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 1,231,470 A→C 45.3% M39L (ATG→CTG)  stp → Serine/threonine phosphatase stp

Read alignment evidence...
  seq id position ref new freq score (cons/poly) reads annotation genes product
*USA300TCH1516_ALE1,231,4700AC45.3% 9.3 / 63.3 55M39L (ATG→CTG) stpSerine/threonine phosphatase stp
Reads supporting (aligned to +/- strand):  ref base A (17/13);  new base C (16/9);  total (33/22)
Fisher's exact test for biased strand distribution p-value = 7.83e-01
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 1.00e+00

CAAGTAGAAACGAGGTAAAGACAAATGCTAGAGGCACAATTTTTTACTGATACTGGACAACATAGAGATAAGAATGAAGATGCGGGTGGTATTTTTTATAATCAAACTAATCAACAACTTTTAGTTCTGTGTG‑ATGGTATGGGTGGCCATAAAGCAGGAGAAGTTGCAAGTAAATTTGTTACAGATGAGTTGAAATCCCGTTTTGAAGCGGAAAATCTTATAGAACAACATCAAGCTGAAAATTGGTTGCGTAATAATATAAAAGATATAAATTTTC  >  USA300TCH1516_ALE/1231332‑1231608
                                                                                                                                           |                                                                                                                                          
cAAGTAGAAACGAGGTAAAGACAAATGCTAGAGGCACAATTTTTTACTGATACTGGACAACATAGAGATAAGAATGAAGATGCGGGTGGTATTTTTTATAATCAAACTAATCAACAACTTTTAGTTCTGTGTG‑ATGGTATg                                                                                                                                          >  2:538330/1‑141 (MQ=255)
    tAGAAACGAGGTAAAGACAAATGCTAGAGGCACAATTTTTTACTGATACTGGACAACATAGAGATAAGAATGAAGATGCGGGTGGTATTTTTTATAATCCAACTAATCAACAACTTTTAGTTGTGAGTG‑ATGGTCTGGTTg                                                                                                                                      >  2:419225/1‑141 (MQ=255)
       aaaCGAGGTAAAGACAAATGCTAGAGGCACAATTTTTTACTGATACTGGACAACATAGAGATAAGAATGAAGATGCGGGTGGTATTTTTTATAATCAAACTAATCAACAACTTTTAGTTCTGTGTG‑ATGGTCTGGGTGGcc                                                                                                                                   >  2:213863/1‑141 (MQ=255)
       aaaCGAGGTAAAGACAAATGCTAGAGGCACAATTTTTTACTGATACTGGACAACATAGAGATAAGAATGAAGATGCGGGTGGTATTTTTTATAATCAAACTAATCAACAACTTTTAGTTCTGTGTG‑ATGGTATGGGTGGcc                                                                                                                                   <  2:257942/141‑1 (MQ=255)
        aaCGAGGTAAAGACAAATGCTAGAGGCACAATTTTTTACTGATACTGTACTACATATGTATAAGAATGAAGATGCGGGTGGTATTTTTTATAATCAAACTAATCAACAACTTTTAGTTCTGTGTG‑ATGGTATGGGTGGCCa                                                                                                                                  <  2:208390/141‑1 (MQ=255)
        aaCGAGGTAAAGACAAATGCTAGAGGCACAATTTTTTAATGATACGGGACAACATAGAGATAAGAATGAAGATGCGGGTGGTATTTTTTATAATCCAACTAATCAACACCTTTTAGTTCTGTGTG‑ATGGTCTGGGTgtcaa                                                                                                                                  >  2:251376/1‑137 (MQ=255)
