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 2,919,462 G→C 22.6% G78G (GGC→GGG)  argI ← ornithine carbamoyltransferase 1

Read alignment evidence...
  seq id position ref new freq score (cons/poly) reads annotation genes product
*minE2,919,4620GC22.6% 242.0 / 70.0 128G78G (GGC→GGG) argIornithine carbamoyltransferase 1
Reads supporting (aligned to +/- strand):  ref base G (52/47);  new base C (24/5);  total (76/52)
Fisher's exact test for biased strand distribution p-value = 4.67e-03
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 9.98e-01

Only 100 of 140 total aligned reads displayed.

ATACATGCGACCAAGCACGCGGGCAGTGTCTTTAATCGACTCTTTATGACCAATCTGGCTGCCGCTTGGGCCGAGATAAGTAACGCGAGCACCCTGGTCATATGCGGCAACTTCGAAAGAGCATCGGGTACGAGTCG  >  minE/2919393‑2919529
                                                                     |                                                                   
aTACATGCGACCAAGCACGCGGGCAGTGTCTTTAATCGACTCTTTATGACCAATCTGGCTGCCGCTTGGGc                                                                    >  1:923912/1‑71 (MQ=255)
aTACATGCGACCAAGCACGCGGGCAGTGTCTTTAATCGACTCTTTATGACCAATCTGGCTGCCGCTTGGGc                                                                    >  1:3595857/1‑71 (MQ=255)
 tACATCCGCCCGAGAACCCGCGCGGTGTCCTTAATTGACTCTTTATGCCCAATCTGGCTGCCGCTCGGccc                                                                   >  1:3542633/1‑71 (MQ=255)
  aCATGCGACCAAGCACGCGGGCAGTGTCTTTAATCGACTCTTTATGACCAATCTGGCTGCCGCTTGGGcc                                                                   >  1:4259163/1‑70 (MQ=255)
  aCATCCGCCCGAGAACCCGCGCGGTGTCCTTAATTGACTCTTTATGCCCAATCTGGCTGCCGCTCGGccc                                                                   >  1:4988122/1‑70 (MQ=255)
   cATGCGACCAAGCACGCGGGCAGTGTCTTTAATCGACTCTTTATGACCAATCTGGCTGCCGCTTGGGcc                                                                   >  1:5194333/1‑69 (MQ=255)
   cATCCGCCCGAGAACCCGCGCGGTGTCCTTAATTGACTCTTTATGCCCAATCTGGCTGCCGCTCGGcccta                                                                 <  1:2485555/71‑3 (MQ=255)
     tGCGACCAAGCACGCGGGCAGTGTCTTTAATCGACTCTTTATGACCAATCTGGCTGCCGCTTGGGcc                                                                   >  1:3635020/1‑67 (MQ=255)
      gCGACCAAGCACGCGGGCAGTGTCTTTAATCGACTCTTTATGACCAATCTGGCTGCCGCTTGGGCCgaga                                                               >  1:4028116/1‑70 (MQ=255)
          ccAAGCACGCGGGCAGTGTCTTTAATCGACTCTTTATGACCAATCTGGCTGCCGCTTGGGCCGAGATAAGt                                                          <  1:22761/71‑1 (MQ=255)
           cAAGCACGCGGGCAGTGTCTTTAATCGACTCTTTATGACCAATCTGGCTGCCGCTTGGGCCGAGATAAGTa                                                         <  1:3437969/71‑1 (MQ=255)
           cAAGCACGCGGGCAGTGTCTTTAATCGACTCTTTATGACCAATCTGGCTGCCGCTTGGGCCGAGATAAGTa                                                         <  1:4491596/71‑1 (MQ=255)
             aGCACGCGGGCAGTGTCTTTAATCGACTCTTTATGACCAATCTGGCTGCCGCTTGGGCCGAGATAAGTaa                                                        <  1:4695923/70‑1 (MQ=255)
              gCACGCGGGCAGTGTCTTTAATCGACTCTTTATGACCAATCTGGCTGCCGCTTGGGCCGAGATaa                                                            >  1:5623959/1‑65 (MQ=255)
               cACGCGGGCAGTGTCTTTAATCGACTCTTTATGACCAATCTGGCTGCCGCTTGGGcc                                                                   <  1:4417167/57‑1 (MQ=255)
               cACGCGGGCAGTGTCTTTAATCGACTCTTTATGACCAATCTGGCTGCCGCTTGGGCCGAGATAAGt                                                          >  1:2871870/1‑66 (MQ=255)
