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 1,976,135 T→C 59.7% T286T (ACT→ACC)  galP → D‑galactose transporter

Read alignment evidence...
  seq id position ref new freq score (cons/poly) reads annotation genes product
*minE1,976,1350TC59.7% 58.3 / 86.4 124T286T (ACT→ACC) galPD‑galactose transporter
Reads supporting (aligned to +/- strand):  ref base T (31/19);  new base C (31/43);  total (62/62)
Fisher's exact test for biased strand distribution p-value = 4.35e-02
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 7.62e-01

Only 100 of 124 total aligned reads displayed.

TGAACGTCATCATGTATTACGCGCCGAAAATCTTCGAACTGGCGGGTTATACCAACACTACCGAGCAAATGTGGGGGACCGTGATTGTCGGCCTGACCAACGTACTTGCCACCTTTATCGC  >  minE/1976077‑1976197
                                                          |                                                              
tGAACGTCATCATGTATTACGCGCCGAAAATCTTCGAACTGGCGGGTTATACCAACACTACCGAGCaaa                                                      <  1:1725094/69‑1 (MQ=255)
tGAACGTCATCATGTATTACGCGCCGAAAATCTTCGAACTGGCGGGTTATACCAACACTACCGAGCaaa                                                      <  1:1950240/69‑1 (MQ=255)
tGAACGTCATCATGTATTACGCGCCGAAAATCTTCGAACTGGCGGGTTATACCAACACTACCGAGCaaa                                                      <  1:3063331/69‑1 (MQ=255)
  aaCGTCATCATGTATTACGCGCCGAAAATCTTCGAACTGGCGGGTTATACCAACACTACCGAGCAAAtg                                                    <  1:389994/69‑1 (MQ=255)
   aCGTCATCATGTATTACGCGCCGAAAATCTTCGAACTGGCGGGTTATACCAACACTACCGAGCATAtg                                                    <  1:230015/68‑1 (MQ=255)
    cGTCATCATGTATTACGCGCCGAAAATCTTCGAACTGGCGGGTTATACCAACACTACCGAGCAAAtgtg                                                  >  1:963454/1‑69 (MQ=255)
    cGTCATCATGTATTACGCGCCGAAAATCTTCGAACTGGCGGGTTATACCAACACTACCGAGCAAAtgtg                                                  >  1:273716/1‑69 (MQ=255)
    cGTCATCATGTATTACGCGCCGAAAATCTTCGAACTGGCGGGTTATACCAACACTACCGAGCAAAtgtg                                                  >  1:2918386/1‑69 (MQ=255)
    cGTCATCATGTATTACGCGCCGAAAATCTTCGAACTGGCGGGTTATACCAACACTACCGAGCAAAtg                                                    <  1:1233188/67‑1 (MQ=255)
       catcatGTATTACGCGCCGAAAATCTTCGAACTGGCGGGTTATACCAACACTACCGAGCAAATGTgggg                                               >  1:890772/1‑69 (MQ=255)
        atcatGTATTACGCGCCGAAAATCTTCGAACTGGCGGGTTATACCAACACTACCGAGCAAATGTggggg                                              >  1:2951483/1‑69 (MQ=255)
             gTATTACGCGCCGAAAATCTTCGAACTGGCGGGTTATACCAACACTACCGAGCAAATGTGGGGGACCGt                                         >  1:3266538/1‑69 (MQ=255)
             gTATTACGCGCCGAAAATCTTCGAACTGGCGGGTTATACCAACACTACCGAGCAAATGTGGGGGACCGt                                         >  1:3062096/1‑69 (MQ=255)
              tATTACGCGCCGAAAATCTTCGAACTGGCGGGTTATACCAACACTACCGAGCAAATGTGGGGGACCGTg                                        >  1:364434/1‑69 (MQ=255)
              tATTACGCGCCGAAAATCTTCGAACTGGCGGGTTATACCAACACTACCGAGCAAATGTGGGGGACCGTg                                        >  1:1224801/1‑69 (MQ=255)
              tATTACGCGCCGAAAATCTTCGAACTGGCGGGTTATACCAACACTACCGAGCAAATGTGGGGGACCGTg                                        >  1:3022339/1‑69 (MQ=255)
