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 2,919,516 T→A 30.3% R60R (CGA→CGT)  argI ← ornithine carbamoyltransferase 1

Read alignment evidence...
  seq id position ref new freq score (cons/poly) reads annotation genes product
*minE2,919,5160TA30.3% 149.7 / 79.0 102R60R (CGA→CGT) argIornithine carbamoyltransferase 1
Reads supporting (aligned to +/- strand):  ref base T (27/44);  new base A (16/15);  total (43/59)
Fisher's exact test for biased strand distribution p-value = 2.76e-01
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 1.00e+00

Only 100 of 103 total aligned reads displayed.

TCTGGCTGCCGCTTGGGCCGAGATAAGTAACGCGAGCACCCTGGTCATATGCGGCAACTTCGAAAGAGCATCGGGTACGAGTCGAGTCTTTTTCGAAGATGAGCGCGATGTTTTTACCAGTGAGTTTGGCTTCTTCTT  >  minE/2919446‑2919583
                                                                      |                                                                   
tCTGGCTGCCGCTTGGGCCGAGATAAGTAACGCGAGCACCCTGGTCATATGCGGCAACTTCGAAAGAGCAt                                                                     >  1:1266996/1‑71 (MQ=255)
  tGGCTGCCGCTTGGGCCGAGATAAGTAACGCGAGCACCCTGGTCATATGCGGCAACTTCGAAAGAGCATCg                                                                   >  1:1136939/1‑71 (MQ=255)
     cTGCCGCTCGGCCCTAAATAGGTAACGCGCGCGCCCTGGTCAAATGCGGCAACTTCGAAAGAGCAACGGGt                                                                <  1:1150435/71‑1 (MQ=255)
        ccGCTTGGGCCGAGATAAGTAACGCGAGCACCCTGGTCATATGCGGCAACTTCGAAAGAGCATCGGGTAc                                                              >  1:1021955/1‑70 (MQ=255)
        ccGCTCGGCCCTAAATAGGTAACGCGCGCGCCCTGGTCAAATGCGGCAACTTCGAAAGAGCAACGGGTAc                                                              >  1:1352634/1‑70 (MQ=255)
         cGCTTGGGCCGAGATAAGTAACGCGAGCACGCTGGTCATATGCGGCAACTTCGAAAGAGCATCGGGTAc                                                              <  1:1755589/69‑1 (MQ=255)
         cGCTTGGGCCGAGATAAGTAACGCGAGCACCCTGGTCATATGCGGCAACTTCGAAAGAGCATCGGGTAcga                                                            <  1:47219/71‑1 (MQ=255)
          gCTTGGGCCGAGATAAGTAACGCGAGCACCCTGGTCATATGCGGCAACTTCGAAAGAGCATCGGGTAcgag                                                           <  1:3292804/71‑1 (MQ=255)
           cTTGGGCCGAGATAAGTAACGCGAGCACCCTGGTCATATGCGGCAACTTCGAAAGAGCATc                                                                    <  1:3930069/61‑1 (MQ=255)
           cTTGGGCCGAGATAAGTAACGCGAGCACCCTGGTCATATGCGGCAACTTCGAAAGAGCATCGGGTAcgagt                                                          >  1:175560/1‑71 (MQ=255)
             tGGGCCGAGATAAGTAACGCGAGCACCCTGGTCATATGCGGCAACTTCGAAAGAGCATCGGGTAcgagtc                                                         >  1:764412/1‑70 (MQ=255)
              gggCCGAGATAAGTAACGCGAGCACCCTGGTCATATGCGGCAACTTCGAAAGAGCATCGGGTAcgagtcg                                                        <  1:2916072/70‑1 (MQ=255)
              gggCCGAGATAAGTAACGCGAGCACCCTGGTCATATGCGGCAACTTCGAAAGAGCATCGGGTAcgagtc                                                         <  1:3227791/69‑1 (MQ=255)
              gggCCGAGATAAGTAACGCGAGCACCCTGGTCATATGCGGCAACTTCGAAAGAGCATCGGGTAcgagtc                                                         <  1:733628/69‑1 (MQ=255)
               ggCCGAGATAAGTAACGCGAGCACCCTGGTCATATGCGGCAACTTCGAAAGAGCATCGGGTAcgagtcgag                                                      <  1:509753/71‑1 (MQ=255)
                  cGAGATAAGTAACGCGAGCACCCTGGTCATATGCGGCAACTTCGAAAGAGCATCGGGTACGAGTCGAGTCt                                                   >  1:676457/1‑71 (MQ=255)
