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 494,741 C→T 50.5% Q184Q (CAG→CAA)  galM ← galactose‑1‑epimerase

Read alignment evidence...
  seq id position ref new freq score (cons/poly) reads annotation genes product
*minE494,7410CT50.5% ‑6.0 / 89.0 95Q184Q (CAG→CAA) galMgalactose‑1‑epimerase
Reads supporting (aligned to +/- strand):  ref base C (10/37);  new base T (24/24);  total (34/61)
Fisher's exact test for biased strand distribution p-value = 5.15e-03
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 1.00e+00

CCGCCTTCATCAACCGGCAGATATTCGTCCGCCAGAATCTGCAACTTGTGATTGCGCACGTCAGACTGCTCGCCGTCAAGATTGAAATAGACGTGATTAGTCATATTCACCGGGCAAGGTTTATCAACTG  >  minE/494676‑494805
                                                                 |                                                                
ccgccTTCATCAACCGGCAGATATTCGTCCGCCAGAATCTGCAACTTGTGATTGCGCACGTCAGACTGc                                                               >  1:998775/1‑69 (MQ=255)
     ttCATCAACCGGCAGATATTCGTCCGCCAGAATCTGCAACTTGTGATTGCGCACGTCAGACTGCTCGcc                                                          >  1:1692573/1‑69 (MQ=255)
     ttCATCAACCGGCAGATATTCGTCCGCCAGAATCTGCAACTTGTGATTGCGCACGTCAGACTGCTCGcc                                                          >  1:3031118/1‑69 (MQ=255)
     ttCATCAACCGGCAGATATTCGTCCGCCAGAATCTGCAACTTGTGATTGCGCACGTCAGACTGCTCGcc                                                          >  1:3411532/1‑69 (MQ=255)
     ttCATCAACCGGCAGATATTCGTCCGCCAGAATCTGCAACTTGTGATTGCGCACGTCAGACTGCTCGcc                                                          >  1:702111/1‑69 (MQ=255)
     ttCATCAACCGGCAGATATTCGTCCGCCAGAATCTGCAACTTGTGATTGCGCACGTCAGACTGCTCGcc                                                          >  1:2141638/1‑69 (MQ=255)
     ttCATCAACCGGCAGATATTCGTCCGCCAGAATCTGCAACTTGTGATTGCGCACGTCAGACTGCTCGcc                                                          >  1:267648/1‑69 (MQ=255)
      tcatcaACCGGCAGATATTCGTCCGCCAGAATCTGCAACTTGTGATTGCGCACGTCAGACTGCTCGCCg                                                         <  1:479391/69‑1 (MQ=255)
      tcatcaACCGGCAGATATTCGTCCGCCAGAATCTGCAACTTGTGATTGCGCACGTCAGACTGCTCGCCg                                                         <  1:1869108/69‑1 (MQ=255)
      tcatcaACCGGCAGATATTCGTCCGCCAGAATCTGCAACTTGTGATTGCGCACGTCAGACTGCTCGCCg                                                         <  1:1711848/69‑1 (MQ=255)
      tcatcaACCGGCAGATATTCGTCCGCCAGAATCTGCAACTTGTGATTGCGCACGTCAGACTGCTCGCCg                                                         <  1:1690856/69‑1 (MQ=255)
                  aGATATTCGTCCGCCAGAATCTGCAACTTGTGATTGCGCACGTCAGACTGCTCGCCGTCAAGATTGaaa                                             <  1:2135192/69‑1 (MQ=255)
                  aGATATTCGTCCGCCAGAATCTGCAACTTGTGATTGCGCACGTCAGACTGCTCGCCGTCAAGATTGaaa                                             <  1:2109738/69‑1 (MQ=255)
                  aGATATTCGTCCGCCAGAATCTGCAACTTGTGATTGCGCACGTCAGACTGCTCGCCGTCAAGATTGaaa                                             <  1:2702955/69‑1 (MQ=255)
                  aGATATTCGTCCGCCAGAATCTGCAACTTGTGATTGCGCACGTCAGACTGCTCGCCGTCAAGATTGaaa                                             <  1:2263547/69‑1 (MQ=255)
