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 I1 R1	62	44.4	970160	98.1%	951726	147.0

Breseq alignment

BRESEQ :: Evidence

Predicted mutation
evidence	seq id	position	mutation	annotation	gene	description
RA	USA300TCH1516_ALE	169,407	G→A	G82E (GGA→GAA)	repE →	Replication initiation protein

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	USA300TCH1516_ALE	169,407	0	G	A	100.0%	100.0 / NA	30	G82E (GGA→GAA)	repE	Replication initiation protein
Reads supporting (aligned to +/- strand): ref base G (0/0); new base A (15/15); total (15/15)

CATTTATTAACTCACGAAGAAGAGGAATGGGGAAATTTAGAAAGACGTACTAAAAATAAATATAGAGATAAGTTGAAAAATATAGCGTCTATTGATTTGACAGATTTAATGAAAATATCTTTAAGAGGAAATGAAAACCAATTGCAAAAACAAATCGACTTTTGGTTGAATTAATTATTATAACTAAAGAACTATGTTCACTTATGCTCATCTACTTAAAATAAGTATTTTTTTGTTGGTTTTTAAAAGTAGTTGAAATGT  >  USA300TCH1516_ALE/169280‑169540

aaTTTATTAACGCACGAAGAAGAGGAATGGGGAAATTTAGAAAGACGTACTAAAAATAAATATAGAGATAAGTTGAAAAATATATCGTCTATTGATTTGACAGATTTAATGAAAATATCTTTAAGAGAAAATGAAAACCaa                                                                                                                          <  1:30568/140‑1 (MQ=255)

       taACTCACGAAGAAGAGGAATGGGGAAATTTAGAAAGACGTACTAAAAATAAATATAGAGATAAGTTGAAAAATATAGCGTCTATTGATTTGACAGATTTAATGAAAATATCTTTAAGAGAAAATGAAAACCAATTGCAAAAACAAAt                                                                                                            >  4:49732/1‑148 (MQ=255)

       taACTCACGAAGAAGAGGAATGGGGAAATTTAGAAAGACGTACTAAAAATAAATATAGAGATAAGTTGAAAAATATAGCGTCTATTGATTTGACAGATTTAATGAAAATATCTTTAAGAGAAAATGAAAACCAATTGCAAAAACAAAt                                                                                                            >  4:149063/1‑148 (MQ=255)

       taACTCACGAAGAAGAGGAATGGGGAAATTTAGAAAGACGTACTAAAAATAAATATAGAGATAAGTTGAAAAATATAGCGTCTATTGATTTGACAGATTTAATGAAAATATCTTTAAGAGAAAATGAAAACCAATTGCAAAAACAAAt                                                                                                            >  3:284589/1‑148 (MQ=255)

          cTCACGAAGAAGGGGAATGGGGAAATTTAGAAAGACGTACTAAAAATAAATATAGAGATAAGTTGAAAAATATAGCGTCTATTGATTTGACAGATTTAATGAAAATATCTTTAAGAGAAAATGAAAACCAATTGCAAAAACAAATCGa                                                                                                         >  4:353894/1‑148 (MQ=255)

          cTCACGAAGAAGAGGAATGGGGAAATTTAGAAAGACGTACTAAAAATAAATATAGAGATAAGTTGAAAAATATAGCGTCTATTGATTTGACAGATTTAATGAAAATATCTTTAAGAGAAAATGAAAACCAATTGCAAAAACAAATCGa                                                                                                         >  4:347703/1‑148 (MQ=255)

          cTCACGAAGAAGAGGAATGGGGAAATTTAGAAAGACGTACTAAAAATAAATATAGAGATAAGTTGAAAAATATAGCGTCTATTGATTTGACAGATTTAATGAAAATATCTTTAAGAGAAAATGAAAACCAATTGCAAAAACAAATCGa                                                                                                         >  4:269428/1‑148 (MQ=255)

                aagaagAGGAATGGGGAAATTTAGAAAGACGTACTAAAAATAAATATAGAGATAAGTTGAAAAATATAGCGTCTATTGATTTGACAGATTTAATGAAAATATCTTTAAGAGAAAATGAAAACCAATTGCAAAAACAAATCGACTTTTg                                                                                                   <  3:16486/148‑1 (MQ=255)

                aagaagAGGAATGGGGAAATTTAGAAAGAAGTACTAAAAATAAATATAGAGATAAGTTGAAAAATATAGCGTCTATTGATTTGACAGATTTAATGAAAATATCTTTAAGAGAAAATGAAAAACAATTGAAAAAACAAATCGACTTTTg                                                                                                   <  4:15704/148‑1 (MQ=255)

