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 2,366,628 C→T 43.9% K275K (AAG→AAA)  pepQ ← proline dipeptidase

Read alignment evidence...
  seq id position ref new freq score (cons/poly) reads annotation genes product
*minE2,366,6280CT43.9% 34.4 / 90.5 116K275K (AAG→AAA) pepQproline dipeptidase
Reads supporting (aligned to +/- strand):  ref base C (46/19);  new base T (19/32);  total (65/51)
Fisher's exact test for biased strand distribution p-value = 3.64e-04
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 8.92e-01

Only 100 of 116 total aligned reads displayed.

CACATAGCTGACGCCTGCTTTCATGGTGGCGATCAGCGCCAGTTGTTCATCATTAACGTCCTTCACCAGCTGCGCGTAGTCGTTGTCACTTTTTGCCGACCAGGTACGGGTCAGGTCAGCCGCATAG  >  minE/2366568‑2366694
                                                            |                                                                  
cacaTAGCTGACGCCTGCTTTCATGGTGGCGATCAGCGCCAGTTGTTCATCATTAACGTCCTTCACCAg                                                            >  1:1977393/1‑69 (MQ=255)
cacaTAGCTGACGCCTGCTTTCATGGTGGCGATCAGCGCCAGTTGTTCATCATTAACGTCCTTCACCAg                                                            >  1:973310/1‑69 (MQ=255)
cacaTAGCTGACGCCTGCTTTCATGGTGGCGATCAGCGCCAGTTGTTCATCATTAACGTCCTTCACCAg                                                            >  1:1236692/1‑69 (MQ=255)
cacaTAGCTGACGCCTGCTTTCATGGTGGCGATCAGCGCCAGTTGTTCATCATTAACGTCCTTCACCAg                                                            >  1:750618/1‑69 (MQ=255)
cacaTAGCTGACGCCTGCTTTCATGGTGGCGATCAGCGCCAGTTGTTCATCATTAACGTCCTTCACCAg                                                            >  1:2289113/1‑69 (MQ=255)
cacaTAGCTGACGCCTGCTTTCATGGTGGCGATCAGCGCCAGTTGTTCATCATTAACGTCCTTCACCAg                                                            >  1:2311924/1‑69 (MQ=255)
cacaTAGCTGACGCCTGCTTTCATGGTGGCGATCAGCGCCAGTTGTTCATCATTAACGTCCTTCACCAg                                                            >  1:2760092/1‑69 (MQ=255)
cacaTAGCTGACGCCTGCTTTCATGGTGGCGATCAGCGCCAGTTGTTCATCATTAACGTCCTTCACCAg                                                            >  1:2918564/1‑69 (MQ=255)
           cGCCTGCTTTCATGGTGGCGATCAGCGCCAGTTGTTCATCATTAACGTCCTTCACCAGCTGCGCGTAGt                                                 >  1:1914606/1‑69 (MQ=255)
           cGCCTGCTTTCATGGTGGCGATCAGCGCCAGTTGTTCATCATTAACGTCCTTCACCAGCTGCGCGTAGt                                                 >  1:2223819/1‑69 (MQ=255)
           cGCCTGCTTTCATGGTGGCGATCAGCGCCAGTTGTTCATCATTAACGTCCTTCACCAGCTGCGCGTAGt                                                 >  1:3289871/1‑69 (MQ=255)
           cGCCTGCTTTCATGGTGGCGATCAGCGCCAGTTGTTCATCATTAACGTCCTTCACCAGCTGCGCGTAGt                                                 >  1:408790/1‑69 (MQ=255)
           cGCCTGCTTTCATGGTGGCGATCAGCGCCAGTTGTTCATCATTAACGTCCTTCACCAGCTGCGCGTAGt                                                 >  1:548641/1‑69 (MQ=255)
           cGCCTGCTTTCATGGTGGCGATCAGCGCCAGTTGTTCATCATTAACGTCCTTCACCAGCTGCGCGTAGt                                                 >  1:738628/1‑69 (MQ=255)
              cTGCTTTCATGGTGGCGATCAGCGCCAGTTGCTCATCATTTACGTCTTTCACCAGCTGTGCGTAGTCGt                                              >  1:1781320/1‑69 (MQ=255)
              cTGCTTTCATGGTGGCGATCAGCGCCAGTTGCTCATCATTTACGTCTTTCACCAGCTGTGCGTAGTCGt                                              >  1:1240817/1‑69 (MQ=255)