                  aGATATTCGTCCGCCAGAATCTGCAACTTGTGATTGCGCACGTCAGACTGCTCGCCGTCAAGATTGaaa                                             <  1:3065675/69‑1 (MQ=255)
                  aGATATTCGTCCGCCAGAATCTGCAACTTGTGATTGCGCACGTCAGACTGCTCGCCGTCAAGATTGaaa                                             <  1:1731519/69‑1 (MQ=255)
                  aGATATTCGTCCGCCAGAATCTGCAACTTGTGATTGCGCACGTCAGACTGCTCGCCGTCAAGATTGaaa                                             <  1:3057516/69‑1 (MQ=255)
                  aGATATTCGTCCGCCAGAATCTGCAACTTGTGATTGCGCACGTCAGACTGCTCGCCGTCAAGATTGaaa                                             <  1:3128737/69‑1 (MQ=255)
                  aGATATTCGTCCGCCAGAATCTGCAACTTGTGATTGCGCACGTCAGACTGCTCGCCGTCAAGATTGaaa                                             <  1:3299419/69‑1 (MQ=255)
                         cGTCCGCCAGAATCTGCAACTTGTGATTGCGCACGTCAGACTGCTCGCCGTCAAGATTGAGATAGACGt                                      <  1:1932974/69‑1 (MQ=255)
                         cGTCCGCCAGAATCTGCAACTTGTGATTGCGCACGTCAGACTGCTCGCCGTCAAGATTGAAATAGACGt                                      <  1:1289573/69‑1 (MQ=255)
                         cGTCCGCCAGAATCTGCAACTTGTGATTGCGCACGTCAGACTGCTCGCCGTCAAGATTGAAATAGACGt                                      <  1:3193261/69‑1 (MQ=255)
                         cGTCCGCCAGAATCTGCAACTTGTGATTGCGCACGTCAGACTGCTCGCCGTCAAGATTGAAATAGACGt                                      <  1:2334872/69‑1 (MQ=255)
                         cGTCCGCCAGAATCTGCAACTTGTGATTGCGCACGTCAGACTGCTCGCCGTCAAGATTGAAATAGACGt                                      <  1:2853155/69‑1 (MQ=255)
                         cGTCCGCCAGAATCTGCAACTTGTGATTGCGCACGTCAGACTGCTCGCCGTCAAGATTGAAATAGACGt                                      <  1:1930092/69‑1 (MQ=255)
                         cGTCCGCCAGAATCTGCAACTTGTGATTGCGCACGTCAGACTGCTCGCCGTCAAGATTGAAATAGACGt                                      <  1:2022925/69‑1 (MQ=255)
                         cGTCCGCCAGAATCTGCAACTTGTGATTGCGCACGTCAGACTGCTCGCCGTCAAGATTGAAATAGACGt                                      <  1:2242216/69‑1 (MQ=255)
                         cGTCCACCAGAATCTGCAACTTGTGATTGCGCACGTCAGACTGCTCGCCGTCAAGATTGAAATAGACGt                                      <  1:2382666/69‑1 (MQ=255)
                          gTCCGCCAGAATCTGCAACTTGTGATTGCGCACGTCAGACTGCTCGCCGTCAAGATTGAAATAGACGt                                      <  1:2440377/68‑1 (MQ=255)
                          gTCCGCCAGAATCTGCAACTTGTGATTGCGCACGTCAGACTGCTCGCCGTCAAGATTGAAATAGACGt                                      <  1:1777978/68‑1 (MQ=255)
                           tCCGCCAGAATCTGCAACTTGTGATTGCGCACGTCAGACTGCTCGCCGTCAAGATTGAAATAGACGt                                      <  1:2251004/67‑1 (MQ=255)
                               ccAGAATCTGCAACTTGTGATTGCGCACGTCAGATTGCTCGCCGTCAAGATTGAAATAGACGTGATTa                                 <  1:1124086/68‑1 (MQ=255)
                               ccAGAATCTGCAACTTGTGATTGCGCACGTCAGATTGCTCGCCGTCAAGATTGAAATAGACGTGATTa                                 <  1:1143287/68‑1 (MQ=255)
                               ccAGAATCTGCAACTTGTGATTGCGCACGTCAGATTGCTCGCCGTCAAGATTGAAATAGACGTGATTa                                 <  1:2669866/68‑1 (MQ=255)
                               ccAGAATCTGCAACTTGTGATTGCGCACGTCAGATTGCTCGCCGTCAAGATTGAAATAGACGTGATTa                                 <  1:1364207/68‑1 (MQ=255)
