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 F59 I0 R1	41	42.9	928050	95.2%	883503	140.9

Breseq alignment

BRESEQ :: Evidence

Predicted mutation
evidence	seq id	position	mutation	freq	annotation	gene	description
RA	CP000730	396,540	G→A	100%	A208T (GCA→ACA)	USA300HOU_0364 →	possible lipoprotein

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	CP000730	396,540	0	G	A	100.0%	164.9 / ‑6.5	52	A208T (GCA→ACA)	USA300HOU_0364	possible lipoprotein
Reads supporting (aligned to +/- strand): ref base G (0/1); new base A (21/30); total (21/31)
Rejected as polymorphism: E-value score below prediction cutoff.
Rejected as polymorphism: Frequency below/above cutoff threshold.
Rejected as polymorphism: Variant not supported by required number of reads on each strand.

CATTAGATATCATACCAAAATTAATGTTACAAGGTTCTGTTGACCTATTAAATGAAGTTGCAACTTCTAAAATCACAGGTGAAGAAGAAATTTATTCACATACAGATTTATATGATTTTAAAGCGAACGTTGAAGGCGCACAAAAAATTTATGACTTATTTAAACCTATTTTAGAGAAAAAAGATAAAAAATTAAGTGATGATATCCAAATGAACTTCGATAAAGTGAATCAATTATTGGATAAATATAAAGATAACAACGGCGGTTATG  >  CP000730/396403‑396672

cATTAGATATCATACAAAAATTAATGTTACAAGGTTCTGTTGACCTATTAAATGAAGTTGCAACTTCTAAAATCACAGGTGAAGAAGAAATTTATTCACATACAGATTTATATGATTTTAAAGCGAACGTTGAAGGCacac                                                                                                                                   <  1:210614/141‑1 (MQ=255)

  ttAGATACCATAACAAAATTAATGTTACAAGGTTCTGTTGACCTATTAAATGAAGTTGCAACTTCTAAAATCACAGGTGAAGAAGAAATTTATTCACATACAGATTTATATGATTTTAAAGCGAACGTTGAAGGCACACaa                                                                                                                                 <  2:27511/141‑1 (MQ=255)

      atatCATACCAAAATTAATGTTACAAGGTTCTGTTGACCTATTAAATGAAGTTGCAACTTCTAAAATCACAGGTGAAGAAGAAATTTATTCACATACAGATTTATATGATTTTAAAGCGAACGTTGAAGGCACACaaaaaa                                                                                                                             <  2:376731/141‑1 (MQ=255)

       tattatACCAAAATTAATTTTACAAGGTTCTGTTGACCTATTAAATGAAGTTGCAACTTCTAAAATCACAGGTGAAGAAGAAATTTATTCACATACAGATTTATATGATTTTAACGCGAACGTTGAAGTCACACAAAAAAt                                                                                                                            <  2:386963/141‑1 (MQ=255)

           aTACCAAAATTAATGTTACAAGGTTCTGTTGACCTATTAAATGAAGTTGCAACTTCTAAAATCACAGGTGAAGAAGAAATTTATTCACATACAGATTTATATGATTTTAAAGCGAACGTTGAAGGCACACAAAAAATTTAt                                                                                                                        <  1:347973/141‑1 (MQ=255)

            tACCAAAATTAATGTTACAAGGTTCTGGTGACCTATTAAATGAAGTTGCAACTTCTAAAAACACAGGTGAAGAAGAAATTTATTCACATACAGATTTATATGATTTTAAAGCGAACGTTGAAGGCACACAAAAAATTTATg                                                                                                                       <  1:152168/141‑1 (MQ=255)

             aCCAAAATTAATGTTACAAGGTTCTGTTGACCTATTAAATGAAGTTGCAACTTCTAAAATCACAGGTGAAGAAGAAATTTATTCACATACAGATTTATATGATTTTAAAGCGAACGTTGAAGGCACACAAAAAATTTATGa                                                                                                                      >  1:163420/1‑141 (MQ=255)

              ccAAAATTAATGTTACAAGGTTCTGTTGACCTATTAAATGAAGTTGCAACTTCTAGAATCACAGGTGAAGAAGAAATTTATTCACATACAGATTTATATGATTTGAAAGCGAACGTTGAAGGCACACAAAAAATTTATGAc                                                                                                                     <  2:385286/141‑1 (MQ=255)

