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 1,308,306 T→C 37.7% S162S (TCA→TCG)  yeeY ← predicted DNA‑binding transcriptional regulator

Read alignment evidence...
  seq id position ref new freq score (cons/poly) reads annotation genes product
*minE1,308,3060TC37.7% 45.8 / 59.0 90S162S (TCA→TCG) yeeYpredicted DNA‑binding transcriptional regulator
Reads supporting (aligned to +/- strand):  ref base T (30/26);  new base C (27/7);  total (57/33)
Fisher's exact test for biased strand distribution p-value = 1.47e-02
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 4.43e-01

GCTAACGGATGATGAGGCGCGACCGCAAAGACTTGTTCCAGATCGCCCAACCGTGAAAAACCAAACTCACTGGAAGATGGTGGCTCATGCATCGCGCCAACAATAATATCCGCTCG  >  minE/1308253‑1308368
                                                     |                                                              
gCTAACGGATGATGAGGCGCGACCGCAAAGACTTGTTCCAGATCGCCCAACCGTGAAAAACCAAACTCa                                                 >  1:2402050/1‑69 (MQ=255)
gCTAACGGATGATGAGGCGCGACCGCAAAGACTTGTTCCAGATCGCCCAACCGTGAAAAACCAAACTCa                                                 >  1:2000533/1‑69 (MQ=255)
gCTAACGGATGATGAGGCGCGACCGCAAAGACTTGTTCCAGATCGCCCAACCGTGAAAAACCAAACTCa                                                 >  1:1041707/1‑69 (MQ=255)
gCTAACGGATGATGAGGCGCGACCGCAAAGACTTGTTCCAGATCGCCCAACCGTGAAAAACCAAACTCa                                                 >  1:940436/1‑69 (MQ=255)
gCTAACGGATGATGAGGCGCGACCGCAAAGACTTGTTCCAGATCGCCCAACCGTGAAAAACCAAACTCa                                                 >  1:1463501/1‑69 (MQ=255)
gCTAACGGATGATGAGGCGCGACCGCAAAGACTTGTTCCAGATCGCCCAACCGTGAAAAACCAAACTCa                                                 >  1:1379094/1‑69 (MQ=255)
gCTAACGGATGATGAGGCGCGACCGCAAAGACTTGTTCCAGATCGCCCAACCGTGAAAAACCAAACTCa                                                 >  1:1189699/1‑69 (MQ=255)
gCTAACGGATGATGAGGCGCGACCGCAAAGACTTGTTCCAGATCGCCCAACCGTGAAAAACCAAACTCa                                                 >  1:1236486/1‑69 (MQ=255)
gCTAACGGATGATGAGGCGCGACCGCAAAGACTTGTTCCAGATCGCCCAACCGTGAAAAACCAAACTCa                                                 >  1:1247653/1‑69 (MQ=255)
gCTAACGGATGATGAGGCGCGACCGCAAAGACTTGTTCCAGATCGCCCAACCGTGAAAAACCAAACTCa                                                 >  1:1375107/1‑69 (MQ=255)
gCTAACGGATGATGAG‑‑GCGACCGCAAAGACTTGTTCCAGATCGCCCAACCGt                                                                >  1:2495465/1‑52 (MQ=255)
 cTAACGGATGATGAGGCGCGACCGCAAAGACTTGTTCCAGATCGCCCAACCGTGAAAAACCAAACTCAc                                                >  1:3010244/1‑69 (MQ=255)
      ggATGATGAGGCGCGACCGCAAATACTTGTTCCAGATCGCCCAACCGTGAAAAACCAAACTCACTGGaa                                           <  1:1181745/69‑1 (MQ=255)
         tgatgaGGCGCGACCGCAAAGACTTGTTCCAGATCGCCCAACCGTGAAAAACCAAACTCACTGGAAGAt                                        <  1:1468636/69‑1 (MQ=255)
         tgatgaGGCGCGACCGCAAAGACTTGTTCCAGATCGCCCAACCGTGAAAAACCAAACTCACTGGAAGAt                                        <  1:880363/69‑1 (MQ=255)
          gatgaGGCGCGACCGCAAAGACTTGTTCCAGATCGCCCAACCGTGAAAAACCAAACTc                                                  >  1:3100873/1‑58 (MQ=255)
          gatgaGGCGCGACCGCAAAGACTTGTTCCAGATCGCCCAACCGTGAAAAACCAAACTCa                                                 >  1:1881504/1‑59 (MQ=255)
          gatgaGGCGCGACCGCAAAGACTTGTTCCAGATCGCCCAACCGTGAAAAACCAAACTCa                                                 >  1:2435228/1‑59 (MQ=255)
          gatgaGGCGCGACCGCAAAGACTTGTTCCAGATCGCCCAACCGTGAAAAACCAAACTCa                                                 >  1:786598/1‑59 (MQ=255)
