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 435,813 T→A 34.6% A97A (GCA→GCT)  ybfF ← conserved hypothetical protein

Read alignment evidence...
  seq id position ref new freq score (cons/poly) reads annotation genes product
*minE435,8130TA34.6% 70.3 / 64.7 84A97A (GCA→GCT) ybfFconserved hypothetical protein
Reads supporting (aligned to +/- strand):  ref base T (21/33);  new base A (9/20);  total (30/54)
Fisher's exact test for biased strand distribution p-value = 6.32e-01
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 8.80e-01

ATAGTCGACCGGCGCGATATCGATCGCCACCAGTTTATCGATGCGATCGGAGGCTAGTGCAGTAAGTGCCATTACCGCTTTACCGCCCATGGAGTGACCGATAAATGTTGCTTTGTCGATCTGCTGTGCATCCAG  >  minE/435747‑435881
                                                                  |                                                                    
aTAGTCGACCGGCGCGATATCGATCGCCACTAGTTTATCGATGCGATCGGAGGCTAGTGCAGTAAGTGc                                                                    <  1:363184/69‑1 (MQ=255)
aTAGTCGACCGGCGCGATATCGATCGCCACCAGTTTATCGATGCGATCGGAGGCTAGTGCAGTAAGTGc                                                                    <  1:1800670/69‑1 (MQ=255)
aTAGTCGACCGGCGCGATATCGATCGCCACCAGTTTATCGATGCGATCGGAGGCTAGTGCAGTAAGTGc                                                                    <  1:1798406/69‑1 (MQ=255)
aTAGTCGACCGGCGCGATATAGATCGCCACCAGTTTATCGATGCGATCGGAGGATAGTGCAGTAAGTGc                                                                    <  1:995257/69‑1 (MQ=255)
   gTCGACCGGCGCGATATCGATCGCCACCAGTTTATCGATGCGATCGGAGGCTAGTGCAGTAAGTGCCaa                                                                 >  1:1872537/1‑68 (MQ=255)
   gTCGACCGGCGCGATATCGATCGCCACCAGTTTATCGATGCGATCGGAGGCTAGTGCAGTAAGTGCCAt                                                                 >  1:1086598/1‑69 (MQ=255)
   gTCGACCGGCGCGATATCGATCGCCACCAGTTTATCGATGCGATCGGAGGCTAGTGCAGTAAGTGCCAt                                                                 >  1:2512218/1‑69 (MQ=255)
   gTCGACCGGCGCGATATCGATCGCCACCAGTTTATCGATGCGATCGGAGGCTAGTGCAGTAAGTGCCAt                                                                 >  1:1996639/1‑69 (MQ=255)
   gTCGACCGGCGCGATATCGATCGCCACCAGTTTATCGATGCGATCGGAGGCTAGTGCAGTAAGTGCCAt                                                                 >  1:1856927/1‑69 (MQ=255)
   gTCGACCGGCGCGATATCGATCGCCACCAGTTTATCGATGCGATCGGAGGCTAGTGCAGTAAGTGCCAt                                                                 >  1:1725172/1‑69 (MQ=255)
   gTCGACCGGCGCGATATCGATCGCCACCAGTTTATCGATGCGATCGGAGGCTAGTGCAGTAAGTGCCAt                                                                 >  1:586351/1‑69 (MQ=255)
                  atcgatcgCCACCAGTTTATCGATGCGATCGTAGGCTAGTGCAGTAAGTGCCATTACCGCtt                                                         <  1:3047010/62‑1 (MQ=255)
                  atcgatcgCCACCAGTTTATCGATGCGATCGGAGGCTAGTGCAGTAAGTGCCATTACCGCtt                                                         <  1:145890/62‑1 (MQ=255)
                  atcgatcgCCACCAGTTTATCGATGCGATCGGAGGCTAGTGCAGTAAGTGCCATTACCGCtt                                                         <  1:3179921/62‑1 (MQ=255)
                  atcgatcgCCACCAGTTTATCGATGCGATCGGAGGCTAGTGCAGTAAGTGCCATTACCGCtt                                                         <  1:3170360/62‑1 (MQ=255)
                  atcgatcgCCACCAGTTTATCGATGCGATCGGAGGCTAGTGCAGTAAGTGCCATTACCGCtt                                                         <  1:230274/62‑1 (MQ=255)
                  atcgatcgCCACCAGTTTATCGATGCGATCGGAGGCTAGTGCAGTAAGTGCCATTACCGCtt                                                         <  1:1229678/62‑1 (MQ=255)
