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%	160.8 / NA	51	*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 (28/23);  total (28/23)

AAAAAATTAGAACGGAAGGGCATCATTCAACATCAGAGTGATAGCGCAAACTGTTCTTATTATCTCGTCACCGAAAAATACTCCCATTTTATGAAGTTATTCTGGAACAGCAGGAGTAGACGTTTTAATCGTTAGCTTACTGTGTGCTTCTCCAACCATCGGCGCGCACCAGTTTCGGTTTTAAATGTTTTGCTTTTGGTATACGTCATGGCAGTGAACGTTCCATCCTGGTTGGGGAACACGCCGCACACCAGGGATTCGT  >  NC_000913/1419025‑1419286                                                                                                                                       |                                                                                                                                aaaaaaTTAGAACGGAAGGGCATCATTCAACATCAGAGTGATAGCGCAAACTGTTCTTATTATCTCGTCACCGAAAAATACTCCCATTTTATGAAGTTATTCTGGAACAGCAGGAGTAGACGTTTTAATCGTTAACTTa                                                                                                                             >  2:228758/1‑139 (MQ=255)           aaCGGAAGGGCATCATTCAACATCAGAGTGATAGCGCAAACTGTTCTTATTATCTCGTCACCGAAAAATACTCCCATTTTATGAAGTTATTCTGGAACAGCAGGAGTAGACGTTTTAATCGTTAACTTACTGTGTGCtt                                                                                                                   <  2:873584/139‑1 (MQ=255)                        catTCAACATCAGAGTGATAGCGCAAACTGTTCTTATTATCTCGTCACCGAAAAATACTCCCATTTTATGAAGTTATTCTGGAACAGCAGGAGTAGACGTTTTAATCGTTAACTTACTGTGTGCTTCTCCAACCATCgg                                                                                                      >  1:1081484/1‑139 (MQ=255)                                  cAGAGTGATAGTGCAAACTGTTCTTATTATCTCGTCACCGAAAAATACTCCCATTTTATGAAGTTATTCTGGAACAGCAGGAGTAGACGTTTTAATCGTTAACTTACTGTGTGCTTCTCCAACCATCGGCGCGCACCAg                                                                                            >  2:502732/1‑139 (MQ=255)                                     agTGATAGCGCAAACTGTTCTTATTATCTCGTCACCGAAAAATACTCCCATTTTATGAAGTTATTCTGGAACAGCAGGAGTAGACGTTTTAATCGTTAACTTACTGTGTGCTTCTCCAACCATCGGCGCGCACCAGttt                                                                                         >  2:187744/1‑139 (MQ=255)                                     agTGATAGCGCAAACTGTTCTTATTATCTCGTCACCGAAAAATACTCCCATTTTATGAAGTTATTCTGGAACAGCAGGAGTAGACGTTTTAATCGTTAACTTACTGTGTGCTTCTCCAACCATCGGCGCGCACCAGttt                                                                                         >  1:97094/1‑139 (MQ=255)                                         aTAGCGCAAACTGTTCTTATTATCTCGTCACCGAAAAATACTCCCATTTTATGAAGTTATTCTGGAACAGCAGGAGTAGACGTTTTAATCGTTAACTTACTGTGTGCTTCTCCAACCATCGGCGCGCACCAGTTTCGGt                                                                                     >  1:1293454/1‑139 (MQ=255)                                         aTAGCGCAAACTGTTCTTATTATCTCGTCACCGAAAAATACTCCCATTTTATGAAGTTATTCTGGAACAGCAGGAGTAGACGTTTTAATCGTTAACTTACTGTGTGCTTCTCCAACCATCGGCGCGCACCAGTTTCGGt                                                                                     >  2:155116/1‑139 (MQ=255)                                               cAAACTGTTCTTATTATCTCGTCACCGAAAAATACTCCCATTTTATGAAGTTATTCTGGAACAGCAGGAGTAGACGTTTTAATCGTTAACTTACTGTGTGCTTCTCCAACCATCGGCGCGCACCAGTTTCGGTTTTaaa                                                                               >  1:705227/1‑139 (MQ=255)                                                          tattatCTCGTCACCGAAAAATACTCCCATTTTATGAAGTTATTCTGGAACAGCAGGAGTAGACGTTTTAATCGTTAACTTACTGTGTGCTTCTCCAACCATCGGCGCGCACCAGTTTCGGTTTTAAATGTTTTGCttt                                                                    <  2:1081484/139‑1 (MQ=255)                                                              atCTCGTCACCGAAAAATACTCCCATTTTATGAAGTTATTCTGGAACAGCAGGAGTAGACGTTTTAATCGTTAACTTACTGTGTGCTTCTCCAACCATCGGCGCGCACCAGTTTCGGTTTTAAATGTTTTGCTTTTGGt                                                                >  2:463472/1‑139 (MQ=255)                                                               