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 2,366,622 A→T 47.6% V277V (GTT→GTA)  pepQ ← proline dipeptidase

Read alignment evidence...
  seq id position ref new freq score (cons/poly) reads annotation genes product
*minE2,366,6220AT47.6% 12.5 / 126.8 107V277V (GTT→GTA) pepQproline dipeptidase
Reads supporting (aligned to +/- strand):  ref base A (44/12);  new base T (19/32);  total (63/44)
Fisher's exact test for biased strand distribution p-value = 1.57e-05
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 9.83e-01

Only 100 of 118 total aligned reads displayed.

GTAATCCACATAGCTGACGCCTGCTTTCATGGTGGCGATCAGCGCCAGTTGTTCATCATTAACGTCCTTCACCAGCTGCGCGTAGTCGTTGTCACTTTTTGCCGACCAGGTACGGGTCAGGTCAGCCGC  >  minE/2366562‑2366690
                                                            |                                                                    
gTAATCCACATAGCTGACGCCTGCTTTCATGGTGGCGATCAGCGCCAGTTGTTCATCATTAAc                                                                    <  1:248507/63‑1 (MQ=255)
gTAATCCACATAGCTGACGCCTGCTTTCATGGTGGCGATCAGCGCCAGTTGTTCATCATTAAc                                                                    <  1:2031063/63‑1 (MQ=255)
gTAATCCACATAGCTGACGCCTGCTTTCATGGTGGCGATCAGCGCCAGTTGTTCATCATTAAc                                                                    <  1:2166534/63‑1 (MQ=255)
gTAATCCACATAGCTGACGCCTGCTTTCATGGTGGCGATCAGCGCCAGTTGTTCATCATTAAc                                                                    <  1:2185313/63‑1 (MQ=255)
gTAATCCACATAGCTGACGCCTGCTTTCATGGTGGCGATCAGCGCCAGTTGTTCATCATTAAc                                                                    <  1:653015/63‑1 (MQ=255)
      cacaTAGCTGACGCCTGCTTTCATGGTGGCGATCAGCGCCAGTTGTTCATCATTAACGTCCTTCACCAg                                                        >  1:750618/1‑69 (MQ=255)
      cacaTAGCTGACGCCTGCTTTCATGGTGGCGATCAGCGCCAGTTGTTCATCATTAACGTCCTTCACCAg                                                        >  1:2918564/1‑69 (MQ=255)
      cacaTAGCTGACGCCTGCTTTCATGGTGGCGATCAGCGCCAGTTGTTCATCATTAACGTCCTTCACCAg                                                        >  1:1977393/1‑69 (MQ=255)
      cacaTAGCTGACGCCTGCTTTCATGGTGGCGATCAGCGCCAGTTGTTCATCATTAACGTCCTTCACCAg                                                        >  1:2311924/1‑69 (MQ=255)
      cacaTAGCTGACGCCTGCTTTCATGGTGGCGATCAGCGCCAGTTGTTCATCATTAACGTCCTTCACCAg                                                        >  1:2289113/1‑69 (MQ=255)
      cacaTAGCTGACGCCTGCTTTCATGGTGGCGATCAGCGCCAGTTGTTCATCATTAACGTCCTTCACCAg                                                        >  1:2760092/1‑69 (MQ=255)
      cacaTAGCTGACGCCTGCTTTCATGGTGGCGATCAGCGCCAGTTGTTCATCATTAACGTCCTTCACCAg                                                        >  1:973310/1‑69 (MQ=255)
      cacaTAGCTGACGCCTGCTTTCATGGTGGCGATCAGCGCCAGTTGTTCATCATTAACGTCCTTCACCAg                                                        >  1:1236692/1‑69 (MQ=255)
            gCTGACGCCTGCTTTCATGGTGGCGATCAGCGCCAGTTGTTCATCATTAACGTCCTTCACCAGCTgcgc                                                  >  1:1471043/1‑69 (MQ=255)