              cTGCTTTCATGGTGGCGATCAGCGCCAGTTGCTCATCATTTACGTCTTTCACCAGCTGTGCGTAGTCGt                                              >  1:741394/1‑69 (MQ=255)
               tGCTTTCATGGTGGCGATCAGCGCCAGTTGTTCATCATTAACGTCCTTCACCAGCTGCGCGTAGTCGtt                                             >  1:3140172/1‑69 (MQ=255)
               tGCTTTCATGGTGGCGATCAGCGCCAGTTGTTCATCATTAACGTCCTTCACCAGCTGCGCGTAGTCGtt                                             >  1:97441/1‑69 (MQ=255)
               tGCTTTCATGGTGGCGATCAGCGCCAGTTGTTCATCATTAACGTCCTTCACCAGCTGCGCGTAGTCGtt                                             >  1:1844028/1‑69 (MQ=255)
               tGCTTTCATGGTGGCGATCAGCGCCAGTTGTTCATCATTAACGTCCTTCACCAGCTGCGCGTAGTCGtt                                             >  1:2088719/1‑69 (MQ=255)
               tGCTTTCATGGTGGCGATCAGCGCCAGTTGTTCATCATTAACGTCCTTCACCAGCTGCGCGTAGTCGtt                                             >  1:2388451/1‑69 (MQ=255)
               tGCTTTCATGGTGGCGATCAGCGCCAGTTGTTCATCATTAACGTCCTTCACCAGCTGCGCGTAGTCGtt                                             >  1:2440508/1‑69 (MQ=255)
               tGCTTTCATGGTGGCGATCAGCGCCAGTTGTTCATCATTAACGTCCTTCACCAGCTGCGCGTAGTCGtt                                             >  1:2486834/1‑69 (MQ=255)
               tGCTTTCATGGTGGCGATCAGCGCCAGTTGTTCATCATTAACGTCCTTCACCAGCTGCGCGTAGTCGtt                                             >  1:2867775/1‑69 (MQ=255)
               tGCTTTCATGGTGGCGATCAGCGCCAGTTGTTCATCATTAACGTCCTTCACCAGCTGCGCGTAGTCGtt                                             >  1:2960638/1‑69 (MQ=255)
               tGCTTTCATGGTGGCGATCAGCGCCAGTTGTTCATCATTAACGTCCTTCACCAGCTGCGCGTAGTCGtt                                             >  1:3033615/1‑69 (MQ=255)
                    tCATGGTGGCGATCAGCGCCAGTTGCTCATCATTTACGTCTTTCACctgctgtg                                                       <  1:2570419/54‑3 (MQ=37)
                    tCATGGTGGCGATCAGCGCCAGTTGCTCATCATTTACGTCTTTCACCAGc                                                           >  1:142243/1‑50 (MQ=38)
                    tCATGGTGGCGATCAGCGCCAGTTGCTCATCATTTACGTCTTTCACCAGCTgtg                                                       <  1:3413863/54‑3 (MQ=37)
                    tCATGGTGGCGATCAGCGCCAGTTGCTCATCATTTACGTCTTTCACCAGCTgtg                                                       <  1:1100219/54‑3 (MQ=37)
                    tCATGGTGGCGATCAGCGCCAGTTGCTCATCATTTACGTCTTTCACCAGCTgtg                                                       <  1:2598634/54‑3 (MQ=37)
                    tCATGGTGGCGATCAGCGCCAGTTGCTCATCATTTACGTCTTTCACCAGCTgtg                                                       <  1:2674506/54‑3 (MQ=37)
                    tCATGGTGGCGATCAGCGCCAGTTGCTCATCATTTACGTCTTTCACCAGCTgtg                                                       <  1:2723982/54‑3 (MQ=37)
                    tCATGGTGGCGATCAGCGCCAGTTGCTCATCATTTACGTCTTTCACCAGCTgtg                                                       <  1:2885293/54‑3 (MQ=37)
                    tCATGGTGGCGATCAGCGCCAGTTGCTCATCATTTACGTCTTTCACCAGCTgtg                                                       <  1:1484030/54‑3 (MQ=37)
                    tCATGGTGGCGATCAGCGCCAGTTGCTCATCATTTACGTCTTTCACCAGCTgtg                                                       <  1:2962286/54‑3 (MQ=37)
