Predicted mutation
evidence	seq id	position	mutation	annotation	gene	description
RA	NC_000913	2,073,616	A→G	D693G (GAC→GGC)	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
*	NC_000913	2,073,616	0	A	G	100.0%	199.3 / NA	52	D693G (GAC→GGC)	flu	CP4‑44 prophage, antigen 43 (Ag43) phase‑variable biofilm formation autotransporter
Reads supporting (aligned to +/- strand):  ref base A (0/0);  new base G (28/24);  total (28/24)

TGCGTCGGGGCTGGCGACCAGCGGTAAGGGTATTCAGGTGGTGGAAGCCATTAACGGTGCCACCACGGAGGAAGGGGCCTTTGTCCAGGGGAACAGGCTGCAGGCCGGTGCCTTTAACTACTCCCTCAACCGGGACAGTGATGAGAGCTGGTATCTGCGCAGTGAAAATGCTTATCGTGCAGAAGTCCCCCTGTATGCCTCCATGCTGACACAGGCAATGGACTATGACCGGATTGTGGCAGGCTCCCGCAGCCATCAGACCGGTGTAA  >  NC_000913/2073482‑2073750                                                                                                                                       |                                                                                                                                       tGCGTCGGGGCTGGCGACCAGCGGTAAGGGTATTCAGGTGGTGGAAGCCATTAACGGTGCCACCACGGAGGAAGGGGCCTTTGTCCAGGGGAACAGGCTGCAGGCCGGTGCCTTTAACTACTCCCTCAACCGGGGCAGt                                                                                                                                    >  2:985133/1‑139 (MQ=255)  gCGTCGGGGCTGGCGACCAGCGGTAAGGGTATTCAGGTGGTGGAAGCCATTAACGGTGCCACCACGGAGGAAGGGGCCTTTGTCCAGGGGAACAGGCTGCAGGCCGGTGCCTTTAACTACTCCCTCAACCGGGGCAGtg                                                                                                                                   >  1:1136943/1‑139 (MQ=255)    gTCGGGGCTGGCGACCAGCGGTAAGGGTATTCAGGTGGTGGAAGCCATTAACGGTGCCACCACGGAGGAAGGGGCCTTTGTCCAGGGGAACAGGCTGCAGGCCGGTGCCTTTAACTACTCCCTCAACCGGGGCAGtgat                                                                                                                                 <  1:1320078/139‑1 (MQ=255)           cTGGCGACCAGCGGTAAGGGTATTCAGGTGGTGGAAGCCATTAACGGTGCCACCACGGAGGAAGGGGCCTTTGTCCAGGGGAACAGGCTGCAGGCCGGTGCCTTTAACTACTCCCTCAACCGGGGCAGTGATGAGAGCt                                                                                                                          <  1:50512/139‑1 (MQ=255)             ggCGACCAGCGGTAAGGGTATTCAGGTGGTGGAAGCCATTAACGGTGCCACCACGGAGGAAGGGGCCTTTGTCCAGGGGAACAGGCTGCAGGCCGGTGCCTTTAACTACTCCCTCAACCGGGGCAGTGATGAGAGCTgg                                                                                                                        <  1:21393/139‑1 (MQ=255)                   cAGCGGTAAGGGTATTCAGGTGGTGGAAGCCATTAACGGTGCCACCACGGAGGAAGGGGCCTTTGTCCAGGGGAACAGGCTGCAGGCCGGTGCCTTTAACTACTCCCTCAACCGGGGCAGTGATGAGAGCTGGTATCTg                                                                                                                  <  1:985133/139‑1 (MQ=255)                                aTTCAGGTGGTGGAAGCCATTAACGGTGCCACCACGGAGGAAGGGGCCTTTGTCCAGGGGAACAGGCTGCAGGCCGGTGCCTTTAACTACTCCCTCAACCGGGGCAGtgatga                                                                                                                               <  2:371510/113‑1 (MQ=255)                                aTTCAGGTGGTGGAAGCCATTAACGGTGCCACCACGGAGGAAGGGGCCTTTGTCCAGGGGAACAGGCTGCAGGCCGGTGCCTTTAACTACTCCCTCAACCGGGGCAGtgatga                                                                                                                               >  1:371510/1‑113 (MQ=255)                                