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 F1 I0 R1 2892 75.3 5698161 66.1% 3766484 59.5

Breseq alignment

BRESEQ :: Evidence
Predicted mutation
evidence seq id position mutation freq annotation gene description
RA minE 312,540 C→G 17.3% L111L (CTG→CTC)  acrB ← multidrug efflux system protein

Read alignment evidence...
  seq id position ref new freq score (cons/poly) reads annotation genes product
*minE312,5400CG17.3% 271.9 / 41.4 110L111L (CTG→CTC) acrBmultidrug efflux system protein
Reads supporting (aligned to +/- strand):  ref base C (52/39);  new base G (10/9);  total (62/48)
Fisher's exact test for biased strand distribution p-value = 8.01e-01
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 9.41e-01

Only 100 of 113 total aligned reads displayed.

TGGATGATTTCTCAACGCTCACCCCTTGCTGCTGAACTTCTTGCGGCAGCAACGGCATCGCCAGCTGCAGTTTGTTCTGCACCTGAACCTGCGCGATATCCGCATCAGTACCAGACTCAAAGGTCAGGGTGATCTGCA  >  minE/312473‑312610
                                                                   |                                                                      
tgGATGATTTCTCAACGCTCACCCCTTGCTGCTGAACTTCTTGCGGCAGCAACGGCATCGCCAGCTGCAGt                                                                     >  1:563107/1‑71 (MQ=255)
 ggATGATTTCTCAACGCTCACCCCTTGCTGCTGAACTTCTTGCGGCAGCAACGGCATCGCCAGCTGCAGtt                                                                    >  1:2160592/1‑71 (MQ=255)
  gatgatTTCTCAACGCTCACCCCTTGCTGCTGAACTTCTTGCGGCAGCAACGGCATCGCCAGCTGCAGttt                                                                   >  1:1003350/1‑71 (MQ=255)
   atgatTTCTCAACGCTCACCCCTTGCTGCTGAACTTCTTGCGGCAGCAACGGCATCGCCAGCTGCAGTTTg                                                                  <  1:168728/71‑1 (MQ=255)
    tgatTTCTCAACGCTCACCCCTTGCTGCTGAACTTCTTGCGGCAGCAACGGCATCGCCAGCTGCAGTTTGt                                                                 <  1:2535880/71‑1 (MQ=255)
     gatTTCTCAACGCTCACCCCTTGCTGCTGAACTTCTTGCGGCAGCAACGGCATCGCCAGCTGCAGTTTGtt                                                                >  1:2136240/1‑71 (MQ=255)
      atTTCTCAACGCTCACCCCTTGCTGCTGAACTTCTTGCGGCAGCAACGGCATCGCCAGCTGCAGTTTGTTc                                                               >  1:3648995/1‑71 (MQ=255)
       tttCTCAACGCTCACCCCTTGCTGCTGAACTTCTTGCGGCAGCAACGGCATCGCCAGCTGCAGTTTGTTCt                                                              >  1:2938909/1‑71 (MQ=255)
         tctcAACGCTCACCCCTTGCTGCTGAACTTCTTGCGGCAGCAACGGCATCGCCAGCTGCAGTTTGTTCTg                                                             >  1:4675381/1‑70 (MQ=255)
         tctcAACGCTCACCCCTTGCTGCTGAACTTCTTGCGGCAGCAACGGCATCGCCAGCTGCAGTTTGTTCTg                                                             >  1:1653928/1‑70 (MQ=255)
          ttcAACACTGATCCCCTGCTGCTGAACCTCCTGCGGCAGCAACGGCGTGGCGAGCTGGAGTTTGTTCTGCa                                                           >  1:3473372/2‑71 (MQ=255)
          ttcAACACTGATCCCCTGCTGCTGAACCTCCTGCGGCAGCAACGGCGTGGCGAGCTGGAGTTTGTTCTGCa                                                           >  1:2213787/2‑71 (MQ=255)