                    tCATGGTGGCGATCAGCGCCAGTTGCTCATCATTTACGTCTTTCACCAGCTgtg                                                       <  1:3057358/54‑3 (MQ=37)
                    tCATGGTGGCGATCAGCGCCAGTTGCTCATCATTTACGTCTTTCACCAGCTgtg                                                       <  1:1899891/54‑3 (MQ=37)
                    tCATGGTGGCGATCAGCGCCAGTTGCTCATCATTTACGTCTTTCACCAGCTgtg                                                       <  1:405945/54‑3 (MQ=37)
                    tCATGGTGGCGATCAGCGCCAGTTGCTCATCATTTACGTCTTTCACCAGCTgtg                                                       <  1:515858/54‑3 (MQ=37)
                    tCATGGTGGCGATCAGCGCCAGTTGCTCATCATTTACGTCTTTCACCAGCTgtg                                                       <  1:1361122/54‑3 (MQ=37)
                    tCATGGTGGCGATCAGCGCCAGTTGCTCATCATTTACGTCTTTCACCAGCTgtg                                                       <  1:634262/54‑3 (MQ=37)
                    tCATGGTGGCGATCAGCGCCAGTTGCTCATCATTTACGTCTTTCACCAGCTgtg                                                       <  1:688731/54‑3 (MQ=37)
                    tCATGGTGGCGATCAGCGCCAGTTGCTCATCATTTACGTCTTTCACCAGCTgtg                                                       <  1:726937/54‑3 (MQ=37)
                    tCATGGTGGCGATCAGCGCCAGTTGCTCATCATTTACGTCTTTCACCAGCTgtg                                                       <  1:130358/54‑3 (MQ=37)
                    tCATGGTGGCGATCAGCGCCAGTTGCTCATCATTTACGTCTTTCACCAGCTgtg                                                       <  1:941553/54‑3 (MQ=37)
                    tCATGGTGGCGATCAGCGCCAGTTGCTCATCATTTACGTCTTTCACCAGCTgtg                                                       <  1:1656584/54‑3 (MQ=37)
                    tCATGGTGGCGATCAGCGCCAGTTGCTCATCATTTACGTCTTTCACCAGCTgtg                                                       <  1:191512/54‑3 (MQ=37)
                    tCATGGTGGCGATCAGCGCCAGTTGCTCATCATTTACGTCTTTCACCAGCTgtg                                                       <  1:1861165/54‑3 (MQ=37)
                    tCATGGTGGCGATCAGCGCCAGTTGCTCATCATTTACGTCTTTCACCAGCTgtg                                                       <  1:1697251/54‑3 (MQ=37)
                    tCATGGTGGCGATCAGCGCCAGTTGCTCATCATTTACGTCTTTCACCAGCTgtg                                                       <  1:2092735/54‑3 (MQ=37)
                    tCATGGTGGCGATCAGCGCCAGTTGCTCATCATTTACGTCTTTCACCAGCTgtg                                                       <  1:2134321/54‑3 (MQ=37)
                    tCATGGTGGCGATCAGCGCCAGTTGCTCATCATTTACGTCTTTCACCAGCTgtg                                                       <  1:1730907/54‑3 (MQ=37)
                    tCATGGTGGCGATCAGCGCCAGTTGCTCATCATTTACGTCTTTCACCAGCTgtg                                                       <  1:1721484/54‑3 (MQ=37)
                    tCATGGTGGCGATCAGCGCCAGTTGCTCATCATTTACGTCTTTCACCAGCTgtg                                                       <  1:2294597/54‑3 (MQ=37)
                    tCATGGTGGCGATCAGCGCCAGTTGCTCATCATTTACGTCTTTCACCAGCTGTGCGTAGTCGTTGTcgc                                        >  1:1567342/1‑67 (MQ=255)
                    tCATGGTGGCGATCAGCGCCAGTTGCTCATCATTTACGTCTTTCACCAGCTGTGCGTAGTCGTTGTcgc                                        >  1:885521/1‑67 (MQ=255)
                    tCATGGTGGCGATCAGCGCCAGTTGCTCATCATTTACGTCTTTCACCAGCTGTGCGTAGTCGTTGTcgc                                        >  1:1358553/1‑67 (MQ=255)
