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
A2 F1 I0 R1 4577 57.4 3436498 77.7% 2670158 63.4

Breseq alignment

BRESEQ :: Evidence
Predicted mutation
evidence seq id position mutation freq annotation gene description
RA minE 1,932,405 C→A 27.5% L75L (CTG→CTT)  yqeF ← predicted acyltransferase

Read alignment evidence...
  seq id position ref new freq score (cons/poly) reads annotation genes product
*minE1,932,4050CA27.5% 175.7 / 60.8 116L75L (CTG→CTT) yqeFpredicted acyltransferase
Reads supporting (aligned to +/- strand):  ref base C (37/47);  new base A (9/23);  total (46/70)
Fisher's exact test for biased strand distribution p-value = 1.40e-01
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 9.99e-01

Only 100 of 116 total aligned reads displayed.

AGATGCAGTGCTTTAAGCCCGGAACCGCAAACGTCATTAATAGTGATTGCAGAAACGCTATTAGGCAGACCACCTTTAATAGCCGATTGCCTTGCCGGATTCTGCCCTGCCCCTGCAGTC  >  minE/1932340‑1932459
                                                                 |                                                      
aGATGCAGTGCTTTAAGCCCGGAACCGCAAACGTCATTAATAGTGATTGCAGAAACGCTATTAGGCAg                                                      >  1:2119285/1‑68 (MQ=255)
aGATGCAGTGCTTTAAGCCCGGAACCGCAAACGTCATTAATAGTGATTGCAGAAACGCTATTAGGCAg                                                      >  1:653163/1‑68 (MQ=255)
aGATGCAGTGCTTTAAGCCCGGAACCGCAAACGTCATTAATAGTGATTGCAGAAACGCTATTAGGCAg                                                      >  1:1270912/1‑68 (MQ=255)
    gCAGTGCTTTAAGCCCGGAACCGCAAACGTCATTAATAGTGATTGCAGAAACGCTATTAGGCAGaccac                                                 <  1:947294/69‑1 (MQ=255)
    gCAGTGCTTTAAGCCCGGAACCGCAAACGTCATTAATAGTGATTGCAGAAACGCTATTAGGCAGaccac                                                 <  1:2202759/69‑1 (MQ=255)
    gCAGTGCTTTAAGCCCGGAACCGCAAACGTCATTAATAGTGATTGCAGAAACGCTATTAGGCAGaccac                                                 <  1:15781/69‑1 (MQ=255)
    gCAGTGCTTTAAGCCCGGAACCGCAAACGTCATTAATAGTGATTGCAGAAACGCTATTAGGCAGaccac                                                 <  1:2434550/69‑1 (MQ=255)
    gCAGTGCTTTAAGCCCGGAACCGCAAACGTCATTAATAGTGATTGCAGAAACGCTATTAGGCAGaccac                                                 >  1:2597679/1‑69 (MQ=255)
    gCAGTGCTTTAAGCCCGGAACCGCAAACGTCATTAATAGTGATTGCAGAAACGCTATTAGGCAGaccac                                                 <  1:2919646/69‑1 (MQ=255)
    gCAGTGCTTTAAGCCCGGAACCGCAAACGTCATTAATAGTGATTGCAGAAACGCTATTAGGCAGaccac                                                 <  1:2935560/69‑1 (MQ=255)
    gCAGTGCTTTAAGCCCGGAACCGCAAACGTCATTAATAGTGATTGCAGAAACGCTATTAGGCAGaccac                                                 <  1:298149/69‑1 (MQ=255)
    gCAGTGCTTTAAGCCCGGAACCGCAAACGTCATTAATAGTGATTGCAGAAACGCTATTAGGCAGaccac                                                 <  1:137138/69‑1 (MQ=255)
    gCAGTGCTTTAAGCCCGGAACCGCAAACGTCATTAATAGTGATTGCAGAAACGCTATTAGGCAGaccac                                                 >  1:322909/1‑69 (MQ=255)
    gCAGTGCTTTAAGCCCGGAACCGCAAACGTCATTAATAGTGATTGCAGAAACGCTATTAGGCAGaccac                                                 <  1:733543/69‑1 (MQ=255)
     cAGTGCTTTAAGCCCGGAACCGCAAACGTCATTAATAGTGATTGCAGAAACGCTATTAGGCAGaccac                                                 <  1:125819/68‑1 (MQ=255)
