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 835,327 G→A 43.7% K15K (AAG→AAA)  narH → nitrate reductase 1, beta (Fe‑S) subunit

Read alignment evidence...
  seq id position ref new freq score (cons/poly) reads annotation genes product
*minE835,3270GA43.7% 57.0 / 147.7 128K15K (AAG→AAA) narHnitrate reductase 1, beta (Fe‑S) subunit
Reads supporting (aligned to +/- strand):  ref base G (30/42);  new base A (24/32);  total (54/74)
Fisher's exact test for biased strand distribution p-value = 1.00e+00
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 8.77e-01

Only 100 of 139 total aligned reads displayed.

AATGACCAGGTACAGGAGAGCG‑TAAAATGAAAATTCGTTCACAAGTCGGCATGGTGCTGAATCTCGATAAGTGCATCGGCTGCCACACCTGTTCAGTTACCTGTAAAAACGTCTGGACCAGCCGTGAAGGCGTGGAATATG  >  minE/835257‑835397
                                                                       |                                                                      
aaTGACCAGGTACAGGAGAGCG‑TAAAATGAAAATTCGTTCACAAGTCGGCATGGTGCTGAATCTCGATAAg                                                                        >  1:4002944/1‑71 (MQ=255)
 aTGACCAGGTACAGGAGAGCG‑TAAAATGAAAATTCGTTCACAAGTCGGCATGGTGCTGAATCTCGATAAg                                                                        >  1:1670486/1‑70 (MQ=255)
    aCCAGGTACAGGAGAGCG‑TAAAATGAAAATTCGTTCACAAGTCGGCATGGTGCTGAATCTCGATAAGTGCa                                                                    >  1:233830/1‑71 (MQ=255)
     tcAGGTACAGGAG‑GCGAAAAAATGAAAATCCGTTCACAAGTCGGCATGGTGCTTAACCTCGACAAATGTAt                                                                   >  1:3005167/2‑71 (MQ=255)
     tcAGGTACAGGAG‑GCGAAAAAATGAAAATCCGTTCACAAGTCGGCATGGTGCTTAACCTCGACAAATGTAt                                                                   >  1:2954352/2‑71 (MQ=255)
     ccAGGTACAGGAGAGCG‑TAAAATGAAAATTCGTTCACAAGTCGGCATGGTGCTGAATCTCGATAAGTGCa                                                                    <  1:3122629/70‑1 (MQ=255)
      cAGGTACAGGAG‑GCGAAAAAATGAAAATCCGTTCACAAGTCGGCATGGTGCTTAACCTCGACAAATgt                                                                     >  1:484887/1‑67 (MQ=255)
      cAGGTACAGGAG‑GCGAAAAAATGAAAATCCGTTCACAAGTCGGCATGGTGCTTAACCTCGACAAATGTATc                                                                  >  1:4734300/1‑71 (MQ=255)
      cAGGTACAGGAG‑GCGAAAAAATGAAAATCCGTTCACAAGTCGGCATGGTGCTTAACCTCGACAAATGTATc                                                                  >  1:2118422/1‑71 (MQ=255)
      cAGGTACAGGAG‑GCGAAAAAATGAAAATCCGTTCACAAGTCGGCATGGTGCTTAACCTCGACAAATGTATc                                                                  >  1:556670/1‑71 (MQ=255)
       aGGTACAGGAGAGCG‑TAAAATGAAAATTCGTTCACAAGTCGGCATGGTGCTGAATCTCGATAAGTGCATCg                                                                 >  1:1446184/1‑71 (MQ=255)
           aCAGGAGAGCG‑TAAAATGAGAATTCGTTCACAAGTCGGCATGGTGCTGAATCTCGATAAGTGCATCGGCTg                                                             >  1:2227744/1‑71 (MQ=255)
           aCAGGAGAGCG‑TAAAATGAAAATTCGTTCACAAGTCGGCATGGTGCTGAATCTCGATAAGTGCATCGGCTg                                                             >  1:1495309/1‑71 (MQ=255)
               gagaGCG‑TAAAATGAAAATTCGTTCACAAGTCGGCATGGTGCTGAATCTCGATAAGTGCATCGGCTGCcac                                                         <  1:3211809/71‑1 (MQ=255)
                  agCG‑TAAAATGAAAATTCGTTCACAAGTCGGCATGGTGCTGAATCTCGATAAGTGCATCGGCTGCCACAcc                                                      <  1:104920/71‑1 (MQ=255)
                      aaaaaaTGAAAATCCGTTCACAAGTCGGCATGGTGCTTAACCTCGACAAATGTATCGGCTGCCATACCTGt                                                   <  1:892720/69‑1 (MQ=255)