                   gagaTAAGTAACGCGAGCACCCTGGTCATATGCGGCAACTTCGAAAGAGCATCGGGt                                                                >  1:3365593/1‑57 (MQ=255)
                     gaTAAGTAACGCGAGCACCCTGGTCATATGCGGCAACTTCGAAAGAGCATCGGGTACGAGTCGAGTCtttt                                                >  1:2066507/1‑71 (MQ=255)
                      aTAAGTAACGCGAGCACCCTGGTCATATGCGGCAACTTCGAAAGAGCATCGGGTACGAGTCGAGTCttttt                                               <  1:1716666/71‑1 (MQ=255)
                          gTAACGCGAGCACCCTGGTCATATGCGGCAACTTCGAAAGAGCATCGGGTACGAGTCGAGTCTTTTTCGaa                                           <  1:2915227/71‑1 (MQ=255)
                            aaCGCGCGCGCCCTGGTCAAATGCGGCAACTTCGAAAGAGCAACGGGTAcgagtcg                                                        <  1:1874776/56‑1 (MQ=255)
                             aCGCGCGCGCCCTGGTCAAATGCGGCAACTTCGAAAGAGCAACGGGTACGAGTCGAGTCTTTTTCGAAGAt                                        <  1:3790563/71‑1 (MQ=255)
                             aCGCGAGCACCCTGGTCATATGCGGCAACTTCGAAAGAGCATCGGGTACGAGTCGAGTCTTTTTc                                              <  1:635119/65‑1 (MQ=255)
                             aCGCGAGCACCCTGGTCATATGCGGCAACTTCGAAAGAGCATCGGGTACGAGTCGAGTCTTTTTCGAAGAt                                        <  1:902519/71‑1 (MQ=255)
                             aCGCGAGCACCCTGGACATATGCGGCAACTTCGAAAGAGCATCGGGTACGAGTCGAGTCTTTTTCGAAGAt                                        <  1:3738397/71‑1 (MQ=255)
                              cgcgcgcgCCCTGGTCAAATGCGGCAACTTCGAAAGAGCAACGGGTACGAGTCGAGTCGTTTTCGAAGAt                                        >  1:1109394/1‑70 (MQ=255)
                              cgcgAGCACCCTGGTCATATGCGGCAACTTCGAAAGAGCATCGGGt                                                                <  1:278775/46‑1 (MQ=255)
                               gcgcgcgcCCTGGTCAAATGCGGCAACTTCGAAAGAGCAACGGGTACGAGTCGAGTCTTTTTCGAAGAt                                        <  1:590861/69‑1 (MQ=255)
                               gcgAGCACCCTGGTCATATGCGGCAACTTCGAAAGAGCATCGGGTACGAGTCGAGTCTTTTTCGAAGAt                                        >  1:1052411/1‑69 (MQ=255)
                               gcgAGCACCCTGGTCATATGCGGCAACTTCGAAAGAGCATCGGGTACGAGTCGAGTCTTTTTCGAAGATGa                                      <  1:360040/71‑1 (MQ=255)
                                cgAGCACCCTGGTCATATGCGGCAACTTCGAAAGAGCATCGGGTACGAGTCGAGTCTTTTTCGAAGATGAg                                     <  1:2008898/71‑1 (MQ=255)
                                 gAGCACCCTGGTCATATGCGGCAACTTCGAAAGAGCATCGGGTACGAGTCGAGTCTTTTTCGAAg                                          >  1:1141367/1‑65 (MQ=255)
                                   gcgcccTGGTCAAATGCGGGAACTTCGAAAGAGCAACGGGTACGAGTCGAGTCTTTTTCGAAGATGAgcgc                                  >  1:45921/4‑71 (MQ=255)
                                   gcgcccTGGTCAAATGCGGCAACTTCGAAAGAGCAACGGGTACGAGTCGAGTCTTTTTCGAAGATGAgcgc                                  >  1:3311355/4‑71 (MQ=255)
                                    cACCCTGGTCATATGCTGCAACTTCGAAAGAGCATCGGGTACGAGTCGAGTCTTTTTCGAAGATGAGcgcg                                 <  1:2405417/71‑1 (MQ=255)
                                    cACCCTGGTCATATGCGGCAACTTCGAAAGAGCATCGGGTAc                                                              <  1:764474/42‑1 (MQ=255)
                                    cACCCTGGTCATATGCGGCAACTTCGAAAGAGCATCGGGTACGAGTCGAGTCTTTTTCGAAGATGAgc                                    <  1:2483171/68‑1 (MQ=255)
                                     gcccTGGTCAAATGCGGCAACTTCGAAAGAGCAACGGGTACGAGTCGAGTCTTTTTCGAAGATGAGCGCGa                                <  1:2332387/70‑1 (MQ=255)
