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 2,919,480 A→C 30.2% A72A (GCT→GCG)  argI ← ornithine carbamoyltransferase 1

Read alignment evidence...
  seq id position ref new freq score (cons/poly) reads annotation genes product
*minE2,919,4800AC30.2% 131.3 / 124.7 139A72A (GCT→GCG) argIornithine carbamoyltransferase 1
Reads supporting (aligned to +/- strand):  ref base A (40/57);  new base C (32/10);  total (72/67)
Fisher's exact test for biased strand distribution p-value = 1.87e-04
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 9.82e-01

Only 100 of 143 total aligned reads displayed.

GGCAGTGTCTTTAATCGACTCTTTATGACCAATCTGGCTGCCGCTTGGGCCGAGATAAGTAACGCGAGCACCCTGGTCATATGCGGCAACTTCGAAAGAGCATCGGGTACGAGTCGAGTCTTTTTCGAAGAT  >  minE/2919414‑2919545
                                                                  |                                                                 
   aGTGTCTTTAATCGACTCTTTATGACCAATCTGGCTGCCGCTTGGGCCGAGATAAGTAACGCGAGCACCCt                                                            <  1:4949510/71‑1 (MQ=255)
    gtgtCTTTAATCGACTCTTTATGACCAATCTGGCTGCCGCTTGGGCCGAGATAAGTAACGCGAGCACCCTg                                                           >  1:3233839/1‑71 (MQ=255)
    gtgtCCTTAATTGACTCTTTATGCCCAATCTGGCTGCCGCTCGGCCCTAAATAGGTAACGCGCGCGCCCTg                                                           >  1:2540900/1‑71 (MQ=255)
     tgtCTTTAATCGACTCTTTATGACCAATCTGGCTGCCGCTTGGGCCGAGATAAGTAACGCGAGCAcc                                                              <  1:5352630/67‑1 (MQ=255)
       tCTTTAATCGACTCTTTATGACCAATCTGGCTGCCGCTTGGGCCGAGATAAGTAACGCGAGCa                                                                <  1:4228580/63‑1 (MQ=255)
         tttAATCGACTCTTTATGACCAATCTGGCTGCCGCTTGGGCCGAGATAAGTAACGCGa                                                                   >  1:523689/1‑58 (MQ=255)
         tttAATCGACTCTTTATGACCAATCTGGCTGCCGCTTGGGCCGAGATAAGTAACGCGAGCACCCTGGTCa                                                       >  1:5383000/1‑70 (MQ=255)
         cttAATTGACTCTTTATGCCCAATCTGGCTGCCGCTCGGCCCTAAATAGGTAACGCGCGCGCCCTGGTCa                                                       >  1:228556/2‑70 (MQ=255)
           tAATTGACTCTTTATGCCCAATCTGGCTGCCGCTCGGCCCTAAATAGGTAACGCGCGCGCCCTGGTCaaat                                                    >  1:1306106/1‑71 (MQ=255)
           tAATCGACTCTTTATGACCAATCTGGCTGCCGCTTGGGCCGAGATAAGTAACGCGAGCACCCTGGTCatat                                                    >  1:4699447/1‑71 (MQ=255)
           tAATCGACTCTTTATGACCAATCTGGCTGCCGCTTGGGCCGAGATAAGTAACGCGAGCACCCTGGTCa                                                       <  1:3904649/68‑1 (MQ=255)
           tAATCGACTCTTTATGACCAATCTGGCTGCCGCTTGGGCCGAGATAAGTAACGCGAGCACCCTGGTCa                                                       <  1:4431115/68‑1 (MQ=255)
            aaTCGACTCTTTATGACCAATCTGGCTGCCGCTTGGGCCGAGATAAGTAACGCGa                                                                   >  1:1250657/1‑55 (MQ=255)
             aTCGACTCTTTATGACCAATCTGGCTGCCGCTTGGGCCGAGATAAGTAACGCGAGCACCCTGGt                                                         >  1:5045680/1‑64 (MQ=255)
              ttgACTCTTTATGCCCAATCTGGCTGCCGCTCGGCCCTAAATAGGTAACGCGCGCGCCCTGGTCAAATGCg                                                 >  1:4575185/3‑71 (MQ=255)
              ttgACTCTTTATGCCCAATCTGGCTGCCGCTCGGCCCTAAATAGGTAACGCGCGCGCCCTGGTCAAATGCg                                                 >  1:1819107/3‑71 (MQ=255)
