Predicted mutation
evidence	seq id	position	mutation	annotation	gene	description
RA	NC_000913	2,769,486	G→A	*274* (TAG→TAA)	yfjQ →	CP4‑57 prophage, uncharacterized protein

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NC_000913	2,769,486	0	G	A	100.0%	117.3 / NA	37	*274* (TAG→TAA)	yfjQ	CP4‑57 prophage, uncharacterized protein
Reads supporting (aligned to +/- strand):  ref base G (0/0);  new base A (17/20);  total (17/20)

GGGCGGACTCAGTGGGCGTAATGCTAAAGGCGGACGAACTCATACTCGTGCCGTGCGTGGCATTGACGGGGATGTGAAGCTTAACCGTGCGCTGTGGGTGATGGCAGAAACACTGCTCACGCAACTGCAGTAGACGTTTCATGTTGCCACGTTGTTAATATCGGACACCACCTGTCCGCATCGCTATGTGCTCGTGTGCCTCAATCCCCCGGTTATAGCTTTTAACCCCCGTTACATCTGGCTTTTGCAGAAATAAAAAATAGTTT  >  NC_000913/2769354‑2769619                                                                                                                                     |                                                                                                                                      gggCGGACTCAGTGGGCGTAATGCTAAAGGCGGACGAACTCATACTCGTGCCGTGCGTGGCATTGACGGGGATGTGAAGCTTAACCGTGCGCTGTGGGTGATGGCAGAAACACTGCTCACGCAACTGCAGTAAACGttt                                                                                                                                 >  2:39498/1‑139 (MQ=255)            gTGGGCGTAATGCTAAAGGCGGACGAACTCATACTCGTGCCGTGCGTGGCATTGACGGGGATGTGAAGCTTAACCGTGCGCTGTGGGTGATGGCAGAAACACTGCTCACGCAACTGCAGTAAACGTTTCATGTTGCCAc                                                                                                                      <  1:120206/139‑1 (MQ=255)            gTGGGCGTAATGCTAAAGGCGGACGAACTCATACTCGTGCCGTGCGTGGCATTGACGGGGATGTGAAGCTTAACCGTGCGCTGTGGGTGATGGCAGAAACACTGCTCACGCAACTGCAGTAAACGTTTCATGTTGCCAc                                                                                                                      <  2:348740/139‑1 (MQ=255)                   tAATGCTAAAGGCGGACGAACTCATACTCGTGCCGTGCGTGGCATTGACGGGGATGTGAAGCTTAACCGTGCGCTGTGGGTGATGGCAGAAACACTGCTCACGCAACTGCAGTAAACGTTTCATGTTGCCACGTTGTTa                                                                                                               >  1:9781/1‑139 (MQ=255)                           aaGGCGGACGAACTCATACTCGTGCCGTGCGTGGCATTGACGGGGATGTGAAGCTTAACCGTGCGCTGTGGGTGATGGCAGAAACACTGCTCACGCAACTGCAGTAAACGTTTCATGTTGCCACGTTGTTAATATCGGa                                                                                                       <  1:39498/139‑1 (MQ=255)                                     aaCTCATACTCGTGCCGTGCGTGGCATTGACGGGGATGTGAAGCTTAACCGTGCGCTGTGGGTGATGGCAGAAACACTGCTCACGCAACTGCAGTAAACGTTTCATGTTGCCACGTTGTTAATATCGGACACCACCTGt                                                                                             <  2:882819/139‑1 (MQ=255)                                          aTACTCGTGCCGTGCGTGGCATTGACGGGGATGTGAAGCTTAACCGTGCGCTGTGGGTGATGGCAGAAACACTGCTCACGCAACTGCAGTAAACGTTTCATGTTGCCACGTTGTTAATATCGGACACCACCTGTCCGCa                                                                                        <  1:1025455/139‑1 (MQ=255)                                                 tgccgtgcGTGGCATTGACGGGGATGTGAAGCTTAACCGTGCGCTGTGGGTTATGGCAGAAACACTGCTCACGCAACTGCAGTAAACGTTTCATGTTGcc                                                                                                                        >  2:431003/1‑100 (MQ=255)                                                 tgccgtgcGTGGCATTGACGGGGATGTGAAGCTTAACCGTGCGCTGTGGGTGATGGCAGAAACACTGCTCACGCAACTGCAGTAAACGTTTCATGTTGcc                                                                                                                        <  1:431003/100‑1 (MQ=255)                                                      tgcgtgGCATTGACGGGGATGTGAAGCTTAACCGTGCGCTGTGGGTGATGGCAGAAACACTGCTCACGCAACTGCAGTAAACGTTTCATGTTGcc                                                                                                                        >  2:745899/1‑95 (MQ=255)                                                      tgcgtgGCATTGACGGGGATGTGAAGCTTAACCGTGCGCTGTGGGTGATGGCAGAAACACTGCTCACGCAACTGCAGTAAACGTTTCATGTTGcc                                                                                                                        <  1:745899/95‑1 (MQ=255)                                                          tgGCATTGACGGGGATGTGAAGCTTAACCGTGCGCTGTGGGTGATGGCAGAAACACTGCTCACGCAACTGCAGTAAACGTTTCATGTTGCCACGTTGTTAATATCGGACACCACCTGTCCGCa                                                                                        <  1:493666/123‑1 (MQ=255)                                                          tgGCATTGACGGGGATGTGAAGCTTAACCGTGCGCTGTGGGTGATGGCAGAAACACTGCTCACGCAACTGCAGTAAACGTTTCATGTTGCCACGTTGTTAATATCGGACACCACCTGTCCGCa                                                                                        >  2:493666/1‑123 (MQ=255)                                                            gCATTGACGGGGATGTGAAGCTTAACCGTGCGCTGTGGGTGATGGCAGAAACACTGCTCACGCAACTGCAGTAAACGTTTCATGTTGCCACGTTGTTAATATCGGACACCACCTGTCCGCATCGCTATGTGCTCGtgtg                                                                      >  1:862278/1‑139 (MQ=255)                                                                 gACGGGGATGTGAAGCTTAACCGTGCGCTGTGGGTGATGGCAGAAACACTGCTCACGCAACTGCAGTAAACGTTTCATGTTGCCACGTTGTTAATATCGGACACCACCTGTCCGCATCGCTATGTGCTCGTGTGCCTCa                                                                 <  1:669850/139‑1 (MQ=255)                                                                       gATGTGAAGCTTAACCGTGCGCTGTGGGTGATGGCAGAAACACTGCTCACGCAACTGCAGTAAACGTTTCATGTTGCCACGTTGTTAATATCGGACACCACCTGTCCGCATCGCTATGTGCTCGTGTGCCTCAATccc                                                            >  1:494660/1‑138 (MQ=255)                                                                       gATGTGAAGCTTAACCGTGCGCTGTGGGTGATGGCAGAAACACTGCTCACGCAACTGCAGTAAACGTTTCATGTTGCCACGTTGTTAATATCGGACACCACCTGTCCGCATCGCTATGTGCTCGTGTGCCTCAATccc                                                            <  2:494660/138‑1 (MQ=255)                                                                             aaGCTTAACCGTGCGCTGTGGGTGATGGCAGAAACACTGCTCACGCAACTGCAGTAAACGTTTCATGTTGCCACGTTGTTAATATCGGACACCACCTGTCCGCATCGCTATGTGCTCGTGTTCCTCAATcccc                                                           >  2:622134/1‑133 (MQ=255)                                                                             aaGCTTAACCGTGCGCTGTGGGTGATGGCAGAAACACTGCTCACGCAACTGCAGTAAACGTTTCATGTTGCCACGTTGTTAATATCGGACACCACCTGTCCGCATCGCTATGTGCTCGTGTGCCTCAATcccc                                                           <  1:622134/133‑1 (MQ=255)                                                                                       gTGCGCTGTGGGTGATGGCAGAAACACTGCTCACGCAACTGCAGTAAACGTTTCATGTTGCCACGTTGTTAATATCGGACACCACCTGTCCGCATCGCTATGTGCTCGTGTGCCTCAATCCCCCGGTTATAGCTTTTaa                                           <  2:391200/139‑1 (MQ=255)                                                                                        tGCGCTGTGGGTGATGGCAGAAACACTGCTCACGCAACTGCAGTAAACGTTTCATGTTGCCACGTTGTTAATATCGGACACCACCTGTCCGCATCGCTATGTGCTCGTGTGCCTCAATCCCCCGGTTATAGCTTTTAAc                                          <  2:1013248/139‑1 (MQ=255)                                                                                         gcgcTGTGGGTGATGGCAGAAACACTGCTCACGCAACTGCAGTAAACGTTTCATGTTGCCACGTTGTTAATATCGGACACCACCTGTCCGCATCGCTATGTGCTCGTGTGCCTCAATCCCCCGGTTATAGCTTTTAAcc                                         <  2:9781/139‑1 (MQ=255)                                                                                          cgcTGTGGGTGATGGCAGAAACACTGCTCACGCAACTGCAGTAAACGTTTCATGTTGCCACGTTGTTAATATCGGACACCACCTGTCCGCAt                                                                                       >  2:139736/1‑92 (MQ=255)                                                                                          cgcTGTGGGTGATGGCAGAAACACTGCTCACGCAACTGCAGTAAACGTTTCATGTTGCCACGTTGTTAATATCGGACACCACCTGTCCGCAt                                                                                       <  1:139736/92‑1 (MQ=255)                                                                                                  gTGATGGCAGAAACACTGCTCACGCAACTGCAGTAAACGTTTCATGTTGCCACGTTGTTAATATCGGACACCACCTGTCCGCATCGCTATGTGCTCGTGTGCCTCAATCCCCCGGTTATAGCTTTTAACCCCCGTTACa                                >  