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 2,595,530 A→G 21.8% V356V (GTT→GTC)  arsB ← arsenite/antimonite transporter

Read alignment evidence...
  seq id position ref new freq score (cons/poly) reads annotation genes product
*minE2,595,5300AG21.8% 256.8 / 70.9 133V356V (GTT→GTC) arsBarsenite/antimonite transporter
Reads supporting (aligned to +/- strand):  ref base A (52/52);  new base G (19/10);  total (71/62)
Fisher's exact test for biased strand distribution p-value = 1.48e-01
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 9.00e-01

Only 100 of 137 total aligned reads displayed.

CCAATTGGGGTAATTTTCGGTCCCAAATCGCAGCCAATCACATTGGCATAAACCATCGCTTCTTTGATAACGCCAGATGCCGTGCTGCCATCAATGGACAACGCGCCAACCAGTACCGTCGGCATATTGTTCATAATA  >  minE/2595462‑2595599
                                                                    |                                                                     
ccAATTGGGGTAATTTTCGGTCCCAAATCGCAGCCAATCACATTGGCATAAACCATCGCTTCTTTGATaa                                                                      <  1:496167/70‑1 (MQ=255)
 cAATTGGGGTAATTTTCGGTCCCAAATCGCAGCCAATCACATTGGCATAAACCATCGCTTCTTTGATAACg                                                                    >  1:3597233/1‑71 (MQ=255)
  aaTCGGGGTGATTTTCGGGCCTAAATCACAGCCGATCACATTGGCATAAATCATTGCCTCTTTGACGACGc                                                                   >  1:1067913/1‑71 (MQ=255)
  aaTCGGGGTGATTTTCGGGCCTAAATCACAGCCAATCACATTGGCATAAATCATTGCCTCTTTGACGACGc                                                                   <  1:2056505/71‑1 (MQ=255)
    ttGGGGTAATTTTCGGTCCCAAATCGCAGCCAATCACATTGGCATAAACCATCGCTTCTTTGATAACGCCa                                                                 <  1:966097/71‑1 (MQ=255)
       gggTGATTTTCGGGCCTAAATCACAGCCAATCACATTGGCATAAATCATTGCCTCTTTGACGACGCCAgtc                                                              <  1:1039489/71‑3 (MQ=255)
         gTAATTTTCTGTCCCAAATCGCAGCCAATCACATTGGCATAAACCATCGCTTCTTTGATAACGCCAGATGc                                                            >  1:3629754/1‑71 (MQ=255)
          tAATTTTCGGTCCCAAATCGCAGCCAATCACATTGGCATAAACCATCGCTTCTTTGATAACGCCAGATGcc                                                           <  1:1716718/71‑1 (MQ=255)
           aaTTTTCGGTCCCAAATCGCAGCCAATCACATTGGCATAAACCATCGCTTCTTTGATAACGCCAGATGCCg                                                          >  1:3548375/1‑71 (MQ=255)
            aTTTTCGGTCCCAAATCGCAGCCAATCACATTGGCATAAACCATCGCTTCTTTGATAAGGCCAGATGCCGt                                                         >  1:3657593/1‑71 (MQ=255)
            aTTTTCGGTCCCAAATCGCAGCCAATCACATTGGCATAAACCATCGCTTCTTTGATAACGCCAGATGCCGt                                                         >  1:2282745/1‑71 (MQ=255)
            aTTTTCGGGCCTAAATCACAGCCAATCACATTGGCATAAATCATTGCCTCTTTGACGACGCCAg                                                                <  1:373726/64‑1 (MQ=255)
             ttttCGGGCCTAAATCACAGCTAATCACATTGGCATAAATCATTGCCTCTTTGACGACGCCAGTCGCCGta                                                        <  1:281000/71‑2 (MQ=255)
               ttCGGTCCCAAATCGCAGCCAATCACATTGGCATAAACCATCGCTTCTTTGATAACGCCAGATGCCGtgct                                                      >  1:1318215/1‑71 (MQ=255)
               ttCGGTCCCAAATCGCAGCCAATCACATTGGCATAAACCATCGCTTCTTTGATAACGCCAGATGCCGtgct                                                      >  1:1834918/1‑71 (MQ=255)
                tCGGTCCCAAATCGCAGCCAATCACATTGGCATAAACCATCGCTTCTTTGATAACGCCAGATGCCGtgctg                                                     >  1:1079007/1‑71 (MQ=255)
