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
A19 F57 I0 R1	30	35.6	800162	95.7%	765755	140.9

Breseq alignment

BRESEQ :: Evidence

Predicted mutation
evidence	seq id	position	mutation	freq	annotation	gene	description
RA	USA300TCH1516_ALE	2,532,298	A→T	100%	T15T (ACA→ACT)	femA_3 →	Aminoacyltransferase FemA

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	USA300TCH1516_ALE	2,532,298	0	A	T	97.6%	130.6 / ‑3.4	41	coding (45/1251 nt)	femA_3	Aminoacyltransferase FemA
Reads supporting (aligned to +/- strand): ref base A (0/0); major base T (17/23); minor base . (1/0); total (18/23)
Fisher's exact test for biased strand distribution p-value = 4.39e-01
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 1.00e+00
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.

GTGTATTTGTAATCAGTTTTTGATAAAATAAAAAAATAGCATTATTAATAAATTCAAAAATTATAGTTCAATTCAGAGAGGGATGGGATAAAATGAACTTTGTAACGTTGACTTCGGATGAGTTCAATGCGTTTACAACAAAG‑CATTTTTCACATTACACACAATCAGCTATTCATTACAATCATAGAGTTGATTTAAAAGGCGATGTGCATCTTGTAGGGGTTAAAGATGACAATGGTCAAGTGATTGCAGGATGCTTATTGAC  >  USA300TCH1516_ALE/2532162‑2532426

gtgtATTTGTAATCAGTTTTTGATAAAATAAAAAAATAGCATTATTAATAAATTCAAAAATTATAGTTCAATTCAGAGAGGGATGGGATAAAATGAACTTTGTAACGTTGACTTCGGATGAGTTCAATGCGTTTActacaa                                                                                                                               <  2:148460/141‑1 (MQ=255)

     tttGTAATCAGTTTTTGATAAAATAAAAAAATAGCATTATTAATAAATTCAAAAATTATAGTTCAATTCAGAGAGGGATGGGATAAAATGAACTTTGTAACGTTGACTTCGGATGAGTTCAATGCGTTTACTACAAAG‑CAt                                                                                                                         <  1:50075/141‑1 (MQ=255)

       tGTAATCAGTTTTTGATAAAATAAAAAAATAGCATTATTAATAAATTCAAAAATTATAGTTCAATTCAGAGAGGGATGGGATAAAATGAACTTTGTAACGTTGACTTCGGATGAGTTCAATGCGTTTACTACAAAG‑CAttt                                                                                                                       <  1:139385/141‑1 (MQ=255)

             cAGTTTTTGATAAAATAAAAAAATAGCATTATTAATAAATTCAAAAATTATAGTTCAATTCAGAGAGGGATGGGATAAAATGAACTTTGTAACGTTGACTTCGGATGAGTTCAATGCGTTTACTACAAAG‑CATTTTTcaca                                                                                                                 <  2:300457/141‑1 (MQ=255)

              aGTTTTTGATAAAATAAAAAAATAGCATTATTAATAAATTCAAAAATTATAGTTCAATTCAGAGAGGGATGGGATAAAATGAACTTTGTAACGTTGACTTCGGATGAGTTCAATGCGTTTACTACAAAG‑CATTTTTCACAt                                                                                                                >  1:114055/1‑141 (MQ=255)

                 ttttGATCAAATAAAAAAATAGCATTATTAATAAATTCAAAAATTATAGTTCAATTCAGAGAGGGATGGGATAAAATGAACTTTGTAACGTTGACTTCGGATGAGTTCAATGCGTTAAC‑TCAAAGTCATTTTTCACATTac                                                                                                             >  2:38213/1‑141 (MQ=255)

                    tGATAAAATAAAAAAATAGCATTATTAATAAATTCAAAAATTATAGTTCAATTCAGAGAGGGATGGGATAAAATGAACTTTGTAACGTTGACTTCGGATGAGTTCAATGCGTTTACTACAAAG‑CATTTTTCACATTacaca                                                                                                          <  1:114918/141‑1 (MQ=255)

                        aaaataaaaAAATAGCATTATTAATAAATTCAAAAATTATAGTTCAATTCAGAGAGGGATGGGATAAAATGAACTTTGTAACGTTGACTTCGGATGAGTTCAATGCGTTTACTACAAAG‑CATTTTTCACATTACACACAAt                                                                                                      <  1:134442/141‑1 (MQ=255)