2:1021172/1‑139 (MQ=255)                                                                                                     aTGGCAGAAACACTGCTCACGCAACTGCAGTAAACGTTTCATGTTGCCACGTTGTTAATATCGGACACCACCTGTCCGCATCGCTATGTGCTCGTGTGCCTCAATCCCCCGGTTATAGCTTTTAACCCCCGTTACATCt                             <  1:292615/139‑1 (MQ=255)                                                                                                         cAGAAACACTGCTCACGCAACTGCAGTAAACGTTTCATGTTGCCACGTTGTTAATATCGGACACCACCTGTCAGCATCGCTATGTGCTCGTGTGCCTCAGTCCCCCGGTTATAGCTTTTAACCCCCGTTACATCTGGCt                         >  1:689904/1‑139 (MQ=255)                                                                                                           gAAACACTGCTCACGCAACTGCAGTAAACGTTTCATGTTGCCACGTTGTTAATATCGGACACCACCTGTCCGCa                                                                                        <  2:754759/74‑1 (MQ=255)                                                                                                           gAAACACTGCTCACGCAACTGCAGTAAACGTTTCATGTTGCCACGTTGTTAATATCGGACACCACCTGTCCGCa                                                                                        >  1:754759/1‑74 (MQ=255)                                                                                                            aaaCACTGCTCACGCAACTGCAGTAAACGTTTCATGTTGCCACGTTGTTAATATCGGACACCACCTGTCCGCATCGCTATGTGCTCGTGTGCCTCAATccc                                                            >  2:986762/1‑101 (MQ=255)                                                                                                            aaaCACTGCTCACGCAACTGCAGTAAACGTTTCATGTTGCCACGTTGTTAATATCGGACACCACCTGTCCGCATCGCTATGTGCTCGTGTGCCTCAATccc                                                            <  1:986762/101‑1 (MQ=255)                                                                                                                  tGCTCACGCAACTGCAGTAAACGTTTCATGTTGCCACGTTGTTAATATCGGACACCACCTGTCCTCATCGCTATGTGCTCGTGTGCCTCAATCCCCCGGTTATAGCTTTTa                                            >  1:610806/1‑111 (MQ=255)                                                                                                                  tGCTCACGCAACTGCAGTAAACGTTTCATGTTGCCACGTTGTTAATATCGGACACCACCTGTCCGCATCGCTATGTGCTCGTGTGCCTCAATCCCCCGGTTATAGCTTTTa                                            <  2:610806/111‑1 (MQ=255)                                                                                                                      cACGCAACTGCAGTAAACGTTTCATGTTGCCACGTTGTTAATATCGGACACCACCTGTCCGCATCGCTATGTGCTCGTGTGCCTCAATCCCCCGGTTATAGCTTTTAACCCCCGTTACATCTGGCTTTTGCAGAAATaa            >  1:1038562/1‑139 (MQ=255)                                                                                                                       aCGCAACTGCAGTAAACGTTTCATGTTGCCACGTTGTTAATATCGGACACCACCTGTCCGCATCGCTATGTGCTCGTGTGCCTCAATccc                                                            >  2:858303/1‑90 (MQ=255)                                                                                                                       aCGCAACTGCAGTAAACGTTTCATGTTGCCACGTTGTTAATATCGGACACCACCTGTCCGCATCGCTATGTGCTCGTGTGCCTCAATccc                                                            <  1:858303/90‑1 (MQ=255)                                                                                                                                cAGTAAACGTTTCATGTTGCCACGTTGTTAATATCGGACACCACCTGTCCGCATCGCTATGTGCTCGTGTGCCTCAATCCCCCGGTTATAGCTTTTAACCCCCGTTACATCTGGCTTTTGCAGAAATAAAAAATAGttt  >  2:73094/1‑139 (MQ=255)                                                                                                                                     |                                                                                                                                      GGGCGGACTCAGTGGGCGTAATGCTAAAGGCGGACGAACTCATACTCGTGCCGTGCGTGGCATTGACGGGGATGTGAAGCTTAACCGTGCGCTGTGGGTGATGGCAGAAACACTGCTCACGCAACTGCAGTAGACGTTTCATGTTGCCACGTTGTTAATATCGGACACCACCTGTCCGCATCGCTATGTGCTCGTGTGCCTCAATCCCCCGGTTATAGCTTTTAACCCCCGTTACATCTGGCTTTTGCAGAAATAAAAAATAGTTT  >  NC_000913/2769354‑2769619

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: ‑