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 665,392 T→G 18.3% L79* (TTA→TGA)  paiA_1 → Spermidine/spermine N(1)‑acetyltransferase

Read alignment evidence...
  seq id position ref new freq score (cons/poly) reads annotation genes product
*USA300TCH1516_ALE665,3920TG18.3% 111.3 / 18.8 60L79* (TTA→TGA) paiA_1Spermidine/spermine N(1)‑acetyltransferase
Reads supporting (aligned to +/- strand):  ref base T (27/21);  new base G (6/5);  total (33/27)
Fisher's exact test for biased strand distribution p-value = 1.00e+00
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 9.98e-01

ACAACAGTTAATCACTTGTTAGAAGCTTCATATAA‑TGAACATCATTTAAAGAAAAGACTTCAAGAACAATTATTCTTAGTCGTTGAAGAAGGTAATGACATCGTTGGCTTTGCTAACTTTATTTACGGTGAAGAATTATATTTATCAGCTCATTATGTTAAACCAGAATCGCAACATACAGGTTATGGTACAGCATTGTTAAATGAAGGATTATCACGTTTTGAAGATAAATTTGAAGGTGTTTACTTAGAAGTAGATAATAAAAAT  >  USA300TCH1516_ALE/665256‑665522
                                                                                                                                         |                                                                                                                                  
acaacaGTTAATCACTTGTTAGAAGCTTCATATAA‑TGAACATCATTTAAAGAAAAGACTTCAAGAACAATTATTCTTAGTCGTGGAAGAAGGTAATGACAGCGTTGGCTTTGCTAACTTTATTTACGGTGAAGAATGatat                                                                                                                                >  2:172129/1‑141 (MQ=255)
    caGTTAATCACTTGTTAGAAGCTTCATATAA‑TGAACATCATTTAAAGAAAAGACTTCAAGAACAATTATTCTTAGTCGTTGAAGAAGGTAATGACATCGTTGGCTTTGCTAACTTTATTTACGGTGAAGAATTATATTTAt                                                                                                                            >  2:431991/1‑141 (MQ=255)
        tAATCACTTGTTAGAAGCTTCATATAA‑TGAACATCATTTAAAGAAAAGACTTCAAGAACAATTATTCTTAGTCGTTGAAGAAGGTAATGACATCGTTGGCTTTGCTAACTTTATTTACGGTGAAGAATTATATTTATCAGc                                                                                                                        >  2:134248/1‑141 (MQ=255)
          aTCACTTGTTAGAAGCTTCATATAA‑TGAACATCATTTAAAGAAAAGACTTCAAGAACAATTATTCTTAGTCGTTGAAGAAGGTAATGACATCGTTGGCTTTGCTAACTTTATTTACGGTGAAGAATTATATTTATCAGCTc                                                                                                                      >  1:112777/1‑141 (MQ=255)
          aTCACTTGTTAGAAGCTTCATATAA‑TGAACATCATTTAAAGAAAAGACTTCAAGAACAATTATTCTTAGTCGTTGAAGAAGGTAATGACATCGTTGGCTTTGCTAACTTTATTTACGGTGAAGAATTATATTTATCAGCTc                                                                                                                      <  1:522189/141‑1 (MQ=255)
           tCACTTGTTAGAAGCTTCATATAA‑TGAACATCATTTAAAGAAAAGACTTCAAGAACAATTATTCTTAGTCGTTGAAGAAGGTAATGACATCGTTGGCTTTGCTAACTTTATTTACGGTGAAGAATTCTATTTATGAGCTcc                                                                                                                     >  1:157080/1‑140 (MQ=255)
                tGTTAGAAGCTTCATATAA‑TGAACATCATTTAAAGAAAAGACTTCAAGAACAATTATTCTTAGTCGTTGAAGAAGGTAATGACATCGTTGGCTTTGCTAACTTTATTTACGGTGAAGAATTATATTTATCAGCTCATTATg                                                                                                                >  2:255240/1‑141 (MQ=255)
