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 2,588,902 A→G 30.1% N141N (AAT→AAC)  gadE ← DNA‑binding transcriptional activator

Read alignment evidence...
  seq id position ref new freq score (cons/poly) reads annotation genes product
*minE2,588,9020AG30.1% 107.4 / 55.6 116N141N (AAT→AAC) gadEDNA‑binding transcriptional activator
Reads supporting (aligned to +/- strand):  ref base A (24/57);  new base G (8/27);  total (32/84)
Fisher's exact test for biased strand distribution p-value = 5.05e-01
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 9.45e-01

Only 100 of 151 total aligned reads displayed.

TCATACGTCTTAGTTTCAGCTTGTACATAATGTTGAATTTCTGAATCTTTAATGTTTGTTGCGAAATATTGAGCGTCGACGTGATATTGCTTTCATTTTTATTTTTCAGAATCAGTTGCATAATTTTGAACTGAT  >  minE/2588835‑2588969
                                                                   |                                                                   
tCATACGTCTTAGTTTCAGCTTGTACATAATGTTGAATTTCTGAATCTTTAATGTTTGTTGCGAAata                                                                     <  1:2527415/68‑1 (MQ=255)
tCATACGTCTTAGTTTCAGCTTGTACATAATGTTGAATTTCTGAATCTTTAATGTTTGTTGCGAAata                                                                     <  1:2746143/68‑1 (MQ=255)
tCATACGTCTTAGTTTCAGCTTGTACATAATGTTGAATTTCTGAATCTTTAATGTTTGTTGCGAAata                                                                     <  1:339221/68‑1 (MQ=255)
 cATACGTCTTAGTTTCAGCTTGTACATAATGTTGAATTTCTGAATCTTTAATGTTTGTTGCGAAata                                                                     <  1:2510040/67‑1 (MQ=255)
    aCGTCTTAGTTTCAGCTTGTACATAATGTTGAATTTCTGAATCTTTAATGTTTGTTGCGAAATATTg                                                                  <  1:1891374/67‑1 (MQ=255)
    aCGTCTTAGTTTCAGCTTGTACATAATGTTGAATTTCTGAATCTTTAATGTTTGTTGCGAAATATTg                                                                  <  1:2062896/67‑1 (MQ=255)
    aCGTCTTAGTTTCAGCTTGTACATAATGTTGAATTTCTGAATCTTTAATGTTTGTTGCGAAATATTg                                                                  <  1:1746370/67‑1 (MQ=255)
    aCGTCTTAGTTTCAGCTTGTACATAATGTTGAATTTCTGAATCTTTAATGTTTGTTGCGAAATATTg                                                                  <  1:2311292/67‑1 (MQ=255)
    aCGTCTTAGTTTCAGCTTGTACATAATGTTGAATTTCTGAATCTTTAATGTTTGTTGCGAAATATTg                                                                  <  1:2553746/67‑1 (MQ=255)
    aCGTCTTAGTTTCAGCTTGTACATAATGTTGAATTTCTGAATCTTTAATGTTTGTTGCGAAATATTg                                                                  <  1:1583759/67‑1 (MQ=255)
    aCGTCTTAGTTTCAGCTTGTACATAATGTTGAATTTCTGAATCTTTAATGTTTGTTGCGAAATATTg                                                                  <  1:1406605/67‑1 (MQ=255)
    aCGTCTTAGTTTCAGCTTGTACATAATGTTGAATTTCTGAATCTTTAATGTTTGTTGCGAAATATTg                                                                  <  1:3169343/67‑1 (MQ=255)
    aCGTCTTAGTTTCAGCTTGTACATAATGTTGAATTTCTGAATCTTTAATGTTTGTTGCGAAATATTg                                                                  <  1:3295554/67‑1 (MQ=255)
    aCGTCTTAGTTTCAGCTTGTACATAATGTTGAATTTCTGAATCTTTAATGTTTGTTGCGAAATATTg                                                                  <  1:794265/67‑1 (MQ=255)
    aCGTCTTAGTTTCAGCTTGTACATAATGTTGAATTTCTGAATCTTTAATGTTTGTTGCGAAATATTGAg                                                                <  1:2275720/69‑1 (MQ=255)
    aCGTCTTAGTTTCAGCTTGTACATAATGTTGAATTTCTGAATCTTTAATGTTTGTTGCGAAATATTGAg                                                                <  1:2734239/69‑1 (MQ=255)