                                     gcccTGGTCAAATGCGGCAACTTCGAAAGAGCAACGGGTACGAGTCGAGTCTTTTTCGAAGATGAGCGCGa                                <  1:3713242/70‑1 (MQ=255)
                                      cccTGGTCATATGCGGCAACTTCGAAAGAGCATCGGGTACGTGTCGAGTCTTTTTCGAAGATGAGCGCGAt                               >  1:3537270/1‑71 (MQ=255)
                                      cccTGGTCATATGCGGCAACTTCGAAAGAGCATCGGGTACGAGTCGAGTCTTTTTCGAAGATGAGcgcg                                 >  1:3466483/1‑69 (MQ=255)
                                      cccTGGTCATATGCGGCAACTTCGAAAGAGCATCGGGTACGAGTCGAGTCTTTTTCGAAGATGAGCGCGAt                               >  1:499683/1‑71 (MQ=255)
                                       ccTGGTCATATGCGGCAACTTCGAAAGAGCATCGGGTAcga                                                            >  1:616707/1‑41 (MQ=255)
                                       ccTGGTCATATGCGGCAACTTCGAAAGAGCATCGGGTACGAGTCGAGTCttt                                                 <  1:274598/52‑1 (MQ=255)
                                         tGGTCATATGCGGCAACTTCGAAAGAGCATCGGGTAcg                                                             <  1:2148317/38‑1 (MQ=255)
                                         tGGTCAAATGCGGCAACTTCGAAAGAGCAACGGGTa                                                               >  1:1809294/1‑36 (MQ=38)
                                         tGGTCAAATGCGGCAACTTCGAAAGAGCAACGGGTACGAGTCGAGTCTTTTTCGaa                                           >  1:3894423/1‑56 (MQ=255)
                                           gTCATATGCGGCAACTTCGAAAGAGCATCGGGTAcgag                                                           >  1:91274/1‑38 (MQ=255)
                                           gTCATATGCGGCAACTTCGAAAGAGCATCGGGTAcga                                                            >  1:874462/1‑37 (MQ=255)
                                           gTCATATGCGGCAACTTCGAAAGAGCATCGGGTACGAGTCGAGTCTTTTTCGAAGATGAGCGCGATGttt                           <  1:3354898/70‑1 (MQ=255)
                                           gTCAAATGCGGCAACTTCGAAAGAGCAACGGGTAcgagtcgagt                                                     >  1:2425440/1‑44 (MQ=255)
                                            tCATATGCGGCAACTTCGAAAGAGCATCGGGTAcgagtc                                                         <  1:1912777/39‑1 (MQ=255)
                                            tCATATGCGGCAACTTCGAAAGAGCATCGGGTACGAGTCGAGTCTTTTTCGAAGATGAGCGCGAt                               >  1:2341495/1‑65 (MQ=255)
                                              atatGCGGCAACTTCGAAAGAGCATCGGGTAcgagtcga                                                       >  1:3707273/1‑39 (MQ=255)
                                              atatGCGGCAACTTCGAAAGAGCATCGGGTACGAGTCGAGTCTTTTTCGAAGATGAGCGCGATGt                             <  1:2381121/65‑1 (MQ=255)
                                              atatGCGGCAACTTCGAAAGAGCATCGGGTACGAGTCGAGTCTTTTTCGAAGATGAGCGCGATGTTTTTAc                       >  1:2691091/1‑71 (MQ=255)
                                              atatGCGGCAACTTCGAAAGAGCATCGGGTACGAGTCGAGTCTTTTTCGAAGATGAGCGCGATGTTTTTAc                       >  1:1518154/1‑71 (MQ=255)
                                              aaatGCGGCAACTTCGAAAGAGCAACGGGTACGAGTCGAGTCTTTTTCGAAGATGa                                      >  1:1032924/3‑56 (MQ=255)
                                              aaatGCGGCAACTTCGAAAGAGCAACGGGTACGAGTCGAGTCTTTTTCGAAGATGAGCGCGATGTTTTTAc                       <  1:1216422/69‑1 (MQ=255)