                        gCTTTATATAA‑TGAACATCATTTAAAGAAAAGACTTCAAGAACTATTAGTCTTAGTCGTTGGAGAAGGTAATGACATCGTTGGCTTTGCTAACTTTATTTACGGTGAAGAATTATATTTATCAGCTCTTTATGTTAATCCa                                                                                                        <  2:292230/141‑1 (MQ=255)
                        agttCATATAATTGAAAAT‑ATTTTAAGAAAAGACTTCAAGAACAATTATTCTTAGTCGTTGAAGAAGGTAATGACTTCGTTGGCTTTGCTAACTTGATTTACGGTGAAGAATTATATTTATCAGCTCATTATGTTAAACCa                                                                                                        <  2:188501/139‑1 (MQ=255)
                          ttCATATAA‑TGAACATCATTTAAAGAAAAGACTTCAAGAACAATTATTCTTAGTCGTTGAAGAAGGTAATGACATCGTTGGCGTTGCTAACTTTATTTACGGTGAAGAATTATATTTATCAGCTCATTATGTTAAACCAGa                                                                                                      <  2:231251/141‑1 (MQ=255)
                                    tGAACATCATTTAAAGAAAAGACTTCAAGAACAATTATTCTTAGTGGTTGAAGAAGGTAATGACATCGTTGGCTTTGCTAACTTTATTTACGGTGAAGAATTATATTTATCAGCCCGTTATTGTAAACCAGAGTGGCacga                                                                                             >  1:489825/1‑138 (MQ=255)
                                    agAACATCATTTAAAGAAAAGACATCAAGAACAATTATTCTTAGTCGTTGAAGAAGGTAATGACATCGTTGGCTTTGCTAACTTTATTTACGGTGAAGAATTATATTTATCAGCTCATTATGTTAAACCAGAATCGCAACa                                                                                             <  2:581134/140‑1 (MQ=255)
                                      aaCATCATTTAAAGAAAAGACTTCAAGAACAATTATTCTTAGTCGTTGAAGAAGGTAATGACATCGTTGGCTTTGCTAACTTTATTTACGGTGAAGAATTATATTTATCAGCTCATTATGTTAAACCAGAATCGCAACATa                                                                                           <  1:138975/141‑1 (MQ=255)
                                       aCAGCATTTAAAGAAAAGACTTCAAGAACAATTATTCTTAGTCGTTGAAGAAGGTAATGACATCGTTGGCTTTGCTAACTTTATTTACGGTGAAGAATTATATTTATCAGCTCATTATGTTAAACCAGAATCGCAACATAc                                                                                          <  2:177348/141‑1 (MQ=255)
                                            atTTAAAGAAAAGACTTCAAGAACAATTATTCTTAGTCGTTGAAGAAGGTAATGACATCGTTGGCTTTGCTAACTTTATTTACGGTGAAGAATTATATTTATCAGCTCATTATGTTAAACCAGAATCGCAACATACAGGtt                                                                                     >  1:309402/1‑141 (MQ=255)
                                             tttAAAGAAAAGACTTCAAGAACAATTATTCTTAGTCGTTGAAGAAGGTAATGACATCGTTGGCTTTGCTAACTTTATTTACGGTGAAGAATTATATTTATCAGCTCATTATGTTAAACCAGAATCGCAACATACAGGTTa                                                                                    >  1:191110/1‑141 (MQ=255)
                                              tgaaagatgagaCTTCAAGAACAATTATTCTTAGTCGTTGAAGAAGGTAATGACATCGTTGGCTTTGCTAACTTTATTTACGGTGAAGAATTATATTTATCAGCTCATTATGTTAAGCCAGAATCGCACCATACAGGTTAt                                                                                   >  2:5838/3‑141 (MQ=255)
                                                aaagaaaagaCTTCAAGAACAATTATTCTTAGTCGTTGAAGAAGGTAATGACATCGTTGGCTTTGCTAACTTTATTTACGGTGAAGAATTATATTTATCAGCTCATTATGTTAAACCAGAATCGCAACATACAGGTTATgg                                                                                 >  2:287624/1‑141 (MQ=255)