          ctcAACGCTCACCCCTTGCTGCTGAACTTCTTGCGGCAGCAACGGCATCGCCAGCTGCAGTTTGTTCTGc                                                            <  1:2942190/70‑1 (MQ=255)
             aaCGCTCACCCCTTGCTGCTGAACTTCTTGCGGCAGCAACGGCATCGCCAGCTGCAGTTTGTTCTGCACCt                                                        >  1:5522174/1‑71 (MQ=255)
               cGCTCACCCCTTGCTGCTGAACTTCTTGCGGCAGCAACGGCATCGCCAGCTGCAGTTTGTTCTGCACCTg                                                       <  1:381890/70‑1 (MQ=255)
               cGCTCACCCCTTGCTGCTGAACTTCTTGCGGCAGCAACGGCATCGCCAGCTGCAGTTTGTTCTGCACCTGa                                                      <  1:4243671/71‑1 (MQ=255)
               cGCTCACCCCTTGCTGCTGAACTTCTTGCGGCAGCAACGGCATCGCCAGCTGCAGTTTGTTCTGCACCTGa                                                      <  1:5650579/71‑1 (MQ=255)
               cGCTCACCCCTTGCTGCTGAACTTCTTGCGGCAGCAACGGCATCGCCAGCTGCAGTTTGTTCTGCACCTGa                                                      <  1:1460206/71‑1 (MQ=255)
                gCTCACCCCTTGCTGCTGAACTTCTTGCGGCAGCAACGGCATCGCCAGCTGCAGTTTGTTCTGCACCTGaa                                                     >  1:2302376/1‑71 (MQ=255)
                 cTCACCCCTTGCTGCTGAACTTCTTGCGGCAGCAACGGCATCGCCAGCTGCAGt                                                                     <  1:5464836/54‑1 (MQ=255)
                 cTCACCCCTTGCTGCTGAACTTCTTGCGGCAGCAACGGCATCGCCAGCTGCAGTTTGTTCTGCACCTGAAc                                                    >  1:4415100/1‑71 (MQ=255)
                 cTCACCCCTTGCTGCTGAACTTCTTGCGGCAGCAACGGCATCGCCAGCTGCAGTTTGTTCTGCACCTGAAc                                                    >  1:5181787/1‑71 (MQ=255)
                 cTCACCCCTTGCTGCTGAACTTCTTGCGGCAGCAACGGCATCGCCAGCTGCAGTTTGTTCTGCACCTGAAc                                                    >  1:5188030/1‑71 (MQ=255)
                  tCACCCCTTGCTGCTGAACTTCTTGCGGCAGCAACGGCATCGCCAGCTGCAGTTTGTTCTGCACCTGAAcc                                                   >  1:2304822/1‑71 (MQ=255)
                    aCCCCTTGCTGCTGAACTTCTTGCGGCAGCAACGGCATCGCCAGCTGCAGTTTGTTCTGCACCTGAACCt                                                  <  1:1199429/70‑1 (MQ=255)
                    aCCCCTTGCTGCTGAACTTCTTGCGGCAGCAACGGCATCGCCAGCTGCAGTTTGTTCTGCACCTGAACCTg                                                 >  1:444578/1‑71 (MQ=255)
                    aCCCCTTGCTGCTGAACTTCTTGCGGCAGCAACGGCATCGCCAGCTGCAGTTTGTTCTGCACCTGAACCTg                                                 >  1:124613/1‑71 (MQ=255)
                      cccTTGCTGCTGAACTTCTTGCGGCAGCAACGGCATCGCCAGCTGCAGTTTg                                                                  <  1:1997438/52‑1 (MQ=255)
                      cccTTGCTGCTGAACTTCTTGCGGCAGCAACGGCATCGCCAGCTGCAGTTTGTTCTGCACCTGAACCTgcg                                               >  1:5373523/1‑71 (MQ=255)
                      cccTTGCTGCTGAACTTCTTGCGGCAGCAACGGCATCGCCAGCTGCAGTTTGTTCTGCACCTGAACCTgcg                                               >  1:3268437/1‑71 (MQ=255)
