Predicted mutation
evidence	seq id	position	mutation	annotation	gene	description
RA	NC_000913	2,072,980	T→C	L481P (CTG→CCG)	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	2,072,980	0	T	C	100.0%	199.3 / NA	56	L481P (CTG→CCG)	flu	CP4‑44 prophage, antigen 43 (Ag43) phase‑variable biofilm formation autotransporter
Reads supporting (aligned to +/- strand):  ref base T (0/0);  new base C (32/24);  total (32/24)

CGGACTGTTCACCGCCAGGGGCGGCACACTGGCGGGCACCACCACGCTGAATAACGGCGCCATACTTACCCTTTCCGGGAAGACGGTGAACAACGATACCCTGACCATCCGTGAAGGCGATGCACTCCTGCAGGGAGGCTCTCTCACCGGTAACGGCAGCGTGGAAAAATCAGGAAGTGGCACACTCACTGTCAGCAACACCACACTCACCCAGAAAGCCGTCAACCTGAATGAAGGCACGCTGACGCTGAACGACAGTACC  >  NC_000913/2072852‑2073113                                                                                                                                 |                                                                                                                                      cGGACTGTTCACCGCCAGGGGCGGCACACTGGCGGGCACCACCACGCTGAATAACGGCGCCATACTTACCCTTTCCGGGAAGACGGTGAACAACGATACCCTGACCATCCGTGAAGGCGATGCACTCCCGCAGGGAGGc                                                                                                                             <  2:360757/139‑1 (MQ=255) cGGACTGTTCACCGCCAGGGGCGGCACACTGGCGGGCACCACCACGCTGAATAACGGCGCCATACTTACCCTTTCCGGGAAGACGGTGAACAACGATACCCTGACCATCCGTGAAGGCGATGCACTCCCGCAGGGAGGc                                                                                                                             >  1:290389/1‑139 (MQ=255)   gACTGTTCACCGCCAGGGGCGGCACACTGGCGGGCACCACCACGCTGAATAACGGCGCCATACTTACCCTTTCCGGGAAGACGGTGAACAACGATACCCTGACCATCCGTGAAGGCGATGCACTCCCGCAGGGAGGctc                                                                                                                           >  1:716464/1‑139 (MQ=255)        ttCACCGCCAGGGGCGGCACACTGGCGGGCACCACCACGCTGAATAACGGCGCCATACTTACCCTTTCCGGGAAGACGGTGAACAACGATACCCTGACCATCCGTGAAGGCGATGCACTCCCGCAGGGAGGCTCTCTCa                                                                                                                      <  1:522461/139‑1 (MQ=255)               ccAGGGGCGGCACACTGGCGGGCACCACCACGCTGAATAACGGCGCCATACTTACCCTTTCCGGGAAGACGGTGAACAACGATACCCTGACCATCCGTGAAGGCGATGCACTCCCGCAGGGAGGCTCTCTCACCGGaaa                                                                                                               >  2:571/1‑139 (MQ=255)                cAGGGGCGGCACACTGGCGGGCACCACCACGCTGAATAACGGCGCCATACTTACCCTTTCCGGGAAGACGGTGAACAACGATACCCTGACCATCCGTGAAGGCGATGCACTCCCGCAGGGAGGCTCTCTCACCGGTAAc                                                                                                              >  1:357165/1‑139 (MQ=255)                  ggggCGGCACACTGGCGGGCACCACCACGCTGAATAACGGCGCCATACTTACCCTTTCCGGGAAGACGGTGAACAACGATACCCTGACCATCCGTGAAGGCGATGCACTCCCGCAGGGa                                                                                                                                >  2:974688/1‑119 (MQ=255)                  ggggCGGCACACTGGCGGGCACCACCACGCTGAATAACGGCGCCATACTTACCCTTTCCGGGAAGACGGTGAACAACGATACCCTGACCATCCGTGAAGGCGATGCACTCCCGCAGGGa                                                                                                                                <  1:974688/119‑1 (MQ=255)                  ggggCGGCACACTGGCGGGCACCACCACGCTGAATAACGGCGCCATACTTACCCTTTCCGGGAAGACGGTGAACAACGATACCCTGACCATCCGTGAAGGCGATGCACTCCCGCAGGGAGGCTCTCTCACCGGTAACgg                                                                                                            >  1:1143499/1‑139 (MQ=255)                  