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
A1 F28 I2 R2 356 55.1 4139924 95.4% 3949487 63.8

Breseq alignment

BRESEQ :: Evidence
Predicted mutation
evidence seq id position mutation annotation gene description
RA W3110S.gb 3,518,471 T→C intergenic (‑305/‑120) yiiU ← / → glpF conserved hypothetical protein/glycerol facilitator

Read alignment evidence...
  seq id position ref new freq score (cons/poly) reads annotation genes product
*W3110S.gb3,518,4710TC91.2% 945.5 / 54.7 298intergenic (‑305/‑120)yiiU/glpFconserved hypothetical protein/glycerol facilitator
Reads supporting (aligned to +/- strand):  ref base T (3/23);  new base C (127/144);  total (131/167)
Fisher's exact test for biased strand distribution p-value = 3.42e-04
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 1.00e+00

Only 100 of 298 total aligned reads displayed.

TCATGTACAATCAGATGGAATAAATGGCGCGATAACGCTCATTTTATGACGAGGCACACACATTTTAAGTTCGATATTTCTCGTTTTTGCTCGTTAACGATAAGTTTACAGCATGCCTACAAGCATCGTG  >  W3110S.gb/3518408‑3518537
                                                               |                                                                  
tcatGTACAATCAGATGGAATAAATGGCGCGATAACGCTCATTTTATGACGAGGCACACACATCTTAAGt                                                              >  1:1481987/1‑70 (MQ=255)
    gTACAATCAGATGGAATAAATGGCGCGATAACGCTCATTTTATGACGAGGCACACACATCTTAAGTTCGa                                                          >  1:3345351/1‑70 (MQ=255)
       cAATCAGATGGAATAAATGGCGCGATAACGCTCATTTTATGACGAGGCACACACATCTTAAGTTCGa                                                          <  1:1168980/67‑1 (MQ=255)
       cAATCAGATGGAATAAATGGCGCGATAACGCTCATTTTATGACGAGGCACACACATCTTAAGTTCGATAtt                                                      >  1:1912495/1‑71 (MQ=255)
       cAATCAGATGGAATAAATGGCGCGATAACGCTCATTTTATGACGAGGCACACACATCTTAAGTTCGATAtt                                                      >  1:290571/1‑71 (MQ=255)
       cAATCAGATGGAATAAATGGCGCGATAACGCTCATTTTATGACGAGGCACACACATCTTAAGTTCGATAtt                                                      >  1:2518983/1‑71 (MQ=255)
           cAGATGGAATAAATGGCGCGATAACGCTCATTTTATGACGAGGCACACACATCTTAAGTTCGATATTtctc                                                  >  1:1745262/1‑71 (MQ=255)
           cAGATGGAATAAATGGCGCGATAACGCTCATTTTATGACGAGGCACACACATCTTAAGTTCGATATTtctc                                                  >  1:2703801/1‑71 (MQ=255)
           cAGATGGAATAAATGGCGCGATAACGCTCATTTTATGACGAGGCACACACATCTTAAGTTCGATATTtctc                                                  >  1:3890700/1‑71 (MQ=255)
           cAGATGGAATAAATGGCGCGATAACGCTCATTTTATGACGAGGCACACACATCTTAAGTTCGATATTtctc                                                  >  1:3605994/1‑71 (MQ=255)
            aGATGGAATAAATGGCGCGATAACGCTCATTTTATGACGAGGCACACACATCTTAAGTTCGATATTTCTCg                                                 >  1:1054061/1‑71 (MQ=255)
                   aTAAATGGCGCGATAACGCTCATTTTATGACGAGGCACACACATCTTAAGTTCGATATTTCTCGTTTTTGc                                          <  1:727621/71‑1 (MQ=255)
                   aTAAATGGCGCGATAACGCTCATTTTATGACGAGGCACACACATCTTAAGTTCGATATTTCTCGTTTTTGc                                          <  1:774972/71‑1 (MQ=255)
                   aTAAATGGCGCGATAACGCTCATTTTATGACGAGGCACACACATCTTAAGTTCGATATTTCTCGTTTTTGc                                          <  1:3822704/71‑1 (MQ=255)
                   aTAAATGGCGCGATAACGCTCATTTTATGACGAGGCACACACATCTTAAGTTCGATATTTCTCGTTTTTGc                                          <  1:1536322/71‑1 (MQ=255)
