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
A23 F58 I0 R1	19	25.6	590480	94.5%	558003	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	100.0%	93.0 / NA	32	T15T (ACA→ACT)	femA_3	Aminoacyltransferase FemA
Reads supporting (aligned to +/- strand): ref base A (0/0); new base T (10/22); total (10/22)
Rejected as polymorphism: Frequency below/above cutoff threshold.
Rejected as polymorphism: Variant not supported by required number of reads on each strand.

TGTGTATTTGTAATCAGTTTTTGATAAAATAAAAAAATAGCATTATTAATAAATTCAAAAATTATAGTTCAATTCAGAGAGGGATGGGATAAAATGAACTTTGTAACGTTGACTTCGGATG‑AGTTCAATGCGTTTACAACAAAGCATTTTTC‑ACAT‑TACACACAATCAGCTATTCATTACAATCATAGAGTTGATTTAAAAGGCGATGTGCATCTTGTAGGGGTTAAAGATGACAATGGTCAAGTGATTGCAGGATGCTTATTGACAGAAGC  >  USA300TCH1516_ALE/2532161‑2532432

tgtgTATTTGTAATCAGTTTTTGATAAAATAAAAAAATAGCATTATTAATAAATTCAAAAATTATAGTTCAATTCAGAGAGGGATGGGATAAAATGAACTTTGTAACGTTGACTTCGGATG‑AGTTCAATGCGTTTactaca                                                                                                                                       >  1:75587/1‑141 (MQ=255)

    tctttGTAAGCAGTTTTTGATAAAATAAAAAAATAGCATTATTAATAAATTCAAAAATTATAGTTCAATTCAGAGAGGGATGGGATAAAATGAACTTTGTAACGTTGACTTCGGATG‑AGTTCAATGCGTTTACTACAAAGc                                                                                                                                   <  1:287337/139‑1 (MQ=255)

    tATTTGTAATCAGTTTTTGATAAAATAAAAAAATAGCATTATTAATAAATTCAAAAATTATAGTTCAATTCAGAGAGGGATGGGATAAAATGAACTTTGTAACGTTGACTTCGGATG‑AGTTCAATGCGTTTACTACAAAGc                                                                                                                                   <  1:233281/141‑1 (MQ=255)

    tATTTGTAATCAGTTTTTGATAAAATAAAAAAATAGCATTATTAATAAATTCAAAAATTATAGTTCAATTCAGAGAGGGATGGGATAAAATGAACTTTGTAACGTTGACTTCGGATG‑AGTTCAATGCGTTTACTACAAAGc                                                                                                                                   <  1:288064/141‑1 (MQ=255)

             tCAGTTTTTGATAAAATAAAAAAATAGCATTATTAATAAATTCAACAATTATAGTTCAATTCCGAGAGGGATGGGATAAAATGAACTTTGTAACGTTGACTTCGGATG‑CGTTCACTGCGTTTACTACAAGGCATCTTTc‑ac                                                                                                                         >  1:42553/1‑141 (MQ=255)

                  ttttGATAAAATAAAAAAATAGCATTATTAATAAATTCAAAAATTATAGTTCAATTCAGAGAGGGATGGGATAAAATGAACTTTGTAACGTTGACTTCGGATG‑AGTTCAATGCGTTTACTACAAAGCATTTTTC‑ACAT‑Tac                                                                                                                   >  2:205090/1‑141 (MQ=255)

                    ttGATAAAATAAAAAAATAGCATTATTAATAAATTCAAAAATTATAGTTCAATTCAGAGAGGGATGGGATAAAATGAACTTTGTAACGTTGACTTCGGATG‑AGTTCAATGCGTTTACTACAAAGCATTTTTC‑ACAT‑Tacac                                                                                                                 >  1:287530/1‑141 (MQ=255)

                      gATAAGAAAAAAAAATAGCATTATGAATAAATTCAAAAATGATAGTTGAAGTCAGAGAGGGATGGGATAAAATGAACTTTGTAACGTTGACTTCGGATG‑AGTTCAATGCGTTTACTACAAAGCATTTTTC‑ACAT‑Tacacac                                                                                                               <  2:225386/141‑1 (MQ=255)

                             taaaaAAATAGCATTATTAATAAATTCAAAAATTATAGTTCAATTCAGAGAGGGATGGGATAAAATGAACTTTGTAACGTTGACTTCGGATG‑AGTTCAATGCGTTTACTACAAAGCATTTTTC‑ACAT‑TACACACAATCAGc                                                                                                        <  1:202636/141‑1 (MQ=255)

                              aaataaatAGCATTATTAATAAATTCAAAAATTATAGTTCAATTCAGAGAGGGATGGGATAAAATGAACTTTGTAACGTTGACTTCGGATG‑AGTTCAATGCGTTTACTACAAAGCATTTTTC‑ACAT‑TACACACAATCAGCt                                                                                                       <  2:270218/141‑1 (MQ=255)

