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 F104 I0 R1	54	57.6	1336546	96.4%	1288430	141.0

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%	141.9 / NA	44	A208T (GCA→ACA)	efeM	putative iron uptake system component EfeM
Reads supporting (aligned to +/- strand): ref base G (0/0); new base A (27/17); total (27/17)
Rejected as polymorphism: Frequency below/above cutoff threshold.
Rejected as polymorphism: Variant not supported by required number of reads on each strand.

ATTAGATATCATACCAAAATTAATGTTACAAGGTTCTGTTGACCTATTAAATGAAGTTGCAACTTCTAAAATCACAGGTGAAGAAGAAATTTATTCACATACAGATTTATATGATTTTAAAGCGAACGTTGAAGGCGCACAAAAAATTTATGACTTATTTAAACCTATTTTAGAGAAAAAAGATAAAAAATTAAGTGATGATATCCAAATGAACTTCGATAAAGTGAATCAATTATTGGATAAATATAAAGATAACAACGGCGGTTA  >  USA300TCH1516_ALE/396404‑396670

aTTAGATATCATGCCAAAATTAATGTTACAAGGTTCTGTTGACCTATTAAATGAAGTTGCAACTTCTAAAATCACAGGTGAAGAAGAAATTTATTCACATACAGATTTATATGATTTTAAAGCGAACGTTGAAGGcacaca                                                                                                                                <  2:113084/141‑1 (MQ=255)

aTTAGATATCATACCAAAATTAACGTTACAAGGTTCTGTTGACCTATTAAATGAAGTTGCAACTTCTAAAATCACAGGTGAAGAAGAAATTTATTCACATACAGATTTATATGATTTTAAAGCGAACGTTGAAGGcacaca                                                                                                                                <  1:507263/141‑1 (MQ=255)

       atCATACCAAAATTAATGTTACAAGGTTCTGTTGACCTATTAAATGAAGTTGCAACTTCTAAAATCACAGGTGAAGAAGAAATTTATTCACATACAGATTTATATGATTTTAAAGCGAACGTTGAAGGCACACAAAAAAtt                                                                                                                         >  1:439842/1‑141 (MQ=255)

         cATACCAAAATGACTGTTACAACGCTCTGTTGACCTATTAAATGAAGTTGCAACTTCTAAAATCACAGGTGAAGAAGAAATTTATTCACATACAGATTTATATGATTTTAAAGCGAACGTTGAAGGCACACAAAAAATTTa                                                                                                                       <  1:499260/141‑1 (MQ=255)

          aTACCAAAATTAATGTTACAAGGTTCTGTTGACCTATTAAATGAAGTTGCAACTTCTAAAATCACAGGTGAAGAAGAAATTTATTCACATACAGATTTATATGATTTTAAAGCGAACGTTGAAGGCACACAAAAAATTTAt                                                                                                                      >  2:458033/1‑141 (MQ=255)

                aaaTTAATGTTACAAGGTTCTGTTGACCTATTAAATGAAGTTGCAACTTCTAAAATCACAGGTGAAGAAGAAATTTATTCACATACAGATTTATATGATTTTAAAGCGAACGTTGAAGGCACACAAAAAATTTATGACTTa                                                                                                                >  1:104562/1‑141 (MQ=255)

                aaaTTAATGTTACAAGGTTCTGTTGACCTATTAAATGAAGTTGCAACTTCTAAAATCACAGGTGAAGAAGAAATTTATTCACATACAGATTTATATGATTTGAAAGCGAACGTTGAAGGCACACAAAAAATTTATGACTTa                                                                                                                >  1:513404/1‑141 (MQ=255)

                                gTTCTGTTGACCTATTAAATGAAGTTGCAACTTCTAAAACCACAGGTGAAGAAGAAATTTATTCACATACAGATTTATATGATTTTAAAGCGAACGTTGAAGGCACACAAAAAATTTATGACTTATTTAAACCTATTTTag                                                                                                >  2:56525/1‑141 (MQ=255)

                                       tGACCTATTAAATGAAGTTGCAACTTCTAAAATCACAGGTGAAGAAGAAATTTATTCACATACAGATTTATATGATTTTAAAGCGAACGTTGAAGGCACACAAAAAATTTATGACTTATTTAAACCTATTTTAGAGaaaaa                                                                                         >  2:552854/1‑141 (MQ=255)

                                           ccatcaaaTGAAGTTGCAACTTCTAAAATCACAGGTGAAGAAGAAATTTATTCACATACAGATTTATATGATTTTAAAGCGAACATTGAAGGCACACAAAAAATTTATGACTTATTTAAACCTATTTTAGAGAAAAAAGAt                                                                                     >  2:576606/6‑141 (MQ=255)

