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 552,606 C→T 26.5% T306T (ACG→ACA)  ybiW ← predicted pyruvate formate lyase

Read alignment evidence...
  seq id position ref new freq score (cons/poly) reads annotation genes product
*minE552,6060CT26.5% 161.1 / 52.9 135T306T (ACG→ACA) ybiWpredicted pyruvate formate lyase
Reads supporting (aligned to +/- strand):  ref base C (39/60);  new base T (24/12);  total (63/72)
Fisher's exact test for biased strand distribution p-value = 6.28e-03
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 1.00e+00

Only 100 of 135 total aligned reads displayed.

CTTGTTCACTTCCAGCAGTTTCAGCCAGCAGCTATGCAGCATCTCGATGGCGTGTTCGCGATCCAGCGTCTGGTTGAGTTCAACGTCGCGGCGATAGTACGGGTAGAGATACTGGTCCATACGACCAAACGAT  >  minE/552540‑552672
                                                                  |                                                                  
cTTGTTCACTTCCAGCAGTTTCAGCCAGCAGCTATGCAGCATCTCGATGGCGTGTTCGCGATCCAGCg                                                                   >  1:2616481/1‑68 (MQ=255)
        cTTCCAGCAGTTTCAGCCAGCAGCTATGCAGCATCTCGATGGCGTGTTCGCGATCCAGCGTCTGGTTg                                                           <  1:1182388/68‑1 (MQ=255)
        cTTCCAGCAGTTTCAGCCAGCAGCTATGCAGCATCTCGATGGCGTGTTCGCGATCCAGCGTCTGGTTg                                                           <  1:3193563/68‑1 (MQ=255)
        cTTCCAGCAGTTTCAGCCAGCAGCTATGCAGCATCTCGATGGCGTGTTCGCGATCCAGCGTCTGGTTg                                                           <  1:272147/68‑1 (MQ=255)
        cTTCCAGCAGTTTCAGCCAGCAGCTATGCAGCATCTCGATGGCGTGTTCGCGATCCAGCGTCTGGTTg                                                           <  1:2208768/68‑1 (MQ=255)
                       gccagcAGCTATGCAGCATCTCGATGGCGTGTTCGCGATCCAGCGTCTGGTTGAGTTCAACGTCgcggc                                           >  1:620428/1‑69 (MQ=255)
                       gccagcAGCTATGCAGCATCTCGATGGCGTGTTCGCGATCCAGCGTCTGGTTGAGTTCAACGTCgcggc                                           >  1:1077876/1‑69 (MQ=255)
                       gccagcAGCTATGCAGCATCTCGATGGCGTGTTCGCGATCCAGCGTCTGGTTGAGTTCAACGTCgcggc                                           >  1:2522456/1‑69 (MQ=255)
                       gccagcAGCTATGCAGCATCTCGATGGCGTGTTCGCGATCCAGCGTCTGGTTGAGTTCAACGTCgcggc                                           >  1:1475864/1‑69 (MQ=255)
                            cagcTATGCAGCATCTCGATGGCGTGTTCGCGATCCAGCGTCTGGTTGAGTTCAACGTCGCGGCGATAg                                      <  1:1696422/69‑1 (MQ=255)
                             agcTATGCAGCATCTCGATGGCGTGTTCGCGATCCAGCGTCTGGTTGAGTTCAACGTCGCGGCGATAGt                                     >  1:205389/1‑69 (MQ=255)
                              gcTATGCAGCATCTCGATGGCGTGTTCGCGATCCAGCGTCTGGTTGAGTTCAACGTCGCGGCGATAGTa                                    >  1:1046834/1‑69 (MQ=255)
                              gcTATGCAGCATCTCGATGGCGTGTTCGCGATCCAGCGTCTGGTTGAGTTCAACGTCGCGGCGATAGTa                                    <  1:2520088/69‑1 (MQ=255)
                               cTATGCAGCATCTCGATGGCGTGTTCGCGATCCAGCGTCTGGTTGAGTTCAACGTCGCGGCGATAGTAc                                   <  1:1667705/69‑1 (MQ=255)
                               cTATGCAGCATCTCGATGGCGTGTTCGCGATCCAGCGTCTGGTTGAGTTCAACGTCGCGGCGATAGTAc                                   <  1:1967663/69‑1 (MQ=255)
                               cTATGCAGCATCTCGATGGCGTGTTCGCGATCCAGCGTCTGGTTGAGTTCAACGTCGCGGCGATAGTAc                                   <  1:2034262/69‑1 (MQ=255)
