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 1,566,887 T→G 40.2% A213A (GCT→GCG)  yfeO → predicted ion channel protein

Read alignment evidence...
  seq id position ref new freq score (cons/poly) reads annotation genes product
*minE1,566,8870TG40.2% 40.4 / 93.7 97A213A (GCT→GCG) yfeOpredicted ion channel protein
Reads supporting (aligned to +/- strand):  ref base T (41/17);  new base G (15/24);  total (56/41)
Fisher's exact test for biased strand distribution p-value = 3.08e-03
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 1.00e+00

GCGGCAGCAGCTGGTGCACTTACTACCGGATTATTTTTCCATCCTCATTTTTCACTGCCCATTGCTCATTACGGACAGATGGAAATGACCGATATTCTCAGCGGTGCAATTGTCGCGGCGATTGCCATCGC  >  minE/1566822‑1566952
                                                                 |                                                                 
gcggcAGCAGCTGGTGCACTTACTACCGGATTATTTTTCCATCCTCATTTTTCACTGCCCATTGCTCAt                                                                >  1:100489/1‑69 (MQ=255)
gcggcAGCAGCTGGTGCACTTACTACCGGATTATTTTTCCATCCTCATTTTTCACTGCCCATTGCTCAt                                                                >  1:1583027/1‑69 (MQ=255)
gcggcAGCAGCTGGTGCACTTACTACCGGATTATTTTTCCATCCTCATTTTTCACTGCCCATTGCTCAt                                                                <  1:2485429/69‑1 (MQ=255)
gcggcAGCAGCTGGTGCACTTACTACCGGATTATTTTTCCATCCTCATTTTTCACTGCCCATTGCTCAt                                                                <  1:2361853/69‑1 (MQ=255)
gcggcAGCAGCTGGTGCACTTACTACCGGATTATTTTTCCATCCTCATTTTTCACTGCCCATTGCTCAt                                                                >  1:319757/1‑69 (MQ=255)
gcggcAGCAGCTGGTGCACTTACTACCGGATTATTTTTCCATCCTCATTTTTCACTGCCCATTGCTCAt                                                                <  1:3119039/69‑1 (MQ=255)
gcggcAGCAGCTGGTGCACTTACTACCGGATTATTTTTCCATCCTCATTTTTCACTGCCCATTGCTCAt                                                                <  1:742517/69‑1 (MQ=255)
gcggcAGCAGCTGGTGCACTTACTACCGGATTATTTTTCCATCCTCATTTTTCACTGCCCATTGCTCAt                                                                <  1:670758/69‑1 (MQ=255)
gcggcAGCAGCTGGTGCACTTACTACCGGATTATTTTTCCATCCTCATTTTTCACTGCCCATTGCTCAt                                                                <  1:3151994/69‑1 (MQ=255)
gcggcAGCAGCTGGTGCACTTACTACCGGATTATTTTTCCATACTCATTTTTCACTGCCCATTGCTCAt                                                                >  1:3401155/1‑69 (MQ=255)
     agcagcTGGTGCACTTACTACCGGATTATTTTTCCATTCTCATTTTTCACTGCCCATTGCGCATTACg                                                            >  1:2663870/1‑68 (MQ=255)
     agcagcTGGTGCACTTACTACCGGATTATTTTTCCATCCTCATTTTTCACTGCCCATTGCGCAt                                                                >  1:412761/1‑64 (MQ=255)
     agcagcTGGTGCACTTACTACCGGATTATTTTTCCATCCTCATTTTTCACTGCCCATTGCGCATTACg                                                            >  1:3308556/1‑68 (MQ=255)
     agcagcTGGTGCACTTACTACCGGATTATTTTTCCATCCTCATTTTTCACTGCCCATTGCGCATTACg                                                            >  1:3333841/1‑68 (MQ=255)
     agcagcTGGTGCACTTACTACCGGATTATTTTTCCATCCTCATTTTTCACTGCCCATTGCGCATTACg                                                            >  1:391703/1‑68 (MQ=255)
     agcagcTGGTGCACTTACTACCGGATTATTTTTCCATCCTCATTTTTCACTGCCCATTGCGCATTACg                                                            >  1:506284/1‑68 (MQ=255)