                                            tATTAAATGAAGTTGCAACTTCTAAAATCACAGGTGAAGAAGAAATTTATACACATACAGATTTATATGATTTTAAAGCGAACGTTGAAGGCACACAAAAAATTTATGACTTATTTAAGCCTATTTTAGAGAAAAAAGATa                                                                                    <  2:560714/141‑1 (MQ=255)

                                             aTTAAATGAAGTTGCAACTTCTAAAATCACAGGTGAAGAAGAAATTTATTCACATACAGATTTATATGATTTTAAAGCGAACGTTGAAGGCACACAAAAAATTTATGACTTATTTAAACCTATTTTAGAGAAAAAAGATaa                                                                                   <  1:410959/141‑1 (MQ=255)

                                             aTTAAATGAAGTTACAACTTCTAAAATCACAGGTGAAGAAGAAATTTATTCACATACAGATTTATATGATTTTAAAGCGAACGTTGAAGGCACACAAAAAATTTATGACTTATTTAAACCTATTTTAGAGAAAAAAGATaa                                                                                   <  2:358412/141‑1 (MQ=255)

                                                aaaTGAAGTTGCAACTTCTAAAATCAAAGGTGAAGAAGAAATTTATTCACATACAGATTTATATGATTTTAAAGCGAACGTTGAAGGCACACAAAAAATTTATGACTTATTTAAACCTATTTTAGAGAAAAAAGATaaaaa                                                                                <  2:652605/141‑1 (MQ=255)

                                                  aTGAAGTTGCAACTTCTAAAATCACAGGTGAAGAAGAAATTTATTCACATCCAGATTTATGTGATTTTAAAGCGAACGTTGAAGTCACACAAAAAATTTATGACTTATTTCAACCTATTTTAGAGAAAAACGAGCAAAAAt                                                                              >  1:178001/1‑141 (MQ=255)

                                                     aaGTTGCAACTTCTAAAATCACAGGTGAAGAAGAAATTTATTCACATACAGATTTATATGATTTTAAAGCGAACGTTGAAGGCACACAAAAAATTTATGACTTATTTAAACCTATTTTAGAGAAAAAAGATCAAAAATTaa                                                                           >  1:241155/1‑141 (MQ=255)

                                                         tGCAACTTCTAAAATCACAGGTGAAGAAGAAATTTATTCACATACAGATTTATATGATTTTAAAGCGAACGTTGAAGGCACACAAAAAATTTATGACTTATTTAAACCTATTTTAGAGAAAAAAGATAAAAAATTAAGtga                                                                       >  1:253544/1‑141 (MQ=255)

                                                          gCAACTTCTAAAATCACAGGTGAAGAAGAAATTTATTCACATACAGATTTATATGATTTTAAAGCGAACGTTGAAGGCACACAAAAAATTTATGACTTATTTAAACCTATTTTAGAGAAAAAAGATAAAAAATTAAGtgat                                                                      >  2:600722/1‑141 (MQ=255)

                                                             aCTTCTAAAATCACAGGTGAAGAAGAAATTTATTCACATACAGATTTATATGATTTTAAAGCGAACGTTGAAGGCACACAAAAAATTTATGACTTATTTAAACCTATTTTAGAGAAAAAAGATAAAAAATTAAGTgatgat                                                                   >  1:663890/1‑141 (MQ=255)

                                                                tCTAAAATCACAGGTGAAGAAGAAATTTATTCACATACAGATTTATATGATTTTAAAGCGAACGTTGAAGGCACACAAAAAATTTATGACTTATTTAAACCTATTTTAGAGAAAAAAGATAAAAAATTAAGTGATGATATc                                                                <  1:43886/141‑1 (MQ=255)

                                                                                      aaaTTTATTCACATACAGATTTATATGATTTTAAAGCGAACGTTGAAGGCACACAAAAAATTTATGACTTATTTAAACCTATTTTAGAGAAAAAAGATAAAAAATTAAGTGATGATATCCAAATGAACTTCGATAAAGTGa                                          >  1:357481/1‑141 (MQ=255)

                                                                                       aaTTTATTCAAATACCGATTTATATGATTTTAAAGCGAACGTTGAAGGCACACAAAAAATTTATGACTTATTTAAACCTATTTTAGAGAAAAAAGAAAAAAAATTAAGTGATGATATCCAAATGAACTTCGATAAAGTGaa                                         <  2:3375/141‑1 (MQ=255)

                                                                                           tATTCACATACAGATTTATATGATTTTAAAGCGAACGTTGAAGGCACACAAAAAATTTATGACTTATTTAAACCTATTTTAGAGAAAAAAGATAAAAAATTAAGTGATGATATCCAAATGAACTTCGATAAAGTGAATCaa                                     >  1:475865/1‑141 (MQ=255)

