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 2,643,149 C→T 34.7% L261L (CTG→TTG)  gntR → DNA‑binding transcriptional repressor

Read alignment evidence...
  seq id position ref new freq score (cons/poly) reads annotation genes product
*minE2,643,1490CT34.7% 67.6 / 51.1 92L261L (CTG→TTG) gntRDNA‑binding transcriptional repressor
Reads supporting (aligned to +/- strand):  ref base C (14/46);  new base T (27/5);  total (41/51)
Fisher's exact test for biased strand distribution p-value = 1.59e-08
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 1.00e+00

CGCAGCTGGATGGCGTGTTCTGTACGAATGATGACCTGGCGGTCGGCGCGGCGTTTGAATGTCAGCGTCTGGGGTTAAAAGTTCCTGACGATATGGCGATTGCCGGTTTCCACGGTCATGACATTGGTCAGGTGA  >  minE/2643081‑2643215
                                                                    |                                                                  
cGCAGCTGGATGGCGTGTTCTGTACGAATGATGACCTGGCGGTCGGCGCGGCGTTTGAATGTCAGCGTc                                                                    <  1:2499561/69‑1 (MQ=255)
cGCAGCTGGATGGCGTGTTCTGTACGAATGATGACCTGGCGGTCGGCGCGGCGTTTGAATGTCAGCGTc                                                                    <  1:2308536/69‑1 (MQ=255)
cGCAGCTGGATGGCGTGTTCTGTACGAATGATGACCTGGCGGTCGGCGCGGCGTTTGAATGTCAGCGTc                                                                    <  1:1206248/69‑1 (MQ=255)
cGCAGCTGGATGGCGTGTTCTGTACGAATGATGACCTGGCGGTCGGCGCGGCGTTTGAATGTCAGCGTc                                                                    <  1:1215449/69‑1 (MQ=255)
cGCAGCTGGATGGCGTGTTCTGTACGAATGATGACCTGGCGGTCGGCGCGGCGTTTGAATGTCAGCGTc                                                                    <  1:2388210/69‑1 (MQ=255)
 gCAGCTGGATGGCGTGTTCTGTACGAATGATGACCTGGCGGTCGGCGCGGCGTTTGAATGTCAGCGTc                                                                    <  1:3296946/68‑1 (MQ=255)
     cTGGATGGCGTGTTCTGTACGAATGATGACCTGGCGGTCGGCGCGGCGTTTGAATGTCAGCGTCTggg                                                                >  1:2263507/1‑68 (MQ=255)
     cTGGATGGCGTGTTCTGTACGAATGATGACCTGGCGGTCGGCGCGGCGTTTGAATGTCAGCGTCTggg                                                                >  1:2514866/1‑68 (MQ=255)
     cTGGATGGCGTGTTCTGTACGAATGATGACCTGGCGGTCGGCGCGGCGTTTGAATGTCAGCGTCTggg                                                                >  1:3114869/1‑68 (MQ=255)
     cTGGATGGCGTGTTCTGTACGAATGATGACCTGGCGGTCGGCGCGGCGTTTGAATGTCAGCGTCTggg                                                                >  1:2380239/1‑68 (MQ=255)
     cTGGATGGCGTGTTCTGTACGAATGATGACCTGGCGGTCGGCGCGGCGTTTGAATGTCAGCGTCTggg                                                                >  1:4597/1‑68 (MQ=255)
     cTGGATGGCGTGTTCTGTACGAATGATGACCTGGCGGTCGGCGCGGCGTTTGAATGTCAGCGTCTggg                                                                >  1:1909568/1‑68 (MQ=255)
     cTGGATGGCGTGTTCTGTACGAATGATGACCTGGCGGTCGGCGCGGCGTTTGAATGTCAGCGTCTggg                                                                >  1:1286646/1‑68 (MQ=255)
     cTGGATGGCGTGTTCTGTACGAATGATGACCTGGCGGTCGGCGCGGCGTTTGAATGTCAGCGTCTggg                                                                >  1:606541/1‑68 (MQ=255)
     cTGGATGGCGTGTTCTGTACGAATGATGACCTGGCGGTCGGCGCGGCGTTTGAATGTCAGCGTCTggg                                                                >  1:1127343/1‑68 (MQ=255)
     cTGGATGGCGTGTTCTGTACGAATGATCACCTGGCGGTCGGCGCGGCGTTTGAATGTCAGCGTCTggg                                                                >  1:2353820/1‑68 (MQ=255)