          gatgaGGCGCGACCGCAAAGACTTGTTCCAGATCGCCCAACCGTGAAAAACCAAACTCa                                                 >  1:2197178/1‑59 (MQ=255)
          gatgaGGCGCGACCGCAAAGACTTGTTCCAGATCGCCCAACCGTGAAAAACCAAACTCa                                                 >  1:496961/1‑59 (MQ=255)
          gatgaGGCGCGACCGCAAAGACTTGTTCCAGATCGCCCAACCGTGAAAAACCAAACTCa                                                 >  1:815911/1‑59 (MQ=255)
          gatgaGGCGCGACCGCAAAGACTTGTTCCAGATCGCCCAACCGTGAAAAACCAAACTCa                                                 >  1:1310769/1‑59 (MQ=255)
          gatgaGGCGCGACCGCAAAGACTTGTTCCAGATCGCCCAACCGTGAAAAACCAAACTCa                                                 >  1:468626/1‑59 (MQ=255)
          gatgaGGCGCGACCGCAAAGACTTGTTCCAGATCGCCCAACCGTGAAAAACCAAACTCa                                                 >  1:1561323/1‑59 (MQ=255)
          gatgaGGCGCGACCGCAAAGACTTGTTCCAGATCGCCCAACCGTGAAAAACCAAACTCa                                                 >  1:3036826/1‑59 (MQ=255)
          gatgaGGCGCGACCGCAAAGACTTGTTCCAGATCGCCCAACCGTGAAAAACCAAACTCa                                                 >  1:1306348/1‑59 (MQ=255)
          gatgaGGCGCGACCGCAAAGACTTGTTCAAGATCGCCCAACCGCGaga                                                            >  1:2127841/1‑46 (MQ=255)
          gatgaGGCGCGACCGCAAAGACTTGTTCAAGATCGCCCAACCGCGAGAAAc                                                         >  1:3399835/1‑51 (MQ=255)
          gatgaGGCGCGACCGCAAAGACTTGTTCAAGATCGCCCAACCGCGAGAAAc                                                         >  1:2639174/1‑51 (MQ=255)
          gatgaGGCGCGACCGCAAAGACTTGTTCAAGATCGCCCAACCGCGAGAAAc                                                         >  1:3356193/1‑51 (MQ=255)
          gatgaGGCGCGACCGCAAAGACTTGTTCAAGATCGCCCAACCGCGAGAAAc                                                         >  1:2788440/1‑51 (MQ=255)
          gatgaGGCGCGACCGCAAAGACTTGTTCAAGATCGCCCAACCGCGAGAAAc                                                         >  1:540796/1‑51 (MQ=255)
          gatgaGGCGCGACCGCAAAGACTTGTTCAAGATCGCCCAACCGCGAGAAAc                                                         >  1:2851266/1‑51 (MQ=255)
          gatgaGGCGCGACCGCAAAGACTTGTTCAAGATCGCCCAACCGCGAGAAAc                                                         >  1:660570/1‑51 (MQ=255)
          gatgaGGCGCGACCGCAAAGACTTGTTCAAGATCGCCCAACCGCGAGAAAc                                                         >  1:661270/1‑51 (MQ=255)
          gatgaGGCGCGACCGCAAAGACTTGTTCAAGATCGCCCAACCGCGAGAAAc                                                         >  1:2717239/1‑51 (MQ=255)
          gatgaGGCGCGACCGCAAAGACTTGTTCAAGATCGCCCAACCGCGAGAAAc                                                         >  1:2404330/1‑51 (MQ=255)
          gatgaGGCGCGACCGCAAAGACTTGTTCAAGATCGCCCAACCGCGAGAAAc                                                         >  1:2119537/1‑51 (MQ=255)
          gatgaGGCGCGACCGCAAAGACTTGTTCAAGATCGCCCAACCGCGAGAAAc                                                         >  1:1531119/1‑51 (MQ=255)
          gatgaGGCGCGACCGCAAAGACTTGTTCAAGATCGCCCAACCGCGAGAAAc                                                         >  1:1095280/1‑51 (MQ=255)
          gatgaGGCGCGACCGCAAAGACTTGTTCAAGATCGCCCAACCGCGAGAAAc                                                         >  1:1106925/1‑51 (MQ=255)
          gatgaGGCGCGACCGCAAAGACTTGTTCAAGATCGCCCAACCGCGAGAAAc                                                         >  1:1127922/1‑51 (MQ=255)
          gatgaGGCGCGACCGCAAAGACTTGTTCAAGATCGCCCAACCGCGAGAAAc                                                         >  1:1359373/1‑51 (MQ=255)