                        gAATGGGGAAATTTAGAAAGACGTACTAAAAATAAATATAGAGATAAGTTGAAAAATATAGCGTCTATTGATTTGACAGATTTAATGAAAATATCTTTAAGAGAAAATGAAAACCAATTGCAAAAACAAATCGACTTTTGGTTGaatt                                                                                           <  4:313639/148‑1 (MQ=255)

                        gAATGGGGAAATTTAGAAAGACGTACTAAAAATAAATATAGAGATAAGTTGAAAAATATAGCGTCTATTGATTTGACAGATTTAATGAAAATATCTTTAAGAGAAAATGAAAACCAATTGCAAAAACAAATCGACTTTTGGTTGaatt                                                                                           <  4:186668/148‑1 (MQ=255)

                                          aGACGTACTAAAAATAAATATAGAGATAAGTTGAAAAATATAGCGTCTATTGATTTGACAGATTTAATGAAAATATCTTTAAGAGAAAATGAAAACCAATTGCAAAAACAAATCGACTTTTGGTTGAATTAATTATTATAACTAAAGa                                                                         <  3:228283/148‑1 (MQ=255)

                                          aGACGTACTAAAAATAAATATAGAGATAAGTTGAAAAATATAGCGTCTATTGATTTGACAGATTTAATGAAAATATCTTTAAGAGAAAATGAAAACCAATTGCAAAAACAAATCGACTTTTGGTTGAATTAATTATTATAACTAAAGa                                                                         <  3:401242/148‑1 (MQ=255)

                                                     aaataaatATAGAGATAAGTTGAAAAATATAGCGTCTATTGATTTGACAGATTTAATGAAAATATCTTTAAGAGAAAATGAAAACCAATTGCAAAAACAAATCGACTTTTGGTTGAATTAATTATTATAACTAAAGAACTATGTTCAc                                                              >  3:374490/1‑148 (MQ=255)

                                                        taaataTATATATAAGTTGAAAAATATAGCTTCTATTGATTTGACAGATTTAAAAAAAATATCTTTAATAGAAAATGAAAAAAAAAAAAAAAAACAAATCGACTTTTGGTTGAATTAATTATTATAACTAAAGAACTATGTTCACTTa                                                           <  4:273444/148‑1 (MQ=255)

                                                           atatAGAGATAAGTTGAAAAATATAGCGTCTATTGATTTGACAGATTTAATGAAAATATCTTTAAGAGAAAATGAAAACCAATTGCAAAAACAAATCGACTTTTGGTTGAATTAATTATTATAACTAAAGAACTATGTTCACTTATGc                                                        >  4:29992/1‑148 (MQ=255)

                                                             ataGAGATAAGTTGAAAAATATAGCGTCTATTGATTTGACAGATTTAATGAAAATATCTTTAAGAGAAAATGAAAACCAATTGCAAAAACAAATCGACTTTTGGTTGAATTAATTATTATAACTAAAGAACTATGTTCACTTATGCTc                                                      <  3:193226/148‑1 (MQ=255)

                                                               agagATAAGTTGAAAAATATAGCGTCTATTGATTTGACAGATTTAATGAAAATATCTTTAAGAGAAAATGAAAACCAATTGCAAAAACAAATCGACTTTTGGTTGAATTAATTATTATAACTAAAGAACTATGTTCACTTATGCTCAt                                                    >  3:378276/1‑148 (MQ=255)

                                                                     aaGTTGAAAAATATAGCGTCTATTGATTTGACAGATTTAATGAAAATATCTTTAAGAGAAAATGAAAACCAATTGCAAAAACAAATCGACTTTTGGTTGAATTAATTATTATAACTAAAGAACTATGTTCACTTATGCTCATCTACtt                                              <  4:227705/148‑1 (MQ=255)

                                                                        ttGAAAAATATAGCGTCTATTGATTTGACAGATTTAATGAAAATATCTTTAAGAGAAAATGAAAACCAATTGCAAAAACAAATCGACTTTTGGTTGAATTAATTATTATAACAAAAGAACTATGTTCACTTATGCTCATCTACTTaaa                                           >  3:167143/1‑148 (MQ=255)

                                                                        ttGAAAAATATAGCGTCTATTGATGTGACAGATTTAATGAAAATATCTTTAAGAGAAAATGAAAACCAATTGCAAAAACAAATCGACTTTTGGTTGAATTAATTATTATAACTAAAGAACTATGTTCACTTATGCTCATCTACTTaaa                                           >  4:301220/1‑148 (MQ=255)