                               cTATGCAGCATCTCGATGGCGTGTTCGCGATCCAGCGTCTGGTTGAGTTCAACGTCGCGGCGATAGTAc                                   <  1:2343482/69‑1 (MQ=255)
                               cTATGCAGCATCTCGATGGCGTGTTCGCGATCCAGCGTCTGGTTGAGTTCAACGTCGCGGCGATAGTAc                                   <  1:2384340/69‑1 (MQ=255)
                               cTATGCAGCATCTCGATGGCGTGTTCGCGATCCAGCGTCTGGTTGAGTTCAACGTCGCGGCGATAGTAc                                   <  1:1310733/69‑1 (MQ=255)
                               cTATGCAGCATCTCGATGGCGTGTTCGCGATCCAGCGTCTGGTTGAGTTCAACGTCGCGGCGATAGTAc                                   <  1:519068/69‑1 (MQ=255)
                               cTATGCAGCATCTCGATGGCGTGTTCGCGATCCAGCGTCTGGTTGAGTTCAACGTCGCGGCGATAGTAc                                   <  1:52555/69‑1 (MQ=255)
                               cTATGCAGCATCTCGATGGCGTGTTCGCGATCCAGCGTCTGGTTGAGTTCAACGTCGCGGCGATAGTAc                                   <  1:65499/69‑1 (MQ=255)
                                tATGCAGCATCTCGATGGCGTGTTCGCGATCCAGCGTCTGGTTGAGTTCAACGTCGCGGCGATAGTAc                                   <  1:104371/68‑1 (MQ=255)
                                 aTGCAGCATCTCGATGGCGTGTTCGCGATCCAGCGTCTGGTTGAGTTCAACGTCGCGGCGATAg                                      <  1:2179043/64‑1 (MQ=255)
                                  tGCAGCATCTCGATGGCGTGTTCGCGATCGAGCGTCTGGTTGAGTTCAACGTCGCGGCGATAGTAc                                   <  1:3424823/66‑1 (MQ=255)
                                    cagcaTCTCGATGGCGTGTTCGCGATCCAGCGTCTGGTTGAGTTCAACGTCGCGGCGATAGTa                                    <  1:2928884/63‑1 (MQ=255)
                                    cagcaTCTCGATGGCGTGTTCGCGATCCAGCGTCTGGTTGAGTTCAACGTCGCGGCGATAGTa                                    <  1:1183604/63‑1 (MQ=255)
                                    cagcaTCTCGATGGCGTGTTCGCGATCCAGCGTCTGGTTGAGTTCAACGTCGCGGCGATAGTa                                    <  1:2699647/63‑1 (MQ=255)
                                    cagcaTCTCGATGGCGTGTTCGCGATCCAGCGTCTGGTTGAGTTCAACGTCGCGGCGATAGTa                                    <  1:1510761/63‑1 (MQ=255)
                                    cagcaTCTCGATGGCGTGTTCGCGATCCAGCGTCTGGTTGAGTTCAACGTCGCGGCGATAGTa                                    <  1:121731/63‑1 (MQ=255)
                                    cagcaTCTCGATGGCGTGTTCGCGATCCAGCGTCTGGTTGAGTTCAACGTCGCGGCGATAGTa                                    <  1:3270544/63‑1 (MQ=255)
                                    cagcaTCTCGATGGCGTGTTCGCGATCCAGCGTCTGGTTGAGTTCAACGTCGCGGCGATAGTa                                    <  1:2819501/63‑1 (MQ=255)
                                    cagcaTCTCGATGGCGTGTTCGCGATCCAGCGTCTGGTTGAGTTCAACGTCGCGGCGATAGTa                                    <  1:2478387/63‑1 (MQ=255)
                                    cagcaTCTCGATGGCGTGTTCGCGATCCAGCGTCTGGTTGAGTTCAACGTCGCGGCGATAGTACggg                                >  1:1884032/1‑67 (MQ=255)
                                    cagcaTCTCGATGGCGTGTTCGCGATCCAGCGTCTGGTTGAGTTCAACGTCGCGGCGATAGTACggg                                >  1:360069/1‑67 (MQ=255)
                                    cagcaTCTCGATGGCGTGTTCGCGATCCAGCGTCTGGTTGAGTTCAACGTCGCGGCGATAGTACggg                                >  1:796820/1‑67 (MQ=255)
                                    cagcaTCTCGATGGCGTGTTCGCGATCCAGCGTCTGGTTGAGTTCAACGTCGCGGCGATAGTACggg                                >  1:1858812/1‑67 (MQ=255)
                                    cagcaTCTCGATGGCGTGTTCGCGATCCAGCGTCTGGTTGAGTTCAACGTCGCGGCGATAGTACggg                                >  1:3068446/1‑67 (MQ=255)
