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 834,677 G→C 20.8% L1045L (CTG→CTC)  narG → nitrate reductase 1, alpha subunit

Read alignment evidence...
  seq id position ref new freq score (cons/poly) reads annotation genes product
*minE834,6770GC20.8% 264.7 / 63.8 130L1045L (CTG→CTC) narGnitrate reductase 1, alpha subunit
Reads supporting (aligned to +/- strand):  ref base G (40/63);  new base C (14/13);  total (54/76)
Fisher's exact test for biased strand distribution p-value = 2.74e-01
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 4.54e-01

Only 100 of 135 total aligned reads displayed.

ACAACGCCGGTTACACCAACGTTCACGAGCTGATCCCATGGCGTACGCTCTCTGGTCGTCAGCAACTGTATCAGGATCACCAGTGGATGCGTGATTTCGGTGAAAGCCTGCTGGTTTATCGTCCGCCGATCGACACCC  >  minE/834610‑834747
                                                                   |                                                                      
ataaCGCGGGATACACCAACGTTCATGAGTTAATTCCGTGGCGCACGCTGTCGGGACGCCAGCAGCTCTAt                                                                     >  1:924770/3‑71 (MQ=255)
 cAACGCCGGTTACACCAACGTTCACGAGCTGATCCCATGGCGTACGCTCTCTGGTCGTCAGCAACTGTATc                                                                    <  1:3411846/71‑1 (MQ=255)
  aaCGCGGGATACACCAACGTTCATGAGTTAATTCCGTGGCGCACGCTGTCGGGACGCCAGCAGCTCTAt                                                                     >  1:3529316/1‑69 (MQ=255)
  aaCGCCGGTTACACCAACGTTCACGAGCTGATCCCATGGCGTACGCTCTCTGGTCGTCAGCAACTGTAt                                                                     >  1:3079501/1‑69 (MQ=255)
  aaCGCCGGTTACACCAACGTTCACGAGCTGATCCCATGGCGTACGCTCTCTGGTCGTCAGCAACTGTAt                                                                     >  1:2246712/1‑69 (MQ=255)
  aaCGCCGGTTACACCAACGTTCACGAGCTGATCCCATGGCGTACGCTCTCTGGTCGTCAGCAACTGTATCa                                                                   <  1:615685/71‑1 (MQ=255)
  aaCGCCGGTTACACCAACGTTCACGAGCTGATCCCATGGCGTACGCTCTCTGGTCGTCAGCAACTGTATCa                                                                   <  1:3459054/71‑1 (MQ=255)
  aaCGCCGGTTACACCAACGTTCACGAGCTGATCCCATGGCGTACGCTCTCTGGTCGTCAGCAACTGTATCa                                                                   <  1:5049300/71‑1 (MQ=255)
   aCGCCGGTTACACCAACGTTCACGAGCTGATCCCATGGCGTACGCTCTCTGGTCGTCAGCAACTGTATCa                                                                   <  1:5645872/70‑1 (MQ=255)
     gCCGGTTACACCAACGTTCACGAGCTGATCCCATGGCGTACGCTCTCTGGTCGTCAGCAACTGTATCAGGa                                                                <  1:4554497/71‑1 (MQ=255)
       cGGTTACACCAACGTTCACGAGCTGATCCCATGGCGTACGCTCTCTGGTCGTCAGCAACTGTATCAGGATc                                                              <  1:1855271/71‑1 (MQ=255)
          ttACACCAACGTTCACGAGCTGATCCCATGGCGTACGCTCTCTGGTCGTCAGCAACTGTATCAg                                                                  <  1:2815240/64‑1 (MQ=255)
          ttACACCAACGTTCACGAGCTGATCCCATGGCGTACGCTCTCTGGTCGTCAGCAACTGTATCAGGATCAcc                                                           <  1:3237351/71‑1 (MQ=255)
          ttACACCAACGTTCACGAGCTGATCCCATGGCGTACGCTCTCTGGTCGTCAGCAACTGTATCAGGATCAcc                                                           <  1:1293817/71‑1 (MQ=255)
          atACACCAACGTTCATGAGTTAATTCCGTGGCGCACGCTGTCGGGACGCCAGCAGCTCTATCAGGATCatc                                                           >  1:3748264/2‑69 (MQ=255)
           tACACCAACGTTCATGAGTTAATTCCGTGGCGCACGCTGTCGGGACGCCAGCAGCTCTATCAGGa                                                                <  1:4099391/65‑1 (MQ=255)
