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 678,513 T→C 37.2% G690G (GGA→GGG)  yccS ← predicted inner membrane protein

Read alignment evidence...
  seq id position ref new freq score (cons/poly) reads annotation genes product
*minE678,5130TC37.2% 41.8 / 49.4 79G690G (GGA→GGG) yccSpredicted inner membrane protein
Reads supporting (aligned to +/- strand):  ref base T (29/20);  new base C (19/10);  total (49/30)
Fisher's exact test for biased strand distribution p-value = 6.36e-01
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 9.85e-01

TCCTGCGGAACTTGAGTAATCTGGCGTTGCAGACGACCAATCTCAGGCAGTAATGCAATCAATAATCCAACTTGTTGTACGACCAGAGGTTCTTTGCTGTCTGCCCGTGGTTCAAGTTGCTGCATCCGCTGT  >  minE/678448‑678579
                                                                 |                                                                  
tCCTGCGGATCTTGAGTAATCTGGCGTTGCAGACGACCAATCTCAGGCAGTAATGCAATCAATAATCCa                                                                 >  1:2299899/1‑69 (MQ=255)
       gAACTTGAGTAATCTGGCGTTGCAGACGACCAATCTCAGGCAGTAATGCAATCAATAATCCAACttgt                                                           <  1:948448/68‑1 (MQ=255)
       gAACTTGAGTAATCTGGCGTTGCAGACGACCAATCTCAGGCAGTAATGCAATCAATAATCCAACttgt                                                           <  1:2947189/68‑1 (MQ=255)
       gAACTTGAGTAATCTGGCGTTGCAGACGACCAATCTCAGGCAGTAATGCAATCAATAATCCAACttgt                                                           <  1:3431384/68‑1 (MQ=255)
       gAACTTGAGTAATCTGGCGTTGCAGACGACCAATCTCAGGCAGTAATGCAATCAATAATCCAACttgt                                                           <  1:700866/68‑1 (MQ=255)
        aaCTTGAGTAATCTGGCGTTGCAGACGACCAATCTCAGGCAGTAATGCAATCAATAATCCAACttgttg                                                         <  1:1532085/69‑1 (MQ=255)
        aaCTTGAGTAATCTGGCGTTGCAGACGACCAATCTCAGGCAGTAATGCAATCAATAATCCAACttgttg                                                         <  1:1294899/69‑1 (MQ=255)
          cTTGAGTAATCTGGCGTTGCAGACGACCAATCTCAGGCAGTAATGCAATCAATAATCCAACTtgttgt                                                        >  1:3227481/1‑68 (MQ=255)
          cTTGAGTAATCTGGCGTTGCAGACGACCAATCTCAGGCAGTAATGCAATCAATAATCCAACTtgttgt                                                        >  1:260686/1‑68 (MQ=255)
          cTTGAGTAATCTGGCGTTGCAGACGACCAATCTCAGGCAGTAATGCAATCAATAATCCAACTtgttgt                                                        >  1:1409475/1‑68 (MQ=255)
          cTTGAGTAATCTGGCGTTGCAGACGACCAATCTCAGGCAGTAATGCAATCAATAATCCAACTtgttgt                                                        >  1:738033/1‑68 (MQ=255)
                  aTCTGGCGTTGCAGACGACCAATCTCAGGCAGTAATGCAATCAATAATCCAACTTGTTGTACGACCaga                                               <  1:2509438/69‑1 (MQ=255)
                  aTCTGGCGTTGCAGACGACCAATCTCAGGCAGTAATGCAATCAATAATCCAACTTGTTGTACGACCaga                                               <  1:2271099/69‑1 (MQ=255)
                  aTCTGGCGTTGCAGACGACCAATCTCAGGCAGTAATGCAATCAATAATCCAACTTGTTGTACGACCaga                                               <  1:2233264/69‑1 (MQ=255)
                  aTCTGGCGTTGCAGACGACCAATCTCAGGCAGTAATGCAATCAATAATCCAACTTGTTGTACGACCaga                                               <  1:2146946/69‑1 (MQ=255)