          tGGCGTGTTCTGTACGAATGATGACCTGGCGGTCGGCGCGGCGTTTGAATGTCAGCGTCTGGGGTTaaa                                                          <  1:3268859/69‑1 (MQ=255)
               tgtTCTGTACGAATGATGACCTGGCGGTCGGCGCGGCGTTTGAATGTCAGCGTc                                                                    <  1:588323/54‑1 (MQ=255)
                     gTACGAATGATGACCTGGCGGTCGGCGCGGCGTTTGAATGTCAGCGTCTGGGGTTAAAAGTTCCTGAc                                                <  1:1910802/68‑1 (MQ=255)
                     gTACGAATGATGACCTGGCGGTCGGCGCGGCGTTTGAATGTCAGCGTCTGGGGTTAAAAGTTCCTGAc                                                <  1:2883095/68‑1 (MQ=255)
                        cgtatgatgACCTGGCGGTCGGCGCGGCGTTTGAATGTCAGCGTCTGGGGTTAAAAGTTCCTGACGa                                              <  1:87493/64‑1 (MQ=255)
                        cGAATGATGACCTGGCGGTCGGCGCGGCGTTTGAATGTCAGCGTCTGGGGTTAAAAGTTCCTGACGa                                              <  1:2722124/67‑1 (MQ=255)
                        cGAATGATGACCTGGCGGTCGGCGCGGCGTTTGAATGTCAGCGTCTGGGGTTAAAAGTTCCTGACGa                                              <  1:2894190/67‑1 (MQ=255)
                        cGAATGATGACCTGGCGGTCGGCGCGGCGTTTGAATGTCAGCGTCTGGGGTTAAAAGTTCCTGACGa                                              <  1:2982307/67‑1 (MQ=255)
                        cGAATGATGACCTGGCGGTCGGCGCGGCGTTTGAATGTCAGCGTCTGGGGTTAAAAGTTCCTGACGa                                              <  1:2459356/67‑1 (MQ=255)
                        cGAATGATGACCTGGCGGTCGGCGCGGCGTTTGAATGTCAGCGTCTGGGGTTAAAAGTTCCTGACGa                                              <  1:2434823/67‑1 (MQ=255)
                        cGAATGATGACCTGGCGGTCGGCGCGGCGTTTGAATGTCAGCGTCTGGGGTTAAAAGTTCCTGACGa                                              <  1:3243197/67‑1 (MQ=255)
                        cGAATGATGACCTGGCGGTCGGCGCGGCGTTTGAATGTCAGCGTCTGGGGTTAAAAGTTCCTGACGa                                              <  1:3245259/67‑1 (MQ=255)
                        cGAATGATGACCTGGCGGTCGGCGCGGCGTTTGAATGTCAGCGTCTGGGGTTAAAAGTTCCTGACGa                                              <  1:45533/67‑1 (MQ=255)
                        cGAATGATGACCTGGCGGTCGGCGCGGCGTTTGAATGTCAGCGTCTGGGGTTAAAAGTTCCTGACGa                                              <  1:544936/67‑1 (MQ=255)
                        cGAATGATGACCTGGCGGTCGGCGCGGCGTTTGAATGTCAGCGTCTGGGGTTAAAAGTTCCTGACGa                                              <  1:609865/67‑1 (MQ=255)
                        cGAATGATGACCTGGCGGTCGGCGCGGCGTTTGAATGTCAGCGTCTGGGGTTAAAAGTTCCTGACGa                                              <  1:720936/67‑1 (MQ=255)
                        cGAATGATGACCTGGCGGTCGGCGCGGCGTTTGAATGTCAGCGTCTGGGGTTAAAAGTTCCTGACGa                                              <  1:1051287/67‑1 (MQ=255)
                        cGAATGATGACCTGGCGGTCGGCGCGGCGTTTGAATGTCAGCGTCTGGGGTTAAAAGTTCCTGACGa                                              <  1:1834382/67‑1 (MQ=255)
                        cGAATGATGACCTGGCGGTCGGCGCGGCGTTTGAATGTCAGCGTCTGGGGTTAAAAGTTCCTGACGa                                              <  1:1605358/67‑1 (MQ=255)
                        cGAATGATGACCTGGCGGTCGGCGCGGCGTTTGAATGTCAGCGTCTGGGGTTAAAAGTTCCTGACGa                                              <  1:2005725/67‑1 (MQ=255)
                        cGAATGATGACCTGGCGGTCGGCGCGGCGTTTGAATGTCAGCGTCTGGGGTTAAAAGTTCCTGACGa                                              <  1:162038/67‑1 (MQ=255)
