Predicted mutation
evidence	seq id	position	mutation	annotation	gene	description
RA	NC_000913	3,797,041	(T)8→9	coding (94/1260 nt)	waaL →	O‑antigen ligase

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NC_000913	3,797,033	1	.	T	97.1%	114.4 / ‑3.4	34	coding (86/1260 nt)	waaL	O‑antigen ligase
Reads supporting (aligned to +/- strand):  ref base . (1/0);  new base T (17/16);  total (18/16)
Fisher's exact test for biased strand distribution p-value = 1.00e+00
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 1.00e+00

ACAGTCAAGCAGTTTTGGAAAAGTTATCATCATTATAAAGGTAAAACATGCTAACATCCTTTAAACTTCATTCATTGAAACCTTACACTCTGAAATCATCAATGATTTTAGAGATAATAACTTATATATTATG‑‑TTTTTTTTCAATGATAATTGCATTCGTCGATAATACTTTCAGCATAAAAATATATAATATCACTGCTATAGTTTGCTTATTGTCACTAATTTTACGTGGCAGACAAGAAAATTATAATATAAAAAACC  >  NC_000913/3796901‑3797161                                                                                                                                      |                                                                                                                                  aCAGTCAAGCAGTTTTGGAAAAGTTATCATCATTATAAAGGTAAAACATGCTAACATCCTTTAAACTTCATTCATTGAAACCTTACACTCTGAAATCATCAATGATTTTAGAGATAATAACTTATATATTATG‑‑ttttttt                                                                                                                           >  1:519481/1‑140 (MQ=255)     tCAAGCAGTTTTGGAAAAGTTATCATCATTATAAAGGTAAAACATGCTAACATCCTTTAAACTTCATTCATTGAAACCTTACACTCTGAAATCATCAATGATTTTAGAGATAATAACTTATATATTATG‑‑tttttttttca                                                                                                                       >  2:1147306/1‑137 (MQ=255)             ttttGGAAAAGTTATCATCATTATAAAGGTAAAACATGCTAACATCCTTTAAACTTCATTCATTGAAACCTTACACTCTGAAATCATCAATGATTTTAGAGATAATAACTTATATATTATGTTTTTTTTTTCAATGATaa                                                                                                                 >  2:1148568/1‑140 (MQ=255)                        ttATCATCATTATAAAGGTAAAACATGCTAACATCCTTTAAACTTCATTCATTGAAACCTTACACTCTGAAATCATCAATGATTTTAGAGATAATAACTTATATATTATGT‑TTTTTTTTCAATGATAATTGCATtcgtcg                                                                                                     <  2:519481/140‑1 (MQ=255)                                 ttATAAAGGTAAAACATGCTAACATCCTTTAAACTTCATTCATTGAAACCTTACACTCTGAAATCATCAATGATTTTAGAGATAATAACTTATATATTATGT‑TTTTTTTTCAATGATAATTGCATTCGTCGATAATACtt                                                                                            >  1:911689/1‑140 (MQ=255)                                  tataAAGGTAAAACATGCTAACATCCTTTAAACTTCATTCATTGAAACCTTACACTCTGAAATCATCAATGATTTTAGAGATAATAACTTATATATTATGT‑TTTTTTTTCAATGATAATTGCATTCGTCGATAATACttt                                                                                           >  2:761092/1‑140 (MQ=255)                                  tataAAGGTAAAACATGCTAACATCCTTTAAACTTCATTCATTGAAACCTTACACTCTGAAATCATCAATGATTTTAGAGATAATAACTTATATATTATGT‑TTTTTTTTCAATGATAATTGCATTCGTCGATAATACttt                                                                                           >  1:625793/1‑140 (MQ=255)                                  tataAAGGTAAAACATGCTAACATCCTTTAAACTTCATTCATTGAAACCTTACACTCTGAAATCATCAATGATTTTAGAGATAATAACTTATATATTATGT‑TTTTTTTTCAATGATAATTGCATTCGTCGATAATACttt                                                                                           >  1:347969/1‑140 (MQ=255)                                       aGGTAAAACATGCTAACATCCTTTAAACTTCATTCATTGAAACCTTACACTCTGAAATCATCAATGATTTTAGAGATAATAACTTATATATTATGT‑TTTTTTTTCAATGATAATTGCATTCGTCGATAATACTTTCAGCa                                                                                      <  2:911689/140‑1 (MQ=255)                                        ggTAAAACATGCTAACATCCTTTAAACTTCATTCATTGAAACCTTACACTCTGAAATCATCAATGATTTTAGAGATAATAACTTATATATTATGTTTTTTTTTTCAATGATAATTGCATTCGTCGATAATACTTTCAGCa                                                                                      <  1:1148568/140‑1 (MQ=255)                                         