     cAGTGCTTTAAGCCCGGAACCACAAACGTCATTAATAGTGATTGCAGAAACGCTATTAGTAAGaccacc                                                <  1:1259002/69‑1 (MQ=255)
     cAGTGCTTTAAGCCCGGAACCACAAACGTCATTAATAGTGATTGCAGAAACGCTATTAGGAAGaccacc                                                <  1:1919524/69‑1 (MQ=255)
     cAGTGCTTTAAGCCCGGAACCACAAACGTCATTAATAGTGATTGCAGAAACGCTATTAGGAAGaccacc                                                <  1:3212600/69‑1 (MQ=255)
     cAGTGCTTTAAGCCCGGAACCACAAACGTCATTAATAGTGATTGCAGAAACGCTATTAGGAAGaccacc                                                <  1:200299/69‑1 (MQ=255)
     cAGTGCTTTAAGCCCGGAACCACAAACGTCATTAATAGTGATTGCAGAAACGCTATTAGGAAGaccacc                                                <  1:2007353/69‑1 (MQ=255)
     cAGTGCTTTAAGCCCGGAACCACAAACGTCATTAATAGTGATTGCAGAAACGCTATTAGGAAGaccacc                                                <  1:2064974/69‑1 (MQ=255)
     cAGTGCTTTAAGCCCGGAACCACAAACGTCATTAATAGTGATTGCAGAAACGCTATTAGGAAGaccacc                                                <  1:1028421/69‑1 (MQ=255)
     cAGTGCTTTAAGCCCGGAACCACAAACGTCATTAATAGTGATTGCAGAAACGCTATTAGGAAGaccacc                                                <  1:2224379/69‑1 (MQ=255)
     cAGTGCTTTAAGCCCGGAACCACAAACGTCATTAATAGTGATTGCAGAAACGCTATTAGGAAGaccacc                                                <  1:619562/69‑1 (MQ=255)
     cAGTGCTTTAAGCCCGGAACCACAAACGTCATTAATAGTGATTGCAGAAACGCTATTAGGAAGaccacc                                                <  1:2384064/69‑1 (MQ=255)
     cAGTGCTTTAAGCCCGGAACCACAAACGTCATTAATAGTGATTGCAGAAACGCTATTAGGAAGaccacc                                                <  1:480626/69‑1 (MQ=255)
     cAGTGCTTTAAGCCCGGAACCACAAACGTCATTAATAGTGATTGCAGAAACGCTATTAGGAAGaccacc                                                <  1:349677/69‑1 (MQ=255)
     cAGTGCTTTAAGCCCGGAACCACAAACGTCATTAATAGTGATTGCAGAAACGCTATTAGGAAGaccacc                                                <  1:275731/69‑1 (MQ=255)
     cAGTGCTTTAAGCCCGGAACCACAAACGTCATTAATAGTGATTGCAGAAACGCTATTAGGAAGaccacc                                                <  1:2806125/69‑1 (MQ=255)
     cAGTGCTTTAAGCCCGGAACCACAAACGTCATTAATAGTGATTGCAGAAACGCTATTAGGAAGaccacc                                                <  1:2904305/69‑1 (MQ=255)
     cAGTGCTTTAAGCCCGGAACCACAAACGTCATTAATAGTGATTGCAGAAACGCTATTAGGAAGaccacc                                                <  1:1442504/69‑1 (MQ=255)
     cAGTGCTTTAAGCCCGGAACCACAAACGTCATTAATAGTGATTGCAGAAACGCTATTAGGAAGaccacc                                                <  1:1054699/69‑1 (MQ=255)
     cAGTGCTTTAAGCCCGGAACCACAAACGTCATTAATAGTGATTGCAGAAACGCTATTAGGAAGaccacc                                                <  1:1115594/69‑1 (MQ=255)
     cAGTGCTTTAAGCCCGGAACCACAAACGTCATTAATAGTGATTGAAGAAACGCTATTAGGAAGaccacc                                                <  1:1091117/69‑1 (MQ=255)
      aGTGCTTTAAGCCCGGAACCACAAACGTCATTAATAGTGATTGCAGAAACGCTATTAGGAAGaccacc                                                <  1:1573897/68‑1 (MQ=255)
          cTTTAAGCCCGGAACCGCAAACGTCATTAATAGTGATTGCAGAAACGCTATTAGGCAGACCACCttt                                             >  1:1950249/1‑67 (MQ=255)
          cTTTAAGCCCGGAACCGCAAACGTCATTAATAGTGATTGCAGAAACGCTATTAGGCAGACCACCttt                                             >  1:1511790/1‑67 (MQ=255)
