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
A9 F110 I0 R1	49	71.1	1529928	95.4%	1459551	140.9

Breseq alignment

BRESEQ :: Evidence

Predicted mutation
evidence	seq id	position	mutation	freq	annotation	gene	description
RA	CP000730	76,969	G→A	100%	intergenic (+1027/‑107)	USA300HOU_0072 → / → USA300HOU_0075	universal stress protein/lysophospholipase

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	CP000730	76,969	0	G	A	100.0%	174.0 / NA	55	intergenic (+1027/‑107)	USA300HOU_0072/USA300HOU_0075	universal stress protein/lysophospholipase
Reads supporting (aligned to +/- strand): ref base G (0/0); new base A (30/25); total (30/25)
Rejected as polymorphism: Frequency below/above cutoff threshold.
Rejected as polymorphism: Variant not supported by required number of reads on each strand.

CTTCAGATCTACGGATTTTCGCCATGCCACGAAATTAGCATCATGCTAGCAAGTTAAGCGAACACTGACATGATAAATTAGTGGTTAGCTATATTTTTTTACTTTGCAACAGAACCTATAAAAAACATGGGCTTAAAGGGTTAATTTATATAGTATTACTGCAAACATTGATTTGGGTCAAAAATTAGGGGTATTAAAAAAATGAATGAATCATAATTTTATCAAGCTGATTGGAGAGGTTAAAATGCATTATATAAAATTTATTGAGTCA  >  CP000730/76832‑77102

ttcgaGATCTACGGGTTTGTGCCATGCCACGAAGTTAGCATCATGCTAGCAAGTTAAGCGAATACTGACATGATAAATTAGTGGTTAGCTATAGTTTTTTACTTTGCAACAGAACCTATAAAAAACATGGGCTTAAAAGGt                                                                                                                                    <  2:57071/137‑1 (MQ=14)

ctTCAGATCTACGGATTTTCGCCATGCCACGAAATTAGCATCATGCTAGCAAGTTAAGCGAACACTGACATGATAAATTAGTGGTTAGCTATATTTTTTTACTTTGCAACAGAACCTATAAAAAACATGGGCTTAAAAGGt                                                                                                                                    >  1:395702/1‑141 (MQ=255)

ctTCAGATCTACGGATCTGCGCGATGCCACGAAATTAGCATCATGCTAGCAAGTTAAGCGAACACTGACATGATAAATTAGTGGTTAGCTATATTTTTTTACTTTGCAACAGAACCTATAAAAAACTTGGGCTTAAAAGGt                                                                                                                                    <  2:515717/141‑1 (MQ=14)

  tcagtgcTACGGATCTTCGCCATGGCACGAAATTAGCATCATGCTAGCAAGTTAAGCGAACACTGACATGATAAATTAGTGGTTAGCTATATTTTTTTACTTTGCAACAGAACCTATAAAAACCATGGTCTTAAAAGGTTa                                                                                                                                  <  2:237672/135‑1 (MQ=14)

          aCGGATTTTCGCCATGCCACGAAATTAGCATCATGCTAGCAAGTTAAGCGAACACTGACATGATAAATTAGTGGTTAGCTATATTTTTTTACTTTGCAACAGAACCTATAAAAAACATGGGCTTAAAAGGTTAATTtatat                                                                                                                          <  2:336306/141‑1 (MQ=255)

               ttttCGCCATGCCACGAAATTAGCATCATGCTAGCAAGTTAAGCGAACACTGACATGATAAATTAGTGGTTAGCTATATTTTTTTACTTTGCAACAGAACCTATAAAAAACATGGGCTTAAAAGGTTAATTTATATAGTAt                                                                                                                     >  1:31740/1‑141 (MQ=255)

                 ttCGCCATGCCGCGAAATTGGCATCATGCTAGCCACTTAAGCGAACACTGCCATGATACATTAGTGGTTAGCTATATTTTTCTACTTTGCAACAGAACCTATAAAAAACATGGGCTTAAAAGGTTAATTTATATAGTATTa                                                                                                                   <  1:18318/141‑1 (MQ=18)

                   cGCCATGCCACGAAATTAGCATCATGCTAGCAAGTTAAGCGAACACTGACATGATAAATTAGTGGTTAGCTATATTTTTTTACTTTGCAACAGCACCTATAAAAAACATGGGCTTAAAAGGTTAATTTATATAGTATTACt                                                                                                                 <  1:399810/141‑1 (MQ=255)