           tACACCAACGTTCACGAGCTGATCCCATGGCGTACGCTCTCTGGTCGTCAGCAACTGTATCAGGATCAc                                                            >  1:2056047/1‑69 (MQ=255)
            acacCAACGTTCACGAGCTGATCCCATGGCGTACGCTCTCTGGTCGTCAGCAACTGTATCAGGATCACCAg                                                         >  1:1594438/1‑71 (MQ=255)
            acacCAACGTTCACGAGCTGATCCCATGGCGTACGCTCTCTGGTCGTCAGCAACTGTATCAGGATCACCAg                                                         >  1:3413186/1‑71 (MQ=255)
            acacAAACGTTCACGAGCTGATCCCATGGCGTACGCTCTCTGGTCGTCAGCAACTGTATCAGGATCACCAg                                                         >  1:2207608/1‑71 (MQ=255)
              acCAACGTTCATGAGTTAATTCCGTGGCGCACGCTGTCGGGACGCCAGCAGCTCTATCAg                                                                  <  1:3148503/60‑1 (MQ=255)
              acCAACGTTCATGAGTTAATTCCGTGGCGCACGCTGTCGGGACGCCAGCAGCTCTATCAGGATCATCCGTg                                                       >  1:5194684/1‑71 (MQ=255)
              acCAACGTTCATGAGTTAATTCCGTGGCGCACGCTGTCGGGACGCCAGCAGCTCTATCAGGATCATCCGTg                                                       <  1:1309397/71‑1 (MQ=255)
               ccAACGTTCATGAGTTAATTCCGTGGCGCACGCTGTCGGGACGCCAGCAGCTCTATCAGGATCATCCGTg                                                       <  1:3916310/70‑1 (MQ=255)
                cAACGTTCACGAGCTGATCCCATGGCGTACGCTCTCTGGTCGTCAGCAACTGTATCAGGATCACCAGTgg                                                      >  1:1090091/1‑70 (MQ=255)
                cAACGTTCACGAGCTGATCCCATGGCGTACGCTCTCTGGTCGTCAGCAACTGTATCAGGATCACCAGTgg                                                      >  1:4225396/1‑70 (MQ=255)
                cAACGTTCACGAGCTGATCCCATGGCGTACGCTCTCTGGTCGTCAGCAACTGTATCAGGATCACCAGTGGa                                                     >  1:2432151/1‑71 (MQ=255)
                cAACGTTCACGAGCTGATCCCATGGCGTACGCTCTCTGGTCGTCAGCAACTGTATCAGGATCACCAGTGGa                                                     >  1:1345052/1‑71 (MQ=255)
                  aCGTTCATGAGTTAATTCCGTGGCGCACGCTGTCGGGACGCCAGCAGCTCTATCAGGATCATCCGTg                                                       >  1:4478099/1‑67 (MQ=255)
                  aCGTTCACGAGCTGATCCCATGGCGTACGCTCTCTGGTCGTCAGTAACTGTATCAGGATCACCAg                                                         <  1:325491/65‑1 (MQ=255)
                  aCGTTCACGAGCTGATCCCATGGCGTACGCTCTCTGGTCGTCAGTAACTGTATCAGGATCACCAg                                                         <  1:872409/65‑1 (MQ=255)
                  aCGTTCACGAGCTGATCCCATGGCGTACGCTCTCTGGTCGTCAGCAACTGTATCAGGATCACCAGTGGAt                                                    >  1:3082494/1‑70 (MQ=255)
                     ttCATGAGTTAATTCCGTGGCGCACGCTGTCGGGACGCCAGCAGCTCTATCAGGATCATCCGTGGATGCGt                                                >  1:1960647/1‑71 (MQ=255)
                     ttCACGAGCTGATCCCATGGCGTACGCTCTCTGGTCGTCAGCAACTGTATCa                                                                   <  1:2628966/52‑1 (MQ=255)
                     ttCACGAGCTGATCCCATGGCGTACGCTCTCTGGTCGTCAGCAACTGTATCa                                                                   <  1:4081904/52‑1 (MQ=255)
                     ttCACGAGCTGATCCCATGGCGTACGCTCTCTGGTCGTCAGCAACTGTATCAGGAt                                                               <  1:1430241/56‑1 (MQ=255)
                     ttCACGAGCTGATCCCATGGCGTACGCTCTCTGGTCGTCAGCAACTGTATCAGGATCACCAGTg                                                       <  1:1613692/64‑1 (MQ=255)
                          gAGCTGATCCCATGGCGTACGCTCTCTGGTCGTCAGCAACTGTATCAGGATCACCAGTGGATGCGTGAttt                                           <  1:4714232/71‑1 (MQ=255)