              acAAAATTAATGTTACAAGGTTCTGTTGACCTATTAAATGAAGTTGCAACTTCTAAAATCACAGGTGAAGAAGAAATTTATTCACATACAGATTTATATGATTTTAAAGCGAACGTTGAAGGCACACAAAAAATTTATGAc                                                                                                                     <  1:233556/140‑1 (MQ=255)

               cataaTTAATGTTATAAGGTTCGGTGGACCTATTAAATGAAGTTGCTAGTTCTAAAATCCCAGGTGAAGAAGAAATTTATTCACATACAGATTTATATGATTTTAAAGCGAACGTTGAAGGCACACAAAAAATTTATGACt                                                                                                                    <  2:136940/138‑1 (MQ=255)

               cAAAATTACTGTTACAAGGCTCTGTTAACCTATTAAATAAAGTTGCAACTTATAAAACCACAAGCGAAGCAGAAATCTATTCACATACAGATTTATATGATTTTAAAGCGAACGTTCCAGAAACACAAAAAATTTATGACt                                                                                                                    <  2:231573/141‑1 (MQ=255)

                  aaTTAATGTTACAAGGTTCTGTTGACCTATTAAATGAAGTTGCAACTTCTAAAATCACAGGTGAAGAAGAAATTTATTCACATACAGATTTATATGATTTTAAAGCGAACGTTGAAGGCACACAAAAAATTTATGACTTAt                                                                                                                 >  1:43168/1‑141 (MQ=255)

                  aaTTAATGTTACAAGGTTCTGTTGACCTATTAAATGAAGTTGCAACTTCTAAAATCACAGGTGAAGAAGAAATTTATTCACATACAGATTTATATGATTTTAAAGCGAACGTTGAAGGCACACAAAAAATTTATGACTTAt                                                                                                                 >  2:371708/1‑141 (MQ=255)

                  aaTTAATGTTACAAGGTTCTGTTGACCTATTAAATGAAGTTGCAACTTCTAAAATCACAGGTGAAGAAGAAATTTATTCACATACAGATTTATATGATTTTAAAGCGAACGTTGAAGGCACACAAAAAATTTATGACTTAt                                                                                                                 >  1:37945/1‑141 (MQ=255)

                   aTTAATGTTACAAGGTTCTGTTGACCTATTAAATGAAGTTGCAACTTCTAAAATCACAGGTGAAGAAGAAATTTATTCACATACAGATTTATATGATTTTAAAGCGAACGTTGAAGGCACACAAAAAATTTATGACTTAtt                                                                                                                <  2:311233/141‑1 (MQ=255)

                        tGTTACAAGGTTCTGTTGACCTATTAAATGAAGTTGCAACTTCTAAAATCACAGGTGAAGAAGAAATTTATTCACATACAGATTTATATGATTTTAAAGCGAACGTTGAAGGCACACAAAAAATTTATGACTTATTTAAAc                                                                                                           >  2:371433/1‑141 (MQ=255)

                                ggTTCTGTTGACCTATTAAATGAAGTTGCAACTTCTAAAATCACAGGTGAAGAAGAAATTTATTCACATACAGATTTATATGATTTTAAAGCGAACGTTGAAGGCACACAAAAAATTTATGACTTATTTAAACCTATTTTa                                                                                                   <  1:161906/141‑1 (MQ=255)

                                ggTTCTGTTGACCTATTAAATGAAGTTGCAACTTCTAAAATCACAGGTGAAGAAGAAATTTATTCACATACAGATTTATATGATTTTAAAGCGAACGTTGAAGGCACACAAAAAATTTATGACTTATTTAAACCTATTTTa                                                                                                   <  1:186815/141‑1 (MQ=255)

                                      gTTGACCTATTAAATGAAGTTGCAACTTCTAAAATCACAGGTGAAGAAGAAATTTATTCACATACAGATTTATATGATTTTAAAGCGAACGTTGAAGGCACACAAAAAATTTATGACTTATTTAAACCTATTTTAGAGaaa                                                                                             >  1:460328/1‑141 (MQ=255)

