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 2,022,917 G→A 30.3% H330H (CAC→CAT)  ygiQ ← conserved hypothetical protein

Read alignment evidence...
  seq id position ref new freq score (cons/poly) reads annotation genes product
*minE2,022,9170GA30.3% 90.0 / 42.0 92H330H (CAC→CAT) ygiQconserved hypothetical protein
Reads supporting (aligned to +/- strand):  ref base G (35/29);  new base A (9/19);  total (44/48)
Fisher's exact test for biased strand distribution p-value = 6.90e-02
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 8.94e-01

GTCCATCTCTTCGGTAGAAAGCGGAATAGCAGGCGGGTTGATCCACACATAGCGGTCGCCGTGTTTTTGCATCAATGCGCGGGCACAGCCTGGGTTGGTTTCGTGGTGCAGAATACGCGAAGCATG  >  minE/2022857‑2022982
                                                            |                                                                 
gTCCATCTCTTCGGTAGAAAGCGGAATAGCAGGCGGGTTGATCCACACATAGCGGTCGCCGTGTTTTTg                                                           <  1:590267/69‑1 (MQ=255)
gTCCATCTCTTCGGTAGAAAGCGGAATAGCAGGCGGGTTGATCCACACATAGCGGTCGCCGTGTTTTTg                                                           <  1:1155530/69‑1 (MQ=255)
gTCCATCTCTTCGGTAGAAAGCGGAATAGCAGGCGGGTTGATCCACACATAGCGGTCGCCGTGTTTTTg                                                           <  1:2561812/69‑1 (MQ=255)
gTCCATCTCTTCGGTAGAAAGCGGAATAGCAGGCGGGTTGATCCACACATAGCGGTCGCCGTGTTTTTg                                                           <  1:1929460/69‑1 (MQ=255)
     tctcTTCGGTAGAAAGCGGAATAGCAGGCGGGTTGATCCACACATAGCGGTCGCCGTGTTTTTGCATc                                                       <  1:1606864/68‑1 (MQ=255)
     tctcTTCGGTAGAAAGCGGAATAGCAGGCGGGTTGATCCACACATAGCGGTCGCCGTGTTTTTGCATc                                                       <  1:802565/68‑1 (MQ=255)
      ctctTCGGTAGGAAGCGGAATAGCAGGCGGGTTGATCCACACATAGCGGTCGCCGTGTTTTTGCATCaa                                                     >  1:1768058/1‑69 (MQ=255)
      ctctTCGGTAGAAAGCGGAATAGCATGCGGGTTGATCCACACATAGCGGTCGCCGTGTTTTTGCATCaa                                                     >  1:2089286/1‑69 (MQ=255)
      ctctTCGGTAGAAAGCGGAATAGCAGGCGGGTTGATCCACACATAGCGGTCGCCGTGTTTTTGCATCaa                                                     >  1:2310764/1‑69 (MQ=255)
      ctctTCGGTAGAAAGCGGAATAGCAGGCGGGTTGATCCACACATAGCGGTCGCCGTGTTTTTGCATCaa                                                     >  1:1667268/1‑69 (MQ=255)
      ctctTCGGTAGAAAGCGGAATAGCAGGCGGGTTGATCCACACATAGCGGTCGCCGTGTTTTTGCATCaa                                                     >  1:30542/1‑69 (MQ=255)
      ctctTCGGTAGAAAGCGGAATAGCAGGCGGGTTGATCCACACATAGCGGTCGCCGTGTTTTTGCATCaa                                                     >  1:2837099/1‑69 (MQ=255)
      ctctTCGGTAGAAAGCGGAATAGCAGGCGGGTTGATCCACACATAGCGGTCGCCGTGTTTTTGCATCaa                                                     >  1:1182125/1‑69 (MQ=255)
       tctTCGGTAGAAAGCGGAATAGCAGGCGGGTTGATCCACACATAGCGGTCGCCGTGTTTTTGCATCaa                                                     >  1:1487783/1‑68 (MQ=255)
       tctTCGGTAGAAAGCGGAATAGCAGGCGGGTTGATCCACACATAGCGGTCGCCGTGTTTTTGCATCAAt                                                    >  1:3026785/1‑69 (MQ=255)
       tctTCGGTAGAAAGCGGAATAGCAGGCGGGTTGATCCACACATAGCGGTCGCCGTGTTTTTGCATCAAt                                                    >  1:2393106/1‑69 (MQ=255)