              tATTACGCGCCGAAAATCTTCGAACTGGCGGGTTATACCAACACTACCGAGCAAATGTGGGGGACCGTg                                        >  1:2796180/1‑69 (MQ=255)
              tATTACGCGCCGAAAATCTTCGAACTGGCGGGTTATACCAACACTACCGAGCAAATGTGGGGGACCGTg                                        >  1:1140046/1‑69 (MQ=255)
              tATTACGCGCCGAAAATCTTCGAACTGGCGGGTTATACCAACACTACCGAGCAAATGTGGGGGACCGTg                                        >  1:2400787/1‑69 (MQ=255)
              tATTACGCGCCGAAAATCTTCGAACTGGCGGGTTATACCAACACTACCGAGCAAATGTGGGGGACCGTg                                        >  1:2379822/1‑69 (MQ=255)
              tATTACGCGCCGAAAATCTTCGAACTGGCGGGTTATACCAACACTACCGAGCAAATGTGGGGGACCGTg                                        >  1:2317071/1‑69 (MQ=255)
                         gAAAATCTTCGAACTGGCGGGTTATACCAACACTACCGAGCAAATGTGGGGGACCGTGATTGTCGGCCt                             <  1:580213/69‑1 (MQ=255)
                         gAAAATCTTCGAACTGGCGGGTTATACCAACACTACCGAGCAAATGTGGGGGACCGTGATTGTCGGCCt                             <  1:691002/69‑1 (MQ=255)
                         gAAAATCTTCGAACTGGCGGGTTATACCAACACTACCGAGCAAATGTGGGGGACCGTGATTGTCGGCCt                             <  1:1048007/69‑1 (MQ=255)
                         gAAAATCTTCGAACTGGCGGGTTATACCAACACTACCGAGCAAATGTGGGGGACCGTGATTGTCGGCCt                             <  1:1348755/69‑1 (MQ=255)
                          aaaaTCTTCGAACTGGCGGGTTATACCAACACTACCGAGCAAATGTGGGGGACCGTGATTGTCGGCCt                             <  1:146330/68‑1 (MQ=255)
                          aaaaTCTTCGAACTGGCGGGTTATACCAACACTACCGAGCAAATGTGGGGGACCGTGATTGTCGGCCt                             <  1:3273397/68‑1 (MQ=255)
                                    aaCTGGCGGGTTATACCAACACTACCGAGCAAATGTGGGGGACCGTGATTGGCGGCCTGACCAACGTa                   <  1:2396679/68‑1 (MQ=255)
                                        ggCGGGTTATACCAACACTACCGAGCAAATGTGGGGGACCGTGATTGTCGGCCTGACCAACGTACtttc              >  1:3241652/1‑67 (MQ=255)
                                        ggCGGGTTATACCAACACTACCGAGCAAATGTGGGGGACCGTGATTGTCGGCCTGACCAACGTACTTg               >  1:854269/1‑68 (MQ=255)
                                        ggCGGGTTATACCAACACTACCGAGCAAATGTGGGGGACCGTGATTGTCGGCCTGACCAACGTACTTGc              >  1:1371578/1‑69 (MQ=255)
                                        ggCGGGTTATACCAACACTACCGAGCAAATGTGGGGGACCGTGATTGTCGGCCTGACCAACGTACTTGc              >  1:2601569/1‑69 (MQ=255)
                                        ggCGGGTTATACCAACACTACCGAGCAAATGTGGGGGACCGTGATTGTCGGCCTGACCAACGTACTTGc              >  1:1832693/1‑69 (MQ=255)
                                        ggCGGGTTATACCAACACTACCGAGCAAATGTGGGGGACCGTGATTGTCGGCCTGACCAACGTACTTGc              >  1:729451/1‑69 (MQ=255)
                                               tataCCAACACCACCGAGCAAATGTGGGGGACAGTTATTGTCGGCCTGACCAACGTACTTGCCACCttt       <  1:473523/69‑1 (MQ=255)
                                               tataCCAACACCACCGAGCAAATGTGGGGGACAGTGATTGTCGGCCTGACCAACGTACTTGCCACCttt       <  1:2508263/69‑1 (MQ=255)
                                               tataCCAACACCACCGAGCAAATGTGGGGGACAGTGATTGTCGGCCTGACCAACGTACTTGCCACCttt       <  1:684869/69‑1 (MQ=255)
