Predicted mutation
evidence	seq id	position	mutation	annotation	gene	description
RA	NC_000913	1,429,453	2 bp→TG	coding (405‑406/3363 nt)	stfR →	putative prophage side tail fiber protein StfR

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NC_000913	1,429,453	0	C	T	100.0%	46.0 / NA	16	S135S (AGC→AGT)	stfR	putative prophage side tail fiber protein StfR
Reads supporting (aligned to +/- strand):  ref base C (0/0);  new base T (7/9);  total (7/9)
*	NC_000913	1,429,454	0	A	G	100.0%	46.6 / NA	16	T136A (ACA→GCA)	stfR	putative prophage side tail fiber protein StfR
Reads supporting (aligned to +/- strand):  ref base A (0/0);  new base G (7/9);  total (7/9)

TACCGTGTATGAAGATTCTCAACCCGGTACGCTGAATGATTTTCTCGGTGCCATGACGGAGGATGATGCCCGTCCGGAGGCACTGCGCCGTTTTGAACTGATGGTGGAAGAGGTGGCGCGTAACGCGTCCGCGGTGGCACAGAACACGGCAGCCGCGAAGAAGTCAGCCAGTGATGCCAGCACATCAGC‑CCGTGAGGCGGCAACCCATGCGG‑CTGATGCTGCGGACTCAGCACGCGCAGCCAGCACGTCAGCCGGACAGGCCGCGTCGTCGGCTCAGTCAGCGTCTTCCAGCGCAGGAACGGCATCAACAAAGGCCACTGAAGCATCAAAAAGTGCTGCCGCT  >  NC_000913/1429273‑1429615                                                                                                                                                                                     ||                                                                                                                                                                    caCCGTGTATGAAGATTCACAACCGGGGACGCTGAATGATTTTCTCTGTGCCATGACGGAGGATGATGCCCGGCCGGAGGTGCTGCGTCGTCTTGAACTGATGGTGGAAGAGGTGGCGCGTAACGCGTCCGTGGTGGCACAGAGTACGGCAGACGCGAAGAAATCAGCCGGCGATGCCAGTGCATCAGC‑TGCTCAGGTCGCGGCCCTTGTGA‑CTGATGCAACTGACTCAGCACGCGCCGCCAGCACGTcc                                                                                               <  2:48041/249‑2 (MQ=255)   ccGTGTATGAAGATGCACATCCGGGGACGCTGAATGATTTTCTCTGTGCCATGACGGAGGATGATGCCCGGCCGGAGGTGCTGCGTCGTCTTGAACTGATGGTGGAAGAGGTGGCGCGTAACGCGTCCGTGGTGGCACAGAGTACGGCAGACGCGAAGAAATCAGCCGGCGATGCCAGTGCATCAGC‑TGCTCAGGTCGCGGCCCTTGTGA‑CTGATGCAACTGACTCAGCACGCGCCGCCAGCACGTCCGcc                                                                                            <  1:243072/251‑1 (MQ=255)         aTGAAGATTCACAACCGGGGACGCTGAAGGATTTTCTCTGGGCCATGACGGAGGATGATGCCCGGCCGGAGGTGCTGCGTCGTCTTGAACTGATGGTGGAAGAGGTGGCGCGTAACGCGTCCGTGGTGGCACAGAGTACGGCAGACGCGAAGAAATCAGCCGGCGATGCCAGTGCATCAGC‑TGCTCAGTTCGCGGCCCTTGTGA‑CTGATGCAACTGACTCAGCACGCGCCGCCAGCACGTCCGCCGGACa                                                                                       <  2:223455/250‑1 (MQ=255)                  cacAACCGGGGACGCTGAATGATTTTCTCTGTGCCATGACGGAGGATGATGCCCGGCCGGAGGTGCTGCTTCGTCTTGAACTGATGGTGGAAGAGGTGGCGCGTAACGCGTCCGTGGTGGCACAGAGTACGGCAGACGCGAAGAAATCAGCCGGCGATGCCAGTGCATCAGC‑TGCTCAGGTCTCGGCCCTTGTGA‑CTGATGCAACTGACTCAGCACGCGCCGCCAGCACGTCCGCCGGACAGGctgcatc                                                                              <  1:164354/248‑7 (MQ=255)                  cacAACCGGGGACGCTGAATGATTTTCTCTGTGCCATGACGGAGGATGATGCCCGGCCGGAGGTGCTGCGTCGTCTTGAACTGATGGTGGAAGAGGTGGCGCGTAACGCGTCCGTGGTGGCACAGAGTACGGCAGACGCGAAGCAATCAGCCGGCGATGCCAGTGCATCAGC‑TGCTCAGGTCGCGGCCCTTGTGA‑CTGATGCAACTGACTCAGCACGCGCCGCCAGCACGTCCGCCGGACAGGctgcatcg                                                                             >  1:111514/3‑244 (MQ=255)                      accggggaCGCTGAATGATTTTCTCTGTGCCATGACGGAGGATGATGCCCGGCCGGAGGTGCTGCGTCGTCTTGAACTGATGGTGGAAGAGGTGGCGCGTAACGCGTCCGTGGTGGCCCAGAGTACGGCAGACGCGAAGAAATCAGCCGGCGATGCCAGTGCATCAGC‑TGCTCAGGTCGCGGCCCTTGTGA‑CTGATGCAACTGACTCAGCACGCGCCGCCAGCACGTCCGCCGGACAGGctgcaccgtc                                                                           >  2:185250/8‑240 (MQ=255)                          gggaCGCTGAATGATTTTCTCTGTGCCATGACGGAGGATGATGCCCGGCCGGAGGTGCTGCGTCGTCTTGAACTGATGGTGGAAGAGGTGGCGCGTAACGCGTCCGTGGTGGCACAGAGTACGGCAGACGCGAAGAAATCAGCCGGCGATGCCAGTGCATCAGC‑TGCTCAGGTCGCGGCCCTTGTGA‑CTGATGCAACTGACTCAGCACGCGCCGCCAGCACGTCCGCCGGACAGGCTGCATCGTCAGCtc                                                                      >  2:128612/4‑250 (MQ=255)                                                    cATGACGGAGGATGATGCCCGGCCGGAGGTGCTGCGTCGTCTTGAACTGATGGTGGAAGAGGTGGCGCGTAACGCGTCCGTGGTGGCACAGAGTACGGCAGACGCGAAGAAATCAGCCGGCGATGCCAGTGCATCAGC‑TGCTCAGGTCGCGGCCCTTGTGA‑CTGATGCAACTGACTCAGCACGCGCCGCCAGCACGTCCGCCGGACAGGCTGCATCGTCAGCTCAGGAAGCGTCCTCCGGCGCAgaagcgg                                           >  1:197314/1‑245 (MQ=255)                                                        aCGGAGGATGATGCCCGGCCGGAGGTGCTGCGTCGTCTTGAACTGATGGTGGAAGAGGTGGCGCGTAACGCGTCCGTGGTGGCACAGAGTACGGCAGACGCGAAGAAATCAGCCGGCGATGCCAGTGCATCAGCTGCG‑CAGGTCGCGGCCCTTGTGA‑CTGATGCAACTGACTCAGCACGCGCCGCCAGCACGTCCGCCGGACAGGCTGCATCGTCAGCTCAGGAAGCGTCCTCCGGCGCAGAAGCGGCATc                                       <  1:157527/251‑1 (MQ=255)                                                                  atgCCCGGCCGGAGGTGCTGCGTCGTCTTGAACTGATGGTGGAAGAGGTGGCGCGTAACGCGTCCGTGGTGGCACAGAGTACGGCAGACGCGAAGAAATCAGCCGGCGATGCCAGTGCATCAGC‑TGCTCAGGTCGCGGCCCTTGTGA‑CTGATGCAACTGACTCAGCACGCGCCGCCAGCACGTCCGCCGGACAGGCTGCATCGTCAGCTCAGGAAGCGTCCTCCGGCGCAGACGCGGCATCAGCAAAggac                             >  2:64283/1‑249 (MQ=255)                                                                        ggcgggaggtgctgcgtcggcttGAACTGATGGTGGAAGAGGTGGCGCGTAACGCGTCCGTGGTGGCACAGAGTACGGCAGACGCGAAGAAATCAGCCGGCGATGCCAGTGCATCAGC‑TGCTCAGGTCGCGGCCCGTGTGA‑CTGATGCAACTGACTCAGCACGCGCCGCCAGCACGTCCGCCGGACAGGCTGCATCGGCAGGTCAGGAAGCGTCCTCGGGCGCAGAAGCGGCAGCAGCAAAGGCCTCTGaa                       <  2:42057/230‑1 (MQ=255)                                                                        ggccGGAGGTGCTGCGTCGTCTTGAACTGATGGTGGAAGAGGTGGCGCGTAACGCGTCCGTGGTGGCACAGAGTACGGCAGACGCGAAGAAATCAGCCGGCGATGCCAGTGCATCAGC‑TGCTCAGGTCGCGGCCCTTGTGA‑CTGATGCAACTGACTCAGCACGCGCCGCCAGCACGTCCGCCGGACAGGCTGCATCGTCAGCTCAGGAAGCGTCCTCCGGCGCAGAAGCGGCATCAGCAAAGGCCACTGa                        >  2:2884/3‑250 (MQ=255)                                                                            ggatgtgcTGCGTCGTCTTGAACTGATGGTGGAAGAGGTGGCGCGTAACGCGTCCGTGGTGGCACAGAGTACGGCAGACGCGAAGAAATCAGCCGGCGCTGCCAGTGCATCAGC‑TGCTCAGGTCGCGGCCATTGTGA‑CTGATGCAACTGACTCAGCACGCGCCGCCAGCACGTCCGCCGGACAGGCTGCATCGTCAGCTCAGAAAGCGTCCTCAGGAGCAGAAGCGGCCTCAGCAAAGGCCACTGCAGcgg                   >  2:73486/8‑249 (MQ=255)                                                                             gaggtgcTGCGTCGTCTTTAACTGATGGTGGAAGAGGTGGCGCGTAACGCGTCCGTGGTGGCACAGAGTACGGCAGACGCGAAGAAATCAGCCGGCGATGCCAGTGCATCAGC‑TGCTCAGGTCGCGGCCCTTGTGA‑CTGATGCAACGGACTCAGCACGCGCCGCCAGCACTTCCGCCGGACAGGCTGCATCGTCAGCTCAGGAAGCGTCCTCCGGCGCAGAAGCGGCATCAGCAAAGGCCACTGAAGcgga                  <  1:120666/245‑4 (MQ=255)                                                                                    ggcgtcgtcttGAACTGATGGTGGAAGAGGTGGCGCGTAACGCGTCCGTGGTGGCACAGAGTACGGCAGACGCGAAGAAATCAGCCGGCGATGCCAGTGCATCAGC‑TGCTCAGGTCGCGGCCCTTGTGA‑CTGATGCAACTGACTCAGCACGCGCCGCCAGCACGTCCGCCGGACAGGCTGCATCGTCAGCTCAGGAAGCGTCCTCCGGCGCAGAAGCGGCATCAGCAAAGGCCACTGAAGcggaaaaaagt           <  2:104673/242‑11 (MQ=255)                                                                                              tGAACTGATGGTGGAAGAGGTGGCGCGTAACGCGTCCGTGGTGTCACAGAGTACGGCAGACGCGAAGAAAGCAGCCGGCGATGCCAGTGCATCAGC‑TGCTCAGGTCGCGGCCC‑TGGGGTCTGATGCAACTGACTCAGCCCGCGCCGCCAGCACGTCCGCGGGACAGGCTGCAGCGTCAGCGCAGGAAGCGTCCTACGGCGCATAAGCGGCATCAGCAAAGGCCACTGAAGctgaaaatagtgccgcagcc  <  2:238391/250‑20 (MQ=255)                                                                                                                                                                                     ||                                                                                                                                                                    TACCGTGTATGAAGATTCTCAACCCGGTACGCTGAATGATTTTCTCGGTGCCATGACGGAGGATGATGCCCGTCCGGAGGCACTGCGCCGTTTTGAACTGATGGTGGAAGAGGTGGCGCGTAACGCGTCCGCGGTGGCACAGAACACGGCAGCCGCGAAGAAGTCAGCCAGTGATGCCAGCACATCAGC‑CCGTGAGGCGGCAACCCATGCGG‑CTGATGCTGCGGACTCAGCACGCGCAGCCAGCACGTCAGCCGGACAGGCCGCGTCGTCGGCTCAGTCAGCGTCTTCCAGCGCAGGAACGGCATCAACAAAGGCCACTGAAGCATCAAAAAGTGCTGCCGCT  >  NC_000913/1429273‑1429615

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 12 ≤ ATCG/ATCG < 14 ≤ ATCG/ATCG < 32 ≤ ATCG/ATCG < 38 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