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 2,146,494 A→T 47.9% T71T (ACT→ACA)  yhbX ← predicted hydrolase, inner membrane

Read alignment evidence...
  seq id position ref new freq score (cons/poly) reads annotation genes product
*minE2,146,4940AT47.9% 16.1 / 203.7 169T71T (ACT→ACA) yhbXpredicted hydrolase, inner membrane
Reads supporting (aligned to +/- strand):  ref base A (73/15);  new base T (48/33);  total (121/48)
Fisher's exact test for biased strand distribution p-value = 1.06e-03
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 1.00e+00

Only 100 of 204 total aligned reads displayed.

GCAAATCCATCATTGAAAGTTGTACCAAAGGTACACCATGAATAGAGGCTAATACTCATGTCTGCCGCAGTCAGTAACACAAATGGTGCGGCAACAAGCAGGCGAAGCGGAAGGGATGATATACGTTT  >  minE/2146426‑2146553
                                                                    |                                                           
gCAAATCCATCATTGAAAGTTGTACCAAAGGTACACCATGAATAGAGGCTAATACTCATGTCTGCCGca                                                             >  1:230717/1‑69 (MQ=255)
gCAAATCCATCATTGAAAGTTGTACCAAAGGTACACCATGAATAGAGGCTAATACTCATGTCTGCCGca                                                             >  1:2281993/1‑69 (MQ=255)
gCAAATCCATCATTGAAAGTTGTACCAAAGGTACACCATGAATAGAGGCTAATACTCATGTCTGCCGca                                                             >  1:1242637/1‑69 (MQ=255)
      ccATCATTGAAAGTTGTACCAAAGGTACACCATGAATAGAGGCTAATACTCATGTCTGCCGcagtcagt                                                       <  1:1428706/69‑1 (MQ=255)
      ccATCATTGAAAGTTGTACCAAAGGTACACCATGAATAGAGGCTAATACTCATGTCTGCCGcagtcagt                                                       <  1:185529/69‑1 (MQ=255)
      ccATCATTGAAAGTTGTACCAAAGGTACACCATGAATAGAGGCTAATACTCATGTCTGCCGcagtcagt                                                       <  1:3013928/69‑1 (MQ=255)
      ccATCATTGAAAGTTGTACCAAAGGTACACCATGAATAGAGGCTAATACTCATGTCTGCCGcagtcagt                                                       <  1:1896988/69‑1 (MQ=255)
      ccATCATTGAAAGTTGTACCAAAGGTACACCATGAATAGAGGCTAATACTCATGTCTGCCGcagtcagt                                                       <  1:2880283/69‑1 (MQ=255)
      ccATCATTGAAAGTTGTACCAAAGGTACACCATGAATAGAGGCTAATACTCATGTCTGCCGcagtcagt                                                       >  1:3313379/1‑69 (MQ=255)
      ccATCATTGAAAGTTGTACCAAAGGTACACCATGAATAGAGGCTAATACTCATGTCTGCCGcagtcagt                                                       <  1:2757551/69‑1 (MQ=255)
      ccATCATTGAAAGTTGTACCAAAGGTACACCATGAATAGAGGCTAATACTCATGTCTGCCGcagtcagt                                                       <  1:423640/69‑1 (MQ=255)
      ccATCATTGAAAGTTGTACCAAAGGTACACCATGAATAGAGGCTAATACTCATGTCTGCCGcagtcagt                                                       >  1:2745422/1‑69 (MQ=255)
      ccATCATTGAAAGTTGTACCAAAGGTACACCATGAATAGAGGCTAATACTCATGTCTGCCGcagtcagt                                                       <  1:143499/69‑1 (MQ=255)
      ccATCATTGAAAGTTGTACCAAAGGTACACCATGAATAGAGGCTAATACTCATGTCTGCCGcagtcagt                                                       <  1:2605111/69‑1 (MQ=255)
      ccATCATTGAAAGTTGTACCAAAGGTACACCATGAATAGAGGCTAATACTCATGTCTGCCGcagtcagt                                                       <  1:1139395/69‑1 (MQ=255)
      ccATCATTGAAAGTTGTACCAAAGGTACACCATGAATAGAGGCTAATACTCATGTCTGCCGcagtcagt                                                       <  1:2373801/69‑1 (MQ=255)