                  aTCTGGCGTTGCAGACGACCAATCTCAGGCAGTAATGCAATCAATAATCCAACTTGTTGTACGACCaga                                               <  1:2609410/69‑1 (MQ=255)
                  aTCTGGCGTTGCAGACGACCAATCTCAGGCAGTAATGCAATCAATAATCCAACTTGTTGTACGACCaga                                               <  1:1168724/69‑1 (MQ=255)
                  aTCTGGCGTTGCAGACGACCAATCTCAGGCAGTAATGCAATCAATAATCCAACTTGTTGTACGACCaga                                               <  1:2953670/69‑1 (MQ=255)
                  aTCTGGCGTTGCAGACGACCAATCTCAGGCAGTAATGCAATCAATAATCCAACTTGTTGTACGACCaga                                               <  1:3297022/69‑1 (MQ=255)
                                          tcAGGCAGTAATGCAATCAATAATCCAACTTGTTGTACGACCAGAGGTTCTTTGCTGTCTGCCCGTgg                        >  1:1959416/1‑68 (MQ=255)
                                          tcAGGCAGTAATGCAATCAATAATCCAACTTGTTGTACGACCAGAGGTTCTTTGCTGTCTGCCCGTgg                        >  1:2415816/1‑68 (MQ=255)
                                          tcAGGCAGTAATGCAATCAATAATCCAACTTGTTGTACGACCAGAGGTTCTTTGCTGTCTGCCCGTgg                        >  1:2378210/1‑68 (MQ=255)
                                          tcAGGCAGTAATGCAATCAATAATCCAACTTGTTGTACGACCAGAGGTTCTTTGCTGTCTGCCCGTgg                        >  1:837338/1‑68 (MQ=255)
                                          tcAGGCAGTAATGCAATCAATAATCCAACTTGTTGTACGACCAGAGGTTCTTTGCTGTCTGCCCGTgg                        >  1:3013150/1‑68 (MQ=255)
                                          tcAGGCAGTAATGCAATCAATAATCCAACTTGTTGTACGACCAGAGGTTCTTTGCTGTCTGCCCGTgg                        >  1:1885354/1‑68 (MQ=255)
                                          tcAGGCAGTAATGCAATCAATAATCCAACTTGTTGTACGACCAGAGGTTCTTTGCTGTCTGCCCGTgg                        >  1:1495224/1‑68 (MQ=255)
                                          tcAGGCAGTAATGCAATCAATAATCCAACTTGTTGTACGACCAGAGGTTCTTTGCTGTCTGCCCGTgg                        >  1:1242581/1‑68 (MQ=255)
                                          tcAGGCAGTAATGCAATCAATAATCCAACTTGTTGTACGACCAGAGGTTCTTTGCTGTCTGCCCGTg                         >  1:1918120/1‑67 (MQ=255)
                                          tcAGGCAGTAATGCAATCAATAATCCAACTTGTTGTACGACCAGAGGTTCTTTGCTGTCTGCCCGTg                         >  1:1002014/1‑67 (MQ=255)
                                                    aTGCAATTAATAACCCAACTTGTTGTACGACCAGAGGTTCTTTGCTGTCTGCCCGTGGTTCAAGTtgc              >  1:1385647/1‑68 (MQ=255)
                                                    aTGCAATCAATAACCCAACTTGTTGTACGACCAGAGGTTCTTTg                                      >  1:583593/1‑44 (MQ=255)
                                                    aTGCAATCAATAACCCAACTTGTTGTACGACCAGAGGTTCTTTGCTGTCTGCCCGTGGTTCAAGTtgc              >  1:1382009/1‑68 (MQ=255)
                                                    aTGCAATCAATAACCCAACTTGTTGTACGACCAGAGGTTCTTTGCTGTCTGCCCGTGGTTCAAGTtgc              >  1:3195174/1‑68 (MQ=255)
                                                    aTGCAATCAATAACCCAACTTGTTGTACGACCAGAGGTTCTTTGCTGTCTGCCCGTGGTTCAAGTtgc              >  1:130514/1‑68 (MQ=255)
                                                    aTGCAATCAATAACCCAACTTGTTGTACGACCAGAGGTTCTTTGCTGTCTGCCCGTGGTTCAAGTtgc              >  1:2436311/1‑68 (MQ=255)