                                      gTTGACCTATTAAATGAAGTTGCAACTTCTAAAATCACAGGTGAAGAAGAAATTTATTCACATACAGATTTATATGATTAAAAATCGAACGTTGAAGGCACACAAAAAATTTATGACTTATTTAAACCTATTTTAGAGaaa                                                                                             >  1:106468/1‑141 (MQ=255)

                                       tttaCCTATTAAATGAAGTTGCAACTTCTAAAATCACAGGTGAAGAAGAAATATATTCACATACAGACTCATATGACTTTAAAGCGCACGTTGAAGGCACACAAAAAATTTATGACTTATTTAAACCTATATTAGCGaaaa                                                                                            >  2:132997/4‑141 (MQ=255)

                                       ttGACCTATTAAATGAAGTTGCAACTTCTAAAATCACAGGTGAAGAAGAAATTTATTCACATACAGATTTATATGATTTTAAAGCGAACGTTGAAGGCACACAAAAAATTTATGACTTATTTAAACCTATTTTAGAGaaaa                                                                                            >  2:10402/1‑141 (MQ=255)

                                       ttGACCTATTAAATGAAGTTGCAACTTCTAAAATCACAGGTGAAGAAGAAATTTATTCACATACAGATTTATATGATTTTAAAGCGAACGTTGAAGGCACACAAAAAATTTATGACTTATTTAAACCTATTTTAGAGaaaa                                                                                            <  1:25169/141‑1 (MQ=255)

                                             aataaaaTGAAGCTGGAAAGTCTAAAATCAAAGGGGAAGAAGAAATTTATTCACATACAGATTTATATGATTTTAAAGCGAACGTTGAAGGCACACAAAAAATTTATGACTTATTTAAACCTATTTTAGAGAAAAAAGATa                                                                                      <  1:395705/137‑1 (MQ=255)

                                             aaTTAAATGAAAGTAAAACTTCCAAAAGCAAAGGTAAATAATAAATTTATTCACATACAGATTTATATGATTTTAAAGCGAACGTTGAAGGCACACAAAAAATTTATTACTTATTTAAACCTATTTTAGAGAAAAAAGATa                                                                                      <  2:346061/140‑1 (MQ=255)

                                               ttAAATGAAGTTGCAACTTCTAAAATCACAGGTGAAGAAGAAATTTATTCACATACAGATTTATATGATTTTAAAGCGAACGTTGAAGGCACACAAAAAATTTATGACTTATTTAAACCTATTTTAGAGAAAAAAGATaaa                                                                                    >  1:191337/1‑141 (MQ=255)

                                               ttAAATGAAGTTGCAACTTCTAAAATCACAGGTGAAGAAGAAATTTATTCACATACAGAATTATATGATTTTAAAGCGAACGTTGAAGGCACCCAAAAAATTTACGACTTATTTCAACCTCTCCTAGAGAACAAACATcaa                                                                                    >  2:310172/1‑141 (MQ=255)

                                                      aaGTTGCAACTTCTAAAATCACAGGTGAAGAAGACATTTATTTACCTAAAGGGGAATAACATGTTAAAGCGAAGGTTGAAGGCACACAAAAAATTTATGACTTATTTAAACCTATTTTAGAGAAAAAAGATAAAAAATTaa                                                                             <  1:87309/141‑1 (MQ=255)

                                                         ttGCAACTTCTAAAATCACAGGTGAAGAAGAAATTTATTCACATACAGATTTATATGATTTTAAAGCGAACGTTGAAGGCACACAAAAAATTTATGACTTATTTAAACCTATTTTAGAGAAAAAAGATAAAAAATTAAGtg                                                                          <  1:434714/141‑1 (MQ=255)

                                                           tgaaCTTCTAAAATCACAGGTGAAAAAGATATTTATTCACATACAGATTTATATGATTTTAAAGCGAACGTTGAAGGCACACAAAAAATTTATGACTTATTTAAACCTATTTTAGAGAAAAAAGATAAAAAATTAAGtgat                                                                        <  1:366367/139‑1 (MQ=255)

                                                             aaCTTCTAAAATCACAGGTGAAGAAGAAATTTATTCACATACAGATTTATATGATTTTAAAGCGAACGTTGAAGGCACACAAAAAACTTATGACTTATTTAAACCTATTTTAGAGAAAAAAGATAAAAAATTAAGtgatga                                                                      <  1:308313/141‑1 (MQ=255)