                                                aaagaaaagaCTTCAAGAACAATTATTCTTAGTCGTTGAAGAAGGTAATGACATCGTTGGCTTTGCTAACTTTATTTACGGTGAAGAATTATATTTATAAGATCATTATGTTAAACCAAAATCGCAACATACAGGTTATgg                                                                                 >  2:324558/1‑141 (MQ=255)
                                                 aagaaaagaCTTCAAGAACAATTATTCTTAGTCGTTGAAGAAGGTAATGACATCGTTGGCTTTGCTAACTTTATTTACGGTGAAGAATTATATTTATCAGCTCATTATGTTAAACCAGAATCGCAACATACAGGTTATGGt                                                                                <  1:329234/141‑1 (MQ=255)
                                                  agaaaagaCTTCAAGAACAATTATTCTTAGTCGTTGAAGAAGGTAATGACATCGTTGGCTTTGCTAACTTTATTTACGGTGAAGAATTATATTTATCAGCTCATTATGTTAAACCAGAATCGCAACCTACAGGTTATGGTa                                                                               >  1:408050/1‑141 (MQ=255)
                                                  agaaaagaCTTCAAGAACAATTATTCTTAGTCGTTGAAGAAGGTAATGACATCGTTGACTTTGCTAACTTTATTTACGGTGAAGAATTATATTTATCAGCTCATTATGTTAAACCAGAATCGCAACATACAGGTTATGGTa                                                                               >  1:90532/1‑141 (MQ=255)
                                                  agaaaagaCTTCAAGAACAATTATTATTAGAAGTTGCAGAAGGTAATGATACAGTTGGCTTTGCTATCTTCCATTCCGGTTAAGCATTATTTTTTTGAGCTCATTATGTTATACCAGAAACACAACTTACAGGTTATggga                                                                               >  2:601341/1‑139 (MQ=255)
                                                   gaaaagaCTTCAAGAACAATTATTCTTAGTCGTTGAAGAAGGTAATGACATCGTTGGCTTTGCTAACTTTATTTACGGTGAAGAATCATATTTATCAGCTCATTATGTTAAACCAGAATCGCAACATACAGGTTATGGTAc                                                                              <  1:396422/141‑1 (MQ=255)
                                                    aaaagaCTTCAAGAACAATTATTCTTAGTCGTTGAAGAAGGTAATGACATCGTTGGCTTTGCTAACTTTATTTACGGTGAAGAATTATATTTATCAGCTCATTATGTTAAACCAGAATCGCAACATACAGGTTATGGTACa                                                                             >  2:384249/1‑141 (MQ=255)
                                                      aagaCTTCAAGAACAATTATTCTTAGTCGTTGAAGAAGGTAATGACATCGTTGGCTTTGCTAACTTTATTTACGGTGAAGAATTATATTTATCAGCTCATTATGTTAAACCAGAATCGCAACATACAGGTTATGGTACAGc                                                                           >  2:38660/1‑141 (MQ=255)
                                                       agaCTTCAAGAACAATTATTCTTAGTCGTTGAAGAAGGTAATGACATCGTTGGCTTTGCTAACTTTATTTACGGTGAAGAATTATATTTATCAGCTCATTATGTTAAACCAGAATCGCAACATACAGGTTATGGTACAGCa                                                                          >  2:30897/1‑141 (MQ=255)
                                                         aCTTCAAGAACAATTATTCTTAGTCGTTGAAGAAGGTAATGACATCGTTGGCTTTGCTAACTTTATTTACGGTGAAGAATTATATTTATCAGCTCATTATGTTAAACCAGAATCGCAACATACAGGTTATGGTACAGCAtt                                                                        >  1:483777/1‑141 (MQ=255)
                                                         aCTTCAAGAACAATTATTCTTAGTCGTTGAAGAAGGTAATGACATCGTTGGCTTTGCTAACTTTATTTACGGTGAAGAATTATATTTATCAGCTCATTATGTTAAACCAGAATCGCAACATACAGGTTATGGTACAGCAtt                                                                        <  1:528826/141‑1 (MQ=255)