                                 aaaaTAGCATTATTAATAAATTCAAAAATTATAGTTCAATTCAGAGAGGGATGGGATAAAATGAACTTTGTAACGTTGACTTCGGATG‑AGTTCAATGCGTTTACTACAAAGCATTTTTC‑ACAT‑TACACACAATCAGCTAtt                                                                                                    >  1:110623/1‑141 (MQ=255)

                                     tAGCATTATTAATAAATTCAAAAATTATAGTTCAATTCAGAGAGGGATGGGATAAAATGAACTTTGTAACGTTGACTTCGGATG‑AGTTCAATGCGTTTACTACAAAGCATTTTT‑‑ACATCTACACACAATCAGCTATTCAtt                                                                                                >  2:176713/1‑141 (MQ=255)

                                         attattAATAAATTCAAAAATTATAGTTCAATTCAGAGAGGGATGGGATAAAATGAACTTTGTAACGTTGACTTCGGATG‑AGTTCAATGCGTTTACTACAAAGCATTTTTC‑ACAT‑TACACACAATCAGCTATTCATTACaa                                                                                            <  1:291648/141‑1 (MQ=255)

                                              taataaATTCAAAAATTATAGTTCAATTCAGAGAGGGATGGGATAAAATGAACTTTGTAACGTTGACTTCGGATG‑AGTTCAATGCGTTTACTACAAAGCATTTTTC‑ACAT‑TACACACAATCAGCTATTCATTACAATCATa                                                                                       >  1:236872/1‑141 (MQ=255)

                                                     ttCAAAAATTATAGTTCAATTCAGAGAGGGATGGGATAAAATGAACTTTGTAACGTTGACTTCGGATG‑AGTTCAATGCGTTTACTACAAAGCATTTTTC‑ACAT‑TACACACAATCAGCTATTCATTACAATCATAGAGTTGa                                                                                <  1:103323/141‑1 (MQ=255)

                                                           aaTTATAGTTCAATTCAGAGAGGGATGGGATAAAATGAACTTTGTAACGTTGACTTCGGATG‑AGTTCAATGCGTTTACTACAAAGCATTTTTC‑ACAT‑TACACACAATCAGCTATTCATTACAATCATAGAGTTGATTTaaa                                                                          <  2:276732/141‑1 (MQ=255)

                                                           aaTTATAGTGCAGTTCAGAGAGGGATGGGATAAAATGAACTTTGTAACGTTGACTTCGGATG‑AGTTCAATGCGTTTACTACAAAGCATTTTTC‑ACAT‑TACACACAATCAGCTATTCATTACAATCATAGAGTTGATTTaaa                                                                          <  2:177775/141‑1 (MQ=255)

                                                                  gTTCAATTCAGAGAGGGATGGGATAAAATGAACTTTGTAACGTTGACTTCGGATG‑AGTTCAATGCGTTTACTACAAAGCCTTTTTC‑ACAT‑TACACACAATCAGCTATTCATTACAATCATAGAGTTGATTTAAAAGGCGAt                                                                   <  1:42027/141‑1 (MQ=255)

                                                                       atgcAGAGAGGGATGGGATAAAATGAACTTTGTAACGTTGACTTCGGATG‑AGTTCAATGCGTTTACTACAAAGCATTTTTC‑ACAT‑TACACACAATCAGCTATTCATTACAATCATAGAGTTGATTTAAAAGGCGATGTGCa                                                              <  2:37360/138‑1 (MQ=255)

                                                                        ttCAGAGAGGGATTGGATAAAATGAACTTTGTAACGTTGACTTCGGATG‑AGTTCAATGCGTTTACTACAAAGCATTTTTC‑ACAT‑TACACACAATCAGCTATTCATTACAATCATAGAGTTGATTTAAAAGGCGATGTGCAt                                                             <  1:241694/141‑1 (MQ=255)

                                                                            gagagGGATGGGATAAAATGAACTTTGTAACGTTGACTTCGGATG‑AGTTCAATGCGTTTACTACAAAGCATTTTTC‑ACAT‑TACACACAATCAGCTATTCATTACAATCATAGAGTTGATTTAAAAGGCGATGTGCATCTTg                                                         >  1:161828/1‑141 (MQ=255)

                                                                            gagagGGATGGGATAAAATGAACTTTGTAACGTTGACTTCGGATG‑AGTTCAATGCGTTTACTACAAAGCATTTTTC‑ACAT‑TACACACAATCAGCTATTCATTACAATCATAGAGTTCATTTAAAAGGCGATGTTCATCTTg                                                         >  2:130860/1‑141 (MQ=255)