      ccATCATTGAAAGTTGTACCAAAGGTACACCATGAATAGAGGCTAATACTCATGTCTGCCGcagtcagt                                                       <  1:939895/69‑1 (MQ=255)
              gAAAGTTGTACCAAAGGTACACCATGAATAGAGGCTAATACTCATGTCTGCCGCAGTCAGTAAcaca                                                 <  1:3287025/67‑1 (MQ=255)
                   ttGTACCAAAGGTACACCATGAATAGAGGCTAATACTCATGTCTGCCGCAGTCAGTAACACAAAt                                              >  1:2362562/1‑65 (MQ=255)
                   ttGTACCAAAGGTACACCATGAATAGAGGCTAATACTCATGTCTGCCGCAGTCAGTAACACAAATGGTg                                          >  1:1742163/1‑69 (MQ=255)
                   ttGTACCAAAGGTACACCATGAATAGAGGCTAATACTCATGTCTGCCGCAGTCAGTAACACAAATGGTg                                          >  1:2162224/1‑69 (MQ=255)
                   ttGTACCAAAGGTACACCATGAATAGAGGCTAATACTCATGTCTGCCGCAGTCAGTAACACAAATGGTg                                          >  1:2113134/1‑69 (MQ=255)
                   ttGTACCAAAGGTACACCATGAATAGAGGCTAATACTCATGTCTGCCGCAGTCAGTAACACAAATGGTg                                          >  1:2189810/1‑69 (MQ=255)
                   ttGTACCAAAGGTACACCATGAATAGAGGCTAATACTCATGTCTGCCGCAGTCAGTAACACAAATGGTg                                          >  1:2724763/1‑69 (MQ=255)
                   ttGTACCAAAGGTACACCATGAATAGAGGCTAATACTCATGTCTGCCGCAGTCAGTAACACAAATGGTg                                          >  1:2043676/1‑69 (MQ=255)
                   ttGTACCAAAGGTACACCATGAATAGAGGCTAATACTCATGTCTGCCGCAGTCAGTAACACAAATGGTg                                          >  1:975835/1‑69 (MQ=255)
                   ttGTACCAAAGGTACACCATGAATAGAGGCTAATACTCATGTCTGCCGCAGTCAGTAACACAAATGGTg                                          >  1:1100920/1‑69 (MQ=255)
                   ttGTACCAAAGGTACACCATGAATAGAGGCTAATACTCATGTCTGCCGCAGTCAGTAACACAAATGGTg                                          >  1:85491/1‑69 (MQ=255)
                   ttGTACCAAAGGTACACCATGAATAGAGGCTAATACTCATGTCTGCCGCAGTCAGTAACACAAATGGTg                                          >  1:829383/1‑69 (MQ=255)
                   ttGTACCAAAGGTACACCATGAATAGAGGCTAATACTCATGTCTGCCGCAGTCAGTAACACAAATGGTg                                          >  1:511767/1‑69 (MQ=255)
                   ttGTACCAAAGGTACACCATGAATAGAGGCTAATACTCATGTCTGCCGCAGTCAGTAACACAAATGGTg                                          >  1:1497247/1‑69 (MQ=255)
                   ttGTACCAAAGGTACACCATGAATAGAGGCTAATACTCATGTCTGCCGCAGTCAGTAACACAAATGGTg                                          >  1:2988265/1‑69 (MQ=255)
                   ttGTACCAAAGGTACACCATGAATAGAGGCTAATACTCATGTCTGCCGCAGTCAGTAACACAAATGGTg                                          >  1:716016/1‑69 (MQ=255)
                    tGTACCAAAGGTACACCATGAATAGAGGCTAATACTCATGTCTGCCGCTGTCAGTAACACAAATg                                             >  1:284236/1‑65 (MQ=255)
                    tGTACCAAAGGTACACCATGAATAGAGGCTAATACTCATGTCTGCCGCTGTCAGTAACACAAATGGTgt                                         >  1:548994/1‑68 (MQ=255)
                    tGTACCAAAGGTACACCATGAATAGAGGCTAATACTCATGTCTGCCGCTGTCAGTAACACAAATGGTgt                                         >  1:760546/1‑68 (MQ=255)
                    tGTACCAAAGGTACACCATGAATAGAGGCTAATACTCATGTCTGCCGCTGTCAGTAACACAAATGGTgt                                         >  1:2640514/1‑68 (MQ=255)