     agcagcTGGTGCACTTACTACCGGATTATTTTTCCATCCTCATTTTTCACTGCCCATTGCGCATTACg                                                            >  1:573592/1‑68 (MQ=255)
     agcagcTGGTGCACTTACTACCGGATTATTTTTCCATCCTCATTTTTCACTGCCCATTGCGCATTACg                                                            >  1:1965741/1‑68 (MQ=255)
     agcagcTGGTGCACTTACTACCGGATTATTTTTCCATCCTCATTTTTCACTGCCCATTGCGCATTACg                                                            >  1:2792678/1‑68 (MQ=255)
     agcagcTGGTGCACTTACTACCGGATTATTTTTCCATCCTCATTTTTCACTGCCCATTGCGCATTACg                                                            >  1:2758269/1‑68 (MQ=255)
     agcagcTGGTGCACTTACTACCGGATTATTTTTCCATCCTCATTTTTCACTGCCCATTGCGCATTACg                                                            >  1:1183032/1‑68 (MQ=255)
     agcagcTGGTGCACTTACTACCGGATTATTTTTCCATCCTCATTTTTCACTGCCCATTGCGCATTACg                                                            >  1:810128/1‑68 (MQ=255)
     agcagcTGGTGCACTTACTACCGGATTATTTTTCCATCCTCATTTTTCACTGCCCATTGCGCATTACg                                                            >  1:91674/1‑68 (MQ=255)
     agcagcTGGTGCACTTACTACCGGATTATTTTTCCATCCTCATTTTTCACTGCCCATTGCGCATTACg                                                            >  1:253760/1‑68 (MQ=255)
     agcagcTGGTGCACTTACTACCGGATTATTTTTCCATACTCATTTTTCACTGCCCATTGCGCATTACg                                                            >  1:2569039/1‑68 (MQ=255)
                    tactacCGGATTATTTTTCCATCCTCATTTTTCACTGCCCATTGCTCATTACGGACAGATGGAAATGa                                             >  1:118915/1‑68 (MQ=255)
                     actacCGGATTATTTTTCCATCCTCATTTTTCACTGCCCATTGCTCATTACGGACAGATGGAAATGAcc                                           >  1:1539849/1‑69 (MQ=255)
                     actacCGGATTATTTTTCCATCCTCATTTTTCACTGCCCATTGCTCATTACGGACAGATGGAAATGAcc                                           >  1:996496/1‑69 (MQ=255)
                     actacCGGATTATTTTTCCATCCTCATTTTTCACTGCCCATTGCTCATTACGGACAGATGGAAATGAcc                                           >  1:2041552/1‑69 (MQ=255)
                     actacCGGATTATTTTTCCATCCTCATTTTTCACTGCCCATTGCTCATTACGGACAGATGGAAATGAcc                                           >  1:759229/1‑69 (MQ=255)
                     actacCGGATTATTTTTCCATCCTCATTTTTCACTGCCCATTGCTCATTACGGACAGATGGAAATGAcc                                           >  1:2219480/1‑69 (MQ=255)
                     actacCGGATTATTTTTACATCCTCATTTTTCACTGCCCATTGCTCATTACGGACAGATGGAAATGAcc                                           >  1:1457524/1‑69 (MQ=255)
                           ggATTATTTTTCCATCCTCATTTTTCACTGCCCATTGCGCATTACGGACAGATGGAAATGACCGata                                       <  1:3110840/67‑1 (MQ=255)
                           ggATTATTTTTCCATCCTCATTTTTCACTGCCCATTGCGCATTACGGACAGATGGAAATGACCGata                                       <  1:2943437/67‑1 (MQ=255)
                           ggATTATTTTTCCATCCTCATTTTTCACTGCCCATTGCGCATTACGGACAGATGGAAATGACCGata                                       <  1:746025/67‑1 (MQ=255)
                           ggATTATTTTTCCATCCTCATTTTTCACTGCCCATTGCGCATTACGGACAGATGGAAATGACCGata                                       <  1:761513/67‑1 (MQ=255)
                           ggATTATTTTTCCATCCTCATTTTTCACTGCCCATTGCGCATTACGGACAGATGGAAATGACCGata                                       <  1:79292/67‑1 (MQ=255)
