Predicted mutation
evidence	seq id	position	mutation	freq	annotation	gene	description
RA	CP009273	2,065,990	G→A	20.0%	G324D (GGC→GAC)	flu →	CP4‑44 prophage; antigen 43 (Ag43) phase‑variable biofilm formation autotransporter

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	CP009273	2,065,990	0	G	A	20.0%	33.3 / 5.8	20	G324D (GGC→GAC)	flu	CP4‑44 prophage; antigen 43 (Ag43) phase‑variable biofilm formation autotransporter
Reads supporting (aligned to +/- strand):  ref base G (9/7);  new base A (2/2);  total (11/9)
Fisher's exact test for biased strand distribution p-value = 1.00e+00
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 6.70e-01

GCGGCGACCAGACTGTACATGGTCACGCACTGGATACCACGCTGAATGGGGGATACCAGTATGTGCACAACGGCGGTACAGCGTCTGACACTGTTGTGAACAGTGACGGCTGGCAGATTGTCAAAAACGGGGGTGTGGCCGGGAATACCACCGTTAATCAGAAGGGCAGACTGCAGGTGGACGCCGGTGGTACAGCCACGAATGTCACCCTGAAGCAGGGCGGCGCACTGGTTACCAGTACGGCTGCAACCGTTACCGGCATAAACCGCCTGGGAGCATTCTCTGTTGTGGAGGGTAAAGCTGATAATGTCGTACTGGAAAATGGCGGACGCCTGGATGTGCTGACCGGACACACAGCCACTAATACCCGCGTGGATGATGGCGGAACGCTGGATGTCCGCAACGGTGGCACCGCCACCACCGTATCCATGGGAAATGGCGGTGTACTGCTGGCCGATTCCGGTGCCGCTGTCAGTGGTACCCGGAGCGACGGAAA  >  CP009273/2065732‑2066227                                                                                                                                                                                                                                                                   |                                                                                                                                                                                                                                              gcggcgACCAGACTGTACATGGTCACGCACTGGATACCACGCTGAATGGGGGATACCAGTATGTGCACAACGGCGGTACAGCGTCTGACACTGTTGTGAACAGTGACGGCTGGCAGATTGTCAAAAACGGGGGTGTGGCCGGGAATACCACCGTTAATCAGAAGGGCAGACTGCAGGTGGACGCCGGTGGTACAGCCACGAATGTCACCCTGAAGCAGGGCGGCGCACTGATTACCAGTACGGCTGCAACCGTTACCGGCATAAACCGCCggggg                                                                                                                                                                                                                               >  1:16900/1‑274 (MQ=255)        ccaaccggTACAGGGGCACGCATGTGATACCACGCTGATGGGGGGATGCCCGTTTGTGCTCCAGTGCGTTTCAGCGTCTTACACTGTTTTTAACAGTGACGGCTGGCAGCTTGTCAAAAACGGGGGTGTGGCCGGGAATACCACCGTTAATCAGAAGGGCAGACTGCAGGTGGACGCCGGTGGTACAGCCACGAATGTCACCCTGAAGCAGGGCGGCGCACTGGTTACCAGTACGGCTGCAACCGTTACCGGCATAAACCGCCTGGGAGCATtct                                                                                                                                                                                                                        <  2:16900/268‑1 (MQ=255)                     ggTCACGCACTGGATACCACGCTGAATGGGGGATACCAGTATGTGCACAACGGCGGTACAGCGTCTGACACTGTTGTGAACAGTGACGGCTGGCAGATTGTCAAAAACGGGGGTGTGGCCGGGAATACCACCGTTAATCAGAAGGGCAGACTGCAGGTGGACGCCGGTGGTACAGCCACGAATGTCACCCTGAAGCAGGGCGGCGCCCTGGTTACCAGTACGGCTGCAACCGTTACCGACATAAACCGCCTGGGAGCAATCTCTGTTGTGAAggg                                                                                                                                                                                                           >  1:295370/1‑275 (MQ=255)                                                       aCCAGTATGTGCACAACGGCGGTACAGCGTCTGACACTGTTGTGAACAGTGACGGCTGGCAGATTGTCAAAAACGGGGGTGTGGCCGGGAATACCACCGTTAATCAGAAGGGCAGACTGCAGGTGGACGCCGGTGGTACAGCCACGAATGTCACCCTGAAGCAGGGCGGCGCACTGGCTACCAGTACGGCTGCAACCGTTACCGGCATAAACCGCCTGGGAGCa                                                                                                                                                                                                                            >  1:242724/1‑224 (MQ=255)                                                                                    tCTGACACTGTTGTGAACAGTGACGGCTGGCAGATTGTCAAAAACGGGGGTGGGGCCGGGAATACCACCGTTAATCAGAAGGGCAGACTGCAGGTGGACGCCGGTGGTACAGCCACGAATGTCACCCTGAAGCAGGGCGGCGCACTGGTTACCCGTACGGCTGCAACCGTTACCGGCATAAACCGCCGGGGCGCATGCTCAGTTGTGGAGGGTAAAGCTGATAATGTCGGACTGGAAAAGGGCGGAAGCGTGGAGGGGCAGACGGGGcaaacaac                                                                                                                                            >  1:161799/1‑273 (MQ=255)                                                                                                                gggagggtggagaaaaAGGGGGNGAGGCCGAGAATACCACCGGTGATACGAAGGGCAGGCTGTAGGTGGACGCCGATGGTACAGCCAAGAATGTCACCCTGAAGCAGGGCGGCGCACTGGTTACCAGTACGGCTGCAACCGTTACCGACATAAACCGCCTGGGAGCATTCTCTGTTGTGGAGGGTAAAGCTGATAATGTCGTACTGGAAAATGGCGGACGCCTGGATGTGCTGACCGGACACACAGCCACTAATACCCGCGTGGATCATGGCg                                                                                                                  <  2:295359/261‑1 (MQ=255)                                                                                                                                   gggTGTGGCCGGGAATACCACCGTTAATCAGAAGGGCAGACTGCAGGTGGACGCCGGTGGTACAGCCACGAATGTCACCCTGAAGCAGGGCGGCGCACTGGTTACCAGTACGGCTGCAACCGTTACCGACATAAACCGCCTGGGAGCATTCTCTGTTGTGGAGGGTAAAGCTGATAATg                                                                                                                                                                                             >  1:212902/1‑179 (MQ=255)                                                                                                                                   gggTGTGGCCGGGAATACCACCGTTAATCAGAAGGGCAGACTGCAGGTGGACGCCGGTGGTACAGCCACGAATGTCACCCTGAAGCAGGGCGGCGCACTGGTTACCAGTACGGCTGCAACCGTTACCGACATAAACCGCCTGGGAGCATTCTCTGTTGTGGAGGGTAAAGCTGATAATg                                                                                                                                                                                             <  2:212893/179‑1 (MQ=255)                                                                                                                                       cttctcGGGAATACCACCGTGAATCAGAAGGGCAGCCTGCACGTGGACGCCGGTGGTCCAGCCACGAAGGTCACCCTGAAGCAGGGCGTCGCACTGGTTACCAGTACGGCTGCAACCGTTACCGGCATAAACCGCCTGGGGGCATTCTCTGTTGTGGAGGGTAAAGCTGATAATGTCGTACTGGAAAATGGCGGACGCCTGGATGTGCTGACCGGACACACAGCCACTAATACCCGCGTGGATGATGGCGGAACGCTGGATGTCCGCAACGGTg                                                                                          <  2:161795/269‑1 (MQ=255)                                                                                                                                                                                                                              ggcgCTCTGGTANCCAGGACGGATGCAACCTGTACCGGCATAAACCGCCTGGGAGCATTCGCTGTTGGGGAGGGTAAAGCTGATAATGTCGTACTGGAAAAGGGCGGACGCCTGGATGTGCTGACCGGACACACAGCCACTAATACCCGCGTGGATGATGGCGGAACGCTGGATGTCCGCAACGGTGGCACCGCCACCACCGTATCCATGGGAAATGGCGGTGTACTGCTGGCCGATTCCGGTGCCGCTGTCAGTGGTACCCGGAGCGACGGa    <  2:375679/273‑1 (MQ=255)                                                                                                                                                                                                                                cgcACTGGTTACCAGTACGGCTGCAACCGTTACCGGCATAAACCACCTGGGAGCATTCTCTGTTGTGGAGGGTAAAGCTGATAATGTCGTACTGGAAAATGGCGGACGCCTGGATGTGCTGACCGGACACACAGCCACTAATACCCGCGTGGAGGATGGCGGAACGCTGGATGTCCGCAACGGNGGCACCGCCACAACCGTATCCATGGGAAATGGCGGTGTACTGCTGGCCGATTCCGGTGCCGCTGTCAGTGGTAACCGGAGCGACGGaaa  >  1:375691/1‑273 (MQ=255)                                                                                                                                                                                                                                  cACTGGTTACCAGTACGGCTGCAACCGTTACCGGCATAAACCGCCTGGGAGCa                                                                                                                                                                                                                            >  1:110579/1‑53 (MQ=255)                                                                                                                                                                                                                                      ggTTACCAGTACGGCTGCAACCGTTACCGGCATAAACCGCCTGGGAGCATtct                                                                                                                                                                                                                        <  2:110578/53‑1 (MQ=255)                                                                                                                                                                                                                                               tACGGCTGCAACCGTTACCGGCATAATCCGCCTGAGAGCa                                                                                                                                                                                                                            >  1:351024/1‑40 (MQ=255)                                                                                                                                                                                                                                                 