                                                                                           tATTCACATACAGATTTATATGATTTTAAAGCGAACGTTGAAGGCACACAAAAAATGTATGACTTATTTAAACATATTTTAGAGCAGACAGATGAAAAATTAAGTGATGATATGCAAATGAACTGCGATAAAGTAAATCaa                                     >  1:20080/1‑141 (MQ=255)

                                                                                            aTTCACATACAGATTTATATGATTTTAAAGCGAACGTTGAAGGCACACAAAAAATTTATGACTTATTTAAACCTATTTTAGAGAAAAAAGATAACAAATTAAGTGATGATATCCAAATGAACTTCGATAAAGTGAATCAat                                    >  2:516262/1‑141 (MQ=255)

                                                                                              tCACATACAGATTTATATGATTTTAAAGCGAACGTTGAAGGCACACAAAAAATTTATGACTTATTTAAACCTATTTTAGAGAAAAAAGATAAAAAATTAAGTGATGATATCCAAATGAACTTCGATAAAGTGAATCAatta                                  >  2:11020/1‑141 (MQ=255)

                                                                                                acaTACAAATTTATAGGAATTTAAAGCCAACCTTGAAAACACAAAAAAAATGTATGACTTATTTAAACCTATTTTAGAGAAAAAAGATAAAAAATTAAGTGATGATATCCAAATGAACTTCGATAAAGTGAATCAattatt                                <  2:441508/141‑1 (MQ=255)

                                                                                                        aTTTATATGATTTTAAAGCGAACGTTGAAGGCACACAAAAAATTTATGACTTATTTAAACCTATTTTAGAGAAAAAAGATAACATCTTAATGAATGATATCCAAATGAACTTCGATAAAGTGAATCAATTATTGGATAAat                        >  1:185093/1‑141 (MQ=255)

                                                                                                        aTTTATATGATTTTAAAGCGAACGTTGAAGGCACACAAAAAATTTATGACTTATTTAAACCTATTTTAGAGAAAAAAGATAAAAAAATAAGGGATGATATCCAAATGAACTTCGATAAAGTGAATCAATTATTGGGTAAat                        >  1:185067/1‑141 (MQ=255)

                                                                                                           tataTGATTTTAAAGCGAACGTTGAAGGCACACAAAAAATTTATGACTTATTTAAACCTATTTTAGAGAAAAAAGATAAAAAATTAAGTGATGATATCCAAATGAACTTCGATAAAGTGAATCAATTATTGGATAAAtata                     >  1:17326/1‑141 (MQ=255)

                                                                                                             tatGATTTTAAAGCGAACGTTGAAGGCACACAAAAAATTTATGACTTATTTAAACCTATTTTAGAGAAAAAAGATAAAAAATTAAGTGATGATATCCAAATGAACTTCGATAAAGTGAATCAATTATTGGATAAATATaaa                   >  1:526103/1‑141 (MQ=255)

                                                                                                             tatGATTTTAAAGCGAACGTTGAAGGCACACAAAAAATTTATGACTTATTTAAACCTATTTTAGAGAAAAAAGATAAAAAATTAAGTGATGATATCCAAATGAACTTCGATAAAGTGAATCAATTATTGGATAAATATaaa                   >  2:360377/1‑141 (MQ=255)

                                                                                                                gATTTTAAAGCTAACGTTGAAGGCACACAAAAAATTTATGACTTATTTAAACCTATTTTAGAGAAAAAAGATAAAAAATTAAGTGATGATATCCAAATGAACTTCGATAAAGTGAATCAATTATTGGATAAATATAAAGAt                <  2:117073/141‑1 (MQ=255)

                                                                                                                gATTTTAAAGCGAACGTTGAAGGCACACAAAAAATTTATGACTTATTTAAACCTATTTTAGAGAAAAAAGATAAAAAATTAAGTGATGATATCCAAATGAACTTCGATAAAGTGAATCAATTATTGGATAAATATAAAGAt                <  1:536545/141‑1 (MQ=255)

                                                                                                                gATTTTAAAGCGAACGTTGAAGGCACACAAAAAATTTATGACTTATTTAAACCTATTTTAGAGAAAAAAGATAAAAAATTAAGTGATGATATCCAAATGAACGTCGATAAAGTGAATCAATTATTGGATAAATATAAAGAt                <  2:241155/141‑1 (MQ=255)

                                                                                                                gATTTTAAAGCGAACGTTGAAGGCAAACAAAAAATTTATGACTTATCTAAACCTATTTTATAGAAAAAAGATAAAAAATTAAGTGATGATATCCAAATGAACTTCGATAAAGTGAATCAATTATTGGATAAATATAAAGAt                <  2:269895/141‑1 (MQ=255)

