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
A5 F178 I0 R1	41	49.4	1100758	95.6%	1052324	140.0

Breseq alignment

BRESEQ :: Evidence

Predicted mutation
evidence	seq id	position	mutation	freq	annotation	gene	description
RA	USA300TCH1516_ALE	396,540	G→A	100%	A208T (GCA→ACA)	efeM →	putative iron uptake system component EfeM

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	USA300TCH1516_ALE	396,540	0	G	A	100.0%	150.1 / ‑6.5	50	A208T (GCA→ACA)	efeM	putative iron uptake system component EfeM
Reads supporting (aligned to +/- strand): ref base G (1/0); new base A (25/24); total (26/24)
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.

CATACCAAAATTAATGTTACAAGGTTCTGTTGACCTATTAAATGAAGTTGCAACTTCTAAAATCACAGGTGAAGAAGAAATTTATTCACATACAGATTTATATGATTTTAAAGCGAACGTTGAAGGCGCACAAAAAATTTATGACTTATTTAAACCTATTTTAGAGAAAAAAGATAAAAAATTAAGTGATGATATCCAAATGAACTTCGATAAAGTGAATCAATTATTGGATAAATATAAAGATAACAACGGCGGTTATGAGT  >  USA300TCH1516_ALE/396413‑396675

cATACCAAAATTAATGTTACAAGGTTCTGTTGACCTATTAAATGAAGTTGCAACTTCTAAAATCACAGGTGAAGAAGAAATTTATTCACATACAGATTTATATGATTTTAAAGCGAACGTTGAAGGCACACAAAAAAttt                                                                                                                             >  2:135738/1‑140 (MQ=255)

cATACCAAAATTAATGTTACAAGGTTCTGTTGACCTATTAAATGAAGTTGCAACTTCTAAAATCACAGGTGAAGAAGAAATTTATTCACATACAGATTTATATGATTTTAAAGCGAACGTTGAAGGCACACAAAAAAttt                                                                                                                             >  1:165797/1‑140 (MQ=255)

cATACCAAAATTAATGTTACAAGGTTCTGTTGAACTATTAAATGAAGTTGCAACTTCTAAAATCACAGGTGAAGAAGAAATTTATTCACATACAGATTTATATGATTTTAAAGCGAACGTTGAAGGCACACAGAAAAttt                                                                                                                             <  2:64681/140‑1 (MQ=255)

 aTACCAAAATTAATGTTACAAGGTTCTGTTGACCTATTAAATGAAGTTGCAACTTCTAAAATCACAGGTGAAGAAGAAATTTATTCACATACAGATTTATATGATTTTAAAGCGAACGTTGAAGGCACACAAAAAATTTa                                                                                                                            <  2:217977/140‑1 (MQ=255)

 aTACCAAAATTAATGTTACAAGGTTCTGTTGACCTATTAAATGAAGTTGCAACTTCTAAAATCACAGGTGAAGAAGAAATTTATTCACATACAGATTTATATGATTTTAAAGCGAACGTTGAAGGCACACAAAAAATTTa                                                                                                                            <  2:452171/140‑1 (MQ=255)

   aCCAAAATTAATGTTACAAGGTTCTGTTGACCTATTAAATGAAGTTGCAACTTCTAAAGTCACAGGTGAAGAAGAAATTTATTCACATACAGATTTATATGATTTTAAAGCGAACGTTGAAGGCACACAAAAAATTTATg                                                                                                                          >  1:332221/1‑140 (MQ=255)

    ccAAAATTAATGTTACAAGGTTCTGTTGACCTATTAAATGAAGTTGCAACTTCTAAAATCACAAGTGAAGAAGAAATTTATTCACATACAGATTTATATGATTTTAAAGCGAACGTTGAAGGCACACAAAAAATTTATGa                                                                                                                         >  2:153234/1‑140 (MQ=255)

     cAAAATTAATGTTACAAGGTTCTGTTGACCTATTAAATGAAGTTGCAACTTCTAAAATCACAGGTGAAGAAGAAATTTATTCACATACAGATTTATATGATTTTAAAGCGAACGTTGAAGGCACACAAAAAATTTATGAc                                                                                                                        <  1:217661/140‑1 (MQ=255)

