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 F21 I0 R2 316 65.6 5147759 97.4% 5013917 60.3

Breseq alignment

BRESEQ :: Evidence
Predicted mutation
evidence seq id position mutation freq annotation gene description
RA W3110S.gb 4,561,090 G→A 37.6% intergenic (‑88/‑585) yjiC ← / → yjiD hypothetical protein/DNA replication/recombination/repair protein

Read alignment evidence...
  seq id position ref new freq score (cons/poly) reads annotation genes product
*W3110S.gb4,561,0900GA37.6% 81.2 / 91.0 85intergenic (‑88/‑585)yjiC/yjiDhypothetical protein/DNA replication/recombination/repair protein
Reads supporting (aligned to +/- strand):  ref base G (30/23);  new base A (14/18);  total (44/41)
Fisher's exact test for biased strand distribution p-value = 2.72e-01
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 1.00e+00

GTATTTCACTGATGTTTAGAAAAATAGATAAATTTTTCTGTAGTAAAAAGAGAAGTAAACAAATGACATGCATGTTTCTGTTGTAGTGATATCAACTCTACACGGTGATATTAAAGGGTAGGAAACACTCTAAAGT  >  W3110S.gb/4561021‑4561156
                                                                     |                                                                  
gTATTTCACTGATGTTTAGAAAAATAGATAAATTTTTCTGTAGTAAAAAGAGAAGTAAACAAATGAcatg                                                                    >  1:2742584/1‑70 (MQ=255)
   tttCACTGATGTTTAGAAAAATAGATAAATTTTTCTGTAGTAAAAAGAGAAGTAAACAAATGAcatgcatg                                                                >  1:1147567/1‑71 (MQ=255)
   tttCACTGATGTTTAGAAAAATAGATAAATTTTTCTGTAGTAAAAAGAGAAGTAAACAAATGAcatgcatg                                                                >  1:137671/1‑71 (MQ=255)
   tttCACTGATGTTTAGAAAAATAGATAAATTTTTCTGTAGTAAAAAGAGAAGTAAACAAATGAcatgcat                                                                 <  1:1896731/70‑1 (MQ=255)
     tCACTGATGTTTAGAAAAATAGATAAATTTTTCTGTAGTAAAAAGAGAAGTAAACAAATGACATACATGtt                                                              >  1:4917854/1‑71 (MQ=255)
     tCACTGATGTTTAGAAAAATAGATAAATTTTTCTGTAGTAAAAAGAGAAGTAAACAAATGACATACATGt                                                               <  1:162863/70‑1 (MQ=255)
     tCACTGATGTTTAGAAAAATAGATAAATTTTTCTGTAGTAAAAAGAGAAGTAAACAAATGACATACATGt                                                               <  1:2316033/70‑1 (MQ=255)
      cACTGATGTTTAGAAAAATAGATAAATTTTTCTGTAGTAAAAAGAGAAGTAAACAAATGACATGCATGttt                                                             >  1:4290369/1‑71 (MQ=255)
      cACTGATGTTTAGAAAAATAGATAAATTTTTCTGTAGTAAAAAGAGAAGTAAACAAATGACATGCATGt                                                               <  1:3156636/69‑1 (MQ=255)
      cACTGATGTTTAGAAAAATAGATAAATTTTTCTGTAGTAAAAAGAGAAGTAAACAAATGACATACATGtt                                                              <  1:4625592/70‑1 (MQ=255)
       aCTGATGTTTAGAAAAATAGATAAATTTTTCTGTAGTAAAAAGAGAAGTAAACAAATGACATGCATGttt                                                             >  1:4529945/1‑70 (MQ=255)
       aCTGATGTTTAGAAAAATAGATAAATTTTTCTGTAGTAAAAAGAGAAGTAAACAAATGACATGCATGttt                                                             <  1:3271451/70‑1 (MQ=255)
       aCTGATGTTTAGAAAAATAGATAAATTTTTCTGTAGTAAAAAGAGAAGTAAACAAATGACATGCATGTTTc                                                            <  1:325048/71‑1 (MQ=255)