                      aaaaaaTGAAAATCCGTTCACAAGTCGGCATGGTGCTTAACCTCGACAAATGTATCGGCTGCCATACCTGt                                                   <  1:2601292/69‑1 (MQ=255)
                       tAAAATGAAAATTCGTTCACAAGTCGGCATGGTGCTGAATCTCGATAAGTGCATCGGCTGCCACACCTGtt                                                  <  1:829840/71‑1 (MQ=255)
                       aaaaaTGAAAATCCGTTCACAAGTCGGCATGGTGCTTAACCTCGACAAATGTATCGGCTGc                                                            >  1:1924013/2‑61 (MQ=255)
                       aaaaaTGAAAATCCGTTCACAAGTCGGCATGGTGCTTAACCTCGACAAATGTATCGGCTGc                                                            >  1:458403/2‑61 (MQ=255)
                       aaaaaTGAAAATCCGTTCACAAGTCGGCATGGTGCTTAACCTCGACAAATGTATCGGCTGCCATACCTGtt                                                  <  1:3431545/70‑1 (MQ=255)
                       aaaaaTGAAAATCCGTTCACAAGTCGGCATGGTGCTTAACCTCGACAAATGTATCGGCTGCCATACCTGtt                                                  <  1:4462691/70‑1 (MQ=255)
                       aaaaaTGAAAATCCGTTCACAAGTCGGCATGGTGATTAACCTCGAGAAATGTATCGGCTGCCATACCTGtt                                                  <  1:515880/70‑1 (MQ=255)
                        aaaaTGAAAATCCGTTCACAAGTCGGCATGGTGCTTAACCTCGACAAATGTAt                                                                   >  1:3815755/1‑53 (MQ=255)
                        aaaaTGAAAATCCGTTCACAAGTCGGCATGGTGCTTAACCTCGACAAATGTATCGGCTGCCATACCTGTTc                                                 >  1:2363345/1‑71 (MQ=255)
                         aaaTGAAAATTCGTTCACAAGTCGGCATGGTGCTGAATCTCGATAAGt                                                                       <  1:3425474/48‑1 (MQ=255)
                         aaaTGAAAATTCGTTCACAAGTCGGCATGGTGCTGAATCTCGATAAGt                                                                       <  1:4634673/48‑1 (MQ=255)
                         aaaTGAAAATTCGTTCACAAGTCGGCATGGTGCTGAATCTCGATAAGTGCATCGGCTGCCACACCTGtt                                                  >  1:1677326/1‑69 (MQ=255)
                         aaaTGAAAATTCGTTCACAAGTCGGCATGGTGCTGAATCTCGATAAGTGCATCGGCTGCCACACCTGTTc                                                 <  1:4398764/70‑1 (MQ=255)
                         aaaTGAAAATCCGTTCACAAGTCGGCATGGTGCTTAACCTCGACAAATGTATCGGCTGCCATACCTGTTcg                                                >  1:2178191/1‑70 (MQ=255)
                          aaTGAAAATCCGTTCACAAGTCGGCATGGTGCTTAACCTCGACAAATgt                                                                     <  1:1707439/49‑2 (MQ=255)
                            tGAAAATCCGTTCACAAGTCGGCATGGTGCTTAACCTCGACAAATg                                                                      <  1:1345615/46‑1 (MQ=255)
                              aaaaTTCGTTCACAAGTCGGCATGGTGCTGAATCTCGATAAGTGCATCGGCTGCCACACCTGTTCAGTTAc                                           >  1:2988737/1‑71 (MQ=255)
                                aaTTCGTTCACAAGTCGGCATGGTGCTGAATCTCGATAAg                                                                        >  1:3674212/1‑40 (MQ=255)
                                aaTTCGTTCACAAGTCGGCATGGTGCTGAATCTCGATAAg                                                                        >  1:1941724/1‑40 (MQ=255)
                                aaTTCGTTCACAAGTCGGCATGGTGCTGAATCTCGATAAg                                                                        >  1:31596/1‑40 (MQ=255)
                                aaTTCGTTCACAAGTCGGCATGGTGCTGAATCTCGATAAg                                                                        >  1:844935/1‑40 (MQ=255)
                                aaTTCGTTCACAAGTCGGCATGGTGCTGAATCTCGATAAGTGCATCGGCTGCCACACCTGTTc                                                 <  1:643041/63‑1 (MQ=255)
