Predicted mutation
evidence	seq id	position	mutation	annotation	gene	description
RA	NC_000913	1,419,159	G→A	*163* (TAG→TAA)  S51S (AGC→AGT)	sieB → ydaF ←	phage superinfection exclusion protein, Rac prophage uncharacterized protein, Rac prophage

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NC_000913	1,419,159	0	G	A	100.0%	163.1 / NA	52	*163* (TAG→TAA)  S51S (AGC→AGT)	sieB ydaF	phage superinfection exclusion protein, Rac prophage uncharacterized protein, Rac prophage
Reads supporting (aligned to +/- strand):  ref base G (0/0);  new base A (25/27);  total (25/27)

AAAATTAGAACGGAAGGGCATCATTCAACATCAGAGTGATAGCGCAAACTGTTCTTATTATCTCGTCACCGAAAAATACTCCCATTTTATGAAGTTATTCTGGAACAGCAGGAGTAGACGTTTTAATCGTTAGCTTACTGTGTGCTTCTCCAACCATCGGCGCGCACCAGTTTCGGTTTTAAATGTTTTGCTTTTGGTATACGTCATGGCAGTGAACGTTCCATCCTGGTTGGGGAACACGCCGCACACCAGGGATTCGTT  >  NC_000913/1419027‑1419287                                                                                                                                     |                                                                                                                                 aaaaTTAGAACGGAAGGGCATCATTCAACATCAGAGTGATAGCGCAAACTGTTCTTATTATCTCGTCACCGAAAAATACTCCCATTTTATGAAGTTATTCTGGAACAGCAGGAGTAGACGTTTTAATCGTTAACTTACt                                                                                                                            <  1:444362/139‑1 (MQ=255)                   catcatTCAACATCAGAGTGATAGCGCAAACTGTTCTTATTATCTCGTCACCGAAAAATACTCCCATTTTATGAAGTTATTCTGGAACAGCAGGAGTAGACGTTTTAATCGTTAACTTACTGTGTGCTTCTCCAACCAt                                                                                                          <  2:1290419/139‑1 (MQ=255)                        ttCAACATCAGAGTGATAGCGCAAACTGTTCTTATTATCTCGTCACCGAAAAATACTCCCATTTTATGAAGTTATTCTGGAACAGCAGGAGTAGACGTTTTAATCGTTAACTTACTGTGTGCTTCTCCAACCATCGgcg                                                                                                     >  2:1007360/1‑139 (MQ=255)                                  gagTGATAGCGCAAACTGTTCTTATTATCTCGTCACCGAAAAATACTCCCATTTTATGAAGTTATTCTGGAACAGCAGGAGTAGACGTTTTAATCGTTAACTTACTGTGTGCTTCTCCAACCATCGGCGCGCACCAGtt                                                                                           >  2:627397/1‑139 (MQ=255)                                   agTGATAGCGCAAACTGTTCTTATTATCTCGTCACCGAAAAATACTCCCATTTTATGAAGTTATTCTGGAACAGCAGGAGTAGACGTTTTAATCGTTAACTTACTGTGTGCTTCTCCAACCATCGGCGCGCACCAGttt                                                                                          >  1:1248719/1‑139 (MQ=255)                                   agTGATAGCGCAAACTGTTCTTATTATCTCGTCACCGAAAAATACTCCCATTTTATGAAGTTATTCTGGAACAGCAGGAGTAGACGTTTTAATCGTTAACTTACTGTGTGCTTCTCCAACCATCGGCGCGCACCAGttt                                                                                          >  1:99744/1‑139 (MQ=255)                                    gTGATAGCGCAAACTGTTCTTATTATCTCGTCACCGAAAAATACTCCCATTTTATGAAGTTATTCTGGAACAGCAGGAGTAGACGTTTTAATCGTTAACTTACTGTGTGCTTCTCCAACCATCGGCGCGCACCAGTTTc                                                                                         <  2:1360379/139‑1 (MQ=255)                                          gcgcAAACTGTTCTTATTATCTCGTCACCGAAAAATACTCCCATTTTATGAAGTTATTCTGGAACAGCAGGAGTAGACGTTTTAATCGTTAACTTACTGTGTGCTTCTCCAACCATCGGCGCGCACCAGTTTCGGtttt                                                                                   >  2:1343658/1‑139 (MQ=255)                                                 cTGTTCTTATTATCTCGTCACCGAAAAATACTCCCATTTTATGAAGTTATTCTGGAACAGCAGGAGTAGACGTTTTAATCGTTAACTTACTGTGTGCTTCTCCAACCATCGGCGCGCACCAGTTTCGGTTTTAAATGtt                                                                            <  1:627397/139‑1 (MQ=255)                                                    ttCTTATTATCTCGTCACCGAAAAATACTCCCATTTTATGAAGTTATTCTGGAACAGCAGGAGTAGACGTTTTAATCGTTAACTTACTGTGTGCTTCTCCAACCATCGGCGCGCACCTGTTTCGGTTTTAAATGTTTTg                                                                         >  2:832231/1‑139 (MQ=255)                                                        tattatCTCGTCACCGAAAAATACTCCCATTTTATGAAGTTATTCTGGAACAGCAGGAGTAGACGTTTTAATCGTTAACTTACTGTGTGCTTCTCCAACCATCGGCGCGCACCAGTTTCGGTTTTAAATGTTTTGCttt                                                                     <  2:995012/139‑1 (MQ=255)                                                        tattatCTCGTCACCGAAAAATACTCCCATTTTATGAAGTTATTCTGGAACAGCAGGAGTAGACGTTTTAATCGTTAACTTACTGTGTGCTTCTCCAACCATCGGCGCGCACCAGTTTCGGTTTTAAATGTTTTGCttt                                                                     <  1:1007360/139‑1 (MQ=255)                                                        tattatCTCGTCACCGAAAAATACTCCCATTTTATGAAGTTATTCTGGAACAGCAGGAGTAGACGTTTTAATCGTTAACTTACTGTGTGCTTCTCCAACCATCGGCGCGCACCAGTTTCGGTTTTAAATGTTTTGCttt                                                                     <  1:1343658/139‑1 (MQ=255)                                                           tatCTCGTCACCGAAAAATACTCCCATTTTATGAAGTTATTCTGGAACAGCAGGAGTAGACGTTTTAATCGTTAACTTACTGTGTGCTTCTCCAACCATCGGCGCGCACCAGTTTCGGTTTTAAATGTTTTGCt                                                                       <  1:581450/134‑1 (MQ=255)                                                           tatCTCGTCACCGAAAAATACTCCCATTTTATGAAGTTATTCTGGAACAGCAGGAGTAGACGTTTTAATCGTTAACTTACTGTGTGCTTCTCCAACCATCGGCGCGCACCAGTTTCGGTTTTAAATGTTTTGCt                                                                       >  2:581450/1‑134 (MQ=255)                                                              ctcGTCACCGAAAAATACTCCCATTTTATGAAGTTATTCTGGAACAGCAGGAGTAGACGTTTTAATCGTTAACTTACTGTGTGCTTCTCCAACCATCGGCGCGCACCAGTTTCGGTTTTAAATGTTTTGCTTTTGGtat                                                               >  2:321278/1‑139 (MQ=255)                                                                 gTCACCGAAAAATACTCGCATTTTATGAAGTTATTCTGGAACAGCAGGAGTAGACGTTTTAATCGTTAACTAACTGTGTGCTTCTCCAACCATCGGCGCGCACCAGTTTCGGTTTTAAATGTTTTGCttt                                                                     >  2:819669/1‑130 (MQ=255)                                                                 gTCACCGAAAAATACTCCCATTTTATGAAGTTATTCTGGAACAGCAGGAGTAGACGTTTTAATCGTTAACTTACTGTGTGCTTCTCCAACCATCGGCGCGCACCAGTTTCGGTTTTAAATGTTTTGCttt                                                                     <  1:819669/130‑1 (MQ=255)                                                                  tCACCGAAAAATACTCCCATTTTATGAAGTTATTCTGGAACAGCAGGAGTAGACGTTTTAATCGTTAACTTACTGTGTGCTTCTCCAACCATCGGCGCGCACCAGTTTCGGTTTTAAATGTTTTGCTTTTGGta                                                                <  1:166094/134‑1 (MQ=255)                                                                  