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 F58 I0 R1 46 56.2 1222162 96.0% 1173275 141.0

Breseq alignment

BRESEQ :: Evidence
Predicted mutation
evidence seq id position mutation freq annotation gene description
RA USA300TCH1516_ALE 396,540 G→A 11.5% 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_ALE396,5400GA11.5% 127.5 / 6.6 50A208T (GCA→ACA) efeMputative iron uptake system component EfeM
Reads supporting (aligned to +/- strand):  ref base G (27/17);  new base A (2/4);  total (29/21)
Fisher's exact test for biased strand distribution p-value = 2.23e-01
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 9.71e-01

ATACATTAGATATCATACCAAAATTAATGTTACAAGGTTCTGTTGACCTATTAAATGAAGTTGCAACTTCTAAAATCACAGGTGAAGAAGAAATTTATTCACATACAGATTTATATGATTTTAAAGCGAACGTTGAAGGCGCACAAAAAATTTATGACTTATTTAAACCTATTTTAGAGAAAAAAGATAAAAAATTAAGTGATGATATCCAAATGAACTTCGATAAAGTGAATCAATTATTGGATAAATATAAAGATAACAACGGCGGTTATGAGTCATTT  >  USA300TCH1516_ALE/396400‑396680
                                                                                                                                            |                                                                                                                                            
aTACATTAGATATCATACCAAAATTAATGTTACAAGGTTCTGTTGACCTATTAAATGAAGTTGCAACTTCTAAAATCACAGGTGAAGAAGAAATTTATTCACATACAGATTTATATGATTTTAAAGCGAACGTTGAAGgcg                                                                                                                                              <  2:377221/141‑1 (MQ=255)
 tACATTAGATATCATACCAAAATTAATGTTCCAAGGTTCTGTTGACCCATTAAATGAAGTTGCAACTTCTAAAATCACAGGTGAAGAAGAAATTTATTCACATACAGATTTATATGATTTTAAAGCGAACGTTGAAGccgc                                                                                                                                             >  2:128963/1‑141 (MQ=255)
 aaCATTAAATATAATACCAAAATTAATGTTACAAGGTTCTGTTGACCTATTCAATGAAGTTGCAACTTCTAAAATCACAGGTTAAGAAGAAATTTATGCACATACAGATTTATATGATTTTAAAGCGAACGTTTAAGgcgc                                                                                                                                             <  2:388674/140‑1 (MQ=255)
   cATTATATATCATACAAAAATTAATGTTACAAGGTTCTGTTGACCTATTAAATGCAGTTGCAACTTCTAAAATCACAGGTGAAGAAGAAATTTATTCACATACAGATTTATATGATTCTAAAGCGAACGTTGAAGGCGcac                                                                                                                                           <  1:72864/141‑1 (MQ=255)
   cATTAGATATCATACCAAAATTAATGTTACAAGGTTCTGTTGACCTATTAAATGAAGTTGCAACTTCTAAAATCACAGGTGAAGAAGAAATTTATTCACATACAGATTTATATGATTTTAAAGCGAACGTTGAAGGCGcac                                                                                                                                           <  2:499226/141‑1 (MQ=255)
     ttAGATATCATACCAAAATTAATGTTACAAGGTTCTGTTGACCTATTAAATGAAGTTGCAACTTCTAAAATCACAGGTGAAGAAGAAATTTATTCACATACAGATTTATATGATTTTAAAGCGAACGTTGAAGGCGCACaa                                                                                                                                         >  2:200728/1‑141 (MQ=255)
           atCATACCAAAATTAATGTTACAAGGTTCTGTTGACCTATTAAATGAAGTTGCAACTTCTAAAATCACAGGTGAAGAAGAAATTTATTCACATACAGATTTATATGATTTTAAAGCGAACGTTGAAGGCGCACAAAAAAtt                                                                                                                                   >  1:522946/1‑141 (MQ=255)
               tACCAAAATTAATGTTACAAGGTTCTGTTGACCTATTAAATGAAGTTGCAACTTCTAAAATCACAGGTGAAGAAGAAATTTATTCACATACAGATTTATATGATTTTAAAGCGAACGTTGAAGGCGCACAAAAAATTTATg                                                                                                                               <  2:399369/141‑1 (MQ=255)