                  atcgatcgCCACCAGTTTATCGATGCGATCGGAGGCTAGTGCAGTAAGTGCCATTACCGCtt                                                         <  1:1290876/62‑1 (MQ=255)
                  atcgatcgCCACCAGTTTATCGATGCGATCGGAGGCTAGTGCAGTAAGTGCCATTACCGCtt                                                         <  1:3059844/62‑1 (MQ=255)
                  atcgatcgCCACCAGTTTATCGATGCGATCGGAGGCTAGTGCAGTAAGTGCCATTACCGCtt                                                         <  1:518403/62‑1 (MQ=255)
                  atcgatcgCCACCAGTTTATCGATGCGATCGGAGGCTAGTGCAGTAAGTGCCATTACCGCtt                                                         <  1:993637/62‑1 (MQ=255)
                  atcgatcgCCACCAGTTTATCGATGCGATCGGAGGCTAGTGCAGTAAGTGCCATTACCGCtt                                                         <  1:974479/62‑1 (MQ=255)
                  atcgatcgCCACCAGTTTATCGATGCGATCGGAGGCTAGTGCAGTAAGTGCCATTACCGCtt                                                         <  1:1464574/62‑1 (MQ=255)
                  atcgatcgCCACCAGTTTATCGATGCGATCGGAGGCTAGTGCAGTAAGTGCCATTACCGCtt                                                         <  1:1657597/62‑1 (MQ=255)
                  atcgatcgCCACCAGTTTATCGATGCGATCGGAGGCTAGTGCAGTAAGTGCCATTACCGCtt                                                         <  1:636981/62‑1 (MQ=255)
                  atcgatcgCCACCAGTTTATCGATGCGATCGGAGGCTAGTGCAGTAAGTGCCATTACCGCtt                                                         <  1:2650061/62‑1 (MQ=255)
                  atcgatcgCCACCAGTTTATCGATGCGATCGGAGGCTAGTGCAGTAAGTGCCATTACCGCtt                                                         <  1:2646078/62‑1 (MQ=255)
                       tcgCCACCAGTTTATCGATGCGATCGGAGGCTAGTGCAGTAAGTGCCATTACCGCTTTACCGCCCATg                                              <  1:2492995/68‑1 (MQ=255)
                       tcgCCACCAGTTTATCGATGCGATCGGAGGCTAGTGCAGTAAGTGCCATTACCGCTTTACCGCCCATg                                              <  1:176115/68‑1 (MQ=255)
                       tcgCCACCAGTTTATCGATGCGATCGGAGGCTAGTGCAGTAAGTGCCATTACCGCTTTACCGCCCATg                                              <  1:2546086/68‑1 (MQ=255)
                       tcgCCACCAGTTTATCGATGCGATCGGAGGCTAGTGCAGTAAGTGCCATTACCGCTTTACCGCCCATg                                              <  1:1533256/68‑1 (MQ=255)
                        cgCCACCAGTTTATCGATGCGATCGGAGGCTAGTGCAGTAAGTGCCATTACCGCTTTACCGCCCATGGa                                            >  1:1527876/1‑69 (MQ=255)
                        cgCCACCAGTTTATCGATGCGATCGGAGGCTAGTGCAGTAAGTGCCATTACCGCTTTACCGCCCATGGa                                            >  1:3082243/1‑69 (MQ=255)
                        cgCCACCAGTTTATCGATGCGATCGGAGGCTAGTGCAGTAAGTGCCATTACCGCTTTACCGCCCATGGa                                            >  1:1291169/1‑69 (MQ=255)
                        cgCCACCAGTTTATCGATGCGATCGGAGGCTAGTGCAGTAAGTGCCATTACCGCTTTACCGCCCATGGa                                            >  1:569878/1‑69 (MQ=255)
                           caccaGTTTATCGATGCGATCGGAGGCTAGTGCAGTAAGTGCCATTACCGCTTTACCGCCCATGGAGt                                          <  1:1129022/68‑1 (MQ=255)
                           caccaGTTTATCGATGCGATCGGAGGCTAGTGCAGTAAGTGCCATTACCGCTTTACCGCCCATGGAGt                                          <  1:3192979/68‑1 (MQ=255)
                           caccaGTTTATCGATGCGATCGGAGGCTAGTGCAGTAAGTGCCATTACCGCTTTACCGCCCATGGAGt                                          <  1:2415669/68‑1 (MQ=255)
                           caccaGTTTATCGATGCGATCGGAGGCTAGTGCAGTAAGTGCCATTACCGCTTTACCGCCCATGGAGt                                          <  1:2478513/68‑1 (MQ=255)