               cACGCGGGCAGTGTCTTTAATCGACTCTTTATGACCAATCTGGCTGCCGCTTGGGCCGAGATAAGTAAcgc                                                     <  1:4518990/71‑1 (MQ=255)
               cACGCGGGCAGTGTCTTTAATCGACTCTTTATGACCAATCTGGCTGCCGCTTGGGCCGAGATAAGTAAcgc                                                     <  1:1254243/71‑1 (MQ=255)
                        aGTGTCTTTAATCGACTCTTTATGACCAATCTGGCTGCCGCTTGGGCCGAGATAAGTAACGCGAGCACCCt                                            <  1:4949510/71‑1 (MQ=255)
                         gtgtCTTTAATCGACTCTTTATGACCAATCTGGCTGCCGCTTGGGCCGAGATAAGTAACGCGAGCACCCTg                                           >  1:3233839/1‑71 (MQ=255)
                         gtgtCCTTAATTGACTCTTTATGCCCAATCTGGCTGCCGCTCGGCCCTAAATAGGTAACGCGCGCGCCCTg                                           >  1:2540900/1‑71 (MQ=255)
                            tccttAATTGACTCTTTATGCCCAATCTGGCTGCCGCTCGGCCATAAATAGGTACCGCGCGCGCCCTGGt                                         >  1:5591149/4‑70 (MQ=255)
                            tCTTTAATCGACTCTTTATGACCAATCTGGCTGCCGCTTGGGCCGAGATa                                                             >  1:450414/1‑50 (MQ=255)
                            tCTTTAATCGACTCTTTATGACCAATCTGGCTGCCGCTTGGGCCGAGATAAGTAACGCGAGCa                                                <  1:4228580/63‑1 (MQ=255)
                              tttAATCGACTCTTTATGACCAATCTGGCTGCCGCTTGGGCCGAGATa                                                             >  1:40336/1‑48 (MQ=255)
                              tttAATCGACTCTTTATGACCAATCTGGCTGCCGCTTGGGCCGAGATAAGTatc                                                       >  1:4138938/1‑52 (MQ=255)
                              tttAATCGACTCTTTATGACCAATCTGGCTGCCGCTTGGGCCGAGATAAGTAAc                                                       >  1:3718214/1‑54 (MQ=255)
                              tttAATCGACTCTTTATGACCAATCTGGCTGCCGCTTGGGCCGAGATAAGTAACGCGa                                                   >  1:523689/1‑58 (MQ=255)
                              tttAATCGACTCTTTATGACCAATCTGGCTGCCGCTTGGGCCGAGATAAGTAACGCGAGCACCCTGGTCa                                       >  1:5383000/1‑70 (MQ=255)
                              cttAATTGACTCTTTATGCCCAATCTGGCTGCCGCTCGGCCCTAAATAGGTAACGCGCGCGCCCTGGTCa                                       >  1:228556/2‑70 (MQ=255)
                                tAATTGACTCTTTATGCCCAATCTGGCTGCCGCTCGGcccta                                                                 <  1:3834253/42‑3 (MQ=21)
                                tAATTGACTCTTTATGCCCAATCTGGCTGCCGCTCGGCCCTAAATAGGTAACGCGCGCGCCCTGGTCaaat                                    >  1:1306106/1‑71 (MQ=255)
                                tAATTGACTCTTTATGCCCAATCTGGCTGCCGCTCGGCCCTAAATAGGTAACGCGCGCGCCCTGGTCaaat                                    >  1:5364924/1‑71 (MQ=255)
                                tAATCGACTCTTTATGACCAATCTGGCTGCCGCTTGGGCCGAGATAAGTAAcgc                                                     <  1:2132330/54‑1 (MQ=255)
                                tAATCGACTCTTTATGACCAATCTGGCTGCCGCTTGGGCCGAGATAAGTAACGCGAGCACCCTGGTCatat                                    >  1:4699447/1‑71 (MQ=255)
                                tAATCGACTCTTTATGACCAATCTGGCTGCCGCTTGGGCCGAGATAAGTAACGCGAGCACCCTGGTCa                                       <  1:3904649/68‑1 (MQ=255)
                                 aaTCGACTCTTTATGACCAATCTGGCTGCCGCTTGGGCCGAGATAAGTAACGCGa                                                   >  1:1250657/1‑55 (MQ=255)
                                   ttgACTCTTTATGCCCAATCTGGCTGCCGCTCGGCCCTAAATAGGTAACGCGCGCGCCCTGGTCAAATGCg                                 >  1:1819107/3‑71 (MQ=255)
