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 435,831 G→A 38.3% G91G (GGC→GGT)  ybfF ← conserved hypothetical protein

Read alignment evidence...
  seq id position ref new freq score (cons/poly) reads annotation genes product
*minE435,8310GA38.3% 42.6 / 49.5 79G91G (GGC→GGT) ybfFconserved hypothetical protein
Reads supporting (aligned to +/- strand):  ref base G (23/25);  new base A (9/21);  total (32/47)
Fisher's exact test for biased strand distribution p-value = 1.57e-01
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 9.77e-01

TCGCCACCAGTTTATCGATGCGATCGGAGGCTAGTGCAGTAAGTGCCATTACCGCTTTACCGCCCATGGAGTGACCGATAAATGTTGCTTTGTCGATCTGCTGTGCATCCAGAGTATC  >  minE/435770‑435887
                                                             |                                                        
tcgCCACCAGTTTATCGATGCGATCGGAGGCTAGTGCAGTAAGTGCCATTACCGCTTTACCGCCCATg                                                    <  1:176115/68‑1 (MQ=255)
tcgCCACCAGTTTATCGATGCGATCGGAGGCTAGTGCAGTAAGTGCCATTACCGCTTTACCGCCCATg                                                    <  1:1533256/68‑1 (MQ=255)
tcgCCACCAGTTTATCGATGCGATCGGAGGCTAGTGCAGTAAGTGCCATTACCGCTTTACCGCCCATg                                                    <  1:2546086/68‑1 (MQ=255)
tcgCCACCAGTTTATCGATGCGATCGGAGGCTAGTGCAGTAAGTGCCATTACCGCTTTACCGCCCATg                                                    <  1:2492995/68‑1 (MQ=255)
 cgCCACCAGTTTATCGATGCGATCGGAGGCTAGTGCAGTAAGTGCCATTACCGCTTTACCGCCCATGGa                                                  >  1:3082243/1‑69 (MQ=255)
 cgCCACCAGTTTATCGATGCGATCGGAGGCTAGTGCAGTAAGTGCCATTACCGCTTTACCGCCCATGGa                                                  >  1:569878/1‑69 (MQ=255)
 cgCCACCAGTTTATCGATGCGATCGGAGGCTAGTGCAGTAAGTGCCATTACCGCTTTACCGCCCATGGa                                                  >  1:1527876/1‑69 (MQ=255)
 cgCCACCAGTTTATCGATGCGATCGGAGGCTAGTGCAGTAAGTGCCATTACCGCTTTACCGCCCATGGa                                                  >  1:1291169/1‑69 (MQ=255)
    caccaGTTTATCGATGCGATCGGAGGCTAGTGCAGTAAGTGCCATTACCGCTTTACCGCCCATGGAGt                                                <  1:764051/68‑1 (MQ=255)
    caccaGTTTATCGATGCGATCGGAGGCTAGTGCAGTAAGTGCCATTACCGCTTTACCGCCCATGGAGt                                                <  1:2478513/68‑1 (MQ=255)
    caccaGTTTATCGATGCGATCGGAGGCTAGTGCAGTAAGTGCCATTACCGCTTTACCGCCCATGGAGt                                                <  1:2415669/68‑1 (MQ=255)
    caccaGTTTATCGATGCGATCGGAGGCTAGTGCAGTAAGTGCCATTACCGCTTTACCGCCCATGGAGt                                                <  1:3192979/68‑1 (MQ=255)
    caccaGTTTATCGATGCGATCGGAGGCTAGTGCAGTAAGTGCCATTACCGCTTTACCGCCCATGGAGt                                                <  1:1129022/68‑1 (MQ=255)
                     gATCGGGGGCTAGTGCAGTAAGAGCCATTACCGCTTTACCACCCATGGAGTGACCGATAAATGTTGCtt                              >  1:2490602/1‑69 (MQ=255)
                     gATCGGGGGCTAGTGCAGTAAGAGCCATTACCGCTTTACCACCCATGGAGTGACCGATAAATGTTGCtt                              >  1:1095962/1‑69 (MQ=255)
                     gATCGGGGGCTAGTGCAGTAAGAGCCATTACCGCTTTACCACCCATGGAGTGACCGATAAATGTTGCtt                              >  1:3035435/1‑69 (MQ=255)
