Predicted mutation
evidence	seq id	position	mutation	annotation	gene	description
RA	NZ_CP009273	2,099,575	A→G	F378S (TTC→TCC)	wzy ←	O16 family O‑antigen polymerase

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NZ_CP009273	2,099,575	0	A	G	100.0%	123.1 / NA	35	F378S (TTC→TCC)	wzy	O16 family O‑antigen polymerase
Reads supporting (aligned to +/- strand):  ref base A (0/0);  new base G (10/25);  total (10/25)

AGAAATGTTTTCATAATCTGAAGCAATGTCCAGTGCATCTTTTCTTGCTTTAAATCCAGCATCGCGTCTAGAGAAATTTAAATCATTCAAAAAATACATTTTCACTTTATTTTCTGGGCCTTAAGAAATTGAGAGAATACTATGATACAAAGAGTTATTTGTATCCAACTGCTAATATTAGTCATGAAGCTTTCATGATAAAAAATGAAAGAAAAGGTATAAATAAAATATGAATAAAATATTTTCACAGATATGTAATTTCGAGA  >  NZ_CP009273/2099440‑2099705                                                                                                                                        |                                                                                                                                   aGAAATGTTTTCATAATCTGAAGCAATGTCCAGTGCATCTTTTCTTGCTTTAAATCCAGCATCGCGTCTAGAGAAATTTAAATCATTCAAAAAATACATTTTCACTTTATTTTCTGGGCCTTAAGAAATTGAGAGGATa                                                                                                                                 <  1:5615/139‑1 (MQ=255)   aaaTGTTTTCATAATCTGAAGCAATGTCCAGTGCATCTTTTCTTGCTTTAAATCCAGCATCGCGTCTAGAGAAATTTAAATCATTCAAAAAATACATTTTCACTTTATTTTCTGGGCCTTAAGAAATTGAGAGGATACt                                                                                                                               <  1:630483/139‑1 (MQ=255)            cATAATCTGAAGCAATGTCCAGTGCATCTTTTCTTGCTTTAAATCCAGCATCGCGTCTAGAGAAATTTAAATCATTCAAAAAATACATTTTCACTTTATTTTCTGGGCCTTAAGAAATTGAGAGGATACTATGATACa                                                                                                                       <  2:1018770/138‑1 (MQ=255)             aTAATCTGAAGCAATGTCCAGTGCATCTTTTCTTGCTTTAAATCCAGCATCGCGTCTAGAGAAATTTAAATCATTCAAAAAATACATTTTCACTTTATTTTCTGGGCCTTAAGAAATTGAGAGGATACTATGATACaa                                                                                                                      <  1:1278847/138‑1 (MQ=255)             aTAATCTGAAGCAATGTCCAGTGCATCTTTTCTTGCTTTAAATCCAGCATCGCGTCTAGAGAAATTTAAATCATTCAAAAAATACATTTTCACTTTATTTTCTGGGCCTTAAGAAATTGAGAGGATACTATGATACaa                                                                                                                      <  1:291673/138‑1 (MQ=255)             aTAATCTGAAGCAATGTCCAGTGCATCTTTTCTTGCTCTAAATCCAGCATCGCGTCTAGAGAAATTTAAATCATTCAAAAAATACATTTTCACTTTATTTTCTGGGCCTTAAGAAATTGAGAGGATACTATGATACaa                                                                                                                      <  2:530563/138‑1 (MQ=255)                 tCTGAAGCAATGTCCAGTGCATCTTTTCTTGCTTTAAATCCAGCATCGCGTCTAGAGAAATTTAAATCATTCAAAAAATACATTTTCACTTTATTTTCTGGGCCTTAAGAAATTGAGAGGATACTATGATACAAAGAGt                                                                                                                 >  2:893612/1‑139 (MQ=255)                    gAAGCAATGTCCAGTGCATCTTTTCTTGCTTTAAATCCAGCATCGCGTCTAGAGAAATTTAAATCATTCAAAAAATACATTTTCACTTTATTTTCTGGGCCTTAAGAAATTGAGAGGATACTATGATACAAAGAGTTAt                                                                                                              >  1:354913/1‑139 (MQ=255)                     aaGCAATGTCCAGTGCATCTTTTCTTGCTTTAAATCCAGCATCGCGTCTAGAGAAATTTAAATCATTCAAAAAATACATTTTCACTTTATTTTCTGGGCCTTAAGAAATTGAGAGGATACTATGATACAAAGAGt                                                                                                                 <  2:1166702/135‑1 (MQ=255)                           tGTCCAGTGCATCTTTTCTTGCTTTAAATCCAGCATCGCGTCTAGAGAAATTTAAATCATTCAAAAAATACATTTTCACTTTATTTTCTGGGCCTTAAGAAATTGAGAGGATa                                                                                                                                 <  2:276668/113‑1 (MQ=255)                           