         aCGAGGAAAAGAAAAATGCAAGAGGGACAATTTTTTACTGATACTGGACAACATAGAGATAAGAATGAAGATGCGGGTGGTATTTTTTATAATCAAACTAATCAACAACTTTTAGTTCTGTGTG‑ATGGTCTGGGTGGCCAt                                                                                                                                 <  2:560114/141‑1 (MQ=255)
                aaaaACAAATGCTAGAGGCACAATTTTTTACTGAGACTGGACAACATAGAGATAAGAATGAAGATGCGGGTGGTATTGTTTATAATCAACCTAATCAACGACTTTTAGTTCTGTGTG‑ATGGTATGGGTGGCCATAAAGCAg                                                                                                                          <  1:564085/141‑1 (MQ=255)
                 aaGACAAATGCTAGAGGCACAATTTTTTACTGATACTGGACAACATAGAGATAAGAATGAAGATGCGGGTGGTATTTTTTATAATCAAACTAATCAACCACCTTTAATTACATTTA‑ATGGTATGGGTGGCCATAAAGCacg                                                                                                                         >  2:126067/1‑139 (MQ=255)
                  aGACAAATGCTAGAGGCACAATTTTTTACTGATACTGGACAACATAGAGATAAGAATGAAGATGCGGGTGGTATTTTTTATAATCAAACTAATCAACAACTTTTAGTTCTGTGTG‑ATGGTATGGGTGGCCATAAAGCAGga                                                                                                                        >  1:489215/1‑141 (MQ=255)
                        aTGCTAGAGGCACAATTTTTTACTGATACTGGACAACATAGAGATAAGAATGAAGATGCGGGTGGTATTTTTTATAATCAAACTAATCAACAACTTTTAGTTCTGTGTG‑AGGGTATGGGTGGCCATAAAGCAGGAGAAGtt                                                                                                                  <  2:602739/141‑1 (MQ=255)
                            tAGAGGCACAATTTTTTACTGATACTGGACAACATAGAGATAAGAATGAAGATGCGGGTGGTATTTTTTATAATCAAACTAATCAACAACTTTTAGTTCTGTGTG‑ATGGTATGGGTGGCCATAAAGCAGGAGCAGTTGCaa                                                                                                              >  1:11398/1‑141 (MQ=255)
                            tAGAGGCACAATTTTTTACTGATACTGGACAACATAGAGATAAGAATGAAGATGCGGGTGGTATTTTTTATAATCAAACTAAGCAACAACTTTTAGTTCTGTGTG‑ATGGTCTGGGTGGCCATAAAGCAGGAGAAGTTGCaa                                                                                                              >  1:201616/1‑141 (MQ=255)
                            tAGAGGCACAATTTTTTACGGATACTGGACAACATAGAGATAAGAATGAAGATGCGGGTGGTATTTTTTATAATCAAACTAATCAACAACTTTTAGTTCTGTGTG‑ATGGTATGGGTGGCCATAAAGCAGGAGAAGTTGCaa                                                                                                              >  1:335907/1‑141 (MQ=255)
                            tAGAGGCACAATTTGTTACAGATACTGGACAACATAGAGATAAGCATGAAGATGCGGGTGGTATTTTTTATAATCAAACTAATCAACAACTTTTAGTTCTGTGTG‑ATGGTATGGGTGGCCATAAAGCAGGAGAAGTTGCaa                                                                                                              >  1:335721/1‑141 (MQ=255)
                               agGCACAATTTTTTACTGATACTGGACAACATAGAGATAAGAATGAAGATGCGGGTGGTATTTTTTATAATCAAACTAATCAACAACTTTTAGTTCTGTGTG‑ATGGTCTGGGTGGCCATAAAGCAGGAGAAGTTGCAAGTa                                                                                                           <  2:381393/141‑1 (MQ=255)
                                      aTTTTTTACTGATACTGGACAACATAGAGATAAGAATGAAGATGCGGGTGGTATTTTTTATAATCAAACTAATCAACAACTTTTAGTTCTGTGTG‑ATGGTCTGGGTGGCCATAAAGCAGGAGAAGTTGCAAGTAAATTTgg                                                                                                    >  1:508322/1‑140 (MQ=255)