                       ccTTGCTGCTGAACTTCTTGCGGCAGCAACGGCATCGCCAGCTGCAGTTTGTTCTGCACCTGAACCTgcgc                                              >  1:1201616/1‑71 (MQ=255)
                       ccTTGCTGCTGAACTTCTTGCGGCAGCAACGGCATCGCCAGCTGCAGTTTGTTCTGCACCTGAACCTgcgc                                              >  1:3131442/1‑71 (MQ=255)
                       ccTTGCTGCTGAACTTCTTGCGGCAGCAACGGCATCGCCAGCTGCAGTTTGTTCTGCACCTGAACCTgcgc                                              >  1:1830243/1‑71 (MQ=255)
                       ccTTGCTGCTGAACTTCTTGCGGCAGCAACGGCATCGCCAGCTGCAGTTTGTTCTGCACCTGAACCTgcgc                                              <  1:1253011/71‑1 (MQ=255)
                       ccTTGCTGCTGAACTTCTTGCGGCAGCAACGGCATCGCCAGCTGCAGTTTGTTCTGCACCTGAACCTgcg                                               >  1:630402/1‑70 (MQ=255)
                        cTTGCTGCTGAACTTCTTGCGGCAGCAACGGCATCGCCAGCTGCAGTTTGTTCTGCAcc                                                         >  1:2674422/1‑59 (MQ=255)
                         ttGCTGCTGAACTTCTTGCGGCAGCAACGGCATCGCCAGCTGCAGtt                                                                    <  1:3360678/47‑1 (MQ=255)
                         ttGCTGCTCAACTTCTTGCGGCAGCAACGGCATCGCCAGCTGCAGTTTGTTCTGCACCTGa                                                      <  1:2550526/61‑1 (MQ=255)
                          tgctgcTGAACCTCCTGCGGCAGCAACGGCGTGGCGAGCTGGAGTTTGTTCTGCACCTGCACTTGCGCGa                                            >  1:2052532/1‑70 (MQ=255)
                           gctgctGAACTTCTTGCGGCAGCAACGGCATCGCCAGCTGCAGt                                                                     >  1:3854876/1‑44 (MQ=255)
                           gctgctGAACTTCTTGCGGCAGCAACGGCATCGCCAGCTGCAGTTTGTTCTGCACCt                                                        >  1:442104/1‑57 (MQ=255)
                           gctgctGAACTTCTTGCGGCAGCAACGGCATCGCCAGCTGCAGTTTGTTCTGCACCTGAACCTGCGCGata                                          >  1:3822746/1‑71 (MQ=255)
                           gctgctGAACTTCTTGCGGCAGCAACGGCATCGCCAGCTGCAGTTTGTTCTGCACCTGAACCTGCGCGata                                          >  1:5065724/1‑71 (MQ=255)
                           gctgctGAACCTCCTGCGGCAGCAACGGCGTGGCGAGCTGGAGtt                                                                    <  1:2431612/45‑1 (MQ=16)
                           gctgctGAACCTCCTGCGGCAGCAACGGCGTGGCGAGCTGGAGTTTGTTc                                                               >  1:3610013/1‑50 (MQ=19)
                           gctgctGAACCTCCTGCGGCAGCAACGGCGTGGCGAGCTGGAGTTTGTTc                                                               >  1:3609236/1‑50 (MQ=19)
                              gctgAACTTCTTGCGGCAGCAACGGCATCGCCAGCTGCAGt                                                                     <  1:4430184/41‑1 (MQ=255)
                              gctgAACTTCTTGCGGCAGCAACGGCATCGCCAGCTGCAGt                                                                     <  1:4092937/41‑1 (MQ=255)
