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 2,919,441 A→C 21.5% G85G (GGT→GGG)  argI ← ornithine carbamoyltransferase 1

Read alignment evidence...
  seq id position ref new freq score (cons/poly) reads annotation genes product
*minE2,919,4410AC21.5% 207.5 / 76.7 130G85G (GGT→GGG) argIornithine carbamoyltransferase 1
Reads supporting (aligned to +/- strand):  ref base A (53/49);  new base C (18/10);  total (71/59)
Fisher's exact test for biased strand distribution p-value = 2.88e-01
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 9.35e-01

Only 100 of 134 total aligned reads displayed.

GCGATACTGAATACCGTCATACATGCGACCAAGCACGCGGGCAGTGTCTTTAATCGACTCTTTATGACCAATCTGGCTGCCGCTTGGGCCGAGATAAGTAACGCGAGCACCCTGGTCATATGCGGCAACTTCGA  >  minE/2919375‑2919508
                                                                  |                                                                   
gcgATACTGAATGCCGTCATACATCCGCCCGAGAACCCGCGCGGTGTCCTTAATTGACTCTTTATGCCCaa                                                                 <  1:1430620/71‑1 (MQ=255)
 cgATACTGAATACCGTCATACATGCGACCAAGCACGCGGGCAGTGTCTTTAATCGACTCTTTATGACCAAt                                                                <  1:705228/71‑1 (MQ=255)
    tACTGAATACCGTCATACATGCGACCAAGCACGCGGGCAGTGTCTTTAATCGACTCTTTATGACCAATCt                                                              <  1:548513/70‑1 (MQ=255)
      cTGAATACCGTCATACATGCGACCAAGCACGCGGGCAGTGTCTTTAATCGACTCTTTATGACCAATCTgg                                                            <  1:63655/70‑1 (MQ=255)
      cTGAATACCGTCATACATGCGACCAAGCACGCGGGCAGTGTCTTTAATCGACTCTTTATGACCAATCTgg                                                            <  1:3782015/70‑1 (MQ=255)
      cTGAATACCGTCATACATGCGACCAAGCACGCGGGCAGTGTCTTTAATCGACTCTTTATGACCAATCTGGc                                                           >  1:5073876/1‑71 (MQ=255)
      cTGAATACCGTCATACATGCGACCAAGCACGCGGGCAGTGTCTTTAATCGACTCTTTATGACCAATCTGGc                                                           >  1:5097980/1‑71 (MQ=255)
        gAATACCGTCATACATGCGACCAAGCACGCGGGCAGTGTCTTTAATCGACTCTTTATGACCAATCTGGCTg                                                         >  1:761281/1‑71 (MQ=255)
           tACCGTCATACATGCGACCAAGCACGCGGGCAGTGTCTTTAATCGACTCTTTATGACCAATCt                                                              >  1:3357756/1‑63 (MQ=255)
              cGTCATACATGCGACCAAGCACGCGGGCAGTGTCTTTAATCGACTCTTTATGACCAATCTGGCTGCCGCtt                                                   <  1:1396736/71‑1 (MQ=255)
              cGTCATACATCCGCCCGAGAACCCGCGCGGTGTCCTTAATTGACTCTTTATGCCCAATCTGGCTGCCGCtc                                                   <  1:1665900/71‑2 (MQ=255)
              cGTCATACATCCGCCCGAGAACCCGCGCGGTGTCCTTAATTGACTCTTTATGCCCAATCTGGCTGCCGCtc                                                   >  1:5537000/1‑70 (MQ=255)
               gTCATACATGCGACCAAGCACGCGGGCAGTGTCTTTAATCGACTCTTTATGACCAATCTGGCTGCCGCTTg                                                  >  1:4752809/1‑71 (MQ=255)
               gTCATACATGCGACCAAGCACGCGGGCAGTGTCTTTAATCGACTCTTTATGACCAATCTGGCTGCCGCTTg                                                  <  1:94395/71‑1 (MQ=255)