                                                                                                                 aTTTTAAAGCGAACGTTGAAGGCACACAAAAAATTTATGACTTATTTAAACCTATTTTAGAGAAAAAAGATAAAAAATTAAGTGATGATATCCAAATGAACTTCGATAAAGTGAATCAATTATTGGATAAATATAAAGATa               >  1:452255/1‑141 (MQ=255)

                                                                                                                     tAAAGCGAACGTTGAATGCACACAAAAAATTTATGACTTATTTAAACCTATTTCAGAGAAAAAAGATAAAAAATTAAGTGATGATATCCAAATGAACTTCGATAAAGTGAATCAATTATTGGATAAATATAAAGATaacaa           <  2:364953/141‑1 (MQ=255)

                                                                                                                     tAAAGCGAACGTTGAAGCCACAAAAAAAATTTATGACTTATTTAAACCTATTTTAGAGAAAAAAGATAAAAAATTAAGTGATGATATCCAAATGAACTTCGATAAAGTGAATCAATTATTGGATAAATATAAAGATaacaa           <  1:265596/141‑1 (MQ=255)

                                                                                                                      aaaGCGAACGTTGAAGGCACACAAAAAATTTATGACTTATTTAAACCTATTTTAGAGAAAAAAGATAAAAAATTAAGTGATGATATCCAAATGAACTTCGATAAAGTGAATCAATTATTGGATAAATATAAAGATaacttc          <  2:120016/141‑4 (MQ=255)

                                                                                                                       aaGCGAACGTTGAAGGCACACAAAAAAATTATGACTTATTTAAACCTATGTTAGAGAAAAAAGATAAAAAATTAAGTGATGAGATCCAAATAAACTATGGTTAAGTGAATCAATTATTGGATAAATATAAAGATaacaaag         >  2:398945/1‑139 (MQ=255)

                                                                                                                         gCGAACGTTGAAGGCACACAAAAAATTTATGACTTATTTAAACCTATTTTAGAGAAAAAAGATAAAAAATTAAGTGATGATATCCAAATGAACTTCGATAAAGTGAATCAATTATAGGATAAAAATAAAGATAACAAcggg       >  2:355853/1‑140 (MQ=255)

                                                                                                                             aCGTTGAAGGCACACAAAAAATTTATGACTTATTTAAACCTATTTTAGAGAAAAAAGATAAAAAATTAAGTGATGATATCCAAATGAACTTCGATAAAGTGAATCAATTATTGGATAAATATAAAGATAACAACGGCGGtt   <  1:11020/141‑1 (MQ=255)

                                                                                                                             aCGTTGAAGGCACACAAAAAATTTATGACTTATTTAAACCTATTTTAGAGAAAAAAGATAAAAAATTAAGTGATGATATCCAAATGAACTTCGATAAAGTGAATCAATTATTGGATAAATATAAAGATAACAACGGAGGtt   >  2:59209/1‑141 (MQ=255)

                                                                                                                              cGTTGAAGGCACACAAAAAATTTATGACTTATTTAAACCTATTTTAGAGAAAAAAGATAAAAAATTAAGTGATGATATCCAAATGAACTTCGATAAAGTGAATCAATTATTGGATAAATATAAAGATAACAACGGCGGTTa  >  1:653524/1‑141 (MQ=255)

                                                                                                                              cGTTGAAGGCACACAAAAAATTTATGACTTATTTAAACCTATTTTAGAGAAAAAAGATAAAAAATTAAGTGATGATATCCAAATGAACTTCGATAAAGTGAATCAATTATTGGATAAATATAAAGATAACAACGGCGGTTa  <  1:535659/141‑1 (MQ=255)

ATTAGATATCATACCAAAATTAATGTTACAAGGTTCTGTTGACCTATTAAATGAAGTTGCAACTTCTAAAATCACAGGTGAAGAAGAAATTTATTCACATACAGATTTATATGATTTTAAAGCGAACGTTGAAGGCGCACAAAAAATTTATGACTTATTTAAACCTATTTTAGAGAAAAAAGATAAAAAATTAAGTGATGATATCCAAATGAACTTCGATAAAGTGAATCAATTATTGGATAAATATAAAGATAACAACGGCGGTTA  >  USA300TCH1516_ALE/396404‑396670

Alignment Legend
Aligned base mismatch/match (shaded by quality score): `ATCG/ATCG` `< 3 ≤` `ATCG/ATCG` `< 12 ≤` `ATCG/ATCG` `< 22 ≤` `ATCG/ATCG` `< 32 ≤` `ATCG/ATCG` `< 41 ≤` `ATCG/ATCG`
Unaligned base: `atcg` Masked matching base: `atcg` Alignment gap: `‑` Deleted base: `‑`

GATK/CNVnator alignment

N/A