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 1,438,595 G→A 42.8% I164I (ATC→ATT)  yojL ← predicted thiamine biosynthesis lipoprotein

Read alignment evidence...
  seq id position ref new freq score (cons/poly) reads annotation genes product
*minE1,438,5950GA42.8% 15.8 / 39.3 56I164I (ATC→ATT) yojLpredicted thiamine biosynthesis lipoprotein
Reads supporting (aligned to +/- strand):  ref base G (28/4);  new base A (20/4);  total (48/8)
Fisher's exact test for biased strand distribution p-value = 7.13e-01
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 1.00e+00

CGGTGGAGAGATCGACATATAAATCCGGCAGGTCTTTTTGCAGATATTGCTGATGCGACTGATTGATGACCGTCAGGTGCTGTAAGCCGGTTTTGGCTTTCATCGCATCGATCTGTTCCTGGCTCGGAA  >  minE/1438531‑1438659
                                                                |                                                                
cGGTGGAGAGATCGACATATAAATCCGGCAGGTCTTTTTGCAGATATTGCTGATGCGACTGATtgatga                                                              <  1:263490/69‑1 (MQ=255)
cGGTGGAGAGATCGACATATAAATCCGGCAGGTCTTTTTGCAGATATTGCTGATGCGACTGATtgatga                                                              <  1:2642857/69‑1 (MQ=255)
cGGTGGAGAGATCGACATATAAATCCGGCAGGTCTTTTTGCAGATATTGCTGATGCGACTGATtgatga                                                              <  1:2881461/69‑1 (MQ=255)
cGGTGGAGAGATCGACATATAAATCCGGCAGGTCTTTTTGCAGATATTGCTGATGCGACTGATtgatga                                                              <  1:294223/69‑1 (MQ=255)
cGGTGGAGAGATCGACATATAAATCCGGCAGGTCTTTTTGCAGATATTGCTGATGCGACTGATtgatga                                                              <  1:3181058/69‑1 (MQ=255)
     gagagaTCGACATATAAATCCGGCAGGTCTTTTTGCAGATATTGCTGATGCGACtgattg                                                                  <  1:3036824/60‑1 (MQ=255)
     gagagaTCGACATATAAATCCGGCAGGTCTTTTTGCAGATATTGCTGATGCGACtgattg                                                                  <  1:2531442/60‑1 (MQ=255)
     gagagaTCGACATATAAATCCGGCAGGTCTTTTTGCAGATATTGCTGATGCGACtgattg                                                                  <  1:2674486/60‑1 (MQ=255)
     gagagaTCGACATATAAATCCGGCAGGTCTTTTTGCAGATATTGCTGATGCGACtgattg                                                                  <  1:2172962/60‑1 (MQ=255)
     gagagaTCGACATATAAATCCGGCAGGTCTTTTTGCAGATATTGCTGATGCGACtgattg                                                                  <  1:1816340/60‑1 (MQ=255)
     gagagaTCGACATATAAATCCGGCAGGTCTTTTTGCAGATATTGCTGATGCGACtgattg                                                                  <  1:295770/60‑1 (MQ=255)
     gagagaTCGACATATAAATCCGGCAGGTCTTTTTGCAGATATTGCTGATGCGACtgattg                                                                  <  1:377925/60‑1 (MQ=255)
     gagagaTCGACATATAAATCCGGCAGGTCTTTTTGCAGATATTGCTGATGCGACtgattg                                                                  <  1:632918/60‑1 (MQ=255)
     gagagaTCGACATATAAATCCGGCAGGTCTTTTTGCAGATATTGCTGATGCGACtgattg                                                                  <  1:75021/60‑1 (MQ=255)
     gagagaTCGACATATAAATCCGGCAGGTCTTTTTGCAGATATTGCTGATGCGACtgattg                                                                  <  1:861257/60‑1 (MQ=255)
     gagagaTCGACATATAAATCCGGCAGGTCTTTTTGCAGATATTGCTGATGCGACtgattg                                                                  <  1:1385127/60‑1 (MQ=255)
     gagagaTCGACATATAAATCCGGCAGGTCTTTTTGCAGATATTGCTGATGCGACtgattg                                                                  <  1:863363/60‑1 (MQ=255)
           tCGACATATAAATCCGGCAGGTCTTTTTGCAGATATTGCTGATGCGACTGATTGATGACCGTCAGGTGc                                                   >  1:1805307/1‑69 (MQ=255)
