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 2,366,613 T→C 51.5% E280E (GAA→GAG)  pepQ ← proline dipeptidase

Read alignment evidence...
  seq id position ref new freq score (cons/poly) reads annotation genes product
*minE2,366,6130TC51.5% 6.8 / 119.3 132E280E (GAA→GAG) pepQproline dipeptidase
Reads supporting (aligned to +/- strand):  ref base T (43/21);  new base C (36/32);  total (79/53)
Fisher's exact test for biased strand distribution p-value = 1.12e-01
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 8.98e-01

Only 100 of 133 total aligned reads displayed.

GGAACTGGATGTGGTAATCCACATAGCTGACGCCTGCTTTCATGGTGGCGATCAGCGCCAGTTGTTCATCATTAACGTCCTTCACCAGCTGCGCGTAGTCGTTGTCACTTTTTGCCGACCAGGTACGGGTCA  >  minE/2366549‑2366680
                                                                |                                                                   
ggAACTGGATGTGGTAATCCACATAGCTGACGCCTGCTTTCATGGTGGCGATCAGCGCCAGTTGTtcat                                                                 <  1:2934691/69‑1 (MQ=255)
ggAACTGGATGTGGTAATCCACATAGCTGACGCCTGCTTTCATGGTGGCGATCAGCGCCAGTTGTtcat                                                                 <  1:2521002/69‑1 (MQ=255)
ggAACTGGATGTGGTAATCCACATAGCTGACGCCTGCTTTCATGGTGGCGATCAGCGCCAGTTGTtcat                                                                 <  1:1020512/69‑1 (MQ=255)
ggAACTGGATGTGGTAATCCACATAGCTGACGCCTGCTTTCATGGTGGCGATCAGCGCCAGTTGTtcat                                                                 <  1:1197528/69‑1 (MQ=255)
ggAACTGGATGTGGTAATCCACATAGCTGACGCCTGCTTTCATGGTGGCGATCAGCGCCAGTTGTtcat                                                                 <  1:2656943/69‑1 (MQ=255)
ggAACTGGATGTGGTAATCCACATAGCTGACGCCTGCTTTCATGGTGGCGATCAGCGCCAGTTGTtcat                                                                 <  1:2201906/69‑1 (MQ=255)
ggAACTGGATGTGGTAATCCACATAGCTGACGCCTGCTTTCATGGTGGCGATCAGCGCCAGTTGTtcat                                                                 <  1:472662/69‑1 (MQ=255)
ggAACTGGATGTGGTAATCCACATAGCTGACGCCTGCTTTCATGGTGGCGATCAGCGCCAGTTGTtcat                                                                 <  1:1814532/69‑1 (MQ=255)
ggAACTGGATGTGGTAATCCACATAGCTGACGCCTGCTTTCATGGTGGCGATCAGCGCCAGTTGTtcat                                                                 <  1:2800374/69‑1 (MQ=255)
    cTGGATATGGTAATCCACATAGCTGACGCCTGCTTTCATGGTGGCGATCAGCGCCAGTTGCtcatc                                                                >  1:973582/1‑66 (MQ=255)
    cTGGATATGGTAATCCACATAGCTGACGCCTGCTTTCATGGTGGCGATCAGCGCCAGTTGCTCATCAtt                                                             >  1:3254581/1‑69 (MQ=255)
    cTGGATATGGTAATCCACATAGCTGACGCCTGCTTTCATGGTGGCGATCAGCGCCAGTTGCTCATCAtt                                                             >  1:3422302/1‑69 (MQ=255)
    cTGGATATGGTAATCCACATAGCTGACGCCTGCTTTCATGGTGGCGATCAGCGCCAGTTGCTCATCAtt                                                             >  1:1710154/1‑69 (MQ=255)
    cTGGATATGGTAATCCACATAGCTGACGCCTGCTTTCATGGTGGCGATCAGCGCCAGTTGCTCATCAtt                                                             >  1:631597/1‑69 (MQ=255)
    cTGGATATGGTAATCCACATAGCTGACGCCTGCTTTCATGGTGGCGATCAGCGCCAGTTGCTCATCAtt                                                             >  1:180502/1‑69 (MQ=255)
    cTGGATATGGTAATCCACATAGCTGACGCCTGCTTTCATGGTGGCGATCAGCGCCAGTTGCTCATCAtt                                                             >  1:1342663/1‑69 (MQ=255)