        aaTTAATGTTACAAGGTTCTGTTGACCTATTAAATGAAGTTGCAACTTCTAAAATCACAGGTGAAGAAGAAATTTATTCACATACAGATTTATATGATTTTAAAGCGAACGTTGAAGGCACACAAAAAATTTATGACttc                                                                                                                     >  2:518965/1‑139 (MQ=255)

        aaTTAATGTTACAAGGTACTGTTGACCTATTAAATAAAGTGGCAACTTCTAAAAACACAGGTCAAGAAGAAATTTATTCACAAACAGATTTATATGATTTTAAAGGGAACGTTAAAGGCACACAAAAAATTTATGACTTa                                                                                                                     >  2:174816/1‑140 (MQ=255)

              tGTTTCAAGGTTCTGTTGACCTATTAAATGAAGTTGCAACTTCTAAAATCACAGGTGAAGAAGAAATTTATTCACATACAGATTTATATGATTTTAAAGCGAACGTTGAAGGCACACAAAAAATTTATGACTTATTTaaa                                                                                                               <  2:441699/140‑1 (MQ=255)

                 tACAAGGTTCTGTTGACCTATTAAATGAAGTTGCAACTTCTAAAATCACAGGTGAAGAAGAAATTTATTCACATACAGATTTATATGATTTTAAAGCGAACGTTGAAGGCACACAAAAAATTTATGACTTATTTAAACCt                                                                                                            <  2:386800/140‑1 (MQ=255)

                       gTTCTGTTGACCTATTAAATGAAGTTGCAACTTCTAAAATCACAGGTGAAGAAGAAATTTATTCACATACAGATTTATATGATTTTAAAGCGAACGTTGAAGGCACACAAAAAATTTATGACTTATTTAAACCTATTTTa                                                                                                      <  1:80789/140‑1 (MQ=255)

                        ttCTGTTGACCTATTAAATGAAGTTGCAACTTCTAAAATCACAGGTGAAGAAGAAATTTATTCACATACAGATTTATATGATTTTAAAGCGAACGTTGAAGGCACACAAAAAATTTATGACTTATTTAAACCTATTTTag                                                                                                     >  1:393124/1‑140 (MQ=255)

                        ttCTGTTGACCTATTAAATGAAGTTGCAACTTCTAAAATCACAGGTGAAGAAGAAATTTATTCACATACAGATTTATATGATTTTAAAGCGAACGTTGAAGGCACACAAAAAATTTATGACTTATTTAAACCTATTTTag                                                                                                     <  2:80198/140‑1 (MQ=255)

                        ttCTGTTGACCTATTAAATGAAGTTGCAACTTATAATATCACAGGTGAAGAAGAAATTTATTCAAATACAGATTTATATGATTTTAAAGCGAACGTTGAAGGCACACAAATCAGGTAAGACGTATTTAAACCTATTTTag                                                                                                     <  1:131566/140‑1 (MQ=255)

                            gTTGACCTATTAAATGAAGTTGCAACTTCTAAAATCACAGGTGAAGAAGCAATTTATTCACATACAGATTTATATGATTTTAAAGCGAACGTTGAAGGCACACAAAAAATTTATGACTTATTTAAAACTATTTTATAGaa                                                                                                 >  2:164059/1‑140 (MQ=255)

                            gTTGACCTATTAAATGAAGTTGCAACTTCTAAAATCACAGGTGAAGAAGAAATTTATTCACATACAGATTTATATGATTTTAAAGCGAACGTTGAAGGCACACAAAAAATTTATGACTTATTTAAACCTATTTTAGAGaa                                                                                                 >  1:436878/1‑140 (MQ=255)

                             ataaCCTATTAAATGAAGTTGCAACTTCTAAAATCACAGGGGAAGAAGAAATTTATTCACATACAGCTTTATATGATTTTAAAGCGAACGTTGAAGGCGCACAAAAAATATATGACTTAGTTAAACCTATTTAAGGGaaa                                                                                                >  2:452696/4‑140 (MQ=255)

