Predicted mutation
evidence	seq id	position	mutation	annotation	gene	description
RA	USA300TCH1516_ALE	2,543,088	G→A	R283K (AGA→AAA)	hlgA →	Gamma‑hemolysin component A

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	USA300TCH1516_ALE	2,543,088	0	G	A	100.0%	129.4 / NA	38	R283K (AGA→AAA)	hlgA	Gamma‑hemolysin component A
Reads supporting (aligned to +/- strand):  ref base G (0/0);  new base A (18/20);  total (18/20)

ACCTCCTTTAATTCAAAGTGGCTTTAATCCATCATTTATTACAACATTGTCACACGAAAGAGGTAAAGGTGATAAAAGCGAGTTTGAAATCACTTACGGCAGAAACATGGATGCTACATATGCTTACGTGACAAGACATCGTTTAGCCGTTGATAGAAAACATGATGCTTTTAAAAACCGAAACGTTACAGTTAAATATGAAGTGAACTGGAAAACACATGAAGTAAAAATTAAAAGCATCACACCTAAGTAAACAGTTCAATCATCTTAAAAAATCC  >  USA300TCH1516_ALE/2542954‑2543231                                                                                                                                       |                                                                                                                                                aCCTCCTTTAATTCAAAGTGGCTTTAATCCATCATTTATTACAACATTGTCACACGAAAGAGGTAAAGGTGATAAAAGCGAGTTTGAAATCACTTACGGCAGAAACATGGATGCTACATATGCTTACGTGACAAAACATCGTTTAGcc                                                                                                                                    <  4:130750/148‑1 (MQ=255) aCCTCCTTTAATTCAAAGTGGCTTTAATCCATCATTTATTACAACATTGTCACACGAAAGAGGTAAAGGTGATAAAAGCGAGTTTGAAATCACTTACGGCAGAAACATGGATGCTACATATGCTTACGTGACAAAACATCGTTTAGcc                                                                                                                                    <  3:361116/148‑1 (MQ=255)            ttCAAAGTGGCTTTAATCCATCATTTATTACAACATTGTCACACGAAAGAGGTAAAGGTGATAAAAGCGAGTTTGAAATCACTTACGGCAGAAACATGGATGCTACATATGCTTACGTGACAAAACATCGTTTAGCCGTTGATAGaaa                                                                                                                         >  3:26644/1‑148 (MQ=255)                   tGGCTTTAATCCATCATTTATTACAACATTGTCACACGAAAGAGGTAAAGGTGATAAAAGCGAGTTTGAAATCACTTACGGCAGAAACATGGATGCTACATATGCTTACGTGACAAAACATCGTTTAGCCGTTGATAGaaa                                                                                                                         >  1:54660/1‑141 (MQ=255)                   tGGCTTTAATCCATCATTTATTACAACATTGTCACACGAAAGAGGTAAAGGTGATAAAAGCGAGTTTGAAATCACTTACGGCAGAAACATGGATGCTACATATGCTTACGTGACAAAACATAGTTTAGCCGTTGATAGaaa                                                                                                                         >  1:43909/1‑141 (MQ=255)                       tttAATCCATCATTTATTACAACATTGTCACACGAAAGAGGTAAAGGTGATAAAAGCGAGTTTGAAATCACTTACGGCAGAAACATGGATGCTACATATGCTTACGTGACAAAACATCGTTTAGCCGTTGATAGAAAACATGATGCtt                                                                                                              >  4:385842/1‑148 (MQ=255)                         tAATCCATCATTTATTACAACATTGTCACACGAAAGAGGTAAAGGTGATAAAAGCGAGTTTGAAATCACTTACGGCAGAAACATGGATGCTACATATGCTTACGTGACAAAACATCGTTTAGCCGTTGATAGAAAACATGATGCtttt                                                                                                            >  4:380851/1‑148 (MQ=255)                            tCCATCATTTATTACAACATTGTCACACGAAAGAGGTAAAGGTGATAAAAGCGAGTTTGAAATCACTTACGGCAGAAACATGGATGCTACATATGCTTACGTGACAAAACATCGTTTAGCCGTTGATAGAAAACATGATGCTTTTaaa                                                                                                         >  3:239563/1‑148 (MQ=255)                               atcatTTATTACAACATTGTCACACGAAAGAGGTAAAGGTGATAAAAGCGAGTTTGAAATCACTTACGGCAGAAACATGGATGCTACATATGCTTACGTGACAAAACATCGTTTAGCCGTTGATAGAAAACATGATGCTTTTAAAAAc                                                                                                      <  4:40669/148‑1 (MQ=255)                                      attaCAACATTGTCACACGAAAGAGGTAAAGGTGATAAAAGCGAGTTTGAAATCACTTACGGCAGAAACATGGATGCTACATATGCTTACGTGACAAAACATCGTTTAGCCGTTGATAGAAAACATGATGCTTTTAAAAACCGAAACg                                                                                               <  3:251182/148‑1 (MQ=255)                                         acaacaTTGTCACACGAAAGAGGTAAAGGTGATAAAAGCGAGTTTGAAATCACTTACGGCAGAAACATGGATGCTACATATGCTTACGTGACAAAACATCGTTTAGCCGTTGATAGAAAACATGATGCTTTTAAAAACCGAAACGTTa                                                                                            >  3:222031/1‑148 (MQ=255)                                         acaacaTTGTCACACGAAAGAGGTAAAGGTGATAAAAGCGAGTTTGAAATCACTTACGGCAGAAACATGGATGCTACATATGCTTACGTGACAAAACATCGTTTAGCCGTTGATAGAAAACATGATGCTTTTAAAAACCGAAACGTTa                                                                                            >  3:150166/1‑148 (MQ=255)                                            acaTTGTCACACGAAAGAGGTAAAGGTGATAAAAGCGAGTTTGAAATCACTTACGGCAGAAACATGGATGCTACATATGCTTACGTGACAAAACATCGTTTAGCCGTTGATAGAAAACATGATGCTTTTAAAAACCGAAACGTTACAg                                                                                         <  4:224307/148‑1 (MQ=255)                                             caTTGTCACACGAAAGAGGTAAAGGTGATAAAAGCGAGTTTGAAATCACTTACGGCAGAAACATGGATGCTACATATGCTTACGTGACAAAACATCGTTTAGCCGTTGATAGAAAACATGATGCTTTTAAAAACCGAAACg                                                                                               >  1:9995/1‑141 (MQ=255)                                             caTTGTCACACGAAAGAGGTAAAGGTGATAAAAGCGAGTTTGAAATCACTTACGGCAGAAACATGGATGCTACATATGCTTACGTGACAAAACATCGTTTAGCCGTTGATAGAAAACATGATGCTTTTAAAAACCGAAACGTTACAGt                                                                                        <  4:20840/148‑1 (MQ=255)                                               ttGTCACACGAAAGAGGTAAAGGTGATAAAAGCGAGTTTGAAATCACTTACGGCAGAAACATGGATGCTACATATGCTTACGTGACAAAACATCGTTTAGCCGTTGATAGAAAACATGATGCTTTTAAAAACCGAAACGTTACAGTTa                                                                                      <  4:196322/148‑1 (MQ=255)                                                   cacaCGAAAGAGGTAAAGGTGATAAAAGCGAGTTTGAAATCACTTACGGCAGAAACATGGATGCTACATATGCTTACGTGACAAAACATCGTTTAGCCGTTGATAGAAAACATGATGCTTTTAAAAACCGAAACGTTACAGTTAAata                                                                                  >  4:129918/1‑148 (MQ=255)                                                    acacGAAAGAGGTAAAGGTGATAAAAGCGAGTTTGAAATCACTTACGGCAGAAACATGGATGCTACATATGCTTACGTGACAAAACATCGTTTAGCCGTTGATAGAAAACATGATGCTTTTAAAAACCGAAACGTTACAGTTAAatat                                                                                 >  3:389768/1‑148 (MQ=255)                                                            