                 cGGGCCTAAATCACAGCCAATCACATTGGCATAAATCATTGCCTCTTTGACGACGCCAGTCGCCGtactc                                                     <  1:1014757/70‑2 (MQ=255)
                  ggTCCCAAATCGCAGCCAATCACATTGGCATAAACCATCGCTTCTTTGATAACGCCAGATGCCGtgctgc                                                    >  1:1098596/1‑70 (MQ=255)
                  ggTCCCAAATCGCAGCCAATCACATTGGCATAAACCATCGCTTCTTTGATAACGCCAGATGCCGtgctgc                                                    <  1:2603902/70‑1 (MQ=255)
                  ggTCCCAAATCGCAGCCAATCACATTGGCATAAACCATCGCTTCTTTGATAACGCCAGATGCCGTGCTGcc                                                   <  1:2138816/71‑1 (MQ=255)
                   gTCCCAAATCGCAGCCAATCACATTGGCATAAACCATCGCTTCTTTGATAACGCCAGATGCCGTGCTGCCa                                                  <  1:3081292/71‑1 (MQ=255)
                   gTCCCAAATCGCAGCCAATCACATTGGCATAAACCATCGCTTCTTTGATAACGCCAGATGCCGTGCTGCCa                                                  <  1:3379826/71‑1 (MQ=255)
                    tCCCAAATCGCAGCCAATCACATTGGCATAAACCATCGCTTCTTTGATAACGCCat                                                                <  1:3070565/56‑2 (MQ=255)
                    tCCCAAATCGCAGCCAATCACATTGGCATAAACCATCGCTTCTTTGATAACGCCAg                                                                <  1:2746220/56‑1 (MQ=255)
                    tCCCAAATCGCAGCCAATCACATTGGCATAAACCATCGCTTCTTTGATAACGCCAGATGCCGtg                                                        <  1:1221579/64‑1 (MQ=255)
                    tCCCAAATCGCAGCCAATCACATTGGCATAAACCATCGCTTCTTTGATAACGCCAGATGCCGtg                                                        <  1:3699881/64‑1 (MQ=255)
                     cccAAATCGCAGCCAATCACATTGGCATAAACCATCGCTTCTTTGATAACGCCAGATGCCGtgctg                                                     >  1:3733789/1‑66 (MQ=255)
                       cAAATCGCAGCCAATCACATTGGCATAAACCATCGCTTCTTTGATAACGCCAGAt                                                              >  1:1126735/1‑55 (MQ=255)
                        aaaTCGCAGCCAATCACATTGGCATAAACCATCGCTTCTTTGATAACGCCAGATGCCGTGCTGCCATCAAt                                             >  1:2797251/1‑71 (MQ=255)
                        aaaTCACAGCCAATCACATTGGCATAAATCATTGCCTCTTTGACGACGCCAgt                                                               >  1:2970104/1‑52 (MQ=255)
                        aaaTCACAGCCAATCACATTGGCATAAATCATTGCCTCTTTGACGACGCCAgt                                                               >  1:609924/1‑52 (MQ=255)
                        aaaTCACAGCCAATCACATTGGCATAAATCATTGCCTCTTTGACGACGCCAGTCGCCGTACTCCCGTCAAt                                             >  1:3493069/1‑71 (MQ=255)
                         aaTCGCAGCCAATCACATTGGCATAAACCATCGCTTCTTTGATAACGCCAGATGCCGtgc                                                       >  1:3524820/1‑60 (MQ=255)
                         aaTCGCAGCCAATCACATTGGCATAAACCATCGCTTCTTTGATAACGCCAGATGCCGtgc                                                       >  1:96736/1‑60 (MQ=255)
                         aaTCGCAGCCAATCACATTGGCATAAACCATCGCTTCTTTGATAACGCCAGATGCCGTGCTGCCATCAATg                                            >  1:2405114/1‑71 (MQ=255)
                         aaTCGCAGCCAATCACATTGGCATAAACCATCGCTTCTTTGATAACGCCAGATGCCGTGCTGCCATCAATg                                            <  1:2865012/71‑1 (MQ=255)
                         aaTCGCAGCCAATCACATTGGCATAAACCATCGCTTCTTTGATAACGCCAGATGCCGTGCTGCCATCAATg                                            >  1:1132875/1‑71 (MQ=255)
                         aaTCGCAGCCAATCACATTGGCATAAACCATCGCTTCTTTGATAACGCCAGATGCCGTGCTGCCATCAATg                                            >  1:2105044/1‑71 (MQ=255)
