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 1,215,319 A→G 41.1% L376L (TTA→TTG)  yebQ → predicted transporter

Read alignment evidence...
  seq id position ref new freq score (cons/poly) reads annotation genes product
*minE1,215,3190AG41.1% 32.5 / 64.8 90L376L (TTA→TTG) yebQpredicted transporter
Reads supporting (aligned to +/- strand):  ref base A (27/26);  new base G (34/3);  total (61/29)
Fisher's exact test for biased strand distribution p-value = 2.97e-05
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 1.00e+00

GCCCGCGTCACCTGCGGATATCAATATTATCTGGCCGATGATCTTATGTGGTGCTGGATTTGGCTTATTCCAGTCACCCAATAACCACACCATTATTACCTCCGCGCCTCGCGAACGTAGCGGTGGAGCCAGT  >  minE/1215253‑1215385
                                                                  |                                                                  
gcCCGCGTCACCTGCGGATATCAATATTATCTGGCCGATGATCTTATGTGGTGCTGGATTTGGCTTAt                                                                   >  1:2246921/1‑68 (MQ=255)
   cgcgTCACCTGCGGATATCAATATTATCTGGCCGATGATCTTATGTGGTGCTGGATTTGGCTTATTcc                                                                <  1:1118311/68‑1 (MQ=255)
   cgcgTCACCTGCGGATATCAATATTATCTGGCCGATGATCTTATGTGGTGCTGGATTTGGCTTATTcc                                                                <  1:1981489/68‑1 (MQ=255)
   cccgTCACCTGCGGATATCAATATTATCTGGCCGATGATCTTATGTGGTGCTGGATTTGGCTTATTcc                                                                <  1:631919/66‑1 (MQ=255)
        cACCTGCGGATATCAATATTATCTGGCCGATGATCTTATGTGGTGCTGGATTTGGCTTATTCCAGTCAc                                                          <  1:1591183/69‑1 (MQ=255)
           cttcGGATATCAATATTATCTGGCCGATGATCTTATGTGGTGCTGGATTTGGCTTGTTCCAGTCAccc                                                        >  1:2373173/4‑68 (MQ=255)
           cTGCGGATATCAATATTATCTGGCCGATGATCTTATGTGGTGCTGGATTTGGCTTGTTCCAGTCAccc                                                        >  1:365855/1‑68 (MQ=255)
           cTGCGGATATCAATATTATCTGGCCGATGATCTTATGTGGTGCTGGATTTGGCTTGTTCCAGTCAccc                                                        >  1:2173466/1‑68 (MQ=255)
           cTGCGGATATCAATATTATCTGGCCGATGATCTTATGTGGTGCTGGATTTGGCTTGTTCCAGTCAccc                                                        >  1:2121027/1‑68 (MQ=255)
           cTGCGGATATCAATATTATCTGGCCGATGATCTTATGTGGTGCTGGATTTGGCTTGTTCCAGTCAccc                                                        >  1:2119689/1‑68 (MQ=255)
           cTGCGGATATCAATATTATCTGGCCGATGATCTTATGTGGTGCTGGATTTGGCTTGTTCCAGTCAccc                                                        >  1:2563230/1‑68 (MQ=255)
           cTGCGGATATCAATATTATCTGGCCGATGATCTTATGTGGTGCTGGATTTGGCTTGTTCCAGTCAccc                                                        >  1:2861415/1‑68 (MQ=255)
           cTGCGGATATCAATATTATCTGGCCGATGATCTTATGTGGTGCTGGATTTGGCTTGTTCCAGTCAccc                                                        >  1:3383590/1‑68 (MQ=255)
           cTGCGGATATCAATATTATCTGGCCGATGATCTTATGTGGTGCTGGATTTGGCTTGTTCCAGTCAccc                                                        >  1:3391348/1‑68 (MQ=255)