    aCGTCTTAGTTTCAGCTTGTACATAATGTTGAATTTCTGAATCTTTAATGTTTGTTGCGAAATATTGAg                                                                <  1:695639/69‑1 (MQ=255)
    aCGTCTTAGTTTCAGCTTGTACATAATGTTGAATTTCTGAATCTTTAATGTTTGTTGAGAAATATTg                                                                  <  1:2599769/67‑1 (MQ=255)
     cGTCTTAGTTTCAGCTTGTACATAATGTTGAATTTCTGAATCTTTAATGTTTGTTGCGAAATATTGa                                                                 >  1:1738351/1‑67 (MQ=255)
     cGTCTTAGTTTCAGCTTGTACATAATGTTGAATTTCTGAATCTTTAATGTTTGTTGCGAAATATTGAGc                                                               >  1:3423825/1‑69 (MQ=255)
     cGTCTTAGTTTCAGCTTGTACATAATGTTGAATTTCTGAATCTTTAATGTTTGTTGCGAAATATTGAGc                                                               >  1:1067800/1‑69 (MQ=255)
     cGTCTTAGTTTCAGCTTGTACATAATGTTGAATTTCTGAATCTTTAATGTTTGTTGCGAAATATTGAGc                                                               >  1:546648/1‑69 (MQ=255)
     cGTCTTAGTTTCAGCTTGTACATAATGTTGAATTTCTGAATCTTTAATGTTTGTTGCGAAATATTGAGc                                                               >  1:1859850/1‑69 (MQ=255)
     cGTCTTAGTTTCAGCTTGTACATAATGTTGAATTTCTGAATCTTTAATGTTTGTTGCGAAATATTGAGc                                                               >  1:906530/1‑69 (MQ=255)
     cGTCATAGTTTCAGCTTGTACATAATGTTGAATTTCTGAATCTTTAATGTTTGTTGCGAAATATTGAGc                                                               >  1:1942355/1‑69 (MQ=255)
         ttAGTTTCAGCTTGTACATAATGTTGAATTTCTGAATCTTTAATGTTTGTTGCGAAATATTGAGCGTCg                                                           >  1:1440101/1‑69 (MQ=255)
         ttAGTTTCAGCTTGTACATAATGTTGAATTTCTGAATCTTTAATGTTTGTTGCGAAATATTGAGCGTCg                                                           >  1:1433840/1‑69 (MQ=255)
         ttAGTTTCAGCTTGTACATAATGTTGAATTTCTGAATCTTTAATGTTTGTTGCGAAATATTGAGCGTCg                                                           >  1:2894780/1‑69 (MQ=255)
         ttAGTTTCAGCTTGTACATAATGTTGAATTTCTGAATCTTTAATGTTTGTTGCGAAATATTGAGCGTCg                                                           >  1:1058316/1‑69 (MQ=255)
         ttAGTTTCAGCTTGTACATAATGTTGAATTTCTGAATCTTTAATGTTTGTTGCGAAATATTGAGCGTCg                                                           >  1:2008389/1‑69 (MQ=255)
         ttAGTTTCAGCTTGTACATAATGTTGAATTTCTGAATCTTTAATGTTTGTTGCGAAATATTGAGCGTCg                                                           >  1:925478/1‑69 (MQ=255)
         ttAATTTCAGCTTGTACATAATGTTGAATTTCTGAATCTTTAATGTTTGTTGCGAAATGTTGAGCGttg                                                           <  1:1045684/69‑3 (MQ=255)
         ttAATTTCAGCTTGTACATAATGTTGAATTTCTGAATCTTTAATGTTTGTTGCGAAATGTTGAGCGttg                                                           <  1:2170305/69‑3 (MQ=255)
         ttAATTTCAGCTTGTACATAATGTTGAATTTCTGAATCTTTAATGTTTGTTGCGAAATGTTGAGCGttg                                                           <  1:643357/69‑3 (MQ=255)
         ttAATTTCAGCTTGTACATAATGTTGAATTTCTGAATCTTTAATGTTTGTTGCGAAATGTTGAGCGttg                                                           <  1:27008/69‑3 (MQ=255)
         ttAATTTCAGCTTGTACATAATGTTGAATTTCTGAATCTTTAATGTTTGTTGCGAAATGTTGAGCGttg                                                           <  1:3384923/69‑3 (MQ=255)
         ttAATTTCAGCTTGTACATAATGTTGAATTTCTGAATCTTTAATGTTTGTTGCGAAATGTTGAGCGttg                                                           <  1:1238100/69‑3 (MQ=255)