                        aaaataaaaAAATAGCATTATTAATAAATTCAAAAATTATAGTTCAATTCAGAGAGGGATGGGATAAAATGAACTTTGTAACGTTGACTTCGGATGAGTTCAATGCGTTTACTACAAAG‑CATTTTTCACATTACACACAAt                                                                                                      <  1:81139/141‑1 (MQ=255)

                              aaaaaaTAGCATTATTAATAAATTCAAAAATTATAGTTCAATTCAGAGAGGGATGGGATAAAATGAACTTTGTAACGTTGACTTCGGATGAGTTCAATGCGTTTACTACAAAG‑CATTTTTCACATTACACACAATCAGCTa                                                                                                >  2:386475/1‑141 (MQ=255)

                              aaaaaaTAGCATTATTAATAAATTCAAAAATTATAGTTCAATTCAGAGAGGGATGGGATAAAATGAACTTTGTAACGTTGACTTCGGATGAGTTCAATGCGTTTACTACAAAG‑CATTTTTCACATTACACACAATCAGCTa                                                                                                >  1:341037/1‑141 (MQ=255)

                               aaaagTAGCATTATTAATAAATTCAAAAATTATAGTTCAATTCAGAGAGGGATGGGATAAAATGAACTTTGTAACGTTGACTTCGGATGAGTTCAATGCGTTTACTACAAAG‑CATTTTTCACATTACACACAATCAGCTAt                                                                                               <  2:195966/141‑1 (MQ=255)

                               aaaaaTAGCATTATTAATAAATTCAAAAATTATAGTTCAATTCAGAGAGGGATGGGATAAAATGAACTTTGTAACGTTGACTTCGGATGAGTTCAATGCGTTTACTACAAAG‑CATTTTTCACATTACACACAATCAGCTAt                                                                                               <  1:13080/141‑1 (MQ=255)

                                 aaaTAGCATTATTAATAAATTCAAAAATAATAGTTCAATTCAGAGAGGGATGGGATAAAATGAACTTTGTAACGTTGACTTCGGATGAGTTCAATGCGTTTACTACAAAG‑CATTTTTCACATTACACACAATCAGCTATTc                                                                                             <  1:277414/141‑1 (MQ=255)

                                    tAGCATTATTAATAAATTCAAAAATTATAGTTCAATTCAGAGAGGGATGGGATAAAATGAACTTTGTAACGTTGACTTCGGATGAGTTCAATGCGTTTACTACAAAG‑CATTTTTCACATTACACACAATCAGCTATTCAtt                                                                                          <  1:2614/141‑1 (MQ=255)

                                    tAGCATTATTAATAAATTCAAAAATTATAGTTCAATTCAGAGAGGGATGGGATAAAATGAACTTTGTAACGTTGACTTCGGATGAGTTCAATGCGTTTACTACAAAG‑CATTTTTCACATTACACACAATCAGCTATTCAtt                                                                                          >  1:119610/1‑141 (MQ=255)

                                          tattaATAAATTCAAAAATTATAGTTCAATTCAGAGAGGGATGGGATAAAATGAACTTTGTAACGTTGACTTCGGATGAGTTCAATGCGTTTACTACAAAG‑CATTTTTCACATTACACACAATCAGCTATTCATTACAATc                                                                                    <  2:131688/141‑1 (MQ=255)

                                           attaATAAATTCAAAAATTATAGTTCAATTCAGAGAGGGATGGGATAAAATGAACTTTGTAACGTTGACTTCGGATGAGTTCAATGCGTTTACTACAAAG‑CATTTTTCACATTACACACAATCAGCTATTCATTACAATCa                                                                                   <  1:49348/141‑1 (MQ=255)

                                           attaATAAATTCAAAAATTATAGTTCAATTCAGAGAGGGATGGGATAAAATGAACTTTGTAACGTTGACTTCGGATGAGTTCAATGCGTTTACTACAAAG‑CATTTTTCACATTACACACAATCAGCTATTCATTACAATCa                                                                                   <  1:184087/141‑1 (MQ=255)

                                              aataaATTCAAAAATTATAGTTCAATTCAGAGAGGGATGGGATAAAATGAACTTTGTAACGTTGACTTCGGATGAGTTCAATGCGTTTACTACAAAG‑CATTTTTCACATTACACACAATCAGCTATTCATTACAATCATag                                                                                <  1:192466/141‑1 (MQ=255)

                                               ataaATTCAAAAATTATAGTTCAATTCAGAGAGGGATGGGATAAAATGAACTTTGTAACGTTGACTTCGGATGAGTTCAATGCGTTTACTACAAAG‑CATTTTTCACATTACACACAATCAGCTATTCATTACAATCATaga                                                                               <  1:240108/141‑1 (MQ=255)