                                                    aTGCAATCAATAACCCAACTTGTTGTACGACCAGAGGTTCTTTGCTGTCTGCCCGTGGTTCAAGTtgc              >  1:897292/1‑68 (MQ=255)
                                                    aTGCAATCAATAACCCAACTTGTTGTACGACCAGAGGTTCTTTGCTGTCTGCCCGTGGTTCAAGTtgc              >  1:1496259/1‑68 (MQ=255)
                                                    aTGCAATCAATAACCCAACTTGTTGTACGACCAGAGGTTCTTTGCTGTCTGCCCGTGGTTCAAGTtgc              >  1:807595/1‑68 (MQ=255)
                                                    aTGCAATCAATAACCCAACTTGTTGTACGACCAGAGGTTCTTTGCTGTCTGCCCGTGGTTCAAGTtgc              >  1:2547310/1‑68 (MQ=255)
                                                    aTGCAATCAATAACCCAACTTGTTGTACGACCAGAGGTTCTTTGCTGTCTGCCCGTGGTTCAAGTtgc              >  1:2198428/1‑68 (MQ=255)
                                                    aTGCAATCAATAACCCAACTTGTTGTACGACCAGAGGTTCTTTGCTGTCTGCCCGTGGTTCAAGTtgc              >  1:2590186/1‑68 (MQ=255)
                                                    aTGCAATCAATAACCCAACTTGTTGTACGACCAGAGGTTCTTTGCTGTCTGCCCGTGGTTCAAGTtgc              >  1:2118335/1‑68 (MQ=255)
                                                    aTGCAATCAATAACCCAACTTGTTGTACGACCAGAGGTTCTTTGCTGTCTGCCCGTGGTTCAAGTtgc              >  1:2104978/1‑68 (MQ=255)
                                                    aTGCAATCAATAACCCAACTTGTTGTACGACCAGAGGTTCTTTGCTGTCTGCCCGTGGTTCAAGTtgc              >  1:292317/1‑68 (MQ=255)
                                                    aTGCAATCAATAACCCAACTTGTTGTACGACCAGAGGTTCTTTGCTGTCTGCCCGTGGTTCAAGTtgc              >  1:1617820/1‑68 (MQ=255)
                                                    aTGCAATCAATAACCCAACTTGTTGTACGACCAGAGGTTCTTTGCTGTCTGCCCGTGGTTCAAGTtgc              >  1:3341383/1‑68 (MQ=255)
                                                    aTGCAATCAATAACCCAACTTGTTGTACGACCAGAGGTTCTTTGCTGTCTGCCCGTGGTTCAAGTtgc              >  1:1800497/1‑68 (MQ=255)
                                                    aTGCAATCAATAACCCAACTTGTTGTACGACCAGAGGTTCTTTGCTGTCTGACCGTGGTTCAAGTtgc              >  1:3412270/1‑68 (MQ=255)
                                                    aTGCAATCAATAAACCAACTTGTTGTACGACCAGAGGt                                            >  1:2318533/1‑38 (MQ=255)
                                                      gCAATCAATAACCCAACTTGTTGTACGACCAGAGGTTCTTTGCTGTCTGCCCGTGGTTCAAGTtgcttc           <  1:2409196/69‑3 (MQ=255)
                                                      gCAATCAATAACCCAACTTGTTGTACGACCAGAGGTTCTTTGCTGTCTGCCCGTGGTTCAAGTtgctgc           <  1:637018/69‑1 (MQ=255)
                                                      gCAATCAATAACCCAACTTGTTGTACGACCAGAGGTTCTTTGCTGTCTGCCCGTGGTTCAAGTtgctgc           <  1:385678/69‑1 (MQ=255)
                                                      gCAATCAATAACCCAACTTGTTGTACGACCAGAGGTTCTTTGCTGTCTGCCCGTGGTTCAAGTtgctgc           <  1:1825080/69‑1 (MQ=255)
                                                      gCAATCAATAACCCAACTTGTTGTACGACCAGAGGTTCTTTGCTGTCTGCCCGTGGTTCAAGTtgctgc           <  1:190680/69‑1 (MQ=255)
                                                      gCAATCAATAACCCAACTTGTTGTACGACCAGAGGTTCTTTGCTGTCTGCCCGTGGTTCAAGTtgctgc           <  1:2965401/69‑1 (MQ=255)