                 cGCCTGCTTTCATGGTGGCGATCAGCGCCAGTTGTTCATCATTAACGTCCTTCACCAGCTGCGCGTAGt                                             >  1:1914606/1‑69 (MQ=255)
                 cGCCTGCTTTCATGGTGGCGATCAGCGCCAGTTGTTCATCATTAACGTCCTTCACCAGCTGCGCGTAGt                                             >  1:3289871/1‑69 (MQ=255)
                 cGCCTGCTTTCATGGTGGCGATCAGCGCCAGTTGTTCATCATTAACGTCCTTCACCAGCTGCGCGTAGt                                             >  1:408790/1‑69 (MQ=255)
                 cGCCTGCTTTCATGGTGGCGATCAGCGCCAGTTGTTCATCATTAACGTCCTTCACCAGCTGCGCGTAGt                                             >  1:2223819/1‑69 (MQ=255)
                 cGCCTGCTTTCATGGTGGCGATCAGCGCCAGTTGTTCATCATTAACGTCCTTCACCAGCTGCGCGTAGt                                             >  1:738628/1‑69 (MQ=255)
                    cTGCTTTCATGGTGGCGATCAGCGCCAGTTGCTCATCATTTACGTCTTTCACCAGCTGTGCGTAGTCGt                                          >  1:1240817/1‑69 (MQ=255)
                    cTGCTTTCATGGTGGCGATCAGCGCCAGTTGCTCATCATTTACGTCTTTCACCAGCTGTGCGTAGTCGt                                          >  1:1781320/1‑69 (MQ=255)
                    cTGCTTTCATGGTGGCGATCAGCGCCAGTTGCTCATCATTTACGTCTTTCACCAGCTGTGCGTAGTCGt                                          >  1:741394/1‑69 (MQ=255)
                     tGCTTTCATGGTGGCGATCAGCGCCAGTTGTTCATCATTAACGTCCTTCACCAGCTGCGCGTAGTCGtt                                         >  1:2867775/1‑69 (MQ=255)
                     tGCTTTCATGGTGGCGATCAGCGCCAGTTGTTCATCATTAACGTCCTTCACCAGCTGCGCGTAGTCGtt                                         >  1:2388451/1‑69 (MQ=255)
                     tGCTTTCATGGTGGCGATCAGCGCCAGTTGTTCATCATTAACGTCCTTCACCAGCTGCGCGTAGTCGtt                                         >  1:2088719/1‑69 (MQ=255)
                     tGCTTTCATGGTGGCGATCAGCGCCAGTTGTTCATCATTAACGTCCTTCACCAGCTGCGCGTAGTCGtt                                         >  1:1844028/1‑69 (MQ=255)
                     tGCTTTCATGGTGGCGATCAGCGCCAGTTGTTCATCATTAACGTCCTTCACCAGCTGCGCGTAGTCGtt                                         >  1:2440508/1‑69 (MQ=255)
                     tGCTTTCATGGTGGCGATCAGCGCCAGTTGTTCATCATTAACGTCCTTCACCAGCTGCGCGTAGTCGtt                                         >  1:97441/1‑69 (MQ=255)
                     tGCTTTCATGGTGGCGATCAGCGCCAGTTGTTCATCATTAACGTCCTTCACCAGCTGCGCGTAGTCGtt                                         >  1:1829327/1‑69 (MQ=255)
                     tGCTTTCATGGTGGCGATCAGCGCCAGTTGTTCATCATTAACGTCCTTCACCAGCTGCGCGTAGTCGtt                                         >  1:3140172/1‑69 (MQ=255)
                     tGCTTTCATGGTGGCGATCAGCGCCAGTTGTTCATCATTAACGTCCTTCACCAGCTGCGCGTAGTCGtt                                         >  1:2960638/1‑69 (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                                                   <  1:515858/54‑3 (MQ=37)
                          tCATGGTGGCGATCAGCGCCAGTTGCTCATCATTTACGTCTTTCACCAGCTgtg                                                   <  1:941553/54‑3 (MQ=37)
                          tCATGGTGGCGATCAGCGCCAGTTGCTCATCATTTACGTCTTTCACCAGCTgtg                                                   <  1:726937/54‑3 (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                                                   <  1:688731/54‑3 (MQ=37)