                                 aTTCGTTCACAAGTCGGCATGGTGCTGAATCTCGATAAGTGCAt                                                                   >  1:2679041/1‑44 (MQ=255)
                                 aTTCGTTCACAAGTCGGCATGGTGCTGAATCTCGATAAGTGCAt                                                                   >  1:1975393/1‑44 (MQ=255)
                                 aTTCGTTCACAAGTCGGCATGGTGCTGAATCTCGATAAGTGCATCGGCTGCCACACCTGTTCAg                                               >  1:5531578/1‑64 (MQ=255)
                                  tccGTTCACAAGTCGGCATGGTGCTTAACCTCGACAAATGTATCGGCTGCCATACCTGTTCGGTGACCt                                         >  1:2955088/3‑69 (MQ=255)
                                   ccGTTCACAAGTCGGCATGGTGCTTAACCTCGACAAATGTATCGGCTGCCATACCTGTTCGGTGACCTg                                        >  1:4929890/2‑69 (MQ=255)
                                     gTTCACAAGTCGGCATGGTGCTTAACCTCGACAAATGTATCGGCTGCCATACCTGTTCGGTGACCTGTaaa                                    <  1:39445/71‑1 (MQ=255)
                                     gTTCACAAGTCGGCATGGTGCTGAATCTCGATAAGTGCATCGGCTGCCACACCTGTTCAGTTACCTGTaa                                     <  1:4627365/70‑1 (MQ=255)
                                     gTTCACAAGTCGGCATGGTGCTGAATCTCGATAAGTGCATCGGCTGCCACACCTGTTCAGTTACCTGTaa                                     <  1:3824596/70‑1 (MQ=255)
                                      ttCACAAGTCGGCATGGTGCTTAACCTCGACAAATGTATCGGCTGCCATACCTGtt                                                  <  1:1244187/56‑1 (MQ=255)
                                      ttCACAAGTCGGCATGGTGCTGAATCTCGATAAGTGCATCGGCTGCCACACCTGTTCAGTTACCTTTaaaa                                   <  1:1391440/71‑1 (MQ=255)
                                      ttCACAAGTCGGCATGGTGCTGAATCTCGATAAGTGCATCGGCTGCCACACCTGTTCAGTTACCTGTaaa                                    <  1:2080557/70‑1 (MQ=255)
                                       tCACAAGTCGGCATGGTGCTGAATCTCGATAAGTGCATCGGCTGc                                                            <  1:2813408/45‑1 (MQ=255)
                                        cacaAGTCGGCATGGTGCTTAACCTCGACAAATGTATCGGCTGCca                                                          >  1:2216369/1‑46 (MQ=255)
                                        cacaAGTCGGCATGGTGCTTAACCTCGACAAATGTATCGGCTGCCATACCTGTTCGGTGACCTGTAAAAAc                                 >  1:2548851/1‑71 (MQ=255)
                                          caAGTCGGCATGGTGCTTAACCTCGACAAATGTATCGGCTGCCATACCTGtt                                                  <  1:807893/52‑1 (MQ=255)
                                              tCGGCATGGTGCTTAACCTCGACAAATGTATCGGCTGCCATACCTGTTCGGTGACCTGTAAAAACGTCTgg                           <  1:5621635/71‑1 (MQ=255)
                                              tCGGCATGGTGCTTAACCTCGACAAATGTATCGGCTGCCATACCTGTTCGGTGACCTGTAAAAACGTCTgg                           <  1:3266844/71‑1 (MQ=255)
                                              tCGGCATGGTGCTTAACCTCGACAAATGTATCGGCTGCCATACCTGTTCGGTGACCTGTAAAAACGTCTg                            <  1:4548543/70‑1 (MQ=255)
                                                ggCATGGTGCTTAACCTCGACAAATGTATCGGCTGCCATACCTGTTCGGTGACCTGTAAAAACGTCTGGAc                         <  1:4918992/71‑1 (MQ=255)
                                                   aTGGTGCTTAACCTCGACAAATGTATCGGCTGCCATACCTGTTCGGTGACCTGTAAAAACGTCTGGAccg                       <  1:401755/70‑2 (MQ=255)
                                                   aTGGTGCTGAATCTCTATAAGTGCATCGGCTGCCACAcc                                                      <  1:1000773/39‑1 (MQ=255)