tGTCCAGTGCATCTTTTCTTGCTTTAAATCCAGCATCGCGTCTAGAGAAATTTAAATCATTCAAAAAATACATTTTCACTTTATTTTCTGGGCCTTAAGAAATTGAGAGGATa                                                                                                                                 >  1:276668/1‑113 (MQ=255)                           tGTCCAGTGCATCTTTTCTTGCTTTAAATCCAGCATCGCGTCTAGAGAAATTTAAATCATTCAAAAAATACATTTTCACTTTATTTTCTGGGCCTTAAGAAATTGAGAGGATACTATGATACAAAGAGTTATTTGTATc                                                                                                       >  1:922917/1‑139 (MQ=255)                             tCCAGTGCATCTTTTCTTGCTTTAAATCCAGCATCGCGTCTAGAGAAATTTAAATCATTCAAAAAATACATTTTCACTTTATTTTCTGGGCCTTAAGAAATTGAGAGGATACTATGATACAAAGAGTTATTTGTATcc                                                                                                      <  2:354913/138‑1 (MQ=255)                             tCCAGTGCATCTTTTCTTGCTTTAAATCCAGCATCGCGTCTAGAGAAATTTAAATCATTCAAAAAATACATTTTCACTTTATTTTCTGGGCCTTAAGAAATTGAGAGGATACTATGATACAAAGAGTTATTTGTATCCa                                                                                                     <  1:792895/139‑1 (MQ=255)                               cAGTGCATCTTTTCTTGCTTTAAATCCAGCATCGCGTCTAGAGAAATTTAAATCATTCAAAAAATACATTTTCACTTTATTTTCTGGGCCTTAAGAAATTGAGAGGATACTATGATACAAAGAGTTATTTGTATCCaa                                                                                                    <  1:493358/138‑1 (MQ=255)                               cAGTGCATCTTTTCTTGCTTTAAATCCAGCATCGCGTCTAGAGAAATTTAAATCATTCAAAAAATACATTTTCACTTTATTTTCTGGGCCTTAAGAAATTGAGAGGATACTATGATACAAAGAGTTATTTGTATCCaa                                                                                                    <  1:275152/138‑1 (MQ=255)                                 gTGCATCTTTTCTTGCTTTAAATCCAGCATCGCGTCTAGAGAAATTTAAATCATTCAAAAAATACATTTTCACTTTATTTTCTGGGCCTTAAGAAATTGAGAGGATACTATGATACAAAGAGTTATTTGTATCCAACTg                                                                                                 <  1:639822/139‑1 (MQ=255)                                       cTTTTCTTGCTTTAAATCCAGCATCGCGTCTAGAGAAATTTAAATCATTCAAAAAATACATTTTCACTTTATTTTCTGGGCCTTAAGAAATTGAGAGGATACTATGATACAAAGAGTTATTTGTATCCAACTGCTAata                                                                                           >  2:151447/1‑139 (MQ=255)                                            cTTGCTTTAAATCCAGCATCGCGTCTAGAGAAATTTAAATCATTCAAAAAATACATTTTCACTTTATTTTCTGGGCCTTAAGAAATTGAGAGGATACTATGATACa                                                                                                                       >  1:125213/1‑106 (MQ=255)                                            cTTGCTTTAAATCCAGCATCGCGTCTAGAGAAATTTAAATCATTCAAAAAATACATTTTCACTTTATTTTCTGGGCCTTAAGAAATTGAGAGGATACTATGATACa                                                                                                                       <  2:125213/106‑1 (MQ=255)                                                cTTTAAATCCAGCATCGCGTCTAGAGAAATTTAAATCATTCAAAAAATACATTTTCACTTTATTTTCTGGGCCTTAAGAAATTGAGAGGATACTATGATACAAAGAGTTATTTGTATCCAACTGCTAATATTAGTCATg                                                                                  <  2:725801/139‑1 (MQ=255)                                                cTTTAAATCCAGCATCGCGTCTAGAGAAATTTAAATCATTCAAAAAATACATTTTCACTTTATTTTCTGGGCCTTAAGAAATTGAGAGGATACTATGATACAAAGAGTTATTTGTATCCAACTGCTAATATTAGTCATg                                                                                  <  1:154037/139‑1 (MQ=255)                                                                       gagaAATTTAAATCATTCAAAAAATACATTTTCACTTTATTTTCTGGGCCTTAAGAAATTGAGAGGATACTATGATACAAAGAGTTATTTGTATCCAACTGCTAATATTAGTCATGAAGCTTTCATGATAAAAAAt                                                              <  2:922917/136‑1 (MQ=255)                                                                           aaTTTAAATCATTCAAAAAATACATTTTCACTTTATTTTCTGGGCCTTAAGAAATTGAGAGGATACTATGATACAAAGAGTTATTTGTATCCAACTGCTAATATTAGTCATGAAGCTTTCATGATAAAAAATgaaagaa                                                       <  2:282932/139‑1 (MQ=255)                                                                           aaTTTAAATCATTCAAAAAATACATTTTCACTTTATTTTCTGGGCCTTAAGAAATTGAGAGGATACTATGATACAAAGAGTTATTTGTATCCAACTGCTAATATTAGTCATGAAGCTTTCATGATAAAAAATgaaagaa                                                       <  1:878067/139‑1 (MQ=255)                                                                           aaTTTAAATCATTCAAAAAATACATTTTCACTTTATTTTCTGGGCCTTAAGAAATTGAGAGGATACTATGATACAAAGAGTTATTTGTATCCAACTGCTAATATTAGTCATGAAGCTTTCATGATAAAAAATgaaagaa                                                       <  1:151447/139‑1 (MQ=255)                                                                            aTTTAAATCATTCAAAAAATACATTTTCACTTTATTTTCTGGGCCTTAAGAAATTGAGAGGATACTATGATACAAAGAGTTATTTGTATCCAACTGCTAATATTAGTCATGAAGCTTTCATGATAAAAAATgaaagaa                                                       >  2:979738/1‑138 (MQ=255)                                                                                 aaTCATTCAAAAAATACATTTTCACTTTATTTTCTGGGCCTTAAGAAATTGAGAGGATACTATGATACAAAGAGTTATTTGTATCCAACTGCTAATATTAGTCATGAAGCTTTCATGATAAAAAATGAAAGAAAAGGt                                                  <  1:1251952/138‑1 (MQ=255)                                                                                                   ttttCACTTTATTTTCTGGGCCTTAAGAAATTGAGAGGATACTATGATACAAAGAGTTATTTGTATCCAACTGCTAATATTAGTCATGAAGCTTTCATGATAAAAAATGAAAGAAAAGGTATAAATAAAATATGAATaa                               <  1:782886/139‑1 (MQ=255)                                                                                                     ttCACTTTATTTTCTGGGCCTTAAGAAATTGAGAGGATACTATGATACAAAGAGTTATTTGTATCCAACTGCTAATATTAGTCATGAAGCTTTCATGATAAAAAATGAAAGAAAAGGTATAAATAAAATATGAATaa                               <  2:227683/137‑1 (MQ=255)                                                                                                     ttCACTTTATTTTCTGGGCCTTAAGAAATTGAGAGGATACTATGATACAAAGAGTTATTTGTATCCAACTGCTAATATTAGTCATGAAGCTTTCATGATAAAAAATGAAAGAAAAGGTATAAATAAAATATGAATaa                               >  1:227683/1‑137 (MQ=255)                                                                                                              ttttCTGGGCCTTAAGAAATTGAGAGGATACTATGATACAAAGAGTTATTTGTATCCAACTGCTAATATTAGTCATGAAGCTTTCATGATAAAAAATGAAAGAAAAGGTATAAATAAAATATGAATAAAATATTTTca                     <  2:39455/138‑1 (MQ=255)                                                                                                                    gggCCTTAAGAAATTGAGAGGATACTATGATACAAAGAGTTATTTGTATCCAACTGCTAATATTAGTCATGAAGCTTTCATGATAAAAAATGAAAGAAAAGGTATAAATAAAATATGAATAAAATATTTTCACAGatat              >  2:843907/1‑139 (MQ=255)                                                                                                                      gCCTTAAGAAATTGAGAGGATACTATGATACAAAGAGTTATTTGTATCCAACTGCTAATATTAGTCATGAAGCTTTCATGATAAAAAATGAAAGAAAAGGTATAAATAAAATATGAATAAAATATTTTCACAGATATGt            <  2:808796/139‑1 (MQ=255)                                                                                                                                 ttGAGAGGATACTATGATACAAAGAGTTATTTGTATCCAACTGCTAATATTAGTCATGAAGCTTTCATGATAAAAAATGAAAGAAAAGGTATAAATAAAATATGAATAAAATATTTTCACAGATATGTAATTTCgaga  >  1:802069/1‑138 (MQ=255)                                                                                                                                        |                                                                                                                                   AGAAATGTTTTCATAATCTGAAGCAATGTCCAGTGCATCTTTTCTTGCTTTAAATCCAGCATCGCGTCTAGAGAAATTTAAATCATTCAAAAAATACATTTTCACTTTATTTTCTGGGCCTTAAGAAATTGAGAGAATACTATGATACAAAGAGTTATTTGTATCCAACTGCTAATATTAGTCATGAAGCTTTCATGATAAAAAATGAAAGAAAAGGTATAAATAAAATATGAATAAAATATTTTCACAGATATGTAATTTCGAGA  >  NZ_CP009273/2099440‑2099705

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 33 ≤ ATCG/ATCG < 37 ≤ ATCG/ATCG < 38 ≤ ATCG/ATCG < 39 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