                                               tataCCAACACCACCGAGCAAATGTGGGGGACAGTGATTGTCGGCCTGACCAACGTACTTGCCACCttt       <  1:2687606/69‑1 (MQ=255)
                                               tataCCAACACCACCGAGCAAATGTGGGGGACAGTGATTGTCGGCCTGACCAACGTACTTGCCACCttt       <  1:1537254/69‑1 (MQ=255)
                                               tataCCAACACCACCGAGCAAATGTGGGGGACAGTGATTGTCGGCCTGACCAACGTACTTGCCACCttt       <  1:2858524/69‑1 (MQ=255)
                                               tataCCAACACCACCGAGCAAATGTGGGGGACAGTGATTGTCGGCCTGACCAACGTACTTGCCACCttt       <  1:1464188/69‑1 (MQ=255)
                                               tataCCAACACCACCGAGCAAATGTGGGGGACAGTGATTGTCGGCCTGACCAACGTACTTGCCACCttt       <  1:457907/69‑1 (MQ=255)
                                               tataCCAACACCACCGAGCAAATGTGGGGGACAGTGATTGTCGGCCTGACCAACGTACTTGCCACCttt       <  1:440510/69‑1 (MQ=255)
                                               tataCCAACACCACCGAGCAAATGTGGGGGACAGTGATTGTCGGCCTGACCAACGTACTTGCCACCttt       <  1:1372053/69‑1 (MQ=255)
                                               tataCCAACACCACCGAGCAAATGTGGGGGACAGTGATTGTCGGCCTGACCAACGTACTTGCCACCttt       <  1:3195586/69‑1 (MQ=255)
                                               tataCCAACACCACCGAGCAAATGTGGGGGACAGTGATTGTCGGCCTGACCAACGTACTTGCCACCttt       <  1:171405/69‑1 (MQ=255)
                                               tataCCAACACCACCGAGCAAATGTGGGGGACAGTGATTGTCGGCCTGACCAACGTACTTGCCACCttt       <  1:897596/69‑1 (MQ=255)
                                               tataCCAACACCACCGAGCAAATGTGGGGGACAGTGATTGTCGGCCTGACCAACGTACTTGCCACCttt       <  1:1893582/69‑1 (MQ=255)
                                               tataCCAACACCACCGAGCAAATGTGGGGGACAGTGATTGTCGGCCTGACCAACGTACTTGCCACCttt       <  1:2013091/69‑1 (MQ=255)
                                               tataCCAACACCACCGAGCAAATGTGGGGGACAGTGATTGTCGGCCTGACCAACGTACTTGCCACCttt       <  1:1065849/69‑1 (MQ=255)
                                               tataCCAACACCACCGAGCAAATGTGGGGGACAGTGATTGTCGGCCTGACCAACGTACTTGCCACCttt       <  1:2257278/69‑1 (MQ=255)
                                               tataCCAACACCACCGAGCAAATGTGGGGGACAGTGATTGTCGGCCTGACCAACGTACTTGCCACCttt       <  1:768696/69‑1 (MQ=255)
                                                ataCCAACACCACCGGGCAAATGTGGGGGACAGTGATTGTCGGCCTGACCAACGTACTTGCCACCTTTa      >  1:2610449/1‑69 (MQ=255)
                                                ataCCAACACCACCGAGCAAATGTGGGGGACAGTGATTGTCGGCCt                             >  1:2154000/1‑46 (MQ=255)
                                                ataCCAACACCACCGAGCAAATGTGGGGGACAGTGATTGTCGGCCTGACCAACGTACTTGCCACCttt       >  1:1870238/1‑68 (MQ=255)
                                                ataCCAACACCACCGAGCAAATGTGGGGGACAGTGATTGTCGGCCTGACCAACGTACTTGCCACCttt       >  1:3233538/1‑68 (MQ=255)
                                                ataCCAACACCACCGAGCAAATGTGGGGGACAGTGATTGTCGGCCTGACCAACGTACTTGCCACCttt       >  1:1704580/1‑68 (MQ=255)
                                                ataCCAACACCACCGAGCAAATGTGGGGGACAGTGATTGTCGGCCTGACCAACGTACTTGCCACCTTTa      >  1:1172641/1‑69 (MQ=255)
                                                ataCCAACACCACCGAGCAAATGTGGGGGACAGTGATTGTCGGCCTGACCAACGTACTTGCCACCTTTa      >  1:69375/1‑69 (MQ=255)