                               ccAGAATCTGCAACTTGTGATTGCGCACGTCAGATTGCTCGCCGTCAAGATTGAAATAGACGTGATTa                                 <  1:2478679/68‑1 (MQ=255)
                               ccAGAATCTGCAACTTGTGATTGCGCACGTCAGATTGCTCGCCGTCAAGATTGAAATAGACGTGATTa                                 <  1:702671/68‑1 (MQ=255)
                               ccAGAATCTGCAACTTGTGATTGCGCACGTCAGATTGCTCGCCGTCAAGATTGAAATAGACGTGATTa                                 <  1:26888/68‑1 (MQ=255)
                               ccAGAATCTGCAACTTGTGATTGCGCACGTCAGATTGCTCGCCGTCAAGATTGAAATAGACGTGATTa                                 <  1:511906/68‑1 (MQ=255)
                               ccAGAATCTGCAACTTGTGATTGCGCACGTCAGATTGCTCGCCGTCAAGATTGAAATAGACGTGATTa                                 <  1:2077588/68‑1 (MQ=255)
                               ccAGAATCTGCAACTTGTGATTGCGCACGTCAGATTGCTCGCCGTCAAGATTGAAATAGACGTGATTa                                 <  1:1704368/68‑1 (MQ=255)
                               ccAGAATCTGCAACTTGTGATTGCGCACGTCAGATTGCTCGCCGTCAAGATTGAAATAGACGTGATTa                                 <  1:2992355/68‑1 (MQ=255)
                               ccAGAATCTGCAACTTGTGATTGCGCACGTCAGATTGCTCGCCGTCAAGATTGAAATAGACGTGATTa                                 <  1:2996038/68‑1 (MQ=255)
                               ccAGAATCTGCAACTTGTGATTGCGCACGTCAGATTGCTCGCCGTCAAGATTGAAATAGACGTGATTa                                 <  1:3149438/68‑1 (MQ=255)
                               ccAGAATCTGCAACTTGTGATTGCGCACGTCAGATTGCTCGCCGTCAAGATTGAAATAGACGTGATTa                                 <  1:1656320/68‑1 (MQ=255)
                                    aTCTGCAACTTGTGATTGCGCACGTCAGACTGCTCGCCGTCAAGATTGAAATAGACGTGATTAGTCata                           <  1:2605844/69‑1 (MQ=255)
                                       tGCAACTTGTGATTGCGCACGTCAGACTGCTCGCCGTCAAGATTGaaa                                             <  1:106848/48‑1 (MQ=255)
                                       tGCAACTTGTGATTGCGCACGTCAGACTGCTCGCCGTCAAGATTGaaa                                             <  1:3045516/48‑1 (MQ=255)
                                       tGCAACTTGTGATTGCGCACGTCAGACTGCTCGCCGTCAAGATTGaaa                                             <  1:1790626/48‑1 (MQ=255)
                                       tGCAACTTGTGATTGCGCACGTCAGACTGCTCGCCGTCAAGATTGaaa                                             <  1:1379994/48‑1 (MQ=255)
                                       tGCAACTTGTGATTGCGCACGTCAGACTGCTCGCCGTCAAGATTGaaa                                             <  1:1809699/48‑1 (MQ=255)
                                       tGCAACTTGTGATTGCGCACGTCAGACTGCTCGCCGTCAAGATTGaaa                                             <  1:1288766/48‑1 (MQ=255)
                                       tGCAACTTGTGATTGCGCACGTCAGACTGCTCGCCGTCAAGATTGaaa                                             <  1:2742959/48‑1 (MQ=255)
                                       tGCAACTTGTGATTGCGCACGTCAGACTGCTCGCCGTCAAGATTGaaa                                             <  1:3125205/48‑1 (MQ=255)
                                       tGCAACTTGTGATTGCGCACGTCAGACTGCTCGCCGTCAAGATTGaaa                                             <  1:742872/48‑1 (MQ=255)