         ttAATTTCAGCTTGTACATAATGTTGAATTTCTGAATCTTTAATGTTTGTTGCGAAATGTTGAGCGttg                                                           <  1:1276739/69‑3 (MQ=255)
         ttAATTTCAGCTTGTACATAATGTTGAATTTCTGAATCTTTAATGTTTGTTGCGAAATGTTGAGCGttg                                                           <  1:1820989/69‑3 (MQ=255)
         ttAATTTCAGCTTGTACATAATGTTGAATTTCTGAATCTTTAATGTTTGTTGCGAAATGTTGAGCGttg                                                           <  1:1520889/69‑3 (MQ=255)
         ttAATTTCAGCTTGTACATAATGTTGAATTTCTGAATCTTTAATGTTTGTTGCGAAATGTTGAGCGttg                                                           <  1:1647829/69‑3 (MQ=255)
         ttAATTTCAGCTTGTACATAATGTTGAATTTCTGAATCTTTAATGTTTGTTGCGAAATGTTGAGCGttg                                                           <  1:1721028/69‑3 (MQ=255)
         ttAATTTCAGATTGTACATAATGTTGAATTTCTGAATCTTTAATGTTTGTTGCGAAATGTTGAGCGttg                                                           <  1:1009978/69‑3 (MQ=255)
             tttCAGCTTGTACATAATGTTGAATTTCTGAATCTTTAATGTTTGTTGCGAAATATTGAGCGTCGa                                                          <  1:3360574/66‑1 (MQ=255)
             tttCAGCTTGTACATAATGTTGAATTTCTGAATCTTTAATGTTTGTTGCGAAATATTGAGCGTCGa                                                          <  1:1304467/66‑1 (MQ=255)
             tttCAGCTTGTACATAATGTTGAATTTCTGAATCTTTAATGTTTGTTGCGAAATATTGAGCGTCGa                                                          <  1:3134319/66‑1 (MQ=255)
             tttCAGCTTGTACATAATGTTGAATTTCTGAATCTTTAATGTTTGTTGCGAAATATTGAGCGTCGa                                                          <  1:746878/66‑1 (MQ=255)
             tttCAGCTTGTACATAATGTTGAATTTCTGAATCTTTAATGTTTGTTGCGAAATATTGAGCGTCGa                                                          <  1:2480216/66‑1 (MQ=255)
             tttCAGCTTGTACATAATGTTGAATTTCTGAATCTTTAATGTTTGTTGCGAAATATTGAGCGTCGa                                                          <  1:2270225/66‑1 (MQ=255)
               tCAGCTTGTACATAATGTTGAATTTCTGAATCTTTAATGTTTGTTGCGAAATATTGAGCGTCGACGTGa                                                     <  1:1586551/69‑1 (MQ=255)
                   cTTGTACATAATGTTGAATTTCTGAATCTTTAATGTTTGTTGCGAAATATTGAGCGTCGACGTGATAtt                                                 <  1:66/69‑1 (MQ=255)
                   cTTGTACATAATGTTGAATTTCTGAATCTTTAATGTTTGTTGCGAAATATTGAGCGTCGACGTGATAtt                                                 <  1:134675/69‑1 (MQ=255)
                   cTTGTACATAATGTTGAATTTCTGAATCTTTAATGTTTGTTGCGAAATATTGAGCGTCGACGTGATAtt                                                 <  1:1517379/69‑1 (MQ=255)
                    ttGTACATAATGTTGAATTTCTGAATCTTTAATGTTTGTTGCGAAATATTGAGCGTCGACGTGATAtt                                                 <  1:2384552/68‑1 (MQ=255)
                     tGTACATAATGTTGAATTTCTGAATCTTTAATGTTTGTTGCGTAATATTGAGCGTc                                                            <  1:1106103/56‑1 (MQ=255)
                     tGTACATAATGTTGAATTTCTGAATCTTTAATGTTTGTTGCGAAATATTGAGCGTc                                                            <  1:1316983/56‑1 (MQ=255)
                     tGTACATAATGTTGAATTTCTGAATCTTTAATGTTTGTTGCGAAATATTGAGCGTc                                                            <  1:1215392/56‑1 (MQ=255)
                         cATAATGTTGAATTTCTGAATCTTTAATGTTTGTTGCGAAATATTGAGCGTCGACGTGa                                                     <  1:2788357/59‑1 (MQ=255)
                         cATAATGTTGAATTTCTGAATCTTTAATGTTTGTTGCGAAATATTGAGCGTCGACGTGa                                                     <  1:2898030/59‑1 (MQ=255)
