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
A6 F21 I0 R2 370 72.1 3738297 91.5% 3420541 62.3

Breseq alignment

BRESEQ :: Evidence
Predicted mutation
evidence seq id position mutation freq annotation gene description
RA minE 2,281,121 A→G 65.0% F67S (TTT→TCT)  fabR ← DNA‑binding transcriptional repressor

Read alignment evidence...
  seq id position ref new freq score (cons/poly) reads annotation genes product
*minE2,281,1210AG65.0% 61.5 / 56.7 60F67S (TTT→TCT) fabRDNA‑binding transcriptional repressor
Reads supporting (aligned to +/- strand):  ref base A (15/6);  new base G (18/21);  total (33/27)
Fisher's exact test for biased strand distribution p-value = 1.02e-01
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 8.24e-01

GTAGCATTAAACCGCTCTCATCAACCATGGTCAGACCCAGTTCGTCTACGTCGCGGAAATGCCGATAAAAAGAGGTGGGAGCAATGCCCGCTTCACGCGCCACTTCACGCAAACTCAGGCTGGCGAAGCTGCGTTC  >  minE/2281053‑2281188
                                                                    |                                                                   
gTAGCATTAAACCGCTCTCATCAACCATGGTCAGACCCAGTTCGTCTACGTCGCGGAAATGCCGATaaa                                                                     >  1:786268/1‑69 (MQ=255)
gTAGCATTAAACCGCTCTCATCAACCATGGTCAGACCCAGTTCGTCTACGTCGCGGAAATGCCGATaaa                                                                     >  1:1544183/1‑69 (MQ=255)
      ttAAACCGCTCTCATCAACCATGGTCAGACCCAGTTCGTCTACGTCGCGGAAATGCCGATAAGAAGAGGTg                                                             >  1:3019771/1‑71 (MQ=255)
      ttAAACCGCTCTCATCAACCATGGTCAGACCCAGTTCGTCTACGTCGCGGAAATGCCGATAAAAAGAGGTg                                                             >  1:2151380/1‑71 (MQ=255)
      ttAAACCGCTCTCATCAACCATGGTCAGACCCAGTTCGTCTACGACGCGGAAATGCCGATAAAAAGAGGTg                                                             >  1:691783/1‑71 (MQ=255)
        aaaCCGCTCTCATCAACCATGGTCAGACCCAGTTCGTCTACGTCGCGGAAATGCCGATAAAAAGAGGTgg                                                            <  1:2101114/70‑1 (MQ=255)
         aaCCGCTCTCATCAACCATGGTCAGACCCAGTTCGTCTACGTCGCGGAAATGCCGATAAGAAGAGGTgg                                                            >  1:3472876/1‑69 (MQ=255)
            cGCTCTCATCAACCATGGTCAGACCCAGTTCGTCTACGTCGCGGAAATGCCGATAAGAAGAGGTGGGAGCa                                                       <  1:3077799/71‑1 (MQ=255)
            cGCTCTCATCAACCATGGTCAGACCCAGTTCGTCTACGTCGCGGAAATGCCGATAAGAAGAGGTGGGAGCa                                                       <  1:1446011/71‑1 (MQ=255)
             gCTCTCATCAACCATGGTCAGACCCAGTTCGTCTACGTCGCGGAAATGCCGATAAGAAGAGGTGGGAGCaa                                                      >  1:1632795/1‑71 (MQ=255)
                ctcATCAACCATGGTCAGACCCAGTTCGTCTACGTCGCGGAAATGCCGATAAGAagag                                                                <  1:2524834/58‑1 (MQ=255)
                ctcATCAACCATGGTCAGACCCAGTTCGTCTACGTCGCGGAAATGCCGATAAGAagag                                                                <  1:3660101/58‑1 (MQ=255)
                  catcaACCATGGTCAGACCCAGTTCGTCTACGTCGCGGAAATGCCGATAAGAAGAGGTGGGAGCAATGcc                                                  >  1:2276804/1‑70 (MQ=255)
                   atcaACCATGGTCAGACCCAGTTCGTCTACGTCGCGGAAATGCCGATAAGAAGAGGTGGGAGCAATGccc                                                 <  1:2165556/70‑1 (MQ=255)
                   atcaACCATGGTCAGACCCAGTTCGTCTACGTCGCGGAAATGCCGATAAGAAGAGGTGGGAGCAATGccc                                                 <  1:3053664/70‑1 (MQ=255)
                   atcaACCATGGTCAGACCCAGTTCGTCTACGTCGCGGAAATGCCGATAAGAAGAGGTGGGAGCAATGccc                                                 <  1:1756450/70‑1 (MQ=255)
                    tcaACCATGGTCAGACCCAGTTCGTCTACGTCGCGGAAATGCCGATAAGAAGAGGTGGGAGCAATGCCCGc                                               <  1:684074/71‑1 (MQ=255)