                                               ataaATTCAAAAATTATAGTTCAATTCAGAGAGGGATGGGATAAAATGAACTTTGTAACGTTGACTTCGGATGAGTTCAATGCGTTTACTACAAAG‑CATTTTTCACATTACACACAATCAGCTATTCATTACAATCATaga                                                                               >  1:181361/1‑141 (MQ=255)

                                                  aaTTCAAAAATTATAGTTCAATTCAGAGAGGGATGGGATAAAATGAACTTTGTAACGTTGACTTCGGATGAGTTCAATGCGTTTACTACAAAG‑CATTTTTCTCATTACACACAATCAGCTATTCATTACAATCATAGAGtt                                                                            >  2:6927/1‑141 (MQ=255)

                                                      cAAAAATTATAGTTAAATTCAGAGAGGGATGGGATAAAATGGACTTTGTAACGTTGACTTCGGATGAGTTCAATGCGTTTACTACAAAG‑CATTTTTCACATTACACACAATCAGCTATTCATTACAATCATAGAGTGGAtt                                                                        >  1:211264/1‑141 (MQ=255)

                                                              ataGTTCAATTCAGAGCGGGATGGGATACAACGAACTTTGTAACGTTGACTTAGGATGAGTTCAATGCGTTTACTACAAAG‑CATTTTTCACCTTCCACACAATAAGCTATTCATTCCAATCATAGAGTTGATTTAACAGGc                                                                >  2:108467/1‑141 (MQ=255)

                                                              ataGTTCAATTCAGAGAGGGATGGGATAAAATGAACTTTGTAACGTTGACTTCGGATGAGTTCAATGCGTTTACTACAAAG‑CATTTTTCACATTACACACAATCAGCCATGCATTACAATCATAGAGTTGATTTAAAAGGc                                                                <  1:192571/141‑1 (MQ=255)

                                                               taGTTCAATTCAGAGAGGGATGGGATAAAATGAACTTTGTAACGTTGACTTCGGATGAGTTCAATGCGTTTACTACAAAG‑CATTTTTCACATTACACACAATCAGCTATTCATTACAATCATAGAGTTGATTTAAAAGGCg                                                               >  2:107565/1‑141 (MQ=255)

                                                                aGTTCAATTCAGAGAGGGATGGGATAAAATGAACTTTGTAACGTTGACTTCGGATGAGTTCAATGCGTTTACTACAAAG‑CATTTTTCACATTACACACAATCAGCTATTCATTACAATCATAGAGTTGATTTAAAAGGCGa                                                              >  1:377248/1‑141 (MQ=255)

                                                                 gTTCAATTCAGAGAGGGATGGGATAAAATGAACTTTGTAACGTTGACTTCGTATGAGTTACGTGAGTTTACTACAAAG‑CATTTTTCACATTACACACAATCAGCTATTCATTCCAATCATAGAGATGAATTAAAAGTCGAt                                                             >  1:54860/1‑141 (MQ=255)

                                                                        tCAGAGAGGGATGGGATAAAATGAACTTTGTAACGTTGACTTCGGATGAGTTCAATGCGTTTACTACAAAG‑CATTTTTCACATTACACACAATCAGCTATTCATTACAATCATAGAGTTGATTTAAAAGGCGATGTGCATc                                                      <  1:317129/141‑1 (MQ=255)

                                                                         cAGAGAGGGATGGGATAAAATGAACTTTGTAACGTTGACTTCGGATGGGGTCGATGCGTTTACTACAAAG‑CATTTTTCACATTACACACAATCAGCTATTCATTACAATCATAGAGTTGATTTAAAAGGCGATGTGCATCt                                                     >  1:77209/1‑141 (MQ=255)

                                                                          agagagGGATGTGATAAAATGAACTTTGTAACGTTGACTTCGGATGAGTTCAATGCGTTTACTACAAAG‑CAGTTTTCACATTACACACAATCAGCTATTCATTACAATCATAGAGTTGATTTAAAAGGCGATGTGCATCtt                                                    <  1:82333/141‑1 (MQ=255)

                                                                          agagagGGATGGGATAAAATGAACTTTGTAACGTTGACTTCGGATGAGTTCAATGCGTTTACTACAAAG‑CATTTTTCACATTACACACAATCAGCTATTCATTACAATCATAGAGTTGATTTAAAAGGCGATGTGCATCtt                                                    <  1:398476/141‑1 (MQ=255)