                          ccaaaaaaTTAGGAGCATGATAGCAAGTTAAACGAACAGTGACATGATAAATTAGTGGTTAGCTATATTTTTTTACTTTGTAAAAAAAAAAAAAAAAAACATGGGCTTAAAAGGTTAATTTATATAGTATTACTGCAAACa                                                                                                          <  2:451314/136‑1 (MQ=18)

                          ccACGAAATTAGCATCATGCTAGCAAGTTAAGCGAACACTGCCATGATAAATTAGTAGTTAGCTATATTTTTTTACTTTGCAACAGAAACTACATAACACATGGGCTTAAAAGGTTAATTTATATAGTATTACTGCAAACa                                                                                                          <  2:193050/141‑1 (MQ=18)

                           cACGAAATTAGCATCATGCTAGCAAGTTAAGCGAACACTGACATGATAAATTAGTGGTTAGCTATATTTTTTTACTTGGCAACAGAACCTATAAAAAACATGGGCTTAAAAGGTTAATTTATATAGTATTACTGCAAACAt                                                                                                         >  1:512398/1‑141 (MQ=255)

                                     gCATCATGCTAGCAAGTTAAGCGAACACTGACATGATAAATTAGTGGTTAGCTATATTTTTTTACTTTGCAACAGAACCTATAAAAAACATGGGCTTAAAAGGTTAATTTATATAGTATTACTGCAAACATTGATTTGGGt                                                                                               <  2:713184/141‑1 (MQ=255)

                                     gCATCATGCTAGCAAGTTAAGCGAACACTGACATGATAAATTAGTGGTAAGCTATATTTTTTTACTTTGCAACAGAACCTATAAAAAACATGGGCTTAAAAGGTTAATTTATATAGTATTACTGCAAACATTGAttttgtt                                                                                               >  1:716900/1‑137 (MQ=255)

                                      catcatGCTAGCAAGTTAAGCGAACACTGACATGATAAATTAGTGGTTAGCTATATTTTTTTACTTTGCAACAGAACCTATAAAAAACATGGGCTTAAAAGGTTAATTTATATAGTATTACTGCAAACATTGATTTGGGTc                                                                                              >  2:675340/1‑141 (MQ=255)

                                      catcatGCTAGCAAGTCAAGCGAACACTGACATGATAAATTAGTGGTTAGCTATATTTTTTTACTTTGCAACAGAACCTATAAAAAACATGGGCTTAAAAGGTTAATTTATATAGTATTACTGCAAACATTGATTTGGGTc                                                                                              >  1:388095/1‑141 (MQ=255)

                                             cTAGCAAGTTAAGCAAACACTGACATGATAAATTAGTGGTTAGCTATATTTTTTTAGTTTGCAACAGAACCTATAAAAAACATGGGCTTAAAAGGTTAATTTATATAGTATTACTGCAAACATTGATTTGGGTCAAAAAtt                                                                                       <  2:441378/141‑1 (MQ=255)

                                              tAGCAAGTTAAGCGAACACTGACATGATAAATTAGTGGTTAGCTATATTTTTTTACTTTGCAACAGAACCTATAAAAAACATGGGCTTAAAAGGTTAATTTATATAGTATTACTGCAAACATTGATTTGGGTCAACAATTa                                                                                      >  2:470520/1‑141 (MQ=255)

                                               aGCAAGTTAAGCGAACACTGACATGATAAATTAGTGGTTAGCTATATTTTTTTACTTTGCAACAGAACCTATAAAAAACATGGGCTTAAAAGGTTAATTTATATAGTATTACTACAAACATTGACTTGGGTCAAAAATTAg                                                                                     >  2:242184/1‑141 (MQ=255)

                                                     ttAAGCGAACACTGACATGATAAATTAGTGGTTAGCTATATTTTTTTACTTTGCAACAGAACCTATAAAAAACATGGGCTTAAAAGGTTAATTTATATAGTATTACTGCAAACATTGATTTGGGTCAAAAATTAGGGGTAt                                                                               <  2:119020/141‑1 (MQ=255)

                                                     ttAAGCGAACACTGAAATGATAAATTAGTGGTTAGGTATAGTTAATTAAAAAATAACAGAACAGAGAAAAAAAATGGGCACAAAATGTTAATCTAGATAGTATTACTGCAAACATTGGTTTGGGTCAAAAAtaaaaaaaaa                                                                               <  2:719075/141‑10 (MQ=255)

