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 2,255,856 A→G 36.5% I394I (ATT→ATC)  rpoC ← RNA polymerase, beta prime subunit

Read alignment evidence...
  seq id position ref new freq score (cons/poly) reads annotation genes product
*minE2,255,8560AG36.5% 46.9 / 49.9 82I394I (ATT→ATC) rpoCRNA polymerase, beta prime subunit
Reads supporting (aligned to +/- strand):  ref base A (26/26);  new base G (23/7);  total (49/33)
Fisher's exact test for biased strand distribution p-value = 2.08e-02
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 9.30e-01

GATAACTTCGTCCAGGATATCCCAAACGACAGCTTCTTCGCGCTCAACCATTTTCTTCGCAGCTTTAATGGTGGTAGCAAGACCACGCAGTTCCAGCTTGCCGTAGATGAACGGTTTGAACAGC  >  minE/2255790‑2255913
                                                                  |                                                         
gATAACTTCGTCCAGGATATCCCAAACGACAGCTTCTTCGCGCTCAACCATTTTCTTCGCAGCTTTAAt                                                         >  1:1000078/1‑69 (MQ=255)
gATAACTTCGTCCAGGATATCCCAAACGACAGCTTCTTCGCGCTCAACCATTTTCTTCGCAGCTTTAAt                                                         >  1:2250412/1‑69 (MQ=255)
          tCCAGGATATCCCAAACGACAGCTTCTTCGCGCTCAACCATTTTCTTCGCAGCTTTAATGGTGGTAGc                                                <  1:199175/68‑1 (MQ=255)
          tCCAGGATATCCCAAACGACAGCTTCTTCGCGCTCAACCATTTTCTTCGCAGCTTTAATGGTGGTAGc                                                <  1:1291080/68‑1 (MQ=255)
           ccAGGATATCCCAAACGACAGCTTCTTCGCGCTCAACCATTTTCTTCGCAGCTTTAATGGTGGTAGc                                                <  1:1527188/67‑1 (MQ=255)
              ggATATCCCAAACGACAGCTTCTTCGCGCTCAACCATTTTCTTCGCAGCTTTAATGGTGGTAGCAAGAc                                           <  1:2419753/69‑1 (MQ=255)
               gATATCCCAAACGACAGCTTCTTCGCGCTCAACCATTTTCTTCGCAGCTTTGATGGTGGTAGCaga                                             >  1:168870/1‑64 (MQ=255)
               gATATCCCAAACGACAGCTTCTTCGCGCTCAACCATTTTCTTCGCAGCTTTGATGGTGGTAGCaa                                              >  1:2788377/1‑65 (MQ=255)
               gATATCCCAAACGACAGCTTCTTCGCGCTCAACCATTTTCTTCGCAGCTTTGATGGTGGTAGCAAg                                             >  1:1413260/1‑66 (MQ=255)
               gATATCCCAAACGACAGCTTCTTCGCGCTCAACCATTTTCTTCGCAGCTTTGATGGTGGTAGCAAGAcc                                          >  1:2789753/1‑69 (MQ=255)
               gATATCCCAAACGACAGCTTCTTCGCGCTCAACCATTTTCTTCGCAGCTTTGATGGTGGTAGCAAGAcc                                          >  1:3287340/1‑69 (MQ=255)
               gATATCCCAAACGACAGCTTCTTCGCGCTCAACCATTTTCTTCGCAGCTTTGATGGTGGTAGCAAGAcc                                          >  1:1006534/1‑69 (MQ=255)
               gATATCCCAAACGACAGCTTCTTCGCGCTCAACCATTTTCTTCGCAGCTTTGATGGTGGTAGCAAGAcc                                          >  1:2532488/1‑69 (MQ=255)
               gATATCCCAAACGACAGCTTCTTCGCGCTCAACCATTTTCTTCGCAGCTTTGATGGTGGTAGCAAGAcc                                          >  1:2487846/1‑69 (MQ=255)
               gATATCCCAAACGACAGCTTCTTCGCGCTCAACCATTTTCTTCGCAGCTTTGATGGTGGTAGCAAGAcc                                          >  1:380872/1‑69 (MQ=255)
               gATATCCCAAACGACAGCTTCTTCGCGCTCAACCATTTTCTTCGCAGCTTTGATGGTGGTAGCAAGAcc                                          >  1:533891/1‑69 (MQ=255)
               gATATCCCAAACGACAGCTTCTTCGCGCTCAACCATTTTCTTCGCAGCTTTGATGGTGGTAGCAAGAcc                                          >  1:606193/1‑69 (MQ=255)