                         aaTCGCAGCCAATCACATTGGCATAAACCATCGCTTCTTTGATAACGCCAGATGCCGTGCTGCCATCAATg                                            <  1:2090554/71‑1 (MQ=255)
                         aaTCGCAGCCAATCACATTGGCATAAACCATCGCTTCTTTGATAACGCCAGATGCCGTGCTGCCATCAATg                                            >  1:1919377/1‑71 (MQ=255)
                         aaTCGCAGCCAATCACATTGGCATAAACCATCGCTTCTTTGATAACGCCAGATGCCGTGCTGCCATCAATg                                            >  1:1673561/1‑71 (MQ=255)
                         aaTCGCAGCCAATCACATTGGCATAAACCATCGCTTCTTTGATAACGCCAGATGCCGTGCTGCCATCAATg                                            >  1:899769/1‑71 (MQ=255)
                         aaTCACAGCCAATCACATTGGCATAAATCATTGCCTCTTTGACGACGCCAGTCGCCGta                                                        >  1:743546/1‑58 (MQ=255)
                         aaTCACAGCCAATCACATTGGCATAAATCATTGCCTCTTTGACGACGCCAGTCGCCGTACTCCCGTCAAtc                                            >  1:453421/1‑70 (MQ=255)
                         aaTCACAGCCAATCACATTGGCATAAATCATTGCCTCTTTGACGACGCCAGTCGCCGTACTCCCGTCAAtc                                            >  1:1814704/1‑70 (MQ=255)
                          aTCGCAGCCAATCACATTGGCATAAACCATCGCTTCTTTGATAACGCCAGATGCCGTGCTGCCa                                                  >  1:3412466/1‑64 (MQ=255)
                          aTCACAGCCAATCACATTGGCATAAATCATTGCCTCTTTGACGACGCCAGTCGCCGTACTCCCGTCaa                                              <  1:3923911/68‑1 (MQ=255)
                               aGCCAATCACATTGGCATAAATCATTGCCTCTTTGACGACGCCAGTCGCCGTACTCCCGTCAATCGACagc                                      >  1:2383520/1‑69 (MQ=255)
                                gCCAATCACATTGGCATAAATCATTGCCTCTTTGACGACGCCAGTCGCCGTACTCCCGTCAATCGACAGcg                                     <  1:925202/71‑1 (MQ=255)
                                 ccAATCACATTGGCATAAACCATCGCTTCTTTGATAACGCCAg                                                                >  1:200458/1‑43 (MQ=255)
                                 ccAATCACATTGGCATAAACCATCGCTTCTTTGATAACGCCAGATGCCGTGCTGCCATCa                                               <  1:1114362/60‑1 (MQ=255)
                                 ccAATCACATTGGCATAAACCATCGCTTCTTTGATAACGCCAGATGCCGTGCTGCCATCAATGGACAAcg                                     >  1:2386721/1‑70 (MQ=255)
                                  gaaTCACATTGGCATAAACCATCGCTTCTTTGATAACGCCAGATGCCGTGCTGCCAGCAATGGACAAcgcg                                   <  1:1149530/70‑1 (MQ=255)
                                  cAATCACATTGGCATAAATCATTGCCTCTTTGACGACGCCAGTCGCCGTACTCCCGTCAATCGACAgcgca                                   >  1:3797257/1‑70 (MQ=255)
                                   aaTCACATTGGCATAAATCATTGCCTCTTTGACGACGCCAGTCGCCGTACTCCCGTCAATCGACAgcgcac                                  >  1:782482/1‑69 (MQ=255)
                                   aaTCACATTGGCATAAATCATTGCCTCTTTGACGACGCCAGTCGCCGTACTCCCGTCAATCGACAgcgca                                   <  1:2834251/70‑2 (MQ=255)
                                   aaTCACATTGGCATAAACCATCGCTTCTTTGATAACGCCAGATGCCGTGCTGCCATc                                                <  1:3800795/57‑1 (MQ=255)
                                   aaTCACATTGGCATAAACCATCGCTTCTTTGATAACGCCAGATGCCGTGCTGCCATCAATGGACAACgcgc                                  <  1:301922/71‑1 (MQ=255)
                                   aaTCACATTGGCATAAACCATCGCTTCTTTGATAACGCCAGATGCCGTGCTGCCATCAATGGACAACgcgc                                  >  1:3837660/1‑71 (MQ=255)
