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 1,231,268 T→A 43.5% G496G (GGA→GGT)  ptrB ← protease II

Read alignment evidence...
  seq id position ref new freq score (cons/poly) reads annotation genes product
*minE1,231,2680TA43.5% 34.4 / 87.8 85G496G (GGA→GGT) ptrBprotease II
Reads supporting (aligned to +/- strand):  ref base T (33/15);  new base A (17/20);  total (50/35)
Fisher's exact test for biased strand distribution p-value = 4.59e-02
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 2.01e-01

CCAGTTTTAACAATGCATCGCAGGCATCAAGATAATCATTAAACGTATTTTTCTTCTTCAGAAATTTTCCGTCTTCGTACCATTGTTGCCCCAGCTCACCACCGCCGCGAACATGGACAATGGCGTA  >  minE/1231201‑1231327
                                                                   |                                                           
ccAGTTTTAACAATGCATCGCAGGCATCAAGATAATCATTAAACGTATTTTTCTTCTTCAGAAAtttt                                                             <  1:825815/68‑1 (MQ=255)
ccAGTTTTAACAATGCATCGCAGGCATCAAGATAATCATTAAACGTATTTTTCTTCTTCAGAAAtttt                                                             <  1:397775/68‑1 (MQ=255)
ccAGTTTTAACAATGCATCGCAGGCATCAAGATAATCATTAAACGTATTTTTCTTCTTCAGAAAtttt                                                             <  1:2817512/68‑1 (MQ=255)
      ttAACAATGCATCGCAGGCATCAAGATAATCATTAAACGTATTTTTCTTCTTCAGAAATTTTCCGTCtt                                                      <  1:1143413/69‑1 (MQ=255)
       tAACAATGCATCGCAGGCATCAAGATAATCATTAAACGTATTTTTCTTCTTCAGAAATTTTCCGTCtt                                                      <  1:2596323/68‑1 (MQ=255)
            aTGCATCGCAGGCATCAAGATAATCATTAAACGTATTTTTCTTCTTCAGAAATTTTCCGTCTTCGTAcc                                                >  1:1515599/1‑69 (MQ=255)
            aTGCATCGCAGGCATCAAGATAATCATTAAACGTATTTTTCTTCTTCAGAAATTTTCCGTCTTCGTAcc                                                >  1:2230136/1‑69 (MQ=255)
            aTGCATCGCAGGCATCAAGATAATCATTAAACGTATTTTTCTTCTTCAGAAATTTTCCGTCTTCGTAcc                                                >  1:240237/1‑69 (MQ=255)
            aTGCATCGCAGGCATCAAGATAATCATTAAACGTATTTTTCTTCTTCAGAAATTTTCCGTCTTCGTAcc                                                >  1:2445085/1‑69 (MQ=255)
            aTGCATCGCAGGCATCAAGATAATCATTAAACGTATTTTTCTTCTTCAGAAATTTTCCGTCTTCGTAcc                                                >  1:2628038/1‑69 (MQ=255)
            aTGCATCGCAGGCATCAAGATAATCATTAAACGTATTTTTCTTCTTCAGAAATTTTCCGTCTTCGTAcc                                                >  1:2726910/1‑69 (MQ=255)
            aTGCATCGCAGGCATCAAGATAATCATTAAACGTATTTTTCTTCTTCAGAAATTTTCCGTCTTCGTAcc                                                >  1:2964598/1‑69 (MQ=255)
            aTGCATCGCAGGCATCAAGATAATCATTAAACGTATTTTTCTTCTTCAGAAATTTTCCGTCTTCGTAcc                                                >  1:3010649/1‑69 (MQ=255)
            aTGCATCGCAGGCATCAAGATAATCATTAAACGTATTTTTCTTCTTCAGAAATTTTCCGTCTTCGTAcc                                                >  1:3060217/1‑69 (MQ=255)
            aTGCATCGCAGGCATCAAGATAATCATTAAACGTATTTTTCTTCTTCAGAAATTTTCCGTCTTCGTAcc                                                >  1:1301908/1‑69 (MQ=255)
            aTGCATCGCAGGCATCAAGATAATCATTAAACGTATTTTTCTTCTTCAGAAATTTTCCGTCTTCGTAcc                                                >  1:3331188/1‑69 (MQ=255)
            aTGCATCGCAGGCATCAAGATAATCATTAAACGTATTTTTCTTCTTCAGAAATTTTCCGTCTTCGTAcc                                                >  1:723432/1‑69 (MQ=255)
            aTGCATCGCAGGCATCAAGATAATCATTAAACGTATTTTTCTTCTTCAGAAATTTTCCGTCTTCGTAcc                                                >  1:913310/1‑69 (MQ=255)
            aTGCATCGCAGGCATCAAGATAATCATTAAACGTATTTTTCTTCTTCAGAAATTTTCCGTCTTCGTAcc                                                >  1:1098163/1‑69 (MQ=255)
