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 F41 I1 R1	11	26.2	606442	94.9%	575513	140.9

Breseq alignment

BRESEQ :: Evidence

Predicted mutation
evidence	seq id	position	mutation	annotation	gene	description
RA	USA300TCH1516_ALE	2,532,298	A→T	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	96.8%	94.2 / ‑4.6	31	T15T (ACA→ACT)	femA_3	Aminoacyltransferase FemA
Reads supporting (aligned to +/- strand): ref base A (0/1); new base T (9/21); total (9/22)
Fisher's exact test for biased strand distribution p-value = 1.00e+00
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 9.91e-01

ATGTGTATTTGTAATCAGTTTTTGATAAAATAAAAAAATAGCATTATTAATAAATTCAAAAATTATAGTTCAATTCAGAGAGGGATGGGATAAAATGAACTTTGTAACGTTGACTTCGGATGAGTTCAATGCGTTTACAACAAAGC‑ATTTTTCACATTACACACAATCAGCTATTCATTACAATCATAGAGTTGATTTAAAAGGCGATGTGCATCTTGTAGGGGTTAAAGATGACAATGGTCAAGTGATTGCAGGATGCTTATTGACAGAAGCA  >  USA300TCH1516_ALE/2532160‑2532433

aaatgtATTTGAAATCAGTTTTTAATAAAATAAAAAAATAGGATTATTAATAAATTCAAAAATTATAGTTCAATTCAGAGAGGGATGGGATAAAATGAACTTTGTAACGTTGACTTCGGATGAGTTCAATGCGTTtactac                                                                                                                                        <  2:66542/138‑1 (MQ=255)

      aTTTGTAATCAGTTTTTGATAAAATAAAAAAATAGCATTATTAATAAATTCAAAAATTATAGTTCAATTCAGAGAGGGATGGGATAAAATGAACTTTGTAACGTTGACTTCGGATGAGTTCAATGCGTTTACTACAAAGC‑a                                                                                                                                 <  1:23252/141‑1 (MQ=255)

        ttGTAATCAGTTTTTGATAAAATAAAAAAATAGCATTATTGATAAATTCAAAAATTATAGTTCAATTCAGAGAGGGATGGGATAAAATGAACTTTGTAACGTTGACTTCGGATGAGTTCAATGCGTTTACTACAAAGC‑Att                                                                                                                               >  1:180650/1‑141 (MQ=255)

            aaTCAGTTTTTGATAAAATAAAAAAATAGCATTATTAATAAATTCAAAAATTATAGTTCAATTCAGAGAGGGATGGGATAAAATGAACTTTGTAACGTTGACTTCGGATGAGTTCAATGCGTTTACTACAAAGC‑ATTTTTc                                                                                                                           >  1:278307/1‑141 (MQ=255)

                  tttatGATAAAATAAAAAAATAGCATTATTAATAAATTCAAAAATTATAGTTCAATTCAGAGAGGGATGGGATAAAATGAACTTTGTAACGTTGACTTCGGATGAGTTCAATGCGTTTACTACAAAGC‑ATTTTTCACATTa                                                                                                                     <  2:228332/141‑1 (MQ=255)

                     ttGATAAAATAAAAAAATAGCATTATTAATAAATTCAAAAATTATAGTTCAATTCAGAGAGGGATGGGATAAAATGAACTTTGTAACGTTGACTTCGGATGAGTTCAATGCGTTTACTACAAAGC‑ATTTTTCACATTacac                                                                                                                  <  1:218072/141‑1 (MQ=255)

                     ttGATAAAATAAAAAAATAGCATTATTAATAAATTCAAAAATTATAGGTCAATTCAGATAGAGATAAGATATTATGAACTTTGTAACGTTGACTTCGGATGAGTTCAATGCGTTTACTACAAAGC‑ATTTTTCACATTacac                                                                                                                  <  1:191010/141‑1 (MQ=255)

                           aaataaaaAAATAGCATTATTAATAAATTCAAAAATTATAGTTCAATTCAGAGAGGGATGGGATAAAATGAACTTTGTAACGTTGACTTCGGATGAGTTCAATGCGTTTACTACAAAGC‑ATTTTTCACATTACACACAATc                                                                                                            >  2:2280/1‑141 (MQ=255)

                              taaaaAAATAGCATTATTAATAAATTCAAAAATTATAGTTCAATTCAGAGAGTGATGGGATAAAATGACATCGGCGCTGGTGACGTGGGGTGAAAGCTCCGCTGTTGCTACAAAGC‑ATTTTTCACATTACACACAATCAGc                                                                                                         <  1:143995/141‑1 (MQ=255)