                                    aTCACATTGGCATAAACCATCGCTTCTTTGATAACGCCAGATGcc                                                           <  1:794708/45‑1 (MQ=255)
                                    aTCACATTGGCATAAACCATCGCTTCTTTGATAACGCCAGATGCCg                                                          >  1:3140959/1‑46 (MQ=255)
                                    aTCACATTGGCATAAACCATCGCTTCTTTGATAACGCCAGATGCCGt                                                         >  1:2633605/1‑47 (MQ=255)
                                    aTCACATTGGCATAAACCATCGCTTCTTTGATAACGCCAGATGCCGTGCTGCCa                                                  <  1:1290411/54‑1 (MQ=255)
                                    aTCACATTGGCATAAACCATCGCTTCTTTGATAACGCCAGATGCCGTGCTGCCATCAATGGACAACgcgc                                  >  1:2994059/1‑70 (MQ=255)
                                     tCACATTGGCATAAACCATCGCTTCTTTGATAACGCCAGATGCCGTGCTGCCATCAATGGACAACGCGcc                                 >  1:2944604/1‑70 (MQ=255)
                                     tCACATTGGCATAAACCATCGCTTCTTTGATAACGCCAGATGCCGTGCTGCCATCAATGGACAACGCGcc                                 >  1:729627/1‑70 (MQ=255)
                                       acaTTGGCATAAATCATTGCCTCTTTGACGACGCCAGTCGCCGTACTCCCGTCAATCGACAGCGCACCaat                              >  1:831528/1‑70 (MQ=255)
                                       acaTTGGCATAAACCATCGCTTCTTTGATAACGCCAGATGCCGTTCTGCCATCAATGGACAACGCGCCAAc                              <  1:3891851/71‑1 (MQ=255)
                                        caTTGGCATAAACCATCGCTTCTTTGATAACGCCAGATGCCGTGCTGCCATCAATGGACAACGCGCCAAcc                             <  1:1891077/71‑1 (MQ=255)
                                        caTTGGCATAAACCATCGCTTCTTTGATAACGCCAGATGCCGTGCTGCCATCAATGGACAACGCGCCAAcc                             <  1:573784/71‑1 (MQ=255)
                                          ttGGCATAAACCATCGCTTCTTTGATATCGCCAGTTGCCGTGCTGCCATCAATGGACAACGCGCCAACCAg                           <  1:1018982/71‑1 (MQ=255)
                                          ttGGCATAAACCATCGCTTCTTTGATAACGCCAGATGCCGTGCTGCCATCAATGGACAACGCGCCAACCAg                           <  1:3657448/71‑1 (MQ=255)
                                           tGGCATAAACCATCGCTTCTTTGATAACGCCAGATGCCGTGCTGCCATCAATGGACAACGCGCCAACCAg                           >  1:283908/1‑70 (MQ=255)
                                           tGGCATAAACCATCGCTTCTTTGATAACGCCAGATGCCGTGCTGCCATCAATGGACAACGCGCCAACCAg                           >  1:2753474/1‑70 (MQ=255)
                                               aTAAACCATCGCTTCTTTGATAACGCCAGATGCCGTGCTGCCATCaa                                              <  1:3334613/47‑1 (MQ=255)
                                               aTAAACCATCGCTTCTTTGATAACGCCAGATGCCGTGCTGCCATCaa                                              <  1:3172012/47‑1 (MQ=255)
                                               aTAAACCATCGCTTCTTTGATAACGCCAGATGCCGTGCTGCCATCAATGGACAAcgc                                    <  1:778934/57‑1 (MQ=255)
                                                tAAACCATCGCTTCTTTGATAACGCCAGATGCCGTGCTGCCATCAATGGACAACGCGCCAACCAGTACCg                      <  1:1832053/70‑1 (MQ=255)
                                                tAAACCATCGCTTCTTTGATAACGCCAGATGCCGTGCTGCCATCAATGGACAACGCGCCAACCAGTACCGt                     >  1:3470445/1‑71 (MQ=255)
                                                 aaaCCATCGCTTCTTTGATAACGCCAGATGCCGTGCTGCCATCAATGGACAACGCGCCAACCAGTACCGTc                    >  1:3243634/1‑71 (MQ=255)
                                                  aaCCATCGCTTCTTTGATAACGCCAGATGCCGtgc                                                       >  1:1411956/1‑35 (MQ=255)
