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
A6 F21 I0 R1 2169 63.0 3952800 76.2% 3012033 62.4

Breseq alignment

BRESEQ :: Evidence
Predicted mutation
evidence seq id position mutation freq annotation gene description
RA minE 1,015,259 C→G 13.9% V270V (GTG→GTC)  fumA ← aerobic Class I fumarate hydratase

Read alignment evidence...
  seq id position ref new freq score (cons/poly) reads annotation genes product
*minE1,015,2590CG13.9% 177.8 / 18.6 72V270V (GTG→GTC) fumAaerobic Class I fumarate hydratase
Reads supporting (aligned to +/- strand):  ref base C (27/35);  new base G (5/5);  total (32/40)
Fisher's exact test for biased strand distribution p-value = 7.43e-01
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 8.94e-01

AGTATTTACCACCAAACTGCGCACCCAGACCAAGATTTTGCGCTTCGATCAGCAATTCTTTTTCCAGTTCCACATCGCGGAACGCCTGACCGTGCTCATTCCCTTCCGTTGGCAGTTCATCATAGTATTTCGCGGAAGC  >  minE/1015189‑1015327
                                                                      |                                                                    
aGTATTTACCACCAAACTGCGCACCCAGACCAAGATTTTGCGCTTCGATCAGCAATTCTTTTTCCAGTTcc                                                                      <  1:1825202/71‑1 (MQ=255)
  tATTTACCACCAAACTGCGCACCCAGACCAAGATTTTGCGCTTCGATCAGCAATTCTTTTTCCAGTTCcac                                                                    <  1:3951433/71‑1 (MQ=255)
   aTTTACCACCAAACTGCGCACCCAGACCAAGATTTTGCGCTTCGATCAGCAATTCTTTTTCCAGTTCcaca                                                                   >  1:2323110/1‑71 (MQ=255)
   aTTTACCACCAAACTGCGCACCCAGACCAAGATTTTGCGCTTCGATCAGCAATTCTTTTTCCAGTTCcaca                                                                   >  1:1578601/1‑71 (MQ=255)
      tACCACCAAACTGCGCACCCAGACCAAGATTTTGCGCTTCGATCAGCAATTCTTTTTCCAGTTCCACATcg                                                                >  1:1425660/1‑71 (MQ=255)
             aaaCTGCGCGCCAAGACCGAGTTTCTGGGCCTCTTCCAGCAGTTCCTGTTCCAGCTGGACATCGCGGAACg                                                         <  1:1363336/71‑1 (MQ=255)
             aaaCTGCGCGCCAAGACCGAGTTTCTGGGCCTCTTCCAGCAGTTCCTGTTCCAGCTGGACATCGCGGAACg                                                         >  1:3231890/1‑71 (MQ=255)
              aaCTGCGCGCCAAGACCGAGTTTCTGGGCCTCTTCCAGCAGTTCCTGTTCCAGCTGGACATCGCGGAACGc                                                        >  1:2134061/1‑71 (MQ=255)
               aCTGCGCACCCAGACCAAGATTTTGCGCTTCGATCAGCAATTCTTTTTCCAGTTCCACATCGCGGAACGcc                                                       >  1:772568/1‑71 (MQ=255)
                cTGCGCACCCAGACCAAGATTTTGCGCTTCGATCAGCAATTCTTTTTCCAGTTCCACAt                                                                  <  1:572389/59‑1 (MQ=255)
                cTGCGCACCCAGACCAAGATTTTGCGCTTCGATCAGCAATTCTTTTTCCAGTTCCACAt                                                                  <  1:3433633/59‑1 (MQ=255)
                cTGCGCACCCAGACCAAGATTTTGCGCTTCGATCAGCAATTCTTTTTCCAGTTCCACATCGCGGAACGCCt                                                      >  1:1216288/1‑71 (MQ=255)
                 tGCGCGCCAAGACCGAGTTTCTGGGCCTCTTCCAGCAGTTCCTGTTCCAGCTGGACATCGCGGAACGCCt                                                      >  1:31996/1‑70 (MQ=255)
                    gcACCCAGACCAAGATTTTGCGCTTCGATCAGCAATTCTTTTTCCAGTTCCACATCGCGGAACGCCTGAcc                                                  <  1:151129/71‑1 (MQ=255)
                    gcACCCAGACCAAGATTTTGCGCTTCGATCAGCAATTCTTTTTCCAGTTCCACATCGCGGAACGCCTGAcc                                                  <  1:164936/71‑1 (MQ=255)
                     cACCCAGACCAAGATTTTGCGCTTCGATCAGCAATTCTTTTTCCAGTTCCACATCGCGGAACGCCTGACCg                                                 <  1:3950693/71‑1 (MQ=255)