ggggCGGCACACTGGCGGGCACCACCACGCTGAATAACGGCGCCATACTTACCCTTTCCGGGAAGACGGTGAACAACGATACCCTGACCATCCGTGAAGGCGATGCACTCCCGCAGGGAGGCTCTCTCACCGGTAACgg                                                                                                            >  2:38718/1‑139 (MQ=255)                  ggggCGGCACACTGGCGGGCACCACCACGCTGAATAACGGCGCCATACTTACCCTTTCCGGGAAGACGGTGAACAACGATACCCTGACCATCCGTGAAGGCGATGCACTCCCGCAGGGAGGCTCTCTCACCGGTAACgg                                                                                                            >  1:534412/1‑139 (MQ=255)                                gCGGGCACCACCACGCTGAATAACGGCGCCATACTTACCCTTTCCGGGAAGACGGTGAACAACGATACCCTGACCATCCGTGAAGGCGATGCACTCCCGCAGGGAGGCTCTCTCACCGGTAACGGCAGCGTGGAAAAAt                                                                                              <  2:966745/139‑1 (MQ=255)                                 cGGGCACCACCACGCTGAATAACGGCGCCATACTTACCCTTTCCGGGAAGACGGTGAACAACGATACCCTGACCATCCGTGAAGGCGATGCACTCCCGCAGGGAGGCTCTCTCACCGGTAACGGCAGCGTGGAAAAATc                                                                                             >  1:528001/1‑139 (MQ=255)                                     caccaccacGCTGAATAACGGCGCCATACTTACCCTTTCCGGGAAGACGGTGAACAACGATACCCTGACCATCCGTGAAGGCGATGCACTCCCGCAGGGAGGCTCTCTCACCGGTAACGGCAGCGTGGaa                                                                                                  <  2:158937/130‑1 (MQ=255)                                     caccaccacGCTGAATAACGGCGCCATACTTACCCTTTCCGGGAAGACGGTGAACAACGATACCCTGACCATCCGTGAAGGCGATGCACTCCCGCAGGGAGGCTCTCTCACCGGTAACGGCAGCGTGGaa                                                                                                  >  1:158937/1‑130 (MQ=255)                                      accaccacGCTGAATAACGGCGCCATACTTACCCTTTCCGGGAAGACGGTGAACAACGATACCCTGACCATCCGTGAAGGCGATGCACTCCCGCAGGGAGGCTCTCTCACCGGTAACGGCAGCGTGGAAAAATCAGGaa                                                                                        >  1:472540/1‑139 (MQ=255)                                            acGCTGAATAACGGCGCCATACTTACCCTTTCCGGGAAGACGGTGAACAACGATACCCTGACCATCCGTGAAGGCGATGCACTCCCGCAGGGAGGCTCTCTCACCGGTAACGGCAGCGTGGAAAAATCAGGAAGTGGca                                                                                  <  2:1143499/139‑1 (MQ=255)                                                tGAATAACGGCGCCATACTTACCCTTTCCGGGAAGACGGTGAACAACGATACCCTGACCATCCGTGAAGGCGATGCACTCCCGCAGGGAGGCTCTCTCACCGGTAACGGCAGCGTGGAAAAATCAGGAAg                                                                                       >  1:628010/1‑130 (MQ=255)                                                tGAATAACGGCGCCATACTTACCCTTTCCGGGAAGACGGTGAACAACGATACCCTGACCATCCGTGAAGGCGATGCACTCCCGCAGGGAGGCTCTCTCACCGGTAACGGCAGCGTGGAAAAATCAGGAAg                                                                                       <  2:628010/130‑1 (MQ=255)                                                tGAATAACGGCGCCATACTTACCCTTTCCGGGAAGACGGTGAACAACGATACCCTGACCATCCGTGAAGGCGATGCACTCCCGCAGGGAGGCTCTCTCACCGGTAACGGCAGCGTGGAAAAATCAGGAAGTGGCAcact                                                                              <  2:1192246/139‑1 (MQ=255)                                                  aaTAACGGCGCCATACTTACCCTTTCCGGGAAGACGGTGAACAACGATACCCTGACCATCCGTGAAGGCGATGCACTCCCGCAGGGAGGCTCTCTCACCGGTAACGGCAGCGTGGAAAAATCAGGAAGTGGCAcactca                                                                            >  2:657807/1‑139 (MQ=255)                                                     