          cTTTAAGCCCGGAACCGCAAACGTCATTAATAGTGATTGCAGAAACGCTATTAGGCAGACCACCttt                                             >  1:328530/1‑67 (MQ=255)
          cTTTAAGCCCGGAACCGCAAACGTCATTAATAGTGATTGCAGAAACGCTATTAGGCAGACCACCttt                                             >  1:1590330/1‑67 (MQ=255)
          cTTTAAGCCCGGAACCGCAAACGTCATTAATAGTGATTGCAGAAACGCTATTAGGCAGACCACCttt                                             >  1:2616835/1‑67 (MQ=255)
          cTTTAAGCCCGGAACCGCAAACGTCATTAATAGTGATTGCAGAAACGATATTAGGCAGACCACCtt                                              >  1:1776768/1‑66 (MQ=255)
                  ccGGAACCGCAAACGTCATTAATAGTGATTGCAGAAACGCTATTAGGCAGACCACCTTTAATAGCCGa                                    >  1:2684038/1‑68 (MQ=255)
                          gCAAACGTCATTAATAGTGATTGCAGAAACGCTATTAGGCAGACCACCttt                                             >  1:521837/1‑51 (MQ=255)
                          gCAAACGTCATTAATAGTGATTGCAGAAACGCTATTAGGCAGACCACCttt                                             >  1:1897291/1‑51 (MQ=255)
                          gCAAACGTCATTAATAGTGATTGCAGAAACGCTATTAGGCAGACCACCttt                                             >  1:1172097/1‑51 (MQ=255)
                          gCAAACGTCATTAATAGTGATTGCAGAAACGCTATTAGGCAGACCACCttt                                             >  1:3182737/1‑51 (MQ=255)
                          gCAAACGTCATTAATAGTGATTGCAGAAACGCTATTAGGCAGACCACCttt                                             >  1:3088039/1‑51 (MQ=255)
                          gCAAACGTCATTAATAGTGATTGCAGAAACGCTATTAGGCAGACCACCttt                                             >  1:555265/1‑51 (MQ=255)
                          gCAAACGTCATTAATAGTGATTGCAGAAACGCTATTAGGCAGACCACCttt                                             >  1:2419023/1‑51 (MQ=255)
                          gCAAACGTCATTAATAGTGATTGCAGAAACGCTATTAGGCAGACCACCttt                                             >  1:2230282/1‑51 (MQ=255)
                          gCAAACGTCATTAATAGTGATTGCAGAAACGCTATTAGGCAGACCACCttt                                             >  1:1582497/1‑51 (MQ=255)
                          ccAAACGTCATTAATAGTGATTGCAGAAACGCTATTAGGCAGACCACCttt                                             >  1:2941541/2‑51 (MQ=255)
                          acAAACGTCATTAATAGTGATTGCAGAAACGCTATTAGGAAGCCCACCTTTAATAGCCGAttgtcttgc                           >  1:2464639/2‑69 (MQ=255)
                          acAAACGTCATTAATAGTGATTGCAGAAACGCTATTAGGAAGACCACCTTTAATAGCCg                                     >  1:2914981/2‑59 (MQ=255)
                          acAAACGTCATTAATAGTGATTGCAGAAACGCTATTAGGAAGACCACCTTTAATAGCCGAttgtcttgc                           >  1:1400751/2‑69 (MQ=255)
                          acAAACGTCATTAATAGTGATTGCAGAAACGCTATTAGGAAGACCACCTTTAATAGCCGAttgtcttgc                           >  1:2586087/2‑69 (MQ=255)
                          acAAACGTCATTAATAGTGATTGCAGAAACGCTATTAGGAAGACCACCTTTAATAGCCGAttgtcttgc                           >  1:1842159/2‑69 (MQ=255)
                             aaCGTCATTAATAGTGATTTCAGAAACGCTATTAGGCAGACCACCTTTAATAGCCGATTGCCTTGCCgg                        <  1:1721758/69‑1 (MQ=255)