                            gCTGATCCCATGGCGTACGCTCTCTGGTCGTCAGCAACTGTATCAGGATCACCAGTGGATGCGTGATTTCg                                         >  1:3534533/1‑71 (MQ=255)
                             cTGATCCCATGGCGTACGCTCTCTGGTCGTCAGCAACTGTATCAGGa                                                                <  1:2412288/47‑1 (MQ=255)
                             cTGATCCCATGGCGTACGCTCTCTGGTCGTCAGCAACTGTATCAGGa                                                                <  1:4053997/47‑1 (MQ=255)
                             cTGATCCCATGGCGTACGCTCTCTGGTCGTCAGCAACTGTATCAGGa                                                                <  1:1846671/47‑1 (MQ=255)
                             cTGATCCCATGGCGTACGCTCTCTGGTCGTCAGCAACTGAATCAGGATCACCAGTGGATGCGTGATTTCgg                                        <  1:5682121/71‑1 (MQ=255)
                              tGATCCCATGGCGTACGCTCTCTGGTCGTCAGCAACTg                                                                        <  1:4889442/38‑1 (MQ=255)
                              tGATCCCATGGCGTACGCTCTCTGGTCGTCAGCAACTg                                                                        <  1:538502/38‑1 (MQ=255)
                                aTCCCATGGCGTACGCTCTCTGGTCGTCAGCAACTGTATCAGGATc                                                              <  1:4344398/46‑1 (MQ=255)
                                aTCCCATGGCGTACGCTCTCTGGTCGTCAGCAACTGTATCAGGATc                                                              <  1:4389639/46‑1 (MQ=255)
                                aTCCCATGGCGTACGCTCTCTGGTCGTCAGCAACTGTATCAGGATc                                                              <  1:5120110/46‑1 (MQ=255)
                                 tCCCATGGCGTACGCTCTCTGGTCGTCAGCAACTGTATCAGGATc                                                              <  1:943826/45‑1 (MQ=255)
                                  cccATGGCGTACGCTCTCTGGTCGTCAGCAACTGTATCAGGATCAcc                                                           >  1:581817/1‑47 (MQ=255)
                                  cccATGGCGTACGCTCTCTGGTCGTCAGCAACTGTATCAGGATCACCAGTGGATGCGTGATTTCGGTg                                      >  1:5589866/1‑68 (MQ=255)
                                  cccATGGCGTACGCTCTCTGGTCGTCAGCAACTGTATCAGGATCACCAGTGGATGCGTGATTTCGGTGa                                     >  1:1361191/1‑69 (MQ=255)
                                  cccATGGCGTACGCTCTCTGGTCGTCAGCAACTGTATCAGGATCACCAGTGGATGCGTGATTTCGGTGa                                     >  1:3302829/1‑69 (MQ=255)
                                  cccATGGCGTACGCTCTCTGGTCGTCAGCAACTGTATCAGGATCACCAGTGGATGCGTCATTTCGGTGa                                     >  1:4694891/1‑69 (MQ=255)
                                   ccgtGGCGCACGCTGTCGGGACGCCAGCAGCTCTATCAGGATCATCCGTGGATGCGTGCTTTTGGTGaaa                                   <  1:5323375/67‑1 (MQ=255)
                                   ccgtGGCGCACGCTGTCGGGACGCCAGCAGCTCTATCAGGATCATCCGTGGATGCGTGCTTTTGGTGAAAg                                  >  1:214927/4‑71 (MQ=255)
                                   ccATGGCGTACGCTCTCTGGTCGTCAGCAACTGTATCAGGATCACCAGTGGATGCGTGATTTCGGTGaaa                                   <  1:275250/70‑1 (MQ=255)
                                   ccATGGCGTACGCTCTCTGGTCGTCAGCAACTGTATCAGGATCACCAGTGGATGCGTGATTTCGGTGaaa                                   <  1:212152/70‑1 (MQ=255)
                                    cATGGCGTACGCTCTCTGGTCGTCAGCAACTGTATCAg                                                                  <  1:1793873/38‑1 (MQ=255)