               gTCATACATGCGACCAAGCACGCGGGCAGTGTCTTTAATCGACTCTTTATGACCAATCTGGCTGCCGCTTg                                                  >  1:1869083/1‑71 (MQ=255)
               gTCATACATGCGACCAAGCACGCGGGCAGTGTCTTTAATCGACTCTTTATGACCAATCTGGCTGCCGCTTg                                                  >  1:5531244/1‑71 (MQ=255)
                tCATACATGCGACCAAGCACGCGGGCAGTGTCTTTAATCGACTCTTTATGACCAATCTg                                                             <  1:632779/59‑1 (MQ=255)
                  aTACATGCGACCAAGCACGCGGGCAGTGTCTTTAATCGACTCTTTATGACCAATCTGGCTGCCGCTTGGGc                                               >  1:3595857/1‑71 (MQ=255)
                  aTACATGCGACCAAGCACGCGGGCAGTGTCTTTAATCGACTCTTTATGACCAATCTGGCTGCCGCTTGGGc                                               >  1:923912/1‑71 (MQ=255)
                  aTACATCCGCCCGAGAACCCGCGCGGTGTCCTTAATTGACTCTTTATGCCCAATCTGGCTGCCGCTCggcc                                               >  1:3962020/1‑69 (MQ=255)
                   tACATCCGCCCGAGAACCCGCGCGGTGTCCTTAATTGACTCTTTATGCCCAATCTGGCTGCCGCTCGGccc                                              >  1:1830407/1‑71 (MQ=255)
                   tACATCCGCCCGAGAACCCGCGCGGTGTCCTTAATTGACTCTTTATGCCCAATCTGGCTGCCGCTCGGccc                                              >  1:3542633/1‑71 (MQ=255)
                    aCATCCGCCCGAGAACCCGCGCGGTGTCCTTAATTGACTCTTTATGCCCAATCTGGCTGCCGCTCGGccc                                              >  1:4988122/1‑70 (MQ=255)
                     cATGCGACCAAGCACGCGGGCAGTGTCTTTAATCGACTCTTTATGACCAATCTGGCTGCCGCTTGGGcc                                              >  1:5194333/1‑69 (MQ=255)
                     cATGCGACCAAGCACGCGGGCAGTGTCTTTAATCGACTCTTTATGACCAATCTGGCTGCCGCTTGGGcc                                              >  1:4151673/1‑69 (MQ=255)
                     cATGCGACCAACCACGCGGGCAGTGTCTTTAATCGACTCTTTATGACCAATCTGGCTGCCGCTTGGGCCga                                            <  1:2594551/71‑1 (MQ=255)
                      aTGCGACCAAGCACGCGGGCAGTGTCTTTAATCGACTCTTTATGACCAATCTg                                                             >  1:4953611/1‑53 (MQ=255)
                      aTGCGACCAAGCACGCGGGCAGTGTCTTTAATCGACTCTTTATGACCAATCTGGCTGCCGCTTGGGcc                                              >  1:4380865/1‑68 (MQ=255)
                       tGCGACCAAGCACGCGGGCAGTGTCTTTAATCGACTCTTTATGACCaa                                                                 <  1:3244587/48‑1 (MQ=255)
                       tGCGACCAAGCACGCGGGCAGTGTCTTTAATCGACTCTTTATGACCAATCTGGCTGCCGCTTGGGcc                                              >  1:3635020/1‑67 (MQ=255)
                       tGCGACCAAGCACGCGGGCAGTGTCTTTAATCGACTCTTTATGACCAATCTGGCTGCCGCTTGGGcc                                              >  1:3080077/1‑67 (MQ=255)
                        gCGACCAAGCACGCGGGCAGTGTCTTTAATCGACTCTTTATGACCAATCTgg                                                            >  1:1002154/1‑52 (MQ=255)
                        gCGACCAAGCACGCGGGCAGTGTCTTTAATCGACTCTTTATGACCAATCTGGCTGCCGCt                                                    >  1:2186677/1‑60 (MQ=255)
                        gCGACCAAGCACGCGGGCAGTGTCTTTAATCGACTCTTTATGACCAATCTGGCTGCCGCTTGGGCCgaga                                          >  1:4028116/1‑70 (MQ=255)