    cTGGATATGGTAATCCACATAGCTGACGCCTGCTTTCATGGTGGCGATCAGCGCCAGTTGCTCATCAtt                                                             >  1:2238833/1‑69 (MQ=255)
    cTGGATATGGTAATCCACATAGCTGACGCCTGCTTTCATGGTGGCGATCAGCGCCAGTTGCTCATCAtt                                                             >  1:2389800/1‑69 (MQ=255)
    cTGGATATGGTAATCCACATAGCTGACGCCTGCTTTCATGGTGGCGATCAGCGCCAGTTGCTCATCAtt                                                             >  1:119791/1‑69 (MQ=255)
    cTGGATATGGTAATCCACATAGCTGACGCCTGCTTTCATGGTGGCGATCAGCGCCAGTTGCTCATCAtt                                                             >  1:1085087/1‑69 (MQ=255)
    cTGGATATGGTAATCCACATAGCTGACGCCTGCTTTCATGATGGCGATCAGCGCCAGTTGCTCATCAtt                                                             >  1:1040041/1‑69 (MQ=255)
             gTAATCCACATAGCTGACGCCTGCTTTCATGGTGGCGATCAGCGCCAGTTGTTCATCATTAAc                                                          <  1:2031063/63‑1 (MQ=255)
             gTAATCCACATAGCTGACGCCTGCTTTCATGGTGGCGATCAGCGCCAGTTGTTCATCATTAAc                                                          <  1:2707982/63‑1 (MQ=255)
             gTAATCCACATAGCTGACGCCTGCTTTCATGGTGGCGATCAGCGCCAGTTGTTCATCATTAAc                                                          <  1:248507/63‑1 (MQ=255)
             gTAATCCACATAGCTGACGCCTGCTTTCATGGTGGCGATCAGCGCCAGTTGTTCATCATTAAc                                                          <  1:653015/63‑1 (MQ=255)
             gTAATCCACATAGCTGACGCCTGCTTTCATGGTGGCGATCAGCGCCAGTTGTTCATCATTAAc                                                          <  1:2166534/63‑1 (MQ=255)
                   cacaTAGCTGACGCCTGCTTTCATGGTGGCGATCAGCGCCAGTTGTTCATCATTAACGTCCTTCACCAg                                              >  1:1977393/1‑69 (MQ=255)
                   cacaTAGCTGACGCCTGCTTTCATGGTGGCGATCAGCGCCAGTTGTTCATCATTAACGTCCTTCACCAg                                              >  1:2760092/1‑69 (MQ=255)
                   cacaTAGCTGACGCCTGCTTTCATGGTGGCGATCAGCGCCAGTTGTTCATCATTAACGTCCTTCACCAg                                              >  1:2311924/1‑69 (MQ=255)
                   cacaTAGCTGACGCCTGCTTTCATGGTGGCGATCAGCGCCAGTTGTTCATCATTAACGTCCTTCACCAg                                              >  1:973310/1‑69 (MQ=255)
                         gCTGACGCCTGCTTTCATGGTGGCGATCAGCGCCAGTTGTTCATCATTAACGTCCTTCACCAGCTgcgc                                        >  1:1471043/1‑69 (MQ=255)
                              cGCCTGCTTTCATGGTGGCGATCAGCGCCAGTTGTTCATCATTAACGTCCTTCACCAGCTGCGCGTAGt                                   >  1:3289871/1‑69 (MQ=255)
                              cGCCTGCTTTCATGGTGGCGATCAGCGCCAGTTGTTCATCATTAACGTCCTTCACCAGCTGCGCGTAGt                                   >  1:408790/1‑69 (MQ=255)
                              cGCCTGCTTTCATGGTGGCGATCAGCGCCAGTTGTTCATCATTAACGTCCTTCACCAGCTGCGCGTAGt                                   >  1:738628/1‑69 (MQ=255)
                              cGCCTGCTTTCATGGTGGCGATCAGCGCCAGTTGTTCATCATTAACGTCCTTCACCAGCTGCGCGTAGt                                   >  1:2223819/1‑69 (MQ=255)
                                 cTGCTTTCATGGTGGCGATCAGCGCCAGTTGCTCATCATTTACGTCTTTCACCAGCTGTGCGTAGTCGt                                >  1:1781320/1‑69 (MQ=255)
                                 cTGCTTTCATGGTGGCGATCAGCGCCAGTTGCTCATCATTTACGTCTTTCACCAGCTGTGCGTAGTCGt                                >  1:1240817/1‑69 (MQ=255)
                                 cTGCTTTCATGGTGGCGATCAGCGCCAGTTGCTCATCATTTACGTCTTTCACCAGCTGTGCGTAGTCGt                                >  1:741394/1‑69 (MQ=255)