                                                     ttAAGCGAACAATGACATGATAAATTAGTGGTTAGCTATATTTTTTTACTTTGCAACAGATCCTATAAAAAACATGGGCTTAAAAGGTTAATTTATATAGTATTACTGCAAACATTGATGTGGGTCAAAAATTAGGGGTAt                                                                               <  1:391544/141‑1 (MQ=255)

                                                     tcaagtcaaCACAGACATGATAAATTAATGGTTAGTTATATTTTTATACATTACAACAAAACCAATAAAAAACATGGGCTTAAAAGGTTAATTCATATAGAATTAGTTCAAACATTGATTTGTCTCAAATATTaaaaaaaa                                                                               <  2:736789/134‑8 (MQ=255)

                                                        aGCGAACACTGACATGATAAATTAGTGGTTAGCTATATTTTTTTACTTTGCAACAGAACCTATAAAAAACATGGGCTTAAAAGGTTAATTTATATAGTATTACTGCAAACATTGATTTGGGTCAAAAATTAGGGGTATTaa                                                                            <  1:521239/141‑1 (MQ=255)

                                                             acacTGACATGATAAATTAGTGGTTAGCTATATTTTTTTACTTTGCAACAGAACCTATAAAAAACATGGGCTTAAAAGGTTAATTTATATAGTATTACTGCAAACATTGATTTGGGTCAAAAATTAGGGGTATTaaaaaaa                                                                       <  1:720226/141‑1 (MQ=255)

                                                                    cATTATAAATTAGTGGTAAGCAATATTTATTAACTTTGCAACAGAATCTATAAAAAACATGGGCTTAAAAGGTTAATTCATATAGTATTTCTGTAAACATTGATTTGTGTCAAAAATTAAAAAAAAAAAAAAAatgaatga                                                                <  2:433805/141‑1 (MQ=255)

                                                                    cATGATAAATTAGTGGTTAGCTATATTTTTTCAGTTTGGCCGTTATCCTATGAAAAACGTGGGCTTAAAAGGTTAATTTATATAGTATTACTGCAAACATTGATTTGGGTCAAAAATTAGGGGAATTAAAAAAatgaatga                                                                >  1:363748/1‑141 (MQ=255)

                                                                     aTGATAAATTAGTGGTTAGCTATATTTTTTTACTTTGCAACAGAACCTATAAAAAACATGGGCTTAAAAGGTTAATTTATATAGTATTACTGCAAACATTGATTTGGGTCAAAAATTAGGGGTATTAAAAAAAtgaatgaa                                                               >  2:186731/1‑141 (MQ=255)

                                                                        ataaataaGTGGTTATCTATATTTTTTTACTTTGCAACAGAACCTATAAAAAACATGGGCTTAAAAGGTTAATTTATATAGTATTACTGCAAACATTGATTTGGGTCAAAAATTAGGGGTATTAAAAAAATGAATGAATCa                                                            <  2:436711/141‑1 (MQ=255)

                                                                        agaaaTGAGTGGTTAGCTATACTTTTTTACTTTTCAACAGAAAGTACAAAAAAAATGTGCATAAAAGGTTAATTTATATAATATTATGGCAAATATTGATTTGGGTCAAAAATTAGGGGTATAAAAAAAATGAATGAATCa                                                            <  2:568528/139‑1 (MQ=255)

                                                                          aaaTTAGTGGTTAGCTATATTTTTTTACTTTGCAACAGAACCTATAAAAAACATGGGCTTAAAAGGTTAATTTATATAGTATTACTGCAAACATTGATTTGGGTCAAAAATTAGGGGTATTAAAAAAATGAATGAATCATa                                                          >  1:369513/1‑141 (MQ=255)

                                                                          aaaTTAGTGGTTAGCTATATTTTTTTACTTTGCAACAGAACCTATAAAAAACATGGGCTTAAAAGGTTAATTTATATAGTATTACTGCAAACATTGATTTGGGTCAAAAATTAGGGGTATTAAAAAAATGAATGAATCATa                                                          >  1:286845/1‑141 (MQ=255)

                                                                                 tGGTTAGCTATATTTTTTTACTTTGCAACAGAACCTATAAAAAACATGGGCTTAAAAGGTTAATTTATATAGTATTACTGCAAACATTGATTTGGGTCAAAAATTAGGGGTATTAAAAAAATGAATGAATCATAATTTTAt                                                   >  2:611855/1‑141 (MQ=255)

