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 1,450,200 A→G 43.3% L261L (CTA→CTG)  atoC → fused response regulator of ato opeon, in two‑component system with AtoS

Read alignment evidence...
  seq id position ref new freq score (cons/poly) reads annotation genes product
*minE1,450,2000AG43.3% 26.7 / 82.2 104L261L (CTA→CTG) atoCfused response regulator of ato opeon, in two‑component system with AtoS
Reads supporting (aligned to +/- strand):  ref base A (25/34);  new base G (26/19);  total (51/53)
Fisher's exact test for biased strand distribution p-value = 1.66e-01
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 9.93e-01

Only 100 of 104 total aligned reads displayed.

ACTCTGCTCCTCGACGAAATTGGCGAAATGCCGCTGGTACTACAAGCCAAATTACTACGCATTCTACAGGAACGGGAATTTGAACGGATTGGCGGCCATCAGACCATAAAAGTTGATATCCGCATCATTGC  >  minE/1450135‑1450265
                                                                 |                                                                 
aCTCTGCTCCTCGACGAAATTGGCGAAATGCCGCTGGTACTACAAGCCAAATTACTACGCATTCTACa                                                                 >  1:3435191/1‑68 (MQ=255)
aCTCTGCTCCTCGACGAAATTGGCGAAATGCCGCTGGTACTACAAGCCAAATTACTACGCATTCTACa                                                                 >  1:1734185/1‑68 (MQ=255)
aCTCTGCTCCTCGACGAAATTGGCGAAATGCCGCTGGTACTACAAGCCAAATTACTACGCATTCTACa                                                                 >  1:1337969/1‑68 (MQ=255)
aCTCTGCTCCTCGACGAAATTGGCGAAATGCCGCTGGTACTACAAGCCAAATTACTACGCATTCTACa                                                                 >  1:1941243/1‑68 (MQ=255)
aCTCTGCTCCTCGACGAAATTGGCGAAATGCCGCTGGTACTACAAGCCAAATTACTACGCATTCTACa                                                                 >  1:657925/1‑68 (MQ=255)
           cgacgaAATTGGCGAAATGCCGCTGTTACTGCAAGCCAAATTACTACGCATTCTGCAGGAACGGGAAt                                                      >  1:2055339/1‑68 (MQ=39)
           cgacgaAATTGGCGAAATGCCGCTGGTACTGCAAGCCAAATTACTACGCATTCTGCAGGAACGGGAAt                                                      >  1:2790609/1‑68 (MQ=39)
           cgacgaAATTGGCGAAATGCCGCTGGTACTGCAAGCCAAATTACTACGCATTCTGCAGGAACGGGAAt                                                      >  1:1808695/1‑68 (MQ=39)
           cgacgaAATTGGCGAAATGCCGCTGGTACTGCAAGCCAAATTACTACGCATTCTGCAGGAACGGGAAt                                                      >  1:811498/1‑68 (MQ=39)
           cgacgaAATTGGCGAAATGCCGCTGGTACTGCAAGCCAAATTACTACGCATTCTGCAGGAACGGGAAt                                                      >  1:575331/1‑68 (MQ=39)
           cgacgaAATTGGCGAAATGCCGCTGGTACTGCAAGCCAAATTACTACGCATTCTGCAGGAACGGGAAt                                                      >  1:497006/1‑68 (MQ=39)
           cgacgaAATTGGCGAAATGCCGCTGGTACTGCAAGCCAAATTACTACGCATTCTGCAGGAACGGGAAt                                                      >  1:2737874/1‑68 (MQ=39)
           cgacgaAATTGGCGAAATGCCGCTGGTACTGCAAGCCAAATTACTACGCATTCTGCAGGAACGGGAAt                                                      >  1:2322474/1‑68 (MQ=39)
           cgacgaAATTGGCGAAATGCCGCTGGTACTGCAAGCCAAATTACTACGCATTCTGCAGGAACGGGAAt                                                      >  1:2873910/1‑68 (MQ=39)
           cgacgaAATTGGCGAAATGCCGCTGGTACTGCAAGCCAAATTACTACGCATTCTGCAGGAACGGGAAt                                                      >  1:2908188/1‑68 (MQ=39)
           cgacgaAATTGGCGAAATGCCGCTGGTACTGCAAGCCAAATTACTACGCATTCTGCAGGAACGGGAAt                                                      >  1:2978434/1‑68 (MQ=39)