                    tGTACCAAAGGTACACCATGAATAGAGGCTAATACTCATGTCTGCCGCTGTCAGTAACACAAATGGTgt                                         >  1:640721/1‑68 (MQ=255)
                    tGTACCAAAGGTACACCATGAATAGAGGCTAATACTCATGTCTGCCGCTGTCAGTAACACAAATGGTgt                                         >  1:383767/1‑68 (MQ=255)
                    tGTACCAAAGGTACACCATGAATAGAGGCTAATACTCATGTCTGCCGCTGTCAGTAACACAAATGGTgt                                         >  1:2800375/1‑68 (MQ=255)
                    tGTACCAAAGGTACACCATGAATAGAGGCTAATACTCATGTCTGCCGCTGTCAGTAACACAAATGGTgt                                         >  1:3222565/1‑68 (MQ=255)
                    tGTACCAAAGGTACACCATGAATAGAGGCTAATACTCATGTCTGCCGCTGTCAGTAACACAAATGGTgt                                         >  1:2580067/1‑68 (MQ=255)
                    tGTACCAAAGGTACACCATGAATAGAGGCTAATACTCATGTCTGCCGCTGTCAGTAACACAAATGGTgt                                         >  1:3033681/1‑68 (MQ=255)
                    tGTACCAAAGGTACACCATGAATAGAGGCTAATACTCATGTCTGCCGCTGTCAGTAACACAAATGGTgt                                         >  1:1350743/1‑68 (MQ=255)
                    tGTACCAAAGGTACACCATGAATAGAGGCTAATACTCATGTCTGCCGCTGTCAGTAACACAAATGGTgt                                         >  1:1636808/1‑68 (MQ=255)
                    tGTACCAAAGGTACACCATGAATAGAGGCTAATACTCATGTCTGCCGCTGTCAGTAACACAAATGGTgt                                         >  1:1399107/1‑68 (MQ=255)
                    tGTACCAAAGGTACACCATGAATAGAGGCTAATACTCATGTCTGCCGCTGTCAGTAACACAAATGGTgt                                         >  1:1688605/1‑68 (MQ=255)
                    tGTACCAAAGGTACACCATGAATAGAGGCTAATACTCATGTCTGCCGCTGTCAGTAACACAAATGGTgt                                         >  1:1269239/1‑68 (MQ=255)
                    tGTACCAAAGGTACACCATGAATAGAGGCTAATACTCATGTCTGCCGCTGTCAGTAACACAAATGGTgt                                         >  1:1171965/1‑68 (MQ=255)
                    tGTACCAAAGGTACACCATGAATAGAGGCTAATACTCATGTCTGCCGCTGTCAGTAACACAAATGGTgt                                         >  1:178156/1‑68 (MQ=255)
                    tGTACCAAAGGTACACCATGAATAGAGGCTAATACTCATGTCTGCCGCTGTCAGTAACACAAATGGTgt                                         >  1:1958698/1‑68 (MQ=255)
                    tGTACCAAAGGTACACCATGAATAGAGGCTAATACTCAAGTCTGCCGCTGTCAGTAACACAAATGGTgt                                         >  1:1996781/1‑68 (MQ=255)
                    tGTACCAAAGGTACACAATGAATAGAGGCTAATACTCATGTCTGCCGCTGTCAGTAACACAAATGGTgt                                         >  1:635408/1‑68 (MQ=255)
                                 cacCATGAATAGAGGCTAATACTCATGTCTGCCGCAGTCAGTAACACAAATGGTGCGGCAACAAGCAg                             >  1:398105/1‑68 (MQ=255)
                                 cacCATGAATAGAGGCTAATACTCATGTCTGCCGCAGTCAGTAACACAAATGGTGCGGCAACAAGCAg                             >  1:951192/1‑68 (MQ=255)
                                 cacCATGAATAGAGGCTAATACTCATGTCTGCCGCAGTCAGTAACACAAATGGTGCGGCAACAAGCAg                             >  1:3082904/1‑68 (MQ=255)
                                 cacCATGAATAGAGGCTAATACTCATGTCTGCCGCAGTCAGTAACACAAATGGTGCGGCAACAAGCAg                             >  1:2529056/1‑68 (MQ=255)
                                    cATGAATAGAGGCTAATACTCATGTCTGCCGCTGTCAGTAACACAAATGGTGTGGCAACAAGCAGGCGa                         <  1:16093/69‑1 (MQ=255)
                                    cATGAATAGAGGCTAATACTCATGTCTGCCGCTGTCAGTAACACAAATGGTGTGGCAACAAGCAGGCGa                         <  1:439815/69‑1 (MQ=255)
