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 R1 4577 57.4 3436498 77.7% 2670158 63.4

Breseq alignment

BRESEQ :: Evidence
Predicted mutation
evidence seq id position mutation freq annotation gene description
RA minE 1,764,751 T→C 36.8% Q703Q (CAA→CAG)  clpB ← protein disaggregation chaperone

Read alignment evidence...
  seq id position ref new freq score (cons/poly) reads annotation genes product
*minE1,764,7510TC36.8% 60.0 / 65.1 103Q703Q (CAA→CAG) clpBprotein disaggregation chaperone
Reads supporting (aligned to +/- strand):  ref base T (26/39);  new base C (19/19);  total (45/58)
Fisher's exact test for biased strand distribution p-value = 4.11e-01
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 9.89e-01

Only 100 of 103 total aligned reads displayed.

AATCAGATCGGAACCGAGGTTAGAGGTCATAATGACGACCGTATTACGGAAGTCGACCGTTCTCCCTTGCCCGTCAGTCAGACGCCCATCATCCAGTACCTGCAACAGAATGTTGAAGACATCCGGATGC  >  minE/1764685‑1764814
                                                                  |                                                               
aaTCAGATCGGAACCGAGGTTAGAGGTCATAATGACGAGCGTATTACGGAAGTCGACCGTTCTCCCCTg                                                               >  1:3330826/1‑69 (MQ=255)
aaTCAGATCGGAACCGAGGTTAGAGGTCATAATGACGACCGTATTACGGAAGTCGACCGTTCTCCCCTg                                                               >  1:1768569/1‑69 (MQ=255)
aaTCAGATCGGAACCGAGGTTAGAGGTCATAATGACGACCGTATTACGGAAGTCGACCGTTCTCCCCTg                                                               >  1:1873723/1‑69 (MQ=255)
aaTCAGATCGGAACCGAGGTTAGAGGTCATAATGACGACCGTATTACGGAAGTCGACCGTTCTCCCCTg                                                               >  1:1230083/1‑69 (MQ=255)
aaTCAGATCGGAACCGAGGTTAGAGGTCATAATGACGACCGTATTACGGAAGTCGACCGTTCTCCCCTg                                                               >  1:642004/1‑69 (MQ=255)
aaTCAGATCGGAACCGAGGTTAGAGGTCATAATGACGACCGTATTACGGAAGTCGACCGTTCTCCCCTg                                                               >  1:1287903/1‑69 (MQ=255)
aaTCAGATCGGAACCGAGGTTAGAGGTCATAATGACGACCGTATTACGGAAGTCGACCGTTCTCCCCTg                                                               >  1:639535/1‑69 (MQ=255)
aaTCAGATCGGAACCGAGGTTAGAGGTCATAATGACGACCGTATTACGGAAGTCGACCGTTCTCCCCTg                                                               >  1:1900928/1‑69 (MQ=255)
aaTCAGATCGGAACCGAGGTTAGAGGTCATAATGACGACCGTATTACGGAAGTCGACCGTTCTCCCCTg                                                               >  1:521228/1‑69 (MQ=255)
aaTCAGATCGGAACCGAGGTTAGAGGTCATAATGACGACCGTATTACGGAAGTCGACCGTTCTCCCCTg                                                               >  1:242102/1‑69 (MQ=255)
   cAGATCGGAACCGAGGTTAGAGGGCATAATGACGACCGTATTACGGAAGTCGACCGTTCTCCCTTGccc                                                            <  1:732670/69‑1 (MQ=255)
         ggAACCGAGGTTAGAGGTCATATTGACGACCGTATTACGGAAGTCGACCGTTCTCCCTTGCCCgtcagt                                                      <  1:3032180/69‑1 (MQ=255)
         ggAACCGAGGTTAGAGGTCATAATGACGACCGTATTACGGAAGTCGACCGTTCTCCCTTGCCCgtcagt                                                      <  1:2755987/69‑1 (MQ=255)
         ggAACCGAGGTTAGAGGTCATAATGACGACCGTATTACGGAAGTCGACCGTTCTCCCTTGCCCgtcagt                                                      <  1:2860003/69‑1 (MQ=255)
         ggAACCGAGGTTAGAGGTCATAATGACGACCGTATTACGGAAGTCGACCGTTCTCCCTTGCCCgtcagt                                                      <  1:1833719/69‑1 (MQ=255)
