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 2,160,046 G→A 21.1% A15A (GCG→GCA)  sfsB → DNA‑binding transcriptional regulator

Read alignment evidence...
  seq id position ref new freq score (cons/poly) reads annotation genes product
*minE2,160,0460GA21.1% 200.2 / 38.1 136A15A (GCG→GCA) sfsBDNA‑binding transcriptional regulator
Reads supporting (aligned to +/- strand):  ref base G (54/53);  new base A (26/3);  total (80/56)
Fisher's exact test for biased strand distribution p-value = 9.40e-05
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 9.98e-01

Only 100 of 136 total aligned reads displayed.

CTTAAGGAGTGAGGAAAAATGGAAAGTAATTTCATTGACTGGCATCCCGCTGACATCATTGCGGGTTTGCGCAAGAAGGGAACGTCAATGGCGGCGGAATCTCGCAGAAATGGTTTGAGTTCCTCA  >  minE/2159984‑2160109
                                                              |                                                               
cTTAAGGAGTGAGGAAAAATGGAAAGTAATTTCATTGACTGGCATCCCGCTTACATCATTGCGGGTTTg                                                           >  1:2237512/1‑69 (MQ=255)
cTTAAGGAGTGAGGAAAAATGGAAAGTAATTTCATTGACTGGCATCCCGCTGACATCATTGCGGGttt                                                            >  1:380406/1‑68 (MQ=255)
cTTAAGGAGTGAGGAAAAATGGAAAGTAATTTCATTGACTGGCATCCCGCTGACATCATTGCGGGTTTg                                                           >  1:3421300/1‑69 (MQ=255)
cTTAAGGAGTGAGGAAAAATGGAAAGTAATTTCATTGACTGGCATCCCGCTGACATCATTGCGGGTTTg                                                           >  1:2780763/1‑69 (MQ=255)
cTTAAGGAGTGAGGAAAAATGGAAAGTAATTTCATTGACTGGCATCCCGCTGACATCATTGCGGGTTTg                                                           >  1:2803124/1‑69 (MQ=255)
cTTAAGGAGTGAGGAAAAATGGAAAGTAATTTCATTGACTGGCATCCCGCTGACATCATTGCGGGTTTg                                                           >  1:2098428/1‑69 (MQ=255)
cTTAAGGAGTGAGGAAAAATGGAAAGTAATTTCATTGACTGGCATCCCGCTGACATCATTGCGGGTTTg                                                           >  1:1837860/1‑69 (MQ=255)
cTTAAGGAGTGAGGAAAAATGGAAAGTAATTTCATTGACTGGCATCCCGCTGACATCATTGCGGGTTTg                                                           >  1:1123463/1‑69 (MQ=255)
cTTAAGGAGTGAGGAAAAATGGAAAGTAATTTCATTGACTGGCATCCCGCTGACATCATTGCGGGTTTg                                                           >  1:1770988/1‑69 (MQ=255)
cTTAAGGAGTGAGGAAAAATGGAAAGTAATTTCATTGACTGGCATCCCGCTGACATCATTGCGGGTTTg                                                           >  1:2269195/1‑69 (MQ=255)
cTTAAGGAGTGAGGAAAAATGGAAAGTAATTTCATTGACTGGCAGCCCGCTGACATCATTGCGGGTTTg                                                           >  1:3308296/1‑69 (MQ=255)
      gAGTGAGGAAAAATGGAAATTAATTTCATTGACTGGCATCCCGCTGACATCATTGCGGGTTTGCGCaag                                                     <  1:1441511/69‑1 (MQ=255)
      gAGTGAGGAAAAATGGAAAGTAATTTCATTGACTGGCATCCCGCTGACATCATTGCGGGTTTGCGCaag                                                     <  1:675420/69‑1 (MQ=255)
      gAGTGAGGAAAAATGGAAAGTAATTTCATTGACTGGCATCCCGCTGACATCATTGCGGGTTTGCGCaag                                                     <  1:744785/69‑1 (MQ=255)
      gAGTGAGGAAAAATGGAAAGTAATTTCATTGACTGGCATCCCGCTGACATCATTGCGGGTTTGCGCaag                                                     <  1:2705121/69‑1 (MQ=255)
      gAGTGAGGAAAAATGGAAAGTAATTTCATTGACTGGCATCCCGCTGACATCATTGCGGGTTTGCGCaag                                                     <  1:2714322/69‑1 (MQ=255)
