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 835,291 T→C 27.3% I3I (ATT→ATC)  narH → nitrate reductase 1, beta (Fe‑S) subunit

Read alignment evidence...
  seq id position ref new freq score (cons/poly) reads annotation genes product
*minE835,2910TC27.3% 209.3 / 92.7 139I3I (ATT→ATC) narHnitrate reductase 1, beta (Fe‑S) subunit
Reads supporting (aligned to +/- strand):  ref base T (49/52);  new base C (23/15);  total (72/67)
Fisher's exact test for biased strand distribution p-value = 2.54e-01
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 1.00e+00

Only 100 of 140 total aligned reads displayed.

ATGAAGAACATTGACTGGTTAGATGGCGAAGGCAATGACCAGGTACAGGAGAGCG‑TAAAATGAAAATTCGTTCACAAGTCGGCATGGTGCTGAATCTCGATAAGTGCATCGGCTGCCACACCTGTTCAGTTACCTGT  >  minE/835224‑835360
                                                                    |                                                                     
 tGAAGAACATTGACTGGTTAGATGGCGAAGGCAATGACCAGGTACAGGAGAGCG‑TAAAATGAAAATTCGtt                                                                   <  1:4242196/71‑1 (MQ=255)
 tGAAGAACATTGACTGGTTAGATGGCGAAGGCAATGACCAGGTACAGGAGAGCG‑TAAAATGAAAATTCGt                                                                    >  1:5310696/1‑70 (MQ=255)
  gaagaaCATTGACTGGTTAGATGGCGAAGGCAATGACCAGGTACAGGAGAGCG‑TAAAATGAAAATTCGtt                                                                   >  1:2637404/1‑70 (MQ=255)
   aagaaCATTGACTGGTTAGATGGCGAAGGCAATGACCAGGTACAGGAGAGCG‑TAAAATGAAAATTCGTTc                                                                  <  1:4788100/70‑1 (MQ=255)
    agaaCGTTAACTGGCTGGATGATGAAGGTCGCGATCAGGTACAGGAG‑GCGAAAAAATGAAAATCCGTTcac                                                                <  1:2320362/71‑1 (MQ=255)
    agaaCATTGACTGGTTAGATGGCGAAGGCAATGACCAGGTACAGGAGAGCG‑TAAAATGAAAATTCGTTca                                                                 >  1:3760167/1‑70 (MQ=255)
     gaaCGTTAACTGGCTGGATGATGAAGGTCGCGATCAGGTACAGGAG‑GCGAAAAAATGAAAATCCGTTcaca                                                               <  1:3837257/71‑1 (MQ=255)
     gaaCATTGACTGGTTAGATGGCGAAGGCAATGACCAGGTACAGGAGAGCG‑TAAAATGAAAATTCGTTcaca                                                               <  1:5561609/71‑1 (MQ=255)
     gaaCATTGACTGGTTAGATGGCGAAGGCAATGACCAGGTACAGGAGAGCG‑TAAAATGAAAATTCGTTcaca                                                               <  1:1974923/71‑1 (MQ=255)
        cATTGACTGGTTAGATGGCGAAGGCAATGACCAGGTACAGGAGAGCG‑TAAAATGAAAATTCGTTCACAAGt                                                            >  1:4031414/1‑71 (MQ=255)
            gACTGGTTAGATGGCGAAGGCAATGACCAGGTACAGGAGAGCG‑TAAAATGAAAATTCGTTCACAAGTCgg                                                         <  1:4125809/70‑1 (MQ=255)
              cTGGTTAGATGGCGAAGGCAATGACCAGGTACAGGAGAGCG‑TAAAATGAAAATTCg                                                                     >  1:4727742/1‑56 (MQ=255)
                ggTTAGATGGCGAAGGCAATGACCAGGTACAGGAGAGCG‑TAAAATGAAAATTCGTTCACaa                                                              <  1:1517586/61‑1 (MQ=255)
                ggTTAGATGGCGAAGGCAATGACCAGGTACAGGAGAGCG‑TAAAATGAAAATTCGTTCACaa                                                              <  1:5350169/61‑1 (MQ=255)
                 gTTAGATGGCGAAGGCAATGACCAGGTACAGGAGAGCG‑TAAAATGAAAATTCGTTCACAAGTCGGCATg                                                     <  1:5165659/69‑1 (MQ=255)
                     gATGGCGAAGGCAATGACCAGGTACAGGAGAGCG‑TAAAATGAAAATTCGTTCACAAGTCGGCATGGTGCt                                                >  1:3769060/1‑70 (MQ=255)
                     gATGGCGAAGGCAATGACCAGGTACAGGAGAGCG‑TAAAATGAAAATTCGTTCACAAGTCGGCATGGTGCTg                                               <  1:236991/71‑1 (MQ=255)
                        ggCGAAGGCAATGACCAGGTACAGGAGAGCG‑TAAAATGAAAATTCGTTcaca                                                               >  1:2531585/1‑52 (MQ=255)
                         gCGAAGGCAATGACCAGGTACAGGAGAGCG‑TAAAATGAAAATTCGTTCACAAGTCGGCATGGTGCTGAAtc                                           <  1:1585040/71‑1 (MQ=255)
