Predicted mutation
evidence	seq id	position	mutation	annotation	gene	description
RA	NC_000913	2,073,667	T→C	V710A (GTC→GCC)	flu →	CP4‑44 prophage; self recognizing antigen 43 (Ag43) autotransporter

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NC_000913	2,073,667	0	T	C	100.0%	71.9 / NA	22	V710A (GTC→GCC)	flu	CP4‑44 prophage; self recognizing antigen 43 (Ag43) autotransporter
Reads supporting (aligned to +/- strand):  ref base T (0/0);  new base C (9/13);  total (9/13)

GGTGCCACCACGGAGGAAGGGGCCTTTGTCCAGGGGAACAGGCTGCAGGCCGGTGCCTTTAACTACTCCCTCAACCGGGACAGTGATGAGAGCTGGTATCTGCGCAGTGAAAATGCTTATCGTGCAGAAGTCCCCCTGTATGCCTCCATGCTGACACAGGCAATGGACTATGACCGGATTGTGGCAGGCTCCCGCAGCCATCAGACCGGTGTAAATGGTGAAAACAACAGCGTCCGTCTCAGCATTCAGGGC  >  NC_000913/2073537‑2073788                                                                                                                                   |                                                                                                                          ggTGCCACCACGGAGGAAGGGGCCTTTGTCCAGGGGAACAGGCTGCAGGCCGGTGCCTTTAACTACTCCCTCAACCGGGACAGTGATGAGAGCTGGTATCTGCGCAGTGAAAATGCTTATCGTGCAGAAGccc                                                                                                                         <  1:599109/133‑1 (MQ=255)   tGCCACCACGGAGGAAGGGGCCTTTGTCCAGGGGAACAGGCTGCAGGCCGGTGCCTTTAACTACTCCCTCAACCGGGACAGTGATGAGAGCTGGTATCTGCGCAGTGAAAATGCTTATCGTGCAGAAGCcccc                                                                                                                       <  2:307/133‑1 (MQ=255)   tGCCACCACGGAGGAAGGGGCCTTTGTCCAGGGGAACAGGCTGCAGGCCGGTGCCTTTAACTACTCCCTCAACCGGGACAGTGATGAGAGCGGGTATCTGGGCAGTGAGAATGCTTATCGTGCAGAAGCcccc                                                                                                                       >  2:189311/1‑133 (MQ=255)    gCCACCACGGAGGAAGGGGCCTTTGTCCAGGGGAACAGGCTGCAGGCCGGTGCCTTTAACTACTCCCTCAACCGGGACAGTGATGAGAGCTGGTATCTGCGCAGTGAAAATGCTTATCGTGCAGAAGcccccc                                                                                                                      >  2:99656/1‑133 (MQ=255)        ccacGGAGGAAGGGGCCTTTGTCCAGGGGAACAGGCTGCAGGCCGGTGCCTTTAACTACTCCCTCAACCGGGACAGTGATGAGAGCTGGTATCTGCGCAGTGAAAATGCTTATCGTGCAGAAGCCCCCCTGTa                                                                                                                  <  1:99656/133‑1 (MQ=255)        ccacGGAGGAAGGGGCCTTTGTCCAGGGGAACAGGCTGCAGGCCGGTGCCTTTAACTACTCCCTCAACCGGGACAGTGATGAGAGCTGGTATCTGCGCAGTGAAAATGCTTATCGTGCAGAAGCCCCCCTGTa                                                                                                                  <  1:605269/133‑1 (MQ=255)                   ggggCCTTTGTCCAGGGGAACAGGCTGCAGGCCGGTGCCTTTAACTACTCCCTCAACCGGGACAGTGATGAGAGCTGGTATCTGCGCAGTGAAAATGCTTATCGTGCAGAAGCCCCCCTGTATGCCTCCATGc                                                                                                       >  1:44341/1‑133 (MQ=255)                    gggCCTTTGTCCAGGGGAACAGGCTGCAGGCCGGTGCCTTTAACTACTCCCTCAACCGGGACAGTGATGAGAGCTGGTATCTGCGCAGTGAAAATGCTTATCGTGCAGAAGCCCCCCTGTATGCCTCCATGCt                                                                                                      >  1:117448/1‑133 (MQ=255)                         tttGTCCAGGGGAACAGGCTGCAGGCCGGTGCCTTTAACTACTCCCTCAACCGGGACAGTGATGAGAGCTGGTATCTGCGCAGTGAAAATGCTTATCGTGCAGAAGCCCCCCTGTATGCCTCCATGCTGacac                                                                                                 <  2:44341/133‑1 (MQ=255)                          ttGTCCAGGGGAACAGGCTGCAGGCCGGTGCCTTTAACTACTCCCTCAACCGGGACAGTGATGAGAGCTGGTATCTGCGCAGTGAAAATGCTTATCGTGCAGAAGCCCCCCTGTATGCCTCCATGCTGAcaca                                                                                                >  2:414438/1‑133 (MQ=255)                          ttGTCCAGGGGAACAGGCTGCAGGCCGGTGCCTTTAACTACTCCCTCAACCGGGACAGTGATGAGAGCTGGTATCTGCGCAGTGAAAATGCTTATCGTGCAGAAGCCCCCCTGTATGCCTCCATGCTGAcaca                                                                                                <  2:117448/133‑1 (MQ=255)                                  