                                          tttACTGATACTGGACAACATAGAGATAAGAATGAAGATGCGGGTGGTATTTTTTATAATCAAACTAATCAACAACTTTTAGTTCTGTGTG‑ATGGTCTGGGTGGCCATAAAGCAGGAGAAGTTGCAAGTAAATTTGTTACa                                                                                                >  1:540952/1‑141 (MQ=255)
                                          tttACTGATACTGGACAACATAGAGATAAGAATGAAGATGCGGGTGGTATTTTTTATAATCAAACTAATCAACAACTTTTAGTCTTGTGAGCATGG‑AGTGGCGGAAATAAACCAGGAGAAGTTGCAAGTAAATTTGTTACa                                                                                                >  1:138541/1‑141 (MQ=255)
                                          tttACTGATACTGGACAACATAGAGATAAGAATGAAGATGCGGGTGGTATTTTGTATAATCAAACTAATCAACAACTTTTAGTTCTGTGTG‑ATGGTATGGGTGGCCATAAAGCAGGCGAAGTTGCAAGTAAATTTGTTACa                                                                                                >  1:387365/1‑141 (MQ=255)
                                           ttACTGATACTGGACAACATAGAGATAAGAATGAAGATGCGGGTGGTATTTTTTATAATCAAACTAATCAACAACTTTTAGTTCTGTGTG‑ATGGTATGGGTGGCCATAAAGCAGGAGAAGTTGCAAGTAAATTTGTTACAg                                                                                               <  1:343061/141‑1 (MQ=255)
                                             aCTGATACTGGACAACATAGAGATAAGAATGAAGATGCGGGTGGTATTTTTTATAATCAAACTAATCAACAACTTTTAGTTCTGTGTG‑ATGGTCTGGGTGGCCATAAAGCAGGAGAAGTTGCAAGTAAATTTGTTACAGAt                                                                                             <  2:284696/141‑1 (MQ=255)
                                                    cTGGACAACATAGAGATAAGAATGAAGATGCGGGTGGTATTTTTTATAATCAAACTAATCAACAACTTTTAGTTCTGTGTG‑ATGGTCTGGGTGGCCATAAAGCAGGAGAAGTTGCTAGTAAATTTCTTACAGATGAGTTGa                                                                                      <  1:307788/141‑1 (MQ=255)
                                                    cTGGACAACATAGAGATAAGAATGAAGATGCGGGTGGTATTTTTTATAATCAAACTAATCAACAACTTTTAGTTCTGTGTG‑ATGGTATGGGTGGCCATAAAGCAGGAGAAGTTGCAAGTAAATTTGTTACAGATGAGTTGa                                                                                      <  1:482276/141‑1 (MQ=255)
                                                          aacaTAGAGGTAAGAATGAAGATGCGGGTGGTATTTTTTATAATCAAACTAATCAACAACTTTTGGTTCTGTGTG‑ATGGTATCGGTGGCCATAAAGCAGGAGAAGTTGCAAGTAAATTTGTTACAGATGAGTTGAAATccg                                                                                >  2:403740/1‑140 (MQ=255)
                                                          aacaTAGAGATAAGAATGAAGATGCGGGTGGTATTTTTTATAATCAAACTAATCAACAACTTTTAGTTCTGTGTG‑ATGGTATGGGTGGCCATAAAGCAGGAGAAGTTGCAAGTAAATTTGTTACAGATGAGTTGAAATccc                                                                                <  2:219975/141‑1 (MQ=255)
                                                          aacaTAGAGATAAGAATGAAGATGCGGGTGGTATTTTTTATAATCAAACTAATCAACAACTTTTAGTTCTGTGTG‑ATGGTATGGGTGGCCATAAAGCAGGAGAAGTTGCAAGTAAATTTGTTACAGATGAGTTGAAATccc                                                                                >  1:436638/1‑141 (MQ=255)
