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 1,971,130 G→A 42.8% D592D (GAC→GAT)  speA ← biosynthetic arginine decarboxylase, PLP‑binding

Read alignment evidence...
  seq id position ref new freq score (cons/poly) reads annotation genes product
*minE1,971,1300GA42.8% 57.9 / 123.9 161D592D (GAC→GAT) speAbiosynthetic arginine decarboxylase, PLP‑binding
Reads supporting (aligned to +/- strand):  ref base G (45/47);  new base A (43/26);  total (88/73)
Fisher's exact test for biased strand distribution p-value = 1.10e-01
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 9.51e-01

Only 100 of 166 total aligned reads displayed.

CATATTGCAGCATGTCCGCCACGGTATCGCCTTCGTCAGACAGTTCTACTTCTACGCTACCGTCAGGGAAGACGAACACGTCAACCGCTTCGGTATCACCGAACAGGTTGTGCATGTTGCCGAGGATC  >  minE/1971069‑1971196
                                                             |                                                                  
cATATTGCAGCATGTCCGCCACGGTATCGCCTTCGTCAGACAGTTCTACTTCTACGCTACCGTCAg                                                                >  1:2305905/1‑66 (MQ=255)
cATATTGCAGCATGTCCGCCACGGTATCGCCTTCGTCAGACAGTTCTACTTCTACGCTACCGTCAg                                                                >  1:1723282/1‑66 (MQ=255)
cATATTGCAGCATGTCCGCCACGGTATCGCCTTCGTCAGACAGTTCTACTTCTACGCTACCGTCAg                                                                >  1:1858434/1‑66 (MQ=255)
cATATTGCAGCATGTCCGCCACGGTATCGCCTTCGTCAGACAGTTCTACTTCTACGCTACAGTCa                                                                 >  1:1620254/1‑65 (MQ=255)
            tGTCCGCCACGGTATCGCCTTCGTCAGACAGTTCTACTTCTACGCTACCGTCAGGGAAGACGAACACg                                                  >  1:678049/1‑68 (MQ=255)
            tGTCCGCCACGGTATCGCCTTCGTCAGACAGTTCTACTTCTACGCTACCGTCAGGGAAGACGAACACg                                                  >  1:1005000/1‑68 (MQ=255)
            tGTCCGCCACGGTATCGCCTTCGTCAGACAGTTCTACTTCTACGCTACCGTCAGGGAAGACGAACACg                                                  >  1:2594706/1‑68 (MQ=255)
            tGTCCGCCACGGTATCGCCTTCGTCAGACAGTTCTACTTCTACGCTACCGTCAGGGAAGACGAACACg                                                  >  1:1192137/1‑68 (MQ=255)
            tGTCCGCCACGGTATCCCCTTCGTCAGACAGTTCTACTTCTACGCTACCGTCAGGGAAGACGAACACg                                                  >  1:288944/1‑68 (MQ=255)
              tCCGCCACGGTATCGCCTTCGTCAGACAGTTCTACTTCTACGCTACCGTCAGGGAAGACg                                                        >  1:1834495/1‑60 (MQ=255)
                cGCCACGGTATCGCCTTTGTCAGACAGTTCTACTTCTACGCTACCGTCAGGGAAGACGAACACGTCAAc                                             <  1:2806043/69‑1 (MQ=255)
                cGCCACGGTATCGCCTTCGTCAGACAGTTCTACTTCTACGCTACCGTCAGGGAAGAGGAACACGTCAAc                                             <  1:1587380/69‑1 (MQ=255)
                cGCCACGGTATCGCCTTCGTCAGACAGTTCTACTTCTACGCTACCGTCAGGGAAGACGAACACGTCAAc                                             <  1:1976576/69‑1 (MQ=255)
                cGCCACGGTATCGCCTTCGTCAGACAGTTCTACTTCTACGCTACCGTCAGGGAAGACGAACACGTCAAc                                             <  1:2755681/69‑1 (MQ=255)
                cGCCACGGTATCGCCTTCGTCAGACAGTTCTACTTCTACGCTACCGTCAGGGAAGACGAACACGTCAAc                                             <  1:2817173/69‑1 (MQ=255)
                cGCCACGGTATCGCCTTCGTCAGACAGTTCTACTTCTACGCTACCGTCAGGGAAGACGAACACGTCAAc                                             <  1:2172516/69‑1 (MQ=255)