                        cGAATGATGACCTGGCGGTCGGCGCGGCGTTTGAATGTCAGCGTCTGGGGTTAAAAGTTCCTGACGa                                              <  1:1397360/67‑1 (MQ=255)
                        cGAATGATGACCTGGCGGTCGGCGCGGCGTTTGAATGTCAGCGTCTGGGGTTAAAAGTTCCTGACGa                                              <  1:1898219/67‑1 (MQ=255)
                        cGAATGATGACCTGGCGGTCGGCGCGGCGTTTGAATGTCAGCGTCTGGGGTTAAAAGTTCCTGACGa                                              <  1:1282452/67‑1 (MQ=255)
                        cGAATGATGACCTGGCGGTCGGCGCGGCGTTTGAATGTCAGCGTCTGGGGTTAAAAGTTCCTGACGa                                              <  1:1622150/67‑1 (MQ=255)
                          aaTGATGACCTGGCGGTCGGCGCGGCGTTTGAATGTCAGCGTTTGGGGTTAAAAGt                                                       >  1:2084875/1‑56 (MQ=255)
                          aaTGATGACCTGGCGGTCGGCGCGGCGTTTGAATGTCAGCGTTTGGGGTTAAAAGTTCCTGCCGATATg                                          >  1:2990037/1‑69 (MQ=255)
                          aaTGATGACCTGGCGGTCGGCGCGGCGTTTGAATGTCAGCGTTTGGGGTTAAAAGTTCCTGACGatat                                           >  1:2356936/1‑68 (MQ=255)
                          aaTGATGACCTGGCGGTCGGCGCGGCGTTTGAATGTCAGCGTTTGGGGTTAAAAGTTCCTGACGatat                                           >  1:2361003/1‑68 (MQ=255)
                          aaTGATGACCTGGCGGTCGGCGCGGCGTTTGAATGTCAGCGTTTGGGGTTAAAAGTTCCTGACGATATg                                          >  1:906561/1‑69 (MQ=255)
                          aaTGATGACCTGGCGGTCGGCGCGGCGTTTGAATGTCAGCGTTTGGGGTTAAAAGTTCCTGACGATATg                                          >  1:388212/1‑69 (MQ=255)
                          aaTGATGACCTGGCGGTCGGCGCGGCGTTTGAATGTCAGCGTTTGGGGTTAAAAGTTCCTGACGATATg                                          >  1:3079155/1‑69 (MQ=255)
                          aaTGATGACCTGGCGGTCGGCGCGGCGTTTGAATGTCAGCGTTTGGGGTTAAAAGTTCCTGACGATATg                                          >  1:903408/1‑69 (MQ=255)
                             gatgaCCTGGCGGTCGGCGCGGCGTTTGAATGTCAGCGTCTGGGGTTAAAAGTTCCTGACGa                                              <  1:721520/62‑1 (MQ=255)
                             gatgaCCTGGCGGTCGGCGCGGCGTTTGAATGTCAGCGTCTGGGGTTAAAAGTTCCTGACGATATGTCg                                       <  1:2961768/69‑1 (MQ=255)
                             gatgaCCTGGCGGTCGGCGCGGCGTTTGAATGTCAGCGTCTGGGGTTAAAAGTTCCTGACGATATGGCg                                       <  1:3323594/69‑1 (MQ=255)
                             gatgaCCTGGCGGTCGGCGCGGCGTTTGAATGTCAGCGTCTGGGGTTAAAAGTTCCTGACGATATGGCg                                       <  1:3011365/69‑1 (MQ=255)
                             gatgaCCTGGCGGTCGGCGCGGCGTTTGAATGTCAGCGTCTGGGGTTAAAAGTTCCTGACGATATGGCg                                       <  1:2599945/69‑1 (MQ=255)
                             gatgaCCTGGCGGTCGGCGCGGCGTTTGAATGTCAGCGTCTGGGGTTAAAAGTTCCTGACGATATGGCg                                       <  1:2558403/69‑1 (MQ=255)
                             gatgaCCTGGCGGTCGGCGCGGCGTTTGAATGTCAGCGTCTGGGGTTAAAAGTTCCTGACGATATGGCg                                       <  1:2553240/69‑1 (MQ=255)
                             gatgaCCTGGCGGTCGGCGCGGCGTTTGAATGTCAGCGTCTGGGGTTAAAAGTTCCTGACGATATGGCg                                       <  1:1441973/69‑1 (MQ=255)
                             gatgaCCTGGCGGTCGGCGCGGCGTTTGAATGTCAGCGTCTGGGGTTAAAAGTTCCTGACGATATGGCg                                       <  1:551169/69‑1 (MQ=255)
                             gatgaCCTGGCGGTCGGCGCGGCGTTTGAATGTCAGCGTCTGGGGTTAAAAGTTCCTGACGATATGGCg                                       <  1:1280609/69‑1 (MQ=255)
