Sample Resequencing Stats

Note: The mutation counts shown below represent unfiltered mutation sets.
ALE, Flask, Isolate Predicted Mutations Mean Coverage Total Reads Percent Mapped Mapped Reads Average Read Length
A1 F169 I1 R1 62 44.4 970160 98.1% 951726 147.0

Breseq alignment

BRESEQ :: Evidence
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_ALE2,543,0880GA100.0% 129.4 / NA 38R283K (AGA→AAA) hlgAGamma‑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: ‑

GATK/CNVnator alignment

N/A