       tctTCGGTAGAAAGCGGAATAGCAGGCGGGTTGATCCACACATAGCGGTCGCCGTGTTTTTGCATCAAt                                                    >  1:3366613/1‑69 (MQ=255)
       tctTCGGTAGAAAGCGGAATAGCAGGCGGGTTGATCCACACATAGCGGTCGCCGTGTTTTTGCATCAAt                                                    >  1:2314161/1‑69 (MQ=255)
       tctTCGGTAGAAAGCGGAATAGCAGGCGGGTTGATCCACACATAGCGGTCGCCGTGTTTTTGCATCAAt                                                    >  1:2300609/1‑69 (MQ=255)
       tctTCGGTAGAAAGCGGAATAGCAGGCGGGTTGATCCACACATAGCGGTCGCCGTGTTTTTGCATCAAt                                                    >  1:391442/1‑69 (MQ=255)
       tctTCGGTAGAAAGCGGAATAGCAGGCGGGTTGATCCACACATAGCGGTCGCCGTGTTTTTGCATCAAt                                                    >  1:1125372/1‑69 (MQ=255)
       tctTCGGTAGAAAGCGGAATAGCAGGCGGGTTGATCCACACATAGCGGTCGCCGTGTTTTTGCATCAAt                                                    >  1:824370/1‑69 (MQ=255)
           cGGTAGAAAGCGGAATAGCAGGCGGGTTGATCCACACATAGCGGTCGCCGTGTTTTTGCATCAATgcgc                                                >  1:158183/1‑69 (MQ=255)
           cGGTAGAAAGCGGAATAGCAGGCGGGTTGATCCACACATAGCGGTCGCCGTGTTTTTGCATCAATgcgc                                                >  1:1118474/1‑69 (MQ=255)
           cGGTAGAAAGCGGAATAGCAGGCGGGTTGATCCACACATAGCGGTCGCCGTGTTTTTGCATCAATgcgc                                                >  1:1542446/1‑69 (MQ=255)
           cGGTAGAAAGCGGAATAGCAGGCGGGTTGATCCACACATAGCGGTCGCCGTGTTTTTGCATCAATgcgc                                                >  1:1495510/1‑69 (MQ=255)
           cGGTAGAAAGCGGAATAGCAGGCGGGTTGATCCACACATAGCGGTCGCCGTGTTTTTGCATCAATgcgc                                                >  1:2981766/1‑69 (MQ=255)
           cGGTAGAAAGCGGAATAGCAGGCGGGTTGATCCACACATAGCGGTCGCCGTGTTTTTGCATCAATgcgc                                                >  1:1389767/1‑69 (MQ=255)
           cGGTAGAAAGCGGAATAGCAGGCGGGTTGATCCACACATAGCGGTCGCCGTGTTTTTGCATCAATgcgc                                                >  1:791758/1‑69 (MQ=255)
           cGGTAGAAAGCGGAATAGCAGGCGGGTTGATCCACACATAGCGGTCGCCGTGTTTTTGCATCAATgcgc                                                >  1:2057515/1‑69 (MQ=255)
               aGAAAGCGGAATAGCAGGCGGGTTGATCCACACATAGCGGTCGCCGTGTTTTTCCATCaa                                                     >  1:366059/1‑60 (MQ=255)
                                  gtgTTGATCCATACATAGCGGTCGCCATGTTTTTGCATCAATGCGCGGGCGCAGCCTGGGTTAGTTTCg                         <  1:2842892/67‑1 (MQ=255)
                                  gggTTGATCCATACATAGCGGTCGCCATGTTTTTGCATCAATGCGCGGGCGCAGCCTGGGTTAGTTTCg                         <  1:2363335/69‑1 (MQ=255)
                                  gggTTGATCCATACATAGCGGTCGCCATGTTTTTGCATCAATGCGCGGGCGCAGCCTGGGTTAGTTTCg                         <  1:398853/69‑1 (MQ=255)
                                  gggTTGATCCATACATAGCGGTCGCCATGTTTTTGCATCAATGCGCGGGCGCAGCCTGGGTTAGTTTCg                         <  1:866687/69‑1 (MQ=255)
                                  gggTTGATCCATACATAGCGGTCGCCATGTTTTTGCATCAATGCGCGGGCGCAGCCTGGGTTAGTTTCg                         <  1:2687296/69‑1 (MQ=255)
                                  gggTTGATCCATACATAGCGGTCGCCATGTTTTTGCATCAATGCGCGGGCGCAGCCTGGGTTAGTTTCg                         <  1:2816681/69‑1 (MQ=255)
                                  gggTTGATCCATACATAGCGGTCGCCATGTTTTTGCATCAATGCGCGGGCGCAGCCTGGGTTAGTTTCg                         <  1:769479/69‑1 (MQ=255)
