCAAATCAACGCAAACCTGCCGGTTGGCGACCTTccc                                                                                                               >  2:389418/1‑43 (MQ=255)                                                                                          ggAACGGCAAATCAACGCAAACCTGCCGGTTGGCGACCTTccc                                                                                                               <  1:389418/43‑1 (MQ=255)                                                                                          ggAACGGCAAATCAACGCAAACCTGCCGGTTGGCGACCTTCCCAACGTTGACACAGAGCGAACTGGCAAACTGTTCCAACGCGATGACTTTTCTGAGGATAGCCATGCCAACGATCCGAAGTTGGTTGGTGATGATTAc               >  2:268556/1‑139 (MQ=255)                                                                                          ggAACGGCAAATCAACGCAAACCTGCCGGTTGGCGACCTTCCCAACGTTGACACAGAGCGAACTGGCAAACTGTTCCAACGCGATGACTTTTCTGAGGATAGCCATGCCAACGATCCGAAGTTGGTTGGTGATGATTAc               >  2:54652/1‑139 (MQ=255)                                                                                          ggAACGGCAAATCAACGCAAACCTGCCGGTTGGCGACCTTCCCAACGTTGACACAGAGCGAACTGGCAAACTGTTCCAACGCGATGACTTTTCTGAGGATAGCCATGCCAACGATCCGAAGTTGGTTGGTGATGATTAc               <  2:578052/139‑1 (MQ=255)                                                                                             aCGGCAAATCAACGCAAACCTGCCGGTTGGCGACCTTCCCAACGTTGACACAGAGCGAACTGGCAAACTGTTCCAACGCGATGACTTTTCTGAGGATAGCCATGCCAACGATCCGAAGTTGGTTGGTGATGATTACGTc            <  1:402982/139‑1 (MQ=255)                                                                                             aCGGCAAATCAACGCAAACCTGCCGGTTGGCGACCTTCCCAACGTTGACACAGAGCGAACTGGCAAACTGTTCCAACGCGATGACTTTTCTGAGGATAGCCATGCCAACGATCCGAAGTTGGTTGGTGATGATTACGTc            <  1:226434/139‑1 (MQ=255)                                                                                                  aaaTCAACGCAAACCTGCCGGTTGGCGACCTTCCCAACGTTGACACAGAGCGAACTGGCAAACTGTTCCAACGCGATGACTTTTCTGAGGATAGCCATGCCAACGATCCGAAGTTGGTTGGTGATGATTACGTCCCCCa       <  1:399100/139‑1 (MQ=255)                                                                                                  aaaTCAACGCAAACCTGCCGGTTGGCGACCTTCCCAACGTTGACACAGAGCGAACTGGCAAACTGTTCCAACGCGATGACTTTTCTGAGGATAGCCATGCCAACGATCCGAAGTTGGTTGGTGATGATTACGTCCCCCa       <  1:236468/139‑1 (MQ=255)                                                                                                       aaCGCAAACCTGCCGGTTGGCGACCTTCCCAACGTTGACACAGAGCGAACTGGCAAACTGTTCCAACGCGATGACTTTTCTGAGGATAGCCATGCCAACGATCCGAAGTTGGTTGGTGATGATTACGTCCCCCAGGCAc  <  1:54652/139‑1 (MQ=255)                                                                                                                       ttGGCGACCTTCCCAACGTTGACACAGAGCGACCTGGCAAACTGTTCCAACGCGATGACTTTTCTGAGGATAGCCATGCCAACGAt                                       >  1:14282/1‑86 (MQ=255)                                                                                                                       ttGGCGACCTTCCCAACGTTGACACAGAGCGAACGGGCAAACTGTTCCAACGCGATGACTTTTCTGAGGATAGCCATGCCAACGAt                                       <  2:14282/86‑1 (MQ=255)                                                                                                                        tGGCGACCTTCCCAACGTTGACACAGAGCGAACTGGCAAACTGTTCCAACGCGATGACTTTTCTGAGGa                                                       <  1:450502/69‑1 (MQ=255)                                                                                                                        tGGCGACCTTCCCAACGTTGACACAGAGCGAACTGGCAAACTGTTCCAACGCGATGACTTTTCTGAGGa                                                       >  2:450502/1‑69 (MQ=255)                                                                                                                             |                                                                                                                     AGCAAGGTGCTTGCCTGGGTGAGCTTATCGCACAAAGACACCTTCACGGGTGCGAAACGGTTTCAATACTTCCAAACGATGTACGACATGGAACGGCAAATCAACGCAAACCTGCCGGTTGGCGGCCTTCCCAACGTTGACACAGAGCGAACTGGCAAACTGTTCCAACGCGATGACTTTTCTGAGGATAGCCATGCCAACGATCCGAAGTTGGTTGGTGATGATTACGTCCCCCAGGCAC  >  NC_000913/2562860‑2563100

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 27 ≤ ATCG/ATCG < 34 ≤ ATCG/ATCG < 39 ≤ ATCG/ATCG < 40 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