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 F56 I1 R1	11	18.4	473212	93.6%	442926	129.0

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	100.0%	31.2 / NA	14	T15T (ACA→ACT)	femA_3	Aminoacyltransferase FemA
Reads supporting (aligned to +/- strand): ref base A (0/0); new base T (6/8); total (6/8)

TCAGTTTTTGATAAAATAAAAAAATAGCATTATTAATAAATTCAAAAATTATAGTTCAATTCAGAGAGGGATGGGATAAAATGAACTTTGTAACGTTGACTTCGGATGAGTTCAATGCGTTTACAACAAAGCATTTTTCACATTACACACAATCAGCTATTCATTACAATCATAGAGTTGATTTAAAAGGCGATGTGCATCTTGTAGGGGTTAAAGATGACAATGGTCAAGTGATTGCAGGATGCTTA  >  USA300TCH1516_ALE/2532174‑2532421

tCAGTTTTTGATAAAATAAAAAAATAGCATTATTAATAAATTCAAAAATTATAGTTCAATTCAGAGAGGGATGGGATAAAATGAACTTTGTAACGTTGACTTCGGATAAGATAAATGCGCTTActacaa                                                                                                                         >  2:137823/1‑129 (MQ=255)

tCAGTTTTTGATAAAATAAAAAAATAGCATTATTAATAAATTCAAAAATTATAGTTAAATTCAGAGAGGGATGGGATAAAATGAACTTTGTAACGTTGACTTCGGATGAGTTCAATGCGTTTAcaccaa                                                                                                                         >  2:231877/1‑129 (MQ=255)

   gTTTTTGATAAAATAAAAAAATAGCATTATTAATAAATTCAAAAATTATAGTTCAATTCAGAGAGGGATGGGATAAAATGAACTTTGTAACGTTGACTTCGGATGAGTTCAATGCGTTTACTACAAAGc                                                                                                                      >  1:131939/1‑129 (MQ=255)

             aaataaaaAAATAGCATTATTAATAAATTAAAAAATTATAGTTTTATTCAGAGAGGGATGGAATAAAATGAACTTTGTAAAGTTGACTTCTGATGATTTGAATGTGTTTACTATATAGCATTTTTctca                                                                                                            >  2:118001/1‑129 (MQ=255)

                        tAGCATTATTAATAAATTCAAAAATTATAGTTCAATTCAGAGAGGGATGGGATAAAATGAACTTTGTAAAGTTAACTTCGGATGAGTTCAATGCGTTTACTACAAAGCATTTTTCACATTACACACAAt                                                                                                 >  1:95410/1‑129 (MQ=255)

                                   ataaATGCAAACATTAAAGTTGCAGTGAGAGAGGGATGGGATAAAATGAACTTTGTAACGTTGACTTCGGATGAGTTCAATGCGTTTACTACAAAGCATTTTTCACATTACACACAATCAGCTATTCAt                                                                                      <  2:152974/129‑1 (MQ=255)

                                       atacAAAAATTATAGTTAAATTCAGAGATGGATGGGATAAAATTAACTTTGTAACGTTGACTTCGGATGAGTTTAATGCTTTTACTATAAAGCATTTTTCACATTACACACAATCAGCTATTCATTACa                                                                                  <  1:11389/126‑1 (MQ=255)

                                                      ttCAATTCAGAGAGGGATGGGATAAAATGAACTTTGTAACGTTGACTTCGGATGAGTTCAATGCGTTTACTACAAAGCATTTTTCACATTACACACAATCAGCTATTCATTACAATCATAGAGTTGAtt                                                                   >  2:209352/1‑129 (MQ=255)

                                                             cAGAGAGGCATGGGATAAAATGAACTTTGTAACGTTGACTTCGGATGAGTTCAATGCGTTTACTACAAAGCATTTTTCACATTACACACAATCAGCTATTCATTACAATCATAGAGTTGATTTAAAAgg                                                            <  2:212699/129‑1 (MQ=255)

                                                                    ggatgggatAAAATGAACTTTGTAACGTTGACTTCGGATGAGTTCAATGCGTTTACTACAAAGCATTTTTCACATTACACACAATCAGCTATTCATTACAATCATAGAGTTCATTTAAAAGGCGAtgtg                                                     <  2:179493/129‑1 (MQ=255)

                                                                     gatgggatAAAAAGAACTTTGTAACGTCGACTTCAGATGAGTTCAATGAGTTTACTACAAAGCATTTTTCACATTACACACAAACAGCTAGTAATTAGAATGATAGAGTTGATTTAAAAGACGATgcgc                                                    >  2:69131/1‑129 (MQ=255)

                                                                          gatAAAAGGAAGTTTGTAACGTTGACTTCGGATGAGTTCAATGCGTTTACTACAAAGTATTTTTCATATTACACATAATCAGCTATTCATTACAATCATAGAGTTGATTTAAAAGGCGATGTGCATCtt                                               <  1:86309/129‑1 (MQ=255)

                                                                           atAAAATGAACTTTGTAACGTTGACTTCGGATGAGTTCAATGCGTTTACTACAAAGCATTTTTCACATTACACACAATCAGCTATTCATTACAATCATAGAGTTGATTTAAAAGGCGATGTGCATCTTg                                              <  2:19690/129‑1 (MQ=255)

                                                                                                           gAGTTCAATGAGTTTACTACAAAGCATTTTTCACATTACACACAATCAGCTATTCATTACAATCATAGAGTTGATTTAAAAGGCGATGTGCATCTTGTAGGGGTTAAAGATGACAATGGTCAAGTGAtt              <  1:171382/129‑1 (MQ=255)

                                                                                                                  aTGCGTTTACTACAAAGCATTTTTCACATTACACACAATCAGCTATTCATTACAATCATAGAGTTGATTTAAAAGGCGATGTGCATCTTGTAGGGGTTAAAGATGACAATGGTCAAGTGATTGCAGGAt       <  2:131939/129‑1 (MQ=255)

                                                                                                                       tttACTACAAAGCATTTTTCACATTACACACAATCAGCTATTCATTACAATCATAGTGTTGATTTAAAAGGCGATGTGCATCTTGTAGGGGTTAAAGATGACACTGGTCAAGTGATTGTAGGATGCTTa  >  2:121036/1‑129 (MQ=255)

TCAGTTTTTGATAAAATAAAAAAATAGCATTATTAATAAATTCAAAAATTATAGTTCAATTCAGAGAGGGATGGGATAAAATGAACTTTGTAACGTTGACTTCGGATGAGTTCAATGCGTTTACAACAAAGCATTTTTCACATTACACACAATCAGCTATTCATTACAATCATAGAGTTGATTTAAAAGGCGATGTGCATCTTGTAGGGGTTAAAGATGACAATGGTCAAGTGATTGCAGGATGCTTA  >  USA300TCH1516_ALE/2532174‑2532421

Alignment Legend
Aligned base mismatch/match (shaded by quality score): `ATCG/ATCG` `< 3 ≤` `ATCG/ATCG` `< 12 ≤` `ATCG/ATCG` `< 13 ≤` `ATCG/ATCG` `< 22 ≤` `ATCG/ATCG` `< 41 ≤` `ATCG/ATCG`
Unaligned base: `atcg` Masked matching base: `atcg` Alignment gap: `‑` Deleted base: `‑`

GATK/CNVnator alignment

N/A