                           gAAGGCAATGACCAGGTACAGGAGAGCG‑TAAAATGAAAATTCGTTCACAAGTCGGCATTGTGCTGAAtctc                                         <  1:5349937/71‑1 (MQ=255)
                            aaGGCAATGACCAGGTACAGGAGAGCG‑TAAAATGAAAATTCGTTCACAAGTCGGCATGGTGCTGAATCTCg                                        <  1:3902747/71‑1 (MQ=255)
                              ggCAATGACCAGGTACAGGAGAGCG‑TAAAATGAAAATTCGTTCACAAGTCGGCATGGTGCTGAATCTCGAt                                      <  1:4381332/71‑1 (MQ=255)
                               gCAATGACCAGGTACAGGAGAGCG‑TAAAATGAAAATTCGTTcac                                                                <  1:5511454/44‑1 (MQ=255)
                               gCAATGACCAGGTACAGGAGAGCG‑TAAAATGAAAATTCGTTCACAAGTCGGCATGGTGCTGAATCTCGAt                                      <  1:4920049/70‑1 (MQ=255)
                                cAATGACCAGGTACAGGAGAGCG‑TAAAATGAAAATTCGTTCACAAGTCGGCATGGTGCTGAATCTCGATaa                                    <  1:3129607/71‑1 (MQ=255)
                                 aaTGACCAGGTACAGGAGAGCG‑TAAAATGAAAATTCGtt                                                                   >  1:3066947/1‑39 (MQ=255)
                                 aaTGACCAGGTACAGGAGAGCG‑TAAAATGAAAATTCGtt                                                                   >  1:3968704/1‑39 (MQ=255)
                                 aaTGACCAGGTACAGGAGAGCG‑TAAAATGAAAATTCGTTCACAAGTCGGCATGGTGCTGAATCTCGAt                                      >  1:178519/1‑68 (MQ=255)
                                 aaTGACCAGGTACAGGAGAGCG‑TAAAATGAAAATTCGTTCACAAGTCGGCATGGTGCTGAATCTCGATAAg                                   >  1:4613436/1‑71 (MQ=255)
                                  aTGACCAGGTACAGGAGAGCG‑TAAAATGAAAATTCGTTCACAAGTCgg                                                         <  1:771026/48‑1 (MQ=255)
                                     aCCAGGTACAGGAGAGCG‑TAAAATGAAAATTCGtt                                                                   >  1:1177935/1‑35 (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                             >  1:2118422/1‑71 (MQ=255)
                                       cAGGTACAGGAG‑GCGAAAAAATGAAAATCCGTTCACAAGTCGGCATGGTGCTTAACCTCGACAAATGTATc                             >  1:556670/1‑71 (MQ=255)
                                       aaGGTACAGGAG‑GCGAAAAAATGAAAATCCGTTCACAAGt                                                            >  1:3302333/2‑40 (MQ=12)
                                        aGGTACAGGAGAGCG‑TAAAATGAAAATTCGTTCACAAGTCGGCATGGTGCTGAATCTCGATAAGTGCATCg                            >  1:1446184/1‑71 (MQ=255)
                                        aGGTACAGGAG‑GCGAAAAAATGAAAATCCGTTCACAAGTCGGCATGGTGCTTAACCTCGACaaat                                  >  1:4363597/1‑63 (MQ=255)
                                            aCAGGAGAGCG‑TAAAATGAGAATTCGTTCACAAGTCGGCATGGTGCTGAATCTCGATAAGTGCATCGGCTg                        >  1:2227744/1‑71 (MQ=255)
                                            aCAGGAGAGCG‑TAAAATGAAAATTCGTTCACAAGTCGGCATg                                                     >  1:383081/1‑42 (MQ=255)
                                            aCAGGAGAGCG‑TAAAATGAAAATTCGTTCACAAGTCGGCATg                                                     >  1:916219/1‑42 (MQ=255)
                                                gagaGCG‑TAAAATGAAAATTCGTTCACAAGTCGGCATGGTGCt                                                <  1:2098594/43‑1 (MQ=255)
                                                gagaGCG‑TAAAATGAAAATTCGTTCACAAGTCGGCATGGTGCTGAATCTCGATAAGTGCATCGGCTGCcac                    <  1:3211809/71‑1 (MQ=255)
                                                 agagCG‑TAAAATGAAAATTCGTTCACAAGTCGGCATGGTGCTGAAtct                                          >  1:3287573/1‑48 (MQ=255)
                                                   agCG‑TAAAATGAAAATTCGTTCACAAGTCGGCATGGTGCTGAATCTCGATAAGTGCATCGGCTGCCACAcc                 <  1:104920/71‑1 (MQ=255)
                                                     cG‑TAAAATGAAAATTCGTTCACAAGTCGGCATGGTGCTGa                                              >  1:3072600/1‑40 (MQ=255)