                           ggATTATTTTTCCATCCTCATTTTTCACTGCCCATTGCGCATTACGGACAGATGGAAATGACCGata                                       <  1:2739637/67‑1 (MQ=255)
                           ggATTATTTTTCCATCCTCATTTTTCACTGCCCATTGCGCATTACGGACAGATGGAAATGACCGata                                       <  1:313532/67‑1 (MQ=255)
                           ggATTATTTTTCCATCCTCATTTTTCACTGCCCATTGCGCATTACGGACAGATGGAAATGACCGata                                       <  1:862324/67‑1 (MQ=255)
                           ggATTATTTTTCCATCCTCATTTTTCACTGCCCATTGCGCATTACGGACAGATGGAAATGACCGata                                       <  1:909178/67‑1 (MQ=255)
                           ggATTATTTTTCCATCCTCATTTTTCACTGCCCATTGCGCATTACGGACAGATGGAAATGACCGata                                       <  1:662536/67‑1 (MQ=255)
                           ggATTATTTTTCCATCCTCATTTTTCACTGCCCATTGCGCATTACGGACAGATGGAAATGACCGata                                       <  1:2590235/67‑1 (MQ=255)
                           ggATTATTTTTCCATCCTCATTTTTCACTGCCCATTGCGCATTACGGACAGATGGAAATGACCGata                                       <  1:2466680/67‑1 (MQ=255)
                           ggATTATTTTTCCATCCTCATTTTTCACTGCCCATTGCGCATTACGGACAGATGGAAATGACCGata                                       <  1:1942771/67‑1 (MQ=255)
                           ggATTATTTTTCCATCCTCATTTTTCACTGCCCATTGCGCATTACGGACAGATGGAAATGACCGata                                       <  1:2112215/67‑1 (MQ=255)
                           ggATTATTTTTCCATCCTCATTTTTCACTGCCCATTGCGCATTACGGACAGATGGAAATGACCGata                                       <  1:1777412/67‑1 (MQ=255)
                           ggATTATTTTTCCATCCTCATTTTTCACTGCCCATTGCGCATTACGGACAGATGGAAATGACCGata                                       <  1:1616253/67‑1 (MQ=255)
                           ggATTATTTTTCCATCCTCATTTTTCACTGCCCATTGCGCATTACGGACAGATGGAAATGACCGata                                       <  1:2262058/67‑1 (MQ=255)
                           ggATTATTTTTCCATCCTCATTTTTCACTGCCCATTGCGCATTACGGACAGATGGAAATGACCGata                                       <  1:1460185/67‑1 (MQ=255)
                           ggATTATTTTTCCATCCTCATTTTTCACTGCCCATTGCGCATTACGGACAGATGGAAATGACCGata                                       <  1:2386191/67‑1 (MQ=255)
                           ggATTATTTTTCCATCCTCATTTTTCACTGCCCATTGCGCATTACGGACAGATGGAAATGACCGata                                       <  1:1324713/67‑1 (MQ=255)
                           ggATTATTTTTCCATCCTCATTTTTCACTGCCCATTGCGCATTACGGACAGATGGAAATGACCGata                                       <  1:1127290/67‑1 (MQ=255)
                           ggATTATTTTTCCATCCTCATTTTTCACTGCCCATTGCGCATTACGGACAGATGGAAATGACCGata                                       <  1:2546862/67‑1 (MQ=255)
                           ggATTATTTTTCCATCCTCATTTTTCACTGCCCATTGCGCATTACGGACAGATGGAAATGACCGata                                       <  1:1024499/67‑1 (MQ=255)
                            gATTATTTTTCCATCCTCATTTTTCACTGCCCATTGCGCATTACGGACAGATGGAAATGACCGata                                       <  1:1976720/66‑1 (MQ=255)
                                           cTCATTTTTCACTGCCCATTGCTCATTACGGACAGATGGAAATGACCGATATTCTCAGCGGTGCAATTg                     >  1:718424/1‑69 (MQ=255)