                             gatgaCCTGGCGGTCGGCGCGGCGTTTGAATGTCAGCGTCTGGGGTTAAAAGTTCCTGACGATATGGCg                                       <  1:2300334/69‑1 (MQ=255)
                             gatgaCCTGGCGGTCGGCGCGGCGTTTGAATGTCAGCGTCTGGGGTTAAAAGTTCCTGACGATATGGCg                                       <  1:708268/69‑1 (MQ=255)
                              atgaCCTGGCGGTCGGCGCGGCGTTTGAATGTCAGCGTCTGGGGTTAAAAGTTCCTGACGATATGGCg                                       <  1:3146923/68‑1 (MQ=255)
                                       cGGTCGGCGCGGCGTTTGAATGTCAGCGTCTGGGGTTAAAAGTTCCTGACGa                                              <  1:156384/52‑1 (MQ=255)
                                         gTCGGCGCGGCGTTTGAATGTCAGCGTTTGGGGTTGAAAGTTCCTGACGATATGGCGATTGCCGGTTTc                           <  1:597032/69‑1 (MQ=255)
                                         gTCGGCGCGGCGTTTGAATGTCAGCGTTTGGGGTTGAAAGTTCCTGACGATATGGCGATTGCCGGTTTc                           <  1:2054812/69‑1 (MQ=255)
                                          tCGGCGCGGCGTTTGAATGTCAGCGTTTGGGGTTGAAAGTTCCTGACGATATGGCGATTGCCGGTTTc                           <  1:2724968/68‑1 (MQ=255)
                                            ggcgcggcgTTTGAATGTCAGCGTTTGGGGTTGAAAGTTCCTGACGATATGGCGATTGCCGGTTTc                           <  1:2667721/66‑1 (MQ=255)
                                              cgcggcgTTTGAATGTCAGCGTTTGGGGTTGAAAGTTCCTGACGatat                                           >  1:621809/1‑48 (MQ=255)
                                              cgcggcgTTTGAATGTCAGCGTTTGGGGTTGAAAGTTCCTGACGATATGGCGATTGCCGGTTTCCACg                       >  1:1860222/1‑68 (MQ=255)
                                              cgcggcgTTTGAATGTCAGCGTTTGGGGTTGAAAGTTCCTGACGATATGGCGATTGCCGGTTTCCACg                       >  1:2027354/1‑68 (MQ=255)
                                              cgcggcgTTTGAATGTCAGCGTTTGGGGTTGAAAGTTCCTGACGATATGGCGATTGCCGGTTTCCACg                       >  1:2073124/1‑68 (MQ=255)
                                              cgcggcgTTTGAATGTCAGCGTTTGGGGTTGAAAGTTCCTGACGATATGGCGATTGCCGGTTTCCACg                       >  1:900656/1‑68 (MQ=255)
                                              cgcggcgTTTGAATGTCAGCGTTTGGGGTTGAAAGTTCCTGACGATATGGCGATTGCCGGTTTCCACg                       >  1:828313/1‑68 (MQ=255)
                                              cgcggcgTTTGAATGTCAGCGTTTGGGGTTGAAAGTTCCTGACGATATGGCGATTGCCGGTTTCCACg                       >  1:635630/1‑68 (MQ=255)
                                              cgcggcgTTTGAATGTCAGCGTTTGGGGTTGAAAGTTCCTGACGATATGGCGATTGCCGGTTTCCACg                       >  1:603732/1‑68 (MQ=255)
                                              cgcggcgTTTGAATGTCAGCGTTTGGGGTTGAAAGTTCCTGACGATATGGCGATTGCCGGTTTCCACg                       >  1:187292/1‑68 (MQ=255)
                                              cgcggcgTTTGAATGTCAGCGTTTGGGGTTGAAAGTTCCTGACGATATGGCGATTGCCGGTTTCCACg                       >  1:1864250/1‑68 (MQ=255)
                                              cgcggcgTTTGAATGTCAGCGTTTGGGGTTGAAAGTTCCTGACGATATGGCGATTGCCGGTTTCCACg                       >  1:1514715/1‑68 (MQ=255)
                                              cgcggcgTTTGAATGTCAGCGTTTGGGGTTGAAAGTTCCTGACGATATGGCGATTGCCGGTTTCCACg                       >  1:1814975/1‑68 (MQ=255)
                                              cgcggcgTTTGAATGTCAGCGTTTGGGGTTGAAAGTTCCTGACGATATGGCGATTGCCGGTTTCCACg                       >  1:3137323/1‑68 (MQ=255)