                   aTAAATGGCGCGATAACGCTCATTTTATGACGAGGCACACACATCTTAAGTTCGATATTTCTCGTTTTTGc                                          <  1:2804115/71‑1 (MQ=255)
                      aaTGGCGCGATAACGCTCATTTTATGACGAGGGACACACATCTTAAGTTCGATATTTCTCGTTTTTGCTc                                        >  1:911600/1‑70 (MQ=255)
                      aaTGGCGCGATAACGCTCATTTTATGACGAGGCACACACATTTTAAGTTCGATATTTCTCGTTTTTGCTCg                                       >  1:214176/1‑71 (MQ=255)
                      aaTGGCGCGATAACGCTCATTTTATGACGAGGCACACACATTTTAAGTTCGATATTTCTCGTTTTTGCTCg                                       >  1:2679464/1‑71 (MQ=255)
                      aaTGGCGCGATAACGCTCATTTTATGACGAGGCACACACATCTTAAGTTCGATATTTCTCGTTTTTGCTCg                                       >  1:1859096/1‑71 (MQ=255)
                      aaTGGCGCGATAACGCTCATTTTATGACGAGGCACACACATCTTAAGTTCGATATTTCTCGTTTTTGCTCg                                       >  1:1129167/1‑71 (MQ=255)
                      aaTGGCGCGATAACGCTCATTTTATGACGAGGCACACACATCTTAAGTTCGATATTTCTCGTTTTTGCTCg                                       >  1:430532/1‑71 (MQ=255)
                      aaTGGCGCGATAACGCTCATTTTATGACGAGGCACACACATCTTAAGTTCGATATTTCTCGTTTTTGCTCg                                       >  1:3493478/1‑71 (MQ=255)
                        tGGCGCGATAACGCTCATTTTATGACGAGGCACACACATCTTAAGTTCGATATTTCTCGTTTTTGCTCGt                                      >  1:3145555/1‑70 (MQ=255)
                        tGGCGCGATAACGCTCATTTTATGACGAGGCACACACATCTTAAGTTCGATATTTCTCGTTTTTGCTCGt                                      >  1:2351394/1‑70 (MQ=255)
                        tGGCGCGATAACGCTCATTTTATGACGAGGCACACACATCTTAAGTTCGATATTTCTCGTTTTTGCTCGt                                      >  1:1035364/1‑70 (MQ=255)
                        tGGCGCGATAACGCTCATTTTATGACGAGGCACACACATCTTAAGTTCGATATTTCTCGTTTTTGCTCGt                                      >  1:923500/1‑70 (MQ=255)
                        tGGCGCGATAACGCTCATTTTATGACGAGGCACACACATCTTAAGTTCGATATTTCTCGTTTTTGCTCGt                                      >  1:1802515/1‑70 (MQ=255)
                        tGGCGCGATAACGCTCATTTTATGACGAGGCACACACATCTTAAGTTCGATATTTCTCGTTTTTGCTCGt                                      >  1:1191458/1‑70 (MQ=255)
                        tGGCGCGATAACGCTCATTTTATGACGAGGCACACACATCTTAAGTTCGATATTTCTCGTTTTTGCTCGt                                      >  1:1412240/1‑70 (MQ=255)
                        tGGCGCGATAACGCTCATTTTATGACGAGGCACACACATCTTAAGTTCGATATTTCTCGTTTTTGCTCGt                                      >  1:464958/1‑70 (MQ=255)
                        tGGCGCGATAACGCTCATTTTATGACGAGGCACACACATCTTAAGTTCGATATTTCTCGTTTTTGCTCGt                                      >  1:1517810/1‑70 (MQ=255)
                        tGGCGCGATAACGCTCATTTTATGACGAGGCACACACATCTTAAGTTCGATATTTCTCGTTTTTGCTCGt                                      >  1:4046720/1‑70 (MQ=255)
                          gcgcGATAACGCTCATTTTATGACGAGGCACACACATCTTAAGTTCGATATTTCTCGTTTTTGCTCGTTaa                                   >  1:2157646/1‑71 (MQ=255)
                          gcgcGATAACGCTCATTTTATGACGAGGCACACACATCTTAAGTTCGATATTTCTCGTTTTTGCTCGTTaa                                   >  1:571848/1‑71 (MQ=255)
                          gcgcGATAACGCTCATTTTATGACGAGGCACACACATCTTAAGTTCGATATTTCTCGTTTTTGCTCGTTaa                                   >  1:3221319/1‑71 (MQ=255)
                           cgcgATAACGCTCATTTTATGACGAGGCACACACATCTTAAGTTCGATATTTCTCGTTTTTGCTCGTTAAc                                  <  1:3310057/71‑1 (MQ=255)