                                                                 tCTAAAATCACAGGTGAAGAAGAAATTTATTCACATACAGATTTATATGATTTTAAAGCGAACGTTGAAGGCACACAAAAAATTTATGACTTATTTAAACCTATTTTAGAGAAAAAAGATAAAAAATTAAGTGATGATATc                                                                  >  1:141134/1‑141 (MQ=255)

                                                                     aaaTCACAGGTGAAGAAGAAATTTATTCACATACAGATTTATATGATTTTAGAGCGAACGTTGAAGGCACACAAAAAATTTATGACTTATTTAAACCTATTTTAGAGAAAAAAGATAAAAAATTAAGTGATGATATCCaaa                                                              >  2:47873/1‑141 (MQ=255)

                                                                     aaaTCACAGGTGAAGAAGAAATTTATTCACATACAGATTTATATGAGTTTAAAGCGAACGTTGAAGGCACACAAAAAATTTATGACTTAGTTAAACCTATTTTAGAGAAAAAAGATAAAAAATTAAGTGATGATATCCaaa                                                              <  2:81064/141‑1 (MQ=255)

                                                                     aaaGCACAGGGGAAGAAGAAATTTATTCACATACAGATTTAGATGATTTTAAAGCGAACGTTGAAGGCACACAAAAAATTTATGACTTATTTAAACCTATTTTAGAGAAAAAAGATAAAAAATTAAGTGATGATATCCaaa                                                              <  2:130072/141‑1 (MQ=255)

                                                                      aaTCACAGGTGAAGAAGAAATTTATTCACATACAGATTTATATGATTTTAAAGCGAACGTTGAAGGCACACAAAAAATTTATGACTTATTTAAACCTATTTTAGAGAAAAAAGATAAAAAATTAAGTGATGATATCCAAAt                                                             >  1:408173/1‑141 (MQ=255)

                                                                           caagtaaaaaagaaATTTATACACATACAAAATTAAATGATTTTAAAGCGAACGTTGAAGGCACACAAAAAATTTATGACTTATTTAAACCTAGTTTAGAGAAAAAAGATAAAAAATTAAGTGATGATATCCAAATGAACt                                                        <  1:319643/132‑1 (MQ=255)

                                                                               tGAAGAAGAAATTTATTCACATACAGATTTATATGATTTTAAAGCGAACGTTGAAGGCACACAAAAAATTTATGACTTATTTAAACCTATTTTAGAGAAAAAAGATAAAAAATTAAGTGATGATATCCAAATGAACTTCGa                                                    >  1:7845/1‑141 (MQ=255)

                                                                               tGAAGAAAAAATTTAATCACATACAGATTTATATGATTGTAAAGCGATCGTTGAAGGCACACAAAAAATGTATGACTTATTTAAACCTATTTGAGAGAAAAAAGATAAAAAATTAAGTGATGATATCCAAATGAACTTCGa                                                    <  2:63392/141‑1 (MQ=255)

                                                                                        aagttATTCACACACAGATTTATATGCTTTTAATGCGAACGTTTAAGGCACAAATAAAATTTATGCCTTATTTAAACCTATATTAGAGAAAAGAGATAAAAAATTAAGTGATGATATCCAATTGAACTTGTATATAGTGaa                                           <  2:258276/138‑1 (MQ=255)

                                                                                                cacaTACAGATTTATATGATTTTAAAGCGAACGTTGAAGGCACACAAAAAATTTATGACTTATTTAAACCTATTTTAGAGAAAAAAGATAAAAAATTAAGTGATGATATCCAAATGAACTTCGATAAAGTGACTCAattat                                   >  2:51213/1‑141 (MQ=255)

                                                                                                cacaTACAGATTTATATGATTTTAAAGCGAACGTTGAAGGCACACAAAAAATTTATGACTTATTTAAACCTATTTTAGAGAAAAAAGATAAAAAATTAAGTGATGATATCCAAATGAACTTCGATAAAGTGAATCAattat                                   >  1:343074/1‑141 (MQ=255)

                                                                                                              tatGATTTTAAAGCGAACGTTGAAGGCACACAAAAAATTTATGACTTATTTAAACCTATTTTAGAGAAAAAAGATAAAAAATTAAGTGATAAAATACAAATGAACTTCGATAAAGTGAATCAATTATTGGATAAATATaaa                     >  1:431621/1‑141 (MQ=255)