           tCGACATATAAATCCGGCAGGTCTTTTTGCAGATATTGCTGATGCGACTGATTGATGACCGTCAGGTGc                                                   >  1:2689382/1‑69 (MQ=255)
           tCGACATATAAATCCGGCAGGTCTTTTTGCAGATATTGCTGATGCGACTGATTGATGACCGTCAGGTGc                                                   >  1:3044851/1‑69 (MQ=255)
           tCGACATATAAATCCGGCAGGTCTTTTTGCAGATATTGCTGATGCGACTGATTGATGACCGTCAGGTGc                                                   >  1:1413873/1‑69 (MQ=255)
           tCGACATATAAATCCGGCAGGTCTTTTTGCAGATATTGCTGATGCGACTGATTGATGACCGTCAGGTGc                                                   >  1:1600008/1‑69 (MQ=255)
           tCGACATATAAATCCGGCAGGTCTTTTTGCAGATATTGCTGATGCGACTGATTGATGACCGTCAGGTGc                                                   >  1:3230030/1‑69 (MQ=255)
           tCGACATATAAATCCGGCAGGTCTTTTTGCAGATATAGCTGATGCGACTGATTGATGACCGTCAGGTGc                                                   >  1:1193848/1‑69 (MQ=255)
                          ggCAGGTCTTTTTGCAGATATTGCTGATGCGACtgattg                                                                  <  1:28957/39‑1 (MQ=255)
                            cAGGTTTTTTTGCAGATATTGCTGATGCGACTGATTAATGACCGTCAGGTGCTGTAAGCCGGTTTTGGc                                  <  1:1348660/69‑1 (MQ=255)
                            cAGGTTTTTTTGCAGATATTGCTGATGCGACTGATTAATGACCGTCAGGTGCTGTAAGCCGGTTTTGGc                                  <  1:1196890/69‑1 (MQ=255)
                            cAGGTTTTTTTGCAGATATTGCTGATGCGACTGATTAATGACCGTCAGGTGCTGTAAGCCGGTTTTGGc                                  <  1:2832108/69‑1 (MQ=255)
                            cAGGTTTTTTTGCAGATATTGCTGATGCGACTGATTAATGACCGTCAGGTGCTGTAAGCCGGTTTTGGc                                  <  1:2493099/69‑1 (MQ=255)
                             aGGTTTTTTTGCAGATATTGCTGATGCGACTGATTAATGACCGTCAGGTGCTGt                                                >  1:2566540/1‑54 (MQ=38)
                             aGGTTTTTTTGCAGATATTGCTGATGCGACTGATTAATGACCGTCAGGTGCTGt                                                >  1:1127271/1‑54 (MQ=38)
                             aGGTTTTTTTGCAGATATTGCTGATGCGACTGATTAATGACCGTCAGGTGCTGt                                                >  1:1218001/1‑54 (MQ=38)
                             aGGTTTTTTTGCAGATATTGCTGATGCGACTGATTAATGACCGTCAGGTGCTGt                                                >  1:2539799/1‑54 (MQ=38)
                             aGGTTTTTTTGCAGATATTGCTGATGCGACTGATTAATGACCGTCAGGTGCTGt                                                >  1:2343105/1‑54 (MQ=38)
                             aGGTTTTTTTGCAGATATTGCTGATGCGACTGATTAATGACCGTCAGGTGCTGt                                                >  1:2229792/1‑54 (MQ=38)
                             aGGTTTTTTTGCAGATATTGCTGATGCGACTGATTAATGACCGTCAGGTGCTGt                                                >  1:2771071/1‑54 (MQ=38)
                             aGGTTTTTTTGCAGATATTGCTGATGCGACTGATTAATGACCGTCAGGTGCTGt                                                >  1:2168664/1‑54 (MQ=38)
                             aGGTTTTTTTGCAGATATTGCTGATGCGACTGATTAATGACCGTCAGGTGCTGt                                                >  1:201918/1‑54 (MQ=38)
                             aGGTTTTTTTGCAGATATTGCTGATGCGACTGATTAATGACCGTCAGGTGCTGt                                                >  1:1732470/1‑54 (MQ=38)
                             aGGTTTTTTTGCAGATATTGCTGATGCGACTGATTAATGACCGTCAGGTGCTGt                                                >  1:3196865/1‑54 (MQ=38)
                                  tttttGCAGATATTGCTGATGCGCCTGATTAATGACCGTCAGGTGCt                                                  >  1:662075/1‑47 (MQ=39)
                                  tttttGCAGATATTGCTGATGCGACTGATTAATGACCGTCAGGTGCt                                                  >  1:2874321/1‑47 (MQ=255)