gagGTAAAGGTGATAAAAGCGAGTTTGAAATCACTTACGGCAGAAACATGGATGCTACATATGCTTACGTGACAAAACATCGTTTAGCCGTTGATAGAAAACATGATGCTTTTAAAAACCGAAACGTTACAGTTAAATATGAAGTGaa                                                                         <  4:379608/148‑1 (MQ=255)                                                            gagGTAAAGGTGATAAAAGCGAGTTTGAAATCACTTACGGCAGAAACATGGATGCTACATATGCTTACGTGACAAAACATCGTTTAGCCGTTGATAGAAAACATGATGCTTTTAAAAACCGAAACGTTACAGTTAAATATGAAGTGaa                                                                         <  4:334333/148‑1 (MQ=255)                                                            gagGTAAAGGTGATAAAAGCGAGTTTGAAATCACTTACGGCAGAAACATGGATGCTACATATGCTTACGTGACAAAACATCGTTTAGCCGTTGATAGAAAACATGATGCTTTTAAAAACCGAAACGTTACAGTTAAATATGAAGTGaa                                                                         <  4:69913/148‑1 (MQ=255)                                                               gTAAAGGTGATAAAAGCGAGTTTGAAATCACTTACGGCAGAAACATGGATGCTACATATGCTTACGTGACAAAACATCGTTTAGCCGTTGATAGAAAACATGATGCTTTTAAAAACCGAAACGTTACAGTTAAATATGAAg                                                                             <  2:836/141‑1 (MQ=255)                                                               gTAAAGGTGATAAAAGCGAGTTTGAAATCACTTACGGCAGAAACATGGATGCTACATATGCTTACGTGACAAAACATCGTTTAGCCGTTGATAGAAAACATGATGCTTTTAAAAACCGAAACGTTACAGTTAAATATGAAGTGAACTg                                                                      <  4:35517/148‑1 (MQ=255)                                                                       gATAAAAGCGAGTTTGAAATCACTTACGGCAGAAACATGGATGCTACATATGCTTACGTGACAAAACATCGTTTAGCCGTTGATAGAAAACATGATGCTTTTAAAAACCGAAACGTTACAGTTAAATATGAAGTGAACTGGAAAacac                                                              <  4:252100/148‑1 (MQ=255)                                                                            aaGCGAGTTTGAAATCACTTACGGCAGAAACATGGATGCTACATATGCTTACGTGACAAAACATCGTTTAGCCGTTGATAGAAAACATGATGCTTTTAAAAACCGAAACGTTACAGTTAAATATGAAGTGAACTGGAAAac                                                                >  1:53231/1‑141 (MQ=255)                                                                                        aaTCACTTACGGCAGAAACATGGATGCTACATATGCTTACGTGACAAAACATCGTTTAGCCGTTGATAGAAAACATGATGCTTTTAAAAACCGAAACGTTACAGTTAAATATGAAGTGAACTGGAAAACACATGAAGTAAAAATTaaa                                             >  3:92451/1‑148 (MQ=255)                                                                                        aaTCACTTACGGCAGAAACATGGATGCTACATATGCTTACGTGACAAAACATCGTTTAGCCGTTGATAGAAAACATGATGCTTTTAAAAACCGAAACGTTACAGTTAAATATGAAGTGAACTGGAAAACACATGAAGTAAAAATTaaa                                             >  3:323208/1‑148 (MQ=255)                                                                                           cACTTACGGCAGAAACATGGATGCTACATATGCTTACGTGACAAAACATCGTTTAGCCGTTGATAGAAAACATGATGCTTTTAAAAACCGAAACGTTACAGTTAAATATGAAGTGAACTGGAAAACACATGAAGTAAAAATTAAAAGc                                          >  3:20470/1‑148 (MQ=255)                                                                                            aCTTACGGCAGAAACATGGATGCTACATATGCTTACGTGACAAAACATCGTTTAGCCGTTGATAGAAAACATGATGCTTTTAAAAACCGAAACGTTACAGTTAAATATGAAGTGAACTGGAAAACACATGAAGTAAAAATTAAAAGCa                                         >  4:325299/1‑148 (MQ=255)                                                                                            