                                                    tGGTGCTTAACCTCGACAAATGTATCGGCTGCCATACCTGtt                                                  <  1:1798066/42‑1 (MQ=255)
                                                    tGGTGCTTAACCTCGACAAATGTATCGGCTGCCATACCTGtt                                                  <  1:3032749/42‑1 (MQ=255)
                                                    tGGTGCTTAACCTCGACAAATGTATCGGCTGCCATACCTGTTc                                                 <  1:2512733/43‑1 (MQ=255)
                                                    tGGTGCTTAACCTCGACAAATGTATCGGCTGCCATACCTGTTc                                                 <  1:836334/43‑1 (MQ=255)
                                                      gTGCTTAACCTCGACAAATGTATCGGCTGCCATACCTGTTCGGTGACCTGTAAAAACGTCTg                            >  1:4608998/1‑62 (MQ=255)
                                                      gTGCTGAATCTCGATAAGTGCATCGGCTGCCACACCTGTTCAGTTACCTGTAAAAACGTCTGGACCAGCCg                   <  1:696788/71‑1 (MQ=255)
                                                        gCTTAACCTCGACAAATGTATCGGCTGCCATACCTGTTCGGTGACCTGTa                                      >  1:921225/1‑50 (MQ=255)
                                                        gCTTAACCTCGACAAATGTATCGGCTGCCATACCTGTTCGGTGACCTGTa                                      >  1:2454457/1‑50 (MQ=255)
                                                        gCTGAATCTCGATAAGTGCATCGGCTTCCACACCTGTTCAGTTACCTGTaa                                     <  1:757831/51‑1 (MQ=255)
                                                        gCTGAATCTCGATAAGTGCATCGGCTGCCACACCTGTTCAGTTACCTGTAAAAACGTCTGGACCAGCCGt                  >  1:4773351/1‑70 (MQ=255)
                                                         cTGAATCTCGATAAGTGCATCGGCTGCCACACCTGTTCAGTTACCTGTAAAAACGTCTGGACCAGCCGt                  >  1:4223772/1‑69 (MQ=255)
                                                         cTGAATCTCGATAAGTGCATCGGCTGCCACACCTGTTCAGTTACCTGTAAAAACGTCTGGACCAGCCGTg                 >  1:1232917/1‑70 (MQ=255)
                                                         cTGAATCTCGATAAGTGCATCGGCTGCCACACCTGTTCAGTTACCTGTAAAAACGTCTGGACCAGCCGTGa                <  1:2550486/71‑1 (MQ=255)
                                                            aacctcGACAAATGTATCGGCTGCCATACCTGTTCGGTGACCTGTAAAAACGTCTGGACCGGGCGCGAAgg             >  1:5108994/4‑71 (MQ=255)
                                                            aaTCTCGATAAGTGCATCGGCTGCCACACCTGTTCAGTTACCTGTAAAAAc                                 >  1:2485647/1‑51 (MQ=255)
                                                            aaTCTCGATAAGTGCATCGGCTGCCACACCTGTTCAGTTACCTGTAAAAAc                                 >  1:290336/1‑51 (MQ=255)
                                                            aaTCTCGATAAGTGCATCGGCTGCCACACCTGTTCAGTTACCTGTAAAAAc                                 >  1:557873/1‑51 (MQ=255)
                                                            aaTCTCGATAAGTGCATCGGCTGCCACACCTGTTCAGTTACCTGTAAAAACGTCTGGACCAGCCGTGaa               <  1:1816674/69‑1 (MQ=255)
                                                             acctcGACAAATGTATCGGCTGCCATACCTGTTCGGTGACCTGTAAAAACGTCTGGACCGGGCGCGAAgg             <  1:1544852/68‑1 (MQ=255)
                                                             aTCTCGATAAGTGCATCGGCTGCCACACCTGTTCAGTTACCTGTAAAAACGTCTGGACCAGCCGTTAAGGc            <  1:2791370/71‑1 (MQ=255)
                                                              tctcGATAAGTGCATCGGCTGCCACACCTGTTCAGt                                              <  1:2025118/36‑1 (MQ=255)
                                                              tctcGATAAGTGCATCGGCTGCCACACCTGTTCAGTTACCTGTAAAAACGt                               <  1:4109947/51‑1 (MQ=255)