                   gCAGGCATCAAGATAATCATTAAACGTATTTTTCTTCTTCAGAAATTTTCCGTCTTCGTACCAttgttg                                         >  1:2793532/1‑69 (MQ=255)
                        aaTCAAGATAATCATTAAACGTATTTTTCTTCTTCAGAAATTTTCCGTCTTCGTACCATTGTTGcccc                                     <  1:917606/67‑1 (MQ=255)
                            aaGATAATCATTAAAGGTATTTTTCTTCTTCAGAAATTTTCCGTCTTCGTACCATTGTTGCCCCAGCTc                                >  1:1935718/1‑69 (MQ=255)
                            aaGATAATCATTAAACGTATTTTTCTTCTTCAGAAATTTTCCGTCtt                                                      >  1:3215076/1‑47 (MQ=255)
                            aaGATAATCATTAAACGTATTTTTCTTCTTCAGAAATTTTCCGTCTTCGTACCa                                               >  1:996275/1‑54 (MQ=255)
                            aaGATAATCATTAAACGTATTTTTCTTCTTCAGAAATTTTCCGTCTTCGTACCATTGTTGCCCCAGCTc                                >  1:995389/1‑69 (MQ=255)
                            aaGATAATCATTAAACGTATTTTTCTTCTTCAGAAATTTTCCGTCTTCGTACCATTGTTGCCCCAGCTc                                >  1:991213/1‑69 (MQ=255)
                              gATAATCATTAAACGTATTTTTCTTCTTCAGAAATTTTCCGTCTTCGTACCATTGTTGCCCCAGCTcac                              <  1:218977/69‑1 (MQ=255)
                              gATAATCATTAAACGTATTTTTCTTCTTCAGAAATTTTCCGTCTTCGTACCATTGTTGCCCCAGCTcac                              <  1:5155/69‑1 (MQ=255)
                              gATAATCATTAAACGTATTTTTCTTCTTCAGAAATTTTCCGTCTTCGTACCATTGTTGCCCCAGCTcac                              <  1:357543/69‑1 (MQ=255)
                              gATAATCATTAAACGTATTTTTCTTCTTCAGAAATTTTCCGTCTTCGTACCATTGTTGCCCCAGCTcac                              <  1:3341001/69‑1 (MQ=255)
                              gATAATCATTAAACGTATTTTTCTTCTTCAGAAATTTTCCGTCTTCGTACCATTGTTGCCCCAGCTcac                              <  1:2435391/69‑1 (MQ=255)
                              gATAATCATTAAACGTATTTTTCTTCTTCAGAAATTTACCGTCCTCGTACCATTGTTGCCCCAGCt                                 <  1:3312771/66‑1 (MQ=255)
                              gATAATCATTAAACGTATTTTTCTTCTTCAGAAATTTACCGTCCTCGTACCATTGTTGCCCCAGCt                                 <  1:3122090/66‑1 (MQ=255)
                              gATAATCATTAAACGTATTTTTCTTCTTCAGAAATTTACCGTCCTCGTACCATTGTTGCCCCAGCt                                 <  1:3012320/66‑1 (MQ=255)
                              gATAATCATTAAACGTATTTTTCTTCTTCAGAAATTTACCGTCCTCGTACCATTGTTGCCCCAGCt                                 <  1:1671912/66‑1 (MQ=255)
                              gATAATCATTAAACGTATTTTTCTTCTTCAGAAATTTACCGTCCTCGTACCATTGTTGCCCCAGCt                                 <  1:2149151/66‑1 (MQ=255)
                              gATAATCATTAAACGTATTTTTCTTCTTCAGAAATTTACCGTCCTCGTACCATTGTTGCCCCAGCt                                 <  1:3295707/66‑1 (MQ=255)
                              gATAATCATTAAACGTATTTTTCTTCTTCAGAAATTTACCGTCCTCGTACCATTGTTGCCCCAGCt                                 <  1:32358/66‑1 (MQ=255)
                              gATAATCATTAAACGTATTTTTCTTCTTCAGAAATTTACCGTCCTCGTACCATTGTTGCCCCAGCt                                 <  1:2786837/66‑1 (MQ=255)
                              gATAATCATTAAACGTATTTTTCTTCTTCAGAAATTTACCGTCCTCGTACCATTGTTGCCCCAGCt                                 <  1:563040/66‑1 (MQ=255)
                              gATAATCATTAAACGTATTTTTCTTCTTCAGAAATTTACCGTCCTCGTACCATTGTTGCCCCAGCt                                 <  1:2754636/66‑1 (MQ=255)
                              gATAATCATTAAACGTATTTTTCTTCTTCAGAAATTTACCGTCCTCGTACCATTGTTGCCCCAGCt                                 <  1:849997/66‑1 (MQ=255)