                     caACCATGGTCAGACCCAGTTCGTCTACGTCGCGGAAATGCCGATAAGAAGAGGTGGGAGCAATGCCCGc                                               >  1:3326513/1‑70 (MQ=255)
                     caACCATGGTCAGACCCAGTTCGTCTACGTCGCGGAAATGCCGATAAGAAGAGGTGGGAGCAATGCCCGc                                               >  1:163855/1‑70 (MQ=255)
                      aaCCATTGTCAGACCCAGTTCGTCTACGTCGCGGAAATGCCGATAAGAAGAGGTGGGAGCAATGCCCGCt                                              <  1:3609565/70‑1 (MQ=255)
                        ccATGGTCAGACCCAGTTCGTCTACGTCGCGGAAATGCCGATAAAAAGAGGTGGGAGCAATGCCCGCTTCa                                           >  1:323018/1‑71 (MQ=255)
                        ccATGGTCAGACCCAGTTCGTCTACGTCGCGGAAATGCCGATAAAAAGAGGTGGGAGCAATGCCCGCTTCa                                           >  1:3297112/1‑71 (MQ=255)
                           tGGTCAGACCCAGTTCGTCTACGTCGCGGAAATGCCGATAAAAAGAGGTGGGAGCAATGCCCGCTTCAcgc                                        >  1:1346096/1‑71 (MQ=255)
                            ggTCAGACCCAGTTCGTCTACGTCGCGGAAATGCCGATAAGAAGAGGTGGGAGCAATGCCCGCTTCAcgc                                        >  1:250372/1‑70 (MQ=255)
                                 gACCCAGTTCGTCTACGTCGCGGAAATGCCGATAAGAAGAGGTGGGAGCAATGCCCGCTTCACGCGCCACt                                  <  1:342691/71‑1 (MQ=255)
                                      aGTTCGTCTACGTCGCGGAAATGCCGATAAGAAGAGGTGGGAGCAATGCCCGCTTCACGCGCCACTTCACg                             >  1:2926846/1‑71 (MQ=255)
                                      aGTTCGTCTACGTCGCGGAAATGCCGATAAGAAGAGGTGGGAGCAATGCCCGCTTCACGCGCCACTTCACg                             >  1:500036/1‑71 (MQ=255)
                                      aGTTCGTCTACGTCGCGGAAATGCCGATAAGAAGAGGTGGGAGCAATGCCCGCTACACGCGCCa                                    >  1:517795/1‑64 (MQ=255)
                                       gTTCGTCTACGTCGCGGAAATGCCGATAAGAAGAGGTGGGAGCAATGCCCGCTTCACGCGCCACTTCAc                              >  1:2654348/1‑69 (MQ=255)
                                        ttCGTCTACGTCGCGGAAATGCCGATAAGAAGAGGTGGGAGCAATGCCCGCtt                                             <  1:295652/53‑1 (MQ=255)
                                        ttCGTCTACGTCGCGGAAATGCCGATAAGAAGAGGTGGGAGCAATGCCCGCtt                                             <  1:294364/53‑1 (MQ=255)
                                        ttCGTCTACGTCGCGGAAATGCCGATAAGAAGAGGTGGGAGCAATGCCCGCTTCACGCGCCACTTCACgaa                           <  1:3685997/71‑3 (MQ=255)
                                        ttCGTCTACGTCGCGGAAATGCCGATAAGAAGAGGTGGGAGCAATGCCCGCTTCACGCGCCACTTCACGCa                           <  1:3542491/71‑1 (MQ=255)
                                          cGTCTACGTCGCGGAAATGCCGATAAGAAGAGGTGGGAGCAATGCCCGCTTCACGCGCCACTTCACGCaaa                         >  1:1800929/1‑71 (MQ=255)
                                          cGTCTACGTCGCGGAAATGCCGATAAAAAGAGGTGGGAGCAATGcc                                                  >  1:3086214/1‑46 (MQ=255)
                                           gTCTACGTCGCGGAAATGCCGATAAAAAGAGGTGGGAGCAATGCCCGCTTCACGCGCCACTTCACGCAAAc                        >  1:1596837/1‑71 (MQ=255)
                                                  tCGCGGAAATGCCGATAAAAAGAGGTGGGAGCAATGCCCGCTTCACGCGCCACtt                                 >  1:229504/1‑55 (MQ=255)
                                                  tCGCGGAAATGCCGATAAAAAGAGGTGGGAGCAATGCCCGCTTCACGCGCCACtt                                 >  1:2064397/1‑55 (MQ=255)
                                                  tCGCGGAAATGCCGATAAAAAGAGGTGGGAGCAATGCCCGCTTCACGCGCCACTTCACGCAAACTCAGGCt                 <  1:3183927/71‑1 (MQ=255)
                                                    gcgGAAATGCCGATAAGAAGAGGTGGGAGCAATGCCCGCTTCACGCGCCACTTCACGCAAACTCAGGCTgg               >  1:2725390/1‑71 (MQ=255)
                                                    gcgGAAATGCCGATAAGAAGAGGTGGGAGCAATGCCCGCTTCACGCGCCACTTCACGCAAACTCAGGCTgg               >  1:2118947/1‑71 (MQ=255)