gggAACAGGCTGCAGGCCGGTGCCTTTAACTACTCCCTCAACCGGGACAGTGATGAGAGCTGGTATCTGCGCAGTGAAAATGCTTATCGTGCAGAAGCCCCCCTGTATGCCTCCATGCTGACACAGGCAATgg                                                                                        >  2:477660/1‑133 (MQ=255)                                     aaCAGGCTGCAGGCCGGTGCCTTTAACTACTCCCTCAACCGGGACAGTGATGAGAGCTGGTATCTGCGCAGTGAAAATGCTTATCGTGCAGAAGCCCCCCTGTATGTCTCCATGCTGACACAGGCAATGGACt                                                                                     >  2:331407/1‑133 (MQ=255)                                                      tGCCTTTAACTACTCCCTCAACCGGGACAGTGATGAGAGCTGGTATCTGCGCAGTGAAAATGCTTATCGTGCAGAAGCCCCCCTGTATGTCTCCATGCTGACACAGGCAATGGACTATGACCGGATTGTGGCa                                                                    <  1:331407/133‑1 (MQ=255)                                                           ttAACTACCCCCTCACCCCGGACAGTGATGAGAGCTGGTATCTGCGCAGTGAAAATGCTTATCGTGCAGAAGCCCCCCTGTATGCCTCCATGCTGACACAGGCAATGGACTATGACCGGATTGTGGCAGGCTc                                                               <  1:189311/133‑1 (MQ=255)                                                                tactCCCTCAACCGGGACAGTGATGAGAGCTGGTATCTGCGCAGTGAAAATGCTTATCGTGCAGAAGCCCCCCTGTATGCCTCCATGCTGACACAGGCAATGGACTATGACCGGATTGTGGCAGGCTCCCGCa                                                          <  1:477660/133‑1 (MQ=255)                                                                         aaCCGGGACAGTGATGAGAGCTGGTATCTGCGCAGTGAAAATGCTTATCGTGCAGAAGCCCCCCTGTATGCCTCCATGCTGACACAGGCAATGGACTATGACCGGATTGTGGCAGGCTCCCGCAGCCATCAGa                                                 >  2:381113/1‑133 (MQ=255)                                                                         aaCCGGGACAGTGATGAGAGCTGGTATCTGCGCAGTGAAAATGCTTATCGTGCAGAAGCCCCCCTGTATGCCTCCATGCTGACACAGGCAATGGACTATGACCGGATTGTGGCAGGCTCCCGCAGCCATCAGa                                                 <  1:500722/133‑1 (MQ=255)                                                                         aaCCGGGACAGTGATGAGAGCTGGTATCTGCGCAGTGAAAATGCTTATCGTGCAGAAGCCCCCCTGTATGCCTCCATGCTGACACAGGAAATGGACTATGACCGGATTGTGGCAGGCTCCCGCAGCCATCAGa                                                 <  1:414438/133‑1 (MQ=255)                                                                          aCCGGGACAGTGATGAGAGCTGGTATCTGCGCAGTGAAAATGCTTATCGTGCAGAAGCCCCCCTGTATGCCTCCATGCTGACACAGGCAATGGACTATGACCGGATTGTGGCAGGCTCCCGCAGCCATCAGAc                                                >  1:587569/1‑133 (MQ=255)                                                                                         agagCTGGTATCTGCGCAGTGAAAATGCTTATCGTGCAGAAGCCCCCCTGTATGCCTCCATGCTGACACAGGCAATGGACTATGACCGGATTGTGGCAGGCTCCCGCAGCTATCCGATCGGTGTAAATGGTGa                                 >  1:218675/1‑133 (MQ=255)                                                                                                      gcgcAGTGAAAATGCTTATCGTGCAGAAGCCCCCCTGTATGCCTCCATGCTGACACAGGCAATGGACTATGACCGGATTGTGGCAGGCTCCCGCAGCCATCAGACCGGTGTAAATGGTGAAAACAACAGcgtc                    <  2:587569/133‑1 (MQ=255)                                                                                                                  tGCTTATCGTGCAGACGCCCCCCTGTATGCCTTCATGCTGAAACAGGCAATGGACTATGACCGGATTGTGGCAGGCTCCCGCAGCCATCAGACCGGTGTAAATGGTGAAAACAACAGCGTCCGTCTCAGCAtt        <  2:218675/133‑1 (MQ=255)                                                                                                                        tCGTGCAGAAGCCCCCCTGTATGCCTCCATGCTGACACAGGCAATGGACTATGACCGGATTGTGGCAGGCTCCCGCAGCCATCAGACCGGTGTAAATGGTGAAAACAACAGCGTCCGTCTCAGCATTCAGGGc  <  1:381113/133‑1 (MQ=255)                                                                                                                                   |                                                                                                                          GGTGCCACCACGGAGGAAGGGGCCTTTGTCCAGGGGAACAGGCTGCAGGCCGGTGCCTTTAACTACTCCCTCAACCGGGACAGTGATGAGAGCTGGTATCTGCGCAGTGAAAATGCTTATCGTGCAGAAGTCCCCCTGTATGCCTCCATGCTGACACAGGCAATGGACTATGACCGGATTGTGGCAGGCTCCCGCAGCCATCAGACCGGTGTAAATGGTGAAAACAACAGCGTCCGTCTCAGCATTCAGGGC  >  NC_000913/2073537‑2073788

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 15 ≤ ATCG/ATCG < 27 ≤ ATCG/ATCG < 33 ≤ ATCG/ATCG < 40 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