                                                            caTAGAGATAAGAATGAAGATGCGGGTGGTATTTTTTATAATCAAACTAATCAACAACTTTTAGTTCTGTGTG‑ATGGTCTGGGTGGCCATAAAGCAGGAGAAGTTGCAAGTAAATTTGTTACAGATGAGTTGAAATCCCGt                                                                              >  1:218369/1‑141 (MQ=255)
                                                             aTAGAGATAAGAATGAGGATGCGGGTGGTATTTTTTATAATCAAACTAATCAACAACTTTTAGTTCTGTGTG‑ATGGTATGGGTGGCCATAAAGCAGGAGAAGTTGCAAGTAAATTTGTTACAGATGAGTTGAAATCCCGtt                                                                             >  1:304925/1‑141 (MQ=255)
                                                                    tAAGAATGAAGATGCGGGTGGTATTTTTTATAATCAAACTAATCAACAACTTTTAGTTCTGTGTG‑ATGGTCTGGGTGGCCATAAAGCAGGAGAAGTTGCAAGTAAATTTGTTACAGATGAGTTGAAATCCCGTTTTGAAGc                                                                      <  1:213863/141‑1 (MQ=255)
                                                                      aGAATGAAGATGCGGGTGGTATTTTTTATAATCAAACTAATCAACAACTTTTAGTTCTGTGTG‑ATGGTATGGGTGGCCATAAAGCAGGAGAAGTTGCAAGTAAATTTGTTACAGATGAGTTGAAATCCCGTTTTGAAGCgg                                                                    >  2:50281/1‑141 (MQ=255)
                                                                      aGAATGAAGATGCGGGTGGTAGTTTTTATAATCAAACTAATCAACAACTTTTAGTTATGTGTG‑ATGGTCTGGGTCGCCATAAAGCAGGAGAAGTTGCAAGTAAATTTGTTACAGATGAGTTGAAATCCCGTTTTGCAGCgg                                                                    <  1:450231/141‑1 (MQ=255)
                                                                         aTGAAGATGCGGGTGGTATTTTTTATAATCAAACTAATCAACAACTTTTAGTTCTGTGTG‑ATGGTCTGGGTGGCCATAAAGCAGGAGAAGTTGCAAGTAAATTTGTTACAGATGGGTTGAAATCCCGTTTTGACGCGGaaa                                                                 >  1:260771/1‑141 (MQ=255)
                                                                         aTGAAGATGCGGGTGGTATTTTTTATAATCAAACTAATCAACAACTTTTAGTTCTGTGTG‑ATGGTCTGGGTGGCCATAAAGCAGGAGAAGTTGCAAGTAAATTTGTTACAGATGAGTTGAAATCCCGTTTTGAAGCGGaaa                                                                 >  1:504331/1‑141 (MQ=255)
                                                                           gAAGATGCGGGTGGTATTTTTTATAATCAAACTAATCACCAACTTTTAGTTCTGTGTG‑ATGGTATGGGTGGCCATAAAGCAGGAGAAGTTGCAAGTAAATTTGTTACAGATGAGTTGAAATCCCGTTTTGAAGCGGAAAAt                                                               <  2:64568/141‑1 (MQ=255)
                                                                              gATGCGGGTGGTATTTTTTATAATCAAACTAATCAACAACTTTTAGTTCTGTGTG‑ATGGTCTGGGTGGCCATAAAGCAGGAGAAGTTGCAAGTAAATTTGTTACAGATGAGTTGAAATCCCGTTTTGAAGCGGAAAATCtt                                                            >  1:479998/1‑141 (MQ=255)
                                                                              gATGCGGGTGATATTTTTTATAATCATACTAATCAACAACTTTTAGTTCTGTGTG‑ATGGTCTAGGTGGCCATAAAGCAGGAGAAGTTGCAAGTAATTTTGTTACAGATGAGTTGAAGTCCGGTTTTGAAACGGAAAATcat                                                            >  2:374415/1‑139 (MQ=255)