                                                                                                               atGATTTTAAAGCGAACGTTGAAGGCACACAAAAAATTTATGACTTATTTAAACCTATTTTAGAGAAAAAAGATAAAAAATTAAGTGATGATATCCAAATGAACTTCGATAAAGTGAATCAATTATTGGATAAATATAAAg                    >  1:450432/1‑141 (MQ=255)

                                                                                                                  aTTTTAAAGCGAACGTTGAAGGCACACAAAAAATTTATGACTTATTTAAACCTATTTTAGAGAAAAAAGATAAAAAATTAAGTGATGATATCCAAATGAACTTCGATAAAGTGAATCAATTATTGGATAAATATAAAGATa                 <  1:20925/141‑1 (MQ=255)

                                                                                                                  aTTTGAAAGCGAACGATGAATGCAGCTAAAAAATTTATGACTTATTTAAAACTATTTTAGAGAAAAAAGATAAAAAATTAAGTGATGATATCCAAATGAACTTCGATAAAGTGAATCAATTATTGGATAAATATAAAGATa                 <  2:394497/141‑1 (MQ=255)

                                                                                                                      tAAAGCGAACGTTGAAGGCACACAAAAAATTTATGACTTATTTAAACCTATTTTAGAGAAAAAAGATAAAAAATTAAGTGATGATATCCAAATGAACTTCGATAAAGTGAATCAATTATTGGATAAATATAAAGATaacaa             <  1:36697/141‑1 (MQ=255)

                                                                                                                         aGCGAACGTTGAAGGCGCACAAAAAATTTATGACTTATTTAAATAAAAAAAAAAAAAAAAAGATAAAAAATTAAGTGATGATATCCAAATGAACTTCGATAAAGTGAATCAATTATTGGATAAATATAAAGATAACAAcgg          <  2:105622/141‑1 (MQ=255)

                                                                                                                         aGCGAACGTTGAAGGCACACAAAAAATTTATGACTTATTTAAACCTATTTTAGAGAAAAAAGATAAAAAATTAAGTGATGATATCCAAATGAACTTCGATAAAGTGAATCAATTATTGGATAAATATAAAGATAACAAcgg          >  1:285058/1‑141 (MQ=255)

                                                                                                                         aGCGAACGTTGAAGGCACACAAAAAATTTATGACTTATTTAAACCTATTTTAGAGAAAAAAGATAAAAAATTAAGTGATGATATCCAAATGAACTTCGATAAAGTGAATCAATTATTGGATAAATATAAAGATAACAAcgg          >  2:237898/1‑141 (MQ=255)

                                                                                                                           cGAACGTTGAAGGCACACAAAAAATTTATGACTTATTTAAACCTATTTTAGAGAAAAAAGATAAAAAATTAAGTGATGATATCCAAATGAACTTCGATAAAGTGAATCAATTATTGGATAAATATAAAGATAACAAcggcg        <  1:371433/141‑1 (MQ=255)

                                                                                                                            gAACGTTGAAGGCACACAAAAAATTTATGACTTATTTAAACCTATTTTAGAGAAAAAAGATAAAAAATTAAGTGATGATATCCAAATGAACTTCGATAAAGTGAATCAATTATTGGATAAATATAAAGATAACAAcggcgg       <  1:177939/141‑1 (MQ=255)

                                                                                                                                 ttGAAGGCACACAAAAAATTTATGACTTATTTAAACCTATTTTAGAGAAAAAAGATAAAAAATTAAGTGATGATATCCAAATGAACTTCGATAAAGTGAATCAATTATTGGATAAATATAAAGATAACAACGGCGGTTATg  <  1:392333/141‑1 (MQ=255)

CATTAGATATCATACCAAAATTAATGTTACAAGGTTCTGTTGACCTATTAAATGAAGTTGCAACTTCTAAAATCACAGGTGAAGAAGAAATTTATTCACATACAGATTTATATGATTTTAAAGCGAACGTTGAAGGCGCACAAAAAATTTATGACTTATTTAAACCTATTTTAGAGAAAAAAGATAAAAAATTAAGTGATGATATCCAAATGAACTTCGATAAAGTGAATCAATTATTGGATAAATATAAAGATAACAACGGCGGTTATG  >  CP000730/396403‑396672

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