                                  tttttGCAGATATTGCTGATGCGACTGATTAATGACCGTCAGGTGCt                                                  >  1:753127/1‑47 (MQ=255)
                                  tttttGCAGATATTGCTGATGCGACTGATTAATGACCGTCAGGTGCt                                                  >  1:996389/1‑47 (MQ=255)
                                  tttttGCAGATATTGCTGATGCGACTGATTAATGACCGTCAGGTGCt                                                  >  1:3347283/1‑47 (MQ=255)
                                  tttttGCAGATATTGCTGATGCGACTGATTAATGACCGTCAGGTGCt                                                  >  1:440091/1‑47 (MQ=255)
                                  tttttGCAGATATTGCTGATGCGACTGATTAATGACCGTCAGGTGCt                                                  >  1:1206684/1‑47 (MQ=255)
                                  tttttGCAGATATTGCTGATGCGACTGATTAATGACCGTCAGGTGCt                                                  >  1:2328774/1‑47 (MQ=255)
                                  tttttGCAGATATTGCTGATGCGACTGATTAATGACCGTCAGGTGCt                                                  >  1:1868909/1‑47 (MQ=255)
                                    tttGCAGATATTGCTGATGCGACTGATTGATGACCGTCAGGTGCTGTAAGCCGGTTTTGGCttt                               <  1:1477797/64‑1 (MQ=255)
                                    tttGCAGATATTGCTGATGCGACTGATTGATGACCGTCAGGTGCTGTAAGCCGGTTTTGGCttt                               >  1:1452330/1‑64 (MQ=255)
                                    tttGCAGATATTGCTGATGCGACTGATTGATGACCGTCAGGTGCTGTAAGCCGGTTTTGGCttt                               <  1:1435971/64‑1 (MQ=255)
                                    tttGCAGATATTGCTGATGCGACTGATTGATGACCGTCAGGTGCTGTAAGCCGGTTTTGGCttt                               <  1:145195/64‑1 (MQ=255)
                                    tttGCAGATATTGCTGATGCGACTGATTGATGACCGTCAGGTGCTGTAAGCCGGTTTTGGCttt                               <  1:1807402/64‑1 (MQ=255)
                                             atTGCTGATGCGACTGATTGATGACCGTCAGGTGCTGTAAGCCGGTTTTGGCTTTCATCGCATCGATCt                 >  1:2399107/1‑69 (MQ=255)
                                              ttGCTGATGCGACTGATTGATGACCGTCAGGTGCTGTAAGcc                                           >  1:2495779/1‑42 (MQ=255)
                                              ttGCTGATGCGACTGATTGATGACCGTCAGGTGCTGTAAGCCGGTTTTGGCTTTcatc                           >  1:218530/1‑58 (MQ=255)
                                              ttGCTGATGCGACTGATTGATGACCGTCAGGTGCTGTAAGCCGGTTTTGGCTTTCATCGCATCGATCt                 >  1:811097/1‑68 (MQ=255)
                                              ttGCTGATGCGACTGATTGATGACCGTCAGGTGCTGTAAGCCGGTTTTGGCTTTCATCGCATCGATCTg                >  1:3188944/1‑69 (MQ=255)
                                              ttGCTGATGCGACTGATTGATGACCGTCAGGTGCTGTAAGCCGGTTTTGGCTTTCATCGCATCGATCTg                >  1:2444651/1‑69 (MQ=255)
                                              ttGCTGATGCGACTGATTGATGACCGTCAGGTGCTGTAAGCCGGTTTTGGCTTTCATCGCATCGATCTg                >  1:409851/1‑69 (MQ=255)
                                              ttGCTGATGCGACTGATTGATGACCGTCAGGTGCTGTAAGCCGGTTTTGGCTTTCATCGCATCGATCTg                >  1:623214/1‑69 (MQ=255)
                                              ttGCTGATGCGACTGATTGATGACCGTCAGGTGCTGTAAGCCGGTTTTGGCTTTCATCGCATCGATCTg                >  1:1359735/1‑69 (MQ=255)
                                              ttGCTGATGCGACTGATTGATGACCGTCAGGTGCTGTAAGCCGGTTTTGGCTTTCATCGCATCGATCTg                >  1:815243/1‑69 (MQ=255)
                                              ttGCTGATGCGACTGATTGATGACCGTCAGGTGCTGTAAGCCGGTTTTGGCTTTCATCGCATCGATCTg                >  1:1070637/1‑69 (MQ=255)
                                              ttGCTGATGCGACTGATTGATGACCGTCAGGTGCTGTAAGCCGGTTTTGGCTTTCATCGCATCGATCTg                >  1:1003667/1‑69 (MQ=255)