           cTGCGGATATCAATATTATCTGGCCGATGATCTTATGTGGTGCTGGATTTGGCTTGTTCCAGTCAccc                                                        >  1:394909/1‑68 (MQ=255)
           cTGCGGATATCAATATTATCTGGCCGATGATCTTATGTGGTGCTGGATTTGGCTTGTTCCAGTCAccc                                                        >  1:1649172/1‑68 (MQ=255)
           cTGCGGATATCAATATTATCTGGCCGATGATCTTATGTGGTGCTGGATTTGGCTTGTTCCAGTCAccc                                                        >  1:600976/1‑68 (MQ=255)
           cTGCGGATATCAATATTATCTGGCCGATGATCTTATGTGGTGCTGGATTTGGCTTGTTCCAGTCAccc                                                        >  1:638187/1‑68 (MQ=255)
           cTGCGGATATCAATATTATCTGGCCGATGATCTTATGTGGTGCTGGATTTGGCTTGTTCCAGTCAccc                                                        >  1:664408/1‑68 (MQ=255)
           cTGCGGATATCAATATTATCTGGCCGATGATCTTATGTGGTGCTGGATTTGGCTTGTTCCAGTCAccc                                                        >  1:664573/1‑68 (MQ=255)
           cTGCGGATATCAATATTATCTGGCCGATGATCTTATGTGGTGCTGGATTTGGCTTGTTCCAGTCAccc                                                        >  1:677625/1‑68 (MQ=255)
           cTGCGGATATCAATATTATCTGGCCGATGATCTTATGTGGTGCTGGATTTGGCTTGTTCCAGTCAccc                                                        >  1:68923/1‑68 (MQ=255)
           cTGCGGATATCAATATTATCTGGCCGATGATCTTATGTGGTGCTGGATTTGGCTTGTTCCAGTCAcc                                                         >  1:2651080/1‑67 (MQ=255)
           cTGCGGACATCAATATTATCTGGCCGATGATCTTATGTGGTGCTGGATTTGGCTTGTTCCAGTCAccc                                                        >  1:556774/1‑68 (MQ=255)
            tGCGGATATCAATATTATCTGGCCGATGATCTTATGTGGTGCTGGATTTGGCTTATTCCAGTCACCCa                                                       >  1:1097913/1‑68 (MQ=255)
            tGCGGATATCAATATTATCTGGCCGATGATCTTATGTGGTGCTGGATTTGGCTTATTCCAGTCACCCa                                                       >  1:523887/1‑68 (MQ=255)
            tGCGGATATCAATATTATCTGGCCGATGATCTTATGTGGTGCTGGATTTGGCTTATTCCAGTCACCCa                                                       >  1:3176341/1‑68 (MQ=255)
            tGCGGATATCAATATTATCTGGCCGATGATCTTATGTGGTGCTGGATTTGGCTTATTCCAGTCACCCa                                                       >  1:3087693/1‑68 (MQ=255)
            tGCGGATATCAATATTATCTGGCCGATGATCTTATGTGGTGCTGGATTTGGCTTATTCCAGTCACCCa                                                       >  1:2668395/1‑68 (MQ=255)
            tGCGGATATCAATATTATCTGGCCGATGATCTTATGTGGTGCTGGATTTGGCTTATTCCAGTCACCCa                                                       >  1:664922/1‑68 (MQ=255)
            tGCGGATATCAATATTATCTGGCCGATGATCTTATGTGGTGCTGGATTTGGCTTATTCCAGTCACCCa                                                       >  1:1455819/1‑68 (MQ=255)
            tGCGGATATCAATATTATCTGCCCGATGATCTTATGTGGTGCTGGATTTGGCTTATTCCAGTCACCCa                                                       >  1:2967993/1‑68 (MQ=255)
                gATATCAATATTATCTGGCCGATGATCTTATGTGGTGCTGGATTTGGCTTATTCCAGTCACCCAATAAc                                                  <  1:3135694/69‑1 (MQ=255)
                   atCAATATTATCTGGCCGATGATCTTATGTGGTGCTGGATTTGGCTTGTTCCAGTCACCCAATAACcac                                               <  1:3251486/69‑1 (MQ=255)