          gatgaGGCGCGACCGCAAAGACTTGTTCAAGATCGCCCAACCGCGAGAAAc                                                         >  1:1379620/1‑51 (MQ=255)
          gatgaGGCGCGACCGCAAAGACTTGTTCAAGATCGCCCAACCGCGAGAAAc                                                         >  1:1507939/1‑51 (MQ=255)
          gatgaGGCGCGACCGCAAAGACTTGTTCAAGATCGCCCAACCGCGAGAAAc                                                         >  1:724142/1‑51 (MQ=255)
          gatgaGGCGCGACCGCAAAGACTTGTTCAAGATCGCCCAACCGCGAGAAAc                                                         >  1:2000392/1‑51 (MQ=255)
          gatgaGGCGCGACCGCAAAGACTTGTTCAAGATCGCCCAACCGCGAGAAAc                                                         >  1:810039/1‑51 (MQ=255)
          gatgaGGCGCGACCGCAAAGACTTGTTCAAGATCGCCCAACCGCGAGAAAc                                                         >  1:2124485/1‑51 (MQ=255)
          gatgaGGCGCGACCGCAAAGACTTGTTCAAGATCGCCCAACCGCGAGAAAc                                                         >  1:2226504/1‑51 (MQ=255)
          gatgaGGCGCGACCGCAAAGACTTGTTCAAGATCGCCCAACCGCGAGAAAc                                                         >  1:773706/1‑51 (MQ=255)
          gatgaGGCGCGACCGCAAAGACTTGTTCAAGATCGCCCAACCGCGAGAAAc                                                         >  1:2299343/1‑51 (MQ=255)
          gatgaGGCGCGACCGCAAAGACTTGTTCAAGATCGCCCAAACGCGAGAAAc                                                         >  1:3209374/1‑51 (MQ=255)
             gaGGCGCGACCGCAAAGACTTGTTCCAGATCGCCCAACCGTGAAAAACCAAACTCACTGGAAGAtggt                                     <  1:1178178/68‑1 (MQ=255)
             gaGGCGCGACCGCAAAGACTTGTTCCAGATCGCCCAACCGTGAAAAACCAAACTCACTGGAAGAtggt                                     >  1:3026891/1‑68 (MQ=255)
                    gACCGCAAAGACTTGTTCCAGATCGCCCAACCGTGAAAAACCAAACTCACTGGAAGATGGTGGCTCATg                             <  1:854233/69‑1 (MQ=255)
                    gACCGCAAAGACTTGTTCCAGATCGCCCAACCGTGAAAAACCAAACTCACTGGAAGATGGTGGCTCATg                             <  1:906192/69‑1 (MQ=255)
                    gACCGCAAAGACTTGTTCCAGATCGCCCAACCGTGAAAAACCAAACTCACTGGAAGATGGTGGCTCATg                             <  1:3231496/69‑1 (MQ=255)
                    gACCGCAAAGACTTGTTCCAGATCGCCCAACCGTGAAAAACCAAACTCACTGGAAGATGGTGGCTCATg                             <  1:942739/69‑1 (MQ=255)
                    gACCGCAAAGACTTGTTCCAGATCGCCCAACCGTGAAAAACCAAACTCACTGGAAGATGGTGGCTCATg                             <  1:2334534/69‑1 (MQ=255)
                    gACCGCAAAGACTTGTTCCAGATCGCCCAACCGTGAAAAACCAAACTCACTGGAAGATGGTGGCTCATg                             <  1:1943310/69‑1 (MQ=255)
                                       aGATCGCCCAACCGTGAAAAACCAAACTCACTGGAAGATGGTGGCTCATGCATCGCGCCAACaataat           <  1:2978024/68‑1 (MQ=255)
                                       aGATCGCCCAACCGTGAAAAACCAAACTCACTGGAAGATGGTGGCTCATGCATCGCGCCAACaataat           <  1:2263825/68‑1 (MQ=255)
                                       aGATCGCCCAACCGTGAAAAACCAAACTCACTGGAAGATGGTGGCTCATGCATCGCGCCAACaataat           <  1:2065072/68‑1 (MQ=255)
                                       aGATCGCCCAACCGTGAAAAACCAAACTCACTGGAAGATGGTGGCTCATGCATCGCGCCAACaataat           <  1:2467398/68‑1 (MQ=255)
                                       aGATCGCCCAACCGTGAAAAACCAAACTCACTGGAAGATGGTGGCTCATGCATCGCGCCAACaataat           <  1:58725/68‑1 (MQ=255)
                                       aGATCGCCCAACCGTGAAAAACCAAACTCACTGGAAGATGGTGGCTCATGCATCGCGCCAACaataat           <  1:2578877/68‑1 (MQ=255)