                            ccAAGCACGCGGGCAGTGTCTTTAATCGACTCTTTATGACCAATCTGGCTGCCGCTTGGGCCGAGATAAGt                                     <  1:22761/71‑1 (MQ=255)
                             cAAGCACGCGGGCAGTGTCTTTAATCGACTCTTTATGACCAATCTGGCTGCCGCTTGGGCCGAGATAAGt                                     <  1:867675/70‑1 (MQ=255)
                             cAAGCACGCGGGCAGTGTCTTTAATCGACTCTTTATGACCAATCTGGCTGCCGCTTGGGCCGAGATAAGTa                                    <  1:4491596/71‑1 (MQ=255)
                             cAAGCACGCGGGCAGTGTCTTTAATCGACTCTTTATGACCAATCTGGCTGCCGCTTGGGCCGAGATAAGTa                                    <  1:3437969/71‑1 (MQ=255)
                              aaGCACGCGGGCAGTGTCTTTAATCGACTCTTTATGACCAATCTGGCTGCCGCTTGGGCCGAGATAAGTaa                                   >  1:3226887/1‑71 (MQ=255)
                               aGCACGCGGGCAGTGTCTTTAATCGACTCTTTATGACCAATCTGGCTGCCGCtt                                                   <  1:2231518/54‑1 (MQ=255)
                                gCACGCGGGCAGTGTCTTTAATCGACTCTTTATGACCAATCTGGCTGCCGCTTGGGCCGAGATaa                                       >  1:5623959/1‑65 (MQ=255)
                                 cACGCGGGCAGTGTCTTTAATCGACTCTTTATGACCAATCTgg                                                            >  1:1145620/1‑43 (MQ=255)
                                 cACGCGGGCAGTGTCTTTAATCGACTCTTTATGACCAATCTgg                                                            >  1:4376206/1‑43 (MQ=255)
                                 cACGCGGGCAGTGTCTTTAATCGACTCTTTATGACCAATCTgg                                                            >  1:4564316/1‑43 (MQ=255)
                                 cACGCGGGCAGTGTCTTTAATCGACTCTTTATGACCAATCTgg                                                            >  1:2877340/1‑43 (MQ=255)
                                 cACGCGGGCAGTGTCTTTAATCGACTCTTTATGACCAATCTGGCTGCCGCTTGGGCCGAGATAAGTAAcgc                                >  1:3650320/1‑71 (MQ=255)
                                  aCGCGGGCAGTGTCTTTAATCGACTCTTTATGACCAATCTGGCTGCCGCTTGGGCCGAGATAAGTAAcgc                                <  1:5614383/70‑1 (MQ=255)
                                          aGTGTCTTTAATCGACTCTTTATGACCAATCTGGCTGCCGCTTGGGCCGAGATAAGTAACGCGAGCACCCt                       <  1:4949510/71‑1 (MQ=255)
                                           gtgtCTTTAATCGACTCTTTATGACCAATCTGGCTGCCGCTTGGGCCGAGATAAGTAACGCGAGCACCCTg                      >  1:3233839/1‑71 (MQ=255)
                                           gtgtCCTTAATTGACTCTTTATGCCCAATCTGGCTGCCGCTCGGCCCTAAATAGGTAACGCGCGCGCCCTg                      >  1:2540900/1‑71 (MQ=255)
                                             gtCTTTAATCGACTCTTTATGACCAATCTGGCTGCCGc                                                     <  1:3099466/38‑1 (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)
                                                tttAATCGACTCTTTATGACCAATCTGGCTGCCGCTTGGGCCGAGATAAGTAAcgcg                               <  1:1259835/57‑1 (MQ=255)
                                                tttAATCGACTCTTTATGACCAATCTGGCTGCCGCTTGGGCCGAGATAAGTAAc                                  >  1:3718214/1‑54 (MQ=255)
                                                tttAATCGACTCTTTATGACCAATCTGGCTGCCGCTTGGGCCGAGATAAGTAACGCGa                              >  1:523689/1‑58 (MQ=255)