                    tCAATATTATCTGGCCGATGATCTTATGTGGTGCTGGATTTGGCTTGTTCCAGTCACCCAATAACcac                                               <  1:2254659/68‑1 (MQ=255)
                    tCAATATTATCTGGCCGATGATCTTATGTGGTGCTGGATTTGGCTTGTTCCAGTCACCCAATAACcac                                               <  1:3094253/68‑1 (MQ=255)
                         attatCTGGCCGATGATCTTATGTGGTGCTGGATTTGGCTTATTCCAGTCACCCAATAACCACACCatt                                         >  1:47970/1‑69 (MQ=255)
                          ttatCTGGCCGATGATCTTATGTGGTGCTGGATTTGGCTTATTCCAGTCACCCAATAACCACACCatt                                         >  1:2691704/1‑68 (MQ=255)
                           tatCTGGCCGATGATCTTATGTGGTGCTGGATTTGGCTTATTCCa                                                               <  1:1061736/45‑1 (MQ=255)
                           tatCTGGCCGATGATCTTATGTGGTGCTGGATTTGGCTTATTCCa                                                               <  1:2978938/45‑1 (MQ=255)
                            atCTGGCCGATGATCTTATGTGGTGCTGGATTTGGCTTAt                                                                   >  1:2327833/1‑40 (MQ=255)
                            atCTGGCCGATGATCTTATGTGGTGCTGGATTTGGCTTATTCCa                                                               >  1:504306/1‑44 (MQ=255)
                            atCTGGCCGATGATCTTATGTGGTGCTGGATTTGGCTTATTCCa                                                               >  1:2919873/1‑44 (MQ=255)
                            atCTGGCCGATGATCTTATGTGGTGCTGGATTTGGCTTATTCCa                                                               >  1:2187636/1‑44 (MQ=255)
                            atCTGGCCGATGATCTTATGTGGTGCTGGATTTGGCTTATTCCa                                                               >  1:1159270/1‑44 (MQ=255)
                            atCTGGCCGATGATCTTATGTGGTGCTGGATTTGGCTTATTCCa                                                               >  1:67084/1‑44 (MQ=255)
                            atCTGGCCGATGATCTTATGTGGTGCTGGATTTGGCTTATTCCa                                                               >  1:780172/1‑44 (MQ=255)
                            atCTGGCCGATGATCTTATGTGGTGCTGGATTTGGCTTATTCCa                                                               >  1:968601/1‑44 (MQ=255)
                            atCTGGCCGATGATCTTATGTGGTGCTGGATTTGGCTTATTCCa                                                               >  1:23465/1‑44 (MQ=255)
                            atCTGGCCGATGATCTTATGTGGTGCTGGATTTGGCTTATTCCa                                                               >  1:2803949/1‑44 (MQ=255)
                            atCTGGCCGATGATCTTATGTGGTGCTGGATTTGGCTTATTCCa                                                               >  1:224558/1‑44 (MQ=255)
                            atCTGGCCGATGATCTTATGTGGTGCTGGATTTGGCTTATTCCAGTCACCCAATAACCACACCattatt                                      <  1:590649/69‑1 (MQ=255)
                            atCTGGCCGATGATCTTATGTGGTGCTGGATTTGGCTTATTCCAGTCACCCAATAACCACACCattatt                                      <  1:2248974/69‑1 (MQ=255)