aCTTACGGCAGAAACATGGATGCTACATATGCTTACGTGACAAAACATCGTTTAGCCGTTGATAGAAAACATGATGCTTTTAAAAACCGAAACGTTACAGTTAAATATGAAGTGAACTGGAAAACACATGAAGTAAAAATTAAAAGCa                                         >  3:281653/1‑148 (MQ=255)                                                                                                   gCAGAAACATGGATGCTACATATGCTTACGTGACAAAACATCGTTTAGCCGTTGATAGAAAACATGATGCTTTTAAAAACCGAAACGTTACAGTTAAATATGTAGTGAACTGGAAAACACATGAAGTAAAAATTAAAAGCa                                         <  1:65094/141‑1 (MQ=255)                                                                                                           aTGGATGCTACATATGCTTACGTGACAAAACATCGTTTAGCCGTTGATAGAAAACATGATGCTTTTAAAAACCGAAACGTTACAGTTAAATATGAAGTGAACTGGAAAACACATGAAGTAAAAATTAAAAGCATCACACCt                                 <  2:53231/141‑1 (MQ=255)                                                                                                             ggATGCTACATATGCTTACGTGACAAAACATCGTTTAGCCGTTGATAGAAAACATGATGCTTTTAAAAACCGAAACGTTACAGTTAAATATGAAGTGAACTGGAAAACACATGAAGTAAAAATTAAAAGCATCACACCTAAGTAAACa                        >  3:347424/1‑148 (MQ=255)                                                                                                             ggATGCTACATATGCTTACGTGACAAAACATCGTTTAGCCGTTGATAGAAAACATGATGCTTTTAAAAACCGAAACGTTACAGTTAAATATGAAGTGAACTGGAAAACACATGAAGTAAAAATTAAAAGCATCACACCTAAGTAAACa                        <  3:278230/148‑1 (MQ=255)                                                                                                                   aaCATATGCTTACCTGACAAAACATCGTTTAGCAGTTGATAGAAAACATGATGCTTTTAAAAACCGAAACGTAAAAGTTAAATATGAAGTGATCTGGAAAAAAAAAAAAAAAAAAATTAAAAGCATCACACCTAAGTAAACAGTTCaa                  <  4:308202/147‑1 (MQ=255)                                                                                                                      atatGCTTACGTGACAAAACATCGTTTAGCCGTTGATAGAAAACATGATGCTTTTAAAAACCGAAACGTTACAGTTAAATATGAAGTGAACTGGAAAACACATGAAGTAAAAATTAAAAGCATCACACCTAAGTAAACAGTTCAatca               <  3:282605/148‑1 (MQ=255)                                                                                                                                   aCAAAACATCGTTTAGCCGTTGATAGAAAACATGATGCTTTTAAAAACCGAAACGTTACAGTTAAATATGAAGTGAACTGGAAAACACATGAAGTAAAAATTAAAAGCATCACACCTAAGTAAACAGTTCAATCATCTTAAAAAATcc  <  4:212046/148‑1 (MQ=255)                                                                                                                                   aCAAAACATCGTTTAGCCGTTGATAGAAAACATGATGCTTTTAAAAACCGAAACGTTACAGTTAAATATGAAGTGAACTGGAAAACACATGAAGTAAAAATTAAAAGCATCACACCTAAGTAAACAGTTCAATCATCTTAAAAAATcc  <  4:70525/148‑1 (MQ=255)                                                                                                                                       |                                                                                                                                                ACCTCCTTTAATTCAAAGTGGCTTTAATCCATCATTTATTACAACATTGTCACACGAAAGAGGTAAAGGTGATAAAAGCGAGTTTGAAATCACTTACGGCAGAAACATGGATGCTACATATGCTTACGTGACAAGACATCGTTTAGCCGTTGATAGAAAACATGATGCTTTTAAAAACCGAAACGTTACAGTTAAATATGAAGTGAACTGGAAAACACATGAAGTAAAAATTAAAAGCATCACACCTAAGTAAACAGTTCAATCATCTTAAAAAATCC  >  USA300TCH1516_ALE/2542954‑2543231

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 22 ≤ ATCG/ATCG < 32 ≤ ATCG/ATCG < 41 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