         ggAACCGAGGTTAGAGGTCATAATGACGACCGTATTACGGAAGTCGACCGTTCTCCCTTGCCCgtcagt                                                      <  1:2882613/69‑1 (MQ=255)
         ggAACCGAGGTTAGAGGTCATAATGACGACCGTATTACGGAAGTCGACCGTTCTCCCTTGCCCgtcagt                                                      <  1:1338523/69‑1 (MQ=255)
         ggAACCGAGGTTAGAGGTCATAATGACGACCGTATTACGGAAGTCGACCGTTCTCCCTTGCCCgtcagt                                                      <  1:818162/69‑1 (MQ=255)
         ggAACCGAGGTTAGAGGTCATAATGACGACCGTATTACGGAAGTCGACCGTTCTCCCTTGCCCgtcagt                                                      <  1:894508/69‑1 (MQ=255)
          gAACCGAGGTTAGAGGTCATAATGACGACCGTATTACGGAAGTCGACCGTTCTCCCTTGCCCgtcagt                                                      <  1:2531738/68‑1 (MQ=255)
          gAACCGAGGTTAGAGGTCATAATGACGACCGTATTACGGAAGTCGACCGTTCTCCCTTGCCCgtcagt                                                      <  1:1871178/68‑1 (MQ=255)
                aGGTTAGAGGCCATAATGACGACCGTATTACGGAAGTCGACCGTTCTCCCTTGccc                                                            <  1:2330515/56‑1 (MQ=255)
                    tAGAGGTCATAATGACGACCGTATTACGGAAGTCGACCGTTCTCCCTTGCCCgtcagt                                                      <  1:3391491/58‑1 (MQ=255)
                       agGTCATAATGACGACCGTATTACGGAAGTCGACCGTTCTCCCCTGCCTGTCAGTCAGACGTCcatca                                         <  1:435254/68‑1 (MQ=255)
                       agGTCATAATGACGACCGTATTACGGAAGTCGACCGTTCTCCCCTGCCCGTCAGTCAGACGCCcatca                                         <  1:2101153/68‑1 (MQ=255)
                       agGTCATAATGACGACCGTATTACGGAAGTCGACCGTTCTCCCCTGCCCGTCAGTCAGACGCCcatca                                         <  1:47496/68‑1 (MQ=255)
                       agGTCATAATGACGACCGTATTACGGAAGTCGACCGTTCTCCCCTGCCCGTCAGTCAGACGCCcatca                                         <  1:2930316/68‑1 (MQ=255)
                       agGTCATAATGACGACCGTATTACGGAAGTCGACCGTTCTCCCCTGCCCGTCAGTCAGACGCCcatca                                         <  1:2276886/68‑1 (MQ=255)
                       agGTCATAATGACGACCGTATTACGGAAGTCGACCGTTCTCCCCTGCCCGTCAGTCAGACGCCcatca                                         <  1:2838373/68‑1 (MQ=255)
                       agGTCATAATGACGACCGTATTACGGAAGTCGACCGTTCTCCCCTGCCCGTCAGTCAGACGCCcatca                                         <  1:1705289/68‑1 (MQ=255)
                       agGTCATAATGACGACCGTATTACGGAAGTCGACCGTTCTCCCCTGCCCGTCAGTCAGACGCCcatca                                         <  1:1521604/68‑1 (MQ=255)
                       agGTCATAATGACGACCGTATTACGGAAGTCGACCGTTCTCCCCTGCCCGTCAGTCAGACGCCcatca                                         <  1:576779/68‑1 (MQ=255)
                       agGTCATAATGACGACCGTATTACGGAAGTCGACCGTTCTCCCCTGCCCGTCAGTCAGACGCCcatca                                         <  1:697021/68‑1 (MQ=255)
                       agGTCATAATGACGACCGTATTACGGAAGTCCACCGTTCTCCCCTGCCCGTCAGTCAGACGCCcatca                                         <  1:3344030/68‑1 (MQ=255)
                         gTCATAATGACGACCGTATTACGGAAGTCGACCGTTCTCCCTTGCCCGTCAGTCAGACGCCCATCATcc                                      >  1:954370/1‑69 (MQ=255)
                           cATAATGACGACCGTATTACGGAAGTCGACCGTTCTCCCTTGCCCGTCAGTCAGACGCCCATCATCCAg                                    >  1:3407841/1‑69 (MQ=255)
                           cATAATGACGACCGTATTACGGAAGTCGACCGTTCTCCCTTGCCCGTCAGTCAGACGCCCATCATCCAg                                    >  1:2404301/1‑69 (MQ=255)