                                       tGCAACTTGTGATTGCGCACGTCAGACTGCTCGCCGTCAAGATTGaaa                                             <  1:2148507/48‑1 (MQ=255)
                                       tGCAACTTGTGATTGCGCACGTCAGACTGCTCGCCGTCAAGATTGaaa                                             <  1:2635124/48‑1 (MQ=255)
                                                     gcgcACGTCAGACTGCTCGCCGTCAAGATTGAAATAGACGTGATTAGTCATATTCACCGGGCAAGGttt          >  1:2075839/1‑69 (MQ=255)
                                                     gcgcACGTCAGACTGCTCGCCGTCAAGATTGAAATAGACGTGATTAGTCATATTCACCGGGCAAGGttt          >  1:3068090/1‑69 (MQ=255)
                                                     gcgcACGTCAGACTGCTCGCCGTCAAGATTGAAATAGACGTGATTAGTCATATTCACCGGGCAAGGtt           >  1:3391826/1‑68 (MQ=255)
                                                            tCAGATTGCTCGCCGTCAAGATTGAAATAGACGTGATTAGTCatat                          >  1:927721/1‑46 (MQ=255)
                                                            tCAGATTGCTCGCCGTCAAGATTGAAATAGACGTGATTAGTCATATTCACCGGGCAAGGTTTATCAACt   >  1:1473047/1‑69 (MQ=255)
                                                            tCAGATTGCTCGCCGTCAAGATTGAAATAGACGTGATTAGTCATATTCACCGGGCAAGGTTTATCAACt   >  1:3241553/1‑69 (MQ=255)
                                                            tCAGATTGCTCGCCGTCAAGATTGAAATAGACGTGATTAGTCATATTCACCGGGCAAGGTTTATCAACt   >  1:1414131/1‑69 (MQ=255)
                                                            tCAGATTGCTCGCCGTCAAGATTGAAATAGACGTGATTAGTCATATTCACCGGGCAAGGTTTATCAACt   >  1:3349366/1‑69 (MQ=255)
                                                            tCAGATTGCTCGCCGTCAAGATTGAAATAGACGTGATTAGTCATATTCACCGGGCAAGGTTTATCAACt   >  1:3081878/1‑69 (MQ=255)
                                                            tCAGATTGCTCGCCGTCAAGATTGAAATAGACGTGATTAGTCATATTCACCGGGCAAGGTTTATCAACt   >  1:1580385/1‑69 (MQ=255)
                                                            tCAGATTGCTCGCCGTCAAGATTGAAATAGACGTGATTAGTCATATTCACCGGGCAAGGTTTATCAACt   >  1:41995/1‑69 (MQ=255)
                                                            tCAGATTGCTCGCCGTCAAGATTGAAATAGACGTGATTAGTCATATTCACCGGGCAAGGTTTATCAACt   >  1:469885/1‑69 (MQ=255)
                                                            tCAGATTGCTCGCCGTCAAGATTGAAATAGACGTGATTAGTCATATTCACCGGGCAAGGTTTATCAACt   >  1:1313226/1‑69 (MQ=255)
                                                            tCAGATTGCTCGCCGTCAAGATTGAAATAGACGTGATTAGTCATATTCACCGGGCAAGGTTTATCAACt   >  1:691949/1‑69 (MQ=255)
                                                            tCAGATTGCTCGCCGTCAAGATTGAAATAGACGTGATTAGTCATATTCACCGGGCAAGGTTTATCAACt   >  1:1260484/1‑69 (MQ=255)
                                                            tCAGATTGCTCGCCGTCAAGATTGAAATAGACGTGATTAGTCATATTCACCGGGCAAGGTTTATCAACt   >  1:787759/1‑69 (MQ=255)
                                                            tCAGATTGCTCGCCGTCAAGATTGAAATAGACGTGATTAGTCATATTCACCGGGCAAGGTTTATCAACt   >  1:863907/1‑69 (MQ=255)
                                                            tCAGATTGCTCGCCGTCAAGATTGAAATAGACGTGATTAGTCATATTCACCGGGCAAGGTTTATCAACt   >  1:1018421/1‑69 (MQ=255)
                                                            tCAGATTGCTCGCCGTCAAGATTGAAATAGACGTGATTAGTCATATTCACCGGGCAAGGTTTATCAACt   >  1:3066858/1‑69 (MQ=255)
