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 I0 R1	75	34.0	794130	95.7%	759982	140.9

Breseq alignment

BRESEQ :: Evidence

Predicted mutation
evidence	seq id	position	mutation	freq	annotation	gene	description
RA	USA300TCH1516_ALE	2,543,088	G→A	100%	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%	107.0 / ‑6.5	39	R283K (AGA→AAA)	hlgA	Gamma‑hemolysin component A
Reads supporting (aligned to +/- strand): ref base G (0/0); major base A (16/22); minor base C (1/0); total (17/22)
Rejected as polymorphism: E-value score below prediction cutoff.
Rejected as polymorphism: Frequency below/above cutoff threshold.
Rejected as polymorphism: Variant not supported by required number of reads on each strand.

CTCCTTTAATTCAAAGTGGCTTTAATCCATCATTTATTACAACATTGTCACACGAAAGAGGTAAAGGTGATAAAAGCGAGTTTGAAATCACTTACGGCAGAAACATGGATGCTACATATGCTTACGTGACAAGACATCGTTTAGCCGTTGATAGAAAACATGATGCTTTTAAAAACCGAAACGTTACAGTTAAATATGAAGTGAACTGGAAAACACATGAAGTAAAAATTAAAAGCATCACACCTAAGTAAACAGTTCAATCATCTTAAA  >  USA300TCH1516_ALE/2542956‑2543225

ctcctTTAATTCAAAGTGGCTTTAATCCATCATTTATTACAACATTGTCACACGAAAGAGGTAAAGGTGATAAAAGCGAGTTTGAAATCACTTACGGCAGAAACATGGATGCTACATATGCTTACGTGACAAAACATCCtt                                                                                                                                   >  2:201276/1‑141 (MQ=255)

      tAATTCAAAGTGGCTTTAATCCATCATTTATTACAACATTGTCACACGAAAGAGGTAAAGGTGATAAAAGCGAGTTTGAAATCACTTACGGCAGAAACATGGATGCTACATATGCTTACGTGACAAAACATCGTTTAGCCg                                                                                                                             <  1:120596/141‑1 (MQ=255)

             aaGTGGCTTTAATCCATCATTTATTACAACATTGTCACACGAAAGAGGTAAAGGTGATAAAAGCGAGTTTGAAATCACTTACGGCAGAAACATGGATGCTACATATGCTTACGTGACAAAACATCGTTTAGCCGTTGATAg                                                                                                                      >  1:83632/1‑141 (MQ=255)

             aaGTGGCTTTAATCCATCATTTATTACAACATTGTCACACGAAAGAGGTAAAGGTGATAAAAGCGAGTTTGAAATCACTTACGGCAGAAACATGGATGCTACATATGCTTACGTGACAAAACATCGTTTAGCCGTTGATAg                                                                                                                      <  1:318250/141‑1 (MQ=255)

             aaGTGGCTTTAATCCATCATTTATTACAACATTGTCACACGAAAGAGGTAAAGGTGATAAAAGCGAGTTTGAAATCACTTACGGCAGAAACATGGATGCTACATATGCTTACGTGACAAAACATCGTTTAGCCGTTGATAg                                                                                                                      >  1:277057/1‑141 (MQ=255)

               gTGGCTTTAATCCATCATTTATTACAACATTGTCACACGAAAGAGGTAAAGGTGATAAAAGCGAGTTTGAAATCACTTGCGGCAGAAACATGGATGCTACATCTGCTTACGTGACAAAACATCGTTTAGCCGTTGATAGaa                                                                                                                    <  1:63148/141‑1 (MQ=255)

                         tCCATAATTTATGATAACATTGTCAAACGAAAGAGGTAAAGGTGATAAAAGCGAGTTTGAAATCACTTACGGCAGAAACATGGATGCTACATATGCTTACGTGACAAAACATCGTTTAGCCGTTGATAGAAAACATGATGc                                                                                                          <  2:6859/141‑1 (MQ=255)

                                 ttattaCAACATTGTCACACGCAAGAGGTAAAGGTGATAAAAGCGAGTTTGAAATCACTTACGGCAGAAACATGGATGCTACATATGCTTACGTGACAAAACATCGTTTAGCCGTTGATAGAAAACATGATGCTTTTaaaa                                                                                                  >  2:352959/1‑141 (MQ=255)