                                                      gCAATCAATAACCCAACTTGTTGTACGACCAGAGGTTCTTTGCTGTCTGCCCGTGGTTCAAGTtgctgc           <  1:2682481/69‑1 (MQ=255)
                                                      gCAATCAATAACCCAACTTGTTGTACGACCAGAGGTTCTTTGCTGTCTGCCCGTGGTTCAAGTtgctgc           <  1:2542428/69‑1 (MQ=255)
                                                      gCAATCAATAACCCAACTTGTTGTACGACCAGAGGTTCTTTGCTGTCTGCCCGTGGTTCAAGTtgctgc           <  1:228258/69‑1 (MQ=255)
                                                       caatcaatAATCCAACTTGTTGTACGACCAGAGGTTCTTTGCTGTCTGCCCGTGGTTCAAGTTGCTGCa          <  1:2226062/69‑1 (MQ=255)
                                                       caatcaatAATCCAACTTGTTGTACGACCAGAGGTTCTTTGCTGTCTGCCCGTGGTTCAAGTTGCTGCa          >  1:1588031/1‑69 (MQ=255)
                                                       caatcaatAATCCAACTTGTTGTACGACCAGAGGTTCTTTGCTGTCTGCCCGTGGTTCAAGTTGCTGCa          >  1:1392381/1‑69 (MQ=255)
                                                       caatcaatAATCCAACTTGTTGTACGACCAGAGGTTCTTTGCTGTCTGCCCGTGGTTCAAGTTGCTGCa          >  1:784269/1‑69 (MQ=255)
                                                       caatcaatAATCCAACTTGTTGTACGACCAGAGGTTCTTTGCTGTCTGCCCGTGGTTCAAGTTGCTGCa          <  1:78788/69‑1 (MQ=255)
                                                       caatcaatAATCCAACTTGTTGTACGACCAGAGGTTCTTTGCTGTCTGCCCGTGGTTCAAGTTGCTGCa          <  1:1840948/69‑1 (MQ=255)
                                                       caatcaatAATCCAACTTGTTGTACGACCAGAGGTTCTTTGCTGTCTGCCCGTGGTTCAAGTTGCTGCa          >  1:2529492/1‑69 (MQ=255)
                                                       caatcaatAATCCAACTTGTTGTACGACCAGAGGTTCTTTGCTGTCTGCCCGTGGTTCAAGTTGCTGCa          <  1:2788764/69‑1 (MQ=255)
                                                       caatcaatAATCCAACTTGTTGTACGACCAGAGGTTCTTTGCTGTCTGCCCGTGGTTCAAGTTGCTGCa          >  1:2051502/1‑69 (MQ=255)
                                                       caatcaatAATCCAACTTGTTGTACGACCAGAGGTTCTTTGCTGTCTGCCCGTGGTTCAAGTTGCTGCa          <  1:2155975/69‑1 (MQ=255)
                                                       caatcaatAATCCAACTTGTTGTACGACCAGAGGTTCTTTGCTGTCTGCCCGTGGTTCAAGTTGCTGCa          <  1:1073426/69‑1 (MQ=255)
                                                       caatcaatAACCCAACTTGTTGTACGACCAGAGGTTCTTTGCTGTCTGCCCGTGGTTCAAGTtgctgc           <  1:230982/68‑1 (MQ=255)
                                                         atcaatAATCCAACTTGTTGTACGACCAGAGGTTCTTTg                                      >  1:2857384/1‑39 (MQ=255)
                                                         atcaatAATCCAACTTGTTGTACGACCAGAGGTTCTTTGCTGt                                  >  1:2195395/1‑43 (MQ=255)
                                                         atcaatAATCCAACTTGTTGTACGACCAGAGGTTCTTTGCTGTCTGCCCGTGGTTCAAGTTGCTGCAt         >  1:1553228/1‑68 (MQ=255)
                                                         atcaatAATCCAACTTGTTGTACGACCAGAGGTTCTTTGCTGTCTGCCCGTGGTTCAAGTTGCTGCATc        >  1:1987540/1‑69 (MQ=255)
                                                         atcaatAATCCAACTTGTTGTACGACCAGAGGTTCTTTGCTGTCTGCCCGTGGTTCAAGTTGCTGCATc        >  1:2535962/1‑69 (MQ=255)