                                              aaatGCGGCAACTTCGAAAGAGCAACGGGTACGAGTCGAGTCTTTTTCGAAGATGAGCGCGATGTTTTTAc                       >  1:1619642/3‑71 (MQ=255)
                                               tatGCGGCAACTTCGAAAGAGCATCGGGTACGAGTCGAGTCTTTTTCGAAGATGa                                      <  1:2539659/55‑1 (MQ=255)
                                                atGCGGCAACTTCGAAAGAGCATCGGGTACGAGTCGAGTCTTTTTCGAAGATGAGCGCGATGTTTTTAc                       >  1:2359750/1‑69 (MQ=255)
                                                atGCGGCAACTTCGAAAGAGCAACGGGTACGAGTCGAGTCTTTTTCGAAGATGAGGGCGATGTTTTTAccg                     <  1:2047002/71‑2 (MQ=255)
                                                  gCGGCAACTTCGAAAGAGCAACGGGTACGAGTCGAGTCTTTTTCGAAg                                          >  1:2088466/1‑48 (MQ=255)
                                                   cGGCAACTTCGAAAGAGCAACGGGTACGAGTCGAGTCTTTTTCGAAGATGAGCGCGATGtttt                          >  1:1999660/1‑63 (MQ=255)
                                                    ggCAACTTCGAAAGAGCATCGGGTACGAGTCGAGTCTTTTTCg                                             <  1:865483/43‑1 (MQ=255)
                                                    ggCAACTTCGAAAGAGCAACGGGTACGAGTCGAGTCTTTTTCGAAGATGAgcgc                                  <  1:3763794/54‑1 (MQ=255)
                                                      cAACTTCGAAAGAGCATCGGGTACGAGTCGAGTCTTTTTCGAAGATGAGCGCGATGTTTTTACCAGTGAg                <  1:573463/70‑1 (MQ=255)
                                                      cAACTTCGAAAGAGCATCGGGTACGAGTCGAGTCTTTTTCGAAGATGAGCGCGATGTTTTTACCAGTGAGt               <  1:2060975/71‑1 (MQ=255)
                                                      cAACTTCGAAAGAGCAACGGGTACGAGTCGAGTCTTTTTCGAAGATGAGCGCGATGTTTTTACCGGTAAgc               <  1:1477191/71‑2 (MQ=255)
                                                       aaCTTCGAAAGAGCATCGGGTACGAGTCGAGTCTTTTTCGAAg                                          <  1:2409388/43‑1 (MQ=255)
                                                       aaCTTCGAAAGAGCATCGGGTACGAGTCGAGTCTTTTTCGAAGATGAGCGCGATGTTTTTACCAGTGAGtt              <  1:2673147/71‑1 (MQ=255)
                                                       aaCTTCGAAAGAGCAACGGGTACGAGTCGAGTCTTTTTCGAAGATGAGCGCGATGTTTTTACCGGTAAgct              <  1:3128023/71‑3 (MQ=255)
                                                       aaCTTCGAAAGAGCAACGGGTACGAGTCGAGTCTTTTTCGAAGATGAGCGCGATGTTTTTACCGGTAAgct              >  1:261907/1‑69 (MQ=255)
                                                       aaCTTCGAAAGAGCAACGGGTACGAGTCGAGTCTTTATCGAAGATGA‑‑GCGATGTTTTTACCGGTAAGcttc            >  1:1687322/1‑70 (MQ=255)
                                                        aCTTCGAAAGAGCATCGGGTACGAGTCGAGTCTTTTTCGAAGATGAGCGCGATGttttt                         >  1:3109281/1‑59 (MQ=255)
                                                        aCTTCGAAAGAGCATCGGGTACGAGTCGAGTCTTTTTCGAAGATGAGCGCGATGTTTTTACCAGTGAGttt             <  1:823246/71‑1 (MQ=255)
                                                        aCTTCGAAAGAGCATCGGGTACGAGTCGAGTCTTTTTCGAAGATGAGCGCGATGTTTTTACCAGTGAGttt             >  1:3420171/1‑71 (MQ=255)
                                                        aCTTCGAAAGAGCATCGGGTACGAGTCGAGTCTTTTTCGAAGATGAGCGCGATGTTTTTACCAGTGAGttt             <  1:2970049/71‑1 (MQ=255)
                                                          ttCGAAAGAGCATCGGGTACGAGTCGAGTCttttt                                               <  1:3590903/35‑1 (MQ=255)
                                                          ttCGAAAGAGCATCGGGTACGAGTCGAGTCttttt                                               <  1:3797261/35‑1 (MQ=255)