                                 ttattaCAACATTGTCACACGAAAGATGTAAAGGTGATAAAAGCGAGTTTGAAATCACTTACGGCAGAAACATGGATGCTACATATGCTTACGTGACAAAACATCGTTTAGCCGTTGATAGAAAACATGATGCTTTTaaaa                                                                                                  <  1:303690/141‑1 (MQ=255)

                                 ttattaCAACATTGTCACACGAAAGAGGTAAAGGTGATAAAAGCGAGTTTGAAATCACTTACGGCAGAAACATGGATGCTACATATGCTTACGTGACAAAACATCGTTTAGCCGTTGATAGAAAACATGATGCTTTTaaaa                                                                                                  >  1:127834/1‑141 (MQ=255)

                                    ttaCAACATTGTCACACGAAAGAGGTAAAGGTGATAAAAGCGAGTTTGAAATCACTTACGGCAGAAACATGGATGCTACATATGCTTACGTGACAAAACATCGTTTAGCCGTTGATAGAAAACATGATGCTTTTCAAAAcc                                                                                               >  1:58803/1‑141 (MQ=255)

                                      acaacaTGGTCACACGAAAGAGGTAAAGGTGATAAAAGCGAGTTTGAAATCACTTACGGCAGAAACATGGATGCTACCTATGCTTACGTGACAAAAGAGCGTTTAGCCGTTGATAGAAAACATGATGCTTTTAAAAACCGa                                                                                             <  2:142703/141‑1 (MQ=255)

                                      acaacaTCGTCACACGAAAGAGGTAAAGGTGATAAAAGCGAGTCTGAAATCACTTACGGCAGAAACATGGATGCTACATATGCTTACGTGACAAAACATCGTTTAGCCGTTGATAGAAAACATGATGCTTTTAAAAACCGa                                                                                             <  1:131556/141‑1 (MQ=255)

                                            ttGTCACACGAAAGAGTTAAACGTGATAAAAGCTGGTTTGCCCCCAGGACCTTCATAAACAGGGATGCTACATATGCTTACGTGACAAAACATCGTTTAGCCGTTGATAGAAAACATGATGCTTTTAAAAACCGAAACGtt                                                                                       <  1:285786/141‑1 (MQ=255)

                                             tGTCACACGAAAGAGGTAAAGGTGATAAAAGCGAGTTTGAAATCACTTACGGCAGAAACATGGATGCTACATATGCTTACGTGACAAAACATCGTTTAGCCGTTGATAGAAAACATGATGCTTTTAAAAACCGAAACGTTa                                                                                      >  2:13344/1‑141 (MQ=255)

                                                 acacGAAAGAGGTAAAGGTGATAAAAGCGAGTTTGAAATCACTTACGGCAGAAACATGGATGCTACATATGCTTACGTGACAAAACATCGTTTAGCCGTTGATAGAAAACATGATGCTTTTAAAAACCGAAACGTTACAGt                                                                                  >  2:330693/1‑141 (MQ=255)

                                                     gAAAGAGGTAAAGGTGATAAAAGCGAGTTTGAAATCACTTACGGCAGAAACATGGATGCTACATATGCTTACGTGACAAAACATCGTTTAGCCGTTGATAGAAGACATGATGCTTTTAAAAACCGAAACGTTACAGTTaaa                                                                              <  1:232208/141‑1 (MQ=255)

                                                       aaGAGGTAAAGGTGATAAAAGCGAGTTTGAAATCACTTACGGCAGAAACATGGATGCTACATATGCTTACGTGACAAAACATCGTTTAGCCGTTGATAGAAAACATGATGCTTTTAACAACAAAAACGTTACAGTTAAata                                                                            >  2:61353/1‑141 (MQ=255)

                                                       aaGAGGTAAAGGTGATAAAAGCGAGTTTGAAATCACTTACGGCAGAAACATGGATGCTACAGATGCTTACGTGACAAAACATCGGTTGGCCGTTGATAGAAAACATGATGCTTTTAAAAACCGAACCGTTACAGTTaaaaa                                                                            >  1:360657/1‑139 (MQ=255)