                                  gggTTGATCCATACATAGCGGTCGCCATGTTTTTGCATCAATGCGCGGGCGCAGCCTGGGTTAGTTTCg                         <  1:2840562/69‑1 (MQ=255)
                                  gggTTGATCCATACATAGCGGTCGCCATGTTTTTGCATCAATGCGCGGGCGCAGCCTGGGTTAGTTTCg                         <  1:688120/69‑1 (MQ=255)
                                  gggTTGATCCATACATAGCGGTCGCCATGTTTTTGCATCAATGCGCGGGCGCAGCCTGGGTTAGTTTCg                         <  1:661782/69‑1 (MQ=255)
                                  gggTTGATCCATACATAGCGGTCGCCATGTTTTTGCATCAATGCGCGGGCGCAGCCTGGGTTAGTTTCg                         <  1:657783/69‑1 (MQ=255)
                                  gggTTGATCCATACATAGCGGTCGCCATGTTTTTGCATCAATGCGCGGGCGCAGCCTGGGTTAGTTTCg                         <  1:337131/69‑1 (MQ=255)
                                  gggTTGATCCATACATAGCGGTCGCCATGTTTTTGCATCAATGCGCGGGCGCAGCCTGGGTTAGTTTCg                         <  1:20975/69‑1 (MQ=255)
                                  gggTTGATCCATACATAGCGGTCGCCATGTTTTTGCATCAATGCGCGGGCGCAGCCTGGGTTAGTTTCg                         <  1:161787/69‑1 (MQ=255)
                                  gggTTGATCCATACATAGCGGTCGCCATGTTTTTGCATCAATGCGCGGGCGCAGCCTGGGTTAGTTTCg                         <  1:1591747/69‑1 (MQ=255)
                                  gggTTGATCCATACATAGCGGTCGCCATGTTTTTGCATCAATGCGCGGGCGCAGCCTGGGTTAGTTTCg                         <  1:2086360/69‑1 (MQ=255)
                                  gggTTGATCCATACATAGCGGTCGCCATGTTTTTGCATCAATGCGCGGGCGCAGCCTGGGTTAGTTTCg                         <  1:1812754/69‑1 (MQ=255)
                                  gggTTGATCCATACATAGCGGTCGCCATGTTTTTGCATCAATGCGCGGGCGCAGCCTGGGTTAGTTTCg                         <  1:1388037/69‑1 (MQ=255)
                                  gggTTGATCCATACATAGCGGTCGCCATGTTTTTGCATCAATGCGCGGGCGCAGCCTGGGTTAGTTTCg                         <  1:1969538/69‑1 (MQ=255)
                                  gggTTGATCCACACATAGCTGTCGCCGTGTTTTTGCATCAATGCGCGGGCACAGCCTGggttggt                             <  1:1585849/65‑1 (MQ=255)
                                  gggTTGATCCACACATAGCGGTCGCCGTGTTTTTGCATCAATGCGCGGGCACAGCCTGggttggt                             <  1:1602754/65‑1 (MQ=255)
                                  gggTTGATCCACACATAGCGGTCGCCGTGTTTTTGCATCAATGCGCGGGCACAGCCTGggttggt                             <  1:3134171/65‑1 (MQ=255)
                                  gggTTGATCCACACATAGCGGTCGCCGTGTTTTTGCATCAATGCGCGGGCACAGCCTGggttggt                             <  1:1430781/65‑1 (MQ=255)
                                  gggTTGATCCACACATAGCGGTCGCCGTGTTTTTGCATCAATGCGCGGGCACAGCCTGggttggt                             <  1:2924466/65‑1 (MQ=255)
                                  gggTTGATCCACACATAGCGGTCGCCGTGTTTTTGCATCAATGCGCGGGCACAGCCTGggttggt                             <  1:820201/65‑1 (MQ=255)
                                  gggTTGATCCACACATAGCGGTCGCCGTGTTTTTGCATCAATGCGCGGGCACAGCCTGggttggt                             <  1:2392297/65‑1 (MQ=255)
                                  gggTTGATCCACACATAGCGGTCGCCGTGTTTTTGCATCAATGCGCGGGCACAGCCTGggttggt                             <  1:2558357/65‑1 (MQ=255)
                                   ggTTGATCCACACATAGCGGTCGCCGTGTTTTTGCATCAATGCGCGGGCACAGCCTGggttggt                             <  1:794522/64‑1 (MQ=255)