                gACTCTTTATGCCCAATCTGGCTTCCGCTCGGCCCTAAATAGGTAACGCGCGCGCCCTGGTCAAATGCgg                                                >  1:4404883/1‑70 (MQ=255)
                gACTCTTTATGCCCAATCTGGCTGCCGCTCGGCCCTAAATAGGTAACGCGCGCGCCCTGGTCAAATGCg                                                 >  1:717621/1‑69 (MQ=255)
                gACTCTTTATGACCAATCTGGCTGCCGCTTGGGCCGAGATAAGTAACGGGAGCACCCTGGTCATATGCGGc                                               <  1:1807272/71‑1 (MQ=255)
                gACTCTTTATGACCAATCTGGCTGCCGCTTGGGCCGAGATAAGTAACGCGAGCACCCTGGTCATATGCgg                                                >  1:2110440/1‑70 (MQ=255)
                gACTCTTTATGACCAATCTGGCTGCCGCTTGGGCCGAGATAAGTAACGCGAGCACCCTGGTCATATGCgg                                                >  1:3092168/1‑70 (MQ=255)
                 aCTCTTTATGACCAATCTGGCTGCCGCTTGGGCCGAGATAAGTAACGCGAGCAccc                                                             <  1:136070/56‑1 (MQ=255)
                     tttATGACCAATCTGGCTGCCGCTTGGGCCGAGATAAGTAACGCGAGCACCCTGGTCata                                                     >  1:2714018/1‑60 (MQ=255)
                     tttATGACCAATCTGGCTGCCGCTTGGGCCGAGATAAGTAACGCGAGCACCCTGGTCATATGCGGc                                               <  1:3622142/66‑1 (MQ=255)
                     tttATGACCAATCTGGCTGCCGCTTGGGCCGAGATAAGTAACGCGAGCACCCTGGTCATATGCGGCAACt                                           >  1:1653631/1‑70 (MQ=255)
                      ttATGACCAATCTGGCTGCCGCTTGGGCCGAGATAAGTAACGCGAGCACCCTGGTCATATGCGGCAACTTc                                         >  1:153013/1‑71 (MQ=255)
                      ttATGACCAATCTGGCTGCCGCTTGGGCCGAGATAAGTAACGCGAGCACCCTGGTCATATGCGGCAACTTc                                         >  1:2903921/1‑71 (MQ=255)
                       tATGCCCAATCTGGCTGCCGCTCGGCCCTAAATAGGTAACGCGCGCGCCCTGGTCAAATGCGGCAACTTc                                         >  1:3443826/1‑70 (MQ=255)
                       tATGACCAATCTGGCTGCCGCTTGGGCCGAGATAAGTAACGCGAGCACCCTGGTCATATGCGGCaa                                             >  1:5332485/1‑66 (MQ=255)
                       tATGACCAATCTGGCTGCCGCTTGGGCCGAGATAAGTAACGCGAGCACCCTGGTCATATGCGGCAACTTc                                         >  1:3174424/1‑70 (MQ=255)
                         tgcccAATCTGGCTGCCGCTCGGCCCTAAATAGGTAACGCGCGCGCCCTGGTCAAATGCGGCAACTTCGa                                       <  1:280392/67‑1 (MQ=255)
                         tgcccAATCTGGCTGCCGCTCGGCCCTAAATAGGTAACGCGCGCGCCCTGGTCAAATGCGGCAACTTCGa                                       <  1:3845007/67‑1 (MQ=255)
                         tGACCAATCTGGCTGCCGCTTGGGCCGAGATAAGTAACGCGAGCACCCTGGTCATATGCGGCAACTTCGa                                       <  1:3818374/70‑1 (MQ=255)
                         tGACCAATCTGGCTGCCGCTTGGGCCGAGATAAGTAACGCGAGCACCCTGGTCATATGCGGCAACTTCGa                                       <  1:2969478/70‑1 (MQ=255)
                           aCCAATCTGGCTGCCGCTTGGGCCGAGATAAGTAACGCGAGCACCCTGGTCATATGCGGCAACTTc                                         <  1:4730925/66‑1 (MQ=255)
                           aCCAATCTGGCTGCCGCTTGGGCCGAGATAAGTAACGCGAGCACCCTGGTCATATGCGGCAACTTc                                         <  1:2384455/66‑1 (MQ=255)
                           aCCAATCTGGCTGCCGCTTGGGCCGAGATAAGTAACGCGACCACCCTGGTCATATGCGGCAACTTCGa                                       >  1:3750491/1‑68 (MQ=255)