                                    cATGAATAGAGGCTAATACTCATGTCTGCCGCTGTCAGTAACACAAATGGTGTGGCAACAAGCAGGCGa                         <  1:3371384/69‑1 (MQ=255)
                                    cATGAATAGAGGCTAATACTCATGTCTGCCGCTGTCAGTAACACAAATGGTGTGGCAACAAGCAGGCGa                         <  1:2378003/69‑1 (MQ=255)
                                    cATGAATAGAGGCTAATACTCATGTCTGCCGCTGTCAGTAACACAAATGGTGTGGCAACAAGCAGGCGa                         <  1:2417223/69‑1 (MQ=255)
                                    cATGAATAGAGGCTAATACTCATGTCTGCCGCTGTCAGTAACACAAATGGTGTGGCAACAAGCAGGCGa                         <  1:3206036/69‑1 (MQ=255)
                                    cATGAATAGAGGCTAATACTCATGTCTGCCGCTGTCAGTAACACAAATGGTGTGGCAACAAGCAGGCGa                         <  1:1020527/69‑1 (MQ=255)
                                    cATGAATAGAGGCTAATACTCATGTCTGCCGCTGTCAGTAACACAAATGGTGTGGCAACAAGCAGGCGa                         <  1:2608222/69‑1 (MQ=255)
                                    cATGAATAGAGGCTAATACTCATGTCTGCCGCTGTCAGTAACACAAATGGTGTGGCAACAAGCAGGCGa                         <  1:2219881/69‑1 (MQ=255)
                                    cATGAATAGAGGCTAATACTCATGTCTGCCGCTGTCAGTAACACAAATGGTGTGGCAACAAGCAGGCGa                         <  1:2694404/69‑1 (MQ=255)
                                    cATGAATAGAGGCTAATACTCATGTCTGCCGCTGTCAGTAACACAAATGGTGTGGCAACAAGCAGGCGa                         <  1:602071/69‑1 (MQ=255)
                                     aTGAATAGAGGCTAATACTCATGTCTGCCGCTGTCAGTAACACAAATGGTGTGGCAACAAGCAGGCGa                         <  1:2085267/68‑1 (MQ=255)
                                      tGAATAGAGGCTAATACTCATGTCTGCCGCTGTCAGTAACACAAATGGTGTGGCAACAAGCAGGCGa                         <  1:1069636/67‑1 (MQ=255)
                                      tGAATAGAGGCTAATACTCATGTCTGCCGCTGTCAGTAACACAAATGGTGTGGCAACAAGCAGGCGa                         <  1:358464/67‑1 (MQ=255)
                                       gAATAGAGCCTAATACTCATGTCTGCCGCTGTCAGTAACACAAATGGTGTGGCAACAAGCAGGCGa                         <  1:3133533/66‑1 (MQ=255)
                                            gagGCTAATACTCATGTCTGCCGCAGTCAGTAACACAAATGGTGCGGcaaca                                  <  1:2237879/52‑1 (MQ=255)
                                            gagGCTAATACTCATGTCTGCCGCAGTCAGTAACACAAATGGTGCGGCAACAAGCAGGCGAAGCgg                    <  1:464358/66‑1 (MQ=255)
                                                      cTCATGTCTGCCGCAGTCAGTAACACAAATGGTGCGGCAACAAGCAGGCGAAGCGGAAGGGATGAtata       >  1:66699/1‑69 (MQ=255)
                                                      cTCATGTCTGCCGCAGTCAGTAACACAAATGGTGCGGCAACAAGCAGGCGAAGCGGAAGGGATGAtata       >  1:615943/1‑69 (MQ=255)
                                                      cTCATGTCTGCCGCAGTCAGTAACACAAATGGTGCGGCAACAAGCAGGCGAAGCGGAAGGGATGAtata       >  1:92048/1‑69 (MQ=255)
                                                      cTCATGTCTGCCGCAGTCAGTAACACAAATGGTGCGGCAACAAGCAGGCGAAGCGGAAGGGATGAtata       >  1:528797/1‑69 (MQ=255)
                                                      cTCATGTCTGCCGCAGTCAGTAACACAAATGGTGCGGCAACAAGCAGGCGAAGCGGAAGGGATGAtata       >  1:1047779/1‑69 (MQ=255)
                                                        cATGTCTGCCGCAGTCAGTAACACAAATGGTGCGGCAACAAGCAGGCGAAGCGGAAGGgatga           >  1:587788/1‑63 (MQ=255)
                                                        cATGTCTGCCGCAGTCAGTAACACAAATGGTGCGGCAACAAGCAGGCGAAGCGGAAGGgatga           >  1:567892/1‑63 (MQ=255)