                                  cTATTAAATGAAGTTGCAACTTCTAACATCACAGGTGAAGAAGAAATTTATTCACATACAGATTTATATGATTTTAAAGCGAACGTTGAAGGCACACAAAAAATTTATGACTTATTTAAACCTATTTTAGAGAAAAAAGa                                                                                           <  2:193916/140‑1 (MQ=255)

                                  atATTAAATGAAGTTGCAACTTATAAAATAACAGGTGAAGAAGAAATTTATTCACATACAGATTTATATGATTTTAAAGCGAACGTTGAAGGCACACAAAAAATTTATGACTTATTTAAACCTATTTTAGAGAAAAAAGa                                                                                           <  1:250056/139‑1 (MQ=255)

                                     ttAAATGAAGTTGCAACTTCTAAAATCACAGGTGAAGAAGAAATTTATTCACATACAGATTTATATGATTTTAAAGCGAACGTTGAAGGCACACAAAAAATTTATGACTTATTTAAACCTATTTTAGAGAAAAAAGATaa                                                                                        >  1:515158/1‑140 (MQ=255)

                                         aTGAAGTTGCAACTTCTAAAATCACAGGTGAATAAGAAATTTATTCACATACAGATTTATATGATTTTAAAGCGAACGTTGAAGGCACACAAAAAATTTATGACTTATTTAAACCTATTTTAGAGAAAAAAGATaaaaaa                                                                                    <  1:314010/140‑1 (MQ=255)

                                         aTGAAGGTGCAACTTCTAAAATCACAGGTGAAGAAGAAATTTATTCACATACAGATTTATATGATTTTAAAGCGAACGTTGAAGGCACACAAAAAATTTATGACTTATTTAAACCTATTTTAGAGAAAAAAGATaaaaaa                                                                                    <  2:466026/140‑1 (MQ=255)

                                           gAAGTTGCAACTTCTAAAATCACAGGTGAAGAAGAAATTTATTCACATACAGATTTATATGATTTTAAAGCGAACGTTGAAGGCACACAAAAAATTTATGACTTATTTAAACCTATTTTAAAGAAAAAAGATAAAAAAtt                                                                                  >  1:364203/1‑140 (MQ=255)

                                             aGTTGCAACTTCTAAAATCACAGGTGAAGAAGAAATTTATTCACATACAGATTTATATGATTTTAAAGCGAACGTTGAAGGCACACAAAAAATTTATGACTTATTTAAACCTATTTTAGAGAAAAAAGATAAAAAGTTaa                                                                                >  2:399953/1‑140 (MQ=255)

                                                 gCAACTTCTAAAATCCCGAGAAAATGAGAAATTTATTCACATACAGATTTATATGATTTTAAAGCGAACGTTGAAGGCACACAAAAAATTTATAACTTATTTAAACCTATTTTAGAGAAAAAAGATAAAAAATTAAGtga                                                                            >  2:530184/1‑140 (MQ=255)

                                                  cAACTTCTAAAATCACAGGTGAAGAAGAAATTTATTCACATACAGATTTATATGATTTTAAAGCGAACGTTGAAGGCACACAAAAAATTTATGACTTATTTAAACCTATTTTAGAGAAAAAAGATAAAAAATTAAGtgat                                                                           <  2:500190/140‑1 (MQ=255)

                                                    aCTTCTAAAATCACAGGTGAAGAAGAAATTTATTCACATACAGATTTATATGATTTTAAAGCGAACGTTGAAGGCACACAAAAAATTTATGACTTATTTAAACCTATTTTAGAGAAAAAAGATAAAAAATTAAGtgatga                                                                         >  2:394255/1‑140 (MQ=255)

                                                          aaaaTCACAGGTGAAGAAGAAATTTAATCACATACAGATTTATATGATTTTAAAGCGAACGTTGAAGGCACACAAAAAATTTATGACTTATTTAAACCTATTTTAGAGAAAAAAGATAAAAAATTAAGTGATGATATCCa                                                                   >  2:330563/1‑140 (MQ=255)