                     gATCGGGGGCTAGTGCAGTAAGAGCCATTACCGCTTTACCACCCATGGAGTGACCGATAAATGTTGCtt                              >  1:337607/1‑69 (MQ=255)
                     gATCGGGGGCTAGTGCAGTAAGAGCCATTACCGCTTTACCACCCATGGAGTGACCGATAAATGTTGCtt                              >  1:3397462/1‑69 (MQ=255)
                     gATCGGGGGCTAGTGCAGTAAGAGCCATTACCGCTTTACCACCCATGGAGTGACCGATAAATGTTGCtt                              >  1:2839000/1‑69 (MQ=255)
                     gATCGGGGGCTAGTGCAGTAAGAGCCATTACCGCTTTACCACCCATGGAGTGACCGATAAATGTTGCtt                              >  1:554452/1‑69 (MQ=255)
                     gATCGGGGGCTAGTGCAGTAAGAGCCATTACCGCTTTACCACCCATGGAGTGACCGATAAATGTTGCtt                              >  1:84979/1‑69 (MQ=255)
                     gATCGGGGGCTAGTGCAGTAAGAGCCATTACCGCTTTACCACCCATGGAGTGACCGATAAATGTTGCtt                              >  1:1701250/1‑69 (MQ=255)
                            ggCTAGTGCAGTAAGTGCCATTACCGCTTTACCGCCCATGGAGTGACCGATAAATGTTGCTTTGTCGAt                       >  1:3285094/1‑69 (MQ=255)
                               tAGTGCAGTAAGTGCCATTACCGCTTTACCGCCCATGGAGTGACCGATAAATGTTGCTTTGTCGATctg                    >  1:2576846/1‑69 (MQ=255)
                                   gCAGTAAGCGCCATTACCGCTTTACCACCCATGGAGTGACCGATAAATGTTGCTTTGTCGATctgct                  <  1:3107478/67‑1 (MQ=255)
                                   gCAGTAAGAGCCATTACCGCTTTACCACCCATGGAGTGACCGATAAATGTTGCTTTGTCGATctgct                  <  1:2365041/67‑1 (MQ=255)
                                   gCAGTAAGAGCCATTACCGCTTTACCACCCATGGAGTGACCGATAAATGTTGCTTTGTCGATctgct                  <  1:2628789/67‑1 (MQ=255)
                                   gCAGTAAGAGCCATTACCGCTTTACCACCCATGGAGTGACCGATAAATGTTGCTTTGTCGATctgct                  <  1:2574658/67‑1 (MQ=255)
                                   gCAGTAAGAGCCATTACCGCTTTACCACCCATGGAGTGACCGATAAATGTTGCTTTGTCGATctgct                  <  1:2571506/67‑1 (MQ=255)
                                   gCAGTAAGAGCCATTACCGCTTTACCACCCATGGAGTGACCGATAAATGTTGCTTTGTCGATctgct                  <  1:929972/67‑1 (MQ=255)
                                   gCAGTAAGAGCCATTACCGCTTTACCACCCATGGAGTGACCGATAAATGTTGCTTTGTCGATctgct                  <  1:2494385/67‑1 (MQ=255)
                                   gCAGTAAGAGCCATTACCGCTTTACCACCCATGGAGTGACCGATAAATGTTGCTTTGTCGATctgct                  <  1:2681687/67‑1 (MQ=255)
                                   gCAGTAAGAGCCATTACCGCTTTACCACCCATGGAGTGACCGATAAATGTTGCTTTGTCGATctgct                  <  1:278070/67‑1 (MQ=255)
                                   gCAGTAAGAGCCATTACCGCTTTACCACCCATGGAGTGACCGATAAATGTTGCTTTGTCGATctgct                  <  1:1458924/67‑1 (MQ=255)
                                   gCAGTAAGAGCCATTACCGCTTTACCACCCATGGAGTGACCGATAAATGTTGCTTTGTCGATctgct                  <  1:1504144/67‑1 (MQ=255)
                                   gCAGTAAGAGCCATTACCGCTTTACCACCCATGGAGTGACCGATAAATGTTGCTTTGTCGATctgct                  <  1:1615621/67‑1 (MQ=255)
                                   gCAGTAAGAGCCATTACCGCTTTACCACCCATGGAGTGACCGATAAATGTTGCTTTGTCGATctgct                  <  1:227337/67‑1 (MQ=255)
                                   gCAGTAAGAGCCATTACCGCTTTACCACCCATGGAGTGACCGATAAATGTTGCTTTGTCGATctgct                  <  1:1650056/67‑1 (MQ=255)