                                  tGCTTTCATGGTGGCGATCAGCGCCAGTTGTtcat                                                                 <  1:594612/35‑1 (MQ=255)
                                  tGCTTTCATGGTGGCGATCAGCGCCAGTTGTTCATCATTAACGTCCTTCACCAGCTGCGCGTAGTCGtt                               >  1:97441/1‑69 (MQ=255)
                                  tGCTTTCATGGTGGCGATCAGCGCCAGTTGTTCATCATTAACGTCCTTCACCAGCTGCGCGTAGTCGtt                               >  1:2867775/1‑69 (MQ=255)
                                  tGCTTTCATGGTGGCGATCAGCGCCAGTTGTTCATCATTAACGTCCTTCACCAGCTGCGCGTAGTCGtt                               >  1:2388451/1‑69 (MQ=255)
                                  tGCTTTCATGGTGGCGATCAGCGCCAGTTGTTCATCATTAACGTCCTTCACCAGCTGCGCGTAGTCGtt                               >  1:2486834/1‑69 (MQ=255)
                                  tGCTTTCATGGTGGCGATCAGCGCCAGTTGTTCATCATTAACGTCCTTCACCAGCTGCGCGTAGTCGtt                               >  1:3140172/1‑69 (MQ=255)
                                  tGCTTTCATGGTGGCGATCAGCGCCAGTTGTTCATCATTAACGTCCTTCACCAGCTGCGCGTAGTCGtt                               >  1:3033615/1‑69 (MQ=255)
                                  tGCTTTCATGGTGGCGATCAGCGCCAGTTGTTCATCATTAACGTCCTTCACCAGCTGCGCGTAGTCGtt                               >  1:2960638/1‑69 (MQ=255)
                                  tGCTTTCATGGTGGCGATCAGCGCCAGTTGTTCATCATTAACGTCCTTCACCAGCTGCGCGTAGTCGtt                               >  1:1829327/1‑69 (MQ=255)
                                  tGCTTTCATGGTGGCGATCAGCGCCAGTTGTTCATCATTAACGTCCTTCACCAGCTGCGCGTAGTCGtt                               >  1:1844028/1‑69 (MQ=255)
                                  tGCTTTCATGGTGGCGATCAGCGCCAGTTGTTCATCATTAACGTCCTTCACCAGCTGCGCGTAGTCGt                                >  1:341839/1‑68 (MQ=255)
                                  tGCTTTCATGGTGGCGATCAGAGCCAGTTGTTCATCATTAACg                                                         >  1:3428928/1‑43 (MQ=255)
                                       tCATGGTGGCGATCAGCGCCAGTTGCTCATCATTTACGTCTTTCACctgctgtg                                         <  1:2570419/54‑3 (MQ=37)
                                       tCATGGTGGCGATCAGCGCCAGTTGCTCATCATTTACGTCTTTCACCAGc                                             >  1:142243/1‑50 (MQ=38)
                                       tCATGGTGGCGATCAGCGCCAGTTGCTCATCATTTACGTCTTTCACCAGCTgtg                                         <  1:1100219/54‑3 (MQ=37)
                                       tCATGGTGGCGATCAGCGCCAGTTGCTCATCATTTACGTCTTTCACCAGCTgtg                                         <  1:130358/54‑3 (MQ=37)
                                       tCATGGTGGCGATCAGCGCCAGTTGCTCATCATTTACGTCTTTCACCAGCTgtg                                         <  1:726937/54‑3 (MQ=37)
                                       tCATGGTGGCGATCAGCGCCAGTTGCTCATCATTTACGTCTTTCACCAGCTgtg                                         <  1:688731/54‑3 (MQ=37)
                                       tCATGGTGGCGATCAGCGCCAGTTGCTCATCATTTACGTCTTTCACCAGCTgtg                                         <  1:515858/54‑3 (MQ=37)
                                       tCATGGTGGCGATCAGCGCCAGTTGCTCATCATTTACGTCTTTCACCAGCTgtg                                         <  1:1484030/54‑3 (MQ=37)
                                       tCATGGTGGCGATCAGCGCCAGTTGCTCATCATTTACGTCTTTCACCAGCTgtg                                         <  1:1656584/54‑3 (MQ=37)