                           cATAATGACGACCGTATTACGGAAGTCGACCGTTCTCCCTTGCCCGTCAGTCAGACGCCCATCATCCAg                                    >  1:3052121/1‑69 (MQ=255)
                           cATAATGACGACCGTATTACGGAAGTCGACCGTTCTCCCTTGCCCGTCAGTCAGACGCCCATCATCCAg                                    >  1:350839/1‑69 (MQ=255)
                           cATAATGACGACCGTATTACGGAAGTCGACCGTTCTCCCTTGCCCGTCAGTCAGACGCCCATCATCCAg                                    >  1:1504525/1‑69 (MQ=255)
                           cATAATGACGACCGTATTACGGAAGTCGACCGTTCTCCCTTGCCCGTCAGTCAGACGCCCATCATCCAg                                    >  1:136143/1‑69 (MQ=255)
                            aTAATGACGACCGTATTACGGAAGTCGACCGTTCTCCCTTTCCCGTCAGTCAGACGCCCATCATCCAGt                                   <  1:763247/69‑1 (MQ=255)
                            aTAATGACGACCGTATTACGGAAGTCGACCGTTCTCCCTTGCCCGTCAGTCAGACGCCcat                                           >  1:1850837/1‑61 (MQ=255)
                            aTAATGACGACCGTATTACGGAAGTCGACCGTTCTCCCTTGCCCGTCAGTCAGACGCCCATCATCCAGt                                   >  1:3396843/1‑69 (MQ=255)
                            aTAATGACGACCGTATTACGGAAGTCGACCGTTCTCCCTTGCCCGTCAGTCAGACGCCCATCATCCAGt                                   >  1:2698944/1‑69 (MQ=255)
                            aTAATGACGACCGTATTACGGAAGTCGACCGTTCTCCCTTGCCCGTCAGTCAGACGCCCATCATCCAGt                                   >  1:2768438/1‑69 (MQ=255)
                            aTAATGACGACCGTATTACGGAAGTCGACCGTTCTCCCTTGCCCGTCAGTCAGACGCCCATCATCCAGt                                   >  1:549909/1‑69 (MQ=255)
                            aTAATGACGACCGTATTACGGAAGTCGACCGTTCTCCCTTGCCCGTCAGTCAGACGCCCATCATCCAGt                                   >  1:1049287/1‑69 (MQ=255)
                            aTAATGACGACCGTATTACGGAAGTCGACCGTTCTCCCTTGCCCGTCAGTCAGACGCCCATCATCCAGt                                   >  1:2695130/1‑69 (MQ=255)
                            aTAATGACGACCGTATTACGGAAGTCGACCGTTCTCCCTTGCCCGTCAGTCAGACGCCCATCATCCAGt                                   >  1:1186590/1‑69 (MQ=255)
                            aTAATGACGACCGTATTACGGAAGTCGACCGTTCTCCCTTGCCCGTCAGTCAGACGCCCATCATCCAGt                                   >  1:1149784/1‑69 (MQ=255)
                               aTGACGACCGTATTACGGAAGTCGACCGTTCTCCCTTGCCCGTCAGTCAGACGCCCatcatc                                       <  1:1106861/62‑1 (MQ=255)
                               aTGACGACCGTATTACGGAAGTCGACCGTTCTCCCTTGCCCGTCAGTCAGACGCCCatcatc                                       <  1:827797/62‑1 (MQ=255)
                               aTGACGACCGTATTACGGAAGTCGACCGTTCTCCCTTGCCCGTCAGTCAGACGCCCATCATCCAGTAcc                                >  1:577275/1‑69 (MQ=255)
                               aTGACGACCGTATTACGGAAGTCGACCGTTCTCCCTTGCCCGTCAGTCAGACGCCCATCATCCAGTAcc                                >  1:729739/1‑69 (MQ=255)
                               aTGACGACCGTATTACGGAAGTCGACCGTTCTCCCTTGCCCGTCAGTCAGACGCCCATCATCCAGTAcc                                >  1:2881306/1‑69 (MQ=255)
                               aTGACGACCGTATTACGGAAGTCGACCGTTCTCCCTTGCCCGTCAGTCAGACGCCCATCATCCAGTAcc                                >  1:2507599/1‑69 (MQ=255)
                               aTGACGACCGTATTACGGAAGTCGACCGTTCTCCCTTGCCCGTCAGTCAGACGCCCATCATCCAGTAc                                 >  1:2017055/1‑68 (MQ=255)
                                 gacgacCGTATTACGGAAGTCGACCGTTCTCCCTTGccc                                                            <  1:1841362/39‑1 (MQ=255)