                cGCCACGGTATCGCCTTCGTCAGACAGTTCTACTTCTACGCTACCGTCAGGGAAGACGAACACGTCAAc                                             <  1:391856/69‑1 (MQ=255)
                cGCCACGGTATCGCCTTCGTCAGACAGTTCTACTTCTACGCTACCGTCAGGGAAGACGAACACGTCAAc                                             <  1:2822020/69‑1 (MQ=255)
                cGCCACGGTATCGCCTTCGTCAGACAGTTCTACTTCTACGCTACCGTCAGGGAAGACGAACACGTCAAc                                             <  1:256885/69‑1 (MQ=255)
                cGCCACGGTATCGCCTTCGTCAGACAGTTCTACTTCTACGCTACCGTCAGGGAAGACGAACACGTCAAc                                             <  1:507615/69‑1 (MQ=255)
                cGCCACGGTATCGCCTTCGTCAGACAGTTCTACTTCTACGCTACCGTCAGGGAAGACGAACACGTCAAc                                             <  1:1405867/69‑1 (MQ=255)
                cGCCACGGTATCGCCTTCGTCAGACAGTTCTACTTCTACGCTACCGTCAGGGAAGACGAACACGTCAAc                                             <  1:522537/69‑1 (MQ=255)
                      ggTATCGCCTTCGTCAGACAGTTCTACTTCTACGCTACCGTCAGGGAAGACGAACACGTCAAc                                             <  1:1565954/63‑1 (MQ=255)
                      ggTATCGCCTTCGTCAGACAGTTCTACCTCTATGCTACCATCAGGGAAGACGAACACGTCAACCGCTTc                                       >  1:2586320/1‑69 (MQ=255)
                      ggTATCGCCTTCGTCAGACAGTTCTACCTCTACGCTACCATCAGGGAAGACGAACACGTCAACCGCTTc                                       >  1:527966/1‑69 (MQ=255)
                      ggTATCGCCTTCGTCAGACAGTTCTACCTCTACGCTACCATCAGGGAAGACGAACACGTCAACCGCTTc                                       >  1:2297596/1‑69 (MQ=255)
                      ggTATCGCCTTCGTCAGACAGTTCTACCTCTACGCTACCATCAGGGAAGACGAACACGTCAACCGCTTc                                       >  1:2258864/1‑69 (MQ=255)
                      ggTATCGCCTTCGTCAGACAGTTCTACCTCTACGCTACCATCAGGGAAGACGAACACGTCAACCGCTTc                                       >  1:2850760/1‑69 (MQ=255)
                      ggTATCGCCTTCGTCAGACAGTTCTACCTCTACGCTACCATCAGGGAAGACGAACACGTCAACCGCTTc                                       >  1:1140530/1‑69 (MQ=255)
                      ggTATCGCCTTCGTCAGACAGTTCTACCTCTACGCTACCATCAGGGAAGACGAACACGTCAACCGCTTc                                       >  1:1204680/1‑69 (MQ=255)
                      ggTATCGCCTTCGTCAGACAGTTCTACCTCTACGCTACCATCAGGGAAGACGAACACGTCAACCGCTTc                                       >  1:2041557/1‑69 (MQ=255)
                      ggTATCGCCTTCGTCAGACAGTTCTACCTCTACGCTACCATCAGGGAAGACGAACACGTCAACCGCTTc                                       >  1:884118/1‑69 (MQ=255)
                      ggTATCGCCTTCGTCAGACAGTTCTACCTCTACGCTACCATCAGGGAAGACGAACACGTCAACCGCTTc                                       >  1:2929613/1‑69 (MQ=255)
                      ggTATCGCCTTCGTCAGACAGTTCTACCTCTACGCTACCATCAGGGAAGACGAACACGTCAACCGCTTc                                       >  1:3088800/1‑69 (MQ=255)
                      ggTATCGCCTTCGTCAGACAGTTCTACCTCTACGCTACCATCAGGGAAGACGAACACGTCAACCGCTTc                                       >  1:3155877/1‑69 (MQ=255)
                      ggTATCGCCTTCGTCAGACAGTTCTACCTCTACGCTACCATCAGGGAAGACGAACACGTCAACCGCTTc                                       >  1:3173621/1‑69 (MQ=255)
                      ggTATCGCCTTCGTCAGACAGTTCTACCTCTACGCTACCATCAGGGAAGACGAACACGTCAACCGCTTc                                       >  1:240658/1‑69 (MQ=255)