      gAGTGAGGAAAAATGGAAAGTAATTTCATTGACTGGCATCCCGCTGACATCATTGCGGGTTTGCGCaag                                                     <  1:2908664/69‑1 (MQ=255)
      gAGTGAGGAAAAATGGAAAGTAATTTCATTGACTGGCATCCCGCTGACATCATTGCGGGTTTGCGCaag                                                     <  1:848611/69‑1 (MQ=255)
           aGGAAAAATGGAAAGTAATTTCATTGACTGGCATCCCGCTGACATCATTGCGGGTTTGCGCaag                                                     >  1:260502/1‑64 (MQ=255)
           aGGAAAAATGGAAAGTAATTTCATTGACTGGCATCCCGCTGACATCATTGCGGGTTTGCGCaag                                                     >  1:1921593/1‑64 (MQ=255)
           aGGAAAAATGGAAAGTAATTTCATTGACTGGCATCCCGCTGACATCATTGCGGGTTTGCGCaag                                                     >  1:2488766/1‑64 (MQ=255)
           aGGAAAAATGGAAAGTAATTTCATTGACTGGCATCCCGCTGACATCATTGCGGGTTTGCGCaag                                                     >  1:3115160/1‑64 (MQ=255)
           aGGAAAAATGGAAAGTAATTTCATTGACTGGCATCCCGCTGACATCATTGCGGGTTTGCGCaag                                                     >  1:2059377/1‑64 (MQ=255)
           aGGAAAAATGGAAAGTAATTTCATTGACTGGCATCCCGCTGACATCATTGCGGGTTTGCGCAAGAAggg                                                <  1:3035606/69‑1 (MQ=255)
           aGGAAAAATGGAAAGTAATTTCATTGACTGGCATCCCGCTGACATCATTGCGGGTTTGCGCAAGAAggg                                                >  1:3171243/1‑69 (MQ=255)
           aGGAAAAATGGAAAGTAATTTCATTGACTGGCATCCCGCTGACATCATTGCGGGTTTGCGCAAGAAggg                                                >  1:810143/1‑69 (MQ=255)
           aGGAAAAATGGAAAGTAATTTCATTGACTGGCATCCCGCTGACATCATTGCGGGTTTGCGCAAGAAggg                                                >  1:1914375/1‑69 (MQ=255)
                 gaTGGAAAGTAATTTCATTGACTGGCATCCCGCTGACATCATTGCAGGTTTGCGCAAGAAGGGAACGTc                                          <  1:1961425/68‑1 (MQ=255)
                 gaTGGAAAGTAATTTCATTGACTGGCATCCCGCTGACATCATTGCAGGTTTGCGCAAGAAGGGAACGTc                                          <  1:265033/68‑1 (MQ=255)
                 gaTGGAAAGTAATTTCATTGACTGGCATCCCGCTGACATCATTGCAGGTTTGCCCAAGAAGGGAACGTc                                          <  1:359589/68‑1 (MQ=255)
                 aaTGGAAAGTAATTTCATTGACTGGCATCCCGCTGACATCATTGCGGGTTTGCGCAAGAAGGGAACGTc                                          <  1:2833779/69‑1 (MQ=255)
                 aaTGGAAAGTAATTTCATTGACTGGCATCCCGCTGACATCATTGCGGGTTTGCGCAAGAAGGGAACGTc                                          <  1:2946861/69‑1 (MQ=255)
                 aaTGGAAAGTAATTTCATTGACTGGCATCCCGCTGACATCATTGCGGGTTTGCGCAAGAAGGGAACGTc                                          <  1:818838/69‑1 (MQ=255)
                 aaTGGAAAGTAATTTCATTGACTGGCATCCCGCTGACATCATTGCGGGTTTGCGCAAGAAGGGAACGTc                                          <  1:960051/69‑1 (MQ=255)
                 aaTGGAAAGTAATTTCATTGACTGGCATCCCGCTGACATCATTGCGGGTTTGCGCAAGAAGGGAACGTc                                          <  1:1066408/69‑1 (MQ=255)
                 aaTGGAAAGTAATTTCATTGACTGGCATCCCGCTGACATCATTGCGGGTTTGCGCAAGAAGGGAACGTc                                          <  1:1498281/69‑1 (MQ=255)
                 aaTGGAAAGTAATTTCATTGACTGGCATCCCGCTGACATCATTGCGGGTTTGCGCAAGAAGGGAACGTc                                          <  1:1828994/69‑1 (MQ=255)