               gATATCCCAAACGACAGCTTCTTCGCGCTCAACCATTTTCTTCGCAGCTTTGATGGTGGTAGCAAGAcc                                          >  1:2146826/1‑69 (MQ=255)
               gATATCCCAAACGACAGCTTCTTCGCGCTCAACCATTTTCTTCGCAGCTTTGATGGTGGTAGCAAGAcc                                          >  1:691362/1‑69 (MQ=255)
               gATATCCCAAACGACAGCTTCTTCGCGCTCAACCATTTTCTTCGCAGCTTTGATGGTGGTAGCAAGAcc                                          >  1:985025/1‑69 (MQ=255)
               gATATCCCAAACGACAGCTTCTTCGCGCTCAACCATTTTCTTCGCAGCTTTGATGGTGGTAGCAAGAcc                                          >  1:1973492/1‑69 (MQ=255)
               gATATCCCAAACGACAGCTTCTTCGCGCTCAACCATTTTCTTCGCAGCTTTGATGGTGGTAGCAAGAcc                                          >  1:179047/1‑69 (MQ=255)
               gATATCCCAAACGACAGCTTCTTCGCGCTCAACCATTTTCTTCGCAGCTTTGATGGTGGTAGCAAGAcc                                          >  1:1748191/1‑69 (MQ=255)
               gATATCCCAAACGACAGCTTCTTCGCGCTCAACCATTTTCTTCGCAGCTTTGATGGTGGTAGCAAGAcc                                          >  1:1237671/1‑69 (MQ=255)
               gATATCCCAAACGACAGCTTCTTCGCGCTCAACCATTTTCTTCGCAGCTTTGATGGTGGTAGCAAGAc                                           >  1:3108498/1‑68 (MQ=255)
               gATATCCCAAACGACAGCTTCTTCGCGCTCAACCATTTTCTTCGCAGCTTTGATGGTGGTAGCAAGAc                                           >  1:3069852/1‑68 (MQ=255)
               gATATCCCAAACGACAGCTTCTTCGCGCTCAACCATTTTCTTCGCAGCTTTGATGGTGGTAGCAAGAc                                           >  1:1394460/1‑68 (MQ=255)
               gATATCCCAAACGACAGCTTCTTCGCGCTCAACCATTTTCTTCGCAGCTTTGATGGTGGTAGCAAGAc                                           >  1:667045/1‑68 (MQ=255)
               gATATCCCAAACGACAGCTTCTTCGCGCTCAACCATTTTCTTCGCAGCTTTGATGGTGGTAGCAAGAc                                           >  1:939303/1‑68 (MQ=255)
                 tatCCCAAACGACAGCTTCTTCGCGCTCAACCATTTTCTTCGCAGCTTTAATGGTGGTAGCAAGACCa                                         >  1:3060649/1‑68 (MQ=255)
                 tatCCCAAACGACAGCTTCTTCGCGCTCAACCATTTTCTTCGCAGCTTTAATGGTGGTAGCAAGACCa                                         >  1:401663/1‑68 (MQ=255)
                   tCCCAAACGACAGCTTCTTCGCGCTCAACCATTTTCTTCGCAGCTTTAATGGTGGTAGCAAGACCACGc                                      >  1:831391/1‑69 (MQ=255)
                   tCCCAAACGACAGCTTCTTCGCGCTCAACCATTTTCTTCGCAGCTTTAATGGTGGTAGCAAGACCACGc                                      >  1:33781/1‑69 (MQ=255)
                   tCCCAAACGACAGCTTCTTCGCGCTCAACCATTTTCTTCGCAGCTTTAATGGTGGTAGCAAGACCACGc                                      >  1:3400056/1‑69 (MQ=255)
                   tCCCAAACGACAGCTTCTTCGCGCTCAACCATTTTCTTCGCAGCTTTAATGGTGGTAGCAAGACCACGc                                      >  1:1741751/1‑69 (MQ=255)
                   tCCCAAACGACAGCTTCTTCGCGCTCAACCATTTTCTTCGCAGCTTTAATGGTGGTAGCAAGACCACGc                                      >  1:2600326/1‑69 (MQ=255)
                   tCCCAAACGACAGCTTCTTCGCGCTCAACCATTTTCTTCGCAGCTTTAATGGTGGTAGCAAGACCACGc                                      >  1:2813935/1‑69 (MQ=255)
                   tCCCAAACGACAGCTTCTTCGCGCTCAACCATTTTCTTCGCAGCTTTAATGGTGGTAGCAAGACCACGc                                      >  1:2066640/1‑69 (MQ=255)
                   tCCCAAACGACAGCTTCTTCGCGCTCAACCATTTTCTTCGCAGCTTTAATGGTGGTAGCAAGACCACGc                                      >  1:2969517/1‑69 (MQ=255)