                                                                             gagGGATGGGATAAAATGAACTTTGTAACGTTGACTTCGGATGAGTTCAATGCGTTTACTACAAAG‑CATTTTTCACATTACACACAATCAGCTATTCATTACAATCATAGAGTTGATTTAAAAGGCGATGTGCATCTTGTa                                                 <  1:350025/141‑1 (MQ=255)

                                                                              agGGATGGGATAAAATGAACTTTGTAACGTTGACTTCGGATGAGTTCAATGCGTTTACTACAAAG‑CATTTTTCACATTACACACAATCAGCTATTCATTACAATCATAGAGTTGATTTAAAAGGCGATGTGCATCTTGTAg                                                >  1:105346/1‑141 (MQ=255)

                                                                                       agaacaTGGACTTGGTAACGTTGACGTCGGATGAGTTCAATGCGTTTACTACAAAG‑CATTTTTCACATTACACACAATCAGCTATTCAGTACAATCATAGAGTTGATTTAAAAGGCGATGTGCATCTTGTAGGGGTTAAAg                                       <  2:59623/136‑1 (MQ=255)

                                                                                               aaCTTTGTAACGTTGACTTCGGATGAGTTCAATGCGTTTACTACAAAG‑CATTTTTCACATTGCACACAATCAGCTAGTCATTACAATCATAGAGATAATTAAAAAGGCGATGTGCATCTAGTAGGGGTTAAAGATGACAAt                               >  2:186080/1‑141 (MQ=255)

                                                                                                        aCGTTGACTTCGGATGAGTTCAATGCGTTTACTACAAAG‑CATTTTTCACATTACACACAATCAGCTATTCATTACAATCCCTGATGGGATTTAAAAGGCGATGTGCATCTTGTAGGGGTTAAAGATGACAATGGTCAAGTg                      >  1:91940/1‑141 (MQ=255)

                                                                                                          gtggACTTCGGATGAGTTCAATGCGTTTACTACAAAG‑CATTTTTCACATTACACACAATCAGCTATTCATTACAATCATAGAGTTGATTTAAAAGGCGATGTGCATCTTGTAGGGGTTAAAGATGACAATGGTCAAGTGAt                    <  2:167999/138‑1 (MQ=255)

                                                                                                                  cGGATGAGTTCAATGCGTTTACTACAAAG‑CATTTTTCAAATTACACACAATCAGCTATTCATTACAATCATAGAGTTGATTTAAAAGGCGATGTGCATCTTGTAGGGGTTAAAGATGACAATGGTCAAGTGATTGCAGGAt            >  2:65874/1‑141 (MQ=255)

                                                                                                                        aGTTCAATGCGTTTACTACAAAG‑CATTTTTCACATTACACACAATCAGCTATTCATTACAATCATAGAGTTGATTTAAAAGGCGATGTGCATCTTGTAGGGGTTAAAGATGACAATGGTCAAGTGATTGCAGGATGCTTAt      >  1:255362/1‑141 (MQ=255)

                                                                                                                            cAATGCGTTTACTACAAAG‑CATTTTTCACATTACACACAATCAGCTATTCATTACAATCATAGAGTTGATTTAAAAGGCGATGTGCATCTTGTAGGGGTTAAAGATGACAATGGTCAAGTGATTGCAGGATGCTTATTGAc  <  1:251078/141‑1 (MQ=255)

GTGTATTTGTAATCAGTTTTTGATAAAATAAAAAAATAGCATTATTAATAAATTCAAAAATTATAGTTCAATTCAGAGAGGGATGGGATAAAATGAACTTTGTAACGTTGACTTCGGATGAGTTCAATGCGTTTACAACAAAG‑CATTTTTCACATTACACACAATCAGCTATTCATTACAATCATAGAGTTGATTTAAAAGGCGATGTGCATCTTGTAGGGGTTAAAGATGACAATGGTCAAGTGATTGCAGGATGCTTATTGAC  >  USA300TCH1516_ALE/2532162‑2532426

Alignment Legend
Aligned base mismatch/match (shaded by quality score): `ATCG/ATCG` `< 3 ≤` `ATCG/ATCG` `< 12 ≤` `ATCG/ATCG` `< 22 ≤` `ATCG/ATCG` `< 37 ≤` `ATCG/ATCG` `< 41 ≤` `ATCG/ATCG`
Unaligned base: `atcg` Masked matching base: `atcg` Alignment gap: `‑` Deleted base: `‑`

GATK/CNVnator alignment

N/A