Predicted mutation
evidence	seq id	position	mutation	annotation	gene	description
RA	W3110S.gb	2,074,177	G→A	V168I (GTC→ATC)	flu →	antigen 43 (Ag43) phase‑variable biofilm formation autotransporter

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	W3110S.gb	2,074,177	0	G	A	100.0%	103.5 / NA	35	V168I (GTC→ATC)	flu	antigen 43 (Ag43) phase‑variable biofilm formation autotransporter
Reads supporting (aligned to +/- strand):  ref base G (0/0);  new base A (15/20);  total (15/20)

AACACCACGCTGAATGGTGGCGAACAGTGGATGCATGAGGGGGCGATAGCCACAGGAACCGTCATTAATGATAAGGGCTGGCAGGTCGTCAAGCCCGGTACAGTGGCAACGGATACCGTTGTTAATAC  >  W3110S.gb/2074117‑2074244                                                             |                                                                    aaCACCACGCTGAATGGTGGCGAATAGTGGATGCATGAGGGGGCGATAGCCACAGGAACCATCATTAATGa                                                           <  1:3880816/71‑1 (MQ=255) aaCACCACGCTGAATGGTGGCGAATAGTGGATGCATGAGGGGGCGATAGCCACAGGAACCATCATTAATGa                                                           <  1:2607573/71‑1 (MQ=255)  acacCACGCTGAATGGTGGCGAATAGTGGATGCATGAGGGGGCGATAGCCACAGGAACCATCAtt                                                                <  1:722630/65‑1 (MQ=255)       acGCTGAATGGTGGCGAATAGTGGATGCATGAGGGGGCGATAGCCACAGGAACCATCATTAATGATAAggg                                                     >  1:3353554/1‑71 (MQ=255)       acGCTGAATGGTGGCGAATAGTGGATGCATGAGGGGGCGATAGCCACAGGAACCATCATTAATGATAAggg                                                     >  1:4365567/1‑71 (MQ=255)                 gtggCGAATAGTGTATGCATGAGGGGGCGATAGCCACAGGAACCATCATTAATGATAAGGGCTGGCAGgtc                                           >  1:1464507/1‑71 (MQ=255)                 gtggCGAATAGTGGATGCATGAGGGGGCGATAGCCACAGGAACCATCATTAATGATAAGGGCTGGCAGgtc                                           >  1:941190/1‑71 (MQ=255)                 gtggCGAATAGTGGATGCATGAGGGGGCGATAGCCACAGGAACCATCATTAATGATAAGGGCTGGCAGgtc                                           >  1:2754740/1‑71 (MQ=255)                 gtggCGAATAGTGGATGCATGAGGGGGCGATAGCCACAGGAACCATCATTAATGATAAGGGCTGGCAGgtc                                           >  1:238156/1‑71 (MQ=255)                     cGAATAGTGGATGCATGAGGGGGCGATAGCCACAGGAACCATCATTAATGATAAGGGCTGGCAGGTCGTCa                                       <  1:2512666/71‑1 (MQ=255)                           gTGGATGCATGAGGGGGCGATAGCCACAGGAACCATCATTAATGATAAGGGCTGGCAGGTCGTCAAGCCCg                                 >  1:1481582/1‑71 (MQ=255)                             ggATGCATGAGGGGGCGATAGCCACAGGAACCATCATTAATGATAAGGGCTGGCAGGTCGTCAAGCCCgg                                >  1:3980277/1‑70 (MQ=255)                              gATGCATGAGGGGGCGATAGCCACAGGAACCATCATTAATGATAAGGGCTGGCAGGTCGTCAAGCCCGGTa                              >  1:323961/1‑71 (MQ=255)                              gATGCATGAGGGGGCGATAGCCACAGGAACCATCATTAATGATAAGGGCTGGCAGGTCGTCAAGCCCGGTa                              >  1:3162738/1‑71 (MQ=255)                              gATGCATGAGGGGGCGATAGCCACAGGAACCATCATTAATGATAAGGGCTGGCAGGTCGTCAAGCCCGGTa                              >  1:3596782/1‑71 (MQ=255)                              gATGCATGAGGGGGCGATAGCCACAGGAACCATCATTAATGATAAGGGCTGGCAGGTCGTCAAGCCCGGTa                              >  1:1075018/1‑71 (MQ=255)                                