                            atCTGGCCGATGATCTTATGTGGTGCTGGATTTGGCTTATTCCAGTCACCCAATAACCACACCattatt                                      <  1:2578523/69‑1 (MQ=255)
                            atCTGGCCGATGATCTTATGTGGTGCTGGATTTGGCTTATTCCAGTCACCCAATAACCACACCattatt                                      <  1:1956304/69‑1 (MQ=255)
                            atCTGGCCGATGATCTTATGTGGTGCTGGATTTGGCTTATTCCAGTCACCCAATAACCACACCattatt                                      <  1:1560499/69‑1 (MQ=255)
                            atCTGGCCGATGATCTTATGTGGTGCTGGATTTGGCTTATTCCAGTCACCCAATAACCACACCattatt                                      <  1:1979122/69‑1 (MQ=255)
                            atCTGGCCGATGATCTTATGTGGTGCTGGATTTGGCTTATTCCAGTCACCCAATAACCACACCattatt                                      <  1:585049/69‑1 (MQ=255)
                            atCTGGCCGATGATCTTATCTGGTGCTGGATTTGGCTTATTCCa                                                               >  1:884107/1‑44 (MQ=255)
                                 gCCGATGATCTTATGTGGTGCTGGATTTGGCTTATTCCAGTCACCCAATAACCACACCATTATTAc                                    <  1:881323/66‑1 (MQ=255)
                                 gCCGATGATCTTATGTGGTGCTGGATTTGGCTTATTCCAGTCACCCAATAACCACACCATTATTAc                                    <  1:256829/66‑1 (MQ=255)
                                 gCCGATGATCTTATGTGGTGCTGGATTTGGCTTATTCCAGTCACCCAATAACCACACCATTATTAc                                    <  1:3303917/66‑1 (MQ=255)
                                 gCCGATGATCTTATGTGGTGCTGGATTTGGCTTATTCCAGTCACCCAATAACCACACCATTATTAc                                    <  1:3345222/66‑1 (MQ=255)
                                 gCCGATGATCTTATGTGGTGCTGGATTTGGCTTATTCCAGTCACCCAATAACCACACCATTATTAc                                    <  1:2404020/66‑1 (MQ=255)
                                 gCCGATGATCTTATGTGGTGCTGGATTTGGCTTATTCCAGTCACCCAATAACCACACCATTATTAc                                    <  1:635372/66‑1 (MQ=255)
                                          cTTATGTGGTGCTGGATTTGGCTTATTCCAGTCACCCAATAACCACACCATTATTACCTCCGCGCCTc                         >  1:53095/1‑68 (MQ=255)
                                          cTTATGTGGTGCTGGATTTGGCTTATTCCAGTCACCCAATAACCACACCATTATTACCTCCGCGCCTc                         >  1:1964400/1‑68 (MQ=255)
                                          cTTATGTGGTGCTGGATTTGGCTTATTCCAGTCACCCAATAACCACACCATTATTACCTCCGCGCCTc                         >  1:3421092/1‑68 (MQ=255)
                                          cTTATGTGGTGCTGGATTTGGCTTATTCCAGTCACCCAATAACCACACCATTATTACCTCCGCGCCTc                         >  1:2949846/1‑68 (MQ=255)
                                                    gCTGGATTTGGCTTATTCCAGTCACCCAATAACCACACCATTATTACCTCCGCGCCTCGCGAACGTAGc              <  1:1250226/69‑1 (MQ=255)
                                                     cTGGATTTGGCTTATTCCAGTCACCCAATAACCACACCattatt                                      <  1:2846700/44‑1 (MQ=255)
                                                          tttGGCTTGTTCCAGTCACCCAATAACCACACCATTATTACCTCCGCTCCTCGCGAACGTAGCGGTGGa        >  1:1298164/1‑69 (MQ=255)
                                                          tttGGCTTGTTCCAGTCACCCAATAACCACACCATTATTACCTCCGCTCCTCGCGAACGTAGCGGTGGa        >  1:2031183/1‑69 (MQ=255)