                      ggTATCGCCTTCGTCAGACAGTTCTACCTCTACGCTACCATCAGGGAAGACGAACACGTCAACCGCTTc                                       >  1:3399746/1‑69 (MQ=255)
                      ggTATCGCCTTCGTCAGACAGTTCTACCTCTACGCTACCATCAGGGAAGACGAACACGTCAACCGCTTc                                       >  1:1693408/1‑69 (MQ=255)
                      ggTATCGCCTTCGTCAGACAGTTCTACCTCTACGCTACCATCAGGGAAGACGAACACGTCAACCGCTTc                                       >  1:477470/1‑69 (MQ=255)
                      ggTATCGCCTTCGTCAGACAGTTCTACCTCTACGCTACCATCAGGGAAGACGAACACGTCAACCGCTTc                                       >  1:445546/1‑69 (MQ=255)
                      ggTATCGCCTTCCTCAGACAGATCTACCTCTACGCTACCATCAGGGAAGACGAACACGTCAACCGCTTc                                       >  1:1154943/1‑69 (MQ=255)
                          tCGCCTTCGTCAGACAGTTCTACTTCTACGCTACCGTCAGGGAAGACGAAGACGTCAACCGCTTCGGTa                                   <  1:3158955/69‑1 (MQ=255)
                          tCGCCTTCGTCAGACAGTTCTACTTCTACGCTACCGTCAGGGAAGACGAACACGTCAACCGCTTCGGTa                                   <  1:3040574/69‑1 (MQ=255)
                          tCGCCTTCGTCAGACAGTTCTACTTCTACGCTACCGTCAGGGAAGACGAACACGTCAACCGCTTCGGTa                                   <  1:2248933/69‑1 (MQ=255)
                            gCCTTCGTCAGACAGTTCTACTTCTACGCTACCGTCAGGGAAGACGAACACGTCAACCGCTTCGGTATc                                 >  1:2710537/1‑69 (MQ=255)
                            gCCTTCGTCAGACAGTTCTACTTCTACGCTACCGTCAGGGAAGACGAACACGTCAACCGCTTCGGTATc                                 >  1:2212677/1‑69 (MQ=255)
                            gCCTTCGTCAGACAGTTCTACTTCTACGCTACCGTCAGGGAAGACGAACACGTCAACCGCTTCGGTATc                                 >  1:1728579/1‑69 (MQ=255)
                            gCCTTCGTCAGACAGTTCTACTTCTACGCTACCGTCAGGGAAGACGAACACGTCAACCGCTTCGGTATc                                 >  1:1663755/1‑69 (MQ=255)
                            gCCTTCGTCAGACAGTTCTACTTCTACGCTACCGTCAGGGAAGACGAACACGTCAACCGCTTCGGTATc                                 >  1:1327902/1‑69 (MQ=255)
                            gCCTTCGTCAGACAGTTCTACTTCTACGCTACCGTCAGGGAAGACGAACACGTCAACCGCTTCGGTATc                                 >  1:982781/1‑69 (MQ=255)
                               ttCGTCAGACAGTTCTACTTCTACGCTACCGTCAGGGAAGACGAACACGTCAACCGCTTc                                       >  1:2864572/1‑60 (MQ=255)
                               ttCGTCAGACAGTTCTACTTCTACGCTACCGTCAGGGAAGACGAACACGTCAACCGCTTc                                       <  1:3309195/60‑1 (MQ=255)
                               ttCGTCAGACAGTTCTACTTCTACGCTACCGTCAGGGAAGACGAACACGTCAACCGCTTc                                       <  1:409809/60‑1 (MQ=255)
                               ttCGTCAGACAGTTCTACTTCTACGCTACCGTCAGGGAAGACGAACACGTCAACCGCTTc                                       <  1:697757/60‑1 (MQ=255)
                               ttCGTCAGACAGTTCTACTTCTACGCTACCGTCAGGGAAGACGAACACGTCAACCGCTTc                                       <  1:798305/60‑1 (MQ=255)
                               ttCGTCAGACAGTTCTACTTCTACGCTACCGTCAGGGAAGACGAACACGTCAACCGCTTc                                       >  1:2545137/1‑60 (MQ=255)
                               ttCGTCAGACAGTTCTACTTCTACGCTACCGTCAGGGAAGACGAACACGTCAACCGCTTc                                       >  1:1292671/1‑60 (MQ=255)
                               ttCGTCAGACAGTTCTACTTCTACGCTACCGTCAGGGAAGACGAACACGTCAACCGCTTc                                       >  1:2697279/1‑60 (MQ=255)