tctcGTCACCGAAAAATACTCCCATTTTATGAAGTTATTCTGGAACAGCAGGAGTAGACGTTTTAATCGTTAACTTACTGTGTGCTTCTCCAACCATCGGCGCGCACCAGTTTCGGTTTTAAATGTTTTGCTTTTGGta                                                               <  1:502732/139‑1 (MQ=255)                                                                   gTCACCGAAAAATACTCCCATTTTATGAAGTTATTCTGGAACAGCAGGAGTAGACGTTTTAATCGTTAACTTACTGTGTGCTTCTCCAACCATCGGCGCGCACCAGTTTCGGTTTTAAATGTTTTGCTTTTGGTATACg                                                           >  1:685986/1‑139 (MQ=255)                                                                             aaTACTCCCATTTTATGAAGTTATTCTGGAACAGCAGGAGTAGACGTTTTAATCGTTAACTTACTGTGTGCTTCTCCAACCATCGGCGCGCACCAGTTTCGGTTTTAAATGTTTTGCTTTTGGTATACGTCATGGCAGt                                                 >  1:578044/1‑139 (MQ=255)                                                                               tACTCCCATTTTATGAAGTTATTCTGGAACAGCAGGAGTAGACGTTTTAATCGTTAACTTACTGTGTGCTTCTCCAACCATCGGCGCGCACCAGTTTCGGTTTTAAATGTTTTGCTTTTGGTATACGTCATGGCAGTGa                                               <  2:1243915/139‑1 (MQ=255)                                                                                  tCCCATTTTATGAAGTTATTCTGGAACAGCAGGAGTAGACGTTTTAATCGTTAACTTACTGTGTGCTTCTCCAACCATCGGCGCGCACCAGTTTCGGTTTTAAATGTTTTGCTTTTGGTATACGTCATGGCAGTGAACg                                            >  1:1080833/1‑139 (MQ=255)                                                                                  tCCCATTTTATGAAGTTATTCTGGAACAGCAGGAGTAGACGTTTTAATCGTTAACTTACTGTGTGCTTCTCCAACCATCGGCGCGCACCAGTTTCGGTTTTAAATGTTTTGCTTTTGGTATACGTCATGGCAGTGAACg                                            <  2:705227/139‑1 (MQ=255)                                                                                    cccttttATGAAGTTATTCTGGAACAGCAGGAGTAGACGGTTTAATCGTTAACTTACTGTGTGCTTCTCCAACCATCGGCGCGCACCAGTTTCGGTTTTAAATGTTTTGCTTTTGGTATACGTCATGGCAGTGAACGtt                                          <  1:1282281/136‑1 (MQ=255)                                                                                    ccATTTTATGAAGTTATTCTGGAACAGCAGGAGTAGACGTTTTAATCGTTAACTTACTGTGTGCTTCTCCAACCATCGGCGCGCACCAGTTTCGGTTTTAAATGTTTTGCTTTTGGTATACGTCATGGCAGTGAACGtt                                          >  1:562260/1‑139 (MQ=255)                                                                                           aTGAAGTTATTCTGGAACAGCAGGAGTAGACGTTTTAATCGTTAACTTACTGTGTGCTTCTCCAACCATCGGCGCGCACCAGTTTCGGTTTTAAATGTTTTGCTTTTGGta                                                               <  1:53242/111‑1 (MQ=255)                                                                                           aTGAAGTTATTCTGGAACAGCAGGAGTAGACGTTTTAATCGTTAACTTACTGTGTGCTTCTCCAACCATCGGCGCGCACCAGTTTCGGTTTTAAATGTTTTGCTTTTGGta                                                               >  2:53242/1‑111 (MQ=255)                                                                                            tGAAGTTATTCTGGAACAGCAGGAGTAGACGTTTTAATCGTTAACTTACTGTGTGCTTCTCCAACCATCGGCGCGTACGAGTTTCGGTTTTAAATGTTTTGCTTTTGGTATACGTCATGGCAGTGAACTTTCCATCCTg                                  >  1:136370/1‑139 (MQ=255)                                                                                              aaGTTATTCTGGAACAGCAGGAGTAGACGTTTTAATCGTTAACTTACTGTGTGCTTCTCCAACCATCGGCGCGCACCAGTTTCGGTTTTAAATGTTTTGCTTTTGGta                                                               <  1:260551/108‑1 (MQ=255)                                                                                              aaGTTATTCTGGAACAGCAGGAGTAGACGTTTTAATCGTTAACTTACTGTGTGCTTCTCCAACCATCGGCGCGCACCAGTTTCGGTTTTAAATGTTTTGCTTTTGGta                                                               >  2:260551/1‑108 (MQ=255)                                                                                                gTTATTCTGGAACAGCAGGAGTAGACGTTTTAATCGTTAACTTACTGTGTGCTTCTCCAACCATCGGCGCGCACCAGTTTCGGTTTTAAATGTTTTGCt                                                                      <  1:13758/99‑1 (MQ=255)                                                                                                