                  cAAAATTAATGTTACAAGGTTCTGTTGACCTATTAAATGAAGTTGCAACTTCTAAAATCACAGGTGAAGAAGAAATTTATTCACATACAGATTTATATGATTTTAAAGCGAACGTTGAAGGCACACAAAAAATTTATGACt                                                                                                                            <  1:544827/141‑1 (MQ=255)
                  cAAAATTAATGTTACAAGGTTCTGTTGACCTATTAAATGAAGTTGCAACTTCTAAAATCACAGGTGAAGAAGAAATTTATTCACATACAGATTTATATGATTTTAAAGCGAACGTTGAAGGCACACAAAAAATTTATGACt                                                                                                                            <  1:249009/141‑1 (MQ=255)
                  cAAAATTAATGTTACAAGGTTCTGTTGACCTATTAAATGAAGTTGCAACTTCTAAAATCACAGGTGAAGAAGAAATTTATTCACATACAGATTTATATGATTTTAAAGCGAACGTTGAAGGCACACAAAAAATTTATGACt                                                                                                                            <  1:571919/141‑1 (MQ=255)
                      aTTAATGTTACAAGGTTCTGTTGACCTATTAAATGAAGTTGCAACTTCTAAAATCACAGGTGAAGAAGAAATTTATTCACATACAGATTTATATGATTTTAAAGCGAACGTTGAAGGCGCACAAAAAATTTATGACTTAtt                                                                                                                        >  2:334026/1‑141 (MQ=255)
                        tAATGTTACAAGGTTCTGTTGACCTATTAAATGAAGTTGCAACTTCTAAAATCACAGGTGAAGAAGAAATTTATTCACATACAGATTTATATGATTTTAAAGCGAACGTTGAAGGCGCACAAAAAATTTATGACTTATTTa                                                                                                                      >  1:117200/1‑141 (MQ=255)
                          aTGTTACAAGGTTCTGTTGACCTATTAAATGAAGTTGCAACTTCTAAAATCACAGGTGAAGAAGAAATTTATTCACATACAGATTTATATGATTTTAAAGCGAACGTTGAAGGCGCACAAAAAATTTATGACTTATTTaaa                                                                                                                    >  2:394413/1‑141 (MQ=255)
                            gTTACAAGGTTCTGTTGACCTATTAAATGAAGTTGCAACTTCTAAAATCACAGGTGAAGAAGAAATTTATTCACATACAGATTTATATGATTTTAAAGCGAACGTTGAAGGCGCACAAAAAATTTATGACTTATTTAAAcc                                                                                                                  >  2:21455/1‑141 (MQ=255)
                                                   tAAATGAAGTTGCAACTTCTAAAATCACAGGTGAAGAAGAAATTTATTCACATACAGATTTATATGATTTTAAAGCGAACGTTGAAGGCGCACAAAAAATTTATGACTTATTTAAACCTATTTTAGAGAAAAAAGATaaaa                                                                                           >  2:319528/1‑141 (MQ=255)
                                                     aaTGAAGTTGCAACTTCTAAAATCACAGGTGAAGAAGAAATTTATTCACATACAGATTTATATGATTTTAAAGCGAACGTTGAAGGCGCACAAAAAATTTATGACTTATTTAAACCTATTTTAGAGAAAAAAGATaaaaaa                                                                                         >  2:443039/1‑141 (MQ=255)
                                                     aaTGAAGTTGCAACTTCTAAAATCACAGGTGAAGAAGAAATTTATTCACATACAGATTTATATGATTTTAAAGCGAACGTTGAAGGCGCACAAAAAATTTATGACTTATTTAAACCTATTTTAGAGAAAAAAGATaaaaaa                                                                                         >  1:500056/1‑141 (MQ=255)
                                                         aaGTTGCAACTTCTAAAATCACAGGTGAAGAAGAAATTTATTCACATACAGATTTATATGATTTTAAAGCGAACGTTGAAGGCGCACAAAAAATTTATGACTTATTTAAACCTATTTTAGAGAAAAAAGATAAAAAATTaa                                                                                     >  1:181980/1‑141 (MQ=255)
                                                            ttGCAACTTCTAAAATCACAGGTGAAGAAGAAATTTATTCACATACAGATTTATATGATTTTAAAGCGAACGTTGAAGGCGCACAAAAAATTTATGACTTATTTAAACCTATTTTAGAGAAAAAAGATAAAAAATTAAGtg                                                                                  >  2:18309/1‑141 (MQ=255)