                          tCATGGTGGCGATCAGCGCCAGTTGCTCATCATTTACGTCTTTCACCAGCTgtg                                                   <  1:634262/54‑3 (MQ=37)
                          tCATGGTGGCGATCAGCGCCAGTTGCTCATCATTTACGTCTTTCACCAGCTgtg                                                   <  1:3413863/54‑3 (MQ=37)
                          tCATGGTGGCGATCAGCGCCAGTTGCTCATCATTTACGTCTTTCACCAGCTgtg                                                   <  1:3057358/54‑3 (MQ=37)
                          tCATGGTGGCGATCAGCGCCAGTTGCTCATCATTTACGTCTTTCACCAGCTgtg                                                   <  1:2885293/54‑3 (MQ=37)
                          tCATGGTGGCGATCAGCGCCAGTTGCTCATCATTTACGTCTTTCACCAGCTgtg                                                   <  1:2569689/54‑3 (MQ=37)
                          tCATGGTGGCGATCAGCGCCAGTTGCTCATCATTTACGTCTTTCACCAGCTgtg                                                   <  1:2962286/54‑3 (MQ=37)
                          tCATGGTGGCGATCAGCGCCAGTTGCTCATCATTTACGTCTTTCACCAGCTgtg                                                   <  1:2942502/54‑3 (MQ=37)
                          tCATGGTGGCGATCAGCGCCAGTTGCTCATCATTTACGTCTTTCACCAGCTgtg                                                   <  1:1721484/54‑3 (MQ=37)
                          tCATGGTGGCGATCAGCGCCAGTTGCTCATCATTTACGTCTTTCACCAGCTgtg                                                   <  1:1730907/54‑3 (MQ=37)
                          tCATGGTGGCGATCAGCGCCAGTTGCTCATCATTTACGTCTTTCACCAGCTgtg                                                   <  1:2294597/54‑3 (MQ=37)
                          tCATGGTGGCGATCAGCGCCAGTTGCTCATCATTTACGTCTTTCACCAGCTgtg                                                   <  1:1697251/54‑3 (MQ=37)
                          tCATGGTGGCGATCAGCGCCAGTTGCTCATCATTTACGTCTTTCACCAGCTgtg                                                   <  1:2134321/54‑3 (MQ=37)
                          tCATGGTGGCGATCAGCGCCAGTTGCTCATCATTTACGTCTTTCACCAGCTgtg                                                   <  1:1484030/54‑3 (MQ=37)
                          tCATGGTGGCGATCAGCGCCAGTTGCTCATCATTTACGTCTTTCACCAGCTgtg                                                   <  1:1861165/54‑3 (MQ=37)
                          tCATGGTGGCGATCAGCGCCAGTTGCTCATCATTTACGTCTTTCACCAGCTgtg                                                   <  1:2092735/54‑3 (MQ=37)
                          tCATGGTGGCGATCAGCGCCAGTTGCTCATCATTTACGTCTTTCACCAGCTgtg                                                   <  1:1361122/54‑3 (MQ=37)
                          tCATGGTGGCGATCAGCGCCAGTTGCTCATCATTTACGTCTTTCACCAGCTgtg                                                   <  1:1656584/54‑3 (MQ=37)
                          tCATGGTGGCGATCAGCGCCAGTTGCTCATCATTTACGTCTTTCACCAGCTgtg                                                   <  1:191512/54‑3 (MQ=37)
                          tCATGGTGGCGATCAGCGCCAGTTGCTCATCATTTACGTCTTTCACCAGCTgtg                                                   <  1:1899891/54‑3 (MQ=37)