                                                          tttGGCTTGTTCCAGTCACCCAATAACCACACCATTATTACCTCCGCTCCTCGCGAACGTAGCGGTGGa        >  1:1533994/1‑69 (MQ=255)
                                                          tttGGCTTGTTCCAGTCACCCAATAACCACACCATTATTACCTCCGCTCCTCGCGAACGTAGCGGTGGa        >  1:2038120/1‑69 (MQ=255)
                                                          tttGGCTTGTTCCAGTCACCCAATAACCACACCATTATTACCTCCGCTCCTCGCGAACGTAGCGGTGGa        >  1:2129724/1‑69 (MQ=255)
                                                          tttGGCTTGTTCCAGTCACCCAATAACCACACCATTATTACCTCCGCTCCTCGCGAACGTAGCGGTGGa        >  1:1627314/1‑69 (MQ=255)
                                                          tttGGCTTGTTCCAGTCACCCAATAACCACACCATTATTACCTCCGCTCCTCGCGAACGTAGCGGTGGa        >  1:1773440/1‑69 (MQ=255)
                                                          tttGGCTTGTTCCAGTCACCCAATAACCACACCATTATTACCTCCGCTCCTCGCGAACGTAGCGGTGGa        >  1:2030300/1‑69 (MQ=255)
                                                          tttGGCTTGTTCCAGTCACCCAATAACCACACCATTATTACCTCCGCTCCTCGCGAACGTAGCGGTGGa        >  1:1774550/1‑69 (MQ=255)
                                                          tttGGCTTGTTCCAGTCACCCAATAACCACACCATTATTACCTCCGCTCCTCGCGAACGTAGCGGTGGa        >  1:374390/1‑69 (MQ=255)
                                                          tttGGCTTGTTCCAGTCACCCAATAACCACACCATTATTACCTCCGCTCCTCGCGAACGTAGCGGTGGa        >  1:1778417/1‑69 (MQ=255)
                                                          tttGGCTTGTTCCAGTCACCCAATAACCACACCATTATTACCTCCGCTCCTCGCGAACGTAGCGGTGGa        >  1:1838230/1‑69 (MQ=255)
                                                          tttGGCTTGTTCCAGTCACCCAATAACCACACCATTATTACCTCCGCTCCTCGCGAACGTAGCGGTGGa        >  1:2017167/1‑69 (MQ=255)
                                                          tttGGCTTGTTCCAGTCACCCAATAACCACACCATTATTACCTCCGCTCCTCGCGAACGTAGCGGTGGa        >  1:3046221/1‑69 (MQ=255)
                                                          tttGGCTTGTTCCAGTCACCCAATAACCACACCATTATTACCTCCGCTCCTCGCGAACGTAGCGGTGGa        >  1:2654343/1‑69 (MQ=255)
                                                              gCTTATTCCAGTCACCCAATAACCACACCATTATTACCTCCGCGCCTCGCGAACGTAGCGGTGGAGcc     <  1:3362915/68‑1 (MQ=255)
                                                                ttATTCCAGTCACCCAATAACCACACCATTATTACCTCCGCGCCTCGCGAACGTAGCGGTGGAGCCAGt  <  1:1150758/69‑1 (MQ=255)
                                                                ttATTCCAGTCACCCAATAACCACACCATTATTACCTCCGCGCCTCGCGAACGTAGCGGTGGAGCCAGt  <  1:1907852/69‑1 (MQ=255)
                                                                 tATTCCAGTCACCCAATAACCACACCATTATTACCTCCGCGCCTCGCGAACGTAGCGGTGGAGCCAGt  <  1:1864006/68‑1 (MQ=255)
                                                                  |                                                                  
GCCCGCGTCACCTGCGGATATCAATATTATCTGGCCGATGATCTTATGTGGTGCTGGATTTGGCTTATTCCAGTCACCCAATAACCACACCATTATTACCTCCGCGCCTCGCGAACGTAGCGGTGGAGCCAGT  >  minE/1215253‑1215385

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