                       aaGTAATTTCATTGACTGGCATCCCGCTGACATCATTGCGGGTTTGCGCAAGAAGGGAACGTCAATggc                                    >  1:1683320/1‑69 (MQ=255)
                                       tGGCATCCCGCTGACATCATTGCGGGTTTGCGCAAGAAGGGAACGTCAATGGCGGCGGAATCTCGCAGa                    <  1:1164579/69‑1 (MQ=255)
                                       tGGCATCCCGCTGACATCATTGCGGGTTTGCGCAAGAAGGGAACGTCAATGGCGGCGGAATCTCGCAGa                    <  1:1313530/69‑1 (MQ=255)
                                       tGGCATCCCGCTGACATCATTGCGGGTTTGCGCAAGAAGGGAACGTCAATGGCGGCGGAATCTCGCAGa                    <  1:3141885/69‑1 (MQ=255)
                                       tGGCATCCCGCTGACATCATTGCGGGTTTGCGCAAGAAGGGAACGTCAATGGCGGCGGAATCTCGCAGa                    <  1:1384693/69‑1 (MQ=255)
                                       tGGCATCCCGCTGACATCATTGCGGGTTTGCGCAAGAAGGGAACGTCAATGGCGGCGGAATCTCGCAGa                    <  1:1447307/69‑1 (MQ=255)
                                       tGGCATCCCGCTGACATCATTGCGGGTTTGCGCAAGAAGGGAACGTCAATGGCGGCGGAATCTCGCAGa                    <  1:1220752/69‑1 (MQ=255)
                                       tGGCATCCCGCTGACATCATTGCGGGTTTGCGCAAGAAGGGAACGTCAATGGCGGCGGAATCTCGCAGa                    <  1:1739455/69‑1 (MQ=255)
                                       tGGCATCCCGCTGACATCATTGCGGGTTTGCGCAAGAAGGGAACGTCAATGGCGGCGGAATCTCGCAGa                    <  1:1096300/69‑1 (MQ=255)
                                       tGGCATCCCGCTGACATCATTGCGGGTTTGCGCAAGAAGGGAACGTCAACGGCGGCGGAATCTCGCAGa                    <  1:824462/69‑1 (MQ=255)
                                       tGGCATCCCGCTGACATCATTGCAGGTTTGCGCAAGAAGTGAACGTCAATgg                                     >  1:1365245/1‑52 (MQ=255)
                                       tGGCATCCCGCTGACATCATTGCAGGTTTGCGCAAGAAGGGAACGTCAATggcg                                   >  1:1289384/1‑54 (MQ=255)
                                       tGGCATCCCGCTGACATCATTGCAGGTTTGCGCAAGAAGGGAACGTCAATggcg                                   >  1:3231419/1‑54 (MQ=255)
                                       tGGCATCCCGCTGACATCATTGCAGGTTTGCGCAAGAAGGGAACGTCAATggcg                                   >  1:2081736/1‑54 (MQ=255)
                                       tGGCATCCCGCTGACATCATTGCAGGTTTGCGCAAGAAGGGAACGTCAATggcg                                   >  1:1436992/1‑54 (MQ=255)
                                       tGGCATCCCGCTGACATCATTGCAGGTTTGCGCAAGAAGGGAACGTCAATggcg                                   >  1:3377278/1‑54 (MQ=255)
                                       tGGCATCCCGCTGACATCATTGCAGGTTTGCGCAAGAAGGGAACGTCAATggcg                                   >  1:2988261/1‑54 (MQ=255)
                                       tGGCATCCCGCTGACATCATTGCAGGTTTGCGCAAGAAGGGAACGTCAATggcg                                   >  1:2096699/1‑54 (MQ=255)
                                       tGGCATCCCGCTGACATCATTGCAGGTTTGCGCAAGAAGGGAACGTCAATggcg                                   >  1:1833108/1‑54 (MQ=255)
                                       tGGCATCCCGCTGACATCATTGCAGGTTTGCGCAAGAAGGGAACGTCAATggcg                                   >  1:34134/1‑54 (MQ=255)
                                       tGGCATCCCGCTGACATCATTGCAGGTTTGCGCAAGAAGGGAACGTCAATggcg                                   >  1:2331800/1‑54 (MQ=255)
                                       tGGCATCCCGCTGACATCATTGCAGGTTTGCGCAAGAAGGGAACGTCAATggcg                                   >  1:2215301/1‑54 (MQ=255)