                             aaCGTCATTAATAGTGATTGCAGAAACGCTATTAGGCAGACCACCTTTAATAGCCGATTGCCTTGCCgg                        <  1:180567/69‑1 (MQ=255)
                             aaCGTCATTAATAGTGATTGCAGAAACGCTATTAGGCAGACCACCTTTAATAGCCGATTGCCTTGCCgg                        <  1:148100/69‑1 (MQ=255)
                             aaCGTCATTAATAGTGATTGCAGAAACGCTATTAGGCAGACCACCTTTAATAGCCGATTGCCTTGCCgg                        <  1:714470/69‑1 (MQ=255)
                             aaCGTCATTAATAGTGATTGCAGAAACGCTATTAGGCAGACCACCTTTAATAGCCGATTGCCTTGCCgg                        <  1:1293215/69‑1 (MQ=255)
                             aaCGTCATTAATAGTGATTGCAGAAACGCTATTAGGCAGACCACCTTTAATAGCCGATTGCCTTGCCgg                        <  1:2963881/69‑1 (MQ=255)
                             aaCGTCATTAATAGTGATTGCAGAAACGCTATTAGGCAGACCACCTTTAATAGCCGATTGCCTTGCCgg                        <  1:489179/69‑1 (MQ=255)
                             aaCGTCATTAATAGTGATTGCAGAAACGCTATTAGGCAGACCACCTTTAATAGCCGATTGCCTTGCCgg                        <  1:826634/69‑1 (MQ=255)
                              aCGTCATTAATAGTGATTGCAGAAACGCTATTAGGCAGACCACCTTTAATAGCCGATTGCCTTGCCgg                        <  1:1993058/68‑1 (MQ=255)
                                 tCATTAATAGTGATTGCAGAAACGCTATTAGGAAGaccacc                                                <  1:2588124/41‑1 (MQ=255)
                                   aTTAATAGTGATTGCAGAAACGCTATTAGGCAGACCACCTTTAATAGCCGATTGCCTTGCCGGATTctg                  <  1:1403820/69‑1 (MQ=255)
                                   aTTAATAGTGATTGCAGAAACGCTATTAGGCAGACCACCTTTAATAGCCGATTGCCTTGCCGGATTctg                  <  1:3154998/69‑1 (MQ=255)
                                   aTTAATAGTGATTGCAGAAACGCTATTAGGCAGACCACCTTTAATAGCCGATTGCCTTGCCGGATTctg                  <  1:313860/69‑1 (MQ=255)
                                   aTTAATAGTGATTGCAGAAACGCTATTAGGCAGACCACCTTTAATAGCCGATTGCCTTGCCGGATTctg                  <  1:3240776/69‑1 (MQ=255)
                                   aTTAATAGTGATTGCAGAAACGCTATTAGGCAGACCACCTTTAATAGCCGATTGCCTTGCCGGATTctg                  <  1:444678/69‑1 (MQ=255)
                                   aTTAATAGTGATTGCAGAAACGCTATTAGGCAGACCACCTTTAATAGCCGATTGCCTTGCCGGATTctg                  <  1:1107397/69‑1 (MQ=255)
                                   aTTAATAGTGATTGCAGAAACGCTATTAGGCAGACCACCTTTAATAGCCGATTGCCTTGCCGGATTctg                  <  1:302307/69‑1 (MQ=255)
                                   aTTAATAGTGATTGCAGAAACGCTATTAGGCAGACCACCTTTAATAGCCGATTGCCTTGCCGGATTctg                  <  1:1995267/69‑1 (MQ=255)
                                   aTTAATAGTGATTGCAGAAACGCTATTAGGCAGACCACCTTTAATAGCCGATTGCCTTGCCGGATTctg                  <  1:3012089/69‑1 (MQ=255)
                                   aTTAATAGTGATTGCAGAAACGCTATTAGGCAGACCACCTTTAATAGCCGATTGCCTTGCCGGATTctg                  <  1:2398004/69‑1 (MQ=255)
                                   aTTAATAGTGATTGCAGAAACGCTATTAGGAAGaccacc                                                <  1:1025548/39‑1 (MQ=255)
                                     tAATAGTGATTGCAGAAACGCTATTAGGCAGACCACCTTTAATAGCCGATTGCCTTGCCGGATTctgc                 <  1:584175/68‑1 (MQ=255)
                                     tAATAGTGATTGCAGAAACGCTATTAGGCAGACCACCTTTAATAGCCGATTGCCTTGCCGGATTctgc                 <  1:1263022/68‑1 (MQ=255)