gTTATTCTGGAACAGCAGGAGTAGACGTTTTAATCGTTAACTTACTGTGTGCTTCTCCAACCATCGGCGCGCACCAGTTTCGGTTTTAAATGTTTTGCt                                                                      >  2:13758/1‑99 (MQ=255)                                                                                                 ttATTCTGGAACAGCAGGAGTAGACGTTTTAATCGTTAACTTACTGTGTGCTTCTCCAACCATCGGCGCGCACCAGTTTCGGTTTTAAATGtt                                                                           >  1:426394/1‑93 (MQ=255)                                                                                                 ttATTCTGGAACAGCAGGAGTAGACGTTTTAATCGTTAACTTACTGTGTGCTTCTCCAACCATCGGCGCGCACCAGTTTCGGTTTTAAATGtt                                                                           <  2:426394/93‑1 (MQ=255)                                                                                                       tGGAACAGCAGGAGTAGACGTTTTAATCGTTAACTTACTGTGTGCTTCTCCAACCATCGGCGCGCACCAGTTTCGGTTTTAAATGTTTTGCTTTTGGTATACGTCATGGCAGTGAACGTTCCATCCTGGTTGGGGAaca                       <  2:97094/139‑1 (MQ=255)                                                                                                       tGGAACAGCAGGAGTAGACGTTTTAATCGTTAACTTACTGTGTGCTTCTCCAACCATCGGCGCGCACCAGTTTCGGTTTTAAATGTTTTGCTTTTGGTATACGTCATGGCAGTGAACGTTCCATCCTGGTTGGGGAaca                       <  2:685986/139‑1 (MQ=255)                                                                                                           aCAGCAGGAGTAGACGTTTTAATCGTTAACTTACTGTGTGCTTCTCCAACCATCGGCGCGCACCAGTTTCGGTTTTAAATGTTTTGCTTTTGGTATACGTCATGGCAGTGAACGTTCCATCCTGGTTGGGGAACAcgcc                   >  1:762793/1‑139 (MQ=255)                                                                                                            cagcagGAGTAGACGTTTTAATCGTTAACTTACTGTGTGCTTCTCCAACCATCGGCGCGCACCAGTTTCGGTTTTAAATGTTTTGCTTTTGGTATACGTCATGGCAGTGAACGTTCCATCCTGGTTGGGGAACAcgccg                  <  1:520890/139‑1 (MQ=255)                                                                                                            cagcagGAGTAGACGTTTTAATCGTTAACTTACTGTGTGCTTCTCCAACCATCGGCGCGCACCAGTTTCGGTTTTAAATGTTTTGCTTTTGGTATACGTCATGGCAGTGAACGTTCCATCCTGGTTGGGGAACAcgccg                  <  2:355256/139‑1 (MQ=255)                                                                                                               cagGAGTAGACGTTTTAATCGTTAACTTACtgtgtg                                                                                                                      >  1:581388/1‑36 (MQ=255)                                                                                                               cagGAGTAGACGTTTTAATCGTTAACTTACtgtgtg                                                                                                                      <  2:581388/36‑1 (MQ=255)                                                                                                               cagGAGTAGACGTTTTAATCGTTAACTTACTGTGTGCTTCTCCAACCATCGGCGCGCACCAGttt                                                                                         <  2:172653/65‑1 (MQ=255)                                                                                                               cagGAGTAGACGTTTTAATCGTTAACTTACTGTGTGCTTCTCCAACCATCGGCGCGCACCAGttt                                                                                         >  1:172653/1‑65 (MQ=255)                                                                                                               cagGAGTAGACGTTTTAATCGTTAACTTACTGTGTGCTTCTCCAACCATCGGCGCGCACCAGTTTCGGtttt                                                                                  >  1:184909/1‑72 (MQ=255)                                                                                                               cagGAGTAGACGTTTTAATCGTTAACTTACTGTGTGCTTCTCCAACCATCGGCGCGCACCAGTTTCGGtttt                                                                                  <  2:184909/72‑1 (MQ=255)                                                                                                               