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 713,725 T→C 44.3% E126G (GAA→GGA)  yceB ← predicted lipoprotein

Read alignment evidence...
  seq id position ref new freq score (cons/poly) reads annotation genes product
*minE713,7250TC44.3% 15.3 / 63.2 79E126G (GAA→GGA) yceBpredicted lipoprotein
Reads supporting (aligned to +/- strand):  ref base T (29/15);  new base C (22/13);  total (51/28)
Fisher's exact test for biased strand distribution p-value = 8.16e-01
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 8.59e-01

TAAAGTAATTGCGTAATGCCTGGTTCAAATAGGGAAGCAACGTTTGCATCACCGTTTGCATTTTTTCCGGTTGTACCGTCGCATCGACCACTTCCATCTCTTTCAGGAAGATCGCACCTTTTTCTTTATCA  >  minE/713660‑713790
                                                                 |                                                                 
tAAAGTAATTGCGTAATGCCTGGTTCAAATAGGGAAGCAACGTTTGCATCACCGTTTGCATTTTTTCCg                                                                >  1:2427142/1‑69 (MQ=255)
tAAAGTAATTGCGTAATGCCTGGTTCAAATAGGGAAGCAACGTTTGCATCACCGTTTGCATTTTTTCCg                                                                >  1:2238129/1‑69 (MQ=255)
     tAATTGCGTAATGCCTGGTTCAAATAGGGAAGCAACGTTTGCATCACCGTTTGCATTTTTTCCGGTTGt                                                           <  1:3041699/69‑1 (MQ=255)
          gCGTAATGCCTGGTTCAAATAGGGAAGCAACGTTTGCATCACCGTTTGCATTTTTTCCGGTTGTACCGt                                                      >  1:1860006/1‑69 (MQ=255)
          gCGTAATGCCTGGTTCAAATAGGGAAGCAACGTTTGCATCACCGTTTGCATTTTTTCCGGTTGTACCGt                                                      >  1:1628395/1‑69 (MQ=255)
                tGCCTGGTTCAAATAGGGAAGCAACGTTTGCATCACCGTTTGCATTTTTTCCGGTTGTACCGTCGCATc                                                >  1:3094872/1‑69 (MQ=255)
                tGCCTGGTTCAAATAGGGAAGCAACGTTTGCATCACCGTTTGCATTTTTTCCGGTTGTACCGTCGCATc                                                >  1:2333661/1‑69 (MQ=255)
                           aaTAGGGAAGCAACGTTTGCATCACCGTTTGCATTTTTCCCGGTTGTACCGTCGCATCGACCACTTcc                                      >  1:2910203/1‑68 (MQ=255)
                           aaTAGGGAAGCAACGTTTGCATCACCGTTTGCATTTTTCCCGGTTGTACCGTCGCATCGACCACTTcc                                      >  1:856696/1‑68 (MQ=255)
                           aaTAGGGAAGCAACGTTTGCATCACCGTTTGCATTTTTCCCGGTTGTACCGTCGCATCGACCACTTCCa                                     >  1:807559/1‑69 (MQ=255)
                           aaTAGGGAAGCAACGTTTGCATCACCGTTTGCATTTTTCCCGGTTGTACCGTCGCATCGACCACTTCCa                                     >  1:525844/1‑69 (MQ=255)
                           aaTAGGGAAGCAACGTTTGCATCACCGTTTGCATTTTTCCCGGTTGTACCGTCGCATCGACCACTTCCa                                     >  1:2909388/1‑69 (MQ=255)
                           aaTAGGGAAGCAACGTTTGCATCACCGTTTGCATTTTTCCCGGTTGTACCGTCGCATCGACCACTTCCa                                     >  1:95588/1‑69 (MQ=255)
                             tAGGGAAGCAACGTTTGCATCACCGTTTGCATTTTTTCCGGTTGTACCGTCGCATCGACCACTTCCAtc                                   <  1:133907/69‑1 (MQ=255)
                             tAGGGAAGCAACGTTTGCATCACCGTTTGCATTTTTTCCGGTTGTACCGTCGCATCGACCACTTCCAtc                                   <  1:1662079/69‑1 (MQ=255)
                                      aaCGTTTGCATCACCGTTTGCATTTTTCCCGGTTGTACCGTCGCATCGACCACTTCCATCTCTTTCAgg                          <  1:2217020/69‑1 (MQ=255)
                                      aaCGTTTGCATCACCGTTTGCATTTTTCCCGGTTGTACCGTCGCATCGACCACTTCCATCTCTTTCAgg                          <  1:2406085/69‑1 (MQ=255)
                                      aaCGTTTGCATCACCGTTTGCATTTTTCCCGGTTGTACCGTCGCATCGACCACTTCCATCTCTTTCAgg                          <  1:2189093/69‑1 (MQ=255)