                                       tCATGGTGGCGATCAGCGCCAGTTGCTCATCATTTACGTCTTTCACCAGCTgtg                                         <  1:1721484/54‑3 (MQ=37)
                                       tCATGGTGGCGATCAGCGCCAGTTGCTCATCATTTACGTCTTTCACCAGCTgtg                                         <  1:1730907/54‑3 (MQ=37)
                                       tCATGGTGGCGATCAGCGCCAGTTGCTCATCATTTACGTCTTTCACCAGCTgtg                                         <  1:2942502/54‑3 (MQ=37)
                                       tCATGGTGGCGATCAGCGCCAGTTGCTCATCATTTACGTCTTTCACCAGCTgtg                                         <  1:2092735/54‑3 (MQ=37)
                                       tCATGGTGGCGATCAGCGCCAGTTGCTCATCATTTACGTCTTTCACCAGCTgtg                                         <  1:2569689/54‑3 (MQ=37)
                                       tCATGGTGGCGATCAGCGCCAGTTGCTCATCATTTACGTCTTTCACCAGCTgtg                                         <  1:2598634/54‑3 (MQ=37)
                                       tCATGGTGGCGATCAGCGCCAGTTGCTCATCATTTACGTCTTTCACCAGCTgtg                                         <  1:1899891/54‑3 (MQ=37)
                                       tCATGGTGGCGATCAGCGCCAGTTGCTCATCATTTACGTCTTTCACCAGCTgtg                                         <  1:191512/54‑3 (MQ=37)
                                       tCATGGTGGCGATCAGCGCCAGTTGCTCATCATTTACGTCTTTCACCAGCTgtg                                         <  1:2674506/54‑3 (MQ=37)
                                       tCATGGTGGCGATCAGCGCCAGTTGCTCATCATTTACGTCTTTCACCAGCTgtg                                         <  1:2134321/54‑3 (MQ=37)
                                       tCATGGTGGCGATCAGCGCCAGTTGCTCATCATTTACGTCTTTCACCAGCTgtg                                         <  1:2294597/54‑3 (MQ=37)
                                       tCATGGTGGCGATCAGCGCCAGTTGCTCATCATTTACGTCTTTCACCAGCTgtg                                         <  1:1861165/54‑3 (MQ=37)
                                       tCATGGTGGCGATCAGCGCCAGTTGCTCATCATTTACGTCTTTCACCAGCTgtg                                         <  1:2885293/54‑3 (MQ=37)
                                       tCATGGTGGCGATCAGCGCCAGTTGCTCATCATTTACGTCTTTCACCAGCTGTGCGTAGTCGTTGTcgc                          >  1:1358553/1‑67 (MQ=255)
                                       tCATGGTGGCGATCAGCGCCAGTTGCTCATCATTTACGTCTTTCACCAGCTGTGCGTAGTCGTTGTcgc                          >  1:2885810/1‑67 (MQ=255)
                                       tCATGGTGGCGATCAGCGCCAGTTGCTCATCATTTACGTCTTTCACCAGCTGTGCGTAGTCGTTGTcgc                          >  1:711108/1‑67 (MQ=255)
                                       tCATGGTGGCGATCAGCGCCAGTTGCTCATCATTTACGTCTTTCACCAGCTGTGCGTAGTCGTTGTcgc                          >  1:574774/1‑67 (MQ=255)
                                       tCATGGTGGCGATCAGCGCCAGTTGCTCATCATTTACGTCTTTCACCAGCTGTGCGTAGTCGTTGTcgc                          >  1:517002/1‑67 (MQ=255)
                                       tCATGGTGGCGATCAGCGCCAGTTGCTCATCATTTACGTCTTTCACCAGCTGTGCGTAGTCGTTGTcgc                          >  1:885521/1‑67 (MQ=255)
                                       tCATGGTGGCGATCAGCGCCAGTTGCTCATCATTTACGTCTTTCACCAGCTGTGCGTAGTCGTTGTcgc                          >  1:1355122/1‑67 (MQ=255)
                                       tCATGGTGGCGATCAGCGCCAGTTGCTCATCATTTACGTCTTTCACCAGCTGTGCGTAGTCGTTGTcgc                          >  1:1474393/1‑67 (MQ=255)
                                       tCATGGTGGCGATCAGCGCCAGTTGCTCATCATTTACGTCTTTCACCAGCTGTGCGTAGTCGTTGTcgc                          >  1:3296809/1‑67 (MQ=255)