                              gctgAACTTCTTGCGGCAGCAACGGCATCGCCAGCTGCAGTTTGTTCTGCACCTGAAc                                                    <  1:4098675/58‑1 (MQ=255)
                               ctgAACTTCTTGCGGCAGCACCGGCATCGCCAGCTGCAGTTTGTTCTGCACCTGCACCTGCGCGATATCCg                                      >  1:2945349/1‑71 (MQ=255)
                                   aCTTCTTGCGGCAGCAACGGCATCGCCAGCTGCAGTTTGTTCTGCACCTGAACCTGCGCGATATCCGCAt                                   >  1:4642006/1‑70 (MQ=255)
                                   aCTTCTTGCGGCAGCAACGGCATCGCCAGCTGCAGTTTGTTCTGCACCTGAACCTGCGCGATATCCGCAt                                   >  1:448469/1‑70 (MQ=255)
                                   aCTTCTTGCGGCAGCAACGGCATCGCCAGCTGCAGTTTGTTCTGCACCTGAACCTGCGCGATATCCGCAt                                   >  1:515958/1‑70 (MQ=255)
                                    cttcttGCGGCTGCAACGGCATCGCCAGCTGCAGTTTGTTCTGc                                                            <  1:277137/44‑1 (MQ=255)
                                    cttcttGCGGCAGCAACGGCATCGCCAGCTGCAGTTTGTTCTGc                                                            <  1:3342115/44‑1 (MQ=255)
                                    cttcttGCGGCAGCAACGGCATCGCCAGCTGCAGTTTGTTCTGCACCTGAACCt                                                  >  1:2598920/1‑54 (MQ=255)
                                     ttcttGCGGCAGCAACGGCATCGCCAGCTGCAGTTTGTTCTGCACCTGa                                                      <  1:2553563/49‑1 (MQ=255)
                                      tcttGCGGCAGCAACGGCATCGCCAGCTGCAGTTTGTTCTGCACCTGAAc                                                    >  1:1260472/1‑50 (MQ=255)
                                      tcttGCGGCAGCAACGGCATCGCCAGCTGCAGTTTGTTCTGCACCTGAAc                                                    >  1:1774050/1‑50 (MQ=255)
                                       cttGCGGCAGCAACGGCATCGCCAGCTGCAGTTTGTTCTGCACCTGAACCTGCGCGATATCCGCATCAg                                <  1:4296053/69‑1 (MQ=255)
                                        ttGCGGCAGCAACGGCATCGCCAGCTGCAGTTTGTTCTGCACCTGAACCTGCGCGATATCCGCATCAGTAc                             >  1:5200020/1‑71 (MQ=255)
                                        ctGCGGCAGCAACGGCGTGGCGAGCTGGAGTTTGt                                                                 <  1:3209470/34‑1 (MQ=12)
                                        ctGCGGCAGCAACGGCGTGGCGAGCTGGAGTTTGt                                                                 <  1:2746399/34‑1 (MQ=12)
                                         tGCGGCAGCAACGGCATCGCCAGCTGCAGTTTGTTCTGCACCTGAACCTGCGCGATATCCGCATCAGTAc                             >  1:2379489/1‑70 (MQ=255)
                                         tGCGGCAGCAACGGCATCGCCAGCTGCAGTTTGTTCTGCACCTGAACCTGCGCGATATCCGCATCAGTAc                             >  1:4264842/1‑70 (MQ=255)
                                          gCGGCAGCAACGGCGTGGCGAGCTGGAGTTTGTTCTGCACCTGCACTTGCGCGATATCAGGATCGGtc                              <  1:870112/68‑2 (MQ=16)