                          tCATGGTGGCGATCAGCGCCAGTTGCTCATCATTTACGTCTTTCACCAGCTGTGCGTAGTCGTTGTcgc                                    >  1:1474393/1‑67 (MQ=255)
                          tCATGGTGGCGATCAGCGCCAGTTGCTCATCATTTACGTCTTTCACCAGCTGTGCGTAGTCGTTGTcgc                                    >  1:3094585/1‑67 (MQ=255)
                          tCATGGTGGCGATCAGCGCCAGTTGCTCATCATTTACGTCTTTCACCAGCTGTGCGTAGTCGTTGTcgc                                    >  1:3296809/1‑67 (MQ=255)
                          tCATGGTGGCGATCAGCGCCAGTTGCTCATCATTTACGTCTTTCACCAGCTGTGCGTAGTCGTTGTcgc                                    >  1:72151/1‑67 (MQ=255)
                          tCATGGTGGCGATCAGCGCCAGTTGCTCATCATTTACGTCTTTCACCAGCTGTGCGTAGTCGTTGTcgc                                    >  1:1358553/1‑67 (MQ=255)
                          tCATGGTGGCGATCAGCGCCAGTTGCTCATCATTTACGTCTTTCACCAGCTGTGCGTAGTCGTTGTcgc                                    >  1:1355122/1‑67 (MQ=255)
                          tCATGGTGGCGATCAGCGCCAGTTGCTCATCATTTACGTCTTTCACCAGCTGTGCGTAGTCGTTGTcgc                                    >  1:885521/1‑67 (MQ=255)
                          tCATGGTGGCGATCAGCGCCAGTTGCTCATCATTTACGTCTTTCACCAGCTGTGCGTAGTCGTTGTcgc                                    >  1:1567342/1‑67 (MQ=255)
                          tCATGGTGGCGATCAGCGCCAGTTGCTCATCATTTACGTCTTTCACCAGCTGTGCGTAGTCGTTGTcgc                                    >  1:574774/1‑67 (MQ=255)
                          tCATGGTGGCGATCAGCGCCAGTTGCTCATCATTTACGTCTTTCACCAGCTGTGCGTAGTCGTTGTcgc                                    >  1:517002/1‑67 (MQ=255)
                               gtggCGATCAGCGCCAGTTGTTCATCATTAACGTCCTTCACCAGCTGCGCGTAGTCGTTGTCACttttt                               >  1:1173093/1‑69 (MQ=255)
                               gtggCGATCAGCGCCAGTTGTTCATCATTAACGTCCTTCACCAGCTGCGCGTAGTCGTTGTCACttttt                               >  1:1437707/1‑69 (MQ=255)
                               gtggCGATCAGCGCCAGTTGTTCATCATTAACGTCCTTCACCAGCTGCGCGTAGTCGTTGTCACttttt                               >  1:1393182/1‑69 (MQ=255)
                               gtggCGATCAGCGCCAGTTGTTCATCATTAACGTCCTTCACCAGCTGCGCGTAGTCGTTGTCACttttt                               >  1:2771701/1‑69 (MQ=255)
                               gtggCGATCAGCGCCAGTTGTTCATCATTAACGTCCTTCACCAGCTGCGCGTAGTCGTTGTCACttttt                               >  1:91588/1‑69 (MQ=255)
                               gtggCGATCAGCGCCAGTTGTTCATCATTAACGTCCTTCACCAGCTGCGCGTAGTCGTTGTCACttttt                               >  1:1246940/1‑69 (MQ=255)
                                  gCGATCAGCGCCAGTTGCTCATCATTTACGTCTTTCACCAGCTgtg                                                   <  1:502471/46‑3 (MQ=25)
                                    gATCAGCGCCAGTTGCTCATCATTTACGTCTTTCACCATCTgtt                                                   <  1:3046186/44‑3 (MQ=21)
                                     aTCAGCGCCAGTTGTTCATCATTAACGTCCTTCACCAGCTGCGCGTAGTCGTTGTCACTTTTTGCCGAc                         <  1:2362996/69‑1 (MQ=255)
                                     aTCAGCGCCAGTTGTTCATCATTAACGTCCTTCACCAGCTGCGCGTAGTCGTTGTCACTTTTTGCCGAc                         <  1:1607323/69‑1 (MQ=255)