                                    cagcaTCTCGATGGCGTGTTCGCGATCCAGCGTCTGGTTGAGTTCAACGTCGCGGCGATAGTACggg                                >  1:2919035/1‑67 (MQ=255)
                                    cagcaTCTCGATGGCGTGTTCGCGATCCAGCGTCTGGTTGAGTTCAACGTCGCGGCGATAGTACggg                                >  1:3043837/1‑67 (MQ=255)
                                    cagcaTCTCGATGGCGTGTTCGCGATCCAGCGTCTGGTTGAGTTCAACGTCGCGGCGATAGTACGGGTa                              <  1:336475/69‑1 (MQ=255)
                                    cagcaTCTCGATGGCGTGTTCGCGATCCAGCGTCTGGTTGAGTTCAACGTCGCGGCGATAGTACGGGTa                              <  1:2874359/69‑1 (MQ=255)
                                        aTCTCGATGGCGTGTTCGCGATCCAGCGTCTGGTTGAGTTCAACGTCgcggc                                           >  1:2700092/1‑52 (MQ=255)
                                        aTCTCGATGGCGTGTTCGCGATCCAGCGTCTGGTTGAGTTCAACGTCgcggc                                           <  1:2617680/52‑1 (MQ=255)
                                        aTCTCGATGGCGTGTTCGCGATCCAGCGTCTGGTTGAGTTCAACGTCgcggc                                           <  1:1293681/52‑1 (MQ=255)
                                        aTCTCGATGGCGTGTTCGCGATCCAGCGTCTGGTTGAGTTCAACGTCgcggc                                           >  1:2567469/1‑52 (MQ=255)
                                        aTCTCGATGGCGTGTTCGCGATCCAGCGTCTGGTTGAGTTCAACGTCgcggc                                           >  1:2733872/1‑52 (MQ=255)
                                        aTCTCGATGGCGTGTTCGCGATCCAGCGTCTGGTTGAGTTCAACGTCgcggc                                           <  1:2938495/52‑1 (MQ=255)
                                        aTCTCGATGGCGTGTTCGCGATCCAGCGTCTGGTTGAGTTCAACGTCgcggc                                           >  1:2964868/1‑52 (MQ=255)
                                        aTCTCGATGGCGTGTTCGCGATCCAGCGTCTGGTTGAGTTCAACGTCgcggc                                           <  1:2996911/52‑1 (MQ=255)
                                        aTCTCGATGGCGTGTTCGCGATCCAGCGTCTGGTTGAGTTCAACGTCgcggc                                           >  1:139428/1‑52 (MQ=255)
                                        aTCTCGATGGCGTGTTCGCGATCCAGCGTCTGGTTGAGTTCAACGTCgcggc                                           >  1:2474815/1‑52 (MQ=255)
                                        aTCTCGATGGCGTGTTCGCGATCCAGCGTCTGGTTGAGTTCAACGTCgcggc                                           <  1:3008872/52‑1 (MQ=255)
                                        aTCTCGATGGCGTGTTCGCGATCCAGCGTCTGGTTGAGTTCAACGTCgcggc                                           <  1:3013871/52‑1 (MQ=255)
                                        aTCTCGATGGCGTGTTCGCGATCCAGCGTCTGGTTGAGTTCAACGTCgcggc                                           >  1:1030900/1‑52 (MQ=255)
                                        aTCTCGATGGCGTGTTCGCGATCCAGCGTCTGGTTGAGTTCAACGTCgcggc                                           >  1:2067243/1‑52 (MQ=255)
                                        aTCTCGATGGCGTGTTCGCGATCCAGCGTCTGGTTGAGTTCAACGTCgcggc                                           >  1:1515496/1‑52 (MQ=255)
                                        aTCTCGATGGCGTGTTCGCGATCCAGCGTCTGGTTGAGTTCAACGTCgcggc                                           >  1:2010344/1‑52 (MQ=255)
                                        aTCTCGATGGCGTGTTCGCGATCCAGCGTCTGGTTGAGTTCAACGTCgcggc                                           <  1:1563801/52‑1 (MQ=255)
