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
A2 F1 I0 R2 230 93.6 4701257 96.3% 4527310 61.2

Breseq alignment

BRESEQ :: Evidence
Predicted mutation
evidence seq id position mutation freq annotation gene description
RA minE 549,018 A→G 54.1% L321L (TTG→CTG)  ybiU ← hypothetical protein

Read alignment evidence...
  seq id position ref new freq score (cons/poly) reads annotation genes product
*minE549,0180AG54.1% 14.3 / 76.4 61L321L (TTG→CTG) ybiUhypothetical protein
Reads supporting (aligned to +/- strand):  ref base A (12/16);  new base G (20/13);  total (32/29)
Fisher's exact test for biased strand distribution p-value = 2.04e-01
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 1.00e+00

GACGTCGCAGTGCCACCAGACGGAGTCTCCGGCTTCGAGTTTTGGAATGCTGGTTAACGCCTCAATCAACAGTGGATGCCATTGCTCTGATACCGGCAATACTCTTCCGGGCGCTACGCCGCACAGTTCATCCTCCGG  >  minE/548950‑549087
                                                                    |                                                                     
gACGTCGCAGTGCCACCAGACGGAGTCTCCGGCTTCGAGTTTTGGAATGCTGGTTAACGCCTCAATCAAc                                                                      <  1:2051902/70‑1 (MQ=255)
 aCGTCGCAGTGCCACCAGACGGAGTCTCCGGCTTCGAGTTTTGGAATGCTGGTTAACGCCTCAATCAACAg                                                                    >  1:2963641/1‑71 (MQ=255)
       cAGTGCCACCAGACGGAGTCTCCGGCTTCGAGTTTTGGAATGCTGGTTAACGCCTCAATCAACAGTg                                                                  <  1:4428448/67‑1 (MQ=255)
       cAGTGCCACCAGACGGAGTCTCCGGCTTCGAGTTTTGGAATGCTGGTTAACGCCTCAATCAACAGTg                                                                  <  1:72888/67‑1 (MQ=255)
        aGTGCCACCAGACGGAGTCTCCGGCTTCGAGTTTTGGAATGCTGGTTAACGCCTCAATCAACAGTGGATGc                                                             <  1:3099809/71‑1 (MQ=255)
           gCCACCAGACGGAGTCTCCGGCTTCGAGTTTTGGAATGCTGGTTAACGCCTCAATCAACAGTGGAt                                                               >  1:2546829/1‑66 (MQ=255)
            ccaccaGACGGAGTCTCCGGCTTCGAGTTTTGGAATGCTGGTTAACGCCTCAATCAGCAGTGGATGCCAtt                                                         >  1:4548617/1‑71 (MQ=255)
               ccaGACGGAGTCTCCGGCTTCGAGTTTTGGAATGCTGGTTAACGCCTCAATCAACAGTGGATGcc                                                            <  1:3251937/65‑1 (MQ=255)
                 aGACGGAGTCTCCGGCTTCGAGTTTTGGAATGCTGGTTAACGCCTCAATCAGCAGTg                                                                  >  1:2336052/1‑57 (MQ=255)
                 aGACGGAGTCTCCGGCTTCGAGTTTTGGAATGCTGGTTAACGCCTCAATCAGCAGTGGATGCCATTGctct                                                    <  1:3618087/71‑1 (MQ=255)
                 aGACGGAGTCTCCGGCTTCGAGTTTTGGAATGCTGGTTAACGCCTCAATCAGCAGTGGATGCCATTGctc                                                     <  1:1662600/70‑1 (MQ=255)
                 aGACGGAGTCTCCGGCTTCGAGTTTTGGAATGCTGGTTAACGCCTCAATCAACAGTGGAt                                                               >  1:1639560/1‑60 (MQ=255)
                  gACGGAGTCTCCGGCTTCGAGTTTTGGAATGCTGGTTAACGCCTCAATCAGCAGTGGATGCCATTGctct                                                    >  1:3979050/1‑70 (MQ=255)
                  gACGGAGTCTCCGGCTTCGAGTTTTGGAATGCTGGTTAACGCCTCAATCAACAGTGGATGCCATTGctct                                                    >  1:4301616/1‑70 (MQ=255)
                   aCGGAGTCTCCGGCTTCGAGTTTTGGAATGCTGGTTAACGCCtcaatcaa                                                                       <  1:780426/50‑1 (MQ=255)