                                      aaCGTTTGCATCACCGTTTGCATTTTTCCCGGTTGTACCGTCGCATCGACCACTTCCATCTCTTTCAgg                          <  1:2015554/69‑1 (MQ=255)
                                      aaCGTTTGCATCACCGTTTGCATTTTTCCCGGTTGTACCGTCGCATCGACCACTTCCATCTCTTTCAgg                          <  1:999239/69‑1 (MQ=255)
                                      aaCGTTTGCATCACCGTTTGCATTTTTCCCGGTTGTACCGTCGCATCGACCACTTCCATCTCTTTCAgg                          <  1:3255108/69‑1 (MQ=255)
                                      aaCGTTTGCATCACCGTTTGCATTTTTCCCGGTTGTACCGTCGCATCGACCACTTCCATCTCTTTCAgg                          <  1:3361251/69‑1 (MQ=255)
                                      aaCGTTTGCATCACCGTTTGCATTTTTCCCGGTTGTACCGTCGCATCGACCACTTCCATCTCTTTCAgg                          <  1:1605631/69‑1 (MQ=255)
                                      aaCGTTTGCATCACCGTTTGCATTTTTCCCGGTTGTACCGTCGCATCGACCACTTCCATCTCTTTCAgg                          <  1:492338/69‑1 (MQ=255)
                                      aaCGTTTGCATCACCGTTTGCATTTTTCCCGGTTGTACCGTCGCATCGACCACTTCCATCTCTTTCAgg                          <  1:530103/69‑1 (MQ=255)
                                      aaCGTTTGCATCACCGTTTGCATTTTTCCCGGTTGTACCGTCGCATCGACCACTTCCATCTCTTTCAgg                          <  1:565991/69‑1 (MQ=255)
                                      aaCGTTTGCATCACCGTTTGCATTTTTCCCGGTTGTACCGTCGCATCGACCACTTCCATCTCTTTCAgg                          <  1:1272097/69‑1 (MQ=255)
                                      aaCGTTTGCATCACCGTTTGCATTTTTCCCGGTTGTACCGTCGCATCGACCACTTCCATCTCTTTCAgg                          <  1:680564/69‑1 (MQ=255)
                                         gTTTGCATCACCGTTTGCATTTTTTCCGGTTGTACCGTCGCATCGACCACTTCCATCTCTTTCAGGAAg                       <  1:3400295/69‑1 (MQ=255)
                                         gTTTGCATCACCGTTTGCATTTTTTCCGGTTGTACCGTCGCATCGACCACTTCCATCTCTTTCAGGAAg                       <  1:307458/69‑1 (MQ=255)
                                         gTTTGCATCACCGTTTGCATTTTTTCCGGTTGTACCGTCGCATCGACCACTTCCATCTCTTTCAGGAAg                       <  1:341644/69‑1 (MQ=255)
                                         gTTTGCATCACCGTTTGCATTTTTTCCGGTTGTACCGTCGCATCGACCACTTCCATCTCTTTCAGGAAg                       <  1:470118/69‑1 (MQ=255)
                                         gTTTGCATCACCGTTTGCATTTTTTCCGGTTGTACCGTCGCATCGACCACTTCCATCTCTTTCAGGAAg                       <  1:2603789/69‑1 (MQ=255)
                                         gTTTGCATCACCGTTTGCATTTTTTCCGGTTGTACCGTCGCATCGACCACTTCCATCTCTTTCAGGAAg                       <  1:626626/69‑1 (MQ=255)
                                         gTTTGCATCACCGTTTGCATTTTTTCCGGTTGTACCGTCGCATCGACCACTTCCATCTCTTTCAGGAAg                       <  1:1060456/69‑1 (MQ=255)
                                         gTTTGCATCACCGTTTGCATTTTTTCCGGTTGTACCGTCGCATCGACCACTTCCATCTCTTTCAGGAAg                       <  1:211132/69‑1 (MQ=255)
                                                 cACCGTTTGCATTTTTTCCGGTTGTACCGTCGCATCGACCACTTCCATCTCTTTCAGGAAGAt                     >  1:741794/1‑63 (MQ=255)
                                                 cACCGTTTGCATTTTTTCCGGTTGTACCGTCGCATCGACCACTTCCATCTCTTTCAGGAAGATCGCAcc               >  1:881929/1‑69 (MQ=255)
                                                 cACCGTTTGCATTTTTTCCGGTTGTACCGTCGCATCGACCACTTCCATCTCTTTCAGGAAGATCGCAcc               >  1:866221/1‑69 (MQ=255)
                                                 cACCGTTTGCATTTTTTCCGGTTGTACCGTCGCATCGACCACTTCCATCTCTTTCAGGAAGATCGCAcc               >  1:421474/1‑69 (MQ=255)
                                                 cACCGTTTGCATTTTTTCCGGTTGTACCGTCGCATCGACCACTTCCATCTCTTTCAGGAAGATCGCAcc               >  1:657530/1‑69 (MQ=255)
                                                 cACCGTTTGCATTTTTTCCGGTTGTACCGTCGCATCGACCACTTCCATCTCTTTCAGGAAGATCGCAcc               >  1:578153/1‑69 (MQ=255)