                    tCATGGTGGCGATCAGCGCCAGTTGCTCATCATTTACGTCTTTCACCAGCTGTGCGTAGTCGTTGTcgc                                        >  1:72151/1‑67 (MQ=255)
                    tCATGGTGGCGATCAGCGCCAGTTGCTCATCATTTACGTCTTTCACCAGCTGTGCGTAGTCGTTGTcgc                                        >  1:574774/1‑67 (MQ=255)
                    tCATGGTGGCGATCAGCGCCAGTTGCTCATCATTTACGTCTTTCACCAGCTGTGCGTAGTCGTTGTcgc                                        >  1:3296809/1‑67 (MQ=255)
                    tCATGGTGGCGATCAGCGCCAGTTGCTCATCATTTACGTCTTTCACCAGCTGTGCGTAGTCGTTGTcgc                                        >  1:3174928/1‑67 (MQ=255)
                    tCATGGTGGCGATCAGCGCCAGTTGCTCATCATTTACGTCTTTCACCAGCTGTGCGTAGTCGTTGTcgc                                        >  1:1474393/1‑67 (MQ=255)
                    tCATGGTGGCGATCAGCGCCAGTTGCTCATCATTTACGTCTTTCACCAGCTGTGCGTAGTCGTTGTcgc                                        >  1:2885810/1‑67 (MQ=255)
                         gtggCGATCAGCGCCAGTTGTTCATCATTAACGTCCTTCACCAGCTgcgc                                                      >  1:175399/1‑50 (MQ=255)
                         gtggCGATCAGCGCCAGTTGTTCATCATTAACGTCCTTCACCAGCTGCGCGTAGTCGTTGTCACttttt                                   >  1:1437707/1‑69 (MQ=255)
                         gtggCGATCAGCGCCAGTTGTTCATCATTAACGTCCTTCACCAGCTGCGCGTAGTCGTTGTCACttttt                                   >  1:1173093/1‑69 (MQ=255)
                         gtggCGATCAGCGCCAGTTGTTCATCATTAACGTCCTTCACCAGCTGCGCGTAGTCGTTGTCACttttt                                   >  1:1889379/1‑69 (MQ=255)
                         gtggCGATCAGCGCCAGTTGTTCATCATTAACGTCCTTCACCAGCTGCGCGTAGTCGTTGTCACttttt                                   >  1:91588/1‑69 (MQ=255)
                         gtggCGATCAGCGCCAGTTGTTCATCATTAACGTCCTTCACCAGCTGCGCGTAGTCGTTGTCACttttt                                   >  1:1246940/1‑69 (MQ=255)
                         gtggCGATCAGCGCCAGTTGTTCATCATTAACGTCCTTCACCAGCTGCGCGTAGTCGTTGTCACttttt                                   >  1:1393182/1‑69 (MQ=255)
                            gCGATCAGCGCCAGTTGCTCATCATTTACGTCTTTCACCAGCTgtg                                                       <  1:502471/46‑3 (MQ=25)
                              gATCAGCGCCAGTTGCTCATCATTTACGTCTTTCACCATCTgtt                                                       <  1:3046186/44‑3 (MQ=21)
                               aTCAGCGCCAGTTGTTCATCATTAACGTCCTTCACCAGCTGCGCGTAGTCGTTGTCACTTTTTGCCGAc                             <  1:2362996/69‑1 (MQ=255)
                                tCAGCGCCAGTTGTTCATCATTAACGTCCTTCACCAGCTGCGCGTAGTCGTTGTCACTTTTTGCCGAc                             <  1:1168595/68‑1 (MQ=255)
                                 cAGCGCCAGTTGTTCATCATTAACGTCCTTCACCAGCTGCGCGTAGTCGTTGTCACTTTTTGCCGACCa                           >  1:416825/1‑69 (MQ=255)
                                 cAGCGCCAGTTGTTCATCATTAACGTCCTTCACCAGCTGCGCGTAGTCGTTGTCACTTTTTGCCGACCa                           >  1:3050827/1‑69 (MQ=255)
                                 cAGCGCCAGTTGTTCATCATTAACGTCCTTCACCAGCTGCGCGTAGTCGTTGTCACTTTTTGCCGACCa                           >  1:512433/1‑69 (MQ=255)
                                 cAGCGCCAGTTGTTCATCATTAACGTCCTTCACCAGCTGCGCGTAGTCGTTGTCACTTTTTGCCGACCa                           >  1:1488143/1‑69 (MQ=255)
                                 cAGCGCCAGTTGTTCATCATTAACGTCCTTCACCAGCTGCGCGTAGTCGTTGTCACTTTTTGCCGACCa                           >  1:2310686/1‑69 (MQ=255)