                                       tGGCATCCCGCTGACATCATTGCAGGTTTGCGCAAGAAGGGAACGTCAATggcg                                   >  1:2775350/1‑54 (MQ=255)
                                       tGGCATCCCGCTGACATCATTGCAGGTTTGCGCAAGAAGGGAACGTCAATggcg                                   >  1:1216752/1‑54 (MQ=255)
                                       tGGCATCCCGCTGACATCATTGCAGGTTTGCGCAAGAAGGGAACGTCAATggcg                                   >  1:547003/1‑54 (MQ=255)
                                       tGGCATCCCGCTGACATCATTGCAGGTTTGCGCAAGAAGGGAACGTCAATggcg                                   >  1:924540/1‑54 (MQ=255)
                                       tGGCATCCCGCTGACATCATTGCAGGTTTGCGCAAGAAGGGAACGTCAATggca                                   >  1:1769539/1‑53 (MQ=255)
                                       tGGCATCACGCTGACATCATTGCAGGTTTGCGCAAGAAGGGAACGTCAAt                                       >  1:2055760/1‑50 (MQ=255)
                                       tGGCATACCGCTGACATCATTGCAGGTTTGCGCAAGAAGGGAACGTCAATggcg                                   >  1:2500093/1‑54 (MQ=255)
                                             cccGCTGACATCATTGCGGGTTTGCGCAAGAAGGGAACGTc                                          <  1:1307012/41‑1 (MQ=255)
                                              ccGCTGACATCATTGCGGGTTTGCGCAAGAAGGGAACGTCa                                         >  1:732962/1‑41 (MQ=255)
                                              ccGCTGACATCATTGCGGGTTTGCGCAAGAAGGGAACGTCa                                         <  1:421758/41‑1 (MQ=255)
                                              ccGCTGACATCATTGCGGGTTTGCGCAAGAAGGGAACGTCa                                         <  1:428533/41‑1 (MQ=255)
                                              ccGCTGACATCATTGCGGGTTTGCGCAAGAAGGGAACGTCa                                         >  1:1107128/1‑41 (MQ=255)
                                              ccGCTGACATCATTGCGGGTTTGCGCAAGAAGGGAACGTCa                                         <  1:437695/41‑1 (MQ=255)
                                              ccGCTGACATCATTGCGGGTTTGCGCAAGAAGGGAACGTCa                                         <  1:736293/41‑1 (MQ=255)
                                              ccGCTGACATCATTGCGGGTTTGCGCAAGAAGGGAACGTCa                                         <  1:3309270/41‑1 (MQ=255)
                                              ccGCTGACATCATTGCGGGTTTGCGCAAGAAGGGAACGTCa                                         <  1:3190867/41‑1 (MQ=255)
                                              ccGCTGACATCATTGCGGGTTTGCGCAAGAAGGGAACGTCa                                         <  1:187227/41‑1 (MQ=255)
                                              ccGCTGACATCATTGCGGGTTTGCGCAAGAAGGGAACGTCa                                         >  1:3014967/1‑41 (MQ=255)
                                              ccGCTGACATCATTGCGGGTTTGCGCAAGAAGGGAACGTCa                                         <  1:2852379/41‑1 (MQ=255)
                                              ccGCTGACATCATTGCGGGTTTGCGCAAGAAGGGAACGTCa                                         >  1:1805309/1‑41 (MQ=255)
                                              ccGCTGACATCATTGCGGGTTTGCGCAAGAAGGGAACGTCa                                         >  1:1104619/1‑41 (MQ=255)
                                              ccGCTGACATCATTGCGGGTTTGCGCAAGAAGGGAACGTCa                                         <  1:3239796/41‑1 (MQ=255)