                                                  aCCGTTTGCATTTTTTCCGGTTGTACCGTCGCATCGAcc                                            >  1:1786093/1‑39 (MQ=255)
                                                  aCCGTTTGCATTTTTTCCGGTTGTACCGTCGCATCGAcc                                            >  1:2005597/1‑39 (MQ=255)
                                                  aCCGTTTGCATTTTTTCCGGTTGTACCGTCGCATCGAcc                                            >  1:1761396/1‑39 (MQ=255)
                                                  aCCGTTTGCATTTTTTCCGGTTGTACCGTCGCATCGAcc                                            >  1:804035/1‑39 (MQ=255)
                                                  aCCGTTTGCATTTTTTCCGGTTGTACCGTCGCATCGAcc                                            >  1:1303438/1‑39 (MQ=255)
                                                  aCCGTTTGCATTTTTTCCGGTTGTACCGTCGCATCGAcc                                            >  1:624328/1‑39 (MQ=255)
                                                  aCCGTTTGCATTTTTTCCGGTTGTACCGTCGCATCGAcc                                            >  1:1914504/1‑39 (MQ=255)
                                                  aCCGTTTGCATTTTTTCCGGTTGTACCGTCGCATCGAc                                             >  1:1762559/1‑38 (MQ=255)
                                                  aCCGTTTGCATTTTTTCCGGTTGTACCGTCGCATCGACCACTTcc                                      >  1:1425369/1‑45 (MQ=255)
                                                  aCCGTTTGCATTTTTTCCGGTTGTACCGTCGCATCGACCACTTcc                                      >  1:1500309/1‑45 (MQ=255)
                                                  aCCGTTTGCATTTTTTCCGGTTGTACCGTCGCATCGACCACTTcc                                      >  1:483851/1‑45 (MQ=255)
                                                  aCCGTTTGCATTTTTTCCGGTTGTACCGTCGCATCGACCACTTcc                                      >  1:1074503/1‑45 (MQ=255)
                                                  aCCGTTTGCATTTTTTCCGGTTGTACCGTCGCATCGACCACTTCCATCTCTTTCAGGAAGATCGCACCt              >  1:1305900/1‑69 (MQ=255)
                                                  aCCGTTTGCATTTTTTCCGGTTGTACCGTCGCATCGACCACTTCCATCTCTTTCAGGAAGATCGCACCt              >  1:708304/1‑69 (MQ=255)
                                                  aCCGTTTGCATTTTTTCCGGTTGTACCGTCGCATCGACCACTTCCATCTCTTTCAGGAAGATCGCACCt              >  1:1221653/1‑69 (MQ=255)
                                                  aCCGTTTGCATTTTTTCCGGTTGTACCGTCGCATCGACCACTTCCATCTCTTTCAGGAAGATCGCACCt              >  1:2209396/1‑69 (MQ=255)
                                                  aCCGTTTGCATTTTTTCCGGTTGTACCGTCGCATCGACCACTTCCATCTCTTTCAGGAAGATCCCACCt              >  1:1978138/1‑69 (MQ=255)
                                                    cGTTTGCATTTTTCCCGGTTGTACCGTCGCATCGACCACTTCCATCTCTTTCAGGAAGATCGcg                 >  1:521971/1‑63 (MQ=255)
                                                    cGTTTGCATTTTTCCCGGTTGTACCGTCGCATCGACCACTTCCATCTCTTTCAGGAAGATCGCGCCttt            >  1:328142/1‑69 (MQ=255)
                                                    cGTTTGCATTTTTCCCGGTTGTACCGTCGCATCGACCACTTCCATCTCTTTCAGGAAGATCGCGCCttt            >  1:1838513/1‑69 (MQ=255)
                                                    cGTTTGCATTTTTCCCGGTTGTACCGTCGCATCGACCACTTCCATCTCTTTCAGGAAGATCGCGCCttt            >  1:109065/1‑69 (MQ=255)
                                                    cGTTTGCATTTTTCCCGGTTGTACCGTCGCATCGACCACTTCCATCTCTTTCAGGAAGATCGCGCCttt            >  1:2928537/1‑69 (MQ=255)
                                                    cGTTTGCATTTTTCCCGGTTGTACCGTCGCATCGACCACTTCCATCTCTTTCAGGAAGATCGCGCCtt             >  1:1030813/1‑68 (MQ=255)