                                                                               aTGCGGGTGGTATTTTTTATAATCAAACTAATCAACAACTTTTAGTTCTGTGTG‑ATGGTATGGGTGGCCATAAAGCAGGAGAAGTTGCAAGTAAATTTGTTACAGATGAGTTGAAATCCCGTTTTGAAGCGGAAAATCTta                                                           <  2:99368/141‑1 (MQ=255)
                                                                                 gCGGGTGGTATTTTTTATAATCAAACTAATCAACAACTTTTAGTTCTGTGTG‑ATGGTCTGGGTGGCCATAAAGCAGGAGAAGTTGCAAGTAAATTTGTTACAGATGAGTTGAAATCCCGTTTTGAAGCGGAAAATCTtata                                                         >  2:244276/1‑141 (MQ=255)
                                                                                   gggTGGTATTTTTTATAATCAAACTAATCAACAACTTTTAGTTCTGTGTG‑ATGGTATGGGTGGCCATAAAGCAGGAGAAGTTGCAAGTAAATTTGTTACAGGTGAGTTGAAATCCCGTGTTGAAGCGGAAAATCTTATAGa                                                       >  2:420483/1‑141 (MQ=255)
                                                                                       ggtATTTTTTGTAATCCACCTAATCAACACCTTTTAGTTCTGTGTG‑ATGGTCTGGGTGGCCATAAAGCAGGAGAAGTTGCAAGTAAATTTGTTACAGATGAGTTGAAATCCCGTTTTGAAGCGGAAAATCTTATAGaacaa                                                   <  2:201616/141‑1 (MQ=255)
                                                                                        gtATTTTTTATAATCAAACTAATCAACAACTTTTAGTTCTGTGTG‑ATGGTCTGGGTGGCCATAAAGCAGGAGAAGTTGCAAGTAAATTTGTTACAGATGAGTTGAAATCCCGTTTTGAAGCGGAAAATCTTATAGaacaac                                                  >  1:154749/1‑141 (MQ=255)
                                                                                            tttttATAATCAAACTAATCAACAACTTTTAGTTCTGTGTG‑ATGGTCTGGGTGGCCATAAAGCAGGAGAAGTTGCAAGTAAATTTGTTACAGATGAGTTGAAATCCCGTTTTGAAGCGGAAAATCTTATAGAACAACATCa                                              <  1:280796/141‑1 (MQ=255)
                                                                                               ttATAATCAAACTAATCAACAACTTTTAGTTATGTGTG‑ATGGTATGGGTGGCCATAAAGCAGGAGAAGTTGCAAGTAAATTTGTTACAGATGAGTTGAAATCCCGTTTTGAAGCGGAAAATCTTATAGAACAACATCAAGc                                           >  2:325933/1‑141 (MQ=255)
                                                                                                  taATCAAACTAATCAACAACTTTTAGTTCTGTGTG‑ATGGTATGGGTGGCCATAAAGCAGGAGAAGTTGCAAGTAAATTTGTTACAGATGAGTTGAAATCCCGTTTTGAAGCGGAAAATCTTATAGAACAACATCAAGCTGa                                        >  1:89913/1‑141 (MQ=255)
                                                                                                  taATCAAACTAATCAAAAACTTTTAGTTCTGTGTG‑ATGGTATGGGTGGCCATAAAGCAGGAGAAGTTGCAAGTAAATTTGTTACAGATGAGTTGAAATCCCGTTTTGAAGCGGAAAATCTTATAGAACAACATCAAGCTGa                                        <  2:129013/141‑1 (MQ=255)
                                                                                                      cAAACTAATCAACAACTTTTAGTTCTGTGTG‑ATGGTCTGGGTGGCCATAAAGCAGGAGAAGTTGCAAGTAAATTTGTTACAGATGAGTTGAAATCCCGTTTTGAAGCGGAAAATCTTATAGAACAACATCAAGCTGAAAAt                                    >  1:258064/1‑141 (MQ=255)