                            ccAATCTGGCTGCCGCTTGGGGCGAGATAAGTAACGCGAGCACCCTGGTCATATGCGGCAACTTCGaaa                                     >  1:4659433/1‑69 (MQ=255)
                             cAATCTGGCTGCCGCTTGGGCCGAGATAAGTAACGCGAGCACCCTGGTCATATGCGGCAACTTCGaaa                                     >  1:5187240/1‑68 (MQ=255)
                             cAATCTGGCTGCCGCTCGGCCCTAAATAGGTAACGCGCGCGCCCTGGTCAAATGCGGCaa                                             >  1:2786265/1‑60 (MQ=255)
                              aaTCTGGCTGCCGCTCGGCCCTAAATAGGTAACGCGCGCGCCCTGGTCAAATGCGGCAACTTCGAAagag                                  >  1:4736921/1‑70 (MQ=255)
                               aTCTGGCTGCCGCTTGGGCCGAGATAAGTAACGCGAGCa                                                                >  1:5562645/1‑39 (MQ=255)
                                 cTGGCTGCCGCTTGGGCCGAGATAAGTAACGCGAGCACCCTGGTCATATGCg                                                 >  1:5238320/1‑52 (MQ=255)
                                 cTGGCTGCCGCTTGGGCCGAGATAAGTAACGCGAGCACCCTGGTCATATGCg                                                 >  1:1385077/1‑52 (MQ=255)
                                 cTGGCTGCCGCTCGGCCCTAAATAGGTAACGCGCGCGCCCTGGTCAAATGCGGCAACTTCGaaa                                     >  1:495666/1‑64 (MQ=255)
                                 cTGGCTGCCGCTCGGCCCTAAATAGGTAACGCGCGCGCCCTGGTCAAATGCGGCAACTTCGAAAGAGCaac                              >  1:5124203/1‑69 (MQ=255)
                                  tGGCTGCCGCTTGGGCCGAGATAAGTAACGCGAGCACCCTGGTCATATGCGGCAACTTCGAAAGAGCATCg                             >  1:1763425/1‑71 (MQ=255)
                                  tGGCTGCCGCTCGGCCCTAAATAGGTAACGCGCGCGCCCTGGTCAAATGCGGCaa                                             >  1:1343995/1‑55 (MQ=255)
                                  tGGCTGCCGCTCGGCCCTAAATAGGTAACGCGCGCGCCCTGGTCAAATGCGGCAACTTCGAAAGAGCAACg                             >  1:302305/1‑71 (MQ=255)
                                    tcTGCCGCTCGGCCCTAAATAGGTAACGCGCGCGCCCTGGGCAAATGCGGCAACTTCGAAAGAGCaac                              <  1:227589/67‑3 (MQ=255)
                                    gCTGCCGCTTGTGCCGAGATAAGTAACGCGAGCACCCTGGTCATATGCGGCAACTTCGAAAGAGCATCggg                           <  1:2123353/71‑1 (MQ=255)
                                    gCTGCCGCTTGGGCCGAGATAAGTAACGCGAGCACCCTGGTCATATGCGGCAACTTCGAAAGAGCATc                              <  1:2610503/68‑1 (MQ=255)
                                    gCTGCCGCTTGGGCCGAGATAAGTAACGCGAGCACCCTGGTCATATGCGGCAACTTCGAAAGAGCATCgg                            <  1:3465091/70‑1 (MQ=255)
                                    gCTGCCGCTTGGGCCGAGATAAGTAACGCGAGCACCCTGGTCATATGCGGCAACTTCGAAAGAGCATCgg                            <  1:4551957/70‑1 (MQ=255)
                                    gCTGCCGCTCGGCCCTAAATAGGTAACGCGCGCGCCCTGGTCAAATGCGGCAACTTCGAAAGAGCAACggg                           >  1:5339171/1‑71 (MQ=255)
                                    gCTGCCGCTCGGCCCTAAATAGGTAACGCGCGCGCCCTGGTCAAATGCGGCAACTTCGAAAGAGCAACggg                           >  1:726144/1‑71 (MQ=255)
                                     cTGCCGCTCGGCCCTAAATAGGTAACGCGCGCGCCCTGGTCAAATGCGGCAACTTCGAAaga                                   >  1:4036508/1‑62 (MQ=255)
                                     cTGCCGCTCGGCCCTAAATAGGTAACGCGCGCGCCCTGGTCAAATGCGGCAACTTCGAAAGAGCAACggg                           >  1:3978607/1‑70 (MQ=255)
                                     cTGCAGCTTGGGCCGAGATAAGTAACGCGAGCACCCTgg                                                          >  1:225472/1‑39 (MQ=255)