                                                     cG‑TAAAATGAAAATTCGTTCACAAGTCGGCATGGTGCTGa                                              >  1:2775739/1‑40 (MQ=255)
                                                       aaaaaaTGAAAATCCGTTCACAAGTCGGCATGGTGCTTAACCTCGACAAATGTATCGGCTGCCATACCTGt              <  1:2601292/69‑1 (MQ=255)
                                                       aaaaaaTGAAAATCCGTTCACAAGTCGGCATGGTGCTTAACCTCGACAAATGTATCGGCTGCCATACCTGt              <  1:892720/69‑1 (MQ=255)
                                                        tAAAATGAAAATTCGTTCACAAGTCGGCATGGTGCTGAATCTCGATAAGTGCATCGGCTGCCACACCTGtt             <  1:829840/71‑1 (MQ=255)
                                                        aaaaaTGAAAATCCGTTCACAAGTCGGCATGGTGCTTAACCTCGACAAATGTATCGGCTGc                       >  1:1924013/2‑61 (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)
                                                          aaaTGAAAATTCGTTCACAAGTCGGCATGGTGCTGaa                                             >  1:926853/1‑37 (MQ=255)
                                                          aaaTGAAAATTCGTTCACAAGTCGGCATGGTGCTGaa                                             >  1:3621258/1‑37 (MQ=255)
                                                          aaaTGAAAATTCGTTCACAAGTCGGCATGGTGCTGaa                                             >  1:3377056/1‑37 (MQ=255)
                                                          aaaTGAAAATTCGTTCACAAGTCGGCATGGTGCTGaa                                             >  1:2832921/1‑37 (MQ=255)
                                                          aaaTGAAAATTCGTTCACAAGTCGGCATGGTGCTGa                                              <  1:5611580/36‑1 (MQ=255)
                                                          aaaTGAAAATTCGTTCACAAGTCGGCATGGTGCTGAATCTCGa                                       >  1:4103550/1‑43 (MQ=255)
                                                          aaaTGAAAATTCGTTCACAAGTCGGCATGGTGCTGAATCTCGa                                       >  1:485090/1‑43 (MQ=255)
                                                          aaaTGAAAATTCGTTCACAAGTCGGCATGGTGCTGAATCTCGATa                                     <  1:2027004/45‑1 (MQ=255)
                                                          aaaTGAAAATTCGTTCACAAGTCGGCATGGTGCTGAATCTCGATa                                     <  1:5139248/45‑1 (MQ=255)
                                                          aaaTGAAAATTCGTTCACAAGTCGGCATGGTGCTGAATCTCGATa                                     <  1:4720835/45‑1 (MQ=255)
                                                          aaaTGAAAATTCGTTCACAAGTCGGCATGGTGCTGAATCTCGATAAGt                                  <  1:4634673/48‑1 (MQ=255)
                                                          aaaTGAAAATTCGTTCACAAGTCGGCATGGTGCTGAATCTCGATAAGTGCATCGGCTGCCACACCTGtt             >  1:1677326/1‑69 (MQ=255)
                                                          aaaTGAAAATTCGTTCACAAGTCGGCATGGTGCTGAATCTCGATAAGTGCATCGGCTGCCACACCTGTTc            <  1:4398764/70‑1 (MQ=255)
                                                          aaaTGAAAATCCGTTCACAAGTCGGCATGGTGCTTaac                                            >  1:1661258/1‑37 (MQ=38)
                                                          aaaTGAAAATCCGTTCACAAGTCGGCATGGTGCTTaac                                            >  1:4297083/1‑37 (MQ=38)
                                                          aaaTGAAAATCCGTTCACAAGTCGGCATGGTGCTTaac                                            >  1:1654626/1‑37 (MQ=38)
                                                          aaaTGAAAATCCGTTCACAAGTCGGCATGGTGCTTAACCTCGACAAATGTATCGGCTGCCATACCTGTTcg           >  1:2178191/1‑70 (MQ=255)
                                                           aaTGAAAATCCGTTCACAAGTCGGCATGGTGCTTAACCTCGACAAATgt                                <  1:1707439/49‑2 (MQ=255)
                                                           aaTGAAAATCCGTTCACAAGTCGGCATGGTGCTTAACCTCGACAAATgt                                <  1:2977072/49‑2 (MQ=255)