                                                                                                           tAATCAACAACTTTTAGTTTCGTGTG‑ATGGTATCGGTGGCCATAAAGCAGGAGAAGTTGCAAGTAAATTTGTTACAGATGAGTTGAAATCCCGTTTTGAAGCGGAAAATCTTATAGAACAACATCAAGCTGAAAACTGGtt                               <  2:342559/141‑1 (MQ=255)
                                                                                                                  caacTTTTAGTTCTGTGTG‑ATGGTATGGGTGGCCATAAAGCAGGAGAAGTTGCAAGTAAATTTGTTACAGATGAGTTGAAATCCCGTTTTGAAGCGGAAAATCTTATAGAACAACATCAAGCTGAAAATTGGTTGCGtaat                        <  1:50281/141‑1 (MQ=255)
                                                                                                                    acTTTTAGTTCTGTGTG‑ATGGTCTGGGTGGCCATAAAGCAGGAGAAGTTGCAAGTAAATTTGTTACAGATGAGTTGAAATCCCGTTTTGAAGCGGAAAATCTTATAGAACAACATCAAGCTGAAAATTGGTTGCGtaataa                      <  1:217259/141‑1 (MQ=255)
                                                                                                                     cTTTTAGATCTGTGTG‑ATGGCCTGGGTGGCCATAAAGCAGGAGAAGTTGCAAGTAAATTTGTTACAGATGAGTTGAAATCCCGTTTTGAAGCGGAAAATCTTATAGAACAACATCAAGCTGAAAATTGGTTGCGTaataat                     >  1:385094/1‑141 (MQ=255)
                                                                                                                       tttAGTTCTGTGTG‑ATGGTATGGGTGGCCATAAAGCAGGAGAAGTTGCAAGTAAATTTGTTACAGATGAGTTGAAATCCCGTTTTGAAGCGGAAAATCTTATAGAACAACATCAAGCTGAAAATTGGTTGCGTAATAatat                   >  1:540520/1‑141 (MQ=255)
                                                                                                                                gtgtg‑ATGGTATGGGTGGCCATAAAGCAGGAGATGTTGCAAGTAAATTTGATACAGATGAGTTGAACTCCCGTTTTGAAGCGGAAAATCTTATAGAACAACATCAAGCTGAAAATTGGTTGCGTAATAATATAAAatatat          <  1:416106/141‑1 (MQ=255)
                                                                                                                                    g‑ATGGTCTGGGTGGCCATAAAGAAGGAGAAGTTGCAAGTAAATTTGTTACAGATGAGTTGAAATCCCGTTTTGAAGCGGAAAATCTTATAGAACAACATCAAGCTGAAAATTGGTTGCGTAATAATATAAAAGATATAAAt      >  2:492974/1‑141 (MQ=255)
                                                                                                                                         gTATGGGTGGCCATAAAGCAGGAGAAGTTGCAAGTAAATTTGTTACAGATGAGTTGAAATCCCGTTTTGAAGCGGAAAATCTTATAGAACAACATCAAGCTGAAAATTGGTTGCGTAATAATATAAAAGATAAAAATTTTc  >  2:104620/1‑141 (MQ=255)
                                                                                                                                           |                                                                                                                                          
CAAGTAGAAACGAGGTAAAGACAAATGCTAGAGGCACAATTTTTTACTGATACTGGACAACATAGAGATAAGAATGAAGATGCGGGTGGTATTTTTTATAATCAAACTAATCAACAACTTTTAGTTCTGTGTG‑ATGGTATGGGTGGCCATAAAGCAGGAGAAGTTGCAAGTAAATTTGTTACAGATGAGTTGAAATCCCGTTTTGAAGCGGAAAATCTTATAGAACAACATCAAGCTGAAAATTGGTTGCGTAATAATATAAAAGATATAAATTTTC  >  USA300TCH1516_ALE/1231332‑1231608

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