                    gacaGTCTCCGGCTTCGAGTTTTGGAATGCTGGTTAACGCCTCAATCAGCAGTGGATGCCATTGCTCTGa                                                  >  1:3715178/4‑70 (MQ=255)
                    cGGAGTCTCCGGCTTCGAGTTTTGGAATGCTGGTTAACGCCTCAATCAACAGTGGATGCCATTGCTCTGAt                                                 <  1:3453219/71‑1 (MQ=255)
                     ggAGTCTCCGGCTTCGAGTTTTGGAATGCTGGTTAACGCCTCAATCAGCa                                                                     >  1:2779805/1‑50 (MQ=255)
                     ggAGTCTCCGGCTTCGAGTTTTGGAATGCTGGTTAACGCCTCAATCAGCa                                                                     >  1:2338947/1‑50 (MQ=255)
                     ggAGTCTCCGGCTTCGAGTTTTGGAATGCTGGTTAACGCCTCAATCAGCa                                                                     >  1:4657249/1‑50 (MQ=255)
                           tcCGGCTTCGAGTTTTGGAATGCTGGTTAACGCCTCAATCAGCAGTGGATGCCATTGCTCTGATACCGGc                                           >  1:4376556/1‑70 (MQ=255)
                           tcCGGCTTCGAGTTTTGGAATGCTGGTTAACGCCTCAATCAACa                                                                     >  1:2679914/1‑44 (MQ=255)
                           tcCGGCTTCGAGTTTTGGAATGCTGGTTAACGCCTCAATCAACAg                                                                    >  1:2878889/1‑45 (MQ=255)
                            ccGGCTTCGAGTTTTGGAATGCTGGTTAACGCCTCAATCAGCAGTg                                                                  <  1:6369/46‑1 (MQ=255)
                             cGGCTTCGAGTTTTGGAATGCTGGTTAACGCCTCACTCAACAGTGGATGCCATTGCTCTGATACCGGCaa                                         >  1:103142/1‑70 (MQ=255)
                             cGGCTTCGAGTTTTGGAATGCTGGTTAACGCCTCAATCAGCAGTGGATGCCATTGCTCTGATACCTGCaa                                         <  1:3926846/70‑1 (MQ=255)
                             cGGCTTCGAGTTTTGGAATGCTGGTTAACGCCTCAATCAGCAGTGGATGCCATTGCTCTGATACCGGCaa                                         <  1:3908744/70‑1 (MQ=255)
                             cGGCTTCGAGTTTTGGAATGCTGGTTAACGCCTCAATCAGCAGTGGATGCCATTGCTCTGATACCGGCAAt                                        <  1:3323427/71‑1 (MQ=255)
                              ggCTTCGAGTTTTGGAATGCTGGTTAACGCCTCAATCAACAGTGGATGCCATTGCTCTGATACCGGCAATa                                       >  1:538463/1‑71 (MQ=255)
                              ggCTTCGAGTTTTGGAATGCTGGTTAACGCCTCAATCAACAGTGGATGCCATTGCTCTGATACCGGCAATa                                       >  1:1497343/1‑71 (MQ=255)
                               gCTTCGAGTTTTGGAATGCTGGTTAACGCCTCAATCAAc                                                                      <  1:2699521/39‑1 (MQ=255)
                                 ttCGAGTTTTGGAATGCTGGTTAACGCCTCAATCAGCAGTGGATGCCATTGctct                                                    <  1:1027560/55‑1 (MQ=255)
                                 ttCGAGTTTTGGAATGCTGGTTAACGCCTCAATCAACAGTGGATGCCATTGCTCTGATACCGGCAATActc                                    >  1:792226/1‑71 (MQ=255)
                                  tCGAGTTTTGGAATGCTGGTTAACGCCTCAATCAGCAGTg                                                                  >  1:1654630/1‑40 (MQ=255)
                                   cGAGTTTTGGAATGCTGGTTAACTCCTCAATCAGCAGTGGATGCCATTGCTCTGATACCGGCAATActct                                   <  1:4308659/70‑1 (MQ=255)
                                   cGAGTTTTGGAATGCTGGTTAACGCCTCAATCAACAGTGGATGCCATTGCTCTGATACCGGCAATACTCtt                                  >  1:4646006/1‑71 (MQ=255)
                                    gAGTTTTGGAATGCTGGTTAACGCCTCAATCAGCAGTg                                                                  <  1:2234150/38‑1 (MQ=255)
