Predicted mutation
evidence	seq id	position	mutation	annotation	gene	description
RA	NC_000913	4,147,479	G→A	*114* (TAG→TAA)  T280I (ACT→ATT)	frwD → yijO ←	putative enzyme IIB component of PTS AraC family putative transcriptional activator

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NC_000913	4,147,479	0	G	A	97.6%	121.2 / ‑4.0	41	*114* (TAG→TAA)  T280I (ACT→ATT)	frwD yijO	putative enzyme IIB component of PTS AraC family putative transcriptional activator
Reads supporting (aligned to +/- strand):  ref base G (0/1);  new base A (24/16);  total (24/17)
Fisher's exact test for biased strand distribution p-value = 4.15e-01
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 8.39e-01

AGCGATTTGAACATTGCCGCTATGTGCAATGCAGCATCTACGCATTCCTGCGTGAGCCGCAGCGGGTAATGAGCGCGGTGCGCAAAGTGCTTTCTGCGCCGCAGCAAACCCATCTTATTCTGGAGTAGTCGGTTTTTCTGTCAGTTGGCTGTGGTACTGCCGGCGATATTCCGACGGCGAGCGTTCGGTGTTTTTACGAAACAGACGGCAGAAGTAGTTGCTGTCGACAAAGCCGCAGGCGTGCGCCACTTCTTTTACCTT  >  NC_000913/4147352‑4147612                                                                                                                                |                                                                                                                                      aGCGATTTGAACATTGCCGCTATGTGCAATGCAGCATCTACGCATTCCTGCGTGAGCCGCAGCGGGTAATGAGCGCGGTGCGCAAAGTGCTTTCTGCGCCGCAGCAAACCCATCTTATTCTGGAGTAATCGGTTTTTCt                                                                                                                            >  2:535118/1‑139 (MQ=255)       ttGAACATTGCCGCTATGTGCAATGCAGCATCTACGCATTCCTGCGTGAGCCGCAGCGGGTAATGAGCGCGGTGCGCAAAGTGCTTTCTGCGCCGCAGCAAACCCATCTTATTCTGGAGTAATCGGTTTTTCTGTCAGt                                                                                                                      <  2:1409753/139‑1 (MQ=255)                gCCGCTATGTGCAATGCAGCATCTACGCATTCCTGCGTGAGCCGCAGCGGGTAATGAGCGCGGTGCGCAAAGTGCTTTCTGCGCCGCAGCAAACCCATCTTATTCTGGAGTAATCGGTTTTTCTGTCAGTTGGCTGTgg                                                                                                             >  1:477429/1‑139 (MQ=255)                      aTGTGCAATGCAGCATCTACGCATTCCTGCGTGAGCCGCAGCGGGTAATGAGCGCGGTGCGCAAAGTGCTTTCTGCGCCGCAGCAAACCCATCTTATTCTGGAGTAATCGGTTTTTCTGTCAGTTGGCTGTGGTACTGc                                                                                                       <  2:477429/139‑1 (MQ=255)                         tgCAATGCAGCATCTACGCATTCCTGCGTGAGCCGCAGCGGGTAATGAGCGCGGTGCGCAAAGTGCTTTCTGCGCCGCAGCAAACCCATCTTATTCTGGAGTAATCGGTTTTTCTGTCAGTTGGCTGTGGTACTGCCgg                                                                                                    >  1:1247552/1‑139 (MQ=255)                                   caTCTACGCATTCCTGCGTGAGCCGCAGCGGGTAATGAGCGCGGTGCGCAAAGTGCTTTCTGCGCCGCAGCAAACCCATCTTATTCTGGAGTAATCGGTTTTTCTGTCAGTTGGCTGTGGTACTGCCGGCGATATTCCg                                                                                          >  1:1225932/1‑139 (MQ=255)                                     tCTACGCATTCCTGCGTGAGCCGCAGCGGGTAATGAGCGCGGTGCGCAAAGTGCTTTCTGCGCCGCAGCAAACCCATCTTATTCTGGAGTAATCGGTTTTTCTGTCAGTTGGCTGTGGTACTGCCGGCGATATTCCGAc                                                                                        >  2:658718/1‑139 (MQ=255)                                               ccTGCGTGAGCCGCAGCGGGTAATGAGCGCGGTGCGCAAAGTGCTTTCTGCGCCGCAGCAAACCCATCTTATTCTGGAGTAATCGGTTTTTCTGTCAGTTGGCTGTGGTACTGCCGGCGATATTCCGACGGCGAGCGtt                                                                              >  2:1652738/1‑139 (MQ=255)                                                cTGCGTGAGCCGCAGCGGGTAATGAGCGCGGTGCGCAAAGTGCTTTCTGCGCCGCAGCAAACCCATCTTATTCTGGAGTAATCGGTTTTTCTGTCAGTTGGCTGTGGTACTGCCGGCGATATTCCGACGGCGAGCGTTc                                                                             >  1:1535886/1‑139 (MQ=255)                                                cTGCGTGAGCCGCAGCGGGTAATGAGCGCGGTGCGCAAAGTGCTTTCTGCGCCGCAGCAAACCCATCTTATTCTGGAGTAATCGGTTTTTCTGTCAGTTGGCTGTGGTACTGCCGGCGATATTCCGACGGCGAGCGTTc                                                                             >  2:581917/1‑139 (MQ=255)                                                cTGCGTGAGCCGCAGCGGGTAATGAGCGCGGTGCGCAAAGTGCTTTCTGCGCCGCAGCAAACCCATCTTATTCTGGAGTAATCGGTTTTTCTGTCAGTTGGCTGTGGTACTGCCGGCGATATTCCGACGGCGAGCGTTc                                                                             >  1:355556/1‑139 (MQ=255)                                                       aGCCGCAGCGGGTAATGAGCGCGGTGCGCAAAGTGCTTTCTGCGCCGCAGCAAACCCATCTTATTCTGGAGTAATCGGTTTTTCTGTCAGTTGGCTGTGGTACTGcc                                                                                                      >  2:818861/1‑107 (MQ=255)                                                       aGCCGCAGCGGGTAATGAGCGCGGTGCGCAAAGTGCTTTCTGCGCCGCAGCAAACCCATCTTATTCTGGAGTAATCGGTTTTTCTGTCAGTTGGCTGTGGTACTGcc                                                                                                      <  1:818861/107‑1 (MQ=255)                                                        gCCGCAGCGGGTAATGAGCGCGGTGCGCAAAGTGCTTTCTGCGCCGCAGCAAACCCATCTTATTCTGGAGTAATCGGTTTTTCTGTCAGTTGGCTGTGGTACTGCCGGCGATATTCCGACGGCGAGCGTTCGGTGtttt                                                                     >  2:500616/1‑139 (MQ=255)                                                        gCCGCAGCGGGTAATGAGCGCGGTGCGCAAAGTGCTTTCTGCGCCGCAGCAAACCCATCTTATTCTGGAGTAATCGGTTTTTCTGTCAGTTGGCTGTGGTACTGCCGGCGATATTCCGACGGCGAGCGTTCGGTGtttt                                                                     >  2:1193236/1‑139 (MQ=255)                                                            cAGCGGGTAATGAGCGCGGTGCGCAAAGTGCTTTCTGCGCCGCAGCAAACCCATCTTATTCTGGAGTAATCGGTTTTTCTGTCAGTTGGCTGTGGTACTGCCGGCGATATTCCGACGGCGAGCGTTCGGTGTTTTTACg                                                                 >  2:445917/1‑139 (MQ=255)                                                                 ggTAATGAGCGCGGTGCGCAAAGTGCTTTCTGCGCCGCAGCAAACCCATCTTATTCTGGAGTAATCGGTTTTTCTGTCAGTTGGCTGTGGTACTGCCGGCGATATTCCGACGGCGAGCGTTCGGTGTTTTTACGAAACa                                                            >  1:195774/1‑139 (MQ=255)                                                                  gTAATGAGCGCGGTGCGCAAAGTGCTTTCTGCGCCGCAGCAAACCCATCTTATTCTGGAGTAATCGGTTTTTCTGTCAGTTGGCTGTGGTACTGCCGGCGATATTCCGACGGCGAGCGTTCGGTGTTTTTACGAAACAg                                                           <  2:195774/139‑1 (MQ=255)                                                                    aaTGAGCGCGGTGCGCAAAGTGCTTTCTGCGCCGCAGCAAACCCATCTTATTCTGGAGTAGTCGGTTTTTCTGTCAGTTGGCTGTGGTACTGCCGGCGATATTCCGACGGCGAGCGTTCGGCGTTTTTACGAAACAGAc                                                         <  2:1436985/139‑1 (MQ=255)                                                                        