                                                                                  ggTTAGCTATATTTTTTTACTTTGCAACAGAACCTATAAAAAACATGGGCTTAAAAGGTTAATTTATATAGTATTACTGCAAACATTGATTTGGGTCAAAAATTAGGGGTATTAAAAAAATGAATGAATCATAATTTTAta                                                  >  2:741348/1‑140 (MQ=255)

                                                                                          atatTTTTTTACTTTGCAACAGAACCTATAAAAAACATGGGCTTAAAAGGTTAATTTATATAGTATTACTGCAAACATTGATTTGGGTCAAAAATTAGGGGGATTAAAAAAATGAATGAATCATAATTTTATCAAGCTGAt                                          >  2:749816/1‑141 (MQ=255)

                                                                                               tttttACTTTGCAACAGAACCTATAAAAAACATGGGCTTAAAAGGTTAATTTATATAGTATTACTGCAAACATTGATGTGGGTCAAAAATTAGGGGTATTAAAAAAATGAATGAATCATAATTTTATCAAGCTGATTGgag                                     >  1:484802/1‑141 (MQ=255)

                                                                                                     cTTTGCAACAGAACCTATAAAAAACATGGGCTTAAAAGGTTAATTTATATAGTATTACTGCAAACATTGATTTGGGTCAAAAATTAGGGGTATTAAAAAAATGAATGAATCATAATTTTATCAAGCTGATTGGAGAGGTTa                               >  2:422004/1‑141 (MQ=255)

                                                                                                         gCAACAGAACCTATAAAAAACATGGGCTTAAAAGGTTAATTTATATAGTATTACTGCAAACATTGATTTGGGTCAAAAATTAGGGGTATTAAAAAAATGAATGAATCATAATTTTATCAAGCTGATTGGAGAGGTTAAAAt                           >  1:26211/1‑141 (MQ=255)

                                                                                                          cAACAGAACCTATAAAAAACATGGGCTTAAAAGGTTAATTTATATAGTATTACTGCAAACATTGATTTGGGTCAAAAATTAGGGGTATTAAAAAAATGAATGAATCATAATTTTATCAAGCTGATTGGAGAGGTTAAAATg                          <  1:13669/141‑1 (MQ=255)

                                                                                                             cAGAACCTATAAAAAACATGGGCTTAAAAGGTTAATTTATATAGTATTACTGCAAACATTGATTTGGGTCAAAAATTAGGGGTATTAAAAAAATGAATGAATCATAATTTTATCAAGCTGATTGGGGAGGTTAAAATGCAt                       <  1:566515/141‑1 (MQ=255)

                                                                                                             cAGAACCTATAAAAAACATGGGCTTAAAAGGTTAATTTATATAGTATTACTGCAAACATTGATTTGGGTCAAAAATTAGGGGTATTAAAAAAATGAATGAATCATAATTTTATCAAGCTGATTGGAGAGGTTAAAATGCAt                       <  1:27701/141‑1 (MQ=255)

                                                                                                               gAACCTATAAAAAACATGGGCTTAAAAGGTTAATTTATATAGTATTACTGCAAACATTGATTTGGGTCAAAAATTAGGGGTATTAAAAAAATGAATGAATCATAATTTTATCAAGCTGATTGGAGAGGTTAAAATGCATta                     >  2:498244/1‑141 (MQ=255)

                                                                                                               gAACCTATAAAAAACATGGGCTTAAAAGGTTAATTTATATAGTATTACTGCAAACATGGAATTGGGTCAAAAATTAGGGGTATTAAAAAAATGAATGAATCATAATTTTATCAAGCTGATTGGAGAGGTTAAAATGCATta                     >  2:5478/1‑141 (MQ=255)

                                                                                                                aaCCTATAAAAAACATGGGCTTAAAAGGTTAATTTATATAGTATTACTGCAAACATTGATTTGGGTCAAAAATTAGGGGTATTAAAAAAATGAATGAATCATAATTTTATCAAGCTGATTGGAGGGGTTAAAATGCATtaa                    >  1:186744/1‑140 (MQ=255)

                                                                                                                   cTATAAAAAAGAGGGGCTTAAAAGGTTGATATATATAGTATTACTGCAAACATTAAAAAAAAAAAAAAATTAGGGGTATTAAAAAAATGAATGAATCATAATTTTATCAAGCTGATTGGAGAGGTTAAAATGCATtatata                 <  2:174955/141‑1 (MQ=255)