aTTCAGGTGGTGGAAGCCATTAACGGTGCCACCACGGAGGAAGGGGCCTTTGTCCAGGGGAACAGGCTGCAGGCCGGTGCCTTTAACTACTCCCTCAACCGGGGCAGTGATGAGAGCTGGTATCTGCGCAGTGAAAATg                                                                                                     >  1:878786/1‑139 (MQ=255)                                    aGGTGGTGGAAGCCATTAACGGTGCCACCACGGAGGAAGGGGCCTTTGTCCAGGGGAACAGGCTGCAGGCCGGTGCCTTTAACTACTCCCTCAACCGGGGCAGTGATGAGAGCTGGTATCTGCGCAGTGAAAATGCTTa                                                                                                 <  2:1333156/139‑1 (MQ=255)                                        ggtggAAGCCATTAACGGTGCCACCACGGAGGAAGGGGCCTTTGTCCAGGGGAACAGGCTGCAGGCCGGTGCCTTTAACTACTCCCTCAACCGGGGCAGtgat                                                                                                                                 >  2:386224/1‑103 (MQ=255)                                        ggtggAAGCCATTAACGGTGCCACCACGGAGGAAGGGGCCTTTGTCCAGGGGAACAGGCTGCAGGCCGGTGCCTTTAACTACTCCCTCAACCGGGGCAGtgat                                                                                                                                 <  1:386224/103‑1 (MQ=255)                                         gtggAAGCCATTAACGGTGCCACCACGGAGGAAGGGGCCTTTGTCCAGGGGAACAGGCTGCAGGCCGGTGCCTTTAACTACTCCCTCAACCGGGGCAGTGATGAGAGCt                                                                                                                          <  2:207022/109‑1 (MQ=255)                                         gtggAAGCCATTAACGGTGCCACCACGGAGGAAGGGGCCTTTGTCCAGGGGAACAGGCTGCAGGCCGGTGCCTTTAACTACTCCCTCAACCGGGGCAGTGATGAGAGCt                                                                                                                          >  1:207022/1‑109 (MQ=255)                                                  aTTAACGGTGCCACCACGGAGGAAGGGGCCTTTGTCCAGGGGAACAGGCTGCAGGCCGGTGCCTTTAACTACTCCCTCAACCGGGGCAGTGATGAGAGCTGGTATCTGCGCAGTGAAAATGCTTATCGTGCAGAAGTcc                                                                                   <  2:1136943/139‑1 (MQ=255)                                                      aCGGTGCCACCACGGAGGAAGGGGCCTTTGTCCAGGGGAACAGGCTGCAGGCCGGTGCCTTTAACTACTCCCTCAACCGGGGCAGTGATGAGAGCTGGTATCTGCGCAGTGAAAATGCTTATCGTGCAGAAGTCCCCCt                                                                               >  2:1117904/1‑139 (MQ=255)                                                           gCCACCACGGAGGAAGGGGCCTTTGTCCAGGGGAACAGGCTGCAGGCCGGTGCCTTTAACTACTCCCTCAACCGGGGCAGTGATGAGAGCTGGTATCTgcg                                                                                                                <  2:159508/101‑1 (MQ=255)                                                           gCCACCACGGAGGAAGGGGCCTTTGTCCAGGGGAACAGGCTGCAGGCCGGTGCCTTTAACTACTCCCTCAACCGGGGCAGTGATGAGAGCTGGTATCTgcg                                                                                                                >  1:159508/1‑101 (MQ=255)                                                           gCCACCACGGAGGAAGGGGCCTTTGTCCAGGGGAACAGGCTGCAGGCCGGTGCCTTTAACTACTCCCTCAACCGGGGCAGTGATGAGAGCTGGTATCTGCGCAGTGAAAATGCTTATCGTGCAGAAGTCCCCCTGTa                                                                            <  2:1337105/137‑1 (MQ=255)                                                           gCCACCACGGAGGAAGGGGCCTTTGTCCAGGGGAACAGGCTGCAGGCCGGTGCCTTTAACTACTCCCTCAACCGGGGCAGTGATGAGAGCTGGTATCTGCGCAGTGAAAATGCTTATCGTGCAGAAGTCCCCCTGTa                                                                            >  1:1337105/1‑137 (MQ=255)                                                                                tttGTCCAGGGGAACAGGCTGCAGGCCGGTGCCTTTAACTACTCCCTCAACCGGGGCAGTGATGAGAGCTGGTATCTGCGCAGTGAAAATGCTTATCGTGCAGAAGTCCCCCTGTATGCCTCCATGCTGACACAGGCaa                                                     <  1:144161/139‑1 (MQ=255)                                                                                 ttGTCCAGGGGAACAGGCTGCAGGCCGGTGCCTTTAACTACTCCCTCAACCGGGGCAGTGATGAGAGCTGGTATCTGCGCAGTGAAAATGCTTATCGTGCAGAAGTCCCCCTGTATGCCTCCATGCTGACACAGGCAAt                                                    >  2:1189508/1‑139 (MQ=255)                                                                                    tCCAGGGGAACAGGCTGCAGGCCGGTGCCTTTAACTACTCCCTCAACCGGGGCAGTGATGAGAGCTGGTATCTGCGCAGTGAAAATGCTTa                                                                                                 >  2:902926/1‑91 (MQ=255)                                                                                    tCCAGGGGAACAGGCTGCAGGCCGGTGCCTTTAACTACTCCCTCAACCGGGGCAGTGATGAGAGCTGGTATCTGCGCAGTGAAAATGCTTa                                                                                                 <  1:902926/91‑1 (MQ=255)                                                                                              cAGGCTGCAGGCCGGTGCCTTTAACTACTCCCTCAACCGGGGCAGTGATGAGAGCTGGTATCTGCGCAGTGAAAATGCTTATCGTGCAGAAGTCCCCCTGTATGCCTCCATGCTGACACAGGCAATGGACTATGACCgg                                       >  1:1226591/1‑139 (MQ=255)                                                                                              cAGGCTGCAGGCCGGTGCCTTTAACTACTCCCTCAACCGGGGCAGTGATGAGAGCTGGTATCTGCGCAGTGAAAATGCTTATCGTGCAGAAGTCCCCCTGTATGCCTCCATGCTGACACAGGCAATGGACTATGACCgg                                       >  1:186108/1‑139 (MQ=255)                                                                                                   tGCAGGCCGGTGCCTTTAACTACTCCCTCAACCGGGGCAGTGATGAGAGCTGGTATCTGCGCAGTGAAAATGCTTATCGTGc                                                                                           <  2:453814/82‑1 (MQ=255)                                                                                                   tGCAGGCCGGTGCCTTTAACTACTCCCTCAACCGGGGCAGTGATGAGAGCTGGTATCTGCGCAGTGAAAATGCTTATCGTGc                                                                                           >  1:453814/1‑82 (MQ=255)                                                                                                   tGCAGGCCGGTGCCTTTAACTACTCCCTCAACCGGGGCAGTGATGAGAGCTGGTATCTGCGCAGTGAAAATGCTTATCGTGCAGAAGTCCCCCTGTATGCCTCCATGCTGACACAGGCAATGGACTATGACCGGATtgt                                  >  2:590128/1‑139 (MQ=255)                                                                                                     cAGGCCGGTGCCTTTAACTACTCCCTCAACCGGGGCAGtgatga                                                                                                                               >  1:260154/1‑44 (MQ=255)                                                                                                     cAGGCCGGTGCCTTTAACTACTCCCTCAACCGGGGCAGtgatga                                                                                                                               <  2:260154/44‑1 (MQ=255)                                                                                                     cAGGCCGGTGCCTTTAACTACTCCCTCAACCGGGGCAGTGATGAGAGCTGGTATCTGCGCAGTGAAAATGCTTATCGTGCAGAAGTCCCCCTGTATGCCTCCATGCTGacac                                                           >  2:1351632/1‑112 (MQ=255)                                                                                                     cAGGCCGGTGCCTTTAACTACTCCCTCAACCGGGGCAGTGATGAGAGCTGGTATCTGCGCAGTGAAAATGCTTATCGTGCAGAAGTCCCCCTGTATGCCTCCATGCTGacac                                                           <  1:1351632/112‑1 (MQ=255)                                                                                                                       tactCCCTCAACCGGGGCAGTGATGAGAGCTGGTATCTGCGCAGTGAAAATGCTTATCGTGCAGAAGTCCCCCTGTATGCCTCCATGCTGACACAGGCAATGGACTATGACCGGATTGTGGCAGGCTCCCGCAGCCATc              >  1:815924/1‑139 (MQ=255)                                                                                                                         ctCCCTCAACCGGGGCAGTGATGAGAGCTGGTATCTgcg                                                                                                                <  1:168230/39‑1 (MQ=255)                                                                                                                         ctCCCTCAACCGGGGCAGTGATGAGAGCTGGTATCTgcg                                                                                                                >  2:168230/1‑39 (MQ=255)                                                                                                                         ctCCCTCAACCGGGGCAGTGATGAGAGCTGGTATCTGCGCAGTGAAAATGCTTATCGTGCAGAAGTCCCCCTGTATGCCTCCATGCTGacac                                                           >  1:114993/1‑92 (MQ=255)                                                                                                                         ctCCCTCAACCGGGGCAGTGATGAGAGCTGGTATCTGCGCAGTGAAAATGCTTATCGTGCAGAAGTCCCCCTGTATGCCTCCATGCTGacac                                                           <  2:114993/92‑1 (MQ=255)                                                                                                                         ctCCCTCAACCGGGGCAGTGATGAGAGCTGGTATCTGCGCAGTGAAAATGCTTATCGTGCAGAAGTCCCCCTGTATGCCTCCATGCTGACACAGGCAATGGACTATGACCGGATTGTGGCAGGCTCCCGCAGCCATCAg            >  1:1205577/1‑139 (MQ=255)                                                                                                                           cccTCAACCGGGGCAGTGATGGGAGCTGGTATCTGCGCTGTGAAAATGCTTATCGTCCAGAAGTCCCCCTGTATGCTTTCATGCTGACACAGGCAGTGGACTATGACCAGATCGTAGCAGGCTCCCGCAACCATCataa          >  2:951428/1‑136 (MQ=255)                                                                                                                           cccTCAACCGGGGCAGTGATGAGAGCTGGTATCTGCGCAGTGAAAATGCTTATCGTGCAGAAGTCCCCCTGTATGCCTCCATGCTGACACAGGCAATGGACTATGACCGGATTGTGGCAGGCTCCCGCAGCCATCAGAc          <  2:187416/139‑1 (MQ=255)                                                                                                                           cccTCAACCGGGGCAGTGATGAGAGCTGGTATCTGCGCAGTGAAAATGCTTATCGTGCAGAAGTCCCCCTGTATGCCTCCATGCTGACACAGGCAATGGACTATGACCGGATTGTGGCAGGCTCCCGCAGCCATCAGAc          >  2:1348660/1‑139 (MQ=255)                                                                                                                           