                                        aTCTCGATGGCGTGTTCGCGATCCAGCGTCTGGTTGAGTTCAACGTCgcggc                                           <  1:1930010/52‑1 (MQ=255)
                                        aTCTCGATGGCGTGTTCGCGATCCAGCGTCTGGTTGAGTTCAACGTCgcggc                                           <  1:3113074/52‑1 (MQ=255)
                                        aTCTCGATGGCGTGTTCGCGATCCAGCGTCTGGTTGAGTTCAACGTCgcggc                                           >  1:897587/1‑52 (MQ=255)
                                        aTCTCGATGGCGTGTTCGCGATCCAGCGTCTGGTTGAGTTCAACGTCgcggc                                           >  1:972178/1‑52 (MQ=255)
                                        aTCTCGATGGCGTGTTCGCGATCCAGCGTCTGGTTGAGTTCAACGTCGCGGCGATAGTACGGGTAgaga                          <  1:311646/69‑1 (MQ=255)
                                                 gCGTGTTCGCGATCCAGTGTCTGGTTCAGTTCAACGTCACGGCGATAGTATGGATAGAGAt                         >  1:3182202/1‑61 (MQ=255)
                                                 gCGTGTTCGCGATCCAGTGTCTGGTTCAGTTCAACGTCACGGCGATAGTATGGATAGAGATACTgtt                   >  1:2258843/1‑65 (MQ=255)
                                                 gCGTGTTCGCGATCCAGTGTCTGGTTCAGTTCAACGTCACGGCGATAGTATGGATAGAGATACTGGTc                  >  1:3215557/1‑68 (MQ=255)
                                                 gCGTGTTCGCGATCCAGTGTCTGGTTCAGTTCAACGTCACGGCGATAGTATGGATAGAGATACTGGTc                  >  1:3270680/1‑68 (MQ=255)
                                                 gCGTGTTCGCGATCCAGTGTCTGGTTCAGTTCAACGTCACGGCGATAGTATGGATAGAGATACTGGTc                  >  1:111101/1‑68 (MQ=255)
                                                 gCGTGTTCGCGATCCAGTGTCTGGTTCAGTTCAACGTCACGGCGATAGTATGGATAGAGATACTGGTc                  >  1:521025/1‑68 (MQ=255)
                                                 gCGTGTTCGCGATCCAGTGTCTGGTTCAGTTCAACGTCACGGCGATAGTATGGATAGAGATACTGGTc                  >  1:677928/1‑68 (MQ=255)
                                                 gCGTGTTCGCGATCCAGTGTCTGGTTCAGTTCAACGTCACGGCGATAGTATGGATAGAGATACTGGTc                  >  1:731751/1‑68 (MQ=255)
                                                 gCGTGTTCGCGATCCAGTGTCTGGTTCAGTTCAACGTCACGGCGATAGTATGGATAGAGATACTGGTc                  >  1:753528/1‑68 (MQ=255)
                                                 gCGTGTTCGCGATCCAGTGTCTGGTTCAGTTCAACGTCACGGCGATAGTATGGATAGAGATACTGGTc                  >  1:771867/1‑68 (MQ=255)
                                                 gCGTGTTCGCGATCCAGTGTCTGGTTCAGTTCAACGTCACGGCGATAGTATGGATAGAGATACTGGTc                  >  1:987987/1‑68 (MQ=255)
                                                 gCGTGTTCGCGATCCAGTGTCTGGTTCAGTTCAACGTCACGGCGATAGTATGGATAGAGATACTGGTc                  >  1:285360/1‑68 (MQ=255)
                                                 gCGTGTTCGCGATCCAGTGTCTGGTTCAGTTCAACGTCACGGCGATAGTATGGATAGAGATACTGGTc                  >  1:2176948/1‑68 (MQ=255)
                                                 gCGTGTTCGCGATCCAGTGTCTGGTTCAGTTCAACGTCACGGCGATAGTATGGATAGAGATACTGGTc                  >  1:2765119/1‑68 (MQ=255)
                                                 gCGTGTTCGCGATCCAGTGTCTGGTTCAGTTCAACGTCACGGCGATAGTATGGATAGAGATACTGGTc                  >  1:1458542/1‑68 (MQ=255)
                                                 gCGTGTTCGCGATCCAGTGTCTGGTTCAGTTCAACGTCACGGCGATAGTATGGATAGAGATACTGGTc                  >  1:1878207/1‑68 (MQ=255)
                                                 gCGTGTTCGCGATCCAGTGTCTGGTTCAGTTCAACGTCACGGCGATAGTATGGATAGAGATACTGGTc                  >  1:1404161/1‑68 (MQ=255)