       aCTGATGTTTAGAAAAATAGATAAATTTTTCTGTAGTAAAAAGAGAAGTAAACAAATGACATGCATGTTTc                                                            <  1:1342745/71‑1 (MQ=255)
       aCTGATGTTTAGAAAAATAGATAAATTTTTCTGTAGTAAAAAGAGAAGTAAACAAATGACATACATGTTTc                                                            <  1:4648137/71‑1 (MQ=255)
          gATGTTTAGAAAAATAGATAAATTTTTCTGTAGTAAAAAGAGAAGTAAACAAATGACATACATGTTTCtgt                                                         >  1:2789673/1‑71 (MQ=255)
           aTGTTTAGAAAAATAGATAAATTTTTCTGTAGTAAAAAGAGAAGTAAACAAATGACATGCATGTTTCtgtt                                                        >  1:515597/1‑71 (MQ=255)
               ttAGAAAAATAGATAAATTTTTCTGTAGTAAAAAGAGAAGTAAACAAATGACATGCATGTTTCtgttgt                                                      <  1:4071754/69‑1 (MQ=255)
                tAGAAAAATAGATAAATTTTTCTGTAGTAAAAAGAGAAGTAAACAAATGACATGCATGTTTCTGTTGTAGt                                                   >  1:2328146/1‑71 (MQ=255)
                 aGAAAAATAGATAAATTTTTCTGTAGTAAAAAGAGAAGTAAACAAATGACATGCATGTTTCTGTTGTAGt                                                   <  1:276547/70‑1 (MQ=255)
                 aGAAAAATAGATAAATTTTTCTGTAGTAAAAAGAGAAGTAAACAAATGACATACATGTTTCTGTTGTAGt                                                   <  1:3725502/70‑1 (MQ=255)
                     aaaTAGATAAATTTTTCTGTAGTAAAAAGAGAAGTAAACAAATGACATGCATGTTTCTGTTGTa                                                     >  1:2092431/1‑64 (MQ=255)
                     aaaTAGATAAATTTTTCTGTAGTAAAAAGAGAAGTAAACAAATGACATGCATGTTTCTGTTGTAGTGatat                                              >  1:2360062/1‑71 (MQ=255)
                      aaTAGATAAATTTTTCTGTAGTAAAAAGAGAAGTAAACAAATGACATGCATGTTTCTGTTGTAGTGatat                                              >  1:3475299/1‑70 (MQ=255)
                      aaTAGATAAATTTTTCTGTAGTAAAAAGAGAAGTAAACAAATGACATGCATGTTTCTGTTGTAGTGATATc                                             <  1:3391707/71‑1 (MQ=255)
                      aaTAGATAAATTTTTCTGTAGTAAAAAGAGAAGTAAACAAATGACATACATGt                                                               >  1:4713090/1‑53 (MQ=255)
                          gATAAATTTTTCTGTAGTAAAAAGAGAAGTAAACAAATGACATGCATGTTTCTGTTGTAGTGATATCAAct                                         <  1:3653881/71‑1 (MQ=255)
                             aaaTTTTTCTGTAGTAAGAAGAGAAGTAAACAAATGACATGCATGTTTCTGTTGTAGTGATATCAACTCTa                                      >  1:4201940/1‑71 (MQ=255)
                              aaTTTTTCTGTAGTAAAAAGAGAAGTAAACAAATGACATGCATGTTTCTGTTGTAGTGATATCAACTCTa                                      <  1:4689454/70‑1 (MQ=255)
                              aaTTTTTCTGTAGTAAAAAGAGAAGTAAACAAATGACATGCATGTTTCTGTTGTAGTGATATCAACTCTa                                      <  1:2945950/70‑1 (MQ=255)
                              aaTTTTTCTGTAGTAAAAAGAGAAGTAAACAAATGACATACATGTTTCTGTTGTAGTAATATCAACTCTa                                      <  1:1556962/70‑1 (MQ=255)
                                 ttttCTGTAGTAAAAAGAGAAGTAAACAAATGAcatg                                                                    >  1:615551/1‑37 (MQ=255)
                                 ttttCTGTAGTAAAAAGAGAAGTAAACAAATGACATGCATGTTTCTGTTGTAGTGATATCAACTCTACACg                                  >  1:224535/1‑71 (MQ=255)