                                                        cATGTCTGCCGCAGTCAGTAACACAAATGGTGCGGCAACAAGCAGGCGAAGCGGAAGGgatga           >  1:1216846/1‑63 (MQ=255)
                                                        cATGTCTGCCGCAGTCAGTAACACAAATGGTGCGGCAACAAGCAGGCGAAGCGGAAGGgatga           >  1:489982/1‑63 (MQ=255)
                                                        cATGTCTGCCGCAGTCAGTAACACAAATGGTGCGGCAACAAGCAGGCGAAGCGGAAGGgatga           >  1:1616550/1‑63 (MQ=255)
                                                        cATGTCTGCCGCAGTCAGTAACACAAATGGTGCGGCAACAAGCAGGCGAAGCGGAAGGgatga           >  1:1654684/1‑63 (MQ=255)
                                                        cATGTCTGCCGCAGTCAGTAACACAAATGGTGCGGCAACAAGCAGGCGAAGCGGAAGGgatga           <  1:277855/63‑1 (MQ=255)
                                                        cATGTCTGCCGCAGTCAGTAACACAAATGGTGCGGCAACAAGCAGGCGAAGCGGAAGGgatga           >  1:2209379/1‑63 (MQ=255)
                                                        cATGTCTGCCGCAGTCAGTAACACAAATGGTGCGGCAACAAGCAGGCGAAGCGGAAGGgatga           >  1:2464845/1‑63 (MQ=255)
                                                        cATGTCTGCCGCAGTCAGTAACACAAATGGTGCGGCAACAAGCAGGCGAAGCGGAAGGgatga           >  1:2357721/1‑63 (MQ=255)
                                                            tCTGCCGCTGTCAGTAACACAAATGGTGTGGCAACAAGCAGGCGAAGCGGAAGGGATGATATACGttt  >  1:2321606/1‑68 (MQ=255)
                                                            tCTGCCGCTGTCAGTAACACAAATGGTGTGGCAACAAGCAGGCGAAGCGGAAGGGATGATATACGttt  >  1:1119252/1‑68 (MQ=255)
                                                            tCTGCCGCTGTCAGTAACACAAATGGTGTGGCAACAAGCAGGCGAAGCGGAAGGGATGATATACGttt  >  1:1696632/1‑68 (MQ=255)
                                                            tCTGCCGCTGTCAGTAACACAAATGGTGTGGCAACAAGCAGGCGAAGCGGAAGGGATGATATACGttt  >  1:3088485/1‑68 (MQ=255)
                                                            tCTGCCGCTGTCAGTAACACAAATGGTGTGGCAACAAGCAGGCGAAGCGGAAGGGATGATATACGttt  >  1:2867859/1‑68 (MQ=255)
                                                            tCTGCCGCTGTCAGTAACACAAATGGTGTGGCAACAAGCAGGCGAAGCGGAAGGGATGATATACGttt  >  1:2104784/1‑68 (MQ=255)
                                                            tCTGCCGCTGTCAGTAACACAAATGGTGTGGCAACAAGCAGGCGAAGCGGAAGGGATGATATACGttt  >  1:2135814/1‑68 (MQ=255)
                                                            tCTGCCGCTGTCAGTAACACAAATGGTGTGGCAACAAGCAGGCGAAGCGGAAGCgatga           >  1:2507252/1‑59 (MQ=255)
                                                            tCTGCCGCTGTCAGTAACACAAATGGTGTGGCAACAAGCAGGCGAAGCGCAAGGGATGATATACGttt  >  1:1749971/1‑68 (MQ=255)
                                                            tCTGCCGCAGTCAGTAACACAAATGGTGCGGCAACAAGCAGGCGAAGCGGAAGGGATGATATACGttt  >  1:3254476/1‑68 (MQ=255)
                                                            tCTGCCGCAGTCAGTAACACAAATGGTGCGGCAACAAGCAGGCGAAGCGGAAGGGATGATATACGttt  >  1:184477/1‑68 (MQ=255)
                                                                    |                                                           
GCAAATCCATCATTGAAAGTTGTACCAAAGGTACACCATGAATAGAGGCTAATACTCATGTCTGCCGCAGTCAGTAACACAAATGGTGCGGCAACAAGCAGGCGAAGCGGAAGGGATGATATACGTTT  >  minE/2146426‑2146553

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