           cgacgaAATTGGCGAAATGCCGCTGGTACTGCAAGCCAAATTACTACGCATTCTGCAGGAACGGGAAt                                                      >  1:3094802/1‑68 (MQ=39)
           cgacgaAATTGGCGAAATGCCGCTGGTACTGCAAGCCAAATTACTACGCATTCTGCAGGAACGGGAAt                                                      >  1:3179195/1‑68 (MQ=39)
           cgacgaAATTGGCGAAATGCCGCTGGTACTGCAAGCCAAATTACTACGCATTCTGCAGGAACGGGAAt                                                      >  1:3358287/1‑68 (MQ=39)
           cgacgaAATTGGCGAAATGCCGCTGGTACTGCAAGCCAAATTACTACGCATTCTGCAGGAACGGGAAt                                                      >  1:173102/1‑68 (MQ=39)
           cgacgaAATTGGCGAAATGCCGCTGGTACTGCAAGCCAAATTACTACGCATTCTGCAGGAACGGGAAt                                                      >  1:1354389/1‑68 (MQ=39)
           cgacgaAATTGGCGAAATGCCGCTGGTACTGCAAGCCAAATTACTACGCATTCTGCAGGAACGGGAAt                                                      >  1:1420513/1‑68 (MQ=39)
           cgacgaAATTGGCGAAATGCCGCTGGTACTGCAAGCCAAATTACTACGCATTCTGCAGGAACGGGAAt                                                      >  1:1516857/1‑68 (MQ=39)
            gacgaAATTGGGGAAATGCCGCTGGTACTGCAAGCCAAATTACTACGCATTCTGCAGGAACGGGAAtt                                                     >  1:2306005/1‑68 (MQ=39)
            gacgaAATTGGCGAAATGCCGCTGGTACTGCAAGCCAAATTACTACGCATTCTGCAGGAACGGGAAtt                                                     >  1:713037/1‑68 (MQ=39)
            gacgaAATTGGCGAAATGCCGCTGGTACTGCAAGCCAAATTACTACGCATTCTGCAGGAACGGGAAtt                                                     >  1:3201237/1‑68 (MQ=39)
            gacgaAATTGGCGAAATGCCGCTGGTACTGCAAGCCAAATTACTACGCATTCTGCAGGAACGGGAAtt                                                     >  1:1288381/1‑68 (MQ=39)
            gacgaAATTGGCGAAATGCCGCTGGTACTGCAAGCCAAATTACTACGCATTCTGCAGGAACGGGAAtt                                                     >  1:80111/1‑68 (MQ=39)
            gacgaAATTGGCGAAATGCCGCTGGTACTGCAAGCCAAATTACTACGCATTCTGCAGGAACGGGAAtt                                                     >  1:1722745/1‑68 (MQ=39)
            gacgaAATTGGCGAAATGCCGCTGGTACTGCAAGCCAAATTACTACGCATTCTGCAGGAACGGGAAtt                                                     >  1:1398607/1‑68 (MQ=39)
              cgaAATTGGCGAAATGCCGCTGGTACTATAAACCAAATTACTACGCATTCTACAGGAACGGGAATTTg                                                   <  1:1770673/68‑1 (MQ=255)
                 aaTTGGCGAAATGCCGCTGGTACTACAAGCCAAATTACTACGCATTCTACAGGAACGGGAATTTGAACg                                               <  1:2536322/69‑1 (MQ=255)
                  aTTGGCGAAATGCCGCTGGTACTACAAGCCAAATTACTACGCATTCTACAGGAACGGGAATTTGAACgg                                              <  1:2101434/69‑1 (MQ=255)
                  aTTGGCGAAATGCCGCTGGTACTACAAGCCAAATTACTACGCATTCTACAGGAACGGGAATTTGAACgg                                              <  1:258645/69‑1 (MQ=255)
                  aTTGGCGAAATGCCGCTGGTACTACAAGCCAAATTACTACGCATTCTACAGGAACGGGAATTTGAACgg                                              <  1:2522916/69‑1 (MQ=255)
                  aTTGGCGAAATGCCGCTGGTACTACAAGCCAAATTACTACGCATTCTACAGGAACGGGAATTTGAACgg                                              <  1:736194/69‑1 (MQ=255)
                        gAAATGCCGCTGGTACTGCAAGCCAAATTACTACGCATTCTGCAGGAACGGGAATTTGAACGGATTgg                                         <  1:1576882/68‑1 (MQ=255)
                        gAAATGCCGCTGGTACTGCAAGCCAAATTACTACGCATTCTGCAGGAACGGGAATTTGAACGGATTgg                                         <  1:880609/68‑1 (MQ=255)