                                                           aaaTCAGAGGGGAATAAGAAATTTATTCACATATAGAGTTATATGATTTTAAAGCGAACGTTGAAGGCACACAAAAAATTTATGACTTATTTAAACCTATTTTAGAGAAAAAAGATAAAATATTAAGTGATGATATCCaa                                                                  <  2:446881/140‑1 (MQ=255)

                                                            aaTCACAGGTGAAGAAGAAATTTATTCACATACAGATTTATATGATTTTAAATCAAACGTTGAAGGCACACAAAAAATTTATGACTTATTTAAACCTATTTTAGAGAAAAAAGATAAAAAATTAATTGATGATATCCaaa                                                                 <  1:288022/140‑1 (MQ=255)

                                                            aaTCACAGGTGAAGAAGAAATTTATTCACATACAGATTTATATGATTTTAAAGCGAACGTTGAAGGCACACAAAAAATTTATGACTTATTTAAACCTATTTTAGAGAAAAAAGATAAAAAATTAAGTGATGATATCCaaa                                                                 <  2:52300/140‑1 (MQ=255)

                                                                        agaagaaATTTATTCACATACAGATTTATATGATTTTAAAGCGAACGTTTAAGGCACACAAAACATTTATGACTTATTTAAACCTATTTTAGAGAAAAAAGATAAAAAATTAAGTGATGATATCCAAATGAACTTCGATa                                                     >  1:121949/1‑140 (MQ=255)

                                                                               aTTTATTCACATACAGATTTATATGATTTTAAAACGAACGGTGAAGGCACACAAAAAATTTATGACTTATTTAAACCTATTTTAGAGAAAAAAGATAAAAAATTAAGTGATGATATCCAAATGAACTTCGATAAAGTGaa                                              <  1:511352/140‑1 (MQ=255)

                                                                                   aTTCACATACAGATTTATATGATTTTAAAGCGAACGTTGAAGGCACACAAAAAATTTATGACTTATTTAAACCTATTTTAGAGAAAAAAGATAAAAAATTAAGTGATGATATCCAAATGAACTTCGATAAAGTGAATCaa                                          <  2:165103/140‑1 (MQ=255)

                                                                                     tCACATACAGATTTATATGATTTTAAAGCGAACGTTGAAGGCACACAAAAAATTTATGACTTATTTAAACCTATTTTAGTGAAAAAAGATAAAAAATTAAGTGATGATATCCAAATGAACTTCGATAAAGTGAATCAatt                                        <  2:108996/140‑1 (MQ=255)

                                                                                        caTACAGATTTATATGATTTTAAAGCGAACGTTGAAGGCACACAAAAAATTTATGACTTATTTAAACCTATTTTAGATAAAAAAGATAAAAAATTAAGTGATGCTATCCAAATGAACTTCGATAAAGTGAATCAattatt                                     <  1:289341/140‑1 (MQ=255)

                                                                                            cAGATTTATATGATTTTAAAGCGAACGTTGAAGGCACACAAAAAATTTATGACTTATTTAAACCTATTTTAGAGAAAAAAGATAAAAAATTAAGTGATGATATCCAAATGAACTTCGATAAAGTGAATCAATTATTGGAt                                 <  1:219858/140‑1 (MQ=255)

                                                                                              gATTTATATGATTTTAAAGCGAACGTTGAAGGCACACAAAACATTTATGACTTATTTAAACCTATTTTAGAGAAAAAAGAAAAAAAATAAAGTGATGATATCCAAATAAACTTCGATAAAGTGAATCACTTATGGGATaa                               >  1:36835/1‑140 (MQ=255)

                                                                                                        aTTTTAAAGCGAACGTTGAAGGCACACAAAAAATTTATGACTTATTTAAACCTATTTTAGAGAAAAAAGATAAAAAATTAAGTGATGATATCCAAATGAACTTCGATAAAGTGAATCAATGATTGGAAAAATATAAAGAt                     >  2:51697/1‑140 (MQ=255)

                                                                                                        aTTTTAAAGCGAACGTTGAAGGCACACAAAAAATGTATGACTTATTTAAACCTATTTGAGATAAACAAGATAAAAAATTAAGTGATGATATCCAAATGAACTTCGATAAAGTGAATCAATCATTGGATAAACATAAAGAt                     >  2:407241/1‑140 (MQ=255)