                                    cATGGCGTACGCTCTCTGGTCGTCAGCAACTGTATCAGGATCACCAGTGGATGCGTGATTTCGGTGa                                     <  1:4888609/67‑1 (MQ=255)
                                     aTGGCGTACGCTCTCTGGTCGTCAGCAACTGTATc                                                                    <  1:2890176/35‑1 (MQ=255)
                                      tGGCGCACGCTGTCGGGACGCCAGCAGCTCTATCAGGATCATCCGTGGATGCGTGCTTTTGGTGAAAGCct                               <  1:1639736/71‑1 (MQ=255)
                                      tGGCGCACGCTGTCGGGACGCCAGCAGCTCTATCAGGATCATCCGTGGAGGCGTGCTTTTGGTGAAAGCct                               <  1:1222393/71‑1 (MQ=255)
                                        gCGTACGCTCTCTGGTCGTCAGCAACTGTATCAGGATCACCAGTGGATGCGTGATTTCGGTGAAAGCctgc                             <  1:4569211/71‑1 (MQ=255)
                                        gCGTACGCTCTCTGGTCGTCAGCAACTGTATCAGGATCACCAGTGGATGCGTGATTTCGGTGAAAGCctgc                             <  1:3837109/71‑1 (MQ=255)
                                        gCGTACGCTCTCTGGTCGTCAGCAACTGTATCAGGATCACCAGTGGATGCGTGATTTCGGTGAAAGCctgc                             <  1:3485840/71‑1 (MQ=255)
                                         cGTACGCTCTCTGGTCGTCAGCAACTGTATCAGGATCACCAGTGGATGCGTGATTTCGGTGAAAGCctgct                            >  1:802042/1‑71 (MQ=255)
                                         cGTACGCTCTCTGGTCGTCAGCAACTGTATCAGGATCACCAGTGGATGCGTGATTTCGGTGAAAGCctgct                            >  1:3832964/1‑71 (MQ=255)
                                          gTACGCTCTCTGGTCGTCAGCAACTGTATCAGGATCACCa                                                          >  1:4693818/1‑40 (MQ=255)
                                           tACGCTCTCTGGTCGTCAGCAACTGTATCAGGATCAc                                                            <  1:5384262/37‑1 (MQ=255)
                                           tACGCTCTCTGGTCGTCAGCAACTGTATCAGGATCAc                                                            <  1:424938/37‑1 (MQ=255)
                                           tACGCTCTCTGGTCGTCAGCAACTGTATCAGGATCAc                                                            <  1:4558929/37‑1 (MQ=255)
                                           tACGCTCTCTGGTCGTCAGCAACTGTATCAGGATCAc                                                            <  1:181024/37‑1 (MQ=255)
                                             cGCTCTCTGGTCGTCAGCAACTGTATCAGGATCACCAGTGGATGCGTGATTTCGGTGAAAGCCTGCTGGt                         <  1:5029826/70‑1 (MQ=255)
                                              gCTGTCGGGACGCCAGCAGCTCTATCAGGATCATCCGTGGATGCGTGCTTTTGGTGAAAGc                                 >  1:274199/1‑61 (MQ=255)
                                              gCTGTCGGGACGCCAGCAGCTCTATCAGGATCATCCGTGGATGCGTGCTTTTGGTGAAAGc                                 >  1:5330468/1‑61 (MQ=255)
                                              gCTGTCGGGACGCCAGCAGCTCTATCAGGATCATCCGTGGATGCGTGCTTTTGGTGAAAGc                                 >  1:1064415/1‑61 (MQ=255)
                                                     ggTCGTCAGCAACTGTATCAGGATCACCAGTGGATGCGTGATTTCGGTg                                      <  1:5370868/49‑1 (MQ=255)
                                                         gtcAGCAACTGTATCAGGATCACCAGTGGATGCGTGATTTCGGTGAAAGCCTGCTGGTTTATCGTccgccg            <  1:4491433/71‑1 (MQ=255)
                                                         gccagcagCTCTATCAGGATCATCCGTGGATGCGTGCTTTTGGTGAAAGCCTGGTGGctt                       <  1:3311403/58‑1 (MQ=255)
                                                          tcAGCAACTGTATCAGGATCACCAGTGGATGCGTGATTTCGGTGAAAg                                  <  1:2888177/48‑1 (MQ=255)