                                              cgcggcgTTTGAATGTCAGCGTTTGGGGTTGAAAGTTCCTGACGATATGGCGATTGCCGGTTTCCACg                       >  1:2927317/1‑68 (MQ=255)
                                              cgcggcgTTTGAATGTCAGCGTTTGGGGTTGAAAGTTCCTGACGATATGGCGATTGCCGGTTTCCACg                       >  1:3351024/1‑68 (MQ=255)
                                              cgcggcgTTTGAATGTCAGCGTTTGGGGTTGAAAGTTCCTGACGATATGGCGATTGCCGGTTTCCACg                       >  1:1803385/1‑68 (MQ=255)
                                              cgcggcgTTTGAATGTCAGCGTTTGGGGTTGAAAGTTCCTGACGATATGGCGATTGCCGGTTTCCACg                       >  1:1657455/1‑68 (MQ=255)
                                              cgcggcgTTTGAATGTCAGCGTTTGGGGTTGAAAGTTCCTGACGATATGGAGATTGCCGGTTTCCACg                       >  1:747139/1‑68 (MQ=255)
                                              cgcggcgTTTGAATATCAGCGTTTGGGGTTGAAAGTTCCTGACGATATGGCGATTGCCGGTTTCCACg                       >  1:1014453/1‑68 (MQ=39)
                                               gcggcgTTTGAATGTCAGCGTTTGGGGTTGAAAGTTCCTGACGATATGGCGATTGCCGGTTTc                           <  1:318421/63‑1 (MQ=255)
                                                    gTTTGAATGTCAGCGTCTGGGGTTAAAAGTTCCTGACGATATGGCGATTGCCGGTTTCCACGGTCATGa                >  1:2353999/1‑69 (MQ=255)
                                                    gTTTGAATGTCAGCGTCTGGGGTTAAAAGTTCCTGACGATATGGCGATTGCCGGTTTCCACGGTCATGa                >  1:1994381/1‑69 (MQ=255)
                                                     tttGAATGTCAGCGTCTGGGGTTAAAAGTTCCTGACGATATGGCGATTGCCGGTTTCCACGGTCATGAc               <  1:1661573/69‑1 (MQ=255)
                                                     tttGAATGTCAGCGTCTGGGGTTAAAAGTTCCTGACGATATGGCGATTGCCGGTTTCCACGGTCATGAc               <  1:3407873/69‑1 (MQ=255)
                                                       tGAATGTCAGCGTCTGGGGTTAAAAGTTCCTGACGATATGGCGATTGCCGGTTTCCACGGTCATGACAt             >  1:1666587/1‑69 (MQ=255)
                                                              cAGCGTCTGGGGTTAAAAGTTCCTGACGATATGGCGATTGCCGGTTTCCACGGTCATGACATTGGTCAg      >  1:2299486/1‑69 (MQ=255)
                                                                  gTCTGGGGTTAAAAGTTCCTGACGATATGGCGATTGCCGGTTTCCACGGTCATGACATTGGTCAGGTGa  <  1:1167610/69‑1 (MQ=255)
                                                                  gTCTGGGGTTAAAAGTTCCTGACGATATGGCGATTGCCGGTTTCCACGGTCATGACATTGGTCAGGTGa  <  1:2103445/69‑1 (MQ=255)
                                                                  gTCTGGGGTTAAAAGTTCCTGACGATATGGCGATTGCCGGTTTCCACGGTCATGACATTGGTCAGGTGa  <  1:1697455/69‑1 (MQ=255)
                                                                  gTCTGGGGTTAAAAGTTCCTGACGATATGGCGATTGCCGGTTTCCACGGTCATGACATTGGTCAGGTGa  <  1:1811023/69‑1 (MQ=255)
                                                                  gTCTGGGGTTAAAAGTTCCTGACGATATGGCGATTGCCGGTTTCCACGGTCATGACATTGGTCAGGTGa  <  1:1851831/69‑1 (MQ=255)
                                                                   tCTGGGGTTAAAAGTTCCTGACGATATGGCGATTGCCGGTTTCCACGGTCATGACATTGGTCAGGTGa  <  1:3411230/68‑1 (MQ=255)
                                                                    |                                                                  
CGCAGCTGGATGGCGTGTTCTGTACGAATGATGACCTGGCGGTCGGCGCGGCGTTTGAATGTCAGCGTCTGGGGTTAAAAGTTCCTGACGATATGGCGATTGCCGGTTTCCACGGTCATGACATTGGTCAGGTGA  >  minE/2643081‑2643215

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