                                 gacgacCGTATTACGGAAGTCGACCGTTCTCCCCTGCCCGTCAGTCAGACGCCcatca                                         <  1:2077071/58‑1 (MQ=255)
                                      ccGTATTACGGAAGTCGACCGTTCTCCCCTGCCCGTCAGTCAGACGCCCATCATCCAGTACCTGCaa                           >  1:167726/1‑67 (MQ=255)
                                      ccGTATTACGGAAGTCGACCGTTCTCCCCTGCCCGTCAGTCAGACGCCCATCATCCAGTACCTGCAAc                          >  1:3083894/1‑68 (MQ=255)
                                      ccGTATTACGGAAGTCGACCGTTCTCCCCTGCCCGTCAGTCAGACGCCCATCATCCAGTACCTGCAAc                          >  1:2341997/1‑68 (MQ=255)
                                      ccGTATTACGGAAGTCGACCGTTCTCCCCTGCCCGTCAGTCAGACGCCCATCATCCAGTACCTGCAAc                          >  1:2833000/1‑68 (MQ=255)
                                      ccGTATTACGGAAGTCGACCGTTCTCCCCTGCCCGTCAGTCAGACGCCCATCATCCAGTACCTGCAAc                          >  1:669815/1‑68 (MQ=255)
                                      ccGTATTACGGAAGTCGACCGTTCTCCCCTGCCCGTCAGTCAGACGCCCATCATCCAGTACCTGCAAc                          >  1:3247186/1‑68 (MQ=255)
                                      ccGTATTACGGAAGTCGACCGTTCTCCCCTGCCCGTCAGTCAGACGCCCATCATCCAGTACCTGCAAc                          >  1:1129093/1‑68 (MQ=255)
                                      ccGTATTACGGAAGTCGACCGTTCTCCCCTGCCCGTCAGTCAGACGCCCATCATCCAGTACCTGCAAc                          >  1:2916283/1‑68 (MQ=255)
                                      ccGTATTACGGAAGTCGACCGTTCTCCCCTGCCCGTCAGTCAGACGCCCATCATCCAGTACCTGCAAc                          >  1:870534/1‑68 (MQ=255)
                                                  aGTCGAGCGTTCTCCCTTGCCCGTCAGTCAGACGCCCATCATCCAGTACCTGCAACAGAATGTTGAAGa             <  1:1608063/69‑1 (MQ=255)
                                                  aGTCGACCGTTCTCCCTTGCCCGTCAGTCAGACGCGCATCATCCAGTACCTGCAACAGAATGTTGAAGa             <  1:1906210/69‑1 (MQ=255)
                                                  aGTCGACCGTTCTCCCTTGCCCGTCAGTCAGACGCCCATCATCCAGTACCTGCAACAGAATGTTGAAGa             <  1:173172/69‑1 (MQ=255)
                                                  aGTCGACCGTTCTCCCTTGCCCGTCAGTCAGACGCCCATCATCCAGTACCTGCAACAGAATGTTGAAGa             <  1:166704/69‑1 (MQ=255)
                                                    tCGACCGTTCTCCCTTGCCCGTCAGTCAGACGCCCATCATCCAGTACCTGCAACAGAATGTTGAAGACa           <  1:2333400/69‑1 (MQ=255)
                                                    tCGACCGTTCTCCCTTGCCCGTCAGTCAGACGCCCATCATCCAGTACCTGCAACAGAATGTTGAAGACa           <  1:13814/69‑1 (MQ=255)
                                                    tCGACCGTTCTCCCTTGCCCGTCAGTCAGACGCCCATCATCCAGTACCTGCAACAGAATGTTGAAGACa           <  1:1733003/69‑1 (MQ=255)
                                                    tCGACCGTTCTCCCTTGCCCGTCAGTCAGACGCCCATCATCCAGTACCTGCAACAGAATGTTGAAGACa           <  1:1967331/69‑1 (MQ=255)
                                                    tCGACCGTTCTCCCTTGCCCGTCAGTCAGACGCCCATCATCCAGTACCTGCAACAGAATGTTGAAGACa           <  1:2955059/69‑1 (MQ=255)
                                                    tCGACCGTTCTCCCTTGCCCGTCAGTCAGACGCCCATCATCCAGTACCTGCAACAGAATGTTGAAGACa           <  1:1113963/69‑1 (MQ=255)
                                                    tCGACCGTTCTCCCTTGCCCGTCAGTCAGACGCCCATCATCCAGTACCTGCAACAGAATGTTGAAGACa           <  1:2906582/69‑1 (MQ=255)