                                                          ttCGAAAGAGCATCGGGTACGAGTCGAGTCttttt                                               <  1:1898847/35‑1 (MQ=255)
                                                          ttCGAAAGAGCATCGGGTACGAGTCGAGTCTTTTTCGa                                            >  1:245709/1‑38 (MQ=255)
                                                          ttCGAAAGAGCAACGGGTACGAGTCGAGTCttttta                                              >  1:850875/1‑35 (MQ=39)
                                                          ttCGAAAGAGCAACGGGTACGAGTCGAGTCTTTTTCGAAg                                          <  1:1920586/40‑1 (MQ=255)
                                                            cGAAAGAGCATCGGGTACGAGTCGAGTCTTTTTCGAAGATGAGCGCGATGTTTTTACCAGTGAGTTTgg           <  1:2693425/69‑1 (MQ=255)
                                                            cGAAAGAGCATCGGGTACGAGTCGAGTCTTTTTCGAAGATGAGCGCGATGTTTTTACCAGTGAGTTTGGct         >  1:3577608/1‑71 (MQ=255)
                                                            cGAAAGAGCAACGGGTACGAGTCGAGTCTTTTTCGAAGATGAGCGCGATGTTTTTACCGGTAAGcttctg          <  1:963201/70‑4 (MQ=255)
                                                            cGAAAGAGCAACGGGTACGAGTCGAGTCTTTTTCGAAGATGAGCGCGATGTTTTTACCGGTAAGcttctg          >  1:1750826/1‑67 (MQ=255)
                                                            cGAAAGAGCAACGGGTACGAGTCGAGTCTTTTTCGAAGATGAGCGCGATGTTTTTACCGGTAAGcttctg          >  1:3855338/1‑67 (MQ=255)
                                                            cGAAAGAGCAACGGGTACGAGTCGAGTCTTTTTCGAAGATGAGCGCGATGTTTTTACCGGTAAGcttctg          <  1:2668452/70‑4 (MQ=255)
                                                               aaGAGCATCGGGTACGAGTCGAGTCTTTTTCGAAGATGAGCGCGATGTTTTTACCAGt                   <  1:1426296/58‑1 (MQ=255)
                                                               aaGAGCATCGGGTACGAGTCGAGTCTTTTTCGAAGATGAGCGCGATGTTTTTACCAGTGAGTTTGGcttct      >  1:1460845/1‑71 (MQ=255)
                                                                 gagCATCGGGTACGAGTCGAGTCTTTTTCGAAGATGAGCGCGATGTTTTTACCAGTGAGTTTGGcttcttc    <  1:2143960/71‑1 (MQ=255)
                                                                 gagCATCGGGTACGAGTCGAGTCTTTTTCGAAGATGAGCGCGATGTTTTTACCAGTGAGTTTGGcttcttc    <  1:1332095/71‑1 (MQ=255)
                                                                  agCATCGGGTACGAGTCGAGTCTTTTTCGAAGATGAGCGCGATGTTTTTACCAGTGAGTTTGGcttcttct   >  1:2330690/1‑71 (MQ=255)
                                                                  agCATCGGGTACGAGTCGAGTCTTTTTCGAAGATGAGCGCGATGTTTTTACCAGTGAGTTTGGcttcttct   <  1:3049360/71‑1 (MQ=255)
                                                                   gCATCGGGTACGAGTCGAGTCTTTTTCGAAGATGAGCGCGATg                              <  1:3911978/43‑1 (MQ=255)
                                                                   gCATCGGGTACGAGTCGAGTCTTTTTCGAAGATGAGCGCGATGTTTTTACCAGTGAGTTTGGcttcttctt  >  1:2547126/1‑71 (MQ=255)
                                                                    cATCGGGTACGAGTCGAGTCTTTTTCGAAGATGAGCGCGATGTTTTTACCAGTGAGTTTGGcttcttctt  <  1:2522935/70‑1 (MQ=255)
                                                                      |                                                                   
TCTGGCTGCCGCTTGGGCCGAGATAAGTAACGCGAGCACCCTGGTCATATGCGGCAACTTCGAAAGAGCATCGGGTACGAGTCGAGTCTTTTTCGAAGATGAGCGCGATGTTTTTACCAGTGAGTTTGGCTTCTTCTT  >  minE/2919446‑2919583

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