                              gATAATCATTAAACGTATTTTTCTTCTTCAGAAATTTACCGTCCTCGTACCATTGTTGCCCCAGCt                                 <  1:2297949/66‑1 (MQ=255)
                              gATAATCATTAAACGTATTTTTCTTCTTCAGAAATTTACCGTCCTCGTACCATTGTTGCCCCAGCt                                 <  1:2112782/66‑1 (MQ=255)
                              gATAATCATTAAACGTATTTTTCTTCTTCAGAAATTTACCGTCCTCGTACCATTGTTGCCCCAGCt                                 <  1:2410685/66‑1 (MQ=255)
                              gATAATCATTAAACGTATTTTTCTTCTTCAGAAATTTACCGTCCTCGTACCATTGTTGCCCCAGCt                                 <  1:2557658/66‑1 (MQ=255)
                              gATAATCATTAAACGTATTTTTCTTCTTCAGAAATTTACCGTCCTCGTACCATTGTTGCCCCAGCt                                 <  1:2579902/66‑1 (MQ=255)
                              gATAATCATTAAACGTATTTTTCTTCTTCAGAAATTTACCGTCCTCGTACCATTGTTGCCCCAGCt                                 <  1:115287/66‑1 (MQ=255)
                              gATAATCATTAAACGTATTTTTCTTCTTCAGAAATTTACCGTCCTCGTACCATTGTTGCCCCAGCt                                 <  1:1167804/66‑1 (MQ=255)
                              gATAATCATTAAACGTATTTTTCTTCTTCAGAAATTTACCGTCCTCGTACCATTGTTGCCCCAGCt                                 <  1:1218869/66‑1 (MQ=255)
                              gATAATCATTAAACGTATTTTTCTTCTTCAGAAATTTACCGTCCTAGTACCATTGTTGCCCCAGCt                                 <  1:1652884/66‑1 (MQ=255)
                               aTAATCATTAAACGTATTTTTCTTCTTCAGAAATTTTCCGTCTTCGTACCATTGTTGCCCCAGCTcacc                             >  1:2539291/1‑69 (MQ=255)
                                tAATCATTAAACGTATTTTTCTTCTTCAGAAATTTTCCGTCTTCGTACCATTGTTGCCCCAGCTcacca                            >  1:2255484/1‑69 (MQ=255)
                                        aaaCGTATTTTTCTTCTTCAGAAATTTTCCGTCTTCGTACCATTGTTGCCCCAGCTCACCACcgccgc                     >  1:1272446/1‑68 (MQ=255)
                                        aaaCGTATTTTTCTTCTTCAGAAATTTTCCGTCTTCGTACCATTGTTGCCCCAGCTCACCACCGCcgcg                    >  1:1233218/1‑69 (MQ=255)
                                        aaaCGTATTTTTCTTCTTCAGAAATTTTCCGTCTTCGTACCATTGTTGCCCCAGCTCACCACCGCcgcg                    >  1:926884/1‑69 (MQ=255)
                                        aaaCGTATTTTTCTTCTTCAGAAATTTTCCGTCTTCGTACCATTGTTGCCCCAGCTCACCACCGCcgcg                    >  1:892686/1‑69 (MQ=255)
                                        aaaCGTATTTTTCTTCTTCAGAAATTTTCCGTCTTCGTACCATTGTTGCCCCAGCTCACCACCGCcgcg                    >  1:577451/1‑69 (MQ=255)
                                        aaaCGTATTTTTCTTCTTCAGAAATTTTCCGTCTTCGTACCATTGTTGCCCCAGCTCACCACCGCcgcg                    >  1:3201861/1‑69 (MQ=255)
                                        aaaCGTATTTTTCTTCTTCAGAAATTTTCCGTCTTCGTACCATTGTTGCCCCAGCTCACCACCGCcgcg                    >  1:1379060/1‑69 (MQ=255)
                                        aaaCGTATTTTTCTTCTTCAGAAATTTTCCGTCTTCGTACCATTGTTGCCCCAGCTCACCACCGCcgcg                    >  1:2119808/1‑69 (MQ=255)
                                        aaaCGTATTTTTCTTCTTCAGAAATTTTCCGTCTTCGTACCATTGTTGCCCCAGCTCACCACCGCcgcg                    >  1:2029845/1‑69 (MQ=255)
                                        aaaCGTATTTTTCTTCTTCAGAAATTTTCCGTCTTCGTACCATTGTTGCCCCAGCTCACCACCGCcgcg                    >  1:2572244/1‑69 (MQ=255)
                                        aaaCGTATTTTTCTTCTTCAGAAATTTTCCGTCTTCGTACCATTGTTGCACCAGCTCACCACCGCcgcg                    >  1:2807478/1‑69 (MQ=255)
                                          aCGTATTTTTCTTCTTCAGAAATTTACCGTCCTCg                                                    >  1:447056/1‑35 (MQ=37)
                                          aCGTATTTTTCTTCTTCAGAAATTTACCGTCCTCGt                                                   >  1:1092327/1‑36 (MQ=37)