                                                              tctcGATAAGTGCATCGGCTGCCACACCTGTTCAGTTACCTGTAAAAACGt                               <  1:2729899/51‑1 (MQ=255)
                                                              cctcGACAAATGTATCGGCTGCCATACCTGTTCGGTGACCTGTAAAAACGTCTGGACCGGGCGCGAAGGca           <  1:3393405/70‑2 (MQ=255)
                                                               ctcGACAAATGTATCGGCTGCCATACCTGTTCGGTGACCTGTAAAAACGTCTGGACCGGGCGCGAAGGcat          <  1:3733652/71‑3 (MQ=255)
                                                                tcGATAAGTGCATCGGCTGCCACACCTGTTCAGTTa                                            >  1:690910/1‑36 (MQ=255)
                                                                tcGATAAGTGCATCGGCTGCCACACCTGTTCAGTTACCTGTAAAAACGTCTgg                           >  1:511548/1‑53 (MQ=255)
                                                                tcGACAAATGTATCGGCTGCCATACCTGTTCGGTGACCTGTaaa                                    <  1:1253319/44‑1 (MQ=16)
                                                                tcGACAAATGTATCGGCTGCCATACCTGTTCGGTGACCTGTAAAAACGTCTGGACCGGGCGCGAAg              >  1:4838527/1‑66 (MQ=255)
                                                                tcGACAAATGTATCGGCTGCCATACCTGTTCGGTGACCTGTAAAAACGTCTGGACCGGGCGCGAAGGc            <  1:4446910/68‑1 (MQ=255)
                                                                tcGACAAATGTATCGGCTGCCATACCTGTTCGGTGACCTGTAAAAACGTCTGGACCGGGCGCGAAGGc            <  1:1188328/68‑1 (MQ=255)
                                                                 cGATAAGTGCATCGGCTGCCACACCTGTTCAGTTACCTGTAAAAACGTCTg                            >  1:4888898/1‑51 (MQ=255)
                                                                  gATAAGTGCATCGGCTGCCACACCTGTTCAGTTACCTGTAAAAACGTCTGGACCAGCCGTGaa               >  1:225986/1‑63 (MQ=255)
                                                                  gATAAGTGCATCGGCTGCCACACCTGTTCAGTTACCTGTAAAAACGTCTGGACCAGCCGTGAAGGCGTgg        >  1:5387749/1‑70 (MQ=255)
                                                                  gATAAGTGCATCGGCTGCCACACCTGTTCAGTTACCTGTAAAAACGTCTGGACCAGCCGTGAAGGCGTgg        <  1:2055536/70‑1 (MQ=255)
                                                                  gATAAGTGCATCGGCTGCCACACCTGTTCAGTTACCTGTAAAAACGTCTGCACCAGCCGTGAAGGCGTgg        <  1:4789397/70‑1 (MQ=255)
                                                                   aTAAGTGCATCGGCTGCCACACCTGTTCAGTTACCTGTAAAAAc                                 <  1:1283786/44‑1 (MQ=255)
                                                                   aTAAGTGCATCGGCTGCCACACCTGTTCAGTTACCTGTAAAAAc                                 <  1:3557967/44‑1 (MQ=255)
                                                                    tAAGTGCATCGGCTGCCACACCTGTTCAGTTACCTGTAAAAACGTCTGGACAAGCCGTGAAGGCGTGGAat     <  1:5430758/71‑1 (MQ=255)
                                                                      aGTGCATCGGCTGCCACACCTGTTCAGTTACCTGTAAAAACGTCTGGACCAGCCGTGAAGGCGTGGAata    <  1:5479613/70‑1 (MQ=255)
                                                                       gTGCATCGGCTGCCACACCTGTTCAGTTACCTGTAAAAACGTCTGGACCAGCCGTGAAGGCGTGGAATATg  <  1:1222241/71‑1 (MQ=255)
                                                                       |                                                                      
AATGACCAGGTACAGGAGAGCG‑TAAAATGAAAATTCGTTCACAAGTCGGCATGGTGCTGAATCTCGATAAGTGCATCGGCTGCCACACCTGTTCAGTTACCTGTAAAAACGTCTGGACCAGCCGTGAAGGCGTGGAATATG  >  minE/835257‑835397

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