                                   gCAGTAAGAGCCATTACCGCTTTACCACCCATGGAGTGACCGATAAATGTTGCTTTGTCGATctgct                  <  1:3211878/67‑1 (MQ=255)
                                   gCAGTAAGAGCCATTACCGCTTTACCACCCATGGAGTGACCGATAAATGTTGCTTTGTCGATctgct                  <  1:2064077/67‑1 (MQ=255)
                                   gCAGTAAGAGCCATTACCGCTTTACCACCCATGGAGTGACCGATAAATGTTGCTTTGTCGATctgct                  <  1:1954641/67‑1 (MQ=255)
                                   gCAGTAAGAGCCATTACCGCTTTACCACCCATGGAGTGACCGATAAATGTTGCTTTGTCGATctgct                  <  1:1856706/67‑1 (MQ=255)
                                   gCAGTAAGAGCCATTACCGCTTTACCACCCATGGAGTGACCGATAAATGTTGCTTTGTCGATctgct                  <  1:401358/67‑1 (MQ=255)
                                   gCAGTAAGAGCCATTACCGCTTTACCACCCATGGAGTGACCGATAAATGTTGCTTTGTCGATctgct                  <  1:1818648/67‑1 (MQ=255)
                                   gCAGTAAGAGCCATTACCGCTTTACCACCCATGGAGTGACCGATAAATGTTGCTTTGTCGATctgct                  <  1:1778244/67‑1 (MQ=255)
                                      gTAAGTGCCATTACCGCTTTACCGCCCATGGAGTGACCGATAAATGTTGCTTTGTCGATCTGCTGTGCa             <  1:1813870/69‑1 (MQ=255)
                                      gTAAGTGCCATTACCGCTTTACCGCCCATGGAGTGACCGATAAATGTTGCTTTGTCGATCTGCTGTGCa             <  1:3014084/69‑1 (MQ=255)
                                      gTAAGTGCCATTACCGCTTTACCGCCCATGGAGTGACCGATAAATGTTGCTTTGTCGATCTGCTGTGCa             <  1:129370/69‑1 (MQ=255)
                                      gTAAGTGCCATTACCGCTTTACCGCCCATGGAGTGACCGATAAATGTTGCTTTGTCGATCTGCTGTGCa             <  1:216644/69‑1 (MQ=255)
                                       tAAGTGCCATTACCGCTTTACCGCCCATGGAGTGACCGATAAATGTTGCTTTGTCGATCTGCTGTGCa             >  1:3069620/1‑68 (MQ=255)
                                       tAAGTGCCATTACCGCTTTACCGCCCATGGAGTGACCGATAAATGTTGCTTTGTCGATCTGCTGTGCa             >  1:2541980/1‑68 (MQ=255)
                                       tAAGTGCCATTACCGCTTTACCGCCCATGGAGTGACCGATAAATGTTGCTTTGTCGATCTGCTGTGCa             >  1:136106/1‑68 (MQ=255)
                                       tAAGTGCCATTACCGCTTTACCGCCCATGGAGTGACCGATAAATGTTGCTTTGTCGATCTGCTGTGCa             >  1:2827800/1‑68 (MQ=255)
                                         aGTGCCATTACCGCTTTACCGCCCATGGAGTGACCGATa                                        >  1:930986/1‑39 (MQ=255)
                                         aGTGCCATTACCGCTTTACCGCCCATGGAGTGACCGATa                                        >  1:2802751/1‑39 (MQ=255)
                                         aGTGCCATTACCGCTTTACCGCCCATGGAGTGACCGATAAATGTTGCTTTGTCGATCTGCTGTGCa             >  1:295301/1‑66 (MQ=255)
                                         aGTGCCATTACCGCTTTACCGCCCATGGAGTGACCGATAAATGTTGCTTTGTCGATCTGCTGTGCa             >  1:290931/1‑66 (MQ=255)
                                           tGCCATTACCGCTTTACCGCCCATGGAGTGACCGATAAATGTTGCTTTGTCGATCTGCTGTGCATCCag        <  1:1691128/69‑1 (MQ=255)
                                           tGCCATTACCGCTTTACCGCCCATGGAGTGACCGATAAATGTTGCTTTGTCGATCTGCTGTGCATCCag        <  1:1972089/69‑1 (MQ=255)