                           cgcgATAACGCTCATTTTATGACGAGGCACACACATCTTAAGTTCGATATTTCTCGTTTTTGCTCGTTAAc                                  <  1:3195941/71‑1 (MQ=255)
                           cgcgATAACGCTCATTTTATGACGAGGCACACACATCTTAAGTTCGATATTTCTCGTTTTTGCTCGTTAAc                                  <  1:3254152/71‑1 (MQ=255)
                           cgcgATAACGCTCATTTTATGACGAGGCACACACATCTTAAGTTCGATATTTCTCGTTTTTGCTCGTTAAc                                  <  1:2172481/71‑1 (MQ=255)
                           cgcgATAACGCTCATTTTATGACGAGGCACACACATCTTAAGTTCGATATTTCTCGTTTTTGCTCGTTAAc                                  <  1:4115695/71‑1 (MQ=255)
                            gcgATAACGCTCATTTTATGACGAGGCACACACATCTTAAGTTCGATATTTCTCGTTTTTGCTCGTTAAc                                  <  1:967582/70‑1 (MQ=255)
                               aTAACGCTCATTTTATGACGAGGCACACACATCTTAAGTTCGATATTTCTCGTTTTTGc                                          <  1:2951663/59‑1 (MQ=255)
                               aTAACGCTCATTTTATGACGAGGCACACACATCTTAAGTTCGATATTTCTCGTTTTTGCTCGTTAACGAt                               >  1:645672/1‑70 (MQ=255)
                               aTAACGCTCATTTTATGACGAGGCACACACATCTTAAGTTCGATATTTCTCGTTTTTGCTCGTTAACGAt                               >  1:2102647/1‑70 (MQ=255)
                                tAACGCTCATTTTATGACGAGGCACACACATCTTAAGTTCGATATTTCTCGTTTTTGCTCGTTAACGAt                               >  1:3068114/1‑69 (MQ=255)
                                 aaCGCTCATTTTATGACGAGGCACACACATCTTAAGTTCGATATTTCTCGTTTTTGCTCGTTAACGATAAg                            >  1:317534/1‑71 (MQ=255)
                                 aaCGCTCATTTTATGACGAGGCACACACATCTTAAGTTCGATATTTCTCGTTTTTGCTCGTTAACGATAAg                            >  1:872991/1‑71 (MQ=255)
                                 aaCGCTCATTTTATGACGAGGCACACACATCTTAAGTTCGATATTTCTCGTTTTTGCTCGTTAACGATAAg                            >  1:2408165/1‑71 (MQ=255)
                                   cGCTCATTTTATGACGAGGCACACACATCTTAAGTTCGATATTTCTCGTTTTTGCTCGTTAACGATAAGtt                          <  1:2638657/71‑1 (MQ=255)
                                   cGCTCATTTTATGACGAGGCACACACATCTTAAGTTCGATATTTCTCGTTTTTGCTCGTTAACGATAAGtt                          <  1:400368/71‑1 (MQ=255)
                                   cGCTCATTTTATGACGAGGCACACACATCTTAAGTTCGATATTTCTCGTTTTTGCTCGTTAACGATAAGtt                          <  1:1932844/71‑1 (MQ=255)
                                   cGCTCATTTTATGACGAGGCACACACATCTTAAGTTCGATATTTCTCGTTTTTGCTCGTTAACGATAAGtt                          <  1:199754/71‑1 (MQ=255)
                                   cGCTCATTTTATGACGAGGCACACACATCTTAAGTTCGATATTTCTCGTTTTTGCTCGTTAACGATAAGtt                          <  1:2116590/71‑1 (MQ=255)
                                   cGCTCATTTTATGACGAGGCACACACATCTTAAGTTCGATATTTCTCGTTTTTGCTCGTTAACGATAAGtt                          <  1:220120/71‑1 (MQ=255)
                                   cGCTCATTTTATGACGAGGCACACACATCTTAAGTTCGATATTTCTCGTTTTTGCTCGTTAACGATAAGtt                          <  1:3152317/71‑1 (MQ=255)
                                   cGCTCATTTTATGACGAGGCACACACATCTTAAGTTCGATATTTCTCGTTTTTGCTCGTTAACGATAAGtt                          <  1:2769028/71‑1 (MQ=255)
                                   cGCTCATTTTATGACGAGGCACACACATCTTAAGTTCGATATTTCTCGTTTTTGCTCGTTAACGATAAGtt                          <  1:947066/71‑1 (MQ=255)