cccTCAACCGGGGCAGTGATGAGAGCTGGTATCTGCGCAGTGAAAATGCTTATCGTGCAGAAGTCCCCCTGTATGCCTCCATGCTGACACAGGCAATGGACTATGACCGGATTGTGGCAGGCTCCCGCAGCCATCAGAc          >  2:876512/1‑139 (MQ=255)                                                                                                                            ccTCAACCGGGGCAGTGATGAGAGCTGGTATCTGCGCAGTGAAAATGCTTATCGTGCAGAAGTCCCCCTGTATGCCTCCATGCTGACACAGGCAATGGACTATGACCGGATTGTGGCAGGTTCCCGCAGCCATCAGAcc         <  2:815924/139‑1 (MQ=255)                                                                                                                              tCAACCGGGGCAGTGATGAGAGCTGGTATCTGCGCAGTGAAAATGCTTATCGTGCAGAAGTCCCCCTGTATGCCTCCATGCTGACACAGGCAATGGACTATGACCGGATTGTGGCAGGCTCCCGCAGCCATCAGACCgg       >  2:360315/1‑139 (MQ=255)                                                                                                                               cAACCGGGGCAGTGATGAGAGCTGGTATCTGCGCAGTGAAAATGCTTATCGTGCAGAAGTCCCCCTGTATGCCTCCATGCTGACACAGGCAATGGACTATGACCGGATTGTGGCAGGCTCCCGCAGCCATCAg            <  2:509191/133‑1 (MQ=255)                                                                                                                               cAACCGGGGCAGTGATGAGAGCTGGTATCTGCGCAGTGAAAATGCTTATCGTGCAGAAGTCCCCCTGTATGCCTCCATGCTGACACAGGCAATGGACTATGACCGGATTGTGGCAGGCTCCCGCAGCCATCAg            >  1:509191/1‑133 (MQ=255)                                                                                                                               cAACCGGGGCAGTGATGAGAGCTGGTATCTGCGCAGTGAAAATGCTTATCGTGCAGAAGTCCCCCTGTATGCCTCCATGCTGACACAGGCAATGGACTATGACCGGATTGTGGCAGGCTCCCGCAGCCATCAGACCGgt      >  2:1177077/1‑139 (MQ=255)                                                                                                                                   cGGGGCAGTGATGAGAGCTGGTATCTGCGCAGTGAAAATGCTTATCGTGCAGAAGTCCCCCTGTATGCCTCCATGCTGACACAGGCAATGGACTATGACCGGATTGTGGCAGGCTCCCGCAGCCATCAGAc          <  2:823195/131‑1 (MQ=255)                                                                                                                                   cGGGGCAGTGATGAGAGCTGGTATCTGCGCAGTGAAAATGCTTATCGTGCAGAAGTCCCCCTGTATGCCTCCATGCTGACACAGGCAATGGACTATGACCGGATTGTGGCAGGCTCCCGCAGCCATCAGAc          >  1:823195/1‑131 (MQ=255)                                                                                                                                   cGGGGCAGTGATGAGAGCTGGTATCTGCGCAGTGAAAATGCTTATCGTGCAGAAGTCCCCCTGTATGCCTCCATGCTGACACAGGCAATGGACTATGACCGGATTGTGGCAGGCTCCCGCAGCCATCAGACCGGTGTaa  <  2:1226591/139‑1 (MQ=255)                                                                                                                                   cGGGGCAGTGATGAGAGCTGGTATCTGCGCAGTGAAAATGCTTATCGTGCAGAAGTCCCCCTGTATGCCTCCATGCTGACACAGGCAATGGACTATGACCGGATTGTGGCAGGCTCCCGCAGCCATCAGACCGGTGTaa  <  1:1177077/139‑1 (MQ=255)                                                                                                                                       |                                                                                                                                       TGCGTCGGGGCTGGCGACCAGCGGTAAGGGTATTCAGGTGGTGGAAGCCATTAACGGTGCCACCACGGAGGAAGGGGCCTTTGTCCAGGGGAACAGGCTGCAGGCCGGTGCCTTTAACTACTCCCTCAACCGGGACAGTGATGAGAGCTGGTATCTGCGCAGTGAAAATGCTTATCGTGCAGAAGTCCCCCTGTATGCCTCCATGCTGACACAGGCAATGGACTATGACCGGATTGTGGCAGGCTCCCGCAGCCATCAGACCGGTGTAA  >  NC_000913/2073482‑2073750

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: ‑