                                       gCCGCTCGGCCCTAAATAGGTAACGCGCGCGCCCTGGTCAAATGCGGCAACTTCGAAAGAGCAACGGGTAc                        >  1:4940451/1‑71 (MQ=255)
                                        ccGCTTGGGCCGAGATAAGTAACGCGAGCACCCTGGTCa                                                       <  1:1003907/39‑1 (MQ=255)
                                        ccGCTTGGGCCGAGATAAGTAACGCGAGCACCCTGGTCa                                                       <  1:1307294/39‑1 (MQ=255)
                                           cTTGGGCCGAGATAAGTAACGCGAGCACCCTGGTCATATGCGGCAACTTCGAAAGAGCATCGGGTAcgagt                    >  1:342421/1‑71 (MQ=255)
                                              gggCCGAGATAAGTAACGCGAGCACCCTGGTCATATGCGGCAACTTCGAAAGAGCATCGGGTAcgagtc                   <  1:4282139/69‑1 (MQ=255)
                                              gggCCGAGATAAGTAACGCGAGCACCCTGGTCATATGCGGCAACTTCGAAAGAGCATCGGGTAcgagtc                   <  1:685737/69‑1 (MQ=255)
                                                gCCGAGATAAGTAACGCGAGCACCCTGGTCATATGCGGCAACTTCGa                                       <  1:684815/47‑1 (MQ=255)
                                                  cGAGATAAGTAACTCGAGCACCCTGGTCATATGCGGCAACTTCGAAAGAGCATCGGGTACGAGTCGAGTCt             >  1:1494119/1‑71 (MQ=255)
                                                  cGAGATAAGTAACGCGAGCACCGTGGTCATATGCGGCAACTTCGAAAGAGCATCGGGTACGAGTCGAGTCt             <  1:3426440/71‑1 (MQ=255)
                                                  cGAGATAAGTAACGCGAGCACCCTGGTCATATGCGGCAACTTCGa                                       <  1:5400427/45‑1 (MQ=255)
                                                  cGAGATAAGTAACGCGAGCACCCTGGTCATATGCGGCAACTTCGa                                       <  1:3322810/45‑1 (MQ=255)
                                                    aaaTAGGTAACGCGCGCGCCCTGGTCAAATGCGGCAACTTCGAAAGAGCAACGGGTAc                        <  1:1668361/56‑1 (MQ=255)
                                                    aaaTAGGTAACGCGCGCGCCCTGGTCAAATGCGGCAACTTCGAAAGAGCAACGGGTAc                        <  1:1392408/56‑1 (MQ=255)
                                                    aaaTAGGTAACGCGCGCGCCCTGGTCAAATGCGGCAACTTCGAAAGAGCAACGGGTACGAGTCGAGTCttt           >  1:3576672/3‑71 (MQ=255)
                                                     gaTAAGTAACGCGAGCACCCTGGTCATATGCGGCAACTTCGAAAGAGCATCGGGTAcgagtcga                 >  1:887751/1‑64 (MQ=255)
                                                     aaTAGGTAACGCGCGCGCCCTGGTCAAATGCGGCAACTTCGAAAGAGCAACGGGTACGAGTCGAGTCtttt          >  1:234508/2‑71 (MQ=255)
                                                     aaTAGGTAACGCGCGCGCCCTGGTCAAATGCGGCAACTTCGAAAGAGCAACGGGTACGAGTCGAGTCttt           <  1:3762245/69‑1 (MQ=255)
                                                      aTAAGTAACGCGAGCACCCTGGTCATATGCGGCAACTTCg                                        <  1:676513/40‑1 (MQ=255)
                                                      aTAAGTAACGCGAGCACCCTGGTCATATGCGGCAACTTCGAAAGAGCAt                               >  1:854560/1‑49 (MQ=255)
                                                      aTAAGTAACGCGAGCACCCTGGTCATATGCGGCAACTTCGAAAGAGCATCGGGTACGAGTCGAGTCttt           <  1:2889611/69‑1 (MQ=255)
                                                        aggTAACGCGCGCGCCCTGGTCAAATGCGGCAACTTCGAAAGAGCAACGGGTACGAGTCGAGTCtttt          >  1:2723965/3‑68 (MQ=255)
                                                         ggTAACGCGCGCGCCCTGGTCAAATGCGGCAACTTCGAAAGAGCAACGGGTACGAGTCGAGTCTTTTTCg       <  1:3824287/69‑1 (MQ=255)