                                                          tcAGCAACTGTATCAGGATCACCAGTGGATGCGTGATTTCGGTGAAAg                                  <  1:597352/48‑1 (MQ=255)
                                                           cAGCAACTGTATCAGGATCACCAGTGGATGCGTGATTTCTGTGAAAGCCTGCTGGTTTATCGTccgcc             <  1:3695165/68‑1 (MQ=255)
                                                           cAGCAACTGTATCAGGATCACCAGTGGATGCGTGATTTCGGt                                       >  1:3626486/1‑42 (MQ=255)
                                                           cAGCAACTGTATCAGGATCACCAGTGGATGCGTGATTTCGGt                                       >  1:5359591/1‑42 (MQ=255)
                                                            agcagcTCTATCAGGATCATCCGTGGATGCGTGCTTTTGGTGAAAGCCTGGTGGCTTATCGCCCGCCTATc         <  1:2868745/71‑1 (MQ=255)
                                                            agcagcTCTATCAGGATCATCCGTGGATGCGTGCTTTTGGTGAAAGCCTGGTGGCTTATCGCCCGCCTATc         <  1:136506/71‑1 (MQ=255)
                                                            aGCAACTGTATCAGGATCACCAGTGGATGCGTGATTTCGGTGAAAGCCTGCTGGTTTATCGt                  >  1:5052966/1‑62 (MQ=255)
                                                            aGCAACTGTATCAGGATCACCAGTGGATGCGTGATTTCGGTGAAAGCCTGCTGGTTTATCGTCCGCCGa           >  1:1724886/1‑69 (MQ=255)
                                                            aGCAACTGTATCAGGATCACCAGTGGATGCGTGATTTCGGTGAAAGCCTGCTGGTTTATCGTCCGCCGa           >  1:3815079/1‑69 (MQ=255)
                                                            aGCAACTGTATCAGGATCACCAGTGGATGCGTGATTTCGGTGAAAGCCTGCTGGTTTATCGTCCGCCGAt          >  1:2261944/1‑70 (MQ=255)
                                                            aGCAACTGTATCAGGATCACCAGTGGATGCGTGATTTCGGTGAAAGCCTGCTGGTTTATCGTCCGCCGATc         <  1:247980/71‑1 (MQ=255)
                                                            aGCAACTGTATCAGGATCACCAGTGGATGCGTGATTTCGGTGAAAGCCTGCTGGTTTATCGTCCGCCGATc         >  1:2032962/1‑71 (MQ=255)
                                                            aGCAACTGTATCAGGATCACCAGTGGATGCGTGATTTCGGTGAAAGCCTGCTGGTTTATCGTCCGCCGATc         <  1:4205993/71‑1 (MQ=255)
                                                              cAACTGTATCAGGATCACCAGTGGATGCGTGATTTCGGTGAAAGCCTGCTGGttt                       <  1:3942181/55‑1 (MQ=255)
                                                              cAACTGTATCAGGATCACCAGTGGATGCGTGATTTCGGTGAAAGCCTGCTGGTTTATCGTCCGCCGATCg        <  1:837594/70‑1 (MQ=255)
                                                              cAACTGTATCAGGATCACCAGTGGATGCGTGATTTCGGTGAAAGCCTGCTGGTTTATCGTCCGCCGATCGa       <  1:4325118/71‑1 (MQ=255)
                                                              cAACTGTATCAGGATCACCAGTGGATGCGTGATTTCGGTGAAAGCCTGCTGGTTTATCGTCCGCCGATCGa       <  1:4825885/71‑1 (MQ=255)
                                                                aCTGTATCAGGATCACCAGTGGATGCGTGATTTCGGTGAAAGCCTGCTGGTTTATCGTCCGCCGATCGaca     >  1:4505128/1‑71 (MQ=255)
                                                                 cTGTATCAGGATCACCAGTGGATGCGTGATTTCGGTGAAAGCct                               <  1:3298944/44‑1 (MQ=255)
                                                                   |                                                                      
ACAACGCCGGTTACACCAACGTTCACGAGCTGATCCCATGGCGTACGCTCTCTGGTCGTCAGCAACTGTATCAGGATCACCAGTGGATGCGTGATTTCGGTGAAAGCCTGCTGGTTTATCGTCCGCCGATCGACACCC  >  minE/834610‑834747

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