                                   ttgACTCTTTATGCCCAATCTGGCTGCCGCTCGGCCCTAAATAGGTAACGCGCGCGCCCTGGTCAAATGCg                                 >  1:4575185/3‑71 (MQ=255)
                                   tCGACTCTTTATGACCAATCTGGCTGCCGCTTGGGCCGAGATAAGTAACGCGAGCACCCTGGTCa                                       <  1:2831777/65‑1 (MQ=255)
                                     gACTCTTTATGCCCAATCTGGCTTCCGCTCGGCCCTAAATAGGTAACGCGCGCGCCCTGGTCAAATGCgg                                >  1:4404883/1‑70 (MQ=255)
                                     gACTCTTTATGCCCAATCTGGCTGCCGCTCGGCCCTAAATAGGTAACGCGCGCGccc                                             >  1:4104350/1‑57 (MQ=255)
                                     gACTCTTTATGACCAATCTGGCTGCCGCTTGGGCCGAGATAAGTAACGGGAGCACCCTGGTCATATGCGGc                               <  1:1807272/71‑1 (MQ=255)
                                     gACTCTTTATGACCAATCTGGCTGCCGCTTGGGCCGAGATAAGTAACGCGAGCACCCTGGTCATATGCgg                                >  1:3092168/1‑70 (MQ=255)
                                     gACTCTTTATGACCAATCTGGCTGCCGCTTGGGCCGAGATAAGTAACGCGAGCACCCTGGTCATATGCgg                                >  1:2110440/1‑70 (MQ=255)
                                     gACTCTTTATGACCAATCTGGCTGCCGCTTGGGCCGAGATAAGTAACGCGAGCACCCTGGTCATATGCGGc                               <  1:218339/71‑1 (MQ=255)
                                      aCTCTTTATGACCAATCTGGCTGCCGCTTGGGCCGAGATAAGTAACGCGAGCAccc                                             <  1:136070/56‑1 (MQ=255)
                                       ctctTTATGCCCAATCTGGCTGCCGCTCGGCCCTAAATAGGTAAcgcg                                                    <  1:631830/48‑1 (MQ=19)
                                        tctTTATGACCAATCTGGCTGCCGCTTGGGCCgag                                                                <  1:941693/35‑1 (MQ=255)
                                        tctTTATGACCAATCTGGCTGCCGCTTGGGCCGAGATAAg                                                           <  1:3961688/40‑1 (MQ=255)
                                        tctTTATGACCAATCTGGCTGCCGCTTGGGCCGAGATAAGTAACGCGAGCACCCTGGTCa                                       <  1:2669303/60‑1 (MQ=255)
                                         ctTTATGACCAATCTGGCTGCCGCTTGGGCCGAGATAAGTAACGCGa                                                   >  1:45659/1‑47 (MQ=255)
                                          tttATGACCAATCTGGCTGCCGCTTGGGCCGAGATAAGTAACGCGAg                                                  >  1:867150/1‑47 (MQ=255)
                                          tttATGACCAATCTGGCTGCCGCTTGGGCCGAGATAAGTAACGCGAGCACCCTGGTCata                                     >  1:2714018/1‑60 (MQ=255)
                                          tttATGACCAATCTGGCTGCCGCTTGGGCCGAGATAAGTAACGCGAGCACCCTGGTCATATGCGGc                               <  1:3622142/66‑1 (MQ=255)
                                          tttATGACCAATCTGGCTGCCGCTTGGGCCGAGATAAGTAACGCGAGCACCCTGGTCATATGCGGCAACt                           >  1:1653631/1‑70 (MQ=255)
                                           ttATGACCAATCTGGCTGCCGCTTGGGCCGAGATAAGTAACGCGAGCACCCTGGTCATATGCGGCAACTTc                         >  1:2903921/1‑71 (MQ=255)
                                            tATGCCCAATCTGGCTGCCGCTCGGCCCTAAATAGGTAACGCGCGCGCCCTGGTCAAATGCGGCAACTTc                         >  1:3443826/1‑70 (MQ=255)
                                            tATGACCAATCTGGCTGCCGCTTGGGCCGAGATAAGt                                                          >  1:576103/1‑37 (MQ=255)