                                                                                                                    tataAAAAACATGGGCTTAAAAGGTTAATTTATATAGTATTACTGCAAACATTGATTTGGGTCAAAAATTAGGGGTATTAGAACAATTCTCTTTGCATAATTTTATCAAGCTGATTGGAGAGGTTAAAATGCATTAGATaa                >  1:714327/1‑141 (MQ=255)

                                                                                                                      taAAAAACATGGGCTTAAAAGGTTAATTTATATAGTATTACTGCAAACATTGATTTGGGTCAAAAATTAGGGGTATTAAAAAAATGAATGAATCATAATTTTATCAAGCTGATTGGAGAGGTTAAAATGCATTATATaaaa              >  1:523172/1‑141 (MQ=255)

                                                                                                                           aaCATGGGCTTAAAAGGTTAATTTATATAGTATTACTGCAAACATTGATTTGGGTCAAAAATTAGGGGTATTAAAAAAATGAATGAATCATAATTTTATCAAGCTGATTGGAGAGGTTAAAATGCATTATATAAAATTTAt         <  1:426087/141‑1 (MQ=255)

                                                                                                                            aCATGGGCTTAAAAGGTTAATTTATATAGTATTACTGCAAACATTGATTTGGGTCAAAAATTAGGGGTATTAAAAAAATGAATGAATAATACTTTTATCAAGCTGATTGGCGAGGTTAAAATGCATTATATAAAATTTAtt        >  1:530640/1‑141 (MQ=255)

                                                                                                                              aTGGGCTTAAAAGGTTAATTTATATAGTATTACTGCAAACATTGATTTGGGTCAAAAATTAGGGGTATTAAAAAAATGAATGAATCATAATTTTATCAAGCTGATTGGAGAGGTTAAAATGCATTATATAAAATTTATTGa      >  1:263414/1‑141 (MQ=255)

                                                                                                                               tGGGCTTAAAAGGTTAATTTATATAGTATTACTGCAAACATTGATTAGTTTCAAAAATTAGGGGTATTAAAAAAATGAATGAATCATAATTTTATCAAGCTGATTGGAGAGGTTAAAATGCATTATATAAAATTTATTGAg     >  1:593619/1‑141 (MQ=255)

                                                                                                                                gggCTTAAAATGTTAATTTATATAGTATTACTGTAAACATTGATTTGGGTCAAAAATTAGGGGTATTAAAAAAATTAATGAATCATAATTTTATCAAGCTGATTGGAGAGGTTAAAATGCATTATATAAAATTTATTGAGt    <  2:716900/141‑1 (MQ=255)

                                                                                                                                gggCTTAAAAGGTTAATTTATATAGTATTACTGCAAACATTGATTTGGGTCAAAAATTAGGGGTATTAAAAAAATGAATGAATCATAATTTTATCAAGCTGATTGGAGAGGTTAAAATGCATTATATGAGATTTATTGAGt    >  1:89475/1‑141 (MQ=255)

                                                                                                                                gggCTTAAAAGGTTAATTTATATAGTATTACTGCAAACATTGATTTGGGTCAAAAATTAGGGGTATTAAAAAAATGAATGAATCATAATTTTATCAAGCTGATTGGAGAGGTTAAAATGCATTATATAAAATTTATTGAGt    >  1:23145/1‑141 (MQ=255)

                                                                                                                                gggCTTAAAAGGTTAATTTATATAGTATTACTGCAAACATTGATTTGGATCAAAAAATAGGGTTATTAAAAAAATGACTGATTTAAAAGAGGAGCAAGCAGATTGGAGAGGTTAAAATGCATTATATAAAATTTATTGAGt    >  2:731789/1‑141 (MQ=255)

                                                                                                                                  gCTTAAAAGGTTAATTTATATAGTATTACTGCAAACATTGCTTTGGGTCAAAAATTAGGGGTATTAAAAAAATGAATGAATCATAATTTTATCAAGCTGATTGGAGAGGTTAAAATGAATTATATAAAATTTATTGAGTCa  >  2:491775/1‑141 (MQ=255)

CTTCAGATCTACGGATTTTCGCCATGCCACGAAATTAGCATCATGCTAGCAAGTTAAGCGAACACTGACATGATAAATTAGTGGTTAGCTATATTTTTTTACTTTGCAACAGAACCTATAAAAAACATGGGCTTAAAGGGTTAATTTATATAGTATTACTGCAAACATTGATTTGGGTCAAAAATTAGGGGTATTAAAAAAATGAATGAATCATAATTTTATCAAGCTGATTGGAGAGGTTAAAATGCATTATATAAAATTTATTGAGTCA  >  CP000730/76832‑77102

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