                                                                           aaaaaTATAGCGTCTATTGATTTGACAGATTTAATGAAAATATCTTTAAGAGAAAATGAAAACCAATTGCAAAAACAAATCGACTTTTGGTTGAATTAATTATTATAACTAAAGAACTATGTTCACTTATGCTCATCTACTTAAAATa                                        >  4:261319/1‑148 (MQ=255)

                                                                                  taGCGTCTATTGATTTGACAGATTTAATGAAAATATCTTTAAGAGAAAATGAAAACCAATTGCAAAAACAAATCGACTTTTGGTTGAATTAATTATTATAACTAAAGAACTATGTTCACTTATGCTCATCTACTTAAAATa                                        <  2:67295/141‑1 (MQ=255)

                                                                                               tttGACAGATTTAATGAAAATATCTTTAAGAGAAAATGAAAACCAATTGCAAAAACAAATCGACTTTTGGTTGAATTAATTATTATAACTAAAGAACTATGTTCACTTATGCTCATCTACTTAAAATAAGTATTTTTTTGTTGGtttt                    >  3:254632/1‑148 (MQ=255)

                                                                                                     aGATTTAATGAAAATATCTTTAAGAGAAAATGAAAACCAATTGCAAAAACAAATCGACTTTTGGTTGAATTAATTATTATAACTAAAGAACTATGTTCACTTATGCTCATCTACTTAAAATAAGTATTTTTTTGTTGGTTTTTAAAag              <  3:25079/148‑1 (MQ=255)

                                                                                                          tAATGAAAATATCTTTAAGAGAAAATGAAAACCAATTGCAAAAACAAATCGACTTTTGGTTGAATTAATTATTATAACTAAAGAACTATGTTCCCTTATGTTCATCTACTTAAAATAAGTATTTTTTTGTTGGTTTTTaaa                >  1:29569/1‑141 (MQ=255)

                                                                                                              gAAAATATCTTTAAGAGAAAATGAAAACCAATTGCAAAAACAAATCGACTTTTGGTTGAATTAATTATTATAACTAAAGAACTATGTTCACTTATGCTCATCTACTTAAAATAAGTATTTTTTTGTTGGTTTTTAAAAGTAGTTGaaa     <  3:203512/148‑1 (MQ=255)

                                                                                                               aaaaTATCTTTAAGAGAAAATGAAAACCAATTGCAAAAACAAATCGACTTTTGGTTGAATTAATTATTATAACTAAAGAACTATGTTCACTTATGCTCATCTACTTAACATAAGTATTTTTTTGTTGGTTTTTAAAAGTAGTTGAAAt    >  3:307348/1‑148 (MQ=255)

                                                                                                                 aacatCTATAAGAGAAAAAGAAAACAAATAGCAAAAACAAATCGACTTTTGGTTGAATTAATTATTATAACTAAAGAACTATGTTAACTTATGATAATCTACTTAAAATAAGTATTTTTTTGTTGGTTTTTAAAAGTAGTTGAAATGt  <  4:352056/145‑1 (MQ=255)

                                                                                                                 aaTATCTTTAAAAGAAAATGAAATCCAATTGCAAAAACAAATCGACTTTTGGTTGAATTAATTATTATAACTAAAGAACTATGTTCACTTATGCTCATCTACTTAAAATAAGTATTTTTTTGTTGGTTTTTAAAAGTAGtt         <  2:53788/141‑1 (MQ=255)

CATTTATTAACTCACGAAGAAGAGGAATGGGGAAATTTAGAAAGACGTACTAAAAATAAATATAGAGATAAGTTGAAAAATATAGCGTCTATTGATTTGACAGATTTAATGAAAATATCTTTAAGAGGAAATGAAAACCAATTGCAAAAACAAATCGACTTTTGGTTGAATTAATTATTATAACTAAAGAACTATGTTCACTTATGCTCATCTACTTAAAATAAGTATTTTTTTGTTGGTTTTTAAAAGTAGTTGAAATGT  >  USA300TCH1516_ALE/169280‑169540

Alignment Legend
Aligned base mismatch/match (shaded by quality score): `ATCG/ATCG` `< 3 ≤` `ATCG/ATCG` `< 12 ≤` `ATCG/ATCG` `< 27 ≤` `ATCG/ATCG` `< 41 ≤` `ATCG/ATCG`
Unaligned base: `atcg` Masked matching base: `atcg` Alignment gap: `‑` Deleted base: `‑`

GATK/CNVnator alignment

N/A