                         cATAATGTTGAATTTCTGAATCTTTAATGTTTGTTACGAAATATTGAGCGTCGACGTGa                                                     <  1:2009462/59‑1 (MQ=255)
                            aaTGTTGAATTTCTGAATCTTTAATGTTTGTTGCTAAATATTGAGCGTCGACGTGATATTGCTTTCatt                                        >  1:2440647/1‑69 (MQ=255)
                            aaTGTTGAATTTCTGAATCTTTAATGTTTGTTGCGAAATATTGAGCGTCGACGTGATATTGCTTTCatt                                        >  1:1870015/1‑69 (MQ=255)
                               gTTGAATTTCTGAATCTTTAATGTTTGTTGCGAAATATTGAGCGTCGACGTGATATTGCTTTCattttt                                     >  1:2580484/1‑69 (MQ=255)
                               gTTGAATTTCTGAATCTTTAATGTTTGTTGCGAAATATTGAGCGTCGACGTGATATTGCTTTCattttt                                     >  1:613254/1‑69 (MQ=255)
                                ttGAATTTCTGAATCTTTAATGTTTGTTGCGAAATGTTGAGCGTTGACGTGATATTGCTTTCattt                                       <  1:3276901/66‑1 (MQ=255)
                                ttGAATTTCTGAATCTTTAATGTTTGTTGCGAAATGTTGAGCGTTGACGTGATATTGCTTTCattt                                       <  1:3284099/66‑1 (MQ=255)
                                ttGAATTTCTGAATCTTTAATGTTTGTTGCGAAATGTTGAGCGTTGACGTGATATTGCTTTCattt                                       <  1:3414034/66‑1 (MQ=255)
                                ttGAATTTCTGAATCTTTAATGTTTGTTGCGAAATGTTGAGCGTTGACGTGATATTGCTTTCattt                                       <  1:170344/66‑1 (MQ=255)
                                ttGAATTTCTGAATCTTTAATGTTTGTTGCGAAATGTTGAGCGTTGACGTGATATTGCTTTCattt                                       <  1:28309/66‑1 (MQ=255)
                                ttGAATTTCTGAATCTTTAATGTTTGTTGCGAAATGTTGAGCGTTGACGTGATATTGCTTTCattt                                       <  1:3354376/66‑1 (MQ=255)
                                ttGAATTTCTGAATCTTTAATGTTTGTTGCGAAATGTTGAGCGTTGACGTGATATTGCTTTCattt                                       <  1:1768463/66‑1 (MQ=255)
                                ttGAATTTCTGAATCTTTAATGTTTGTTGCGAAATGTTGAGCGTTGACGTGATATTGCTTTCattt                                       <  1:2667090/66‑1 (MQ=255)
                                ttGAATTTCTGAATCTTTAATGTTTGTTGCGAAATATTGAGCGTCGACGTGATATTGCTTTCattttta                                    >  1:2155580/1‑69 (MQ=255)
                                ttGAATTTCTGAATCTTTAATGTTTGTTGCGAAATATTGAGCGTCGACGTGATATTGCTTTCattttta                                    >  1:3139826/1‑69 (MQ=255)
                                ttGAATTTCTGAATCTTTAATGTTTGTTGCGAAATATTGAGCGTCGACGTGATATTGCTTTCattttta                                    >  1:3194242/1‑69 (MQ=255)
                                             tCTTTAATGTTTGTTGCGAAATATTGAGCGTCGACGTGATATTGCTTTCATTTTTATTTTTCAGAATc                        <  1:2469817/68‑1 (MQ=255)
                                                        tgttgCGAAATGTTGAGCGTTGACGTGATATTGCTTTCATTTTTGTTTTTCAGAATCAGTTGCATAAtt            >  1:1830642/1‑69 (MQ=255)
                                                        tgttgCGAAATGTTGAGCGTTGACGTGATATTGCTTTCATTTTTGTTTTTCAGAATCAGTTGCATAAtt            >  1:1219670/1‑69 (MQ=255)
                                                        tgttgCGAAATGTTGAGCGTTGACGTGATATTGCTTTCATTTTTGTTTTTCAGAATCAGTTGCATAAtt            >  1:668581/1‑69 (MQ=255)
                                                        tgttgCGAAATGTTGAGCGTTGACGTGATATTGCTTTCATTTTTGTTTTTCAGAATCAGTTGCATAAtt            >  1:1498226/1‑69 (MQ=255)
                                                        tgttgCGAAATGTTGAGCGTTGACGTGATATTGCTTTCATTTTTGTTTTTCAGAATCAGTTGCATAAtt            >  1:1206429/1‑69 (MQ=255)