                   tCCCAAACGACAGCTTCTTCGCGCTCAACCATTTTCTTCGCAGCTTTAATGGTGGTAGCAAGACCACGc                                      >  1:1153051/1‑69 (MQ=255)
                   tCCCAAACGACAGCTTCTTCGCGCTCAACCATTTTCTTCGCAGCTTTAATGGTGGTAGCAAGACCACGc                                      >  1:573848/1‑69 (MQ=255)
                   tCCCAAACGACAGCTTCTTCGCGCTCAACCATTTTCTTCGCAGCTTTAATGGTGGTAGCAAGACCACGc                                      >  1:1079362/1‑69 (MQ=255)
                   tCCCAAACGACAGCTTCTTCGCGCTCAACCATTTTCTTCGCAGCTTTAATGGTGGTAGCAAGACCACGc                                      >  1:2094735/1‑69 (MQ=255)
                    cccAAACGACAGCTTCTTCGCGCTCAACCATTTTCTTCGCAGCTTTAATGGTGGTAGc                                                <  1:3335646/58‑1 (MQ=255)
                     ccAAACGACAGCTTCTTCGCGCTCAACCATTTTCTTCGCAGCTTTAATGGTGGTAGCAAGACCACGCa                                     >  1:2426932/1‑68 (MQ=255)
                     ccAAACGACAGCTTCTTCGCGCTCAACCATTTTCTTCGCAGCTTTAATGGTGGTAGCAAGACCACGCa                                     >  1:2442464/1‑68 (MQ=255)
                     ccAAACGACAGCTTCTTCGCGCTCAACCATTTTCTTCGCAGCTTTAATGGTGGTAGCAAGACCACGCAg                                    >  1:2403270/1‑69 (MQ=255)
                     ccAAACGACAGCTTCTTCGCGCTCAACCATTTTCTTCGCAGCTTTAATGGTGGTAGCAAGACCACGCAg                                    >  1:3240891/1‑69 (MQ=255)
                                     tcGCGCTCAACCATTTTCTTCGCAGCTTTAATGGTGGTAGCAAGACCACTCAGTTCCAGCTTGCCGTa                     <  1:2671392/68‑1 (MQ=255)
                                     tcGCGCTCAACCATTTTCTTCGCAGCTTTAATGGTGGTAGCAAGACCACGCAGTTCCAGCTTGCCGTa                     <  1:1519348/68‑1 (MQ=255)
                                     tcGCGCTCAACCATTTTCTTCGCAGCTTTAATGGTGGTAGCAAGACCACGCAGTTCCAGCTTGCCGTa                     <  1:2698822/68‑1 (MQ=255)
                                     tcGCGCTCAACCATTTTCTTCGCAGCTTTAATGGTGGTAGCAAGACCACGCAGTTCCAGCTTGCCGTa                     <  1:1986307/68‑1 (MQ=255)
                                     tcGCGCTCAACCATTTTCTTCGCAGCTTTAATGGTGGTAGCAAGACCACGCAGTTCCAGCTTGCCGTa                     <  1:397167/68‑1 (MQ=255)
                                     tcGCGCTCAACCATTTTCTTCGCAGCTTTAATGGTGGTAGCAAGACCACGCAGTTCCAGCTTGCCGTa                     <  1:1583934/68‑1 (MQ=255)
                                     tcGCGCTCAACCATTTTCTTCGCAGCTTTAATGGTGGTAGCAAGACCACGCAGTTCCAGCTTGCCGTa                     <  1:454481/68‑1 (MQ=255)
                                     tcGCGCTCAACCATTTTCTTCGCAGCTTTAATGGTGGTAGCAAGACCACGCAGTTCCAGCTTGCCGTa                     <  1:1673875/68‑1 (MQ=255)
                                              aCCATTTTCTTCGCAGCTTTAATGGTGGTAGCAAGACCACGCAGTTCCAGCTTGCCGTa                     <  1:872129/59‑1 (MQ=255)
                                                 aTTTTCTTCGCAGCTTTAATGGTGGTAGCAAGACCACGCAGTTCCAGCTTGCCGTAGATGAACGGTTTg        <  1:1048150/69‑1 (MQ=255)
                                                 aTTTTCTTCGCAGCTTTAATGGTGGTAGCAAGACCACGCAGTTCCAGCTTGCCGTAGATGAACGGTTTg        <  1:1673942/69‑1 (MQ=255)
                                                 aTTTTCTTCGCAGCTTTAATGGTGGTAGCAAGACCACGCAGTTCCAGCTTGCCGTAGATGAACGGTTTg        <  1:2385503/69‑1 (MQ=255)
                                                 aTTTTCTTCGCAGCTTTAATGGTGGTAGCAAGACCACGCAGTTCCAGCTTGCCGTAGATGAACGGTTTg        <  1:1405202/69‑1 (MQ=255)
                                                 aTTTTCTTCGCAGCTTTAATGGGGGTAGCAAGACCACGCAGTTCCAGCTTGCCGTAGATGAACGGTTTg        <  1:124873/69‑1 (MQ=255)