                     cACCCAGACCAAGATTTTGCGCTTCGATCAGCAATTCTTTTTCCAGTTCCACATCGCGGAACGCCTGACCg                                                 <  1:2768556/71‑1 (MQ=255)
                      aCCCAGACCAAGATTTTGCGCTTCGATCAGCAATTCTTTTTCCAGTTCCACAt                                                                  <  1:3234393/53‑1 (MQ=255)
                        ccAGACCAAGATTTTGCGCTTCGATCAGCAATTCTTTTTCCAGTTCCACATCGCGGAACGCCTGACCGTGc                                              >  1:1908612/1‑71 (MQ=255)
                         cAGACCAAGATTTTGCGCTTCGATCAGCAATTCTTTTTCCAGTTCCACATCGCGGAACGCCTGACCg                                                 <  1:2190500/67‑1 (MQ=255)
                          aGACCAAGATTTTGCGCTTCGATCAGCAATTCTTTTTCCAGTTCCACATCGCGGAACGCCTg                                                     <  1:1935804/62‑1 (MQ=255)
                           gACCAAGATTTTGCGCTTCGATCAGCAATTCTTTTTCCAGTTCca                                                                     >  1:2516226/1‑45 (MQ=255)
                           gACCAAGATTTTGCGCTTCGATCAGCAATTCTTTTTCCAGTTCca                                                                     >  1:2463939/1‑45 (MQ=255)
                           gACAAAGATTTTGCGCTTCGATCAGCAATTCTTTTTCCAGTTCca                                                                     >  1:1728732/1‑45 (MQ=255)
                            aCCAAGATTTTGCGCTTCGATCAGCAATTCTTTTTCCAGTTCCACATCGCGGAACGCCTGa                                                    >  1:1696140/1‑61 (MQ=255)
                                aGATTTTGCGCTTCGATCAGCAATTCTTTTTACAGTTCCACATCGCGGAACGCCTGACCGTGCTCATTccc                                      >  1:3387117/1‑71 (MQ=255)
                                 gATTTTGCGCTTCGATCAGCAATTCTTTTTCCAGTTCCACATCGCGGAACGCCTGa                                                    >  1:1219349/1‑56 (MQ=255)
                                   ttttGCGCTTCGATCAGCAATTCTTTTTCCAGTTCCACATCGCGGaa                                                           >  1:2285161/1‑47 (MQ=255)
                                   ttttGCGCTTCGATCAGCAATTCTTTTTCCAGTTCCACATCGCGGAACGCCTGACCGTGCTCATTCCCTTc                                   >  1:1230565/1‑71 (MQ=255)
                                    tttGCGCTTCGATCAGCAATTCTTTTTCCAGTTCCACATCGCGGAACGCCTg                                                     <  1:920588/52‑1 (MQ=255)
                                    tttGCGCTTCGATCAGCAATTCTTTTTCCAGTTCCACATCGCGGAACGCCTg                                                     <  1:3274110/52‑1 (MQ=255)
                                     ttGCGCTTCGATCAGCAATTCTTTTTCCAGTTCCACATCGCGGAACGCCTGACCGTGCTCATTCCCTTcc                                  <  1:691656/70‑1 (MQ=255)
                                      tGCGCTTCGATCAGCAATTCTTTTTCCAGTTCCACATCGCGGa                                                            <  1:2296884/43‑1 (MQ=255)
                                      tGCGCTTCGATCAGCAATTCTTTTTCCAGTTCCACATCGCGGAACGCCTGACCGTGCTCATTCCCTTCCg                                 <  1:3796645/70‑1 (MQ=255)
                                      tGCGCTTCGATCAGCAATTCTTTTTCCAGTTCCACATCGCGGAACGCCTGACCGTGCTCATTCCCTTCCg                                 <  1:1863658/70‑1 (MQ=255)
                                       gcgcTTCGATCAGCAATTCTTTTTCCAGTTCCACATcg                                                                <  1:617746/38‑1 (MQ=255)
                                        cgcTTCGATCAGCAATTCTTTTTCCAGTTCCACATCGCGGAACGCCTGACCGTGCTCATTCCCTTCCGtt                               <  1:3467956/70‑1 (MQ=255)
                                         gcTTCGATCAGCAATTCTTTTTCCAGTTCCACATCGCGGAACGCCTGACCGTGCTCATTCCCTTCCg                                 <  1:3005636/67‑1 (MQ=255)