                                              ccGCTGACATCATTGCGGGTTTGCGCAAGAAGGGAACGTCa                                         <  1:2644598/41‑1 (MQ=255)
                                              ccGCTGACATCATTGCGGGTTTGCGCAAGAAGGGAACGTCAATGGCGGCGGAATCTCGCAGAAATGGt              >  1:169175/1‑68 (MQ=255)
                                              ccGCTGACATCATTGCGGGTTTGCGCAAGAAGGGAACGTCAATGGCGGCGGAATCTCGCAGAAATGGt              >  1:2299713/1‑68 (MQ=255)
                                              ccGCTGACATCATTGCGGGTTTGCGCAAGAAGGGAACGTCAATGGCGGCGGAATCTCGCAGAAATGGt              >  1:2303573/1‑68 (MQ=255)
                                              ccGCTGACATCATTGCGGGTTTGCGCAAGAAGGGAACGTCAATGGCGGCGGAATCTCGCAGAAATGGt              >  1:49033/1‑68 (MQ=255)
                                              ccGCTGACATCATTGCGGGTTTGCGCAAGAAGGGAACGTCAATGGCGGCGGAATCTCGCAGAAATGGt              >  1:822098/1‑68 (MQ=255)
                                              ccGCTGACATCATTGCGGGTTTGCGCAAGAAGGGAACGTCAATGGCGGCGGAATCTCGCAGAAATGGt              >  1:399045/1‑68 (MQ=255)
                                              ccGCTGACATCATTGCGGGTTTGCGCAAGAAGGGAACGTCAATGGCGGCGGAATCTCGCAGAAATGGt              >  1:2807104/1‑68 (MQ=255)
                                              ccGCTGACATCATTGCGGGTTTGCGCAAGAAGGGAACGTCAATGGCGGCGGAATCTCGCAGAAATGGt              >  1:3159277/1‑68 (MQ=255)
                                                  tGACATCATTGCGGGTTTGCGCAAGAAGGGAACGTCAATGGCGGCGGAATCTCGCAGAAATGGTTTGAg         <  1:1606412/69‑1 (MQ=255)
                                                        catTGCGGGTTTGCGCAAGATGGGAACGTCAATGGCGGCGGAATCTCGCAGAAATGGTTTGAGTTCCTc   >  1:3415222/1‑69 (MQ=255)
                                                        catTGCGGGTTTGCGCAAGAAGGGAACGTCAATGGCGGCGGAATCTCGCAGAAATGGTTTGAGTTCCTc   >  1:1951066/1‑69 (MQ=255)
                                                        catTGCGGGTTTGCGCAAGAAGGGAACGTCAATGGCGGCGGAATCTCGCAGAAATGGTTTGAGTTCCTc   >  1:1045920/1‑69 (MQ=255)
                                                        catTGCGGGTTTGCGCAAGAAGGGAACGTCAATGGCGGCGGAATCTCGCAGAAATGGTTTGAGTTCCTc   >  1:1589995/1‑69 (MQ=255)
                                                        catTGCGGGTTTGCGCAAGAAGGGAACGTCAATGGCGGCGGAATCTCGCAGAAATGGTTTGAGTTCCTc   >  1:1692869/1‑69 (MQ=255)
                                                        catTGCGGGTTTGCGCAAGAAGGGAACGTCAATGGCGGCGGAATCTCGCAGAAATGGTTTGAGTTCCTc   >  1:1697374/1‑69 (MQ=255)
                                                        catTGCGGGTTTGCGCAAGAAGGGAACGTCAATGGCGGCGGAATCTCGCAGAAATGGTTTGAGTTCCTc   >  1:2587074/1‑69 (MQ=255)
                                                        catTGCGGGTTTGCGCAAGAAGGGAACGTCAATGGCGGCGGAATCTCGCAGAAATGGTTTGAGTTCCTc   >  1:2549570/1‑69 (MQ=255)
                                                        catTGCGGGTTTGCGCAAGAAGGGAACGTCAATGGCGGCGGAATCTCGCAGAAATGGTTTGAGTTCCTc   >  1:2007333/1‑69 (MQ=255)
                                                              |                                                               
CTTAAGGAGTGAGGAAAAATGGAAAGTAATTTCATTGACTGGCATCCCGCTGACATCATTGCGGGTTTGCGCAAGAAGGGAACGTCAATGGCGGCGGAATCTCGCAGAAATGGTTTGAGTTCCTCA  >  minE/2159984‑2160109

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