gTAAAACATGCTAACATCCTTTAAACTTCATTCATTGAAACCTTACACTCTGAAATCATCAATGATTTTAGAGATAATAACTTATATATTATG‑‑TTTTTTTTCAATGATAATTGCATTCGTCGATAATACTTTCAGCATaa                                                                                   >  1:1028582/1‑140 (MQ=255)                                          tAAAACATGCTAACATCCTTTAAACTTCATTCATTGAAACCTTACACTCTGAAATCATCAATGATTTTAGAGATAATAACTTATATATTATGT‑TTTTTTTTCAATGATAATTGCATTCGTCGATAATACTTTCAGCATaa                                                                                   <  2:355000/140‑1 (MQ=255)                                          tAAAACATGCTAACATCCTTTAAACTTCATTCATTGAAACCTTACACTCTGAAATCATCAATGATTTTAGAGATAATAACTTATATATTATGT‑TTTTTTTTCAATGATAATTGCATTCGTCGATAATACTTTCAGCATaa                                                                                   <  2:718750/140‑1 (MQ=255)                                            aaaCATGCTAACATCCTTTAAACTTCATTCATTGAAACCTTACACTCTGAAATCATCAATGATTTTAGAGATAATAACTTATATATTATGT‑TTTTTTTTCAATGATAATTGCATTCGTCGATAATACTTTCAGCATaaaa                                                                                 >  1:532907/1‑140 (MQ=255)                                            aaaCATGCTAACATCCTTTAAACTTCATTCATTGAAACCTTACACTCTGAAATCATCAATGATTTTAGAGATAATAACTTATATATTATGT‑TTTTTTTTCAATGATAATTGCATTCGTCGATAATACTTTCAGCATaaaa                                                                                 >  2:400203/1‑140 (MQ=255)                                               cATGCTAACATCCTTTAAACTTCATTCATTGAAACCTTACACTCTGAAATCATCAATGATTTTAGAGATAATAACTTATATATTATGT‑TTTTTTTTCAATGATAATTGCATTCGTCGATAATACTTTCAGCATAAAAata                                                                              <  2:347969/140‑1 (MQ=255)                                                   cTAACATCCTTTAAACTTCATTCATTGAAACCTTACACTCTGAAATCATCAATGATTTTAGAGATAATAACTTATATATTATGT‑TTTTTTTTCAATGATAATTGCATTCGTCGATAATACTTTCAGCATAAAAAtatata                                                                          >  1:194170/1‑140 (MQ=255)                                                     aaCATCCTTTAAACTTCATTCATTGAAACCTTACACTCTGAAATCATCAATGATTTTAGAGATAATAACTTATATATTATGT‑TTTTTTTTCAATGATAATTGCATTCGTCGATAATACTTTCAGCATAAAAATATataat                                                                        <  1:621973/140‑1 (MQ=255)                                                       cATCCTTTAAACTTCATTCATTGAAACCTTACACTCTGAAATCATCAATGATTTTAGAGATAATAACTTATATATTATGT‑TTTTTTTTCAATGATAATTGCATTCGTCGATAATACTTTCAGCATAAAAATATATAatat                                                                      <  2:91638/140‑1 (MQ=255)                                                       cATCCTTTAAACTTCATTCATTGAAACCTTACACTCTGAAATCATCAATGATTTTAGAGATAATAACTTATATATTATGT‑TTTTTTTTCAATGATAATTGCATTCGTCGATAATACTTTCAGCATAAAAATATATAatat                                                                      <  1:1147306/140‑1 (MQ=255)                                                         tCCTTTAAACTTCATTCATTGAAACCTTACACTCTGAAATCATCAATGATTTTAGAGATAATAACTTATATATTATGT‑TTTTTTTTCAATGATAATTGCATTCGTCGATAATACTTTCAGCATAAAAATATATAATATCa                                                                    <  2:194170/140‑1 (MQ=255)                                                            tttAAACTTCATTCATTGAAACCTTACACTCTGAAATCATCAATGATTTTAGAGATAATAACTTATATATTATGT‑TTTTTTTTCAATGATAATTGCATTCGTCGATAATACTTTCAGCATAAAAATATATAatat                                                                      >  1:284186/1‑135 (MQ=255)                                                            tttAAACTTCATTCATTGAAACCTTACACTCTGAAATCATCAATGATTTTAGAGATAATAACTTATATATTATGT‑TTTTTTTTCAATGATAATTGCATTCGTCGATAATACTTTCAGCATAAAAATATATAatat                                                                      <  2:284186/135‑1 (MQ=255)                                                            tttAAACTTCATTCATTGAAACCTTACACTCTGAAATCATCAATGATTTTAGAGATAATAACTTATATATTATGT‑TTTTTTTTCAATGATAATTGCATTCGTCGATAATACTTTCAGCATAAAAATATATAATATCACTg                                                                 >  1:102664/1‑140 (MQ=255)                                                                    