                                                            ttGCAACTTCTAAAAACACAGGTGAAGAAGAAATTTATTCACATACAGATTTATATGATTTTAAAGCGAACGTTGAAGGCGCACAAAAAATTTATGACTTATTTAAACCTATTTTAGAGAAAAAAGATAAAAAATTAAGtg                                                                                  <  1:98949/141‑1 (MQ=255)
                                                            ttGCAACTAATAAAAACACAGGTGAAGAAGAAATTTATTCACATACAGATTTATATGATTTTAAAGCGAACGTTGAAAAAAAAAAAAAAATTTATGACTTATTTAAACCTATTTTAGAGAAAAAAGATAAAAAATTAAGtg                                                                                  <  2:230772/141‑1 (MQ=255)
                                                              gCAACTTCTAAAATCACAGGTGAAGAAGAAATTTATTCACATACAGATTTATATGATTTTAAAGCGAACGTTGAAGGCGCACAAAAAATTTATGACTTATTTAAACCTATTTTAGAGAAAAAAGATAAAAAATTAAGtgat                                                                                >  2:70291/1‑141 (MQ=255)
                                                               cAACTTCTAAAATCACAGGTGAAGAAGAAATTTATTCACATACAGATTTATATGATTTTAAAGCGAACGTTGAAGGCGCACAAAAAATTTATGACTTATTTAAACCTATTTTAGAGAAAAAAGATAAAAAATTAAGtgatg                                                                               <  2:495510/141‑1 (MQ=255)
                                                                   ttCTAAAATCACAGGTGAAGAAGAAATTTATTCACATACAGATTTATATGATTTTAAAGCGAACGTTGAAGGCACACAAAAAATTTATGACTTATTTAAACCTATTTTAGAGAAAAAAAATAAAAAATCAAGTGATGatat                                                                           >  2:201166/1‑141 (MQ=255)
                                                                   ttCTAAAATCACAGGTGAAGAAGAAATTTATTCACATACAGATTTATATGATTTTAAAGAGAACGTTGAAGGCGCACAAAAAATTTATGACTTATTTAAACCTATTTTAGAGAAAAAAGATAAAAAATTAAGTGATGatat                                                                           >  2:134440/1‑141 (MQ=255)
                                                                   tcatAAAAATACAGGTGAAGAAGAAATATATTCACAGAGAGATTTATATGATGTTAAAGCGAACGTTGAAGGCGCACAAAAAATTGATGACTTATTTAAACCTATTTTAGAGAAAAAAGATAAAAAATTAAGTGATGatat                                                                           <  2:472922/138‑1 (MQ=255)
                                                                            cacaGGTGAAGAAGAAATTTATTCACATACAGATTTATATGATTTTAAAGCGAACGTTGAAGGCGCACAAAAAATTTATGACTTATTTAAACCTATTTTAGAGAAAAAAGATAAAAAATTAAGTGATGATATCCAAATGaa                                                                  >  1:190821/1‑141 (MQ=255)
                                                                                ggTGAAGAAGAAATTTATTCACATACAGATTTATATGATTTTAAAGCGAACGTTGAAGGCGCACAAAAAATTTATGACTTATTTAAACCTATTTTAGAGAAAAAAGATAAAAAATTAAGTGATGATATCCAAATGAACTTc                                                              <  1:334026/141‑1 (MQ=255)
                                                                                    aagaagaaATTTATTCACAGACAGACTTACAAGTTGTTAAAGCGAACGTTGAAGGCACACAAAAAATTTATGACTTATTTAAACCTATTTTAGAGAAAAAAGATAAAAAATTAAGTGATGATATCCAAATGAACTTCGATa                                                          >  2:404526/1‑141 (MQ=255)
                                                                                          aaaTTTATTCACATACAGATTTATATGATTTTAAAGCGAACGTTGAAGGCGCACAAAAAATTTATGACTTATTTAAACCTATTTTAGAGAAAAAAGATAAAAAATTAAGTGATGATATCCAAATGAACTTCGATAAAGTGa                                                    >  1:97823/1‑141 (MQ=255)
                                                                                           aaTTTATTCACATACAGATTTATATGATTTTAAAGCGAACGTTGAAGGCGCACAAAAAATTTATGACTTATTTAAACCTATTTTAGAGAAAAAAGATAAAAAATTAAGTGATGATATCCAAATGAACTTCGATAAAGTGaa                                                   <  2:357274/141‑1 (MQ=255)