                                                    cGTTTGCATTTTTCCCGGTTGTACCGTCGCATCGACCACTTCCATCTCTTTCAGGAAGATCGCGCCtt             >  1:3411811/1‑68 (MQ=255)
                                                    cGTTTGCATTTTTCCCGGTTGTACCGTCGCATCGACCACTTCCATCTCTTTCAGGAAGATCGCGCCtt             >  1:2432443/1‑68 (MQ=255)
                                                    cGTTTGCATTTTTCCCGGTTGTACCGTCGCATCGACCACTTCCATCTCTTTCAGGAAGATCGCGCCtt             >  1:2589274/1‑68 (MQ=255)
                                                    cGTTTGCATTTTTCCCGGTTGTACCGTCGCATCGACCACTTCCATCTCTTTCAGGAAGATCGCGCCtt             >  1:2841138/1‑68 (MQ=255)
                                                    cGTTTGCATTTTTCCCGGTTGTACCGTCGCATCGACCACTTCCATCTCTTTCAGGAAGATCGCGCCtt             >  1:2937471/1‑68 (MQ=255)
                                                    cGTTTGCATTTTTCCCGGTTGTACCGTCGCATCGACCACTTCCATCTCTTTCAGGAAGATCGCGCCtt             >  1:555854/1‑68 (MQ=255)
                                                    cGTTTGCATTTTTCCCGGTTGTACCGTCGCATCGACCACTTCCATCTCTTTCAGGAAGATCGCGCCtt             >  1:3097869/1‑68 (MQ=255)
                                                    cGTTTGCATTTTTCCCGGTTGTACCGTCGCATCGACCACTTCCATCTCTTTCAGGAAGATCGCGCCtt             >  1:3160322/1‑68 (MQ=255)
                                                    cGTTTGCATTTTTCCCGGTTGTACCGTCGCATCGACCACTTCCATCTCTTTCAGGAAGATCGCGCCtt             >  1:321948/1‑68 (MQ=255)
                                                    cGTTTGCATTTTTCCCGGTTGTACCGTCGCATCGACCACTTCCATCTCTTTCAGGAAGATCGCGCCtt             >  1:463312/1‑68 (MQ=255)
                                                          cATTTTTTCCGGTTGTACCGTCGCATCGACCACTTCCATCTCTTTCAGGAAGATCGCACCTTTTTCtt       <  1:1856442/68‑1 (MQ=255)
                                                          cATTTTTTCCGGTTGTACCGTCGCATCGACCACTTCCATCTCTTTCAGGAAGATCGCACCTTTTTCtt       <  1:1860375/68‑1 (MQ=255)
                                                          cATTTTTTCCGGTTGTACCGTCGCATCGACCACTTCCATCTCTTTCAGGAAGATCGCACCTTTTTCtt       <  1:1257629/68‑1 (MQ=255)
                                                          cATTTTTTCCGGTTGTACCGTCGCATCGACCACTTCCATCTCTTTCAGGAAGATCGCACCTTTTTCtt       <  1:1505524/68‑1 (MQ=255)
                                                            ttttttCCGGTTGTACCGTCGCATCGACCACTTCCATCTCTTTCAGGAAGATCGCACCTTTTTCTTTa     <  1:2866402/68‑1 (MQ=255)
                                                            ttttttCCGGTTGTACCGTCGCATCGACCACTTCCATCTCTTTCAGGAAGATCGCACCTTTTTCTTTa     <  1:2731647/68‑1 (MQ=255)
                                                              ttttCCGGTTGTACCGTCGCATCGACCACTTCCATCTCTTTCAGGAAGATCGCACCttttt          <  1:595259/61‑1 (MQ=255)
                                                              ttttCCGGTTGTACCGTCGCATCGACCACTTCCATCTCTTTCAGGAAGATCGCACCttttt          <  1:1931155/61‑1 (MQ=255)
                                                              ttttCCGGTTGTACCGTCGCATCGACCACTTCCATCTCTTTCAGGAAGATCGCACCttttt          <  1:2387908/61‑1 (MQ=255)
                                                              ttttCCGGTTGTACCGTCGCATCGACCACTTCCATCTCTTTCAGGAAGATCGCACCTTTTTCTTTATCa  >  1:1340339/1‑69 (MQ=255)
                                                              ttttCCGGTTGTACCGTCGCATCGACCACTTCCATCTCTTTCAGGAAGATCGCACCTTTTTCTTTATCa  >  1:456624/1‑69 (MQ=255)
                                                                 |                                                                 
TAAAGTAATTGCGTAATGCCTGGTTCAAATAGGGAAGCAACGTTTGCATCACCGTTTGCATTTTTTCCGGTTGTACCGTCGCATCGACCACTTCCATCTCTTTCAGGAAGATCGCACCTTTTTCTTTATCA  >  minE/713660‑713790

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