cagGAGTAGACGTTTTAATCGTTAACTTACTGTGTGCTTCTCCAACCATCGGCGCGCACCAGTTTCGGTTTTAAATGTTTTGCTTTTGGTATACGTCATGGCAGTGAACGTTCCATCCTGGTTGGGGAACAcgccg                  >  1:961224/1‑136 (MQ=255)                                                                                                               cagGAGTAGACGTTTTAATCGTTAACTTACTGTGTGCTTCTCCAACCATCGGCGCGCACCAGTTTCGGTTTTAAATGTTTTGCTTTTGGTATACGTCATGGCAGTGAACGTTCCATCCTGGTTGGGGAACAcgccg                  <  2:961224/136‑1 (MQ=255)                                                                                                                 ggAGTAGACGTTTTAATCGTTAACTTACTGTGTGCTTCTCCAACCATCGGCGCGCACCAGTTTCGGTTTTAAATGTTTTGCTTTTGGTATACGTCATGGCAGTGAACGTTCCATCCTGGTTGGGGAACACGCCGCacac             <  1:228758/139‑1 (MQ=255)                                                                                                                       gACGTTTTAATCGTTAACTTACTGTGTGCTTCTCCAACCATCGGCGCGCACCAGTTTCGGTTTTAAATGTTTTGCTTTTGGTATACGTCATGGCAGTGAACGTTCCATCCTGGTTg                              <  1:774568/116‑1 (MQ=255)                                                                                                                       gACGTTTTAATCGTTAACTTACTGTGTGCTTCTCCAACCATCGGCGCGCACCAGTTTCGGTTTTAAATGTTTTGCTTTTGGTATACGTCATGGCAGTGAACGTTCCATCCTGGTTg                              >  2:774568/1‑116 (MQ=255)                                                                                                                            tttAATCGTTAACTTACTGTGTGCTTCTCCAACCATCGGCGCGCACCAGTTTCGGTTTTAAATGTTTTGCTTTTGGTATACGTCATGGCAGTGAACGTTCCATCCTGGTTGGGGAACACGCCGCACACCAGGGATTCgt  >  2:35224/1‑139 (MQ=255)                                                                                                                             ttAATCGTTAACTTACTGTGTGCTTCTCCAACCATCGGCGCGCACCAGTTTCGGTTTTAAATGTTTTGCTTTTGGTATACGt                                                          <  2:1006002/82‑1 (MQ=255)                                                                                                                             ttAATCGTTAACTTACTGTGTGCTTCTCCAACCATCGGCGCGCACCAGTTTCGGTTTTAAATGTTTTGCTTTTGGTATACGt                                                          >  1:1006002/1‑82 (MQ=255)                                                                                                                             ttAATCGTTAACTTACTGTGTGCTTCTCCAACCATCGGCGCGCACCAGTTTCGGTTTTAAATGTTTTGCTTTTGGTATACGTCATGGc                                                    >  1:228761/1‑88 (MQ=255)                                                                                                                             ttAATCGTTAACTTACTGTGTGCTTCTCCAACCATCGGCGCGCACCAGTTTCGGTTTTAAATGTTTTGCTTTTGGTATACGTCATGGc                                                    <  2:228761/88‑1 (MQ=255)                                                                                                                             ttAATCGTTAACTTACTGTGTGCTTCTCCAACCATCGGCGCGCACCAGTTTCGGTTTTAAATGTTTTGCTTTTGGTATACGTCATGGCAGTGAACGTTCCATCCTGGTTGGGGa                          >  2:282846/1‑114 (MQ=255)                                                                                                                             ttAATCGTTAACTTACTGTGTGCTTCTCCAACCATCGGCGCGCACCAGTTTCGGTTTTAAATGTTTTGCTTTTGGTATACGTCATGGCAGTGAACGTTCCATCCTGGTTGGGGa                          <  1:282846/114‑1 (MQ=255)                                                                                                                                       |                                                                                                                                AAAAAATTAGAACGGAAGGGCATCATTCAACATCAGAGTGATAGCGCAAACTGTTCTTATTATCTCGTCACCGAAAAATACTCCCATTTTATGAAGTTATTCTGGAACAGCAGGAGTAGACGTTTTAATCGTTAGCTTACTGTGTGCTTCTCCAACCATCGGCGCGCACCAGTTTCGGTTTTAAATGTTTTGCTTTTGGTATACGTCATGGCAGTGAACGTTCCATCCTGGTTGGGGAACACGCCGCACACCAGGGATTCGT  >  NC_000913/1419025‑1419286

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: ‑