                                                ataCCAACACCACCGAGCAAATGTGGGGGACAGTGATTGTCGGCCTGACCAACGTACTTGCCACCTTTa      <  1:1202211/69‑1 (MQ=255)
                                                ataCCAACACCACCGAGCAAATGTGGGGGACAGTGATTGTCGGCCTGACCAACGTACTTGCCACCTTTa      >  1:417090/1‑69 (MQ=255)
                                                ataCCAACACCACCGAGCAAATGTGGGGGACAGTGATTGTCGGCCTGACCAACGTACTTGCCACCTTTa      <  1:631178/69‑1 (MQ=255)
                                                ataCCAACACCACCGAGCAAATGTGGGGGACAGTGATTGTCGGCCTGACCAACGTACTTGCCACCTTTa      >  1:1027870/1‑69 (MQ=255)
                                                ataCCAACACCACCGAGCAAATGTGGGGGACAGTGATTGTCGGCCTGACCAACGTACTTGCCACCTTTa      <  1:1054258/69‑1 (MQ=255)
                                                ataCCAACACCACCGAGCAAATGTGGGGGACAGTGATTGTCGGCCTGACCAACGTACTTGCCACCTTTa      <  1:553455/69‑1 (MQ=255)
                                                ataCCAACACCACCGAGCAAATGTGGGGGACAGTGATTGTCGGCCTGACCAACGTACTTGCCACCTTTa      >  1:885559/1‑69 (MQ=255)
                                                ataCCAACACCACCGAGCAAATGTGGGGGACAGTGATTGTCGGCCTGACCAACGTACTTGCCACCTTTa      <  1:850113/69‑1 (MQ=255)
                                                ataCCAACACCACCGAGCAAATGTGGGGGACAGTGATTGTCGGCCTGACCAACGTACTTGCCACCTTTa      >  1:809868/1‑69 (MQ=255)
                                                ataCCAACACCACCGAGCAAATGTGGGGGACAGTGATTGTCGGCCTGACCAACGTACTTGCCACCTTTa      >  1:704945/1‑69 (MQ=255)
                                                ataCCAACACCACCGAGCAAATGTGGGGGACAGTGATTGTCGGCCTGACCAACGTACTTGCCACCTTTa      <  1:487121/69‑1 (MQ=255)
                                                ataCCAACACCACCGAGCAAATGTGGGGGACAGTGATTGTCGGCCTGACCAACGTACTTGCCACCTTTa      <  1:534839/69‑1 (MQ=255)
                                                ataCCAACACCACCGAGCAAATGTGGGGGACAGTGATTGTCGGCCTGACCAACGTACTTGCCACCTTTa      >  1:710143/1‑69 (MQ=255)
                                                ataCCAACACCACCGAGCAAATGTGGGGGACAGTGATTGTCGGCCTGACCAACGTACTTGCCACCTTTa      >  1:547653/1‑69 (MQ=255)
                                                ataCCAACACCACCGAGCAAATGTGGGGGACAGTGATTGTCGGCCTGACCAACGTACTTGCCACCTTTa      <  1:159633/69‑1 (MQ=255)
                                                ataCCAACACCACCGAGCAAATGTGGGGGACAGTGATTGTCGGCCTGACCAACGTACTTGCCACCTTTa      >  1:1800198/1‑69 (MQ=255)
                                                ataCCAACACCACCGAGCAAATGTGGGGGACAGTGATTGTCGGCCTGACCAACGTACTTGCCACCTTTa      >  1:1883092/1‑69 (MQ=255)
                                                ataCCAACACCACCGAGCAAATGTGGGGGACAGTGATTGTCGGCCTGACCAACGTACTTGCCACCTTTa      >  1:2011156/1‑69 (MQ=255)
                                                ataCCAACACCACCGAGCAAATGTGGGGGACAGTGATTGTCGGCCTGACCAACGTACTTGCCACCTTTa      >  1:2026236/1‑69 (MQ=255)
                                                ataCCAACACCACCGAGCAAATGTGGGGGACAGTGATTGTCGGCCTGACCAACGTACTTGCCACCTTTa      <  1:2083556/69‑1 (MQ=255)
                                                ataCCAACACCACCGAGCAAATGTGGGGGACAGTGATTGTCGGCCTGACCAACGTACTTGCCACCTTTa      <  1:2094825/69‑1 (MQ=255)
                                                ataCCAACACCACCGAGCAAATGTGGGGGACAGTGATTGTCGGCCTGACCAACGTACTTGCCACCTTTa      >  1:2103735/1‑69 (MQ=255)