                                     cTCATTTTATGACGAGGCACACACATCTTAAGTTCGATATTTCTCGTTTTTGCTCGTTAACGATAAGTTTa                        >  1:2033273/1‑71 (MQ=255)
                                     cTCATTTTATGACGAGGCACACACATCTTAAGTTCGATATTTCTCGTTTTTGCTCGTTAACGATAAGTTTa                        <  1:545044/71‑1 (MQ=255)
                                     cTCATTTTATGACGAGGCACACACATCTTAAGTTCGATATTTCTCGTTTTTGCTCGTTAACGATAAGTTTa                        >  1:1884677/1‑71 (MQ=255)
                                     cTCATTTTATGACGAGGCACACACATCTTAAGTTCGATATTTCTCGTTTTTGCTCGTTAACGATAAGTTTa                        >  1:3870809/1‑71 (MQ=255)
                                     cTCATTTTATGACGAGGCACACACATCTTAAGTTCGATATTTCTCGTTTTTGCTCGTTAACGATAAGTTTa                        <  1:979189/71‑1 (MQ=255)
                                     cTCATTTTATGACGAGGCACACACATCTTAAGTTCGATATTTCTCGTTTTTGCTCGTTAACGATAAGTTTa                        <  1:621157/71‑1 (MQ=255)
                                     cTCATTTTATGACGAGGCACACACATCTTAAGTTCGATATTTCTCGTTTTTGCTCGTTAACGATAAGTTTa                        >  1:3689667/1‑71 (MQ=255)
                                     cTCATTTTATGACGAGGCACACACATCTTAAGTTCGATATTTCTCGTTTTTGCTCGTTAACGATAAGTTTa                        <  1:358398/71‑1 (MQ=255)
                                     cTCATTTTATGACGAGGCACACACATCTTAAGTTCGATATTTCTCGTTTTTGCTCGTTAACGATAAGTTTa                        <  1:3418613/71‑1 (MQ=255)
                                     cTCATTTTATGACGAGGCACACACATCTTAAGTTCGATATTTCTCGTTTTTGCTCGTTAACGATAAGTTTa                        <  1:2481305/71‑1 (MQ=255)
                                     cTCATTTTATGACGAGGCACACACATCTTAAGTTCGATATTTCTCGTTTTTGCTCGTTAACGATAAGTTTa                        <  1:224016/71‑1 (MQ=255)
                                     cTCATTTTATGACGAGGCACACACATCTTAAGTTCGATATTTCTCGTTTTTGCTCGTTAACGATAAGTTTa                        <  1:2282869/71‑1 (MQ=255)
                                      tCATTTTATGACGAGGCACACACATCTTAAGTTCGATATTTCTCGTTTTTGCTCGTTAACGATAAGTTTa                        <  1:256440/70‑1 (MQ=255)
                                        aTTTTATGACGAGGCACACACATCTTAAGTTCGATATTTCTCGTTTTTGCTCGTTAACGATAAGTTTAc                       <  1:3537431/69‑1 (MQ=255)
                                        aTTTTATGACGAGGCACACACATCTTAAGTTCGATATTTCTCGTTTTTGCTCGTTAACGATAAGTTTAc                       <  1:3929947/69‑1 (MQ=255)
                                        aTTTTATGACGAGGCACACACATCTTAAGTTCGATATTTCTCGTTTTTGCTCGTTAACGATAAGTTTAc                       <  1:2302195/69‑1 (MQ=255)
                                        aTTTTATGACGAGGCACACACATCTTAAGTTCGATATTTCTCGTTTTTGCTCGTTAACGATAAGTTTACa                      <  1:3937939/70‑1 (MQ=255)
                                        aTTTTATGACGAGGCACACACATCTTAAGTTCGATATTTCTCGTTTTTGCTCGTTAACGATAAGTTTACAg                     <  1:943124/71‑1 (MQ=255)
                                         ttttATGACGAGGCACACACATCTTAAGTTCGATATTTCTCGTTTTTGCTCGTTAACGATAAGTTTAc                       <  1:127246/68‑1 (MQ=255)
                                         ttttATGACGAGGCACACACATCTTAAGTTCGATATTTCTCGTTTTTGCTCGTTAACGATAAGTTTAc                       <  1:1350883/68‑1 (MQ=255)
                                         ttttATGACGAGGCACACACATCTTAAGTTCGATATTTCTCGTTTTTGCTCGTTAACGATAAGTTTAc                       <  1:3779552/68‑1 (MQ=255)
                                           ttATGCCGAGGCACACACATCTTAAGTTCGATATTTCTCGTTTTTGCTCGTTAACGATAAGttt                         >  1:2872984/1‑64 (MQ=255)