                                                          catCAAGAACAATTATGCTTAGTCGTTGAAGAAGGTGATGAGATCGTTGGCTTTGCTAACGTTATTTACGGTGAAGGATTATATGTATCAGCTCATTATGTTAAACCAGCATCGCAACATACAGGTTATGGTACAGCATTg                                                                       <  2:245274/139‑1 (MQ=255)
                                                          cTTCAAGAACAATTATTCTTAGTCGTTGAAGAAGGTAATGACATCGTTGGCTTTGCTAACTTTATTTACGGTGAAGAATGATATTTATCAGCTCATTATGTTAAACCAGAATCGCAACATACAGGTTATGGTACAGCATTg                                                                       <  2:496887/141‑1 (MQ=255)
                                                          cTTCAAGAACAATTATTCTTAGTCGTTGAAGAAGGTAATGACATCGTTGGCTTTGCTAACTTTATTTACGGTGAAGAATGATATTTATCAGCTCATTATGTTAAACCAGAATCGCAACATACAGGTTATGGTACAGCATTg                                                                       <  2:26894/141‑1 (MQ=255)
                                                           ttCAAGAACAATTATTCTTAGTCGTTGAAGAAGGTAATGACATCGTTGGCTTTGCTAACTTTATTTACGGTGAAGAATTATATTTATCAGCTCATTATGTTAAACCAGAATCGCAACATACAGGTTATGGTACAGCATTGt                                                                      <  1:511094/141‑1 (MQ=255)
                                                              aaGAACAATTATTCTTAGTCGTTGAAGAAGGTAATGACATCGTTGGCTTTGCTAACTTTATTTACGGTGAAGAATGATATTTATCAGCTCATTATGTTAAACCAGAATCGCAACATACAGGTTATGGTACAGCATTGTTaa                                                                   >  1:114197/1‑141 (MQ=255)
                                                              aaGAACAATTATTCTTAGTCGTTGAAGAAGGTAATGACATCGTTGGCTTTGCTAACTTTATTTACGGTGAAGAATGATATTTATCAGCCCATTATGTTAAACCAGAATCGCAACATACAGGTTATGTTACAGCATTGTTaa                                                                   >  1:114311/1‑141 (MQ=255)
                                                                      ttattCTTAGTCGTTGAAGAAGGTAATGACATCGTTGGCTTTGCTAACTTTATTTACGGTGAAGAATTATATTTATCAGCTCATTATGTTAAACCAGAATCGCAACATACAGGTTATGGTACAGCATTGTTAAATGAAGGa                                                           >  1:230475/1‑141 (MQ=255)
                                                                       tattCTTAGTCGTTGAAGAAGGTAATGACATCGTTGGCTTTGCTAACTTTATTTACGGTGAAGAATTATATTTATCAGCTCATTATGTTAAACCAGAATCGCAACATACAGGTTATGGTACAGCATTGTTAAATGAAGGAt                                                          <  1:97950/141‑1 (MQ=255)
                                                                       tattCTTAGTCGTTGAAGAAGGTAATGACATCGTTGGCTTTGCTAACTTTATTTACGGTGAAGAATGATATTTATCAGCTCATTATGTTAAACCAGAATCGCAACATACAGGTTATGGTACAGCATTGTTAAATGAAGGAt                                                          >  1:26863/1‑141 (MQ=255)
                                                                        tttCTTAGTCGTTGAAGAAGGTAATGACATCGTTGGCTTTGCTAACTTTATTTACGGTGAAGAATTATATTTATCAGCTCATTATGTTAAACCAGAATCGCAACATACAGGTTATGGTACAGCATTGTTAAATGAAGGAtt                                                         <  1:596669/140‑1 (MQ=255)
                                                                        attCTTAGTCGTTGAAGAAGGTAATGACATCGTTGGCTTTGCTAACTTTATTTACGGTGAAGAATTATATTTATCAGCTCATTATGTTAAACCAGAATCGCAACATACAGGTTATGGTACAGCATTGTTAAATGAAGGAtt                                                         <  1:461461/141‑1 (MQ=255)