                                                ataCCAACACCACCGAGCAAATGTGGGGGACAGTGATTGTCGGCCTGACCAACGTACTTGCCACCTTTa      <  1:1649091/69‑1 (MQ=255)
                                                ataCCAACACCACCGAGCAAATGTGGGGGACAGTGATTGTCGGCCTGACCAACGTACTTGCCACCTTTa      <  1:2311084/69‑1 (MQ=255)
                                                ataCCAACACCACCGAGCAAATGTGGGGGACAGTGATTGTCGGCCTGACCAACGTACTTGCCACCTTTa      <  1:1623145/69‑1 (MQ=255)
                                                ataCCAACACCACCGAGCAAATGTGGGGGACAGTGATTGTCGGCCTGACCAACGTACTTGCCACCTTTa      <  1:2346434/69‑1 (MQ=255)
                                                ataCCAACACCACCGAGCAAATGTGGGGGACAGTGATTGTCGGCCTGACCAACGTACTTGCCACCTTTa      >  1:1598879/1‑69 (MQ=255)
                                                ataCCAACACCACCGAGCAAATGTGGGGGACAGTGATTGTCGGCCTGACCAACGTACTTGCCACCTTTa      >  1:35078/1‑69 (MQ=255)
                                                ataCCAACACCACCGAGCAAATGTGGGGGACAGTGATTGTCGGCCTGACCAACGTACTTGCCACCTTTa      >  1:2497375/1‑69 (MQ=255)
                                                ataCCAACACCACCGAGCAAATGTGGGGGACAGTGATTGTCGGCCTGACCAACGTACTTGCCACCTTTa      <  1:2503597/69‑1 (MQ=255)
                                                ataCCAACACCACCGAGCAAATGTGGGGGACAGTGATTGTCGGCCTGACCAACGTACTTGCCACCTTTa      >  1:2525806/1‑69 (MQ=255)
                                                ataCCAACACCACCGAGCAAATGTGGGGGACAGTGATTGTCGGCCTGACCAACGTACTTGCCACCTTTa      <  1:269315/69‑1 (MQ=255)
                                                ataCCAACACCACCGAGCAAATGTGGGGGACAGTGATTGTCGGCCTGACCAACGTACTTGCCACCTTTa      >  1:2862813/1‑69 (MQ=255)
                                                ataCCAACACCACCGAGCAAATGTGGGGGACAGTGATTGTCGGCCTGACCAACGTACTTGCCACCTTTa      <  1:2888683/69‑1 (MQ=255)
                                                ataCCAACACCACCGAGCAAATGTGGGGGACAGTGATTGTCGGCCTGACCAACGTACTTGCCACCTTTa      <  1:1507746/69‑1 (MQ=255)
                                                ataCCAACACCACCGAGCAAATGTGGGGGACAGTGATTGTCGGCCTGACCAACGTACTTGCCACCTTTa      >  1:1381909/1‑69 (MQ=255)
                                                ataCCAACACCACCGAGCAAATGTGGGGGACAGTGATTGTCGGCCTGACCAACGTACTTGCCACCTTTa      >  1:334242/1‑69 (MQ=255)
                                                ataCCAACACCACCGAGCAAATGTGGGGGACAGTGATTGTCGGCCTGACAAACGTACTTGCCACCttt       >  1:3013614/1‑68 (MQ=255)
                                                ataCCAACACCACCGAGAAAATGTGGGGGACAGTGATTGTCGGCCTGACCAACGTACTTGCCACCttt       >  1:151378/1‑68 (MQ=255)
                                                     aaCACTACCGAGCAAATGTGGGGGACCGTGATTGTCGGCCTGACCAACGTACTTGCCACCTTTATCGc  <  1:439877/68‑1 (MQ=255)
                                                      acacTACCGAGCAAATGTGGGGGACCGTGATTGTCGGCCTGAc                          >  1:733063/1‑43 (MQ=255)
                                                          |                                                              
TGAACGTCATCATGTATTACGCGCCGAAAATCTTCGAACTGGCGGGTTATACCAACACTACCGAGCAAATGTGGGGGACCGTGATTGTCGGCCTGACCAACGTACTTGCCACCTTTATCGC  >  minE/1976077‑1976197

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