                                      gTTTTGGAATGCTGGTTAACGCCTCAATCAGCAGTGGATGc                                                             <  1:365941/41‑1 (MQ=255)
                                      gTTTTGGAATGCTGGTTAACGCCTCAATCAACAGTg                                                                  <  1:1296299/36‑1 (MQ=255)
                                      gTTTTGGAATGCTGGTTAACGCCTCAATCAACAGTg                                                                  <  1:1663433/36‑1 (MQ=255)
                                       ttttGGAATGCTGGTTAACGCCTCAATCAGCAGTGGATGCCATTGCTCTGATACCGGCAATACTCTTCCgg                              <  1:4119538/71‑1 (MQ=255)
                                       ttttGGAATGCTGGTTAACGCCTCAATCAACAGTgg                                                                 <  1:758370/36‑1 (MQ=255)
                                       ttttGGAATGCTGGTTAACGCCTCAATCAACAGTGGATGCCATTGctct                                                    <  1:1360202/49‑1 (MQ=255)
                                        tttGGAATGCTGGTTAACGCCTCAATCAACAGTGGATGCCATTGCTCTGATACCGGCaa                                         >  1:432704/1‑59 (MQ=255)
                                         ttGGAATGCTGGTTAACGCCTCAATCAGCAGTGGATGCCATTGCTCTGa                                                  >  1:4404326/1‑49 (MQ=255)
                                         ttGGAATGCTGGTTAACGCCTCAATCAGCAGTGGATGCCATTGCTCTGATACCGGCAATACTCTTCCggg                             >  1:4568234/1‑70 (MQ=255)
                                         ttGGAATGCTGGTTAACGCCTCAATCAGCAGTGGATGCCATTGCTCTGATAACGGCAATACTCTTCCGGgc                            >  1:3063119/1‑71 (MQ=255)
                                         ttGGAATGCTGGTTAACGCCTCAATCAGCAGTGGATGCAATTg                                                        >  1:672459/1‑43 (MQ=38)
                                             aaTGCTGGTTAACGCCTCAATCAGCAGTGGATGCCATTGCTCTGATACCGGCAATACTCTTCCGGGCGCTa                        >  1:1857163/1‑71 (MQ=255)
                                             aaTGCTGGTTAACGCCTCAATCAGCAGTGGATGCCATTGCTCTGATACCGGCAATACTCTTCCGGGCGCTa                        >  1:354735/1‑71 (MQ=255)
                                              aTGCTGGTTAACGCCTCAATCAGCAGTGGATGCCATTGCTCTGATACCGGCAAt                                        >  1:1867789/1‑54 (MQ=255)
                                               tGCTGGTTAACGCCTCAATCAACAGTGGATGCCATTGctct                                                    <  1:3187388/41‑1 (MQ=255)
                                               tGCTGGTTAACGCCTCAATCAACAGTGGATGCCATTGctct                                                    <  1:1614850/41‑1 (MQ=255)
                                                    gTTAACGCCTCAATCAGCAGTGGATGCCATTGCTCTGATACCGGc                                           <  1:1755786/45‑1 (MQ=255)
                                                    gTTAACGCCTCAATCAGCAGTGGATGCCATTGCTCTGATACCGGCAATACTCTTCCGGGCGCTACGCCGca                 >  1:820945/1‑71 (MQ=255)
                                                    gTTAACGCCTCAATCAGCAGTGGATGCCATTGCTCTGATACCGGCAATACTCTTCCGGGCGCTACGCCGca                 >  1:3496220/1‑71 (MQ=255)
                                                     ttAACGCCTCAATCAGCAGTGGATGCCATTGCTCTGATACCGGCAATACTCTTCCGGGCGCTACGCCGca                 >  1:1230962/1‑70 (MQ=255)
                                                     ttAACGCCTCAATCAACAGTGGATGCCATTGCTCTGATACCGGCAATACTCTTCCGGGCGCTACGCCGca                 <  1:1748160/70‑1 (MQ=255)