                                                tttAATCGACTCTTTATGACCAATCTGGCTGCCGCTTGGGCCGAGATAAGTAACGCGAGCACCCTGGTCa                  >  1:5383000/1‑70 (MQ=255)
                                                cttAATTGACTCTTTATGCCCAATCTGGCTGCCGc                                                     <  1:5382499/34‑1 (MQ=25)
                                                cttAATTGACTCTTTATGCCCAATCTGGCTGCCGc                                                     <  1:1397946/34‑1 (MQ=25)
                                                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)
                                                  tAATCGACTCTTTATGACCAATCTGGCTGCCGCTTGGGCCGAGATAAGTAACGCGAGCACCCTGGTCatat               >  1:4699447/1‑71 (MQ=255)
                                                  tAATCGACTCTTTATGACCAATCTGGCTGCCGCTTGGGCCGAGATAAGTAACGCGAGCACCCTGGTCa                  <  1:4431115/68‑1 (MQ=255)
                                                  tAATCGACTCTTTATGACCAATCTGGCTGCCGCTTGGGCCGAGATAAGTAACGCGAGCACCCTGGTCa                  <  1:3904649/68‑1 (MQ=255)
                                                   aaTCGACTCTTTATGACCAATCTGGCTGCCGCTTGGGCCGAGATAAGTAACGCGa                              >  1:1250657/1‑55 (MQ=255)
                                                     ttgACTCTTTATGCCCAATCTGGCTGCCGCTCGGCCCTAAATAGGTAACGCGCGCGCCCTGGTCAAATGCg            >  1:4575185/3‑71 (MQ=255)
                                                     ttgACTCTTTATGCCCAATCTGGCTGCCGCTCGGCCCTAAATAGGTAACGCGCGCGCCCTGGTCAAATGCg            >  1:1819107/3‑71 (MQ=255)
                                                     tCGACTCTTTATGACCAATCTGGCTGCCGCTTGGGCCGAGATAAGTAACGCGAGCACCCTGGTCa                  <  1:2831777/65‑1 (MQ=255)
                                                       gACTCTTTATGCCCAATCTGGCTTCCGCTCGGCCCTAAATAGGTAACGCGCGCGCCCTGGTCAAATGCgg           >  1:4404883/1‑70 (MQ=255)
                                                       gACTCTTTATGCCCAATCTGGCTGCCGCTCGGCCCTAAATAGGTAACGCGCGCGCCCTGGTCAAATGCg            >  1:717621/1‑69 (MQ=255)
                                                       gACTCTTTATGACCAATCTGGCTGCCGCTTGGGCCGAGATAAGTAACGGGAGCACCCTGGTCATATGCGGc          <  1:1807272/71‑1 (MQ=255)
                                                       gACTCTTTATGACCAATCTGGCTGCCGCTTGGGCCGAGATAAGTAACGCGAGCACCCTGGTCATATGCgg           >  1:3092168/1‑70 (MQ=255)
                                                       gACTCTTTATGACCAATCTGGCTGCCGCTTGGGCCGAGATAAGTAACGCGAGCACCCTGGTCATATGCgg           >  1:2110440/1‑70 (MQ=255)
                                                       gACTCTTTATGACCAATCTGGCTGCCGCTTGGGCCGAGATAAGTAACGCGAGCACCCTGGTCATATGCGGc          <  1:2767777/71‑1 (MQ=255)
                                                       gACTCTTTATGACCAATCTGGCTGCCGCTTGGGCCGAGATAAGTAACGCGAGCACCCTGGTCATATGCGGc          <  1:218339/71‑1 (MQ=255)
                                                        aCTCTTTATGACCAATCTGGCTGCCGCTTGGGCCGAGATAAGTAACGCGAGCAccc                        <  1:136070/56‑1 (MQ=255)
                                                        aCTCTTTATGACCAATCTGGCTGCCGCTTGGGCCGAGATAAGTAACGCGAGCAccc                        <  1:2929451/56‑1 (MQ=255)