                                                  aCCGCTTTACCTCCCATGGAGTGACCGATAAATGTTGCTTTGTCGa                        <  1:604283/46‑1 (MQ=255)
                                                  aCCGCTTTACCGCCCTTGGAGTGACCGATAAATGTTGCTTTGTCg                         <  1:2481534/45‑1 (MQ=255)
                                                  aCCGCTTTACCGCCCATGGAGTTACCGATAAATGTTGCTTTGTCGATCTGCTGTGCATCCAGAGTATc  >  1:1380991/1‑68 (MQ=255)
                                                  aCCGCTTTACCGCCCATGGAGTGACCGATAAATGTTGCTTTGTCg                         <  1:2186478/45‑1 (MQ=255)
                                                  aCCGCTTTACCGCCCATGGAGTGACCGATAAATGTTGCTTTGTCGa                        <  1:1121199/46‑1 (MQ=255)
                                                  aCCGCTTTACCGCCCATGGAGTGACCGATAAATGTTGCTTTGTCGa                        <  1:1224528/46‑1 (MQ=255)
                                                  aCCGCTTTACCGCCCATGGAGTGACCGATAAATGTTGCTTTGTCGa                        <  1:577962/46‑1 (MQ=255)
                                                  aCCGCTTTACCGCCCATGGAGTGACCGATAAATGTTGCTTTGTCGa                        <  1:521211/46‑1 (MQ=255)
                                                  aCCGCTTTACCGCCCATGGAGTGACCGATAAATGTTGCTTTGTCGa                        <  1:3258184/46‑1 (MQ=255)
                                                  aCCGCTTTACCGCCCATGGAGTGACCGATAAATGTTGCTTTGTCGa                        <  1:2137730/46‑1 (MQ=255)
                                                  aCCGCTTTACCGCCCATGGAGTGACCGATAAATGTTGCTTTGTCGa                        <  1:2446727/46‑1 (MQ=255)
                                                  aCCGCTTTACCGCCCATGGAGTGACCGATAAATGTTGCTTTGTCGa                        <  1:3057373/46‑1 (MQ=255)
                                                  aCCGCTTTACCGCCCATGGAGTGACCGATAAATGTTGCTTTGTCGATCTGCTGTGCATCCAGAGTATc  >  1:2112813/1‑68 (MQ=255)
                                                  aCCGCTTTACCGCCCATGGAGTGACCGATAAATGTTGCTTTGTCGATCTGCTGTGCATCCAGAGTATc  >  1:1889725/1‑68 (MQ=255)
                                                  aCCGCTTTACCGCCCATGGAGTGACCGATAAATGTTGCTTTGTCGATCTGCTGTGCATCCAGAGTATc  >  1:1849037/1‑68 (MQ=255)
                                                  aCCGCTTTACCGCCCATGGAGTGACCGATAAATGTTGCTTTGTCGATCTGCTGTGCATCCAGAGTATc  >  1:3195707/1‑68 (MQ=255)
                                                  aCCGCTTTACCGCCCATGGAGTGACCGATAAATGTTGCTTTGTCGATCTGCTGTGCATCCAGAGTATc  >  1:2619366/1‑68 (MQ=255)
                                                  aCCGCTTTACCGCCCATGGAGTGACCGATAAATGTTGCTTTGTCGATCTGCTGTGCATCCAGAGTATc  >  1:1241277/1‑68 (MQ=255)
                                                  aCCGCTTTACCGCCCATGGAGTGACCGATAAATGTTGCTTTGTCGATCTGCTGTGCATCCAGAGTATc  >  1:2645481/1‑68 (MQ=255)
                                                  aCCGCTTAACCGCCCATGGAGTGACCGATAAATGTTGCTTTGTCGATCTGCTGTGCATCCAGAGTATc  >  1:1732792/1‑68 (MQ=255)
                                                             |                                                        
TCGCCACCAGTTTATCGATGCGATCGGAGGCTAGTGCAGTAAGTGCCATTACCGCTTTACCGCCCATGGAGTGACCGATAAATGTTGCTTTGTCGATCTGCTGTGCATCCAGAGTATC  >  minE/435770‑435887

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