                                                    gcgGAAATGCCGATAAGAAGAGGTGGGAGCAATGCCCGCTTCACGCGCCACTTCACGCAAACTCAGGCTgg               >  1:3680617/1‑71 (MQ=255)
                                                     cgGAAATGCCGATAAGCAGAGGTGGGAGCAATGCGCGCTTCACGCGCCACTTCACGc                            <  1:85927/57‑1 (MQ=255)
                                                     cgGAAATGCCGATAAAAAGAGGTGGGAGCAATGCCCGCTTCACGCGCCACTTCACGCAAACTCAGGCTGGc              >  1:256027/1‑71 (MQ=255)
                                                     cgGAAATGCCGATAAAAAGAGGTGGGAGCAATGCCCGCTTCACGCGCCACTTCACGCAAACTCAGGCTGGc              >  1:134161/1‑71 (MQ=255)
                                                       gAAATGCCGTTAAGAAGAGGTGGGAGCAATGCCCGCTTCACGCGCCACTTCACGCAAACTCAGGCTGGCGa            <  1:1991182/71‑1 (MQ=255)
                                                       gAAATGCCGATAAGAAGAGGGGGGAGCAATGCCCGCTTCACGCGCCACTTCACGCAAACTCAGGCTGGCGa            <  1:2985292/71‑1 (MQ=255)
                                                       gAAATGCCGATAAAAAGAGGTGGGAGCAATGCCCGCTTCACGCGCCACTTCACGCAAACTCAGGCTGGCGa            <  1:2750602/71‑1 (MQ=255)
                                                        aaaTGCCGATAAGAAGAGGTGGGAGCAATGCCCGCTTCACGCGCCACTTCa                               <  1:386797/51‑1 (MQ=255)
                                                        aaaTGCCGATAAGAAGAGGTGGGAGCAATGCCCGCTTCACGCGCCACTTCa                               <  1:3585683/51‑1 (MQ=255)
                                                        aaaTGCCGATAAGAAGAGGTGGGAGCAATGCCCGCTTCACGCGCCACTTCa                               <  1:1964895/51‑1 (MQ=255)
                                                        aaaTGCCGATAAGAAGAGGTGGGAGCAATGCCCGCTTCACGCGCCACTTCACg                             >  1:2954321/1‑53 (MQ=255)
                                                        aaaTGCCGATAAGAAGAGGTGGGAGCAATGCCCGCTTCACGCGCCACTTCACGCAAACTCAGGCTGGCg             >  1:1756543/1‑69 (MQ=255)
                                                        aaaTGCCGATAAGAAGAGGTGGGAGCAATGCCCGCTTCACGCGCCACTTCACGCAAACTCAGGCTGGCg             >  1:1374718/1‑69 (MQ=255)
                                                        aaaTGCCGATAAAAAGAGGTGGGAGCAATGCCCGCTTCACGCGCCACTTCACGCAAACTCAGGCTGGCg             >  1:1256906/1‑69 (MQ=255)
                                                        aaaTGCCGATAAAAAGAGGTGGGAGCAATGCCCGCTTCACGCGCCACTTCACGCAAACTCAGGCTGGCGaa           <  1:1223506/71‑1 (MQ=255)
                                                        aaaTGCCGATAAAAAGAGGTGGGAGCAATGCCCGCTTCACGCGCCACTTCACGCAAACTCAGGCTGGCGa            <  1:2405591/70‑1 (MQ=255)
                                                                aTAAGAAGAGGTGGGAGCAATGCCCGCTTCACGCGCCACTTCACGCAAACTCAGGCTGGCGa            <  1:2167098/62‑1 (MQ=255)
                                                                 tAAAAAGAGGTGGGAGCAATGCCCGCTTCACGCGCCACTTCACGCAAACTCAGGCTGGCGAAGCTGCGtt   >  1:1672120/1‑70 (MQ=255)
                                                                 tAAAAAGAGGTGGGAGCAATGCCCGCTTCACGCGCCACTTCACGCAAACTCAGGCTGGCGAAGCTGCGtt   >  1:633836/1‑70 (MQ=255)
                                                                 tAAAAAGAGGTGGGAGCAATGCCCGCTTCACACGCCACTTCACGCAAACTCAGGCTGGCGAAGCTGCGTTc  <  1:1578987/71‑1 (MQ=255)
                                                                 tAAAAAGAGGTGGGAGCAATGCCAGCTTCACGCGCCACTTCACGCAAACTCAGGCTGGCGAAGCTGCGtt   >  1:2508109/1‑70 (MQ=255)
                                                                    |                                                                   
GTAGCATTAAACCGCTCTCATCAACCATGGTCAGACCCAGTTCGTCTACGTCGCGGAAATGCCGATAAAAAGAGGTGGGAGCAATGCCCGCTTCACGCGCCACTTCACGCAAACTCAGGCTGGCGAAGCTGCGTTC  >  minE/2281053‑2281188

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 14 ≤ ATCG/ATCG < 32 ≤ ATCG/ATCG < 36 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑

GATK/CNVnator alignment

N/A