                                                         atcaatAATCCAACTTGTTGTACGACCAGAGGTTCTTTGCTGTCTGCCCGTGGTTCAAGTTGCTGCATc        >  1:2641921/1‑69 (MQ=255)
                                                         atcaatAATCCAACTTGTTGTACGACCAGAGGTTCTTTGCTGTCTGCCCGTGGTTCAAGTTGCTGCATc        >  1:2454416/1‑69 (MQ=255)
                                                         atcaatAATCCAACTTGTTGTACGACCAGAGGTTCTTTGCTGTCTGCCCGTGGTTCAAGTTGCTGCATc        >  1:3253224/1‑69 (MQ=255)
                                                         atcaatAATCCAACTTGTTGTACGACCAGAGGTTCTTTGCTGTCTGCCCGTGGTTCAAGTTGCTGCATc        >  1:68301/1‑69 (MQ=255)
                                                            aataatCCAACTTGTTGTACGACCAGTGGTTCTTTGCTGTCTGCCCGTGGTTCAAGTTGCTGCATCCGc     <  1:1946195/69‑1 (MQ=255)
                                                            aataatCCAACTTGTTGTACGACCAGAGGTTCTTTGCTGTCTGCCCGTGGTTCAAGTTGCTGGATCCGc     <  1:1161306/69‑1 (MQ=255)
                                                            aataatCCAACTTGTTGTACGACCAGAGGTTCTTTGCTGTCTGCCCGTGGTTCAAGTTGCTGCATCCGc     <  1:1422774/69‑1 (MQ=255)
                                                            aataatCCAACTTGTTGTACGACCAGAGGTTCTTTGCTGTCTGCCCGTGGTTCAAGTTGCTGCATCCGc     <  1:242724/69‑1 (MQ=255)
                                                            aataatCCAACTTGTTGTACGACCAGAGGTTCTTTGCTGTCTGCCCGTGGTTCAAGTTGCTGCATCCGc     <  1:1727218/69‑1 (MQ=255)
                                                            aataatCCAACTTGTTGTACGACCAGAGGTTCTTTGCTGTCTGCCCGTGGTTCAAGTTGCTGCATCCGc     <  1:3301999/69‑1 (MQ=255)
                                                            aataatCCAACTTGTTGTACGACCAGAGGTTCTTTGCTGTCTGCCCGTGGTTCAAGTTGCTGCATCCGc     <  1:1746722/69‑1 (MQ=255)
                                                            aataatCCAACTTGTTGTACGACCAGAGGTTCTTTGCTGTCTGCCCGTGGTTCAAGTTGCTGCATCCGc     >  1:256519/1‑69 (MQ=255)
                                                            aataatCCAACTTGTTGTACGACCAGAGGTTCTTTGCTATCTGCCCGTGGTTCAAGTTGCTGCATCCGc     <  1:1061093/69‑1 (MQ=255)
                                                            aataacCCAACTTGTTGTACGACCAGAGGTTCTTTGCTGTCTGCCCGTGGTTCAAGTtgctgc           <  1:1576475/63‑1 (MQ=255)
                                                                atCCAACTTGTTGTACGACCAGAGGTTCTTTGCTGTCTGCCCGTGGTTCAAGTTGCTGCATCCGCTGt  >  1:3308097/1‑68 (MQ=255)
                                                                atCCAACTTGTTGTACGACCAGAGGTTCTTTGCTGTCTGCCCGTGGTTCAAGTTGCTGCATCCGCTGt  >  1:1247035/1‑68 (MQ=255)
                                                                atCCAACTTGTTGTACGACCAGAGGTTCTTTGCTCTCTGCCCGTGGTTCAAGTTGCTGCATCCGCTGt  >  1:766233/1‑68 (MQ=255)
                                                                atCCAACTTGTTGCACGACCAGAGGTTCTTTGCTGTCTGCCCGTGGTTCAAGTTGCTGCATCCGCTGt  >  1:2014754/1‑68 (MQ=255)
                                                                 |                                                                  
TCCTGCGGAACTTGAGTAATCTGGCGTTGCAGACGACCAATCTCAGGCAGTAATGCAATCAATAATCCAACTTGTTGTACGACCAGAGGTTCTTTGCTGTCTGCCCGTGGTTCAAGTTGCTGCATCCGCTGT  >  minE/678448‑678579

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