                           caccaGTTTATCGATGCGATCGGAGGCTAGTGCAGTAAGTGCCATTACCGCTTTACCGCCCATGGAGt                                          <  1:764051/68‑1 (MQ=255)
                                            gATCGGGGGCTAGTGCAGTAAGAGCCATTACCGCTTTACCACCCATGGAGTGACCGATAAATGTTGCtt                        >  1:337607/1‑69 (MQ=255)
                                            gATCGGGGGCTAGTGCAGTAAGAGCCATTACCGCTTTACCACCCATGGAGTGACCGATAAATGTTGCtt                        >  1:3397462/1‑69 (MQ=255)
                                            gATCGGGGGCTAGTGCAGTAAGAGCCATTACCGCTTTACCACCCATGGAGTGACCGATAAATGTTGCtt                        >  1:554452/1‑69 (MQ=255)
                                            gATCGGGGGCTAGTGCAGTAAGAGCCATTACCGCTTTACCACCCATGGAGTGACCGATAAATGTTGCtt                        >  1:3035435/1‑69 (MQ=255)
                                            gATCGGGGGCTAGTGCAGTAAGAGCCATTACCGCTTTACCACCCATGGAGTGACCGATAAATGTTGCtt                        >  1:1095962/1‑69 (MQ=255)
                                            gATCGGGGGCTAGTGCAGTAAGAGCCATTACCGCTTTACCACCCATGGAGTGACCGATAAATGTTGCtt                        >  1:2839000/1‑69 (MQ=255)
                                            gATCGGGGGCTAGTGCAGTAAGAGCCATTACCGCTTTACCACCCATGGAGTGACCGATAAATGTTGCtt                        >  1:84979/1‑69 (MQ=255)
                                            gATCGGGGGCTAGTGCAGTAAGAGCCATTACCGCTTTACCACCCATGGAGTGACCGATAAATGTTGCtt                        >  1:2490602/1‑69 (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            <  1:1615621/67‑1 (MQ=255)
                                                          gCAGTAAGAGCCATTACCGCTTTACCACCCATGGAGTGACCGATAAATGTTGCTTTGTCGATctgct            <  1:1650056/67‑1 (MQ=255)
                                                          gCAGTAAGAGCCATTACCGCTTTACCACCCATGGAGTGACCGATAAATGTTGCTTTGTCGATctgct            <  1:1504144/67‑1 (MQ=255)
                                                          gCAGTAAGAGCCATTACCGCTTTACCACCCATGGAGTGACCGATAAATGTTGCTTTGTCGATctgct            <  1:1778244/67‑1 (MQ=255)
                                                          gCAGTAAGAGCCATTACCGCTTTACCACCCATGGAGTGACCGATAAATGTTGCTTTGTCGATctgct            <  1:401358/67‑1 (MQ=255)
                                                          gCAGTAAGAGCCATTACCGCTTTACCACCCATGGAGTGACCGATAAATGTTGCTTTGTCGATctgct            <  1:1818648/67‑1 (MQ=255)
                                                          gCAGTAAGAGCCATTACCGCTTTACCACCCATGGAGTGACCGATAAATGTTGCTTTGTCGATctgct            <  1:1856706/67‑1 (MQ=255)
                                                          gCAGTAAGAGCCATTACCGCTTTACCACCCATGGAGTGACCGATAAATGTTGCTTTGTCGATctgct            <  1:1954641/67‑1 (MQ=255)
                                                          gCAGTAAGAGCCATTACCGCTTTACCACCCATGGAGTGACCGATAAATGTTGCTTTGTCGATctgct            <  1:929972/67‑1 (MQ=255)
                                                          gCAGTAAGAGCCATTACCGCTTTACCACCCATGGAGTGACCGATAAATGTTGCTTTGTCGATctgct            <  1:1458924/67‑1 (MQ=255)
                                                          gCAGTAAGAGCCATTACCGCTTTACCACCCATGGAGTGACCGATAAATGTTGCTTTGTCGATctgct            <  1:3211878/67‑1 (MQ=255)
                                                          gCAGTAAGAGCCATTACCGCTTTACCACCCATGGAGTGACCGATAAATGTTGCTTTGTCGATctgct            <  1:2064077/67‑1 (MQ=255)
                                                          gCAGTAAGAGCCATTACCGCTTTACCACCCATGGAGTGACCGATAAATGTTGCTTTGTCGATctgct            <  1:2628789/67‑1 (MQ=255)
                                                          gCAGTAAGAGCCATTACCGCTTTACCACCCATGGAGTGACCGATAAATGTTGCTTTGTCGATctgct            <  1:227337/67‑1 (MQ=255)