                                                                                           aaTTTATTCACAGACAGATTTATATGATTTTAAAGCGAACGTTGAAGGCGCAAAAAAAATTTATGACTTATTTAAACCTATTTAAGAGAAAAAAGATAAAAAATTAAGTGATGCTATCCAAATTAACTTCGATAAAGTGaa                                                   <  2:131208/141‑1 (MQ=255)
                                                                                           aaTTTATTCAAAAACAGAAAAATATGATTTTAAAGCGAACGTTGAAGGCGCAAAAAAAATTTATGACTTATTTAAACAAAAAAAAAAAAAAAAAGATAAAAAATTAAGTGATGATATCCAAATGAACTTCGATAAAGTGaa                                                   <  2:427530/141‑1 (MQ=255)
                                                                                           aaTTTAGTCACATACAGATTTATATGATTTTAAAGCGAACGTTGAAGGCGCACAAAAAATTTATGACTTATTTAAACCTATTTTAGAGAAAAAAGATAAAAAATTAAGTGATGATATCCAAATGAACTTCGATAAAGTGaa                                                   <  2:515267/141‑1 (MQ=255)
                                                                                            aTTTATTCACATACAGATTTATATGATTTTAAAGCGAACGTTGAAGGCGCACAAAAAATTTATGACTTATTTAAACCTATTTTAGAGAAAAAAGATAAAAAATTAAGTGATGATATCCAAATGAACTTCGATAAAGTGAAt                                                  >  1:69023/1‑141 (MQ=255)
                                                                                            aTTTATTCACATACAGATTTATATGATTTTAAAGCGAACGTTGAAGGCGCACAAAAAATTTATGACTTATTTAAACCTATTTTAGAGAAAAAAGATAAAAAATTAAGTGATGATATCCAAATGAACTTCGATAAAGTGAAt                                                  <  2:100823/141‑1 (MQ=255)
                                                                                            aTTTATTCACATACAGATTTATATGATTTTAAAGCGAACGTTGAAGGCGCACAAAAAATTTATGACTTATTTAAACATATTTTAGAGTTAAAAGATAAAAAATTAAGTGATGATATCCAAATGAACTTCGATAAAGTGAAt                                                  >  1:290685/1‑141 (MQ=255)
                                                                                                   cacaTACAGATTTATATGATTTTAAAGCGAACGTTGAAGGCGCACAAAAAATTTATGACTTATTTAAACCTATTTTAGAGAAAAAAGATAAAAAATTAAGTGATGATATCCAAATGAACTTCGATAAAGTGAATCAattat                                           >  2:540270/1‑141 (MQ=255)
                                                                                                   cacaTACAGATTTATATGATTTTAAAGCGAACGTTGAAGGCGCACAAAAAATTTATGACTTATTTAAACCTATTTTAGAGAAAAAAGATAAAAAATTAAGTGATGATATCCAAATGAACTTCGATAAAGTGAATAAattat                                           >  2:115287/1‑141 (MQ=255)
                                                                                                     caTACAGATTTATATGATTTTAAAGCGAACGTTGAAGGCGCACAAAAAATTTATGACTTATTTAAACCTATTTTAGAGAAAAAAGATAAAAAATTAAGTGATGATATCCAAATGAACTTCGATAAAGTGAATCAATTATTg                                         >  2:353400/1‑141 (MQ=255)
                                                                                                            aTTTATATGATTTTAAAGCGAAAGTTGAAGGCGCCCAAAAAATTTATGACTTATTTAAACCTATTTTAGAGAAAAAAGCTAAAAAATTAAGTGATGATATCCAAATGAACTTCGATAAAGTGAATCAATTATTGGATAAat                                  <  1:600444/141‑1 (MQ=255)
                                                                                                               tataTGATTTTAAAGCGAACGTTGAAGGCGCACAAAAAATTTATGACTTATTTAAACCTATTTTAGAGAAAAAAGATAAAAAATTAAGTGATGATATCCAAATGAACTTCGATAAAGTGAATCAATTATTGGATAAAtata                               >  1:215435/1‑141 (MQ=255)
                                                                                                                       tttAAAGCGAACGTTGAAGGCGCACAAAAAATTTATGACTTATTTAAACCTATTTTAGAGAAAAAAGATAAAAAATTAAGTGATGATATCCAAATGAACTTCGATAAAGTGAATCAATTATTGGATAAATATAAAGATaaa                       >  2:468428/1‑140 (MQ=255)