                                           ttATGACGAGGCACACACATCTTAAGTTCGATATTTCTCGTTTTTGCTCGTTAACGATAAGTTTa                        >  1:2747117/1‑65 (MQ=255)
                                            tATGACGAGGCACACACATCTTAAGTTCGATATTTCTCGTTTTTGCTCGTTAACGATAAGTTTACAGCAt                  <  1:826106/70‑1 (MQ=255)
                                            tATGACGAGGCACACACATCTTAAGTTCGATATTTCTCGTTTTTGCTCGTTAACGATAAGTTTACAGCAt                  <  1:2573001/70‑1 (MQ=255)
                                            tATGACGAGGCACACACATCTTAAGTTCGATATTTCTCGTTTTTGCTCGTTAACGATAAGTTTACAGCAt                  <  1:1252352/70‑1 (MQ=255)
                                            tATGACGAGGCACACACATCTTAAGTTCGATATTTCTCGTTTTTGCTCGTTAACGATAAGTTTACAGCAt                  <  1:1556121/70‑1 (MQ=255)
                                             aTGACGAGGCACACACATCTTAAGTTCGATATTTCTCGTTTTTGCTCGTTAACGATAAGTTTACAGCATg                 <  1:3731572/70‑1 (MQ=255)
                                             aTGACGAGGCACACACATCTTAAGTTCGATATTTCTCGTTTTTGCTCGTTAACGATAAGTTTACAGCATg                 <  1:2973494/70‑1 (MQ=255)
                                                  gAGGCACACACATCTTAAGTTCGATATTTCTCGTTTTTGCTCGTTAACGATAAGTTTACAGCATGCCTACa           <  1:3444945/71‑1 (MQ=255)
                                                  gAGGCACACACATCTTAAGTTCGATATTTCTCGTTTTTGCTCGTTAACGATAAGTTTACAGCATGCCTACa           <  1:1650387/71‑1 (MQ=255)
                                                  gAGGCACACACATCTTAAGTTCGATATTTCTCGTTTTTGCTCGTTAACGATAAGTTTACAGCATGCCTACa           <  1:3039327/71‑1 (MQ=255)
                                                  gAGGCACACACATCTTAAGTTCGATATTTCTCGTTTTTGCTCGTTAACGATAAGTTTACAGCATGCCTACa           <  1:2859535/71‑1 (MQ=255)
                                                     gCACACACATCTTAAGTTCGATATTTCTCGTTTTTGCTCGTTAACGATAAGTTTACAGCATGCCTACAAg         >  1:902606/1‑70 (MQ=255)
                                                        cacacaTTTTAAGTTCGATATTTCTCGTTTTTGCTCGTTAACGATAAGTTTACAGCATGCCTACAAGCATc     <  1:1318972/71‑1 (MQ=255)
                                                        cacacaTTTTAAGTTCGATATTTCTCGTTTTTGCTCGTTAACGATAAGTTTACAGCATGCCTACAAGCATc     <  1:840379/71‑1 (MQ=255)
                                                        cacacaTTTTAAGTTCGATATTTCTCGTTTTTGCTCGTTAACGATAAGTTTACAGCATGCCTACAAGCATc     <  1:3007676/71‑1 (MQ=255)
                                                        cacacaTTTTAAGTTCGATATTTCTCGTTTTTGCTCGTTAACGATAAGTTTACAGCATGCCTACAAGCATc     <  1:123274/71‑1 (MQ=255)
                                                         acacaTTTTAAGTTCGATATTTCTCGTTTTTGCTCGTTAACGATAAGTTTACAGCATGCCTACAAGCATc     <  1:1455298/70‑1 (MQ=255)
                                                            caTCTTAAGTTCGATATTTCTCGTTTTTGCTCGTTAACGATAAGTTTa                        <  1:3629324/48‑1 (MQ=255)
                                                            caTCTTAAGTTCGATATTTCTCGTTTTTGCTCGTTAACGATAAGTTTACAg                     <  1:1396698/51‑1 (MQ=255)
                                                            caTCTTAAGTTCGATATTTCTCGTTTTTGCTCGTTAACGATAAGTTTACAg                     <  1:504165/51‑1 (MQ=255)
                                                               |                                                                  
TCATGTACAATCAGATGGAATAAATGGCGCGATAACGCTCATTTTATGACGAGGCACACACATTTTAAGTTCGATATTTCTCGTTTTTGCTCGTTAACGATAAGTTTACAGCATGCCTACAAGCATCGTG  >  W3110S.gb/3518408‑3518537

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