tGCATGAGGGGGCGATAGCCACAGGAACCATCATTAATGATAAGGGCTGGCAGGTCGTCAAGCCCGGTAc                             <  1:2404679/70‑1 (MQ=255)                                tGCATGAGGGGGCGATAGCCACAGGAACCATCATTAATGATAAGGGCTGGCAGGTCGTCAAGCCCGGTAc                             <  1:1577675/70‑1 (MQ=255)                                      aGGGGGCGATAGCCACAGGAACCATCATTAATGATa                                                         >  1:2745334/1‑36 (MQ=255)                                      aGGGGGCGATAGCCACAGGAACCATCATTAATGATAAGGGCTGGCAGGTCGTCAAGCCCGGTACAGTgac                       <  1:3896313/70‑3 (MQ=255)                                      aGGGGGCGATAGCCACAGGAACCATCATTAATGATAAGGGCTGGCAGGTCGTCAAGCCCGGTACAGTGGc                       <  1:1450513/70‑1 (MQ=255)                                      aGGGGGCGATAGCCACAGGAACCATCATTAATGATAAGGGCTGGCAGGTCGTCAAGCCAGGTACAGTGGc                       <  1:1638783/70‑1 (MQ=255)                                         gggCGATAGCCACAGGAACCATCATTAATGATAAGGGCTGGCAGGTCGTCAAGCCCGGTACAGTGGCAACg                   <  1:4679219/71‑1 (MQ=255)                                           gCGATAGCCACAGGAACCATCATTAATGATAAGGGCTGGCAGGTCGTCAAGCCCGGTACAGTGGCAACGGa                 <  1:2405019/71‑1 (MQ=255)                                               tAGCCACAGGAACCATCATTAATGATAAGGGCTTGCAGGTCGTCAAGCCCGGTACAGTGGCAACGGa                 <  1:3665323/67‑1 (MQ=255)                                                aGCCACAGGAACCATCATTAATGATAAGGGCTGGCAGGTCGTCAAGCCCGGTACAGTGGCAACGGATACCg            >  1:1735610/1‑71 (MQ=255)                                                 gCCACAGGAACCATCATTAATGATAAGGGCTGGCAGGTCGTCAAGCCCGGTACAGTGGCAACGGATACCg            <  1:2810117/70‑1 (MQ=255)                                                 gCCACAGGAACCATCATTAATGATAAGGGCTGGCAGGTCGTCAAGCCCGGTACAGTGGCAACGGATACCg            <  1:1944427/70‑1 (MQ=255)                                                   cacaGGAACCATCATTAATGATAAGGGCTGGCAGGTCGTCAAGCCCGGTACAGTGGCAACGGATACCgttg         <  1:4418257/71‑1 (MQ=255)                                                   cacaGGAACCATCATTAATGATAAGGGCTGGCAGGTCGTCAAGCCCGGTACAGTGGCAACGGATACCgttg         <  1:966297/71‑1 (MQ=255)                                                     caGGAACCATCATTAATGATAAGGGCTGGCAGGTCGTCAAGCCCGGTACAGTGGCAACGGATACCgttgtt       <  1:3486843/71‑1 (MQ=255)                                                     caGGAACCATCATTAATGATAAGGGCTGGCAGGTCGTCAAGCCCGGTACAGTGGCAACGGATACCgttgtt       <  1:2258978/71‑1 (MQ=255)                                                     caGGAACCATCATTAATGATAAGGGCTGGCAGGTCGTCAAGCCCGGTACAGTGGCAACGGATACCgttgtt       <  1:996012/71‑1 (MQ=255)                                                      aGGAACCATCATTAATGATAAGGGCTGGCAGGTCGTCAAGCCCGGTACAGTGGCAACGGATACCGTTGTTa      <  1:1775269/71‑1 (MQ=255)                                                          aCCATCATTAATGATAAGGGCTGGCAGGTCGTCAAGCCCGGTACAGTGGCAACGGATACCGTTGTTAATAc  >  1:2664699/1‑71 (MQ=255)                                                             |                                                                    AACACCACGCTGAATGGTGGCGAACAGTGGATGCATGAGGGGGCGATAGCCACAGGAACCGTCATTAATGATAAGGGCTGGCAGGTCGTCAAGCCCGGTACAGTGGCAACGGATACCGTTGTTAATAC  >  W3110S.gb/2074117‑2074244

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 21 ≤ ATCG/ATCG < 32 ≤ ATCG/ATCG < 36 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