                                            tATGACCAATCTGGCTGCCGCTTGGGCCGAGATAAGTaa                                                        >  1:2803130/1‑39 (MQ=255)
                                            tATGACCAATCTGGCTGCCGCTTGGGCCGAGATAAGTAACGCGAGCACCCt                                            >  1:145437/1‑51 (MQ=255)
                                            tATGACCAATCTGGCTGCCGCTTGGGCCGAGATAAGTAACGCGAGCACCCTGGTCATATGCGGCaa                             >  1:5332485/1‑66 (MQ=255)
                                            tATGACCAATCTGGCTGCCGCTTGGGCCGAGATAAGTAACGCGAGCACCCTGGTCATATGCGGCAACTTc                         >  1:3174424/1‑70 (MQ=255)
                                            tATGACCAATCTGGCTGCCGCTTGGGCCGAGATAAGTAACGCGAGCACCCTGGTCATATGCGGCAACTTc                         <  1:694644/70‑1 (MQ=255)
                                              tgcccAATCTGGCTGCCGCTCGGCCCTAAATAGGTAACGCGCGCGCCCTGGTCAAATGCGGCAACTTCGa                       <  1:3845007/67‑1 (MQ=255)
                                              tGACCAATCTGGCTGCCGCTTGGGCCGAGATAAGTAACGCGAGCACCCTGGTCATATGCGGCAACTTCGa                       <  1:3818374/70‑1 (MQ=255)
                                              tGACCAATCTGGCTGCCGCTTGGGCCGAGATAAGTAACGCGAGCACCCTGGTCATATGCGGCAACTTCGa                       <  1:2969478/70‑1 (MQ=255)
                                              tGACCAATCTGGCTGCCGCTTGGGCCGAGATAAGTAACGCGAGCACCCTGGTCATATGCGGCAACTTCGa                       <  1:513397/70‑1 (MQ=255)
                                               gACCAATCTGGCTGCCGCTTGGGCCGAGATAAGTAACGCGAGCACCCTGGTCATATGCGGCAACTTCGa                       <  1:207597/69‑1 (MQ=255)
                                                aCCAATCTGGCTGCCGCTTGGGCCGAGATAAGTAACGCGAGCACCCTGGTCATATGCGGCAACTTc                         <  1:4730925/66‑1 (MQ=255)
                                                aCCAATCTGGCTGCCGCTTGGGCCGAGATAAGTAACGCGACCACCCTGGTCATATGCGGCAACTTCGa                       >  1:3750491/1‑68 (MQ=255)
                                                  cAATCTGGCTGCCGCTCGGCCCTAAATAGGTAACGCGCGCGCCCTGGTCAAATGCggaa                              >  1:4806502/1‑57 (MQ=255)
                                                  cAATCTGGCTGCCGCTCGGCCCTAAATAGGTAACGCGCGCGCCCTGGTCAAATGCGGCaa                             >  1:2786265/1‑60 (MQ=255)
                                                   aaTCTGGCTGCCGCTCGGCCCTAAATAGGTAACGCGCGCGCCCTGGTCAAATGCGGCAACTTCGAAagag                  >  1:4736921/1‑70 (MQ=255)
                                                    aTCTGGCTGCCGCTTGGGCCGAGATAAGTAACGCGAGCa                                                >  1:5562645/1‑39 (MQ=255)
                                                    aTCTGGCTGCCGCTTGGGCCGAGATAAGTAACGCGAGCACCCTGGTCATATGCGGCAACTTCGAAAGAGCa                >  1:3479276/1‑71 (MQ=255)
                                                     tCTGGCTGCCGCTTGGGCCGAGATAAGTAACGCGAGCACCCTGGTCATATGCGGCAACTTCGaaa                     <  1:5384988/65‑1 (MQ=255)
                                                      cTGGCTGCCGCTTGGGCCGAGATAAGTAACGCGAGCACCCTGGTCATATGCg                                 >  1:1385077/1‑52 (MQ=255)
                                                      cTGGCTGCCGCTCGGCCCTAAATAGGTAACGCGCGCGCCCTGGTCAAATGCGGCAACTTCGaaa                     >  1:495666/1‑64 (MQ=255)
                                                      cTGGCTGCCGCTCGGCCCTAAATAGGTAACGCGCGCGCCCTGGTCAAATGCGGCAACTTCGAAAGAGCaac              >  1:5124203/1‑69 (MQ=255)
                                                       tGGCTGCCGCTCGGCCCTAAATAGGTAACGCGCGCGCCCTGGTCAAATGCGGCaa                             >  1:1343995/1‑55 (MQ=255)