                                         gcTTCGATCAGCAATTCTTTTTCCAGTTCCACATCGCGGAACGCCTGACCGTGCTCATTCCCTTCCGTTgg                             >  1:1797452/1‑71 (MQ=255)
                                          cTTCGATCAGCAATTCTTTTTCCAGTTCCACATCGCGGa                                                            >  1:634963/1‑39 (MQ=255)
                                          cTTCGATCAGCAATTCTTTTTCCAGTTCCACATCGCGGAACGCCTGACCGTGCTCa                                           >  1:137271/1‑56 (MQ=255)
                                          cTTCGATCAGCAATTCTTTTTCCAGTTCCACATCGCGGAACGCCTGACCGTGCTCa                                           >  1:2385587/1‑56 (MQ=255)
                                          cTTCGATCAGCAATTCTTTTTCCAGTTCCACATCGCGGAACGCCTGACCGTGCTCa                                           >  1:395392/1‑56 (MQ=255)
                                          cTTCGATCAGCAATTCTTTTTCCAGTTCCACATCGCGGAACGCCTGACCGTGCTCATTCCCTTCCGTTGGc                            <  1:279154/71‑1 (MQ=255)
                                           ttCGATCAGCAATTCTTTTTCCAGTTCCACATCGCGGAACGCCTGAc                                                   <  1:1625035/47‑1 (MQ=255)
                                           ttCGATCAGCAATTCTTTTTCCAGTTCCACATCGCGGAACGCCTGACCGTGCTCATTCCCTTCCGTTgg                             >  1:262112/1‑69 (MQ=255)
                                             cGATCAGCAATTCTTTTTCCAGTTCCACATCGCGGAACGCCTGACCGTg                                               >  1:2446395/1‑49 (MQ=255)
                                             cGATCAGCAATTCTTTTTCCAGTTCCACATCGCGGAACGCCTGACCGTGCTCATTCCCTTCCGTTGGCAGt                         >  1:1567985/1‑71 (MQ=255)
                                             cGATCAGCAATTCTTTTTCCAGTTCCACATCGCGGAACGCCTGACCGTGCTCATTCCCTTCCGTTGGCAGt                         >  1:638593/1‑71 (MQ=255)
                                             cGATCAGCAATTCTTTTTCCAGTTCCACATCGCGGAACGCCTGACCGTGCTCATTCCCTTCCGTTGGCAGt                         >  1:1635787/1‑71 (MQ=255)
                                              gATCAGCAATTCTTTTTCCAGTTCCACATCGCGGAACGCCTGACCGTGCTCATTCCCTTCCGTTGGCAGt                         <  1:1912878/70‑1 (MQ=255)
                                              gATCAGCAATTCTTTTTCCAGTTCCACATCGCGGAACGCCTGACCGTGCTCATTCCCTTCCGTTGGCAGt                         <  1:1938763/70‑1 (MQ=255)
                                               aTCAGCAATTCTTTTTCCAGTTCCACATCGCGGAACGCCTGACCGTGCTCATTCCCTTCCGTTgg                             <  1:479704/65‑1 (MQ=255)
                                                 cagcagTTCCTGTTCCAGCTGGACATCGCGGAACGCCTGACCATGTTCGTTCCCTTCCGTCGGCAGTtcat                     <  1:646300/71‑1 (MQ=255)
                                                 cAGCAATTCTTTTTCCAGTTCCACATCGCGGAACGCCTGACCGTGCTCATTCCCTTCCGTTGGCAGTtcat                     >  1:1757373/1‑71 (MQ=255)
                                                 cAGCAATTCTTTTTCCAGTTCCACATCGCGGAACGCCTGACCGTGCTCATTCCCTTCCGTTGGCAGTtca                      >  1:321642/1‑70 (MQ=255)
                                                   gCAGTTCCTGTTCCAGCTGGACATCGCGGAACGCCTGACCATGTTCGTTCCCTTCCGTCGGCAGTtcatcg                   <  1:3297527/71‑2 (MQ=255)
                                                   gCAGTTCCTGTTCCAGCTGGACATCGCGGAACGCCTGACCATGTTCGTTCCCTTCCGTCGGCAGTtca                      <  1:3419707/68‑1 (MQ=255)
                                                   gCAATTCTTTTTCCAGTTCCACATCGCGGAACGCCTGACCGTGCTCATTCCCTTCCGTTGGCAGTtcatca                   <  1:1664489/71‑1 (MQ=255)
                                                    cAATTCTTTTTCCAGTTCCACATCGCGGAACGCCTGACCGTGCTCATTCCCTTCCGTTGGCAGTTcatcat                  <  1:290090/71‑1 (MQ=255)
                                                       ttCTTTTTCCAGTTCCACATCGCGGAACGCCTGACCGTGCTCAtt                                         >  1:805861/1‑45 (MQ=255)