                                                            tCAGATTGCTCGCCGTCAAGATTGAAATAGACGTGATTAGTCATATTCACCGGGCAAGGTTTATCAACt   >  1:2178916/1‑69 (MQ=255)
                                                            tCAGATTGCTCGCCGTCAAGATTGAAATAGACGTGATTAGTCATATTCACCGGGCAAGGTTTATCAACt   >  1:2999840/1‑69 (MQ=255)
                                                            tCAGATTGCTCGCCGTCAAGATTGAAATAGACGTGATTAGTCATATTCACCGGGCAAGGTTTATCAACt   >  1:1894291/1‑69 (MQ=255)
                                                            tCAGATTGCTCGCCGTCAAGATTGAAATAGACGTGATTAGTCATATTCACCGGGCAAGGTTTATCAACt   >  1:1898256/1‑69 (MQ=255)
                                                            tCAGATTGCTCGCCGTCAAGATTGAAATAGACGTGATTAGTCATATTCACCGGGCAAGGTTTATCAACt   >  1:282428/1‑69 (MQ=255)
                                                            tCAGATTGCTCGCCGTCAAGATTGAAATAGACGTGATTAGTCATATTCACCGGGCAAGGTTTATCAACt   >  1:2804151/1‑69 (MQ=255)
                                                            tCAGATTGCTCGCCGTCAAGATTGAAATAGACGTGATTAGTCATATTCACCGGGCAAGGTTTAT‑AACtg  >  1:2681621/1‑69 (MQ=255)
                                                            tCAGATTGCTCGCCGTCAAGATTGAAATAGACGTGATTAGTCATATTCACCGGCCAAGGTATATc       >  1:2731991/1‑65 (MQ=255)
                                                             cAGATTGCTCTCCGTCAAGATTGAAATAGACGTGATTAGTCATATTCACCGGGCAAGGTTTATCAACtg  <  1:3149208/69‑1 (MQ=255)
                                                             cAGATTGCTCGCCGTCAAGATTGAAATAGACGTGATTAGTCATATTCACCGGGCAAGGTTTATCAACtg  <  1:2633167/69‑1 (MQ=255)
                                                             cAGATTGCTCGCCGTCAAGATTGAAATAGACGTGATTAGTCATATTCACCGGGCAAGGTTTATCAACtg  <  1:2640031/69‑1 (MQ=255)
                                                             cAGATTGCTCGCCGTCAAGATTGAAATAGACGTGATTAGTCATATTCACCGGGCAAGGTTTATCAACtg  <  1:2110525/69‑1 (MQ=255)
                                                             cAGATTGCTCGCCGTCAAGATTGAAATAGACGTGATTAGTCATATTCACCGGGCAAGGTTTATCAACtg  <  1:1306446/69‑1 (MQ=255)
                                                             cAGATTGCTCGCCGTCAAGATTGAAATAGACGTGATTAGTCATATTCACCGGGCAAGGTTTATCAACtg  <  1:2871339/69‑1 (MQ=255)
                                                             cAGATTGCTCGCCGTCAAGATTGAAATAGACGTGATTAGTCATATTCACCGGGCAAGGTTTATCAACtg  <  1:1783688/69‑1 (MQ=255)
                                                             cAGATTGCTCGCCGTCAAGATTGAAATAGACGTGATTAGTCATATTCACCGGGCAAGGTTTATCAACtg  <  1:1739482/69‑1 (MQ=255)
                                                             cAGATTGCTCGCCGTCAAGATTGAAATAGACGTGATTAGTCATATTCACCGGGCAAGGTTTATCAACtg  <  1:323693/69‑1 (MQ=255)
                                                             cAGATTGCTCGCCGTCAAGATTGAAATAGACGTGATTAGTCATATTCACCGGGCAAGGTTTATCAACtg  <  1:1617768/69‑1 (MQ=255)
                                                                 |                                                                
CCGCCTTCATCAACCGGCAGATATTCGTCCGCCAGAATCTGCAACTTGTGATTGCGCACGTCAGACTGCTCGCCGTCAAGATTGAAATAGACGTGATTAGTCATATTCACCGGGCAAGGTTTATCAACTG  >  minE/494676‑494805

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