                                                                                                            tAAAGCGAACGTTGAAGGCACACAAAAAATGTATGACTTAGTGAAACCTATTTTAGAGAAAAAAGATAAAAAATTAAGTTATGATATCCAAATGAACTTCGATAAAGTGAATCAATTATTGGATAAATATAAAGATaaca                 <  1:12981/140‑1 (MQ=255)

                                                                                                             aaaGCGAACGTTGAAGGCACACAAAAAATTTATGACTTATTTAAACCTATTTTAGAGAAAAAAGATAAAAAATTAAGTGATGATATCCAAATGAACTTCGATAAAGTGAATCAATTATTGGATAAATATAAAGATaacaa                >  1:222075/1‑140 (MQ=255)

                                                                                                              aaGCGAACGTTGAAGGCACACAAAAAATTTATGCCTTATTTGAACCTATTTTAGAGAAAAAAGATAAAAAATTAAGTGATGATATCCAAATGAACTTCGATAAAGTGAATCAATTATTGGATAAATATAAAGATaaaaac               >  2:90547/1‑140 (MQ=255)

                                                                                                              aaGCGAACGTTGAAGGCACACAAAAAATTTATGACTTATTTAAACCTATTTTAGAGAAAAAAGATAAAAAATTAAGTGATGATATCCAAATGAACTTCGATAAAGTGAATCAATTATTGGATAAATATAAAGATaacaac               <  1:135738/140‑1 (MQ=255)

                                                                                                                gCGAACGTTGAAGGCACACAAAAAATTTATGACTTATTTAAACCTATTTTAGAGAAAAAAGATAAAAAATTAAGTGATGATATCCAAATGAACTTCGATAAAGTGAATCAATTATTGGATAAATATAACGATAACAAcgg             >  2:202949/1‑140 (MQ=255)

                                                                                                                       ttGAAGGCACACAAAAAATTTATGACTTATTTAAACCTATTTTAGAGAAAAAAGATAAAAAATTAAGTGATGATATCCAAATGAACTTCGATAAAGTGAATCAATTATTGGATAAATATAAAGATAACAACGGCGGTTAt      >  1:530499/1‑140 (MQ=255)

                                                                                                                       ttGAAGGCACACAAAAAATTTATGACTTATTTAAACCTATTTTAGAGAAAAAAGATAAAAAATTAAGTGATGATATCCAAATGAACTTCGATAAAGTGAATCAATTATTGGATAAATATAAAGATAACAACGACGGTGAt      >  2:487212/1‑140 (MQ=255)

                                                                                                                           aGGCACACAAAAAATTTATGACTTATTTAAACCTATTTTAGAGAAAAAAGATAAAAAATTAAGTGATGATATCCAAATGAACTTCGATCAAGTGAATCAATTATTTGATAAATATAAAGATAACAACGACGGTTATGAGt  >  1:512684/1‑140 (MQ=255)

CATACCAAAATTAATGTTACAAGGTTCTGTTGACCTATTAAATGAAGTTGCAACTTCTAAAATCACAGGTGAAGAAGAAATTTATTCACATACAGATTTATATGATTTTAAAGCGAACGTTGAAGGCGCACAAAAAATTTATGACTTATTTAAACCTATTTTAGAGAAAAAAGATAAAAAATTAAGTGATGATATCCAAATGAACTTCGATAAAGTGAATCAATTATTGGATAAATATAAAGATAACAACGGCGGTTATGAGT  >  USA300TCH1516_ALE/396413‑396675

Alignment Legend
Aligned base mismatch/match (shaded by quality score): `ATCG/ATCG` `< 3 ≤` `ATCG/ATCG` `< 12 ≤` `ATCG/ATCG` `< 13 ≤` `ATCG/ATCG` `< 27 ≤` `ATCG/ATCG` `< 41 ≤` `ATCG/ATCG`
Unaligned base: `atcg` Masked matching base: `atcg` Alignment gap: `‑` Deleted base: `‑`

GATK/CNVnator alignment

N/A