                                       tCATGGTGGCGATCAGCGCCAGTTGCTCATCATTTACGTCTTTCACCAGCTGTGCGTAGTCGTTGTcgc                          >  1:1567342/1‑67 (MQ=255)
                                       tCATGGTGGCGATCAGCGCCAGTTGCTCATCATTTACGTCTTTCACCAGCTGTGCGTAGTCGTTGTcgc                          >  1:3174928/1‑67 (MQ=255)
                                       tCATGGTGGCGATCAGCGCCAGTTGCTCATCATTTACGTCTTTCACCAGCTGTGCGTAGTCGTTGTcgc                          >  1:3094585/1‑67 (MQ=255)
                                            gtggCGATCAGCGCCAGTTGTTCATCATTAACGTCCTTCACCAGCTGCGCGTAGTCGTTGTCACttttt                     >  1:1437707/1‑69 (MQ=255)
                                            gtggCGATCAGCGCCAGTTGTTCATCATTAACGTCCTTCACCAGCTGCGCGTAGTCGTTGTCACttttt                     >  1:91588/1‑69 (MQ=255)
                                            gtggCGATCAGCGCCAGTTGTTCATCATTAACGTCCTTCACCAGCTGCGCGTAGTCGTTGTCACttttt                     >  1:1393182/1‑69 (MQ=255)
                                            gtggCGATCAGCGCCAGTTGTTCATCATTAACGTCCTTCACCAGCTGCGCGTAGTCGTTGTCACttttt                     >  1:1246940/1‑69 (MQ=255)
                                            gtggCGATCAGCGCCAGTTGTTCATCATTAACGTCCTTCACCAGCTGCGCGTAGTCGTTGTCACttttt                     >  1:1889379/1‑69 (MQ=255)
                                            gtggCGATCAGCGCCAGTTGTTCATCATTAACGTCCTTCACCAGCTGCGCGTAGTCGTTGTCACttttt                     >  1:1173093/1‑69 (MQ=255)
                                            gtggCGATCAGCGCCAGTTGTTCATCATTAACGTCCTTCACCAGCTGCGCGTAGTCGTTGTCACttttt                     >  1:2771701/1‑69 (MQ=255)
                                               gCGATCAGCGCCAGTTGTTCATCATTAACGTCCTTCACCAGCTGCGCGTAGTCGTTGTCACTTTTTGcc                  >  1:792303/1‑69 (MQ=255)
                                                 gATCAGCGCCAGTTGCTCATCATTTACGTCTTTCACCATCTgtt                                         <  1:3046186/44‑3 (MQ=21)
                                                  aTCAGCGCCAGTTGTTCATCATTAACGTCCTTCACCAGCTGCGCGTAGTCGTTGTCACTTTTTGCCGAc               <  1:1607323/69‑1 (MQ=255)
                                                  aTCAGCGCCAGTTGTTCATCATTAACGTCCTTCACCAGCTGCGCGTAGTCGTTGTCACTTTTTGCCGAc               <  1:2362996/69‑1 (MQ=255)
                                                    cAGCGCCAGTTGTTCATCATTAACGTCCTTCACCAGCTGCGCGTAGTCGTTGTCACTTTTTGCCGACCa             >  1:512433/1‑69 (MQ=255)
                                                    cAGCGCCAGTTGTTCATCATTAACGTCCTTCACCAGCTGCGCGTAGTCGTTGTCACTTTTTGCCGACCa             >  1:416825/1‑69 (MQ=255)
                                                    cAGCGCCAGTTGTTCATCATTAACGTCCTTCACCAGCTGCGCGTAGTCGTTGTCACTTTTTGCCGACCa             >  1:3050827/1‑69 (MQ=255)
                                                    cAGCGCCAGTTGTTCATCATTAACGTCCTTCACCAGCTGCGCGTAGTCGTTGTCACTTTTTGCCGACCa             >  1:2310686/1‑69 (MQ=255)
                                                               gttCATCATTAACGTCCTTCACCAGCTGCGCGTAGTCGTTGTCACTTTTTGCCGACCAGGTACGggtca  >  1:1866249/1‑69 (MQ=255)
                                                                |                                                                   
GGAACTGGATGTGGTAATCCACATAGCTGACGCCTGCTTTCATGGTGGCGATCAGCGCCAGTTGTTCATCATTAACGTCCTTCACCAGCTGCGCGTAGTCGTTGTCACTTTTTGCCGACCAGGTACGGGTCA  >  minE/2366549‑2366680

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