                                                        tCTTTTTCCAGTTCCACATCGCGGAACGCCTGACCGTGCTCATTCCCtt                                    >  1:3218016/1‑49 (MQ=255)
                                                        tCTTTTTCCAGTTCCACATCGCGGAACGCCTGACCGTGCTCATTCCCTTCCGTTGGCAGTtca                      >  1:1262810/1‑63 (MQ=255)
                                                         cTTTTTCCAGTTCCACATCGCGGAACGCCTGACCGTGCTCATTCCCTTCCGTTGGCAGTTCATCATAg                >  1:3740127/1‑68 (MQ=255)
                                                          tttttCCAGTTCCACATCGCGGAACGCCTGACCTTGCTCATTCCCTTCCGtt                               <  1:3130134/52‑1 (MQ=255)
                                                           ttttCCAGTTCCACATCGCGGAACGCCTGACCGTGCTCATTCCCTTCCGTTGGCAGTTCATCATAGTAttt           >  1:2936579/1‑71 (MQ=255)
                                                            tttCCAGTTCCACATCGCGGAACGCCTGACCGTGCTCATTCCCTTCCGTTGTCAGTTCATCATAGTAt             <  1:3444093/68‑1 (MQ=255)
                                                            gttCCAGCTGGACATCGCGGAACGCCTGACCATGTTc                                            >  1:2890939/2‑37 (MQ=12)
                                                             ttCCAGTTCCACATCGCGGAACGCCTGACCGTGCTCATTCCCTTc                                   >  1:3805777/1‑45 (MQ=255)
                                                             ttCCAGTTCCACATCGCGGAACGCCTGACCGTGCTCATTCCCTTCCGTTGGCAGTTCATCATAGTATTTc          <  1:3471748/70‑1 (MQ=255)
                                                             ttCCAGCTGGACATCGCGGAACGCCTGACCATGTTCGTTCCCTTCCGTCGGCAGTtcat                     >  1:2544471/1‑59 (MQ=255)
                                                             ttCCAGCTGGACATCGCGGAACGCCTGACCATGTTCGTTCCCTTCCGTCGGCAGTTCATCGTAATagtg           <  1:1632628/69‑4 (MQ=255)
                                                              tCCAGTTCCACATCGCGGAACGCCTGACCGTGCTCATTCCCTTCCGTTGGCAGTTCATCATAGTATTTcg         <  1:142764/70‑1 (MQ=255)
                                                              tCCAGTTCCACATCGCGGAACGCCTGACCGTGCTCATTCCCTTCCGTTGGCAGTTCATCATAGTATTTcg         <  1:3540392/70‑1 (MQ=255)
                                                               ccAGTTCCACATCGCGGAACGCCTGACCGTGCTCATTCCCTTCGGTTg                              <  1:1109231/48‑1 (MQ=255)
                                                               ccAGTTCCACATCGCGGAACGCCTGACCGTGCTCATTCCCTTCCGTTg                              <  1:383607/48‑1 (MQ=255)
                                                               ccAGTTCCACATCGCGGAACGCCTGACCGTGCTCATTCCCTTCCGTTGGCAGTTCATCATAGTATTTcg         <  1:1381048/69‑1 (MQ=255)
                                                                cAGTTCCACATCGCGGAACGCCTGACCGTGCTCATTCCCTTCCGTTGGCAGTTCATCATAGTATTTCGCgg      <  1:1792455/71‑1 (MQ=255)
                                                                cAGTTCCACATCGCGGAACGCCTGACCGT‑CTCATTCCCTTCCGTTGGCAGTTCATCATAGTATTTCGCgg      <  1:3403505/70‑1 (MQ=255)
                                                                     ccACATCGCGGAACGCCTGACCGTGCTCATTCCCTTCCGTTGGCAGTTCATCATAGTATTTCGCGGAAGc  >  1:63942/1‑70 (MQ=255)
                                                                      |                                                                    
AGTATTTACCACCAAACTGCGCACCCAGACCAAGATTTTGCGCTTCGATCAGCAATTCTTTTTCCAGTTCCACATCGCGGAACGCCTGACCGTGCTCATTCCCTTCCGTTGGCAGTTCATCATAGTATTTCGCGGAAGC  >  minE/1015189‑1015327

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 14 ≤ ATCG/ATCG < 32 ≤ ATCG/ATCG < 36 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑

GATK/CNVnator alignment

N/A