                                                                         ttCTTAGTCGTTGAAGAAGGTAATGACATCGTTGGCTTTGCTGACTTTATTTACGGTGAGGAATTCTATTTATCAGCTCGTTATGTTAATCTAGAATGGCAACATACAGGTTATGGTACAGCATTGTTAAATGAAGGATTa                                                        >  2:288289/1‑141 (MQ=255)
                                                                         ttCTTAGTCGTTGAAGAAGGTAATGACATCGTTAGCTTTGATAACTTTATTTACGGTGAAGAATTATATTTATCAGCTCATTATGTTAAACCAGAATCGCAACATACAGGTTATGGTACAGCATTGTTAAATGAAGGATTa                                                        <  1:429814/141‑1 (MQ=255)
                                                                          tCTTAGTCGTTGAAGAAGGTAATGACATCGTTGGCTTTGCTAACTTTATTTACGGTGAAGAATTATATTTATCAGCTCATTATGTTAAACCAGAATCGCAACATACAGGTTATGGTACAGCATTGTTAAATGAAGGATTAt                                                       >  2:83164/1‑141 (MQ=255)
                                                                          tCTTAGTCGTTGAAGAAGGTAATGACATCGTTGGCTTTGCTAACTTTATTTACGGTGAAGAATTATATTTATCAGCTCATTATGTTAAACCAGAATCGCAACATACAGGTTATGGTACAGCATTGTTAAATGAAGGATTAt                                                       >  2:287772/1‑141 (MQ=255)
                                                                            ttAGTCGTTGAAGAAGGTAATGACATCGTTGGCTTTGCTAACTTTATTTACGGTGAAGAATTATATTTATCAGCTCATTATGTTAAACCAGAATCGCAACATACAGGTTATGGTACAGCATTGTTAAATGAAGGATTATCa                                                     <  1:476854/141‑1 (MQ=255)
                                                                              aGTCGTTGAAGAAGGTAATGACATCGTTGGCTTTGCTAACTTTATTTACGGTGAAGAATTATATTTATCAGCTCATTATGTTAAACCAGAATCGCAACATACAGGTTATGGTACAGCATTGTTAAATGAAGGATTATCACg                                                   <  2:593800/141‑1 (MQ=255)
                                                                                   ttGAAGAAGGTAATGACATCGTTGGCTTTGCTAACTTTATTTACGGTGAAGAATTATATTTATCAGCTCATTATGTTAAACCAGAATCGCAACATACAGGTTATGGTACAGCATTGTTAAATGAAGGATTATCACGtttgg                                              >  2:229033/1‑139 (MQ=255)
                                                                                     gaagaaGGTAATGACATCGTTGGCTTTGCTAACTTTATTTACGGTGAAGAATTATATTTATCAGCTCATTATGTTAAACCAGAATCGCAACATACAGGTTATGGTACAGCATTGTTAAATGAAGGATTATCACGTTTTGaa                                            >  2:422613/1‑141 (MQ=255)
                                                                                        gaagGTAATGACATCGTTGGCTTTGCTAACTTTATTTACGGTGAAGAATGATATTTATCAGCTCATTATGTTAAACCAGAATCGCAACATACAGGTTATGGTACAGCATTGTTAAATGAAGGATTATCACGTTTTGAAGAt                                         <  2:358395/141‑1 (MQ=255)
                                                                                           ggTAATGACATCGTTGGCTTTGCTAACTTTATTTACGGTGAAGAATTATATTTATCAGCTCATTATGTTAAACCAGAATCGCAACATACAGGTTATGGTACAGCATTGTTAAATGAAGGATTATCACGTTTTGAAGATaaa                                      >  1:264486/1‑141 (MQ=255)
                                                                                                tGACATCGTTGGCTTTGCTAACTTTATTTACGGTGAAGAATGATATTTATCAGCTCATTATGTTAAACCAGAATCGCAACATACAGGTTATGGTACAGCATTGTTAAATGAAGGATTATCACGTTTTGAAGATAAATTTGa                                 <  2:240656/141‑1 (MQ=255)