                                                     cGACCGTTCTCCCTTGCCCGTCAGTCAGACGCCCATCATcc                                      <  1:382943/41‑1 (MQ=255)
                                                     cGACCGTTCTCCCTTGCCCGTCAGTCAGACGCCCATCATCCAGTACCTGCAACAGAATGTTGAAGACa           <  1:1291534/68‑1 (MQ=255)
                                                      gACCGTTCTCCCTTGCCCGTCAGTCAGACGCCCATCATcc                                      <  1:2105371/40‑1 (MQ=255)
                                                      gACCGTTCTCCCTTGCCCGTCAGTCAGACGCCCATCATCCAGTACCTGCAACAGAATGTTGAAGACATc         <  1:1278194/69‑1 (MQ=255)
                                                      gACCGTTCTCCCTTGCCCGTCAGTCAGACGCCCATCATCCAGTACCTGCAACAGAATGTTGAAGACATc         <  1:515053/69‑1 (MQ=255)
                                                       aCCGTTCTCCCTTGCCCGTCAGTCAGACGCCCATCATCCAGTACCTGCAACAGAATGTTGAAGACATc         <  1:3197488/68‑1 (MQ=255)
                                                        ccGTTCTCCCTTGCCCGTCAGTCAGACGCCCATCATCCAGTACCTGCAACAGAATGTTGAAGACATCCg       <  1:2602946/69‑1 (MQ=255)
                                                        ccGTTCTCCCTTGCCCGTCAGTCAGACGCCCATCATCCAGTACCTGCAACAGAATGTTGAAGACATCCg       <  1:596398/69‑1 (MQ=255)
                                                        ccGTTCTCCCTTGCCCGTCAGTCAGACGCCCATCATCCAGTACCTGCAACAGAATGTTGAAGACATCCg       <  1:3429473/69‑1 (MQ=255)
                                                         cGTTCTCCCTTGCCCGTCAGTCAGACGCCCATCATCCAGTACCTGCAACAGAATGTTGAAGACATCCg       <  1:2268070/68‑1 (MQ=255)
                                                         cGTTCTCCCCTGCCCGTCAGTCAGACGCCCATCATCCAGTACCTGCAACAGAATGTTGa                <  1:554456/59‑1 (MQ=255)
                                                         cGTTCTCCCCTGCCCGTCAGTCAGACGCCCATCATCCAGTACCTGCAACAGAATGTTGa                <  1:3400205/59‑1 (MQ=255)
                                                         cGTTCTCCCCTGCCCGTCAGTCAGACGCCCATCATCCAGTACCTGCAACAGAATGTTGa                <  1:1845283/59‑1 (MQ=255)
                                                         cGTTCTCCCCTGCCCGTCAGTCAGACGCCCATCATCCAGTACCTGCAACAGAATGTTGa                <  1:3025091/59‑1 (MQ=255)
                                                         cGTTCTCCCCTGCCCGTCAGTCAGACGCCCATCATCCAGTACCTGCAACAGAATGTTGa                <  1:2193186/59‑1 (MQ=255)
                                                         cGTTCTCCCCTGCCCGTCAGTCAGACGCCCATCATCCAGTACCTGCAACAGAATGTTGa                <  1:2332534/59‑1 (MQ=255)
                                                          gTTCTCCCTTGCCCGTCAGTCAGACGCCcatcatg                                       <  1:1095882/35‑2 (MQ=255)
                                                             ctcCCTTGCCCGTCAGTCAGACGCCCATCATCCAGTACCTGCAACAGAATGTTGAAGACATCCGGATgc  >  1:391120/1‑69 (MQ=255)
                                                             ctcCCTTGCCCGTCAGTCAGACGCCCATCATCCAGTACCTGCAACAGAATGTTGAAGACATCCGGATgc  >  1:373495/1‑69 (MQ=255)
                                                             ctcCCTTGCCCGTCAGTCAGACGCCCATCATCCAGTACCTGCAACAGAATGTTGAAGACATCCGGATgc  >  1:2679779/1‑69 (MQ=255)
                                                                  |                                                               
AATCAGATCGGAACCGAGGTTAGAGGTCATAATGACGACCGTATTACGGAAGTCGACCGTTCTCCCTTGCCCGTCAGTCAGACGCCCATCATCCAGTACCTGCAACAGAATGTTGAAGACATCCGGATGC  >  minE/1764685‑1764814

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