                              aaaaaaaaTAGCATTATTAATAAATTCAAAAATTATAGTTCAATTCAGAGAGGGATGGGATATAATGAACTTTGTAACGTTGACTTCGGATGAGTTCAATGCGTTTACTACAAAGC‑ATTTTTCACATTACACACAATCAGc                                                                                                         <  2:183666/140‑1 (MQ=255)

                                  aaaaTAGCATTATTAATAAATTCAAAAATTATAGTTCAATTCAGAGAGGGATGGGATAAAATGAACTTTGTAACGTTGACTTCGGATGAGTTCAATGCGTTTACTACAAAGC‑ATTTTTCACATTACACACAATCAGCTAtt                                                                                                     >  2:118240/1‑141 (MQ=255)

                                                     aTTCAAAAATTATAGTTCAATTCAGAGAGGGATGGGATAAAATGAACTTTGTAACGTTGACTTCGGATGAGTTCAATGCGTTTACTACAAAGC‑ATTTTTCACATTACACACAATCAGCTATTCATTACAATCATAGAGTTg                                                                                  <  1:72077/141‑1 (MQ=255)

                                                              ttATAGTTCAATTCAGAGAGGGATGGGATAAAATGAACTTTGTAACGTTGACTTAGGATGAGGTCAATGCGTCTACTACAAAGC‑ATTTTTCACATTACACACAATCAGCTATTCATTACAATCATAGAGTTGATTTAAAAg                                                                         >  2:50910/1‑141 (MQ=255)

                                                                    ttCAATTCAGAGAGGGATGGGATAAAATGAACTTTGTAACGTTGACTTCGGATGAGTTCAATGCGTTTACTACAAAGC‑ATTTTTCACATTACACACAATCAGCTATTCATTACAATCATAGAGTTGATTTAAAAGGCGAtg                                                                   <  1:209527/141‑1 (MQ=255)

                                                                      aaaatCAGAGATGGATGGGATAAAATGAACTTTGTAACGTTGACTTCGGATGGGTTAAATGCGTTTACTACAAAGC‑ATTTTTCACATTACACACAATCAGCTATTCATTACAATCATAGAGTTGATTTAAAAGGCGAtgtg                                                                 <  2:245810/137‑1 (MQ=255)

                                                                        aTTCAGAGAGGGATGGGATAAAATGAACTTTGTAACGTTGACTTCGGATGAGTTCAATGCGTTTACTACAAAGC‑ATTTTTCACATTACACACAATCAGCTATTCATTACAATCATAGAGTTGATTTAAAAGGCGATGTGCa                                                               <  2:157096/141‑1 (MQ=255)

                                                                          tCAGAGAGGGATGGGATAAAATGAACTTTGTAACGTTGACTTCGGATGAGTTCAATGCGTTTACTACAAAGC‑ATTTTTCACATTACACACAATCAGCTATTCATTACAATCATAGAGTTGATTTAAAAGGCGATGTGCATc                                                             <  1:42930/141‑1 (MQ=255)

                                                                           cAGAGAGGGATGGGATAAAATGAACTTTGTAACGTTGACTTCGGATGAGTTCAATGCGTTTACTACAAAGC‑ATTTTTCACATTACACACAATCAGCTATTCATTACAATCATAGAGTTGATTTAAAAGGCGATGTGCATCt                                                            <  1:186691/141‑1 (MQ=255)

                                                                                     tgggatAAAATGAACTTTGTAACGTTGACTTCGGATGAGTTCAATGCGTTTACTACAAAGC‑ATTTTTCACATTACACACAATCAGCTATTCATTACAATCATAGAGTTGATTTAAAAGGCGATGTGCATCTTGTAGGGGtt                                                  <  1:261518/141‑1 (MQ=255)

                                                                                         atAAAATGAACTTTGTAACGTTGACTTCGGATGAGTTCAATGCGTTTACTACAAAGC‑ATTTTTCACATTACACACAATCAGCTATTCATTACAATCATAGAGTTGATTTAAAAGGCGATGTGCATCTTGTAGGGGTTAAAg                                              <  1:118240/141‑1 (MQ=255)

                                                                                         atAAAATGAACTTTGTAACGTTGACTTCGGATGAGTTCAATGCGTTTACTACAAAGC‑ATTTTTCACATTACACACAATCAGCTATTCATTACAATCATAGAGTTGATTTAAAAGGCGATGTGCATCTTGTAGGGGTTAAAg                                              <  1:123116/141‑1 (MQ=255)