                                                        aCTCTTTATGACCAATCTGGCTGCCGCTTGGGCCGAGATAAGTAACGCGAGCAccc                        <  1:3902671/56‑1 (MQ=255)
                                                        aCTCTTTATGACCAATCTGGCTGCCGCTTGGGCCGAGATAAGTAACGCGAGCACCCTGGTCATATGCGGCa         <  1:3390358/71‑1 (MQ=255)
                                                         ctctTTATGCCCAATCTGGCTGCCGCTCGGCCCTAAATAGGTAAcgcg                               <  1:631830/48‑1 (MQ=19)
                                                          tctTTATGACCAATCTGGCTGCCGCTTGGGCCgag                                           <  1:941693/35‑1 (MQ=255)
                                                          tctTTATGACCAATCTGGCTGCCGCTTGGGCCGAGATAAGTAACGCGAGCACCCTGGTCa                  <  1:2669303/60‑1 (MQ=255)
                                                           ctTTATGACCAATCTGGCTGCCGCTTGGGCCGAGATAAGTAACGCGa                              >  1:45659/1‑47 (MQ=255)
                                                            tttATGACCAATCTGGCTGCCGCTTGGGCCGAGATAAGTAACGCGAg                             >  1:867150/1‑47 (MQ=255)
                                                            tttATGACCAATCTGGCTGCCGCTTGGGCCGAGATAAGTAACGCGAGCACCCTGGTCATATGCGGCAACt      >  1:1653631/1‑70 (MQ=255)
                                                             ttATGACCAATCTGGCTGCCGCTTGGGCCGAGATAAGTAACGCGAGCAcc                         >  1:3580523/1‑50 (MQ=255)
                                                             ttATGACCAATCTGGCTGCCGCTTGGGCCGAGATAAGTAACGCGAGCACCCTGGTCATATGCGGCAACTTc    >  1:153013/1‑71 (MQ=255)
                                                             ttATGACCAATCTGGCTGCCGCTTGGGCCGAGATAAGTAACGCGAGCACCCTGGTCATATGCGGCAACTTc    >  1:2903921/1‑71 (MQ=255)
                                                              tATGACCAATCTGGCTGCCGCTTGGGCCGAGATAAGTaa                                   >  1:2803130/1‑39 (MQ=255)
                                                              tATGACCAATCTGGCTGCCGCTTGGGCCGAGATAAGTAACGCGAGCACCCTGGTCATATGCGGCaa        >  1:5332485/1‑66 (MQ=255)
                                                                tGACCAATCTGGCTGCCGCTTGGGCCGAGATAAGTAACGCGAGCACCCTGGTCATATGCGGCAACTTCGa  <  1:513397/70‑1 (MQ=255)
                                                                 gACCAATCTGGCTGCCGCTTGGGCCGAGATAAGTAACGCGAGCACCCTGGTCATATGCGGCAACTTCGa  <  1:207597/69‑1 (MQ=255)
                                                                 gACCAATCTGGCTGCCGCTTGGGCCGAGATAAGTAACGCGAGCACCCTGGTCATATGCGGCAACTTCGa  <  1:3811750/69‑1 (MQ=255)
                                                                  aCCAATCTGGCTGCCGCTTGGGCCGAGATAAGTAACGCGAGCACCCTGGTCATATGCGGCAACTTc    <  1:2384455/66‑1 (MQ=255)
                                                                  aCCAATCTGGCTGCCGCTTGGGCCGAGATAAGTAACGCGAGCACCCTGGTCATATGCGGCAACTTc    <  1:4730925/66‑1 (MQ=255)
                                                                  |                                                                   
GCGATACTGAATACCGTCATACATGCGACCAAGCACGCGGGCAGTGTCTTTAATCGACTCTTTATGACCAATCTGGCTGCCGCTTGGGCCGAGATAAGTAACGCGAGCACCCTGGTCATATGCGGCAACTTCGA  >  minE/2919375‑2919508

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