                                          aCGTATTTTTCTTCTTCAGAAATTTACCGTCCTCGt                                                   >  1:3219456/1‑36 (MQ=37)
                                          aCGTATTTTTCTTCTTCAGAAATTTACCGTCCTCGt                                                   >  1:185937/1‑36 (MQ=37)
                                          aCGTATTTTTCTTCTTCAGAAATTTACCGTCCTCGt                                                   >  1:2650162/1‑36 (MQ=37)
                                          aCGTATTTTTCTTCTTCAGAAATTTACCGTCCTCGt                                                   >  1:2670974/1‑36 (MQ=37)
                                          aCGTATTTTTCTTCTTCAGAAATTTACCGTCCTCGt                                                   >  1:833188/1‑36 (MQ=37)
                                          aCGTATTTTTCTTCTTCAGAAATTTACCGTCCTCGt                                                   >  1:11692/1‑36 (MQ=37)
                                          aCGTATTTTTCTTCTTCAGAAATTTACCGTCCTCGt                                                   >  1:2772124/1‑36 (MQ=37)
                                          aCGTATTTTTCTTCTTCAGAAATTTACCGTCCTCGt                                                   >  1:39367/1‑36 (MQ=37)
                                          aCGTATTTTTCTTCTTCAGAAATTTACCGTCCTCGt                                                   >  1:1688793/1‑36 (MQ=37)
                                          aCGTATTTTTCTTCTTCAGAAATTTACCGTCCTCGt                                                   >  1:2829566/1‑36 (MQ=37)
                                          aCGTATTTTTCTTCTTCAGAAATTTACCGTCCTCGt                                                   >  1:3055492/1‑36 (MQ=37)
                                          aCGTATTTTTCTTCTTCAGAAATTTACCGTCCTCGt                                                   >  1:1509082/1‑36 (MQ=37)
                                          aCGTATTTTTCTTCTTCAGAAATTTACCGTCCTCGt                                                   >  1:3301050/1‑36 (MQ=37)
                                          aCGTATTTTTCTTCTTCAGAAATTTACAGTCCTCGt                                                   >  1:2764620/1‑36 (MQ=25)
                                          aCGTATTTTTCTTCTTCAGAAAATTACCGTCCTCg                                                    >  1:954791/1‑35 (MQ=25)
                                           cGTATTTTTCTTCTTCAGAAATTTTCCGTCTTCGTACCATTGTTGCCCCAGCTCACCACCGCCGCGaa                  <  1:2016302/68‑1 (MQ=255)
                                                 tttCTTCTTCAGAAATTTTCCGTCTTCGTACCATTGTTGCCCCAGCTCACCACCGCCGCGAACATGGAc           <  1:1836898/69‑1 (MQ=255)
                                                 tttCTTCTTCAGAAATTTTCCGTCTTCGTACCATTGTTGCCCCAGCTCACCACCGCCGCGAACATGGAc           <  1:82253/69‑1 (MQ=255)
                                                 tttCTTCTTCAGAAATTTTCCGTCTTCGTACCATTGTTGCCCCAGCTCACCACCGCCGCGAACATGGAc           <  1:553740/69‑1 (MQ=255)
                                                 tttCTTCTTCAGAAATTTTCCGTCTTCGTACCATTGTTGCCCCAGCTCACCACCGCCGCGAACATGGAc           <  1:405353/69‑1 (MQ=255)
                                                            gAAATTTTCCGTCTTCGTACCATTGTTGCCCCAGCTCACCACCGCCGCGAACATGGACAATGGCGTa  <  1:604021/67‑1 (MQ=255)
                                                            gAAATTTTCCGTCTTCGTACCATTGTTGCCCCAGCTCACCACCGCCGCGAACATGGACAATGGCGTa  <  1:1827258/67‑1 (MQ=255)
                                                                   |                                                           
CCAGTTTTAACAATGCATCGCAGGCATCAAGATAATCATTAAACGTATTTTTCTTCTTCAGAAATTTTCCGTCTTCGTACCATTGTTGCCCCAGCTCACCACCGCCGCGAACATGGACAATGGCGTA  >  minE/1231201‑1231327

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