Predicted mutation
evidence	seq id	position	mutation	annotation	gene	description
RA	NZ_CP009273	3,179,271	G→A	A167T (GCC→ACC)	ygiL →	fimbrial‑like protein

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NZ_CP009273	3,179,271	0	G	A	95.1%	181.3 / ‑1.1	61	A167T (GCC→ACC)	ygiL	fimbrial‑like protein
Reads supporting (aligned to +/- strand):  ref base G (2/1);  new base A (27/31);  total (29/32)
Fisher's exact test for biased strand distribution p-value = 6.00e-01
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 6.48e-01

CTCCGGTAGTAATTACGTTCAACAATACCAACAGCTATCAGGAACTGAATTTCAAAGCTCGTATGGAATCCCCAAGCAAAGATGCCACCCCGGGCAACGTTTACGCTCAGGCTGACTACAAGATTGCTTACGAGTAATCGCATTTGGCCGGGTTCGCCCGGCCACATCATTA  >  NZ_CP009273/3179188‑3179359                                                                                    |                                                                                         cTCCGGTAGTAATTACGTTCAACAATACCAACAGCTATCAGGAACTGAATTTCAAAGCTCGTATGGAATCCCCAAGCAAAGATACCAccc                                                                                    <  2:1226751/90‑1 (MQ=255) cTCCGGTAGTAATTACGTTCAACAATACCAACAGCTATCAGGAACTGAATTTCAAAGCTCGTATGGAATCCCCAAGCAAAGATACCAccc                                                                                    >  1:920066/1‑90 (MQ=255) cTCCGGTAGTAATTACGTTCAACAATACCAACAGCTATCAGGAACTGAATTTCAAAGCTCGTATGGAATCCCCAAGCAAAGATACCAccc                                                                                    >  1:369363/1‑90 (MQ=255) cTCCGGTAGTAATTACGTTCAACAATACCAACAGCTATCAGGAACTGAATTTCAAAGCTCGTATGGAATCCCCAAGCAAAGATACCAccc                                                                                    >  1:1475381/1‑90 (MQ=255) cTCCGGTAGTAATTACGTTCAACAATACCAACAGCTATCAGGAACTGAATTTCAAAGCTCGTATGGAATCCCCAAGCAAAGATACCAccc                                                                                    >  1:1238857/1‑90 (MQ=255)  tCCGGTAGTAATTACGTTCAACAATACCAACAGCTATCAGGAACTGAATTTCAAAGCTCGTATGGAATCCCCAAGCAAAGATACCAcccc                                                                                   >  1:1054081/1‑90 (MQ=255)      gtagtaATTACGTTCAACAATACCAACAGCTATCAGGAACTGAATTTCAAAGCTCGTATGGAATCCCCAAGCAAAGATACCACCCCGGGc                                                                               >  2:762430/1‑90 (MQ=255)           aaTTACGTTCAACAATACCAACAGCTATCAGGAACTGAATTTCAAAGCTCGTATGGAATCCCCAAGCAAAGATACCACCCCGGGCAACGt                                                                          >  1:1152670/1‑90 (MQ=255)           aaTTACGTTCAACAATACCAACAGCTATCAGGAACTGAATTTCAAAGCTCGTATGGAATCCCCAAGCAAAGATACCACCCCGGGCAACGt                                                                          >  1:1359035/1‑90 (MQ=255)             ttACGTTCAACAATACCAACAGCTATCAGGAACTGAATTTCAAAGCTCGTATGGAATCCCCAAGCAAAGATACCACCCCGGGCAACGttt                                                                        <  1:1217486/90‑1 (MQ=255)             ttACGTTCAACAATACCAACAGCTATCAGGAACTGAATTTCAAAGCTCGTATGGAATCCCCAAGCAAAGATACCACCCCGGGCAACGttt                                                                        >  2:143758/1‑90 (MQ=255)             ttACGTTCAACAATACCAACAGCTATCAGGAACTGAATTTCAAAGCTCGTATGGAATCCCCAAGCAAAGATACCACCCCGGGCAACGttt                                                                        <  1:1288381/90‑1 (MQ=255)             ttACGTTCAACAATACCAACAGCTATCAGGAACTGAATTTCAAAGCTCGTATGGAATCCCCAAGCAAAGATACCACCCCGGGCAACGttt                                                                        <  2:1515786/90‑1 (MQ=255)             ttACGTTCAACAATACCAACAGCTATCAGGAACTGAATTTCAAAGCTCGTATGGAATCCCCAAGCAAAGATACCACCCCGGGCAACGttt                                                                        <  1:473119/90‑1 (MQ=255)             ttACGTTCAACAATACCAACAGCTATCAGGAACTGAATTTCAAAGCTCGTATGGAATCCCCAAGCAAAGATACCACCCCGGGCAACGtat                                                                        <  2:632865/90‑3 (MQ=255)              tACGTTCAACAATACCAACAGCTATCAGGAACTGAATTTCAAAGCTCGTATGGAATCCCCAAGCAAAGATACCACCCCGGGCAACGTTTa                                                                       >  2:608541/1‑90 (MQ=255)               aCGTTCAACAATACCAACAGCTATCAGGAACTGAATTTCAAAGCTCGTATGGAATCCCCAAGCAAAGATACCACCCCGGGCAACGTTTAc                                                                      >  2:922837/1‑90 (MQ=255)                    caacaaTACCAACAGCTATCAGGAACTGAATTTCAAAGCTCGTATGGAATCCCCAAGCAAAGATACCACCCCGGGCAACGTTTACGCTCa                                                                 >  1:1344384/1‑90 (MQ=255)                    caacaaTACCAACAGCTATCAGGAACTGAATTTCAAAGCTCGTATGGAATCCCCAAGCAAAGATACCACCCCGGGCAACGTTTACGCTCa                                                                 >  2:666230/1‑90 (MQ=255)                       caaTACCAACAGCTATCAGGAACTGAATTTCAAAGCTCGTATGGAATCCCCAAGCAAAGATACCACCCCGGGCAACGTTTACGCTCAGGc                                                              <  1:229517/90‑1 (MQ=255)                       caaTACCAACAGCTATCAGGAACTGAATTTCAAAGCTCGTATGGAATCCCCAAGCAAAGATACCACCCCGGGCAACGTTTACGCTCAGGc                                                              >  2:1437998/1‑90 (MQ=255)                       caaTACCAACAGCTATCAGGAACTGAATTTCAAAGCTCGTATGGAATCCCCAAGCAAAGATACCACCCCGGGCAACGTTTACGCTCAGGc                                                              >  2:158569/1‑90 (MQ=255)                         aTACCAACAGCTATCAGGAACTGAATTTCAAAGCTCGTATGGAATCCCCAAGCAAAGATACCACCCCGGGCAACGTTTACGCTCAGGCTg                                                            <  1:1163418/90‑1 (MQ=255)                         aTACCAACAGCTATCAGGAACTGAATTTCAAAGCTCGTATGGAATCCCCAAGCAAAGATACCACCCCGGGCAACGTTTACGCTCAGGCTg                                                            <  1:208169/90‑1 (MQ=255)                         aTACCAACAGCTATCAGGAACTGAATTTCAAAGCTCGTATGGAATCCCCAAGCAAAGATACCACCCCGGGCAACGTTTACGCTCAGGCTg                                                            <  2:570543/90‑1 (MQ=255)                         aTACCAACAGCTATCAGGAACTGAATTTCAAAGCTCGTATGGAATCCCCAAGCAAAGATACCACCCCGGGCAACGTTTACGCTCAGGCTg                                                            >  2:629244/1‑90 (MQ=255)                         aTACCAACAGCTATCAGGAACTGAATTTCAAAGCTCGTATGGAATCCCCAAGCAAAGATACCACCCCGGGCAACGTTTACGCTCAGGCTg                                                            <  1:1570364/90‑1 (MQ=255)                         aTACCAACAGCTATCAGGAACTGAATTTCAAAGCTCGTATGGAATCCCCAAGCAAAGATACCACCCCGGGCAACGTTTACGCTCAGGCTg                                                            <  2:809463/90‑1 (MQ=255)                         aTACCAACAGCTATCAGGAACTGAATTTCAAAGCTCGTATGGAATCCCCAAGCAAAGATACCACCCCGGGCAACGTTTACGCTCAGGCTg                                                            >  2:988987/1‑90 (MQ=255)                         aTACCAACAGCTATCAGGAACTGAATTTCAAAGCTCGTATGGAATCCCCAAGCAAAGATACCACCCCGGGCAACGTTTACGCTCAGGCTg                                                            <  1:988181/90‑1 (MQ=255)                         aTACCAACAGCTATCAGGAACTGAATTTCAAAGCTCGTATGGAATCCCCAAGCAAAGATACCACCCCGGGCAACGTTTACGCTCAGGCTg                                                            >  1:126782/1‑90 (MQ=255)                         aTACCAACAGCTATCAGGAACTGAATTTCAAAGCTCGTATGGAATCCCCAAGCAAAAATACCACCCCGGGCAACGTTTACGCTCAGGCTg                                                            >  1:1032291/1‑90 (MQ=255)                         aTACCAACAGCTATCAGGAACTGAATTTCAAAGCTCGTATGGAATCCCCAAGAAAAGATACCACCCCGGGCAACGTTTACGCTCAGGCTg                                                            <  1:406795/90‑1 (MQ=255)                            ccAACAGCTATGAGGAACTGACTTCCACACCTCGTATGGAATCCCCAAGCAAAGATACCCCCCCGGGCAACGTTTACTCTCAGGCTGACt                                                         <  1:969701/90‑1 (MQ=255)                              aaCAGCTATCAGGAACTGAATTTCAAAGCTCGTATGGAATCCCCAAGCAAAGATACCACCCCGGGCAACGTTTACGCTCAGGCTGACTAc                                                       >  1:183820/1‑90 (MQ=255)                                  gCTATCAGGAACTGAATTTCAAAGCTCGTATGGAATCCCCAAGCAAAGATACCACCCCGGGCa                                                                              >  2:66812/1‑63 (MQ=255)                                  gCTATCAGGAACTGAATTTCAAAGCTCGTATGGAATCCCCAAGCAAAGATACCACCCCGGGCa                                                                              <  1:66812/63‑1 (MQ=255)                                   cTATCAGGAACTGAATTTCAAAGCTCGTATGGAATCCCCAAGCAAAGATACCACCCCGGGCAACGTTTACGCTCAGGCTGACTACAAGAt                                                  >  2:1116032/1‑90 (MQ=255)                                   cTATCAGGAACTGAATTTCAAAGCTCGTATGGAATCCCCAAGCAAAGATACCACCCCGGGCAACGTTTACGCTCAGGCTGACTACAAGAt                                                  <  1:1384723/90‑1 (MQ=255)                                   cTATCAGGAACTGAATTTCAAAGCTCGTATGGAATCCCCAAGCAAAGATACCACCCCGGGCAACGTTTACGCTCAGGCTGACTACAAGAt                                                  <  2:183820/90‑1 (MQ=255)                                         ggAACTGAATTTCAAAGCTCGTATGGAATCCCCAAGCAAAGATACCACCCCGGGCAACGTTTACGCTCAGGCTGACTACAAGATTGCTTa                                            <  2:1054081/90‑1 (MQ=255)                                            aCTGAATTTCAAAGCTCGTATGGAATCCCCAAGCAAAGATGCCACCCCGGGCAACGTTTACGCTCAGGCTGACTACAAGATTGCTTACGa                                         >  2:935149/1‑90 (MQ=255)                                            aCTGAATTTCAAAGCTCGTATGGAATCCCCAAGCAAAGATACCACCCCGGGCAACGTTTACGCTCAGGCTGACTACAAGATTGCTTACGa                                         >  1:1098671/1‑90 (MQ=255)                                               gAATTTCAAAGCTCGTATGGAATCCCCAAGCAAAGATACCACCCCGGGCAACGTTTACGCTCAGGCTGACTACAAGATTGCTTACGAGTa                                      >  2:590973/1‑90 (MQ=255)                                                           tCGTATGGAATCCCCAAGCAAAGATACCACCCCGGGCAACGTTTACGCTCAGGCTGACTACAAGATTGCTTACGAGTAATCGCATTTGGc                          <  1:403971/90‑1 (MQ=255)                                                           tCGTATGGAATCCCCAAGCAAAGATACCACCCCGGGCAACGTTTACGCTCAGGCTGACTACAAGATTGCTTACGAGTAATCGCATTTGGc                          <  2:1098671/90‑1 (MQ=255)                                                           tCGTATGGAATCCCCAAGCAAAGATACCACCCCGGGCAACGTTTACGCTCAGGCTGACTACAAGATTGCTTACGAGTAATCGCATTTGGc                          <  2:757512/90‑1 (MQ=255)                                                            cGTATGGAATCCCCAAGCAAAGATACCACCCCGGGCAACGTTTACGCTCAGGCTGACTACAAGATTGCTTACGAGTAATCGCATTTGGcc                         <  1:912709/90‑1 (MQ=255)                                                            cGTATGGAATCCCCAAGCAAAGATACCACCCCGGGCAACGTTTACGCTCAGGCTGACTACAAGATTGCTTACGAGTAATCGCATTTGGcc                         <  1:158569/90‑1 (MQ=255)                                                            cGTATGGAATCCCCAAGCAAAGATACCACCCCGGGCAACGTTTACGCTCAGGCTGACTACAAGATTGCTTACGAGTAATCGCATTTGGcc                         <  1:1437998/90‑1 (MQ=255)                                                                   aaTCCCCAAGCAAAGATACCACCCCGGGCAACGTTTACGCTCAGGCTGACTACAAGATTGCTTACGAGTAATCGCATTTGGCCGGGTTCg                  >  2:1318366/1‑90 (MQ=255)                                                                     tCCCCAAGCAAAGATACCACCCCGGGCAACGTTTACGCTCAGGCTGACTACAAGATTGCTTACGAGTAATCGCATTTGGCCGGGTTCGcc                <  1:1099453/90‑1 (MQ=255)                                                                      ccccAAGCAAAGATACCACCCCGGGCAACGTTTACGCTCAGGCTGACTACAAGATTGCTTACGAGTAATCGCATTTGGCCGGGTTCGccc               <  2:1441000/90‑1 (MQ=255)                                                                      ccccAAGCAAAGATACCACCCCGGGCAACGTTTACGCTCAGGCTGACTACAAGATTGCTTACGAGTAATCGCATTTGGCCGGGTTCGccc               <  2:1305811/90‑1 (MQ=255)                                                                           aGCAAAGATACCCCCCCGGGCAACGTTTACGCTCAGGCTGACTACAAGATTGCTTACGAGTAATCGCATTTGGCCGGGTTCGCCCGGCca          <  2:1152670/90‑1 (MQ=255)                                                                            gCAAAGATACCACCCCGGGCAACGTTTACGCTCAGGCTGACTACAAGATTGCTTACGAGTAATCGCATTTGGCCGGGTTCGCCCGGCcac         <  2:997327/90‑1 (MQ=255)                                                                              aaaGATACCACCCCGGGCAACGTTTACGCTCAGGCTGACTACAAGATTGCTTACGAGTAATCGCATTTGGCCGGGTTCGCCCGGCCAcat       <  2:1238857/90‑1 (MQ=255)                                                                                aGATACCACCCCGGGCAACGTTTACGCTCAGGCTGACTACAAGATTGCTTACGAGTAATCGCATTTGGCCGGGTTCGCCCGGCCAcatca     >  1:891475/1‑90 (MQ=255)                                                                                 gATGCCACCCCGGGCAACGTTTACGCTCAGGCTGACTACAAGATTGCTTACGAGTAATCGCATTTGGCCGGGTTCGCCCGGCCAcatcat    >  1:662176/1‑90 (MQ=255)                                                                                 gATACCACCCCGGGCAACGTTTACGCTCAGGCTGACTACAAGATTTCTTACGAGTAATCGAATTTGGCCGGGCTCGCCCGGCCAcatcat    >  1:1076836/1‑90 (MQ=255)                                                                                   tGCCACCCCGGGCAACGTTTACGCTCAGGCTGACTACAAGATTGCTTACGAGTAATCGCATTTGGCCGGGTTCGCCCGGCCACATCATTa  <  2:662176/90‑1 (MQ=255)                                                                                    |                                                                                         CTCCGGTAGTAATTACGTTCAACAATACCAACAGCTATCAGGAACTGAATTTCAAAGCTCGTATGGAATCCCCAAGCAAAGATGCCACCCCGGGCAACGTTTACGCTCAGGCTGACTACAAGATTGCTTACGAGTAATCGCATTTGGCCGGGTTCGCCCGGCCACATCATTA  >  NZ_CP009273/3179188‑3179359

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 20 ≤ ATCG/ATCG < 31 ≤ ATCG/ATCG < 35 ≤ ATCG/ATCG < 41 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