                                                                                                gAACTTTGTAACGTTGACTTCGGATGAGTTCAATGCGTTTACTACAAAGC‑ATTTTTCACATTACACACAATCAGCTATTCATTACAATCATAGAGTTGATTTAAAAGGCGATGTGCATCTTGTAGGGGTTAAAGATGACaa                                       <  2:235913/141‑1 (MQ=255)

                                                                                                gAACTTTGTAACGTTGACTTCGGATGAGTTCAATGCGTTTACTACAAAGC‑ATTTTTCACATTACACACAATCAGCTATTCATTACAATCATAGAGTTGATTTAAAAGGCGATGTGCATCTTGTAGGGGTTAAAGATGACaa                                       <  1:173991/141‑1 (MQ=255)

                                                                                                gAACTTTGTAACGTTGACTTCGGATGAGTTAAATGCGTTTACTACAAAGC‑ATTTTTCACATTACACACAATCAGCTATTCATTACAATCATAGAGTTGATTTAAAAGGCGATGTTCATCTTGTAGGGGTTAAAGATGACaa                                       >  2:144422/1‑141 (MQ=255)

                                                                                                   cTTTGTAACGTTGACTTCGGATGAGTTCAATGCGTTTA‑ATTGTAGCTGTTGTTCATATTACACACAATCAGCTATTCATTACAATCATAGAGTTGATTTAAAAGGCGATGTGCATCTTGTAGGGGTTAAAGATGACAATgg                                    <  2:214325/141‑1 (MQ=255)

                                                                                                          aCGTTGACTTCGGATGAGGTCAATGCGTTTACTACAAAGC‑ATTTTTCACATTACACACAATCAGCTATTCATTACAATCATAGAGTTGATTTAAAAGGCGATGTGCATCTTGTAGGGGTTAAAGATGACAATGGTCAAGTg                             <  2:180650/141‑1 (MQ=255)

                                                                                                              tcaCTTCGGAGCAGTTGAATGCGTTTAGTACAAATC‑ATTTTTTAAAGTACACACAATCAGCTATGCATTACAATCATAGAGGTGATTTAAAAGGGTATGTGCATCTGGTAGGGGTTAAAGATGACAATGGTCAAGTGATTg                         <  2:300613/139‑1 (MQ=255)

                                                                                                                         gAGTTCAATGCGTTTACTACAAAGC‑ATTTTTCACATTACACACAATCAGCTATTCATTACAATCATAGAGTTGATTTAAAAGGCGATGTGCATCTTGTAGGGGTTAAAGATGACAATGGTCAAGTGATTGCAGGATGCTTa              <  1:74989/141‑1 (MQ=255)

                                                                                                                         gAGTTCAATGCGTTTACTACAAAGC‑ATTTTTCACATTACACACAATCAGCTATTCATTACAATCATAGAGTTGATTTAAAAGGCGATGTGCATCTTGTAGGGGTTAAAGATGACAATGGTCAAGTGATTGCAGGATGCTTa              <  1:2280/141‑1 (MQ=255)

                                                                                                                              cAATGCGTTTACTACAAAGC‑ATTTTTCACATTACACACAATCAGCTATTCATTACAATCATAGAGTTGATTTAAAAGGCGATGTGCATCTTGTAGGGGTTAAAGATGACAATGGTCAAGTGATTGCAGGATGCTTATTGaa         >  1:205737/1‑140 (MQ=255)

                                                                                                                              cAATGCGTTTACTACAAAGC‑ATTTTTCACATTACACACAATCAGCTATTCATTACAATCATAGAGTTGATTTAAAAGGCGATGTGCATCTTGTAGGGGTTAAAGATGACAATGGTCAAGTGATTGCAGGATGCTTATTGAc         >  1:185690/1‑141 (MQ=255)

                                                                                                                                     tttACTACAAAGC‑ATTTTTCACATTACACACAATCAGCTATTCATTACAATCATAGAGTTGATTTAAAAGGCGATGTGCATCTTGTAGGGGTTAAAGATGACAATGGTCAAGTGATTGCAGGATGCTTATTGACAGAAgca  >  1:239656/1‑141 (MQ=255)

ATGTGTATTTGTAATCAGTTTTTGATAAAATAAAAAAATAGCATTATTAATAAATTCAAAAATTATAGTTCAATTCAGAGAGGGATGGGATAAAATGAACTTTGTAACGTTGACTTCGGATGAGTTCAATGCGTTTACAACAAAGC‑ATTTTTCACATTACACACAATCAGCTATTCATTACAATCATAGAGTTGATTTAAAAGGCGATGTGCATCTTGTAGGGGTTAAAGATGACAATGGTCAAGTGATTGCAGGATGCTTATTGACAGAAGCA  >  USA300TCH1516_ALE/2532160‑2532433

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