tCACCGAAAAATACTCCCATTTTATGAAGTTATTCTGGAACAGCAGGAGTAGACGTTTTAATCGTTAACTTACTGTGTGCTTCTCCAACCATCGGCGCGCACCAGTTTCGGTTTTAAATGTTTTGCTTTTGGta                                                                >  2:166094/1‑134 (MQ=255)                                                                  tCACCGAAAAATACTCCCATTTTATGAAGTTATTCTGGAACAGCAGGAGTAGACGTTTTAATCGTTAACTTACTGTGTGCTTCTCCAACCATCGGCGCGCACCAGTTTCGGTTTTAAATGTTTTGCTTTTGGTATACGt                                                           >  2:386360/1‑139 (MQ=255)                                                                     ccGAAAAATACTCCCATTTTATGAAGTTATTCTGGAACAGCAGGAGTAGACGTTTTAATCGTTAACTTACTGTGTGCTTCTCCAACCATCGGCGCGCACCAGTTTCGGTTTTAAATGTTTTGCTTTTGGTATACGTCAt                                                        <  1:832231/139‑1 (MQ=255)                                                                      cGAAAAATACTCCCATTTTATGAAGTTATTCTGGAACAGCAGGAGTAGACGTTTTAATCGTTAACTTACTGTGTGCTTCTCCAACCATCGGCGCGCACCAGTTTCGGTTTTAAATGTTTTGCTTTTGGTATACGTCATg                                                       >  2:1245093/1‑139 (MQ=255)                                                                      cGAAAAATACTCCCATTTTATGAAGTTATTCTGGAACAGCAGGAGTAGACGTTTTAATCGTTAACTTACTGTGTGCTTCTCCAACCATCGGCGCGCACCAGTTTCGGTTTTAAATGTTTTGCTTTTGGTATACGTCATg                                                       <  1:1245093/139‑1 (MQ=255)                                                                             tACTCCCATTTTATGAAGTTATTCTGGAACAGCAGGAGTAGACGTTTTAATCGTTAACTTACTGTGTGCTTCTCCAACCATCGGCGCGCACCAGTTTCGGTTTTAAATGTTTTGCTTTTGGTATACGTCATGGCAGTGa                                                <  2:1248719/139‑1 (MQ=255)                                                                             tACTCCCATTTTATGAAGTTATTCTGGAACAGCAGGAGTAGACGTTTTAATCGTTAACTTACTGTGTGCTTCTCCAACCATCGGCGCGCACCAGTTTCGGTTTTAAATGTTTTGCTTTTGGTATACGTCATGGCAGTGa                                                <  2:171609/139‑1 (MQ=255)                                                                                tCCCATTTTATGAAGTTATTCTGGAACAGCAGGAGTAGACGTTTTAATCGTTAACTTACTGTGTGCTTCTCCAACCATCGGCGCGCACCAGTTTCGGTTTTAAATGt                                                                             >  1:963993/1‑107 (MQ=255)                                                                                tCCCATTTTATGAAGTTATTCTGGAACAGCAGGAGTAGACGTTTTAATCGTTAACTTACTGTGTGCTTCTCCAACCATCGGCGCGCACCAGTTTCGGTTTTAAATGt                                                                             <  2:963993/107‑1 (MQ=255)                                                                                tCCCATTTTATGAAGTTATTCTGGAACAGCAGGAGTAGACGTTTTAATCGTTAACTTACTGTGTGCTTCTCCAACCATCGGCGCGCACCAGTTTCGGTTTTAAATGTTTTGCTTTTGGTATACGTCATGGCAGTGAACg                                             <  1:321278/139‑1 (MQ=255)                                                                                          tGAAGTTATTCTGGAACAGCAGGAGTAGACGTTTTAATCGTTAACTTACTGTGTGCTTCTCCAACCATCGGCGCGCACCAGTTTCGGTTTTAAATGTTTTGCttt                                                                     >  2:1046371/1‑105 (MQ=255)                                                                                          tGAAGTTATTCTGGAACAGCAGGAGTAGACGTTTTAATCGTTAACTTACTGTGTGCTTCTCCAACCATCGGCGCGCACCAGTTTCGGTTTTAAATGTTTTGCttt                                                                     <  1:1046371/105‑1 (MQ=255)                                                                                              gTTATTCTGGAACAGCAGGAGTAGACGTTTTAATCGTTAACTTACTGTGTGCTTCTCCAACCATCGGCGCGCACCAGTTTCGGTTTTAAATGTTTTGCTTTTGGTATACGTCATGGCAGTGAACGTTCCATc                                      <  1:199203/132‑1 (MQ=255)                                                                                              gTTATTCTGGAACAGCAGGAGTAGACGTTTTAATCGTTAACTTACTGTGTGCTTCTCCAACCATCGGCGCGCACCAGTTTCGGTTTTAAATGTTTTGCTTTTGGTATACGTCATGGCAGTGAACGTTCCATc                                      >  2:199203/1‑132 (MQ=255)                                                                                                 aTTCTGGAACAGCAGGAGTAGACGTTTTAATCGTTAACTTACTGTGTGCTTCTCCAACCATCGGCGCGCACCAGTTTCGGTTTTAAATGTTTTGCTTTTGTTATACGTCATGGCAGTGAACGTTCCATCCTGGTTgggg                            >  2:636598/1‑139 (MQ=255)                                                                                                  ttCTGGAACAGCAGGAGTAGACGTTTTAATCGTTAACTTACTGTGTGCTTCTCCAACCAt                                                                                                          <  1:517731/60‑1 (MQ=255)                                                                                                  ttCTGGAACAGCAGGAGTAGACGTTTTAATCGTTAACTTACTGTGTGCTTCTCCAACCAt                                                                                                          >  2:517731/1‑60 (MQ=255)                                                                                                  ttCTGGAACAGCAGGAGTAGACGTTTTAATCGTTAACTTACTGTGTGCTTCTCCAACCATCGgcgc                                                                                                    <  2:994811/66‑1 (MQ=255)                                                                                                  ttCTGGAACAGCAGGAGTAGACGTTTTAATCGTTAACTTACTGTGTGCTTCTCCAACCATCGgcgc                                                                                                    >  1:994811/1‑66 (MQ=255)                                                                                                       gAACAGCAGGAGTAGACGTTTTAATCGTTAACTTACTGTGTGCTTCTCCAACCATCGGCGCGCACCAGTTTCGGTTTTAAATGTTTTGCTTTTGGTATACGTCATGGCAGTGAACGTTCCATCCTGGTTGGGGAACAcg                      <  2:221243/139‑1 (MQ=255)                                                                                                          cagcagGAGTAGACGTTTTAATCGTTAACTTACTGTGTGCTTCTCCAACCATCGGCGCGCACCAGTTTCGGTTTTAAATGTTTTGCTTTTGGTATACGTCATGGCAGTGAACGTTCCATCCTGGTTGGGGAACAcgccg                   <  1:636598/139‑1 (MQ=255)                                                                                                            gcagGAGTAGACGTTTTAATCGTTAACTTACTGTGTGCTTCTCCAACCATCGGCGCGCACCAGTTTCGGTTTTAAATGTTTTGCTTTTGGTATACGTCATGGCAGTGAACGTTCCATCCTGGTTGGGGAaca                        >  1:921041/1‑132 (MQ=255)                                                                                                            gcagGAGTAGACGTTTTAATCGTTAACTTACTGTGTGCTTCTCCAACCATCGGCGCGCACCAGTTTCGGTTTTAAATGTTTTGCTTTTGGTATACGTCATGGCAGTGAACGTTCCATCCTGGTTGGGGAaca                        <  2:921041/132‑1 (MQ=255)                                                                                                             cagGAGTAGACGTTTTAATCGTTAACTTACTGTGTGCTTCTCCAACCATCGGCGCGCACCAGTTTCGGTTTTAAATGTTTTGCTTTTGGTATACTTCATGGCAGTGAACGt                                            >  2:1181706/1‑111 (MQ=255)                                                                                                             cagGAGTAGACGTTTTAATCGTTAACTTACTGTGTGCTTCTCCAACCATCGGCGCGCACCAGTTTCGGTTTTAAATGTTTTGCTTTTGGTATACTTCATGGCAGTGAACGt                                            <  1:1181706/111‑1 (MQ=255)                                                                                                             cagGAGTAGACGTTTTAATCGTTAACTTACTGTGTGCTTCTCCAACCATCGGCGCGCACCAGTTTCGGTTTTAAATGTTTTGCTTTTGGTATACGTCATGGCAGTGAACGTTCCATCCTGGTTGGGGAACACGCCGcac                >  2:615972/1‑139 (MQ=255)                                                                                                                        gTTTTAATCGTTAACTTACTGTGTGCTTCTCCAACCATCGgcgcgc                                                                                                  <  2:230606/46‑1 (MQ=255)                                                                                                                        gTTTTAATCGTTAACTTACTGTGTGCTTCTCCAACCATCGgcgcgc                                                                                                  >  1:230606/1‑46 (MQ=255)                                                                                                                          tttAATCGTTAACTTACTGTGTGCTTCTCCAACCATCGGCGCGCACCAGTTTCGGTTTTAAATGTTTTGCTTTTGGTATACGTCATGGCAGTGAACGTTCCAt                                       >  2:1027725/1‑103 (MQ=255)                                                                                                                          tttAATCGTTAACTTACTGTGTGCTTCTCCAACCATCGGCGCGCACCAGTTTCGGTTTTAAATGTTTTGCTTTTGGTATACGTCATGGCAGTGAACGTTCCAt                                       <  1:1027725/103‑1 (MQ=255)                                                                                                                           ttAATCGTTAACTTACTGTGTGCTTCTCCAACCATCGGCGCGCACCAGTTTCGGTTTTAAATGTTTTGCTTTTGGTATACGTCATGGCAGTGAACGTTCCAt                                       <  2:217118/102‑1 (MQ=255)                                                                                                                           ttAATCGTTAACTTACTGTGTGCTTCTCCAACCATCGGCGCGCACCAGTTTCGGTTTTAAATGTTTTGCTTTTGGTATACGTCATGGCAGTGAACGTTCCAt                                       >  1:217118/1‑102 (MQ=255)                                                                                                                           ttAATCGTTAACTTACTGTGTGCTTCTCCAACCATCGGCGCGCACCAGTTTCGGTTTTAAATGTTTTACATTTGGTATACGTCATGGCAGTGAACGTTCCATCCTGGTTGGGGAACACGCCGCACACCAGGGATTCgtt  >  2:833886/1‑139 (MQ=255)                                                                                                                                     |                                                                                                                                 AAAATTAGAACGGAAGGGCATCATTCAACATCAGAGTGATAGCGCAAACTGTTCTTATTATCTCGTCACCGAAAAATACTCCCATTTTATGAAGTTATTCTGGAACAGCAGGAGTAGACGTTTTAATCGTTAGCTTACTGTGTGCTTCTCCAACCATCGGCGCGCACCAGTTTCGGTTTTAAATGTTTTGCTTTTGGTATACGTCATGGCAGTGAACGTTCCATCCTGGTTGGGGAACACGCCGCACACCAGGGATTCGTT  >  NC_000913/1419027‑1419287

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 27 ≤ ATCG/ATCG < 36 ≤ ATCG/ATCG < 39 ≤ ATCG/ATCG < 40 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