                                            gttCATCATTAACGTCCTTCACCAGCTGCGCGTAGTCGTTGTCACTTTTTGCCGACCAGGTACGggtca                >  1:1866249/1‑69 (MQ=255)
                                                     tAACGTCCTTCACCAGCTGCGCGTAGTCGTTGTCACTTTTTGCCGACCAGGTACGGGTCAGGTCAGCCg       <  1:3173568/69‑1 (MQ=255)
                                                     tAACGTCCTTCACCAGCTGCGCGTAGTCGTTGTCACTTTTTGCCGACCAGGTACGGGTCAGGTCAGCCg       <  1:2381558/69‑1 (MQ=255)
                                                      aaCGTCCTTCACCAGCTGCGCGTAGTCGTTGTCACTTTTTGCCGACCAGGTACGGGTCAGGTCAGCCGc      <  1:2290939/69‑1 (MQ=255)
                                                      aaCGTCCTTCACCAGCTGCGCGTAGTCGTTGTCACTTTTTGCCGACCAGGTACGGGTCAGGTCAGCCGc      <  1:1489203/69‑1 (MQ=255)
                                                      aaCGTCCTTCACCAGCTGCGCGTAGTCGTTGTCACTTTTTGCCGACCAGGTACGGGTCAGGTCAGCCGc      <  1:2908513/69‑1 (MQ=255)
                                                      aaCGTCCTTCACCAGCTGCGCGTAGTCGTTGTCACTTTTTGCCGACCAGGTACGGGTCAGGTCAGCCGc      <  1:779336/69‑1 (MQ=255)
                                                      aaCGTCCTTCACCAGCTGCGCGTAGTCGTTGTCACTTTTTGCCGACCAGGTACGGGTCAGGTCAGCCGc      <  1:1505545/69‑1 (MQ=255)
                                                      aaCGTCCTTCACCAGCTGCGCGTAGTCGTTGTCACTTTTTGCCGACCAGGTACGGGTCAGGTCAGCCGc      <  1:2575520/69‑1 (MQ=255)
                                                      aaCGTCCTTCACCAGCTGCGCGTAGTCGTTGTCACTTTTTGCCGACCAGGTACGGGTCAGGTCAGCCGc      <  1:203128/69‑1 (MQ=255)
                                                      aaCGTCCTTCACCAGCTGCGCGTAGTCGTTGTCACTTTTTGCCGACCAGGTACGGGTCAGGTCAGCCGc      <  1:596717/69‑1 (MQ=255)
                                                      aaCGTCCTTCACCAGCTGCGCGTAGTCGTTGTCACTTTTTGCCGACCAGGTACGGGTCAGGTCAGCCGc      <  1:2689964/69‑1 (MQ=255)
                                                      aaCGTCCTTCACCAGCTGCGCGTAGTCGTTGTCACTTTTTGCCGACCAGGTACGGGTCAGGTCAGCCGc      <  1:2786919/69‑1 (MQ=255)
                                                         gTCCTTCACCAGCTGCGCGTAGTCGTTGTCACTTTTTGCCGACCAGGTACGGGTCAGGTCAGCCGCATa   <  1:623417/69‑1 (MQ=255)
                                                         gTCCTTCACCAGCTGCGCGTAGTCGTTGTCACTTTTTGCCGACCAGGTACGGGTCAGGTCAGCCGCATa   <  1:379188/69‑1 (MQ=255)
                                                          tCCTTCACCAGCTGCGCGTAGTCGTTGTCACTTTTTGCCGACCAGGTACGGGTCAGGTCAGCCGCATa   >  1:2078860/1‑68 (MQ=255)
                                                          tCCTTCACCAGCTGCGCGTAGTCGTTGTCACTTTTTGCCGACCAGGTACGGGTCAGGTCAGCCGCATAg  >  1:863852/1‑69 (MQ=255)
                                                          tCCTTCACCAGCTGCGCGTAGTCGTTGTCACTTTTTGCCGACCAGGTACGGGTCAGGTCAGCCGCATAg  >  1:2415407/1‑69 (MQ=255)
                                                          tCCTTCACCAGCTGCGCGTAGTCGTTGTCACTTTTTGCCGACCAGGTACGGGTCAGGTCAGCCGCATAg  >  1:1428100/1‑69 (MQ=255)
                                                            |                                                                  
CACATAGCTGACGCCTGCTTTCATGGTGGCGATCAGCGCCAGTTGTTCATCATTAACGTCCTTCACCAGCTGCGCGTAGTCGTTGTCACTTTTTGCCGACCAGGTACGGGTCAGGTCAGCCGCATAG  >  minE/2366568‑2366694

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