aaCGGCGCCCTACTTACCCTTTCCGGGAAGACGGTTAACAGCGATACCCTGACCCTCCGTGAAGGCGATGCACTCCCGCAGGGAGGCTCTCTCACCGGTAACGGCAGCGTGGAACAATCAGTAAGTGGCACACACATTg                                                                         <  2:879234/139‑1 (MQ=255)                                                      aCGGCGCCATACTTACCCTTTCCGGGAAGACGGTGAACAACGATACCCTGACCATCCGTGAAGGCGATGCACTCCCGCAGGGAGGCTCTCTCACCGGTAACGGCAGCGTGGAAAAATCAGGAAGTGGCACACTCACTGt                                                                        <  2:539375/139‑1 (MQ=255)                                                       cGGCGCCATACTTACCCTTTCCGGGAAGACGGTGAACAACGATACCCTGACCATCCGTGAAGGCGATGCACTCCCGCAGGGAGGCTCTCTCACCGGTAACGGCAGCGTGGAAAAATCAGGAAGTGGCACACTCACTGTc                                                                       >  1:1088355/1‑139 (MQ=255)                                                         gcgcCATACTTACCCTTTCCGGGAAGACGGTGAACAACGATACCCTGACCATCCGTGAAGGCGATGCACTCCCGCAGGGAGGCTCTCTCACCGGTAACGGCAGCGTGGAAAAATCAGGAAGTGGCACACTCACTGTCAg                                                                     <  2:534412/139‑1 (MQ=255)                                                         gcgcCATACTTACCCTTTCCGGGAAGACGGTGAACAACGATACCCTGACCATCCGTGAAGGCGATGCACTCCCGCAGGGAGGCTCTCTCACCGGTAACGGCAGCGTGGAAAAATCAGGAAGTGGCACACTCACTGTCAg                                                                     <  2:365929/139‑1 (MQ=255)                                                                   tACCCTTTCCGGGAAGACGGTGAACAACGATACCCTGACCATCCGTGAAGGCGATGCACTCCCGCAGGGAGGCTCTCTCACCGGTAACGGCAGCGTGGAAAAATCAGGAAGTGGCACACTCACTGTCAGCAACACcaca                                                           <  2:472540/139‑1 (MQ=255)                                                                    aCCCTTTCCGGGAAGACGGTGAACAACGATACCCTGACCATCCGTGAAGGCGATGCACTCCCGCAGGGAGGCTCTCTCACCGGTAACGGCAGCGTGGAAAAATCAGGAAGTGGCACACTCACTGTCAGCAACACCacac                                                          <  2:357165/139‑1 (MQ=255)                                                                     cccTTTCCGGGAAGACGGTGAACAACGATACCCTGACCATCCGTGAAGGCGATGCACTCCCGCAGGGa                                                                                                                                <  2:420227/68‑1 (MQ=255)                                                                     cccTTTCCGGGAAGACGGTGAACAACGATACCCTGACCATCCGTGAAGGCGATGCACTCCCGCAGGGa                                                                                                                                >  1:420227/1‑68 (MQ=255)                                                                      ccTTTCCGGGAAGACGGTGAACAACGATACCCTGACCATCCGTGAAGGCGATGCACTCCCGCAGGGAGGCTCTCTCACCGGTAACGGCAGCGTGGAAAAATCAGGAAGTGGCACACTCACTGTCAGCAACACCACACTc                                                        <  2:1264582/139‑1 (MQ=255)                                                                         ttCCGGGAAGACGGTGAACAACGATACCCTGACCATCCGTGAAGGCGATGCACTCCCGCAGGGAGGCTCTCTCACCGGTAACGGCAGCGTGGAAAAATCAGGAAGTGGCAcact                                                                              <  2:1164583/114‑1 (MQ=255)                                                                         ttCCGGGAAGACGGTGAACAACGATACCCTGACCATCCGTGAAGGCGATGCACTCCCGCAGGGAGGCTCTCTCACCGGTAACGGCAGCGTGGAAAAATCAGGAAGTGGCAcact                                                                              >  1:1164583/1‑114 (MQ=255)                                                                         ttCCGGGAAGACGGTGAACAACGATACCCTGACCATCCGTGAAGGCGATGCACTCCCGCAGGGAGGCTCTCTCACCGGTAACGGCAGCGTGGAAAAATCAGGAAGTGGCACACTCACTGTCAGCAACACCACACTCAcc                                                     >  1:581673/1‑139 (MQ=255)                                                                         ttCCGGGAAGACGGTGAACAACGATACCCTGACCATCCGTGAAGGCGATGCACTCCCGCAGGGAGGCTCTCTCACCGGTAACGGCAGCGTGGAAAAATCAGGAAGTGGCACACTCACTGTCAGCAACACCACACTCAcc                                                     >  1:901942/1‑139 (MQ=255)                                                                          tCCGGGAAGACGGTGAACAACGATACCCTGACCATCCGTGAAGGCGATGCACTCCCGCAGGGAGGCTCTCTCa                                                                                                                      <  2:189338/73‑1 (MQ=255)                                                                          tCCGGGAAGACGGTGAACAACGATACCCTGACCATCCGTGAAGGCGATGCACTCCCGCAGGGAGGCTCTCTCa                                                                                                                      >  1:189338/1‑73 (MQ=255)                                                                          tCCGGGAAGACGGTGAACAACGATACCCTGACCATCCGTGAAGGCGATGCACTCCCGCAGGGAGGCTCTCTCACCGGTAACGGCAGCGTGGAAAAATCAGGAAGTGGCACACTCACTGTCAGCAACACCACACTCAccc                                                    >  2:733395/1‑139 (MQ=255)                                                                          tCCGGGAAGACGGTGAACAACGATACCCTGACCATCCGTGAAGGCGATGCACTCCCGCAGGGAGGCTCTCTCACCGGTAACGGCAGCGTGGAAAAATCAGGAAGTGGCACACTCACTGTCAGCAACACCACACTCAccc                                                    >  1:673842/1‑139 (MQ=255)                                                                                 aGACGGTGAACAACGATACCCTGACCATCCGTGAAGGCGATGCACTCCCGCAGGGAGGCTCTCTCACCGGTAACGGCAGCGTGGAAAAATCAGGAAGTGGCACACTCACTGTCAGCAACACCACACTCACCCAGAAAGc                                             >  2:440484/1‑139 (MQ=255)                                                                                    cGGTGAACAACGATACCCTGACCATCCGTGAAGGCGATGCACTCCCGCAGGGAGGCTCTCTCACCGGTAACGGCAGCGTGGAAAAATCAGGAAGTGGCACACTCACTGTCAGCAACACCACACTCACCCAGAAAGCCGt                                          <  2:290389/139‑1 (MQ=255)                                                                                                 tACCCTGACCATCCGTGAAGGCGATGCACTCCCGCAGGGAGGCTCTCTCACCGGTAACGGCAGCGTGGAAAAATCAGGAAGTGGCACACTCACTGTCAGCAACACCACACTCACCCAGAAAGCCGTCAACCtgaatgaa                             >  1:707498/1‑139 (MQ=255)                                                                                                   cccTGACCATCCGTGAAGGCGATGCACTCCCGCAGGGAGGCTCTCTCACCGGTAACGGCAGCGTGGAAAAATCAGGAAGt                                                                                      <  2:191836/80‑1 (MQ=255)                                                                                                   cccTGACCATCCGTGAAGGCGATGCACTCCCGCAGGGAGGCTCTCTCACCGGTAACGGCAGCGTGGAAAAATCAGGAAGt                                                                                      >  1:191836/1‑80 (MQ=255)                                                                                                   cccTGACCATCCGTGAAGGCGATGCACTCCCGCAGGGAGGCTCTCTCACCGGTAACGGCAGCGTGGAAAAATCAGGAAGTGGCACACTCACTGTCAGCAACACCACACTCACCCAGAAAGCCGTCAACCTGAATGAAgg                           >  2:979478/1‑139 (MQ=255)                                                                                                      tGACCATCCGTGAAGGCGATGCACTCCCGCAGGGAGGCTCTCTCACCGGTAACGGCAGCGTGGAAAAATCAGGAAGTGGCACACTCACTGTCAGCAACACCACACTCACCCAGAAAGCCGTCAACCTGAATGAAGGCac                        >  2:1145999/1‑139 (MQ=255)                                                                                                        aCCATCCGTGAAGGCGATGCACTCCCGCAGGGAGGCTCTCTCACCGGTAACGGCAGCGTGGAAAAATCAGGAAGTGGCACACTCACTGTCAGCAACACCACACTCACCCAGAAAGCCGTCAACCTGAATGAAGGCacgc                      >  2:55855/1‑139 (MQ=255)                                                                                                           aTCCGTGAAGGCGATGCACTCCCGCAGGGAGGCTCTCTCACCGGTAACGGCAGCGTGGAAAAATCAGGAAGTGGCACACTCACTGTCAGCAACACCACACTCACCCAGAAAGCCGTCAACCTGAATGAAGGCacgctga                   >  1:730865/1‑139 (MQ=255)                                                                                                             ccGTGAAGGCGATGCACTCCCGCAGGGAGGCTCTCTCACCGGTAACGGCAGCGTGGaa                                                                                                  >  1:952205/1‑58 (MQ=255)                                                                                                             ccGTGAAGGCGATGCACTCCCGCAGGGAGGCTCTCTCACCGGTAACGGCAGCGTGGaa                                                                                                  <  2:952205/58‑1 (MQ=255)                                                                                                             ccGTGAAGGCGATGCACTCCCGCAGGGAGGCTCTCTCACCGGTAACGGCAGCGTGGAAAAATCAGGAAGTGGCACACTCACTGTCAGCAACACCACACTCACCCAGAAAGCCGTCAACCTGAATGAAGGCacgctgacg                 >  1:698163/1‑139 (MQ=255)                                                                                                                tGAAGGCGATGCACTCCCGCAGGGAGGCTCTCTCACCGGTAACGGCAGCGTGGAAAAATCAGGAAGTGGCACACTCACTGTCAGCAACACCACACTCACCCAGAAAGCCGTCAACCTGAATGAAGGCacgctgacgctg              <  2:144514/139‑1 (MQ=255)                                                                                                                       gATGCACTCCCGCAGGGAGGCTCTCTCACCGGTAACGGCAGCGTGGAAAAATCAGGAAGTGGCACACTCACTGTCAGCAACACCACACTCACCCAGAAAGCCGTCAACCTGAATGAAGGCACGCTGACGCTGAACGACa       >  2:164135/1‑139 (MQ=255)                                                                                                                        aTGCACTCCCGCAGGGAGGCTCTCTCACCGGTAACGGCAGCGTGGAAAAATCAGGAAGTGGCACACTCACTGTCAGCAACACCACACTCACCCAGAAAGCCGTCAACCTGAATGAAGGCACGCTGACGCTGAACGACAg      >  1:911979/1‑139 (MQ=255)                                                                                                                           cACTCCCGCAGGGAGGCTCTCTCACCGGTAACGGCAGCGTGGAAAAATCAGGAAGTGGCACACTCACTGTCAGCAACACCACACTCACCCAGAAAGCCGTCAACCTGAATGAAGGCACGCTGACGCTGAACGACAGTAc   <  1:55855/139‑1 (MQ=255)                                                                                                                            aCTCCCGCAGGGAGGCTCTCTCACCGGTAACGGCAGCGTGGAAAAATCAGGAAGTGGCACACTCACTGTCAGCAACACCACACTCACCCAGAAAGCCGTCAACCTGAATGAAGGCACGCTGACGCTGAACGACAGTAcc  <  1:1073730/139‑1 (MQ=255)                                                                                                                                 |                                                                                                                                      CGGACTGTTCACCGCCAGGGGCGGCACACTGGCGGGCACCACCACGCTGAATAACGGCGCCATACTTACCCTTTCCGGGAAGACGGTGAACAACGATACCCTGACCATCCGTGAAGGCGATGCACTCCTGCAGGGAGGCTCTCTCACCGGTAACGGCAGCGTGGAAAAATCAGGAAGTGGCACACTCACTGTCAGCAACACCACACTCACCCAGAAAGCCGTCAACCTGAATGAAGGCACGCTGACGCTGAACGACAGTACC  >  NC_000913/2072852‑2073113

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 27 ≤ ATCG/ATCG < 35 ≤ ATCG/ATCG < 39 ≤ ATCG/ATCG < 40 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