aGCGCGGTGCGCAAAGTGCTTTCTGCGCCGCAGCAAACCCATCTTATTCTGGAGTAATCGGTTTTTCTGTCAGTTGGCTGTGGTACTGCCGGCGATATTCCGACGGCGAGCGTTCGGTGTTTTTACGAAACAGACGGCa                                                     <  1:187629/139‑1 (MQ=255)                                                                        aGCGCGGTGCGCAAAGTGCTTTCTGCGCCGCAGCAAACCCATCTTATTCTGGAGTAATCGGTTTTTCTGTCAGTTGGCTGTGGTACTGCCGGCGATATTCCGACGGCGAGCGTTCGGTGTTTTTACGAAACAGACGGCa                                                     <  1:317456/139‑1 (MQ=255)                                                                          cgcgGTGCGCAAAGTGCTTTCTGCGCCGCAGCAAACCCATCTTATTCTGGAGTAATCGGTTTTTCTGTCAGTTGGCTGTGGTACTGCCGGCGATATTCCGACGGCGAGCGTTCGGTGTTTTTACGAAACAGACGGCAGa                                                   <  1:535118/139‑1 (MQ=255)                                                                           gcgGTGCGCAAAGTGCTTTCTGCGCCGCAGCAAACCCATCTTATTCTGGAGTAATCGGTTTTTCTGTCAGTTGGCTGTGGTACTGCCGGCGATATTCCGACGGCGAGCGTTCGGTGTTTTTACGAAACAGACGGCAGaa                                                  >  2:251605/1‑139 (MQ=255)                                                                               tGCGCAAAGTGCTTTCTGCGCCGCAGCAAACCCATCTTATTCTGGAGTAATCGGTTTTTCTGTCAGTTGGCTGTGGTACTGCCGGCGATATTCCGACGGCGAGCGTTCGGTGTTTTTACGAAACAGACGGCAGAagtag                                              >  1:1330028/1‑139 (MQ=255)                                                                                         gCTTTCTGCGCCGCAGCAAACCCATCTTATTCTGGAGTAATCGGTTTTTCTGTCAGTTGGCTGTGGTACTGCCGGCGATATTCCGACGGCGAGCGTTCGGTGTTTTTACGAAACAGACGGCAGAAGTAGTTGCTGTCGa                                    >  2:680278/1‑139 (MQ=255)                                                                                            ttCTGCGCCGCAGCAAACCCATCTTATTCTGGAGTAATCGGTTTTTCTGTCAGTTGGCTGTGGTACTGCCGGCGATATTCCGACGGCGAGCGTTCGGTGTTTTTACGAAACAGACGGCAGAAGTAGTTGCTGTCGACaa                                 <  1:680278/139‑1 (MQ=255)                                                                                                  gccgcAGCAAACCCATCTTATTCTGGAGTAATCGGTTTTTCTGTCAGTTGGCTGTGGTACTGCCGGCGATATTCCGACGGCGAGCGTTCGGTGTTTTTACGAAACAGACGGCAGAagtag                                              >  2:69491/1‑120 (MQ=255)                                                                                                  gccgcAGCAAACCCATCTTATTCTGGAGTAATCGGTTTTTCTGTCAGTTGGCTGTGGTACTGCCGGCGATATTCCGACGGCGAGCGTTCGGTGTTTTTACGAAACAGACGGCAGAagtag                                              <  1:69491/120‑1 (MQ=255)                                                                                                             cccATCTTATTCTGGAGTAATCTGTTTTTCTGTCAGTTGGCTGTGGTACTGCCGGCGATATTCCGACGGCGAGCGTTCGGTGTTTTTACGAAACAGACGGCAGAAGTAGTTGCTGTCGACaa                                 <  2:379863/122‑1 (MQ=255)                                                                                                             cccATCTTATTCTGGAGTAATCGGTTTTTCTGTCAGTTGGCTGTGGTACTGCCGGCGATATTCCGACGGCGAGCGTTCGGTGTTTTTACGAAACAGACGGCAGAAGTAGTTGCTGTCGACaa                                 >  1:379863/1‑122 (MQ=255)                                                                                                              ccATCTTATTCTGGAGTAATCGGTTTTTCTGTCAGTTGGCTGTGGTACTGCCGGCGATATTCCGACGGCGAGCGTTCGGTGTTTTTACGAAACAGACGGCAGAAGTAGTTGCTGTCGACAAAGCCGCAGGCGTGCGCCa               <  1:500616/139‑1 (MQ=255)                                                                                                               