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	59	38.6	831760	90.8%	755238	148.0

Breseq alignment

BRESEQ :: Evidence

Predicted mutation
evidence	seq id	position	mutation	annotation	gene	description
RA	CP000730	169,407	G→A	intergenic (+1374/‑130)	USA300HOU_0157 → / → USA300HOU_0160	nucleotidase/hypothetical protein

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	CP000730	169,407	0	G	A	100.0%	81.7 / NA	26	intergenic (+1374/‑130)	USA300HOU_0157/USA300HOU_0160	nucleotidase/hypothetical protein
Reads supporting (aligned to +/- strand): ref base G (0/0); new base A (14/12); total (14/12)

TAACTCACGAAGAAGAGGAATGGGGAAATTTAGAAAGACGTACTAAAAATAAATATAGAGATAAGTTGAAAAATATAGCGTCTATTGATTTGACAGATTTAATGAAAATATCTTTAAGAGGAAATGAAAACCAATTGCAAAAACAAATCGACTTTTGGTTGAATTAATTATTATAACTAAAGAACTATGTTCACTTATGCTCATCTACTTAAAATAAGTATTTTTTTGTTGGTTTTTAAAAGTAGTTGAAATGT  >  CP000730/169287‑169540

taACTCACGAAGAAGAGGAATGGGGAAATTTAGAAAGACGTACTAAAAATAAATATAGAGATAAGTTGAAAAATATAGCGTCTATTGATTTGACAGATTTAATGAAAATATCTTTAAGAGAAAATGAAAACCAATTGCAAAAACAAAt                                                                                                            >  2:49732/1‑148 (MQ=255)

taACTCACGAAGAAGAGGAATGGGGAAATTTAGAAAGACGTACTAAAAATAAATATAGAGATAAGTTGAAAAATATAGCGTCTATTGATTTGACAGATTTAATGAAAATATCTTTAAGAGAAAATGAAAACCAATTGCAAAAACAAAt                                                                                                            >  2:149063/1‑148 (MQ=255)

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

   cTCACGAAGAAGGGGAATGGGGAAATTTAGAAAGACGTACTAAAAATAAATATAGAGATAAGTTGAAAAATATAGCGTCTATTGATTTGACAGATTTAATGAAAATATCTTTAAGAGAAAATGAAAACCAATTGCAAAAACAAATCGa                                                                                                         >  2:353894/1‑148 (MQ=255)

   cTCACGAAGAAGAGGAATGGGGAAATTTAGAAAGACGTACTAAAAATAAATATAGAGATAAGTTGAAAAATATAGCGTCTATTGATTTGACAGATTTAATGAAAATATCTTTAAGAGAAAATGAAAACCAATTGCAAAAACAAATCGa                                                                                                         >  2:347703/1‑148 (MQ=255)

   cTCACGAAGAAGAGGAATGGGGAAATTTAGAAAGACGTACTAAAAATAAATATAGAGATAAGTTGAAAAATATAGCGTCTATTGATTTGACAGATTTAATGAAAATATCTTTAAGAGAAAATGAAAACCAATTGCAAAAACAAATCGa                                                                                                         >  2:269428/1‑148 (MQ=255)

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

         aagaagAGGAATGGGGAAATTTAGAAAGAAGTACTAAAAATAAATATAGAGATAAGTTGAAAAATATAGCGTCTATTGATTTGACAGATTTAATGAAAATATCTTTAAGAGAAAATGAAAAACAATTGAAAAAACAAATCGACTTTTg                                                                                                   <  2:15704/148‑1 (MQ=255)

                 gAATGGGGAAATTTAGAAAGACGTACTAAAAATAAATATAGAGATAAGTTGAAAAATATAGCGTCTATTGATTTGACAGATTTAATGAAAATATCTTTAAGAGAAAATGAAAACCAATTGCAAAAACAAATCGACTTTTGGTTGaatt                                                                                           <  2:313639/148‑1 (MQ=255)

                 gAATGGGGAAATTTAGAAAGACGTACTAAAAATAAATATAGAGATAAGTTGAAAAATATAGCGTCTATTGATTTGACAGATTTAATGAAAATATCTTTAAGAGAAAATGAAAACCAATTGCAAAAACAAATCGACTTTTGGTTGaatt                                                                                           <  2:186668/148‑1 (MQ=255)

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

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

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

                                                 taaataTATATATAAGTTGAAAAATATAGCTTCTATTGATTTGACAGATTTAAAAAAAATATCTTTAATAGAAAATGAAAAAAAAAAAAAAAAACAAATCGACTTTTGGTTGAATTAATTATTATAACTAAAGAACTATGTTCACTTa                                                           <  2:273444/148‑1 (MQ=255)

                                                    atatAGAGATAAGTTGAAAAATATAGCGTCTATTGATTTGACAGATTTAATGAAAATATCTTTAAGAGAAAATGAAAACCAATTGCAAAAACAAATCGACTTTTGGTTGAATTAATTATTATAACTAAAGAACTATGTTCACTTATGc                                                        >  2:29992/1‑148 (MQ=255)

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

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

                                                              aaGTTGAAAAATATAGCGTCTATTGATTTGACAGATTTAATGAAAATATCTTTAAGAGAAAATGAAAACCAATTGCAAAAACAAATCGACTTTTGGTTGAATTAATTATTATAACTAAAGAACTATGTTCACTTATGCTCATCTACtt                                              <  2:227705/148‑1 (MQ=255)

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

                                                                 ttGAAAAATATAGCGTCTATTGATGTGACAGATTTAATGAAAATATCTTTAAGAGAAAATGAAAACCAATTGCAAAAACAAATCGACTTTTGGTTGAATTAATTATTATAACTAAAGAACTATGTTCACTTATGCTCATCTACTTaaa                                           >  2:301220/1‑148 (MQ=255)

                                                                    aaaaaTATAGCGTCTATTGATTTGACAGATTTAATGAAAATATCTTTAAGAGAAAATGAAAACCAATTGCAAAAACAAATCGACTTTTGGTTGAATTAATTATTATAACTAAAGAACTATGTTCACTTATGCTCATCTACTTAAAATa                                        >  2:261319/1‑148 (MQ=255)

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

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

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

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

                                                                                                          aacatCTATAAGAGAAAAAGAAAACAAATAGCAAAAACAAATCGACTTTTGGTTGAATTAATTATTATAACTAAAGAACTATGTTAACTTATGATAATCTACTTAAAATAAGTATTTTTTTGTTGGTTTTTAAAAGTAGTTGAAATGt  <  2:352056/145‑1 (MQ=255)

TAACTCACGAAGAAGAGGAATGGGGAAATTTAGAAAGACGTACTAAAAATAAATATAGAGATAAGTTGAAAAATATAGCGTCTATTGATTTGACAGATTTAATGAAAATATCTTTAAGAGGAAATGAAAACCAATTGCAAAAACAAATCGACTTTTGGTTGAATTAATTATTATAACTAAAGAACTATGTTCACTTATGCTCATCTACTTAAAATAAGTATTTTTTTGTTGGTTTTTAAAAGTAGTTGAAATGT  >  CP000730/169287‑169540

Alignment Legend
Aligned base mismatch/match (shaded by quality score): `ATCG/ATCG` `< 3 ≤` `ATCG/ATCG` `< 12 ≤` `ATCG/ATCG` `< 32 ≤` `ATCG/ATCG` `< 41 ≤` `ATCG/ATCG`
Unaligned base: `atcg` Masked matching base: `atcg` Alignment gap: `‑` Deleted base: `‑`

GATK/CNVnator alignment

N/A