                                                                 ggTGATAAAAGCGAGTTTGAAATCACTTCCGGCAGAAACATGGATGCTACATATGCTTACGTGACAAAACATCGTTTAACCGTTGATAGAAAACATGATGCTTTTAAAAACCGAAACGTTACAGTTAAAGATGAAGTGAAc                                                                  >  1:147438/1‑141 (MQ=255)

                                                                    gATAAAAGCGAGTTTGAAATCACTTACGGCAGAAACATGGATGCTACATATGCTTACGTGACAAAACATCGTTTAGCCGTTGATAGAAAACATGATGCTTTTAAAAACCGAAACGTTACAGTTAAATATGAAGTGAACTgg                                                               <  1:209729/141‑1 (MQ=255)

                                                                     aTAAAAGCGAGTTTGAAATCACTTACGGCAGAAACATGGATGCTACATATGCTTACGTGACAAAACATCGTTTAGCCGTTGATAGAAAACATGATGCTTTTAAAAACCGAAACGTTACAGTTAAATATGAAGTGAACTGGa                                                              <  1:331215/141‑1 (MQ=255)

                                                                     aTAAAAGCGAGTTTGAAATCACTTACGGCAGAAACATGGATGCTACATATGCTTACGTGACAAAACATCGTTTAGCCGTTGATAGAAAACATGATGCTTTTAAAAACCGAAACGTTACAGTTAAATATGAAGTGAACTGGa                                                              >  1:142541/1‑141 (MQ=255)

                                                                           gCGAGTTTGAAATCACTTACGGCAGAAACATGGATGCTACATATGCTTACGTGACAAAACATCGTTTAGCCGTTGATAGAAAACATGATGCTTTTAAAAACCGAAACGTTACAGTTAAATATGAAGTGAACTGGAAAacac                                                        >  1:99758/1‑141 (MQ=255)

                                                                              aGTTTGAAATGCCTTACGGCAGAAACATGGATGCTACATATGCTTACGTGACAAAACATCGTTTAGCCGTTGATAGAAAACATGATGCTTTTAAAAACCGAAACGTTACAGTTAAATATGAAGTGAACTGGAAAACACATg                                                     <  2:360419/141‑1 (MQ=255)

                                                                               ttttGCAATCACTTACGGCAGAAACATGGATGCTACATATGCTTACGTGACAAAACATCGTTTAGCCGTTGATAGAAAACATGATGCTTTTAAAAACCGAAACGTTACAGTTAAATAAGAAGTGAACTGGAAAACACATGa                                                    <  1:313616/140‑1 (MQ=255)

                                                                                  tgagagcACTTACGGCAGAAACATGGATGCTACATCTGCTTACGTGACAACACATCGTATAGCCGTTGAAAGAAAACATGATGCTTTTAAACACCGAAGCGTTACAGCTAAATATGAAGTGGACTGGAAAACACATGAAgg                                                 >  2:213738/7‑140 (MQ=255)

                                                                                        cACTTACGGCAGAAACATGGATGCTACATATGCTTACGTGACAAACCATCGTTTAGCCGTTGATAGAAAACATGATGCTTTTAAAAACCGAAACGTTACAGTTAAATATGAAGTGAACTGGAAAACACATGAAGTAAAAAt                                           <  1:268358/141‑1 (MQ=255)

                                                                                            tACGGCAGAAACATGGATGCTACATATGCTTACGTGACAAAACATCGTTTAGCCGTTGATAGAAAACATGATGCTTTTAAAAACCGAAACGTTACAGTTAAATATGAAGTGAACTGGAAAACACATGAAGTAAAAATTaaa                                       <  1:63439/141‑1 (MQ=255)

                                                                                             aCGGCAGAAACATGGATGCTACATACGCTTACGTGACAAAACATCGTTTAGCCGTTGATAGAAAACGTGATGCTTTTAAAAACCGAAACGTTACAGTTGAATATGAAGTGAACTGGAAAACACATCAAGTAAAAATTaaaa                                      <  1:295131/141‑1 (MQ=255)

                                                                                              cGGCAGAAACATGGATGCTACATATGCTTACGTGACAAAACATCGTTTAGCCGTTGATAGAAAACATGATGCTTTTAAAAACCGAAACGTTACAGTTAAATATGAAGTGTACTGGAAAACACATGAAGTAAAAATTAAAAg                                     <  2:87320/141‑1 (MQ=255)