                                      tCAGCGCCAGTTGTTCATCATTAACGTCCTTCACCAGCTGCGCGTAGTCGTTGTCACTTTTTGCCGAc                         <  1:1168595/68‑1 (MQ=255)
                                       cAGCGCCAGTTGTTCATCATTAACGTCCTTCACCAGCTGCGCGTAGTCGTTGTCACTTTTTGCCGACCa                       >  1:1488143/1‑69 (MQ=255)
                                       cAGCGCCAGTTGTTCATCATTAACGTCCTTCACCAGCTGCGCGTAGTCGTTGTCACTTTTTGCCGACCa                       >  1:2310686/1‑69 (MQ=255)
                                       cAGCGCCAGTTGTTCATCATTAACGTCCTTCACCAGCTGCGCGTAGTCGTTGTCACTTTTTGCCGACCa                       >  1:3050827/1‑69 (MQ=255)
                                       cAGCGCCAGTTGTTCATCATTAACGTCCTTCACCAGCTGCGCGTAGTCGTTGTCACTTTTTGCCGACCa                       >  1:416825/1‑69 (MQ=255)
                                       cAGCGCCAGTTGTTCATCATTAACGTCCTTCACCAGCTGCGCGTAGTCGTTGTCACTTTTTGCCGACCa                       >  1:512433/1‑69 (MQ=255)
                                                  gttCATCATTAACGTCCTTCACCAGCTGCGCGTAGTCGTTGTCACTTTTTGCCGACCAGGTACGggtca            >  1:1866249/1‑69 (MQ=255)
                                                           tAACGTCCTTCACCAGCTGCGCGTAGTCGTTGTCACTTTTTGCCGACCAGGTACGGGTCAGGTCAGCCg   <  1:3173568/69‑1 (MQ=255)
                                                           tAACGTCCTTCACCAGCTGCGCGTAGTCGTTGTCACTTTTTGCCGACCAGGTACGGGTCAGGTCAGCCg   <  1:2381558/69‑1 (MQ=255)
                                                            aaCGTCCTTCACCAGCTGCGCGTAGTCGTTGTCACTTTTTGCCGACCAGGTACGGGTCAGGTCAGCCGc  <  1:596717/69‑1 (MQ=255)
                                                            aaCGTCCTTCACCAGCTGCGCGTAGTCGTTGTCACTTTTTGCCGACCAGGTACGGGTCAGGTCAGCCGc  <  1:1489203/69‑1 (MQ=255)
                                                            aaCGTCCTTCACCAGCTGCGCGTAGTCGTTGTCACTTTTTGCCGACCAGGTACGGGTCAGGTCAGCCGc  <  1:2908513/69‑1 (MQ=255)
                                                            aaCGTCCTTCACCAGCTGCGCGTAGTCGTTGTCACTTTTTGCCGACCAGGTACGGGTCAGGTCAGCCGc  <  1:1942566/69‑1 (MQ=255)
                                                            aaCGTCCTTCACCAGCTGCGCGTAGTCGTTGTCACTTTTTGCCGACCAGGTACGGGTCAGGTCAGCCGc  <  1:2786919/69‑1 (MQ=255)
                                                            aaCGTCCTTCACCAGCTGCGCGTAGTCGTTGTCACTTTTTGCCGACCAGGTACGGGTCAGGTCAGCCGc  <  1:2290939/69‑1 (MQ=255)
                                                            aaCGTCCTTCACCAGCTGCGCGTAGTCGTTGTCACTTTTTGCCGACCAGGTACGGGTCAGGTCAGCCGc  <  1:779336/69‑1 (MQ=255)
                                                            aaCGTCCTTCACCAGCTGCGCGTAGTCGTTGTCACTTTTTGCCGACCAGGTACGGGTCAGGTCAGCCGc  <  1:2689964/69‑1 (MQ=255)
                                                            aaCGTCCTTCACCAGCTGCGCGTAGTCGTTGTCACTTTTTGCCGACCAGGTACGGGTCAGGTCAGCCGc  <  1:2575520/69‑1 (MQ=255)
                                                            |                                                                    
GTAATCCACATAGCTGACGCCTGCTTTCATGGTGGCGATCAGCGCCAGTTGTTCATCATTAACGTCCTTCACCAGCTGCGCGTAGTCGTTGTCACTTTTTGCCGACCAGGTACGGGTCAGGTCAGCCGC  >  minE/2366562‑2366690

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