                        gAAATGCCGCTGGTACTGCAAGCCAAATTACTACGCATTCTGCAGGAACGGGAATTTGAACGGATTgg                                         <  1:1770064/68‑1 (MQ=255)
                        gAAATGCCGCTGGTACTGCAAGCCAAATTACTACGCATTCTGCAGGAACGGGAATTTGAACGGATTgg                                         <  1:968904/68‑1 (MQ=255)
                        gAAATGCCGCTGGTACTGCAAGCCAAATTACTACGCATTCTGCAGGAACGGGAATTTGAACGGATTgg                                         <  1:2498925/68‑1 (MQ=255)
                        gAAATGCCGCTGGTACTGCAAGCCAAATTACTACGCATTCTGCAGGAACGGGAATTTGAACGGATTgg                                         <  1:245377/68‑1 (MQ=255)
                        gAAATGCCGCTGGTACTGCAAGCCAAATTACTACGCATTCTGCAGGAACGGGAATTTGAACGGATTgg                                         <  1:1820421/68‑1 (MQ=255)
                        gAAATGCCGCTGGTACTGCAAGCCAAATTACTACGCATTCTGCAGGAACGGGAATTTGAACGGATTgg                                         <  1:1716491/68‑1 (MQ=255)
                         aaaTGCCGCTGGTACTGCAAGCCAAATTACTACGCATTCTGCAGGAACGGGAATTTGAACGGATTgg                                         <  1:433910/67‑1 (MQ=255)
                         aaaTGCCGCTGGTACTGCAAGCCAAATTACTACGCATTCTGCAGGAACGGGAATTTGAACGGATTgg                                         <  1:20985/67‑1 (MQ=255)
                          aaTGCCGCTGGTACTGCAAGCCAAATTACTACGCATTCTGCAGGAACGGGAATTTGAACGGATTgg                                         <  1:808940/66‑1 (MQ=255)
                              ccGCTGGTACTACAAGCCAAATTACTACGCATTCTACAGGAACGGGAATTTGAACGGATTGGCGGCCAt                                  <  1:744592/69‑1 (MQ=255)
                              ccGCTGGTACTACAAGCCAAATTACTACGCATTCTACAGGAACGGGAATTTGAACGGATTGGCGGCCAt                                  <  1:1659157/69‑1 (MQ=255)
                                      actacAAGCCAAATTACTACGCATTCTACAGGAACGGGAATTTGAACGGATTGGCGGCCATCAGAc                             >  1:2081799/1‑66 (MQ=255)
                                      actacAAGCCAAATTACTACGCATTCTACAGGAACGGGAATTTGAACGGATTGGCGGCCATCAGACCa                           >  1:1216601/1‑68 (MQ=255)
                                      actacAAGCCAAATTACTACGCATTCTACAGGAACGGGAATTTGAACGGATTGGCGGCCATCAGACCa                           >  1:3325253/1‑68 (MQ=255)
                                      actacAAGCCAAATTACTACGCATTCTACAGGAACGGGAATTTGAACGGATTGGCGGCCATCAGACCa                           >  1:347517/1‑68 (MQ=255)
                                      actacAAGCCAAATTACTACGCATTCTACAGGAACGGGAATTTGAACGGATTGGCGGCCATCAGACCa                           >  1:3018968/1‑68 (MQ=255)
                                      actacAAGCCAAATTACTACGCATTCTACAGGAACGGGAATTTGAACGGATTGGCGGCCATCAGACCa                           >  1:490052/1‑68 (MQ=255)
                                      actacAAGCCAAATTACTACGCATTCTACAGGAACGGGAATTTGAACGGATTGGCGGCCATCAGACCa                           >  1:641836/1‑68 (MQ=255)
                                                        acGCATTCTGCAGGAACGGGAATTTGAACGTATTGGCGGCCATCAGACCATAAAAGTTGATATCCGca         <  1:2326716/68‑1 (MQ=255)
                                                        acGCATTCTGCAGGAACGGGAATTTGAACGGATTGGCGGCCATCAGACCATAAAAGTTGATATCCGca         <  1:1785665/68‑1 (MQ=255)
                                                        acGCATTCTGCAGGAACGGGAATTTGAACGGATTGGCGGCCATCAGACCATAAAAGTTGATATCCGca         <  1:2624433/68‑1 (MQ=255)