tcattcatTGAAACCTTACACTCTGAAATCATCAATGATTTTAGAGATAATAACTTATATATTATGT‑TTTTTTTTCAATGATAATTGCATTCGTCGATAATACTTTCAGCATAAAAATATataat                                                                        <  1:749330/125‑1 (MQ=255)                                                                    tcattcatTGAAACCTTACACTCTGAAATCATCAATGATTTTAGAGATAATAACTTATATATTATGT‑TTTTTTTTCAATGATAATTGCATTCGTCGATAATACTTTCAGCATAAAAATATataat                                                                        >  2:749330/1‑125 (MQ=255)                                                                     cattcattGAAACCTTACACTCTGAAATCATCAATGATTTTAGAGATAATAACTTATATATTATGT‑TTTTTTTTCAATGATAATTGCATTCGTCGATAATACTTTCAGCATAAAAATATATAATATCACTGCTATAGttt                                                        >  2:10720/1‑140 (MQ=255)                                                                               aaCCTTACACTCTGAAATCATCAATGATTTTAGAGATAATAACTTATATATTATGT‑TTTTTTTTCAATGATAATTGCATTCGTCGATAATACTTTCAGCATAAAAATATATAATATCACTGCTATAGTTTGCTTATTGTc                                              >  2:636727/1‑140 (MQ=255)                                                                                    tACACTCTGAAATCATCAATGATTTTAGAGATAATAACTTATATATTATGT‑TTTTTTTTCAAAGATAATTGCATTCGTCGATAATACTTTCAGCATAAAAATATATAATATCACTGCTATAGTTTGCTTATTGTCACTaa                                         >  2:168116/1‑140 (MQ=255)                                                                                                   tcaATGATTTTAGAGATAATAACTTATATATTATGT‑TTTTTTTTCAATGATAATTGCATTCGTCGATAATACTTTCAGCATAAAAATATATAATATCACTGCTATAGTTTGCTTATTGTCACTAATTTTACGTGGCAGAc                          >  1:1049801/1‑140 (MQ=255)                                                                                                          ttttAGAGATAATAACTTATATATTATGT‑TTTTTTTTCAATGATAATTGCATTCGTCGATAATACTTTCAGCATAAAAATATATAATATCACTGCTATAGTTTGCTTATTGTCACTAATTTTACGTGGCAGACAAGaaaa                   <  1:10720/140‑1 (MQ=255)                                                                                                                      taaCTTATATATTATGT‑TTTTTTTTCAATGATAATTGCATTCGTCGATAATACTTTCAGCATAAAAATATATAATATCACTGCTATAGTTTGCTTATTGTCACTAATTTTACGTGGCAGACAAGAAAATTATAATATaaa       <  2:102664/140‑1 (MQ=255)                                                                                                                      taaCTTATATATTATGT‑TTTTTTTTCAATGATAATTGCATTCGTCGATAATACTTTCAGCATAAAAATATATAATATCACTGCTATAGTTTGCTTATTGTCACTAATTTTACGTGGCAGACAAGAAAATTATAATATaaa       <  1:1029391/140‑1 (MQ=255)                                                                                                                            atatatTATGTTTTTTTTTTCAATGATAATTGCATTCGTCGATAATACTTTCAGCATAAAAATATATAATATCACTGCTATAGTTTGCTTATTGTCACTAATTTTACGTGGCAGACAAGAAAATTATAATATAAAAAAcc  >  1:1030176/1‑140 (MQ=255)                                                                                                                            atatatTATGT‑TTTTTTTTCAATGATAATTGCATTCGTCGATAATACTTTCAGCATAAAAATATATAATATCACTGCTATAGTTTGCTTATTGTCACTAATTTTACGTGGCAGACAAGAAAATtata              <  1:534306/127‑1 (MQ=255)                                                                                                                            atatatTATGT‑TTTTTTTTCAATGATAATTGCATTCGTCGATAATACTTTCAGCATAAAAATATATAATATCACTGCTATAGTTTGCTTATTGTCACTAATTTTACGTGGCAGACAAGAAAATtata              >  2:534306/1‑127 (MQ=255)                                                                                                                                      |                                                                                                                                  ACAGTCAAGCAGTTTTGGAAAAGTTATCATCATTATAAAGGTAAAACATGCTAACATCCTTTAAACTTCATTCATTGAAACCTTACACTCTGAAATCATCAATGATTTTAGAGATAATAACTTATATATTATG‑‑TTTTTTTTCAATGATAATTGCATTCGTCGATAATACTTTCAGCATAAAAATATATAATATCACTGCTATAGTTTGCTTATTGTCACTAATTTTACGTGGCAGACAAGAAAATTATAATATAAAAAACC  >  NC_000913/3796901‑3797161

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 27 ≤ ATCG/ATCG < 33 ≤ ATCG/ATCG < 37 ≤ ATCG/ATCG < 40 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