                                                       tGGCTGCCGCTCGGCCCTAAATAGGTAACGCGCGCGCCCTGGTCAAATGCGGCAACTTCGAAAGAGCAACg             >  1:302305/1‑71 (MQ=255)
                                                         tcTGCCGCTCGGCCCTAAATAGGTAACGCGCGCGCCCTGGGCAAATGCGGCAACTTCGAAAGAGCaac              <  1:227589/67‑3 (MQ=255)
                                                         gCTGCCGCTTGGGCCGAGATAAGTAACGCGAGCACCCTGGTCATATGCGGCAACTTCGAAAGAGCATc              <  1:2610503/68‑1 (MQ=255)
                                                         gCTGCCGCTTGGGCCGAGATAAGTAACGCGAGCACCCTGGTCATATGCGGCAACTTCGAAAGAGCATCggg           <  1:1695333/71‑1 (MQ=255)
                                                         gCTGCCGCTCGGCCCTAAATAGGTAACGCGCGCGCCCTGGTCAAATGCGGCAACTTCGAAAGAGCAACggg           >  1:726144/1‑71 (MQ=255)
                                                         gCTGCCGCTCGGCCCTAAATAGGTAACGCGCGCGCCCTGGTCAAATGCGGCAACTTCGAAAGAGCAACggg           >  1:5339171/1‑71 (MQ=255)
                                                          cTGCCGCTCGGCCCTAAATAGGTAACGCGCGCGCCCTGGTCAAATGCGGCAACTTCGAAAGAGCAACggg           >  1:3978607/1‑70 (MQ=255)
                                                            gCCGCTTGGGCCGAGATAAGTAACGCGAGCACCCTGGTCATATGCGGCAACTTCGAAAGAGCATCGGGTa         >  1:3230002/1‑70 (MQ=255)
                                                             ccGCTTGGGCCGAGATAAGTAACGCGAGCACCCTGGTCa                                       <  1:1003907/39‑1 (MQ=255)
                                                              cGCTTGGGCCGAGATAAGTAACGCGAGCACCCTGGTCATATGCGGCAACTTCGAAAGAGCATCGGGTa         >  1:751527/1‑68 (MQ=255)
                                                              cGCTTGGGCCGAGATAAGTAACGCGAGCACCCTGGTCATATGCGGCAACTTCGAAAGAGCATCGGGTa         >  1:1963677/1‑68 (MQ=255)
                                                              cGCTTGGGCCGAGATAAGTAACGCGAGCACCCTGGTCATATGCGGCAACTTCGAAAGAGCATCGGGTAcga      <  1:1587703/71‑1 (MQ=255)
                                                                cTTGGGCCGAGATAAGTAACGCGAGCACCCTGGTCATATGCGGCAACTTCGAAAGAGCATCGGGTAcgagt    >  1:342421/1‑71 (MQ=255)
                                                                cTTGGGCCGAGATAAGTAACGCGAGCACCCTGGTCATATGCGGCAACTTCGAAAGAGCATCGGGTAcgagt    >  1:1326477/1‑71 (MQ=255)
                                                                   gggCCGAGTTAAGTAACGCGAGCACCCTGGTCATATGCCGCAACTTCGAAAGAGCATCGGGTAcgagtcg  <  1:5222055/70‑1 (MQ=255)
                                                                   gggCCGAGATAAGTAACGCGAGCACCCTGGTCATATGCGGCAACTTCGAAAGAGCATCGGGTAcgagtc   <  1:685737/69‑1 (MQ=255)
                                                                   gggCCGAGATAAGTAACGCGAGCACCCTGGTCATATGCGGCAACTTCGAAAGAGCATCGGGTAcgagtc   <  1:4282139/69‑1 (MQ=255)
                                                                    ggCCGAGATAAGTAACGCGAGCACCCTGGTCATATGCGGCAACTTCGAAAGAGCATCGGGTAcgagtc   <  1:3089739/68‑1 (MQ=255)
                                                                     gCCGAGATAAGTAACGCGAGCACCCTGGTCATATGCGGCAACTTCGa                       <  1:1302183/47‑1 (MQ=255)
                                                                     |                                                                   
ATACATGCGACCAAGCACGCGGGCAGTGTCTTTAATCGACTCTTTATGACCAATCTGGCTGCCGCTTGGGCCGAGATAAGTAACGCGAGCACCCTGGTCATATGCGGCAACTTCGAAAGAGCATCGGGTACGAGTCG  >  minE/2919393‑2919529

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