cATCTTATTCTGGAGTAATCGGTTTTTCTGTCAGTTGGCTGTGGTACTGCCGGCGATATTCCGACGGCGAGCGTTCGGTGTTTTTACGAAACAGACGGCAGAAGTAGTTGCTGTCGACAAAGCCGCAGGCGTGCGCCAc              <  1:658718/139‑1 (MQ=255)                                                                                                                aTCTTATTCTGGAGTAATCGGTTTTTCTGTCAGTTGGCTGTGGTACTGCCGGCGATATTCCGACGGCGAGCGTTCGGTGTTTTTa                                                                   <  1:481873/85‑1 (MQ=255)                                                                                                                aTCTTATTCTGGAGTAATCGGTTTTTCTGTCAGTTGGCTGTGGTACTGCCGGCGATATTCCGACGGCGAGCGTTCGGTGTTTTTa                                                                   >  2:481873/1‑85 (MQ=255)                                                                                                                 tCTTATTCTGGAGTAATCGGTTTTTCTGTCAGTTGGCTGTGGTACTGCCGGCGATATTCCGACGGCGAGCGTTCGGTGTTTTTACGAAACAGACGGCAGAAGTAGTTGCTGTCGACAAAGCCGCAGGCGTGCGCCActt            <  2:1330028/139‑1 (MQ=255)                                                                                                                 tCTTATTCTGGAGTAATCGGTTTTTCTGTCAGTTGGCTGTGGTACTGCCGGCGATATTCCGACGGCGAGCGTTCGGTGTTTTTACGAAACAGACGGCAGAAGTAGTTGCTGTCGACAAAGCCGCAGGCGTGCGCCActt            >  2:1028781/1‑139 (MQ=255)                                                                                                                        cTGGAGTAATCGGTTTTTCTGTCAGTTGGCTGTGGTACTGCCGGCGATATTCCGACGGCGAGCGTTCGGTGTTTTTACGAAACAGACGGCAGAAGTAGTTGCTGTCGACAAAGCCGCAGGCGTGCGCCACTTCTTTTAc     >  2:1125284/1‑139 (MQ=255)                                                                                                                           gAGTAATCGGTTTTTCTGTCAGTTGGCTGTGGTACTGCCGGCGATATTCCGACGGCGAGCGTTCGGTGTTTTTACGAAACAGACGGCAGAAGTAGTTGCTGTCGACAAAGCCGCAGGCGTGCGCCACTTCtttt       <  2:653157/134‑1 (MQ=255)                                                                                                                           gAGTAATCGGTTTTTCTGTCAGTTGGCTGTGGTACTGCCGGCGATATTCCGACGGCGAGCGTTCGGTGTTTTTACGAAACAGACGGCAGAAGTAGTTGCTGTCGACAAAGCCGCAGGCGTGCGCCACTTCtttt       >  1:653157/1‑134 (MQ=255)                                                                                                                           gAGTAATCGGTTTTTCTGTCAGTTGGCTGTGGTACTGCCGGCGATATTCCGACGGCGAGCGTTCGGTGTTTTTACGAAACAGACGGCAGAAGTAGTTGCTGTCGACAAAGCCGCAGGCGTGCGCCACTTCTTTTACCtt  >  1:1158712/1‑139 (MQ=255)                                                                                                                           gAGTAATCGGTTTTTCTGTCAGTTGGCTGTGGTACTGCCGGCGATATTCCGACGGCGAGCGTTCGGTGTTTTTACGAAACAGACGGCAGAAGTAGTTGCTGTCGACAAAGCCGCAGGCGTGCGCCACTTCTTTTACCtt  <  1:581917/139‑1 (MQ=255)                                                                                                                                |                                                                                                                                      AGCGATTTGAACATTGCCGCTATGTGCAATGCAGCATCTACGCATTCCTGCGTGAGCCGCAGCGGGTAATGAGCGCGGTGCGCAAAGTGCTTTCTGCGCCGCAGCAAACCCATCTTATTCTGGAGTAGTCGGTTTTTCTGTCAGTTGGCTGTGGTACTGCCGGCGATATTCCGACGGCGAGCGTTCGGTGTTTTTACGAAACAGACGGCAGAAGTAGTTGCTGTCGACAAAGCCGCAGGCGTGCGCCACTTCTTTTACCTT  >  NC_000913/4147352‑4147612

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 30 ≤ ATCG/ATCG < 36 ≤ ATCG/ATCG < 39 ≤ ATCG/ATCG < 40 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