                                          gCGGCAGCAACGGCGTGGCGAGCTGGAGTTTGTTCTGCACCTGCACTTGCGCGATATCAGGATCGGtc                              <  1:2828131/68‑2 (MQ=16)
                                          gCGGCAGCAACGGCGTGGCGAGCTGGAGTTTGTTCTGCACCTGCACTTGCGCGATATCAGGATCGGTcccg                           >  1:3609367/1‑70 (MQ=16)
                                          gCGGCAGCAACGGCATCGCCAGCTGCAGTTTGTTCTGCACCTGAACCTGCGCGATATCCGCATCAGTAc                             <  1:5343728/69‑1 (MQ=255)
                                          gCGGCAGCAACGGCATCGCCAGCTGCAGTTTGTTCTGCACCTGAACCTGCGCGATATCCGCATCAGTAc                             >  1:2560355/1‑69 (MQ=255)
                                           cGGCAGCAACGGCGTGGCGAGCTGGAGTTTGTTCTGCACCTGCACTTGCGCGATATCAGGATCGGTcccgg                          <  1:4162183/71‑3 (MQ=16)
                                           cGGCAGCAACGGCGTGGCGAGCTGGAGTTTGTTCTGCACCTGCACTTGCGCGATATCAGGATCGGTcccg                           <  1:4544287/70‑2 (MQ=16)
                                           cGGCAGCAACGGCATCGCCAGCTGCAGTTTGTTCTGCACCTGAACCTGCGCGATATCCGCATCAGTACCa                           <  1:3411071/70‑1 (MQ=255)
                                               agcaACGGCGTGGCGAGCTGGAGTTTGTTCTGCACCTGCACTTGCGCGATATCAGGATCGGTCCCGGACtg                      <  1:4679745/71‑2 (MQ=16)
                                               agcaACGGCATCGCCAGCTGCAGTTTGTTCTGCACCTGAACCTGCGCGATATCCGCATCAGTACCAGa                         <  1:409901/68‑1 (MQ=255)
                                                gcaACGGCATCGCCAGCTGCAGTTTGTTCTGCACCTGAACCTGCGCGATATCCGCATCAGTACCAGACTCa                     <  1:3845462/71‑1 (MQ=255)
                                                gcaACGGCATCGCCAGCTGCAGTTTGTTCTGCACCTGAACCTGCGCGATATCCGCATCAGTACCAGACTCa                     <  1:4628002/71‑1 (MQ=255)
                                                 caACGGCGTGGCGAGCTGGAGTTTGTTCTGCACCTGCACTTGCGCGATATCAGGATCGGTCCCGGACtgga                    <  1:3355794/71‑4 (MQ=12)
                                                 caACGGCATCGCCAGCTGCAGTTTGTTCTGCACCTGAACCTGCGCGATATCCGCATCAGTACCAGa                         <  1:3765029/66‑1 (MQ=255)
                                                 caACGGCATCGCCAGCTGCAGTTTGTTCTGCACCTGAACCTGCGCGATATCCGCATCAGTACCAGACTCaa                    <  1:1095740/71‑1 (MQ=255)
                                                  aaCGGCGTGGCGAGCTGGAGTTTGTTCTGCACCTGCACTTGCGCGATATCAGGATCGGTCCCGGACtgg                     >  1:4200181/1‑67 (MQ=12)
                                                  aaCGGCATCGCCAGCTGCAGTTTGTTCTGCACCTGAACCTGCGCGATATCCGCATCAGTACCAGACTCaa                    <  1:3928987/70‑1 (MQ=255)
                                                   aCGGCATCGCCAGCTGCAGTTTGTTCTGCACCTGAACCTGCGCGATATCCGCATCAGTACCAGACTCAAAg                  >  1:1332078/1‑71 (MQ=255)
                                                     ggCATCGCCAGCTGCAGTTTGTTCTGCACCTGAACCTGCGCGATATCCGCATCAGTACCAGACTCAAAg                  >  1:3842056/1‑69 (MQ=255)
                                                     ggCATCGCCAGCTGCAGTTTGTTCTGCACCTGAACCTGCGCGATATCCGCATCAGTACCAGACTCAAAGGt                <  1:1776993/71‑1 (MQ=255)