                                                 gCGTGTTCGCGATCCAGTGTCTGGTTCAGTTCAACGTCACGGCGATAGTATGGATAGAGATACTGGTc                  >  1:1431766/1‑68 (MQ=255)
                                                 gCGTGTTCGCGATCCAGTGTCTGGTTCAGTTCAACGTCACGGCGATAGTATGGATAGAGATACTGGTc                  >  1:1859705/1‑68 (MQ=255)
                                                     gtTCGCGATCCAGTGTCTGGTTCAGTTCAACGTCACGGCGATAGTATGGATAGAGTTACTGGTCCATAc             <  1:1059807/69‑1 (MQ=255)
                                                     gtTCGCGATCCAGTGTCTGGTTCAGTTCAACGTCACGGCGATAGTATGGATAGAGATACTGGTCCATAc             <  1:2104811/69‑1 (MQ=255)
                                                     gtTCGCGATCCAGTGTCTGGTTCAGTTCAACGTCACGGCGATAGTATGGATAGAGATACTGGTCCATAc             <  1:2251906/69‑1 (MQ=255)
                                                     gtTCGCGATCCAGTGTCTGGTTCAGTTCAACGTCACGGCGATAGTATGGATAGAGATACTGGTCCATAc             <  1:92417/69‑1 (MQ=255)
                                                     gtTCGCGATCCAGTGTCTGGTTCAGTTCAACGTCACGGCGATAGTATGGATAGAGATACTGGTCCATAc             <  1:1761593/69‑1 (MQ=255)
                                                      ttCGCGATCCAGTGTCTGGTTCAGTTCAACGTCACGGCGATAGTATGGATAGAGATACTGGTCCATAc             <  1:570488/68‑1 (MQ=255)
                                                      ttCGCGATCCAGTGTCTGGTTCAGTTCAACGTCACGGCGATAGTATGGATAGAGATACTGGTCCATAc             <  1:2468129/68‑1 (MQ=255)
                                                      ttCGCGATCCAGTGTCTGGTTCAGTTCAACGTCACGGCGATAGTATGGATAGAGATACTGGTCCATAc             <  1:2540282/68‑1 (MQ=255)
                                                      ttCGCGATCCAGTGTCTGGTTCAGTTCAACGTCACGGCGATAGTATGGATAGAGATACTGGTCCATAc             <  1:680714/68‑1 (MQ=255)
                                                      ttCGCGATCCAGCGTCTGGTTGAGTTCAACGTCGCGGCGATAGTACGGGTAGAGATACTGGTCCATACg            <  1:1737838/69‑1 (MQ=255)
                                                      ttCGCGATCCAGCGTCTGGTTGAGTTCAACGTCGCGGCGATAGTACGGGTAGAGATACTGGTCCATACg            <  1:1301486/69‑1 (MQ=255)
                                                        cgcgATCCAGCGTCTGGTTGAGTTCAACGTCGCGGCGATAGTACGGGTAGAGATACTGGTCCATACGa           >  1:2320135/1‑68 (MQ=255)
                                                        cgcgATCCAGCGTCTGGTTGAGTTCAACGTCGCGGCGATAGTACGGGTAGAGATACTGGTCCATACGa           >  1:1857697/1‑68 (MQ=255)
                                                        cgcgATCCAGCGTCTGGTTGAGTTCAACGTCGCGGCGATAGTACGGGTAGAGATACTGGTCCATACGa           >  1:1570941/1‑68 (MQ=255)
                                                        cgcgATCCAGCGTCTGGTTGAGTTCAACGTCGCGGCGATAGTACGGGTAGAGATACTGGTCCATACGa           >  1:3048753/1‑68 (MQ=255)
                                                          cgATCCAGCGTCTGGTTGAGTTCAACGTCGCGGCGATAg                                      <  1:1053933/39‑1 (MQ=255)
                                                                 gCGTCTGGTTGAGTTCAACGTCGCGGCGATAGTACGGGTAGAGATACTGGTCCATACGACCAAACGAt  <  1:825260/68‑1 (MQ=255)
                                                                  |                                                                  
CTTGTTCACTTCCAGCAGTTTCAGCCAGCAGCTATGCAGCATCTCGATGGCGTGTTCGCGATCCAGCGTCTGGTTGAGTTCAACGTCGCGGCGATAGTACGGGTAGAGATACTGGTCCATACGACCAAACGAT  >  minE/552540‑552672

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