                                                                                                 gACATCGTTGGCTTTGCTAACTTTATTTACGGTGAAGAATGATATTTATCAGCTCATTATGTTAAACCAGAATCGCAACATACAGGTTATGGTACAGCATTGTTAAATGAAGGATTATCACGTTTTGAAGATAAATTTGaa                                >  1:277273/1‑141 (MQ=255)
                                                                                                  aCATCGTTGGCTTTGCTAACTTTATTTACGGTGAAGAATTATATTTATCAGCTCATTATGTTAAACCAGAATCGCAACATACAGGTTATGGTACAGCATTGTTAAATGAAGGATTATCACGTTTTGAAGATAAATTTGAAg                               <  1:494174/141‑1 (MQ=255)
                                                                                                       gTTGGTTTTGCTAACTTTATTTACGGTTAAGAATTATATTTATCAGCTCAGTATGTTAAACCAGAATCGTAACATACAGGTTATGGTACAGCATTGTTAAATGAAGGATTATCACGTTTTGAAGATAAATTTGAAGGTGtt                          <  2:14173/141‑1 (MQ=255)
                                                                                                          ggCTTTGCTAACTTTATTTACGGTGAAGAATTATATTTATCAGCTCATTATGTTAAACCAGAATCGCAACATACAGGTTATGGTACAGCATTGTTAAATGAAGGATTATCACGTTTTGAAGATAAATTTGAAGGTGTTTAc                       >  1:181027/1‑141 (MQ=255)
                                                                                                                    aCTTTATGTACGGTGAAGAATTATATTTATCAGATCATTATGTTAAACCAGAATCGCAACATACAGGTTATGGTACAGCATTGTTAAATGAAGGATTATCACGTTTTGAAGATAAATTTGAAGGTGTTTACTTAGAAGTAg             <  1:98780/141‑1 (MQ=255)
                                                                                                                     ttttatttaCGTGGAAGAATGATATTTATAAGCTAATTATGTTAATCCAGAATCGTAACATACAGGTTATGGTACAGCATTGTTAAATGAAGGATTATCACGTTTTGAAGATAAATTTGAAGGTGTTTACTTAGAAGTAGa            <  2:14349/140‑1 (MQ=255)
                                                                                                                               ggTGAAGAATTATATTTATCAGCTCATTATGTTAAACCAGAATCGCAACATACAGGTTATGGTACAGCATTGTTAAATGAAGGATTATCACGTTTTGAAGATAACTTTGAAGGTGTTTACTTAGAAGTAGATAATAAAAAt  <  2:54802/141‑1 (MQ=255)
                                                                                                                               ggTGAAGAATTATATTTATCAGCTCATTATGTTAAACCAGAATCGCAACATACAGGTTATGGTACAGCATTGTTAAATGAAGGATTATCACGTTATGAAGATAAATTTGAAGGTGTTTACTTAGAAGTAGATAATaaaaag  >  2:247715/1‑140 (MQ=255)
                                                                                                                               ggTGAAGAATGATATTTATCAGCTCATTATGTTAAACCAGAATCGCAACATAAAGGTTATGGTACAGCATTGTTAAATGAAGGTTTATCACGTTTTGAAGATAAATTTGAAGGTGTTTACTTAGAAGTAGATAATAAAAAt  >  2:259261/1‑141 (MQ=255)
                                                                                                                                         |                                                                                                                                  
ACAACAGTTAATCACTTGTTAGAAGCTTCATATAA‑TGAACATCATTTAAAGAAAAGACTTCAAGAACAATTATTCTTAGTCGTTGAAGAAGGTAATGACATCGTTGGCTTTGCTAACTTTATTTACGGTGAAGAATTATATTTATCAGCTCATTATGTTAAACCAGAATCGCAACATACAGGTTATGGTACAGCATTGTTAAATGAAGGATTATCACGTTTTGAAGATAAATTTGAAGGTGTTTACTTAGAAGTAGATAATAAAAAT  >  USA300TCH1516_ALE/665256‑665522

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