                                                     ggCATCGCCAGCTGCAGTTTGTTCTGCACCTGAACCTGCGCGATATCCGCATCAGTACCAGACTCAAAGGt                >  1:1006632/1‑71 (MQ=255)
                                                      gCATCGCCAGCTGCAGTTTGTTCTGCACCTGAACCTGCGCGATATCCGCATCAGTACCAGACTCAAAGGTc               <  1:480879/71‑1 (MQ=255)
                                                        aTCGCCAGCTGCAGTTTGTTCTGCACCTGAACCTGCGCGATATCCGCATCAGTACCAGACTCAAAGGTCAg             >  1:4784177/1‑71 (MQ=255)
                                                         tCGCCAGCTGCAGTTTGTTCTGCACCTGAACCTGCGCGATATCCGCATCAGTACCAGACTCAAAGGTCAgg            >  1:4466570/1‑71 (MQ=255)
                                                           gCCAGCTGCAGTTTGTTCTGCACCTGAACCTGCGCGATATCCGCATCAGTACCAGACTCAAAGGTCAGGGt          >  1:5243350/1‑71 (MQ=255)
                                                           gCCAGCTGCAGTTTGTTCTGCACCTGAACCTGCGCGATATCCGCATCAGTACCAGACTCAAAGGTCAGGGt          >  1:2117113/1‑71 (MQ=255)
                                                            ccAGCTGCAGTTTGTTCTGCACCTGAACCTGCGCGATATCCGCATCAGTACCAGACTCAAAGGTCAGGGTg         <  1:1625862/71‑1 (MQ=255)
                                                              aGCTGCAGTTTGTTCTGCACCTGAACCTGCGCGATATCCGCATCAGTACCAGACTCAAAGGTCAGGGTGa        <  1:3901193/70‑1 (MQ=255)
                                                              aGCTGCAGTTTGTTCTGCACCTGAACCTGCGCGATATCCGCATCAGTACCAGACTCAAAGGTCAGGGTGAt       <  1:2939575/71‑1 (MQ=255)
                                                              aGCTGCAGTTTGTTCTGCACCTGAACCTGCGCGATATCCGCATCAGTACCAGACTCAAAGGTCAGGGTGAt       <  1:3479724/71‑1 (MQ=255)
                                                               gCTGGAGTTTGTTCTGCACCTGCACTTGCGCGATATCAGGATCGGtc                              >  1:5688232/1‑46 (MQ=16)
                                                                  gCAGTTTGTTCTGCACCTGAACCTGCGCGATATCCGCATCa                                 >  1:3125337/1‑41 (MQ=255)
                                                                   cAGTTTGTTCTGCACCTGAACCTGCGCGATATCCGCATCAGTACCAGACTCAAAGGTCAGGGTGATCTGc   <  1:4687738/70‑1 (MQ=255)
                                                                   cAGTTTGTTCTGCACCTGAACCTGCGCGATATCCGCATCAGTACCAGACTCAAAGGTCAGGGTGATCTGCa  <  1:3328822/71‑1 (MQ=255)
                                                                   cAGTTTGTTCTGCACCTGAACCTGCGCGATATCCGCATCAGTACCAGACTCAAAGGTCAGGGTGATCTGCa  <  1:5134130/71‑1 (MQ=255)
                                                                   |                                                                      
TGGATGATTTCTCAACGCTCACCCCTTGCTGCTGAACTTCTTGCGGCAGCAACGGCATCGCCAGCTGCAGTTTGTTCTGCACCTGAACCTGCGCGATATCCGCATCAGTACCAGACTCAAAGGTCAGGGTGATCTGCA  >  minE/312473‑312610

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 27 ≤ ATCG/ATCG < 32 ≤ ATCG/ATCG < 36 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑

GATK/CNVnator alignment

N/A