cGGCTGCAACCGTTACCGGCATAAACCGCCTGGGAGCATTCTCTGTTGTGGAg                                                                                                                                                                                                             >  1:147392/1‑53 (MQ=255)                                                                                                                                                                                                                                                   gCTGCAACCGGTACCGGCATAAACCGCCTGGGAGCATtct                                                                                                                                                                                                                        <  2:351012/40‑1 (MQ=255)                                                                                                                                                                                                                                                     tGCAACCGTTACCGGCATAAACCGCCTGGGAGCATTCTCTGTTGTGGAGGGTa                                                                                                                                                                                                         <  2:147390/53‑1 (MQ=255)                                                                                                                                                                                                                                                      gCAACCGTTACCGGCATAAACCGCCTGGGAGCATTCTCTGTTGTGGAGGGTAAAGCTGATAATGTCGTACTGGAAAATGGCGGACGCCTGGATGTGCTGACCGGACACACAGCCACTAATACCCGCGTGGATGATGGCGGAACGCTGGATGTCCGCAACGGTGGCAcc                                                                                     >  2:257430/1‑168 (MQ=255)                                                                                                                                                                                                                                                          ccGTTACCGGCATAAACCGCCTGGGAGCATTCTCTGTTGTGGAGGGTAAAGCTGATAATGTCGTACTGGAAAATGGCGGACGCCTGGATGTGCTGACCGGACACACAGCCACTAATACCCGCGTGGATGATGGCGGAACGCTGGATGTCCGCAACGGTGGCACCGcca                                                                                 <  1:257439/168‑1 (MQ=255)                                                                                                                                                                                                                                                              tACCGGCATAAACCGCCTGGGAGCATTCTCTGTTGTGGAGGGTAAAGCTGATAATGTCGTACTGGAAAATGGCGGACGCCTGGATGTGCTGACCGGaca                                                                                                                                                  >  1:11099/1‑99 (MQ=255)                                                                                                                                                                                                                                                                  ggCATAAACCGCCTGGGAGCATTCTCTGTTGTGGAGGGTAAAGCTGATAATGTCGTACTGGAAAATGGCGGACGCCTGGATGTGCTGACCGGAcacaca                                                                                                                                              <  2:11099/99‑1 (MQ=255)                                                                                                                                                                                                                                                                   |                                                                                                                                                                                                                                              GCGGCGACCAGACTGTACATGGTCACGCACTGGATACCACGCTGAATGGGGGATACCAGTATGTGCACAACGGCGGTACAGCGTCTGACACTGTTGTGAACAGTGACGGCTGGCAGATTGTCAAAAACGGGGGTGTGGCCGGGAATACCACCGTTAATCAGAAGGGCAGACTGCAGGTGGACGCCGGTGGTACAGCCACGAATGTCACCCTGAAGCAGGGCGGCGCACTGGTTACCAGTACGGCTGCAACCGTTACCGGCATAAACCGCCTGGGAGCATTCTCTGTTGTGGAGGGTAAAGCTGATAATGTCGTACTGGAAAATGGCGGACGCCTGGATGTGCTGACCGGACACACAGCCACTAATACCCGCGTGGATGATGGCGGAACGCTGGATGTCCGCAACGGTGGCACCGCCACCACCGTATCCATGGGAAATGGCGGTGTACTGCTGGCCGATTCCGGTGCCGCTGTCAGTGGTACCCGGAGCGACGGAAA  >  CP009273/2065732‑2066227

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 9 ≤ ATCG/ATCG < 11 ≤ ATCG/ATCG < 30 ≤ ATCG/ATCG < 38 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