                                       aGATCGCCCAACCGTGAAAAACCAAACTCACTGGAAGATGGTGGCTCATGCATCGCGCCAACaataat           <  1:2983452/68‑1 (MQ=255)
                                       aGATCGCCCAACCGTGAAAAACCAAACTCACTGGAAGATGGTGGCTCATGCATCGCGCCAACaataat           <  1:2586172/68‑1 (MQ=255)
                                       aGATCGCCCAACCGTGAAAAACCAAACTCACTGGAAGATGGTGGCTCATGCATCGCGCCAACaataat           <  1:434004/68‑1 (MQ=255)
                                       aGATCGCCCAACCGTGAAAAACCAAACTCACTGGAAGATGGTGGCTCATGCATCGCGCCAACaataat           <  1:2599843/68‑1 (MQ=255)
                                       aGATCGCCCAACCGTGAAAAACCAAACTCACTGGAAGATGGTGGCTCATGCATCGCGCCAACaataat           <  1:270776/68‑1 (MQ=255)
                                       aGATCGCCCAACCGTGAAAAACCAAACTCACTGGAAGATGGTGGCTCATGCATCGCGCCAACaataat           <  1:3353250/68‑1 (MQ=255)
                                       aGATCGCCCAACCGTGAAAAACCAAACTCACTGGAAGATGGTGGCTCATGCATCGCGCCAACaataat           <  1:2716108/68‑1 (MQ=255)
                                       aGATCGCCCAACCGTGAAAAACCAAACTCACTGGAAGATGGTGGCTCATGCATCGCGCCAACaataat           <  1:2728696/68‑1 (MQ=255)
                                       aGATCGCCCAACCGTGAAAAACCAAACTCACTGGAAGATGGTGGCTCATGCATCGCGCCAACaataat           <  1:2782566/68‑1 (MQ=255)
                                        gATCGCCCAACCGTGAAAAACCAAACTCACTGGAAGATGGTGGCTCATGCATCGCGCCAACaataat           <  1:1877212/67‑1 (MQ=255)
                                           cGCCCAACCGTGAAAAACCAAACTCACTGGAAGATGGTGGCTCATGCATCGCGCCAACAataata          >  1:3412939/1‑65 (MQ=255)
                                           cGCCCAACCGTGAAAAACCAAACTCACTGGAAGATGGTGGCTCATGCATCGCGCCAACAATAATATcc       >  1:2912531/1‑68 (MQ=255)
                                           cGCCCAACCGTGAAAAACCAAACTCACTGGAAGATGGTGGCTCATGCATCGCGCCAACAATAATATCCg      >  1:906159/1‑69 (MQ=255)
                                           cGCCCAACCGTGAAAAACCAAACTCACTGGAAGATGGTGGCTCATGCATCGCGCCAACAATAATATCCg      >  1:1167166/1‑69 (MQ=255)
                                           cGCCCAACCGTGAAAAACCAAACTCACTGGAAGATGGTGGCTCATGCATCGCGCCAACAATAATATCCg      >  1:2584008/1‑69 (MQ=255)
                                           cGCCCAACCGTGAAAAACCAAACTCACTGGAAGATGGTGGCTCATGCATCGCGCCAACAATAATATCCg      >  1:2731510/1‑69 (MQ=255)
                                               cAACCGCGAGAAACCAAACTCACTGGAAGATGGTGGCTCATGCATCGCGCCAACGATAATATCCGCTCg  <  1:2287780/69‑1 (MQ=255)
                                               cAACCGCGAGAAACCAAACTCACTGGAAGATGGTGGCTCATGCATCGCGCCAACGATAATATCCGCTCg  <  1:3113997/69‑1 (MQ=255)
                                               cAACCGCGAGAAACCAAACTCACTGGAAGATGGTGGCTCATGCATCGCGCCAACGATAATATCCGCTCg  <  1:1615189/69‑1 (MQ=255)
                                                acccGCGAGAAACCAAACTCACTGGAAGATGGTGGCTCATGCATCGCGCCAACGATAATATCCGCTCg  <  1:1641659/66‑1 (MQ=255)
                                                aaCCGCGAGAAACCAAACTCACTGGAAGATGGTGGCTCATGCATCGCGCCAACGATAATATCCGCTCg  <  1:2461478/68‑1 (MQ=255)
                                                aaCCGCGAGAAACCAAACTCACTGGAAGATGGTGGCTCATGCATCGCGCCAACGATAATATCCGCTCg  <  1:350470/68‑1 (MQ=255)
                                                aaCCGCGAGAAACCAAACTCACTGGAAGATGGTGGCTCATGCATCGCGCCAACGATAATATCCGCTCg  <  1:1159347/68‑1 (MQ=255)
                                                     |                                                              
GCTAACGGATGATGAGGCGCGACCGCAAAGACTTGTTCCAGATCGCCCAACCGTGAAAAACCAAACTCACTGGAAGATGGTGGCTCATGCATCGCGCCAACAATAATATCCGCTCG  >  minE/1308253‑1308368

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