                                                      tAACGCCTCAATCAGCAGTGGATGCCATTGCTCTGATACCGGCAATACTCTTCCGGGCGCTACGCCGca                 >  1:1716413/1‑69 (MQ=255)
                                                       ctggCCTCAATCAACAGTGGATGCCATTGCTCTGATACCGGCAATACTCTTCCGGGCGCTACGCCGCACAg              <  1:4549320/68‑1 (MQ=255)
                                                       aaCGCCTCAATCAACAGTGGATGCCATTGCTCTGATACCGGCAATACTCTTCCGGGCGCTACGCCGcaca               <  1:1064422/70‑1 (MQ=255)
                                                           ccTCAATCAGCAGTGGATGCCATTGCTCTGATACCGGCAATACTCTTCCGGGCGCTACGCCGCACAGTTCa          <  1:3256435/71‑1 (MQ=255)
                                                             tcaatcagCAGTGGATGCCATTGCTCTGATACCGGCAATACTCTTCCGGGCGCTACGCCGCACAGTTCa          <  1:2521749/69‑1 (MQ=255)
                                                             tcaatcaaCAGTGGATGCCATTGCTCTGATACCGGCAATa                                       >  1:1992175/1‑40 (MQ=255)
                                                               aatcagCAGTGGATGCCATTGCTCTGATACCGGCAATa                                       >  1:1136475/1‑38 (MQ=255)
                                                               aatcagCAGTGGATGCCATTGCTCTGATACCGGCAATa                                       >  1:3473075/1‑38 (MQ=255)
                                                               aatcagCAGTGGATGCCATTGCTCTGATACCGGCAATACTCTTCCGGGCGCTAcgc                     >  1:314913/1‑56 (MQ=255)
                                                               aatcaaCAGTGGATGCCATTGCTCTGATACCGGCAATACTCTTCCGGGCGCTACGCCGCACAGTTCAtcct      >  1:954081/1‑71 (MQ=255)
                                                               aatcaaCAGTGGATGCCATTGCTCTGATACCGGCAATACTCTTCCGGGCGCTACGCCGCACAGTTCAtcct      >  1:3476813/1‑71 (MQ=255)
                                                               aatcaaCAGTGGATGCCATTGCTCTGATACCGGCAATACTCTTCCGGGCGCTACGCCGCACAGTTCAtcct      >  1:2107069/1‑71 (MQ=255)
                                                                 tcagCAGTGGATGCCATTGCTCTGATACCGGCAATAct                                     <  1:3138040/38‑1 (MQ=255)
                                                                 tcagCAGTGGATGCCATTGCTCTGATACCGGCAATACTCTTcc                                <  1:2446068/43‑1 (MQ=255)
                                                                 tcagCAGTGGATGCCATTGCTCTGATACCGGCAATACTCTTCCGGGCGCTACGCCGCACAGTTCAtcctcc    >  1:2998272/1‑71 (MQ=255)
                                                                  caaCAGTGGATGCCATTGCTCTGATACCGGCAATACTCTTCCGGGCGCTACGCCGca                 <  1:1605607/57‑1 (MQ=255)
                                                                   aaCAGTGGATGCCATTGCTCTGATACCGGCAATACTCTTCCGGGCGCTACGCCGCACAGt             >  1:3591276/1‑60 (MQ=255)
                                                                   aaCAGTGGATGCCATTGCTCTGATACCGGCAATACTCTTCCGGGCGCTACGCCGCACAGTTCATCCTCCgg  >  1:2436888/1‑71 (MQ=255)
                                                                   aaCAGTGGATGCCATTGCTCTGATACCGGCAATACTCTTCCGGGCGCTACGCCGCACAGTTCATCCTCCgg  >  1:2258468/1‑71 (MQ=255)
                                                                    |                                                                     
GACGTCGCAGTGCCACCAGACGGAGTCTCCGGCTTCGAGTTTTGGAATGCTGGTTAACGCCTCAATCAACAGTGGATGCCATTGCTCTGATACCGGCAATACTCTTCCGGGCGCTACGCCGCACAGTTCATCCTCCGG  >  minE/548950‑549087

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