                                                    ttcttcGCAGCTTTAATGGTGGTAGCAAGACCACGCAGTTCCAGCTTGCCGTAGATGAACGGTTTg        >  1:2191682/1‑66 (MQ=255)
                                                    ttcttcGCAGCTTTAATGGTGGTAGCAAGACCACGCAGTTCCAGCTTGCCGTAGATGAACGGTTTg        >  1:2440243/1‑66 (MQ=255)
                                                    ttcttcGCAGCTTTAATGGTGGTAGCAAGACCACGCAGTTCCAGCTTGCCGTAGATGAACGGTTTGAAc     >  1:1454908/1‑69 (MQ=255)
                                                    ttcttcGCAGCTTTAATGGTGGTAGCAAGACCACGCAGTTCCAGCTTGCCGTAGATGAACGGTTTGAAc     >  1:3282640/1‑69 (MQ=255)
                                                    ttcttcGCAGCTTTAATGGTGGTAGCAAGACCACGCAGTTCCAGCTTGCCGTAGATGAACGGTTTGAAc     >  1:1665217/1‑69 (MQ=255)
                                                    ttcttcGCAGCTTTAATGGTGGTAGCAAGACCACGCAGTTCCAGCTTGCCGTAGATGAACGGTTTGAAc     >  1:752922/1‑69 (MQ=255)
                                                      cttcGCAGCTTTAATGGTGGTAGCAAGACCACGCAGTTCCAGCTTGCCGTAGATGAACGGTTTGAACa    <  1:18131/68‑1 (MQ=255)
                                                      cttcGCAGCTTTAATGGTGGTAGCAAGACCACGCAGTTCCAGCTTGCCGTAGATGAACGGTTTGAACa    <  1:2856760/68‑1 (MQ=255)
                                                      cttcGCAGCTTTAATGGTGGTAGCAAGACCACGCAGTTCCAGCTTGCCGTAGATGAACGGTTTGAACa    <  1:418857/68‑1 (MQ=255)
                                                      cttcGCAGCTTTAATGGTGGTAGCAAGACCACGCAGTTCCAGCTTGCCGTAGATGAACGGTTTGAACa    <  1:2360317/68‑1 (MQ=255)
                                                      cttcGCAGCTTTAATGGTGGTAGCAAGACCACGCAGTTCCAGCTTGCCGTAGATGAACGGTTTGAACa    <  1:2202061/68‑1 (MQ=255)
                                                        tcGCAGCTTTGATGGTGGTAGCAAGACCACGCAGTTCCAGCTTGCCGTAGATGAACGGTTTGAACAGc  <  1:888719/68‑1 (MQ=255)
                                                        tcGCAGCTTTGATGGTGGTAGCAAGACCACGCAGTTCCAGCTTGCCGTAGATGAACGGTTTGAACAGc  <  1:1772533/68‑1 (MQ=255)
                                                        tcGCAGCTTTGATGGTGGTAGCAAGACCACGCAGTTCCAGCTTGCCGTAGATGAACGGTTTGAACAGc  <  1:2299378/68‑1 (MQ=255)
                                                        tcGCAGCTTTGATGGTGGTAGCAAGACCACGCAGTTCCAGCTTGCCGTAGATGAACGGTTTGAACAGc  <  1:1098889/68‑1 (MQ=255)
                                                        tcGCAGCTTTGATGGTGGTAGCAAGACCACGCAGTTCCAGCTTGCCGTAGATGAACGGTTTGAACAGc  <  1:3157570/68‑1 (MQ=255)
                                                        tcGCAGCTTTGATGGTGGTAGCAAGACCACGCAGTTCCAGCTTGCCGTAGATGAACGGTTTGAACAGc  <  1:2758899/68‑1 (MQ=255)
                                                        tcGCAGCTTTGATGGTGGTAGCAAGACCACGCAGTTCCAGCTTGCCGTAGATGAACGGTTTGAACAGc  <  1:294623/68‑1 (MQ=255)
                                                        tcGCAGCTTTAATGGTGGTAGCAAGACCACGCAGTTCCAGCTTGCCGTAGATGAACGGTTTGAACAGc  <  1:659113/68‑1 (MQ=255)
                                                         cGCAGCTTTAATGGTGGTAGCAAGACCACGCAGTTCCAGCTTGCCGTAGATGAACGGTTTGAACAGc  <  1:2084753/67‑1 (MQ=255)
                                                                  |                                                         
GATAACTTCGTCCAGGATATCCCAAACGACAGCTTCTTCGCGCTCAACCATTTTCTTCGCAGCTTTAATGGTGGTAGCAAGACCACGCAGTTCCAGCTTGCCGTAGATGAACGGTTTGAACAGC  >  minE/2255790‑2255913

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