                                                        acGCATTCTGCAGGAACGGGAATTTGAACGGATTGGCGGCCATCAGACCATAAAAGTTGATATCCGca         <  1:3388690/68‑1 (MQ=255)
                                                        acGCATTCTGCAGGAACGGGAATTTGAACGGATTGGCGGCCATCAGACCATAAAAGTTGATATCCGca         <  1:3152491/68‑1 (MQ=255)
                                                        acGCATTCTGCAGGAACGGGAATTTGAACGGATTGGCGGCCATCAGACCATAAAAGTTGATATCCGca         <  1:211577/68‑1 (MQ=255)
                                                         cGCATTCTGCAGGAACGGGAATTTGAACGGATTGGCGGCCATCAGACCATAAAAGTTGATATCCGca         <  1:1941095/67‑1 (MQ=255)
                                                          gCATTCTACAGGAACGGGAATTTGAACGGATTGGCGGCCAt                                  <  1:144521/41‑1 (MQ=255)
                                                               cTACAGGAACGGGAATTTGAACGGATTGGCGGCCATCAGACCATAAAAGTTGATATCCGc          <  1:2694560/60‑1 (MQ=255)
                                                               cTACAGGAACGGGAATTTGAACGGATTGGCGGCCATCAGACCATAAAAGTTGATATCCGc          >  1:852015/1‑60 (MQ=255)
                                                               cTACAGGAACGGGAATTTGAACGGATTGGCGGCCATCAGACCATAAAAGTTGATATCCGc          >  1:894236/1‑60 (MQ=255)
                                                               cTACAGGAACGGGAATTTGAACGGATTGGCGGCCATCAGACCATAAAAGTTGATATCCGc          <  1:3400133/60‑1 (MQ=255)
                                                               cTACAGGAACGGGAATTTGAACGGATTGGCGGCCATCAGACCATAAAAGTTGATATCCGc          <  1:877027/60‑1 (MQ=255)
                                                               cTACAGGAACGGGAATTTGAACGGATTGGCGGCCATCAGACCATAAAAGTTGATATCCGc          <  1:516503/60‑1 (MQ=255)
                                                               cTACAGGAACGGGAATTTGAACGGATTGGCGGCCATCAGACCATAAAAGTTGATATCCGc          <  1:333065/60‑1 (MQ=255)
                                                               cTACAGGAACGGGAATTTGAACGGATTGGCGGCCATCAGACCATAAAAGTTGATATCCGc          <  1:2404063/60‑1 (MQ=255)
                                                               cTACAGGAACGGGAATTTGAACGGATTGGCGGCCATCAGACCATAAAAGTTGATATCCGc          <  1:2597695/60‑1 (MQ=255)
                                                               cTACAGGAACGGGAATTTGAACGGATTGGCGGCCATCAGACCATAAAAGTTGATATCCGc          <  1:2117092/60‑1 (MQ=255)
                                                               cTACAGGAACGGGAATTTGAACGGATTGGCGGCCATCAGACCATAAAAGTTGATATCCGc          <  1:2700747/60‑1 (MQ=255)
                                                               cTACAGGAACGGGAATTTGAACGGATTGGCGGCCATCAGACCATAAAAGTTGATATCCGc          <  1:1826940/60‑1 (MQ=255)
                                                               cTACAGGAACGGGAATTTGAACGGATTGGCGGCCATCAGACCATAAAAGTTGATATCCGc          >  1:1766007/1‑60 (MQ=255)
                                                               cTACAGGAACGGGAATTTGAACGGATTGGCGGCCATCAGACCATAAAAGTTGATATCCGc          <  1:1650146/60‑1 (MQ=255)
                                                               cTACAGGAACGGGAATTTGAACGGATTGGCGGCCATCAGACCATAAAAGTTGATATCCGc          <  1:1340121/60‑1 (MQ=255)
                                                               cTACAGGAACGGGAATTTGAACGGATTGGCGGCCATCAGACCATAAAAGTTGATATCCGc          <  1:313082/60‑1 (MQ=255)
                                                               cTACAGGAACGGGAATTTGAACGGATTGGCGGCCATCAGACCATAAAAGTTGATATCCGc          >  1:3279852/1‑60 (MQ=255)