                                                                                                                          aaaGCGAACGTTGAAGGCGCACAAAAAATTTATGACTTATTTAAACCTATTTTAGAGAAAAAAGATAAAAAATTAAGTGATGATATCCAAATGAACTTCGATAAAGTGAATCAATTATTGGATAAATATAAAGATaacaaa                    >  1:353554/1‑140 (MQ=255)
                                                                                                                            aGCGAACGTTGAAGGCGCACAAAAAATTTATGACTTATTTAAACCTATTTTAGAGAAAAAAGATAAAAAATTAAGTGATGATATCCAAATGAACTTCGATAAAGTGAATCAATTATTGGATAAATATAAAGATAACAAcgg                  >  2:70792/1‑141 (MQ=255)
                                                                                                                            aGCGAACGTTGAAGGCGCACAAAAAATTTATGACTTATTTAAACCTATTTTAGAGAAAAAAGATAAAAAATTAAGTGATGATATCCAAATGAACTTCGATAAAGTGAATCAATTATTGGATAAATATAAAGATAACAAcgg                  >  1:334785/1‑141 (MQ=255)
                                                                                                                            aGCGAACGTTGAAGGAGCACAAAAAATTTATGACTTAGTTCAACCTATTTTAGAGAAAAAAGATAAAAAATTAAGTGATGATATCCAAATGAACTTCGATAAAGTGAATCAATTATTGGATAAATATACAGATAACTAcgg                  <  1:431578/141‑1 (MQ=255)
                                                                                                                              cGAACGTTGAAGGCGCACAAAAAATTTATGACTTATTTAAACCTATTTTAGAGAAAAAAGATAAAAAATTAAGTGATGATATCCAAATGAACTTCGATAAAGTGAATCAATTATTGGATAAATATAAAGATAACAAcggcg                >  1:256355/1‑141 (MQ=255)
                                                                                                                               gAACGTTGAAGGCGCACAAAAAATTTATGACTTATTTAAACCTATTTTAGAGAAAAAAGATAAAAAATTAAGTGATGATATCCAAATGAACTTCGATAAAGTGAATCAATTACTGGATAAATATAAAGATAACAAcggagg               >  2:275455/1‑141 (MQ=255)
                                                                                                                                         ggCGCACAAAAAATTTATGACTTATTTAAACCTATTTTAGAGAAAAAAGATAAAAAATTAAGTGATGATATCCAAATGAACTTCGATAAAGTGACTCAATTATTGGATAAATATAAAGATAACAACGGCGGTTATGAGTCa     <  1:19969/141‑1 (MQ=255)
                                                                                                                                         ggCGCACAAAAAATTTATGACTTATTTAAACCTATTTTAGAGAAAAAAGATAAAAAATTAAGTGATGATATCCAAATGAACTTCGATAAAGTGAATCAATTATTGGATAAATATAAAGATAACAACGGCGGTTATGAGTCa     <  1:70291/141‑1 (MQ=255)
                                                                                                                                         ggCGCACAAAAAATTTATGACTTATTTAAACCTATTTTAGAGAAAAAAGATAAAAAATTAAGTGATGATATCCAAATGAACTTCGATAAAGTGAATCAATTATTGGATAAATATAAAGATAACAACGGCGGTTATGAGTCa     <  1:168814/141‑1 (MQ=255)
                                                                                                                                            gcACAAAAAATTTATGACTTAGTTAAACCTATTTTAGAGAAAAAAGATAAAAAATTAAGTGATGATATCCAAATGAACTTCGATAAAGTGAATCAATTATTGGATAAATATAAAGATAACAACGGCGGTTATGAGTCAttt  <  1:128963/141‑1 (MQ=255)
                                                                                                                                            |                                                                                                                                            
ATACATTAGATATCATACCAAAATTAATGTTACAAGGTTCTGTTGACCTATTAAATGAAGTTGCAACTTCTAAAATCACAGGTGAAGAAGAAATTTATTCACATACAGATTTATATGATTTTAAAGCGAACGTTGAAGGCGCACAAAAAATTTATGACTTATTTAAACCTATTTTAGAGAAAAAAGATAAAAAATTAAGTGATGATATCCAAATGAACTTCGATAAAGTGAATCAATTATTGGATAAATATAAAGATAACAACGGCGGTTATGAGTCATTT  >  USA300TCH1516_ALE/396400‑396680

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