                                           cTCATTTTTCACTGCCCATTGCTCATTACGGACAGATGGAAATGACCGATATTCTCAGCGGTGCAATTg                     >  1:1435025/1‑69 (MQ=255)
                                           cTCATTTTTCACTGCCCATTGCTCATTACGGACAGATGGAAATGACCGATATTCTCAGCGGTGCAATTg                     >  1:2564390/1‑69 (MQ=255)
                                           cTCATTTTTCACTGCCCATTGCTCATTACGGACAGATGGAAATGACCGATATTCTCAGCGGTGCAATTg                     >  1:1200087/1‑69 (MQ=255)
                                           cTCATTTTTCACTGCCCATTGCTCATTACGGACAGATGGAAATGACCGATATTCTCAGCGGTGCAATTg                     >  1:113564/1‑69 (MQ=255)
                                           cTCATTTTTCACTGCCCATTGCTCATTACGGACAGATGGAAATGACCGATATTCTCAGCGGTGCAATTg                     >  1:1605342/1‑69 (MQ=255)
                                           cTCATTTTTCACTGCCCATTGCTCATTACGGACAGATGGAAATGACCGATATTCTCAGCGGTGCAATTg                     >  1:875911/1‑69 (MQ=255)
                                           cTCATTTTTCACTGCCCATTGCTCATTACGGACAGATGGAAATGACCGATATTCTCAGCGGTGCAATTg                     >  1:968730/1‑69 (MQ=255)
                                           cTCATTTTTCACTGCCCATTGCTCATTACGGACAGATGGAAATGACCGATATTCTCAGCGGTGCAATTg                     >  1:331439/1‑69 (MQ=255)
                                           cTCATTTTTCACTGCCCATTGCTCATTACGGACAGATGGAAATGACCGATATTCTCAGCGGTGCAATTg                     >  1:182747/1‑69 (MQ=255)
                                           cTCATTTTTCACTGCCCATTGCTCATTACGGACAGATGGAAATGACCGATATTCTCAGCGGTGCAATTg                     >  1:2662486/1‑69 (MQ=255)
                                           cTCATTTTTCACTGCCCATTGCTCATTACGGACAGATGGAAATGACCGATATTCTCAGCGGTGCAATTg                     >  1:268052/1‑69 (MQ=255)
                                           cTCATTTTTCACTGCCCATTGCTCATTACGGACAGATGGAAATGACCGATATTCTCAGCGGTGCAATTg                     >  1:2775394/1‑69 (MQ=255)
                                           cTCATTTTTCACTGCCCATTGCTCATTACGGACAGATGGAAATGACCGATATTCTCAGCGGTGCAATTg                     >  1:3037430/1‑69 (MQ=255)
                                               tttttCACTGCCCATTGCTCATTACGGACAGATGGAAATGACCGATATTCTCAGCGGTGCAATTGTcgc                 >  1:1580296/1‑69 (MQ=255)
                                               tttttCACTGCCCATTGCTCATTACGGACAGATGGAAATGACCGATATTCTCAGCGGTGCAATTGTcgc                 >  1:1318317/1‑69 (MQ=255)
                                               tttttCACTGCCCATTGCTCATTACGGACAGATGGAAATGACCGATATTCTCAGCGGTGCAATTGTcgc                 >  1:1494812/1‑69 (MQ=255)
                                               tttttCACTGCCCATTGCTCATTACGGACAGATGGAAATGACCGATATTCTCAGCGGTGCAATTGTcgc                 >  1:867407/1‑69 (MQ=255)
                                               tttttCACTGCCCATTGCTCATTACGGACAGATGGAAATGACCGATATTCTCAGCGGTGCAATTGTcgc                 >  1:3169503/1‑69 (MQ=255)
                                               tttttCACTGCCCATTGCTCATTACGGACAGATGGAAATGACCGATATTCTCAGCGGTGCAATTGTcg                  >  1:2569895/1‑68 (MQ=255)
                                               tttttCACTGCCCATTGCTCATTACGGACAGATGGAAATGACCGATATTCTCAGCGGTGCAATTGTcg                  >  1:965307/1‑68 (MQ=255)
                                                   tCACTGCCCATTGCTCATTACGGACAGATGGAAATGACCGATATTCTCAGCGGTGCAATTGTCgcggc              <  1:3426854/68‑1 (MQ=255)