                                                               cTACAGGAACGGGAATTTGAACGGATTGGCGGCCATCAGACCATAAAAGTTGATATCCGc          <  1:3290130/60‑1 (MQ=255)
                                                               cTACAGGAACGGGAATTTGAACGGATTGGCGGCCATCAGACCATAAAAGTTGATATCCGCATCATtgc  >  1:125016/1‑68 (MQ=255)
                                                               cTACAGGAACGGGAATTTGAACGGATTGGCGGCCATCAGACCATAAAAGTTGATATCCGCATCATtgc  <  1:1924049/68‑1 (MQ=255)
                                                               cTACAGGAACGGGAATTTGAACGGATTGGCGGCCATCAGACCATAAAAGTTGATATCCGCATCATtgc  <  1:2364889/68‑1 (MQ=255)
                                                               cTACAGGAACGGGAATTTGAACGGATTGGCGGCCATCAGACCATAAAAGTTGATATCCGCATCATtgc  <  1:258294/68‑1 (MQ=255)
                                                               cTACAGGAACGGGAATTTGAACGGATTGGCGGCCATCAGACCATAAAAGTTGATATCCGCATCATtgc  >  1:735734/1‑68 (MQ=255)
                                                               cTACAGGAACGGGAATTTGAACGGATTGGCGGCCATCAGACCATAAAAGTTGATATCCGCATCATtgc  >  1:2440188/1‑68 (MQ=255)
                                                               cTACAGGAACGGGAATTTGAACGGATTGGCGGCCATCAGACCATAAAAGTTGATATCCGCATCATtgc  <  1:689626/68‑1 (MQ=255)
                                                               cTACAGGAACGGGAATTTGAACGGATTGGCGGCCATCAGACCATAAAAGTTGATATCCGCATCATtgc  >  1:2574530/1‑68 (MQ=255)
                                                               cTACAGGAACGGGAATTTGAACGGATTGGCGGCCATCAGACCATAAAAGTTGATATCCGCATCATtgc  >  1:3346561/1‑68 (MQ=255)
                                                               cTACAGGAACGGGAATTTGAACGGATTGGCGGCCATCAGACCATAAAAGTTGATATCCGCATCATtgc  >  1:615191/1‑68 (MQ=255)
                                                               cTACAGGAACGGGAATTTGAACGGATTGGCGGCCATCAGACCATAAAAGTTGATATCCGCATCATtgc  >  1:572332/1‑68 (MQ=255)
                                                               cTACAGGAACGGGAATTTGAACGGATTGGCGGCCATCAGACCATAAAAGTTGATATCCGCATCATtgc  <  1:2634902/68‑1 (MQ=255)
                                                               cTACAGGAACGGGAATTTGAACGGATTGGCGGCCATCAGACCATAAAAGTTGATATCCGCATCATtgc  >  1:463825/1‑68 (MQ=255)
                                                               cTACAGGAACGGGAATTTGAACGGATTGGCGGCCATCAGACCATAAAAGTTGATATCCGCATCATtgc  <  1:45800/68‑1 (MQ=255)
                                                               cTACAGGAACGGGAATTTGAACGGATTGGCGGCCATCAGACCATAAAAGTTGATATCCGCATCATtgc  <  1:3093898/68‑1 (MQ=255)
                                                               cTACAGGAACGGGAATTTGAACGGATTGGCGGCCATCAGACCATAAAAGTTGATATCCGCATCATtgc  <  1:42280/68‑1 (MQ=255)
                                                               cTACAGGAACGGGAATTTGAACGGATTGGCGGCCATCAGACCACAAAAGTTGATATCCGCATCATtgc  <  1:3028364/68‑1 (MQ=255)
                                                               cTACAGGAACGGGAATTTGAACGGATTGGCGGCCATCAGACAATAAAAGTTGATATCCGCATCATtg   >  1:1229494/1‑67 (MQ=255)
                                                                 |                                                                 
ACTCTGCTCCTCGACGAAATTGGCGAAATGCCGCTGGTACTACAAGCCAAATTACTACGCATTCTACAGGAACGGGAATTTGAACGGATTGGCGGCCATCAGACCATAAAAGTTGATATCCGCATCATTGC  >  minE/1450135‑1450265

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 27 ≤ ATCG/ATCG < 32 ≤ ATCG/ATCG < 36 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑

GATK/CNVnator alignment

N/A