                               ttCGTCAGACAGTTCTACTTCTACGCTACCGTCAGGGAAGACGAACACGTCAACCGCTTc                                       <  1:1438054/60‑1 (MQ=255)
                               ttCGTCAGACAGTTCTACTTCTACGCTACCGTCAGGGAAGACGAACACGTCAACCGCTTc                                       <  1:1274686/60‑1 (MQ=255)
                               ttCGTCAGACAGTTCTACTTCTACGCTACCGTCAGGGAAGACGAACACGTCAACCGCTTc                                       >  1:2341576/1‑60 (MQ=255)
                               ttCGTCAGACAGTTCTACTTCTACGCTACCGTCAGGGAAGACGAACACGTCAACCGCTTc                                       <  1:1817854/60‑1 (MQ=255)
                               ttCGTCAGACAGTTCTACTTCTACGCTACCGTCAGGGAAGACGAACACGTCAACCGCTTc                                       <  1:1624785/60‑1 (MQ=255)
                               ttCGTCAGACAGTTCTACTTCTACGCTACCGTCAGGGAAGACGAACACGTCAACCGCTTc                                       >  1:1697665/1‑60 (MQ=255)
                               ttCGTCAGACAGTTCTACTTCTACGCTACCGTAAGGGAAGACGAACACGTCAACCGCTTc                                       >  1:3009551/1‑60 (MQ=255)
                               ttCGTCAGACAGTTCTACCTCTACGCTACCATCAGGGAAGACGAACACGTCAACCGCTTCGGTATCAc                               >  1:2738759/1‑68 (MQ=255)
                               ttCGTCAGACAGTTCTACCTCTACGCTACCATCAGGGAAGACGAACACGTCAACCGCTTCGGTATCAc                               >  1:1780819/1‑68 (MQ=255)
                               ttCGTCAGACAGTTCTACCTCTACGCTACCATCAGGGAAGACGAACACGTCAACCGCTTCGGTATCAc                               >  1:801119/1‑68 (MQ=255)
                               ttCGTCAGACAGTTCTACCTCTACGCTACCATCAGGGAAGACGAACACGTCAACCGCTTCGGTATCAc                               >  1:2933084/1‑68 (MQ=255)
                               ttCGTCAGACAGTTCTACCTCTACGCTACCATCAGGGAAGACGAACACGTCAACCGCTTCGGTATCAc                               >  1:2168231/1‑68 (MQ=255)
                               ttCGTCAGACAGTTCTACCTCTACGCTACCATCAGGGAAGACGAACACGTCAACCGCTTCGGTATCAc                               >  1:1434283/1‑68 (MQ=255)
                               ttCGTCAGACAGTTCTACCTCTACGCTACCATCAGGGAAGACGAACACGTCAACCGCTTCGGTATCAc                               >  1:2680350/1‑68 (MQ=255)
                                tCGTCAGACAGTTCTACTTCTACGCTACCGTCAGGGAAGACGAACACGTCAACCGCTTc                                       <  1:123351/59‑1 (MQ=255)
                                tCGTCAGACAGTTCTACTTCTACGCTACCGTCAGGGAAGACGAACACGTCAACCGCTTCGGTATCACCg                             <  1:1339/69‑1 (MQ=255)
                                tCGTCAGACAGTTCTACTTCTACGCTACCGTCAGGGAAGACGAACACGTCAACCGCTTCGGTATCACCg                             <  1:3345371/69‑1 (MQ=255)
                                tCGTCAGACAGTTCTACTTCTACGCTACCGTCAGGGAAGACGAACACGTCAACCGCTTCGGTATCACCg                             <  1:968693/69‑1 (MQ=255)
                                            tctacttctacGCTACCGTCAGGGAAGACGAACACGTCAACCGCTTCGGTATCACCGAACAGGTtgtg                  <  1:2976339/68‑1 (MQ=255)
                                            tctacttctacGCTACCGTCAGGGAAGACGAACACGTCAACCGCTTCGGTATCACCGAACAGGTTGTGc                 >  1:95976/1‑69 (MQ=255)
                                             ctacttctacGCTACCGTCAGGGAAGACGAACACGTCAACCGCTTCGGTATCACCGAACAGGTTGTGCa                <  1:1553779/69‑1 (MQ=255)
                                             ctacttctacGCTACCGTCAGGGAAGACGAACACGTCAACCGCTTCGGTATCACCGAACAGGTTGTGCa                <  1:2464011/69‑1 (MQ=255)