                                                          gCAGTAAGAGCCATTACCGCTTTACCACCCATGGAGTGACCGATAAATGTTGCTTTGTCGATctgct            <  1:2574658/67‑1 (MQ=255)
                                                          gCAGTAAGAGCCATTACCGCTTTACCACCCATGGAGTGACCGATAAATGTTGCTTTGTCGATctgct            <  1:2365041/67‑1 (MQ=255)
                                                          gCAGTAAGAGCCATTACCGCTTTACCACCCATGGAGTGACCGATAAATGTTGCTTTGTCGATctgct            <  1:2494385/67‑1 (MQ=255)
                                                          gCAGTAAGAGCCATTACCGCTTTACCACCCATGGAGTGACCGATAAATGTTGCTTTGTCGATctgct            <  1:2571506/67‑1 (MQ=255)
                                                          gCAGTAAGAGCCATTACCGCTTTACCACCCATGGAGTGACCGATAAATGTTGCTTTGTCGATctgct            <  1:2681687/67‑1 (MQ=255)
                                                          gCAGTAAGAGCCATTACCGCTTTACCACCCATGGAGTGACCGATAAATGTTGCTTTGTCGATctgct            <  1:278070/67‑1 (MQ=255)
                                                             gTAAGTGCCATTACCGCTTTACCGCCCATGGAGTGACCGATAAATGTTGCTTTGTCGATCTGCTGTGCa       <  1:129370/69‑1 (MQ=255)
                                                             gTAAGTGCCATTACCGCTTTACCGCCCATGGAGTGACCGATAAATGTTGCTTTGTCGATCTGCTGTGCa       <  1:216644/69‑1 (MQ=255)
                                                             gTAAGTGCCATTACCGCTTTACCGCCCATGGAGTGACCGATAAATGTTGCTTTGTCGATCTGCTGTGCa       <  1:1813870/69‑1 (MQ=255)
                                                             gTAAGTGCCATTACCGCTTTACCGCCCATGGAGTGACCGATAAATGTTGCTTTGTCGATCTGCTGTGCa       <  1:3014084/69‑1 (MQ=255)
                                                              tAAGTGCCATTACCGCTTTACCGCCCATGGAGTGACCGATAAATGTTGCTTTGTCGATCTGCTGTGCa       >  1:2541980/1‑68 (MQ=255)
                                                              tAAGTGCCATTACCGCTTTACCGCCCATGGAGTGACCGATAAATGTTGCTTTGTCGATCTGCTGTGCa       >  1:2827800/1‑68 (MQ=255)
                                                              tAAGTGCCATTACCGCTTTACCGCCCATGGAGTGACCGATAAATGTTGCTTTGTCGATCTGCTGTGCa       >  1:3069620/1‑68 (MQ=255)
                                                              tAAGTGCCATTACCGCTTTACCGCCCATGGAGTGACCGATAAATGTTGCTTTGTCGATCTGCTGTGCa       >  1:136106/1‑68 (MQ=255)
                                                                aGTGCCATTACCGCTTTACCGCCCATGGAGTGACCGATa                                  >  1:2802751/1‑39 (MQ=255)
                                                                aGTGCCATTACCGCTTTACCGCCCATGGAGTGACCGATa                                  >  1:930986/1‑39 (MQ=255)
                                                                aGTGCCATTACCGCTTTACCGCCCATGGAGTGACCGATAAATGTTGCTTTGTCGATCTGCTGTGCa       >  1:290931/1‑66 (MQ=255)
                                                                aGTGCCATTACCGCTTTACCGCCCATGGAGTGACCGATAAATGTTGCTTTGTCGATCTGCTGTGCa       >  1:295301/1‑66 (MQ=255)
                                                                  tGCCATTACCGCTTTACCGCCCATGGAGTGACCGATAAATGTTGCTTTGTCGATCTGCTGTGCATCCag  <  1:1691128/69‑1 (MQ=255)
                                                                  tGCCATTACCGCTTTACCGCCCATGGAGTGACCGATAAATGTTGCTTTGTCGATCTGCTGTGCATCCag  <  1:1972089/69‑1 (MQ=255)
                                                                  |                                                                    
ATAGTCGACCGGCGCGATATCGATCGCCACCAGTTTATCGATGCGATCGGAGGCTAGTGCAGTAAGTGCCATTACCGCTTTACCGCCCATGGAGTGACCGATAAATGTTGCTTTGTCGATCTGCTGTGCATCCAG  >  minE/435747‑435881

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