                                                         aGTAACGCGAGCACCCTGGTCATATGCGGCAACTTCGAAAGAGCATCGGGTACGAGTCGAGTCTTTTTCg       <  1:5149346/70‑1 (MQ=255)
                                                         aGTAACGCGAGCACCCTGGTCATATGCGGCAACTTCGAAAGAGCATCGGGTACGAGTCGAGTCTTTTTCg       <  1:1388748/70‑1 (MQ=255)
                                                         aGTAACGCGAGCACCATGGTCATATGCGGCAACTTCGAAAGAGCATCGGGTAcgagtc                   <  1:274060/58‑1 (MQ=255)
                                                         aGTAACGCGAGCACCATGGTCATATGCGGCAACTTCGAAAGAGCATCGGGTAcgagtc                   <  1:3956849/58‑1 (MQ=255)
                                                          gTAACGCGAGCACCCTGGTCATATGCGGCAACTTCGAAAGAGCATCGGGTACGAGTCGAGTCtttttag       >  1:3370418/1‑67 (MQ=255)
                                                          gTAACGCGAGCACCCTGGTCATATGCGGCAACTTCGAAAGAGCATCGGGTACGAGTCGAGTCttt           <  1:892911/65‑1 (MQ=255)
                                                          gTAACGCGAGCACCCTGGTCATATGCGGCAACTTCGAAAGAGCATCGGGTACGAGTCGAGTCttt           <  1:1094189/65‑1 (MQ=255)
                                                          gTAACGCGAGCACCCTGGTCATATGCGGCAACTTCGAAAGAGCATCGGGTACGAGTCGAGTCttt           <  1:3269978/65‑1 (MQ=255)
                                                           tAACGCGCGCGCCCTGGTCAAATGCGGCAACTTCGAAAGAGCAACGGGTa                         >  1:4805761/1‑50 (MQ=255)
                                                           tAACGCGCGCGCCCTGGTCAAATGCGGCAACTTCGAAAGAGCAACGGGTa                         >  1:2063531/1‑50 (MQ=255)
                                                           tAACGCGAGCACCGTGGTCATATGCGGCAACTTCGAAAGAGCATCGGGTACGAGTCGAGTCTTTTTc        >  1:3337491/1‑67 (MQ=255)
                                                           tAACGCGAGCACCCTGGTCATATGCGGCAACTTCGa                                       <  1:5377826/36‑1 (MQ=255)
                                                           tAACGCGAGCACCCTGGTCATATGCGGCAACTTCGa                                       <  1:771263/36‑1 (MQ=255)
                                                           tAACGCGAGCACCCTGGTCATATGCGGCAACTTCGAAAGAGCATTGGGTAcgag                     >  1:3486198/1‑54 (MQ=255)
                                                             aCGCGAGCACCCTGGTCATATGCGTCAACTTCGAAAGAGCATCTGGTAc                        >  1:2053851/1‑49 (MQ=39)
                                                             aCGCGAGCACCCTGGTCATATGCGGCAACTTCGAAAGAGCATCGGGTACGAGTCGAGTCTTTTTCGAAGa   >  1:3640181/1‑70 (MQ=255)
                                                             aCGCGAGCACCCTGGTCATATGCGGCAACTTCGAAAGAGCATCGGGTACGAGTCGAGTCTTTTTCGAAGAt  <  1:2959156/71‑1 (MQ=255)
                                                                 gAGCACCCTGGTCATATGCGGCAACTTCGAAAGAGCATCGGGTAcgagtcg                  <  1:3494316/51‑1 (MQ=255)
                                                                 gAGCACCCTGGTCATATGCGGCAACTTCGAAAGAGCATCGGGTACGAGTCGAGTCTTTTTCGaa     >  1:4629004/1‑64 (MQ=255)
                                                                  |                                                                 
GGCAGTGTCTTTAATCGACTCTTTATGACCAATCTGGCTGCCGCTTGGGCCGAGATAAGTAACGCGAGCACCCTGGTCATATGCGGCAACTTCGAAAGAGCATCGGGTACGAGTCGAGTCTTTTTCGAAGAT  >  minE/2919414‑2919545

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