                                                  aaCCATCGCTTCTTTGATAACGCCAGATGCCGTGCTGCCATCAATGGACAACGCGCCAACCAGTACCGTc                    <  1:62314/70‑1 (MQ=255)
                                                       tCGCTTCTTTGATAACGCCAGATGCCGTGCTGCCATCAATGGACAACGCGCCAACCAGTACCGTCGGCata              >  1:1873291/1‑71 (MQ=255)
                                                        cGCTTCTTTGATAACGCCAGATGCCGTGCTGCCATCAATGGACAAcgc                                    <  1:1589313/48‑1 (MQ=255)
                                                         gCTTCTTTGATAACGCCAGATGCCGTGCTGCCATCAATGGACAACGCGCCAACCa                            >  1:1827212/1‑55 (MQ=255)
                                                         gCTTCTTTGATAACGCCAGATGCCGTGCTGCCATCAATGGACAACGCGCCAACCAGTACCGTCGGCatat             <  1:1738194/70‑1 (MQ=255)
                                                         gCTTCTTTGATAACGCCAGATGCCGTGCTGCCATCAATGGACAACGCGCCAACCAGTACCGTCGGCATAtt            >  1:1389065/1‑71 (MQ=255)
                                                         gCTTCTTTGATAACGCCAGATGCCGTGCTGCCATCAATGGACAACGCGCCAACCAGTACCGTCGGCATAtt            <  1:1414431/71‑1 (MQ=255)
                                                          cttcttTGATAACGCCAGATGCCGTGCTGCCATCAATGGACAACGCGCCAACCAGTACCGTCGGCATATTg           <  1:2641752/71‑1 (MQ=255)
                                                           ttcttTGATAACGCCAGATGCCGTGCTGCCATCAATGGACAACGCGCCAACCAGTAc                        <  1:280419/57‑1 (MQ=255)
                                                             cttTGATAACGCCAGATGCCGTGCTGCCATCAATGGACAACGCGCCAACCAGTACCGTCGGCATATTGtt         <  1:3518380/70‑1 (MQ=255)
                                                              tttGACGACGCCAGTCGCCGTACTCCCGTCAATCGACAGCGCACCAATCAGCACCGTCGGCATATTGTTCa       >  1:1299074/1‑71 (MQ=255)
                                                                tGATAACGCCAGATGCCGTGCTGCCATCAATGGACAACGCGCCAACCAGTACCGTCGGCATATTGTTCa       <  1:1517361/69‑1 (MQ=255)
                                                                 gATAACGCCAGATGCCGTGCTGCCATCAATGGACAACGCGCCAACCAGTACCGTCGGCATATTGTTCata     <  1:2228124/70‑1 (MQ=255)
                                                                  aTAACGCCAGATGCCGTGCTGCCATCAATGGACAACGCGCCAACCAGTACCGTCGGCATATTGTTCataat   <  1:501691/71‑1 (MQ=255)
                                                                  aTAACGCCAGATGCCGTGCTGCCATCAATGGACAACGCGCCAACCAGTACCGTCGGCATATTGTTCat      >  1:3220389/1‑68 (MQ=255)
                                                                  aTAACGCCAGATGCCGTGCTGCCATCAATGGACAACGCGCCAACCAGTACCGTCGGCATATTGTTCat      >  1:1404703/1‑68 (MQ=255)
                                                                   tAACGCCAGATGCCGTGCTGCCATCAATGGACAACGCGCCAACCAGTACCGTCGGCATATTGTTCataata  <  1:3771082/71‑1 (MQ=255)
                                                                   tAACGCCAGATGCCGTGCTGCCATCAATGGACAACGCGCCAACCAGTACCGTCGGCATATTGTTCataa    >  1:3037491/1‑69 (MQ=255)
                                                                    aaCGCCAGATGCCGTGCTGCCATCAATGGACAACGCGCCAACCAGTAcc                       >  1:1638895/1‑49 (MQ=255)
                                                                    |                                                                     
CCAATTGGGGTAATTTTCGGTCCCAAATCGCAGCCAATCACATTGGCATAAACCATCGCTTCTTTGATAACGCCAGATGCCGTGCTGCCATCAATGGACAACGCGCCAACCAGTACCGTCGGCATATTGTTCATAATA  >  minE/2595462‑2595599

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