                                              ttGCTGATGCGACTGATTGATGACCGTCAGGTGCTGTAAGCCGGTTTTGGCTTTCATCGCATCGATCTg                >  1:1862016/1‑69 (MQ=255)
                                              ttGCTGATGCGACTGATTGATGACCGTCAGGTCCTGTAAGCCGGt                                        >  1:2628146/1‑45 (MQ=255)
                                                   gATGCGACTGATTGATGACCGTCAGGTGCTGTAAGCCGGTTTTGGCTTTCATCGCATCGATCTGTTcc            >  1:3172364/1‑68 (MQ=255)
                                                   gATGCGACTGATTGATGACCGTCAGGTGCTGTAAGCCGGTTTTGGCTTTCATCGCATCGATCTGTTCCt           >  1:1529971/1‑69 (MQ=255)
                                                   gATGCGACTGATTGATGACCGTCAGGTGCTGTAAGCCGGTTTTGGCTTTCATCGCATCGATCTGTTCCt           >  1:1790277/1‑69 (MQ=255)
                                                   gATGCGACTGATTGATGACCGTCAGGTGCTGTAAGCCGGTTTTGGCTTTCATCGCATCGATCTGTTCCt           >  1:564346/1‑69 (MQ=255)
                                                   gATGCGACTGATTGATGACCGTCAGGTGCTGTAAGCCGGTTTTGGCTTTCATCGCATCGATCTGTTCCt           >  1:1373160/1‑69 (MQ=255)
                                                   gATGCGACTGATTGATGACCGTCAGGTGCTGTAAGCCGGTTTTGGCTTTCATCGCATCGATCTGTTCCt           >  1:2877024/1‑69 (MQ=255)
                                                            gattaatGACCGTCAGGTGCTGTAAGCCGGTTTTGGCTTTCATCGCATCGATCTGTTCCTGGCTCGGaa  >  1:2573913/1‑69 (MQ=255)
                                                            gattaatGACCGTCAGGTGCTGTAAGCCGGTTTTGGCTTTCATCGCATCGATCTGTTCCTGGCTCGGaa  >  1:164086/1‑69 (MQ=255)
                                                            gattaatGACCGTCAGGTGCTGTAAGCCGGTTTTGGCTTTCATCGCATCGATCTGTTCCTGGCTCGGaa  >  1:2387557/1‑69 (MQ=255)
                                                            gattaatGACCGTCAGGTGCTGTAAGCCGGTTTTGGCTTTCATCGCATCGATCTGTTCCTGGCTCGGaa  >  1:2337598/1‑69 (MQ=255)
                                                            gattaatGACCGTCAGGTGCTGTAAGCCGGTTTTGGCTTTCATCGCATCGATCTGTTCCTGGCTCGGaa  >  1:2741372/1‑69 (MQ=255)
                                                            gattaatGACCGTCAGGTGCTGTAAGCCGGTTTTGGCTTTCATCGCATCGATCTGTTCCTGGCTCGGaa  >  1:1984636/1‑69 (MQ=255)
                                                            gattaatGACCGTCAGGTGCTGTAAGCCGGTTTTGGCTTTCATCGCATCGATCTGTTCCTGGCTCGGaa  >  1:660825/1‑69 (MQ=255)
                                                            gattaatGACCGTCAGGTGCTGTAAGCCGGTTTTGGCTTTCATCGCATCGATCTGTTCCTGGCTCGGaa  >  1:183910/1‑69 (MQ=255)
                                                            gattaatGACCGTCAGGTGCTGTAAGCCGGTTTTGGCTTTCATCGCATCGATCTGTTCCTGGCTCGGaa  >  1:1780748/1‑69 (MQ=255)
                                                            gattaatGACCGTCAGGTGCTGTAAGCCGGTTTTGGCTTTCATCGCATCGATCTGTTCCTGGCTCGGaa  >  1:1648190/1‑69 (MQ=255)
                                                            gattaatGACCGTCAGGTGCTGTAAGCCGGTTTTGGCTTTCATCGCATCGATCTGTTCCTGGCTCGGaa  >  1:3425991/1‑69 (MQ=255)
                                                            gattaatGACCGTCAGGTGCTGTAAGCCGGTTTTGGCTTTCATCGCATCGATCTGTTCCTGGCTCGGaa  >  1:1479377/1‑69 (MQ=255)
                                                            gattaatGACCGTCAGGTGCTGTAAGCCGGTTTTGGCTTTCATCGCATCGATCTGTTCCTGGCTCGGaa  >  1:148732/1‑69 (MQ=255)
                                                                |                                                                
CGGTGGAGAGATCGACATATAAATCCGGCAGGTCTTTTTGCAGATATTGCTGATGCGACTGATTGATGACCGTCAGGTGCTGTAAGCCGGTTTTGGCTTTCATCGCATCGATCTGTTCCTGGCTCGGAA  >  minE/1438531‑1438659

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