                                               acctctacGCTACCATCAGGGAAGACGAACACGTCAACCGCTTCGGTATCACCGAACAGGTTGTGCAt               <  1:573640/65‑1 (MQ=255)
                                               acctctacGCTACCATCAGGGAAGACGAACACGTCAACCGCTTCGGTATCACCGAACAGGTTGTGCAt               <  1:603951/65‑1 (MQ=255)
                                               acctctacGCTACCATCAGGGAAGACGAACACGTCAACCGCTTCGGTATCACCGAACAGGTTGTGCAt               <  1:1257354/65‑1 (MQ=255)
                                               acctctacGCTACCATCAGGGAAGACGAACACGTCAACCGCTTCGGTATCACCGAACAGGTTGTGCAt               <  1:1045054/65‑1 (MQ=255)
                                               acctctacGCTACCATCAGGGAAGACGAACACGTCAACCGCTTCGGTATCACCGAACAGGTTGTGCAt               <  1:1480579/65‑1 (MQ=255)
                                               acctctacGCTACCATCAGGGAAGACGAACACGTCAACCGCTTCGGTATCACCGAACAGGTTGTGCAt               <  1:3353035/65‑1 (MQ=255)
                                               acctctacGCTACCATCAGGGAAGACGAACACGTCAACCGCTTCGGTATCACCGAACAGGTTGTGCAt               <  1:1735845/65‑1 (MQ=255)
                                               acctctacGCTACCATCAGGGAAGACGAACACGTCAACCGCTTCGGTATCACCGAACAGGTTGTGCAt               <  1:3220187/65‑1 (MQ=255)
                                               acctctacGCTACCATCAGGGAAGACGAACACGTCAACCGCTTCGGTATCACCGAACAGGTTGTGCAt               <  1:3217856/65‑1 (MQ=255)
                                               acctctacGCTACCATCAGGGAAGACGAACACGTCAACCGCTTCGGTATCACCGAACAGGTTGTGCAt               <  1:1803076/65‑1 (MQ=255)
                                               acctctacGCTACCATCAGGGAAGACGAACACGTCAACCGCTTCGGTATCACCGAACAGGTTGTGCAt               <  1:1805268/65‑1 (MQ=255)
                                               acctctacGCTACCATCAGGGAAGACGAACACGTCAACCGCTTCGGTATCACCGAACAGGTTGTGCAt               <  1:1852147/65‑1 (MQ=255)
                                               acctctacGCTACCATCAGGGAAGACGAACACGTCAACCGCTTCGGTATCACCGAACAGGTTGTGCAt               <  1:3031463/65‑1 (MQ=255)
                                               acctctacGCTACCATCAGGGAAGACGAACACGTCAACCGCTTCGGTATCACCGAACAGGTTGTGCAt               <  1:1975226/65‑1 (MQ=255)
                                               acctctacGCTACCATCAGGGAAGACGAACACGTCAACCGCTTCGGTATCACCGAACAGGTTGTGCAt               <  1:2224515/65‑1 (MQ=255)
                                               acctctacGCTACCATCAGGGAAGACGAACACGTCAACCGCTTCGGTATCACCGAACAGGTTGTGCAt               <  1:2400137/65‑1 (MQ=255)
                                               acctctacGCTACCATCAGGGAAGACGAACACGTCAACCGCTGCGGTATCACCGAACAGGTTGTGCAt               <  1:396335/65‑1 (MQ=255)
                                                             gTCAGGGAAGACGAACACGTCAACCGCTTCGGTATCACCGAACAGGTTGTGCATGTTGCCGAGGAtc  <  1:1381683/67‑1 (MQ=255)
                                                             gTCAGGGAAGACGAACACGTCAACCGCTTCGGTATCACCGAACAGGTTGTGCATGTTGCCGAGGAtc  <  1:2615741/67‑1 (MQ=255)
                                                             |                                                                  
CATATTGCAGCATGTCCGCCACGGTATCGCCTTCGTCAGACAGTTCTACTTCTACGCTACCGTCAGGGAAGACGAACACGTCAACCGCTTCGGTATCACCGAACAGGTTGTGCATGTTGCCGAGGATC  >  minE/1971069‑1971196

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