                                 ttttCTGTAGTAAAAAGAGAAGTAAACAAATGACATGCATGTTTCTGTTGTAGTGATATCAACTCTACACg                                  >  1:1627198/1‑71 (MQ=255)
                                        tagtaAAAAGAGAAGTAAACAAATGACATGCATGTTTCTGTTGTAGTGATATCAACTCTACACGGTGatat                           >  1:3069120/1‑71 (MQ=255)
                                        tagtaAAAAGAGAAGTAAACAAATGACATGCATGTTTCTGTTGTAGTGATATCAACTCTACACGGTGatat                           >  1:2321469/1‑71 (MQ=255)
                                        tagtaAAAAGAGAAGTAAACAAATGACATGCATGTTTCTGTTGTAGTGATATCAACTCTACACGGTGatat                           >  1:2849912/1‑71 (MQ=255)
                                        tagtaAAAAGAGAAGTAAACAAATGACATACATGTTTCTGTTGTAGTGa                                                 >  1:4190646/1‑49 (MQ=255)
                                        tagtaAAAAGAGAAGTAAACAAATGACATACATGTTTCTGTTGTAGTGa                                                 >  1:1346202/1‑49 (MQ=255)
                                        tagtaAAAAGAGAAGTAAACAAATGACATACATGTTTCTGTTGTAGTGa                                                 >  1:2003833/1‑49 (MQ=255)
                                        tagtaAAAAGAGAAGTAAACAAATGACATACATGTTTCTGTTGTAGTGa                                                 >  1:3405774/1‑49 (MQ=255)
                                          gtaAAAAGAGAAGTAAACAAATGACATGCATGTTTCTGTTGTAGTGATATCAACTCTACACGGTGATAtt                          <  1:449119/70‑1 (MQ=255)
                                           taAAAAGAGAAGTAAACAAATGACATGCATGTTTCTGTTGTAGTGATATCAACTCTACACGGTGATAtt                          <  1:1796161/69‑1 (MQ=255)
                                           taAAAAGAGAAGTAAACAAATGACATGCATGTTTCTGTTGTAGTGATATCAACTCTACACGGTGATATTa                         >  1:295141/1‑70 (MQ=255)
                                           taAAAAGAGAAGTAAACAAATGACATACATGTTTCTGTTGTAGTGATATCAActc                                        <  1:627711/55‑1 (MQ=255)
                                           taAAAAGAGAAGTAAACAAATGACATACATGTTTCTGTTGTAGTGATATCAActc                                        <  1:1500080/55‑1 (MQ=255)
                                           taAAAAGAGAAGTAAACAAATGACATACATGTTTCTGTTGTAGTGATATCAACTCTa                                      <  1:2241099/57‑1 (MQ=255)
                                            aaaaaGAGAAGTAAACAAATGACATGCATGTTTCTGTTGTAGTGa                                                 >  1:518350/1‑45 (MQ=255)
                                             aaaaGAGAAGTAAACAAATGACATACATGTTTCTGTTGTAGTGa                                                 >  1:547239/1‑44 (MQ=255)
                                             aaaaGAGAAGTAAACAAATGACATACATGTTTCTGTTGTAGTGATATCAACTCTACACGGTGATATTaaa                       >  1:3269290/1‑70 (MQ=255)
                                             aaaaGAGAAGTAAACAAATGACATACATGTTTCTGTTGTAGTGATATCAACTCTACACGGTGATATTAAAg                      >  1:105726/1‑71 (MQ=255)
                                             aaaaGAGAAGTAAACAAATGACATACATGTTTCTGTTGTAGTGATATCAACTCTACACGGTGATATTAAAg                      >  1:3225770/1‑71 (MQ=255)
                                             aaaaGAGAAGTAAACAAATGACATACATGTTTCTGTTGTAGTGATATCAACTCTACACGGTGATATTAAAg                      >  1:3655929/1‑71 (MQ=255)
                                               aaGAGAAGTAAACAAATGACATGCATGTTTCTGTTGTAGTGATATCAACTCTACACGGTGATAtt                          <  1:1754987/65‑1 (MQ=255)