                                                            aTGAAAATTCGTTCACAAGTCGGCATGGTGCTGAATCTCGATAAGTGCATCGGCTGCCACACCTGTTCAGt         >  1:2942982/1‑71 (MQ=255)
                                                             tGAAAATTCGTTCACAAGTCGGCATGGTGCTGAATCTCGATAAGTGCATCGGCTGCCACACCTGTTc            <  1:2007373/67‑1 (MQ=255)
                                                             tGAAAATCCGTTCACAAGTCGGCATGGTGCTTAACCTCGACAAATg                                 <  1:1345615/46‑1 (MQ=255)
                                                               aaaaTTCGTTCACAAGTCGGCATGGTGCTGAATCTCGATAAGTGCATCGGCTTCCACACCTGTTCAGTTAc      >  1:1753273/1‑71 (MQ=255)
                                                               aaaaTTCGTTCACAAGTCGGCATGGTGCTGAATCTCGATAAGTGCATCGGCTGCCACACCTGTTCAGTTa       <  1:2111745/70‑1 (MQ=255)
                                                               aaaaTTCGTTCACAAGTCGGCATGGTGCTGAATCTCGATAAGTGCATCGGCTGCCACACCTGTTCAGTTAc      >  1:2988737/1‑71 (MQ=255)
                                                               aaaaTCCGTTCACAAGTCGGCATGGTGCTTAACCTCGaca                                     <  1:5583323/40‑3 (MQ=255)
                                                               aaaaTCCGTTCACAAGTCGGCATGGTGCTTAACCTCGaca                                     <  1:5576613/40‑3 (MQ=255)
                                                                aaaTCCGTTCACAAGTCGGCATGGTGCTTAACCTCGACAAATGTATCGGCTGCCATACCTGTTCGGTGAcc     >  1:3033300/1‑71 (MQ=255)
                                                                 aaTTCGTTCACAAGTCGGCATGGTGCTGAATCTCGATAAg                                   >  1:1649166/1‑40 (MQ=255)
                                                                 aaTTCGTTCACAAGTCGGCATGGTGCTGAATCTCGATAAg                                   >  1:844935/1‑40 (MQ=255)
                                                                 aaTTCGTTCACAAGTCGGCATGGTGCTGAATCTCGATAAg                                   >  1:3674212/1‑40 (MQ=255)
                                                                 aaTTCGTTCACAAGTCGGCATGGTGCTGAATCTCGATAAg                                   >  1:1941724/1‑40 (MQ=255)
                                                                 aaTTCGTTCACAAGTCGGCATGGTGCTGAATCTCGATAAg                                   >  1:4641487/1‑40 (MQ=255)
                                                                 aaTTCGTTCACAAGTCGGCATGGTGCTGAATCTCGATAAGTGCATCGGCTGCCACACCTGTTc            <  1:643041/63‑1 (MQ=255)
                                                                 aaTTCGTTCACAAGTCGGCATGGTGCTGAATCTCGATAAGTGCATCGGCTGCCACACCTGTTCAGTTAcc     <  1:5463800/70‑1 (MQ=255)
                                                                 aaTCCGTTCACAAGTCGGCATGGTGCTTAACCTCGACAAATGTATCGGCTGCCATACCTGTTCGGTGACCt    <  1:3422085/71‑1 (MQ=255)
                                                                  aTTCGTTCACAAGTCGGCATGGTGCTGAATCTCGATAAGTGCAt                              >  1:1975393/1‑44 (MQ=255)
                                                                  aTTCGTTCACAAGTCGGCATGGTGCTGAATCTCGATAAGTGCAt                              >  1:2679041/1‑44 (MQ=255)
                                                                  aTTCGTTCACAAGTCGGCATGGTGCTGAATCTCGATAAGTGCAt                              >  1:4538003/1‑44 (MQ=255)
                                                                  aTTCGTTCACAAGTCGGCATGGTGCTGAATCTCGATAAGTGCATCGGCTGCCACACCTGTTCAg          >  1:5531578/1‑64 (MQ=255)
                                                                   ttCGTTCACAAGTCGGCATGGTGCTGAATCTCGATAAGTGCATCGGCTGCCACACCTGTTCAGTTACCTGt  <  1:1202460/71‑1 (MQ=255)
                                                                    |                                                                     
ATGAAGAACATTGACTGGTTAGATGGCGAAGGCAATGACCAGGTACAGGAGAGCG‑TAAAATGAAAATTCGTTCACAAGTCGGCATGGTGCTGAATCTCGATAAGTGCATCGGCTGCCACACCTGTTCAGTTACCTGT  >  minE/835224‑835360

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