                                                                                gggatgggatAAAATGAACTTTGTAACGTTGACTTCGGATG‑AGTTCAATGCGTTTACTACAAAGCATTTTTC‑ACAT‑TACACACAATCAGCTATTCATTACAATCATAGAGTTGATTTAAAAGGCGATGTGCATCTTGTAgg                                                     >  1:243195/1‑141 (MQ=255)

                                                                                gggatgggaaTAAATTGAGTTTGTAACGTTGACTTCGGATG‑AGTTAAATGCGTTTACTACAAAGCATTTTTC‑ACAT‑TACACACAATCAGCTATTCATTACAATCATAGGGTTGATTTAAAAGGCGATGTGCATCTTGTAgg                                                     <  2:175540/141‑1 (MQ=255)

                                                                                    tgggatAAAATGAACTTTGTAACGTTGACTTCGGATG‑AGTTCAATGCGTTTACTACACAGCATGTTCCAAAAA‑TTCA‑TTATTCAGCTATTCATTACAATCATAGAGTTGATTTAAAAGGCGATGTGCATCTTGTAGGGGtt                                                 >  1:68659/1‑141 (MQ=255)

                                                                                        atAAAATGAACTTTGTAACGTTGACTTCGGATG‑AGTTCAATGCTTTTACTACAAAGCATTTTTC‑ACAT‑TACACACAATCAGCTATTCATTACAATCATAGAGTTGATTTAAAAGGCGATGTGCATCTTGTAGGGGTTAAAg                                             <  1:240870/141‑1 (MQ=255)

                                                                                             aTGGACTTTGTAACGTTG‑CATGTGTTGTAGTTCAATGCGGTTACTACAAAGCATTTTTC‑ACAT‑TACACACAATCAGCTATTCATTACAATCATAGAGTTGATTTAAAAGGCGATGTGCATCTTGTAGGGGTTAAAGATGAc                                        <  2:253839/141‑1 (MQ=255)

                                                                                             aTGAACTTTGTAACGTTGACTTCGGATG‑AGTTCAATGCGTTTACTACAAAGCATTTTTC‑ACAT‑TACACACAATCAGCTATTCATTACAATCATAGAGTTGATTTAAAAGGCGATGTGCATCTTGTAGGGGTTAAAGATGAc                                        <  2:229703/141‑1 (MQ=255)

                                                                                                             tGACTTCGGATG‑AGTTCAATGCGTTTACTACAAAGCATTTTTC‑ACAT‑TACACACAATCAGCTATTCATTACAATCATAGAGTTGATTTAAAAGGCGATGTGCATCTTGTAGGGGTTAAAGATGACAATGGTCAAGTGATTg                        <  1:270659/141‑1 (MQ=255)

                                                                                                                   cGGATG‑AGTTCAATGCATTTACTACAATGCATTTTTC‑ACAT‑TACACACAATCAGCTATTCATGACAATCATAGAGTTGATTCAAAAGGCGATGTGCGTCTTGTAGGGGTTAAAGATGACAATGGTCAAGTGATTGCAGGAt                  <  2:194976/141‑1 (MQ=255)

                                                                                                                   cGGATG‑AGTTCAAGGCGTTTACTACAAAGCATTTTTC‑ACAT‑TACACACAATCAGCTATTCATTACAATCATAGAGTTGATTTAAAAGGCGAGGTGCATCTTGTAGGGGTTAAAGATGACAATGGTCAAGTGATTGCAGGAt                  <  2:42553/141‑1 (MQ=255)

                                                                                                                          aGTTCAATGCGTTTACTACAAAGCATTTTTC‑ACAT‑TACACACAATCAGCTATTCATTACAATCATAGAGTTGATTTAAAAGGCGATGTGCATCTTGTAGGGGTTAAAGATGACAATGGTCAAGTGATTGCAGGATGCTTAt            <  1:118392/141‑1 (MQ=255)

                                                                                                                                    gTTTACTACAAAGCATTTTTC‑ACAT‑TACACACAATCAGCTATTCATTACAATCATAGAGTTGATTTAAAAGGCGATGTGCATCTTGTAGGGGTTAAAGATGACAATGGTCAAGTGATTGCAGGATGCTTATTGACAGAAgc  <  2:118178/141‑1 (MQ=255)

TGTGTATTTGTAATCAGTTTTTGATAAAATAAAAAAATAGCATTATTAATAAATTCAAAAATTATAGTTCAATTCAGAGAGGGATGGGATAAAATGAACTTTGTAACGTTGACTTCGGATG‑AGTTCAATGCGTTTACAACAAAGCATTTTTC‑ACAT‑TACACACAATCAGCTATTCATTACAATCATAGAGTTGATTTAAAAGGCGATGTGCATCTTGTAGGGGTTAAAGATGACAATGGTCAAGTGATTGCAGGATGCTTATTGACAGAAGC  >  USA300TCH1516_ALE/2532161‑2532432

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