                                     tAATAGTGATTGCAGAAACGCTATTAGGCAGACCACCTTTAATAGCCGATTGCCTTGCCGGATTctgc                 <  1:2842837/68‑1 (MQ=255)
                                     tAATAGTGATTGCAGAAACGCTATTAGGCAGACCACCTTTAATAGCCCATTGCCTTGCCGGATTctgc                 <  1:2745636/68‑1 (MQ=255)
                                      aaTAGTGATTGCAGAAACGCTATTAGGCAGACCACCTTTAATAGCCGATTGCCTTGCCGGATTctgccc               >  1:3140228/1‑69 (MQ=255)
                                          gTGATTTCAGAAACGCTATTAGGCAGACCACCTTTAATAGCCGATTGCCTTGCCGGATTctgccctgcc           >  1:3159976/1‑69 (MQ=255)
                                          gTGATTGCATAAACGCTATTAGGCAGACCACCTTTAATAGCCGATTGCCTTGCCGGATTctgccctgc            >  1:220131/1‑68 (MQ=255)
                                             aTTGCAGAAACGCTATTAGGAAGACCACCTTTAATAGCCGATTGTCTTGCCGGATTctgcact              >  1:3021632/1‑63 (MQ=255)
                                             aTTGCAGAAACGCTATTAGGAAGACCACCTTTAATAGCCGATTGTCTTGCCGGATTCTGccctgcccc         >  1:602241/1‑68 (MQ=255)
                                             aTTGCAGAAACGCTATTAGGAAGACCACCTTTAATAGCCGATTGTCTTGCCGGATTCTGccctgcccc         >  1:583745/1‑68 (MQ=255)
                                                   gAAACGCTATTAGGCAGACCACCTTTAATAGCCGATTGCCTTGCCGGATTCTGCCCTGCCCCTGCAGTc  <  1:2918633/69‑1 (MQ=255)
                                                   gAAACGCTATTAGGCAGACCACCTTTAATAGCCGATTGCCTTGCCGGATTCTGCCCTGCCCCTGCAGTc  <  1:1818945/69‑1 (MQ=255)
                                                   gAAACGCTATTAGGCAGACCACCTTTAATAGCCGATTGCCTTGCCGGATTCTGCCCTGCCCCTGCAGTc  <  1:1688670/69‑1 (MQ=255)
                                                   gAAACGCTATTAGGCAGACCACCTTTAATAGCCGATTGCCTTGCCGGATTCTGCCCTGCCCCTGCAGTc  <  1:1519782/69‑1 (MQ=255)
                                                   gAAACGCTATTAGGCAGACCACCTTTAATAGCCGATTGCCTTGCCGGATTCTGCCCTGCCCCTGCAGTc  <  1:324544/69‑1 (MQ=255)
                                                   gAAACGCTATTAGGCAGACCACCTTTAATAGCCGATTGCCTTGCCGGATTCTGCCCTGCCCCTGCAGTc  <  1:1565125/69‑1 (MQ=255)
                                                   gAAACGCTATTAGGCAGACCACCTTTAATAGCCGATTGCCTTGCCGGATTCTGCCCTGCCCCTGCAGTc  <  1:1541132/69‑1 (MQ=255)
                                                   gAAACGCTATTAGGCAGACCACCTTTAATAGCCGATTGCCTTGCCGGATTCTGCCCTGCCCCTGCAGTc  <  1:2662044/69‑1 (MQ=255)
                                                   gAAACGCTATTAGGCAGACCACCTTTAATAGCCGATTGCCTTGCCGGATTCTGCCCTGCCCCTGCAGTc  <  1:380590/69‑1 (MQ=255)
                                                      aCGCTATTAGGCAGACCACCTTTAATAGCCGATTGCCTTGCCGGATTctgc                 >  1:2339530/1‑51 (MQ=255)
                                                      aCGCTATTAGGCAGACCACCTTTAATAGCCGATTGCCTTGCCGGATTctgc                 >  1:2580291/1‑51 (MQ=255)
                                                      aCGCTATTAGGCAGACCACCTTTAATAGCCGATTGCCTTGCCGGATTctgc                 >  1:838359/1‑51 (MQ=255)
                                                                 |                                                      
AGATGCAGTGCTTTAAGCCCGGAACCGCAAACGTCATTAATAGTGATTGCAGAAACGCTATTAGGCAGACCACCTTTAATAGCCGATTGCCTTGCCGGATTCTGCCCTGCCCCTGCAGTC  >  minE/1932340‑1932459

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