                                                   tCACTGCCCATTGCTCATTACGGACAGATGGAAATGACCGATATTCTCAGCGGTGCAATTGTCgcggc              <  1:3369616/68‑1 (MQ=255)
                                                   tCACTGCCCATTGCTCATTACGGACAGATGGAAATGACCGATATTCTCAGCGGTGCAATTGTCgcggc              <  1:1062360/68‑1 (MQ=255)
                                                   tCACTGCCCATTGCTCATTACGGACAGATGGAAATGACCGATATTCTCAGCGGTGCAATTGTCgcggc              <  1:868167/68‑1 (MQ=255)
                                                      cTGCCCATTGCTCATTACGGACAGATGGAAATGACCGATATTCTCAGCGGTGCAATTGTCGCGGCGa            <  1:2179370/67‑1 (MQ=255)
                                                        gCCCATTGCTCATTACGGACAGATGGAAATGACCGATATTCTCAGCGGTGCAATTGTCGCGGCGATTGc        <  1:2702961/69‑1 (MQ=255)
                                                        gCCCATTGCTCATTACGGACAGATGGAAATGACCGATATTCTCAGCGGTGCAATTGTCGCGGCGATTGc        <  1:2527070/69‑1 (MQ=255)
                                                        gCCCATTGCTCATTACGGACAGATGGAAATGACCGATATTCTCAGCGGTGCAATTGTCGCGGCGATTGc        <  1:2570227/69‑1 (MQ=255)
                                                        gCCCATTGCTCATTACGGACAGATGGAAATGACCGATATTCTCAGCGGTGCAATTGTCGCGGCGATTGc        <  1:402240/69‑1 (MQ=255)
                                                        gCCCATTGCTCATTACGGACAGATGGAAATGACCGATATTCTCAGCGGTGCAATTGTCGCGGCGATTGc        <  1:3326400/69‑1 (MQ=255)
                                                        gCCCATTGCTCATTACGGACAGATGGAAATGACCGATATTCTCAGCGGTGCAATTGTCGCGGCGATTGc        <  1:203783/69‑1 (MQ=255)
                                                               gCTCATTACGGACAGATGGAAATGACCGATATTCTCAGCGGTGCAAt                       >  1:1310218/1‑47 (MQ=255)
                                                               gCTCATTACGGACAGATGGAAATGACCGATATTCTCAGCGGTGCAATTGTCGCGGCGATTGCCATc    >  1:427000/1‑66 (MQ=255)
                                                               gCTCATTACGGACAGATGGAAATGACCGATATTCTCAGCGGTGCAATTGTCGCGGCGATTGCCATCgc  >  1:1060044/1‑68 (MQ=255)
                                                               gCTCATTACGGACAGATGGAAATGACCGATATTCTCAGCGGTGCAATTGTCGCGGCGATTGCCATCgc  >  1:2562767/1‑68 (MQ=255)
                                                               gCTCATTACGGACAGATGGAAATGACCGATATTCTCAGCGGTGCAATTGTCGCGGCGATTGCCATCgc  >  1:2654187/1‑68 (MQ=255)
                                                               gCTCATTACGGACAGATGGAAATGACCGATATTCTCAGCGGTGCAATTGTCGCGGCGATTGCCATCgc  >  1:1196851/1‑68 (MQ=255)
                                                               gCTCATTACGGACAGATGGAAATGACCGATATTCTCAGCGGTGCAATTGTCGCGGCGATTGCCATCgc  >  1:1314038/1‑68 (MQ=255)
                                                               gCTCATTACGGACAGATGGAAATGACCGATATTCTCAGCGGTGCAATTGTCGCGGCGATTGCCATCgc  >  1:2487059/1‑68 (MQ=255)
                                                               gCTCATTACGGACAGATGGAAATGACCGATATTCTCAGCGGTGCAATTGTCGCGGCGATTGCCATCgc  >  1:2345319/1‑68 (MQ=255)
                                                                 |                                                                 
GCGGCAGCAGCTGGTGCACTTACTACCGGATTATTTTTCCATCCTCATTTTTCACTGCCCATTGCTCATTACGGACAGATGGAAATGACCGATATTCTCAGCGGTGCAATTGTCGCGGCGATTGCCATCGC  >  minE/1566822‑1566952

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