                                                        tgttgCGAAATGTTGAGCGTTGACGTGATATTGCTTTCATTTTTGTTTTTCAGAATCAGTTGCATAAt             >  1:1199488/1‑68 (MQ=255)
                                                               aaaTATTGAGCGTCGACGTGATATTGCTTTCATTTTTATTTTTCAGAATCAGTTGCATAATTTTGAACt     <  1:1106174/69‑1 (MQ=255)
                                                                  tatTGAGCGTCGACGTGATATTGCTTTCATTTTTTTTTTTc                              <  1:443146/41‑1 (MQ=255)
                                                                  tatTGAGCGTCGACGTGATATTGCTTTCATTTTTATTTTTc                              <  1:975617/41‑1 (MQ=255)
                                                                  tatTGAGCGTCGACGTGATATTGCTTTCATTTTTATTTTTc                              <  1:1723827/41‑1 (MQ=255)
                                                                  tatTGAGCGTCGACGTGATATTGCTTTCATTTTTATTTTTc                              <  1:2239414/41‑1 (MQ=255)
                                                                  tatTGAGCGTCGACGTGATATTGCTTTCATTTTTATTTTTc                              <  1:2237371/41‑1 (MQ=255)
                                                                  tatTGAGCGTCGACGTGATATTGCTTTCATTTTTATTTTTc                              <  1:1784503/41‑1 (MQ=255)
                                                                  tatTGAGCGTCGACGTGATATTGCTTTCATTTTTATTTTTc                              <  1:1893281/41‑1 (MQ=255)
                                                                  tatTGAGCGTCGACGTGATATTGCTTTCATTTTTATTTTTCAGAATCAGTTGCATAATTTTGAACTGAt  <  1:3326101/69‑1 (MQ=255)
                                                                  tatTGAGCGTCGACGTGATATTGCTTTCATTTTTATTTTTCAGAATCAGTTGCATAATTTTGAACTGAt  <  1:2980185/69‑1 (MQ=255)
                                                                  tatTGAGCGTCGACGTGATATTGCTTTCATTTTTATTTTTCAGAATCAGTTGCATAATTTTGAACTGAt  <  1:2969549/69‑1 (MQ=255)
                                                                  tatTGAGCGTCGACGTGATATTGCTTTCATTTTTATTTTTCAGAATCAGTTGCATAATTTTGAACTGAt  <  1:2543220/69‑1 (MQ=255)
                                                                  tatTGAGCGTCGACGTGATATTGCTTTCATTTTTATTTTTCAGAATCAGTTGCATAATTTTGAACTGAt  <  1:2528953/69‑1 (MQ=255)
                                                                  tatTGAGCGTCGACGTGATATTGCTTTCATTTTTATTTTTCAGAATCAGTTGCATAATTTTGAACTGAt  <  1:2101244/69‑1 (MQ=255)
                                                                  tatTGAGCGTCGACGTGATATTGCTTTCATTTTTATTTTTCAGAATCAGTTGCATAATTTTGAACTGAt  <  1:807879/69‑1 (MQ=255)
                                                                  tatTGAGCGTCGACGTGATATTGCTTTCATTTTTATTTTTCAGAATCAGTTGCATAATTTTGAACTGAt  <  1:1938745/69‑1 (MQ=255)
                                                                  tatTGAGCGGCGACGTGATATTGCTTTCATTTTTATTTTTc                              <  1:2383143/41‑1 (MQ=255)
                                                                   atTGAGCGTCGACGTGATATTGCTTTCATTTTTATTTTTc                              <  1:1499832/40‑1 (MQ=255)
                                                                   |                                                                   
TCATACGTCTTAGTTTCAGCTTGTACATAATGTTGAATTTCTGAATCTTTAATGTTTGTTGCGAAATATTGAGCGTCGACGTGATATTGCTTTCATTTTTATTTTTCAGAATCAGTTGCATAATTTTGAACTGAT  >  minE/2588835‑2588969

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