                                               aaGAGAAGTAAACAAATGACATGCATGTTTCTGTTGTAGTGATATCAACTCTACACGGTGATATTAAAggg                    <  1:4309045/71‑1 (MQ=255)
                                               aaGAGAAGTAAACAAATGACATACATGTTTCTGTTGTAGTGatat                                              >  1:4348357/1‑45 (MQ=255)
                                                agagAAGTAAACAAATGACATGCATGTTTCTGTTGTAGTGATATCAACTCTACACGGTGATATTAAAggg                    >  1:3245786/1‑70 (MQ=255)
                                                    aaGTAAACAAATGACATACATGTATCTGTTGTAGTGATATCAACTCTACACGGTGATATTAAAGGGTAGGa               <  1:2692849/71‑1 (MQ=255)
                                                      gTAAACAAATGACATGCATGTTTCTGTTGTAGTGATATCaa                                           >  1:939018/1‑41 (MQ=255)
                                                      gTAAACAAATGACATGCATGTTTCTGTTGTAGTGATATCaa                                           >  1:191356/1‑41 (MQ=255)
                                                      gTAAACAAATGACATGCATGTTTCTGTTGTAGTGATATCaa                                           >  1:5027803/1‑41 (MQ=255)
                                                      gTAAACAAATGACATGCATGTTTCTGTTGTAGTGATATCAACTCTaca                                    >  1:3843604/1‑48 (MQ=255)
                                                      gTAAACAAATGACATGCATGTTTCTGTTGTAGTGATATCAACTCTaca                                    >  1:3269629/1‑48 (MQ=255)
                                                      gTAAACAAATGACATGCATGTTTCTGTTGTAGTGATATCAACTCTACACGGTGATATTAAAGGGTAGGaaa             >  1:541378/1‑71 (MQ=255)
                                                      gTAAACAAATGACATGCATGTTTCTGTTGTAGTGATATCAACTCTACACGGTGATATTAAAGGGTAGGaaa             >  1:942880/1‑71 (MQ=255)
                                                      gTAAACAAATGACATACATGTTTCTGTTGTAGTGATATCAACTCTACACGGTGATATTAAAGGGTAGGaaa             <  1:601684/71‑1 (MQ=255)
                                                       tAAACAAATGACATACATGTTTCTGTTGTAGTGATATCAACTCTACACGGTGATATTAAAGGGTAGGa               <  1:1862005/68‑1 (MQ=255)
                                                       tAAACAAATGACATACATGTTTCTGTTGTAGTGATATCAACTCTACACGGTGATATTAAAGGGTAGGa               <  1:3703547/68‑1 (MQ=255)
                                                       tAAACAAATGACATACATGTTTCTGTTGTAGTGATATCAACTCTACACGGTGATATTAAAGGGTAGGa               <  1:3348829/68‑1 (MQ=255)
                                                       tAAACAAATGACATACATGTTTCTGTTGTAGTGATATCAACTCTACACGGTGATATTAAAGGGTAGGa               <  1:2579726/68‑1 (MQ=255)
                                                         aaCAAATGACATGCATGTTTCTGTTGTAGTGATATCAACTCTACACGGTGATATTaa                        >  1:1186095/1‑57 (MQ=255)
                                                         aaCAAATGACATGCATGTTTCTGTTGTAGTGATATCAACTCTACACGGTGATATTAAAGGGTAGGAAacac          >  1:377458/1‑71 (MQ=255)
                                                         aaCAAATGACATGCATGTTTCTGTTGTAGTGATATCAACTCTACACGGTGATATTAAAGGGTAGGAAaca           <  1:3983141/70‑1 (MQ=255)
                                                         aaCAAATGACATGCATGTTTCTGTTGTAGTGATATCAACTCTACACGGTGATATTAAAGGGTAGGAAaca           <  1:740361/70‑1 (MQ=255)