                                                                                              aggCAGAAACATGGATGCTACATATGCTTACGTGACAAAACATCGTTTAGCCGTTGATAGAAAACATGATGCTTTTAAAAACCGAAACGTTACAGTTAAATATGAAGTGAACTGGAAAACACATGAAGTAAAAATTAAAAg                                     <  2:344651/140‑1 (MQ=255)

                                                                                               ggCCGAAAGACGGATGCGACAGATGCTTACGTGACAAAACATCGTTTAGCCGTTGATAGAAAACATGATGCTTTTAAAAACCGAAACGTTACAGTTAAATATGAAGTGAACCGGAAAACACATGAAGTAAAAATTAAAAGc                                    <  1:310380/141‑1 (MQ=255)

                                                                                                  aGAAACATGGATGCTACATATGCTTACGTGACAAAACATCGTTTAGCCGTTGATAGAAAACATGATGCTTTTAAAAACCGAAACGTTACAGTTAAATATGAAGTGAACTGGAAAACACATGAAGTAAAAATTAAAAGCATc                                 >  1:50889/1‑141 (MQ=255)

                                                                                                      aCATGGATGCTACATATGCTTACGTGACAAAACATCGTTTAGCCGTTGATAGAAAACATGATGCTTTTAAAAACCGAAACGTTACAGTTAAATATGAAGTGAACGGGAAAACACATGAAGGAAAAATTAAAAGCATCacac                             >  2:77424/1‑141 (MQ=255)

                                                                                                       cATGGATGCTACATATGCTTACGTGACAAAACATCGTTTAGCCGTTGATAGAAAACATGATGCTTTTAAAAACCGAAACGTTACAGTTAAATATGAAGTGAACTGGAAAACACATGAAGTAAAAATTAAAAGCATCACAcc                            >  2:196603/1‑141 (MQ=255)

                                                                                                                   atatGCTTACGTGACAAAACATCGTTTAGCCGTTGATAGAAAACATGATGCTTTTAAAAACCGAAACGTTACAGTTAAATATGAAGTGAACTGGAAAACACATGAAGTAAAAATTAAAAGCATCACACCTAAGTAAACAGt                <  2:356831/141‑1 (MQ=255)

                                                                                                                        cTTACGTGACAAAACATCGTTTAGCCGTTGATAGAAAACATGATGCTTTTAAAAACCGAAACGTTACAGTTAAATATGAAGTGAACTGGAAAACACATGAAGTAAAAATTAAAAGCATCACACCTAAGTAAACAGTTCAat           <  2:99758/141‑1 (MQ=255)

                                                                                                                                 cAAAACATCGTTTAGCCGTTGATAGAAAACATGATGCTTTTAAAAACCGAAACGTTACAGTTAAATATGAAGTGAACTGGAAAACACATGAAGTAAAAATTAAAAGCATCACACCTAAGTAAACAGTTCAATCATCTTaaa  <  2:192508/141‑1 (MQ=255)

CTCCTTTAATTCAAAGTGGCTTTAATCCATCATTTATTACAACATTGTCACACGAAAGAGGTAAAGGTGATAAAAGCGAGTTTGAAATCACTTACGGCAGAAACATGGATGCTACATATGCTTACGTGACAAGACATCGTTTAGCCGTTGATAGAAAACATGATGCTTTTAAAAACCGAAACGTTACAGTTAAATATGAAGTGAACTGGAAAACACATGAAGTAAAAATTAAAAGCATCACACCTAAGTAAACAGTTCAATCATCTTAAA  >  USA300TCH1516_ALE/2542956‑2543225

Alignment Legend
Aligned base mismatch/match (shaded by quality score): `ATCG/ATCG` `< 3 ≤` `ATCG/ATCG` `< 12 ≤` `ATCG/ATCG` `< 13 ≤` `ATCG/ATCG` `< 32 ≤` `ATCG/ATCG` `< 41 ≤` `ATCG/ATCG`
Unaligned base: `atcg` Masked matching base: `atcg` Alignment gap: `‑` Deleted base: `‑`

GATK/CNVnator alignment

N/A