                                                         aaCAAATGACATACATGTTTCTGTTGTAGTGATATCAACTCTACACGGTGATATTAAAGGGTAGGaaa             >  1:2021741/1‑68 (MQ=255)
                                                          aCAAATGACATGCATGTTTCTGTTGTAGTGATATCaa                                           <  1:4384952/37‑1 (MQ=255)
                                                          aCAAATGACATGCATGTTTCTGTTGTAGTGATATCaa                                           <  1:4390962/37‑1 (MQ=255)
                                                            aaaTGACATGCATGTTTCTGTTGTAGTGATATCAACTCTACACGGTGATATTAAAGGGTAGGa               <  1:401429/63‑1 (MQ=255)
                                                             aaTGACATGCATGTTTCTGTTGTAGTGATATCAACTCTACACGGTGATATTAAAGGGTAGGAAACACTCTa      <  1:3963664/71‑1 (MQ=255)
                                                             aaTGACATGCATGTTTCTGTTGTAGTGATATCAACTCTACACGGTGATATTAAAGGGTAGGAAACACTCTa      <  1:853326/71‑1 (MQ=255)
                                                             aaTGACATACATGTTTCTGTTGTAGTGATATCAACTCTACACGGTGATATTAAAGGGTAGGAAACACTCTa      <  1:1957897/71‑1 (MQ=255)
                                                              aTGACATACATGTTTCTGTTGTAGTGATATCAACTCTACACGGTGATATTAAAGGGTAGGAAACACTCTaa     <  1:3039875/71‑1 (MQ=255)
                                                              aTGACATACATGTTTCTGTTGTAGTGATATCAACTCTACACGGTGATATTAAAGGGTAGGAAACACTCTaa     <  1:3184865/71‑1 (MQ=255)
                                                               tGACATGCATGTTTCTGTTGTAGTGATATCAActc                                        <  1:288127/35‑1 (MQ=255)
                                                               tGACATGCATGTTTCTGTTGTAGTGATATCAACTCTACACGGTGATATTAAAGGGTAGGAAACActct       >  1:1410910/1‑68 (MQ=255)
                                                                gACATGCATGTTTCTGTTGTAGTGATATCAACTCTACACGGTGATATTAAAGGGTAGGAAACACTCTAAAg   >  1:2779833/1‑71 (MQ=255)
                                                                 aCATGCATGTTTCTGTTGTAGTGATATCAACTCTa                                      >  1:3245891/1‑35 (MQ=255)
                                                                 aCATGCATGTTTCTGTTGTAGTGATATCAACTCTa                                      >  1:4474029/1‑35 (MQ=255)
                                                                 aCATGCATGTTTCTGTTGTAGTGATATCAACTCTa                                      >  1:872071/1‑35 (MQ=255)
                                                                 aCATGCATGTTTCTGTTGTAGTGATATCAACTCTACACGGTGATATTAAAGGGTAGGAAACACTCTAAAGt  <  1:1643356/71‑1 (MQ=255)
                                                                     gcatgTTTCTGTTGTAGTGATATCAACTCTACACGGTGATATTAAAGGGTAGGa               <  1:220538/54‑1 (MQ=255)
                                                                     |                                                                  
GTATTTCACTGATGTTTAGAAAAATAGATAAATTTTTCTGTAGTAAAAAGAGAAGTAAACAAATGACATGCATGTTTCTGTTGTAGTGATATCAACTCTACACGGTGATATTAAAGGGTAGGAAACACTCTAAAGT  >  W3110S.gb/4561021‑4561156

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 21 ≤ ATCG/ATCG < 32 ≤ ATCG/ATCG < 36 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑

GATK/CNVnator alignment

N/A