                                          ccACACATAGCGGTCGCCGTGTTTTTGCATCAATGCGCGGGCACAGCCTGGGTTGGTTTCGTGGTGCAg                 <  1:895340/69‑1 (MQ=255)
                                              acaTAGCGGTCGCCGTGTTTTTGCATCAATGCGCGGGCACAGCCTGGGTTGGTTTCGTGGTGCAGAATa             <  1:1451155/69‑1 (MQ=255)
                                              acaTAGCGGTCGCCGTGTTTTTGCATCAATGCGCGGGCACAGCCTGGGTTGGTTTCGTGGTGCAGAATa             <  1:2734385/69‑1 (MQ=255)
                                              acaTAGCGGTCGCCGTGTTTTTGCATCAATGCGCGGGCACAGCCTGGGTTGGTTTCGTGGTGCAGAATa             <  1:1755383/69‑1 (MQ=255)
                                              acaTAGCGGTCGCCGTGTTTTTGCATCAATGCGCGGGCACAGCCTGGGTTGGTTTCGTGGTGCAGAATa             <  1:1769760/69‑1 (MQ=255)
                                              acaTAGCGGTCGCCATGTTTTTGCATCAATGCGCGGGCGCAGCCTGggtta                               >  1:1716454/1‑50 (MQ=38)
                                              acaTAGCGGTCGCCATGTTTTTGCATCAATGCGCGGGCGCAGCCTGggtta                               >  1:1379510/1‑50 (MQ=38)
                                              acaTAGCGGTCGCCATGTTTTTGCATCAATGCGCGGGCGCAGCCTGggtta                               >  1:1466352/1‑50 (MQ=38)
                                              acaTAGCGGTCGCCATGTTTTTGCATCAATGCGCGGGCGCAGCCTGggtta                               >  1:147416/1‑50 (MQ=38)
                                              acaTAGCGGTCGCCATGTTTTTGCATCAATGCGCGGGCGCAGCCTGggtta                               >  1:1563738/1‑50 (MQ=38)
                                              acaTAGCGGTCGCCATGTTTTTGCATCAATGCGCGGGCGCAGCCTGggtta                               >  1:286992/1‑50 (MQ=38)
                                              acaTAGCGGTCGCCATGTTTTTGCATCAATGCGCGGGCGCAGCCTGggtta                               >  1:1086223/1‑50 (MQ=38)
                                              acaTAGCGGTCGCCATGTTTTTGCATCAATGCGCGGGCGCAGCCTGggtta                               >  1:1714260/1‑50 (MQ=38)
                                              acaTAGCGGTCGCCATGTTTTTGCATCAATGCGCGGGCGCAGCCTGggtta                               >  1:2257181/1‑50 (MQ=38)
                                                   gCGGTCGCCGTGTTTTTGCATCAATGCGCGGGCACAGCCTGGGTTGGTTTCGTGGTGCAg                 >  1:960381/1‑60 (MQ=255)
                                                   gCGGTCGCCGTGTTTTTGCATCAATGCGCGGGCACAGCCTGGGTTGGTTTCGTGGTGCAg                 >  1:3299418/1‑60 (MQ=255)
                                                   gCGGTCGCCGTGTTTTTGCATCAATGCGCGGGCACAGCCTGGGTTGGTTTCGTGGTGCAg                 >  1:2471142/1‑60 (MQ=255)
                                                   gCGGTCGCCGTGTTTTTGCATCAATGCGCGGGCACAGCCTGGGTTGGTTTCGTGGTGCAg                 >  1:2069125/1‑60 (MQ=255)
                                                   gCGGTCGCCGTGTTTTTGCATCAATGCGCGGGCACAGCCTGGGTTGGTTTCGTGGTGCAg                 >  1:1903925/1‑60 (MQ=255)
                                                   gCGGTCGCCGTGTTTTTGCATCAATGCGCGGGCACAGCCTGGGTTGGTTTCGTGGTGCAg                 >  1:310085/1‑60 (MQ=255)
                                                     ggTCGCCGTGTTTTTGCATCAATGCGCGGGCACAGCCTGGGTTGGTTTCGTGGTGCAGAATACGCGAAg      <  1:7740/69‑1 (MQ=255)
                                                     ggTCGCCGTGTTTTTGCATCAATGCGCGGGCACAGCCTGGGTTGGTTTCGTGGTGCAGAATACGCGAAg      <  1:1613834/69‑1 (MQ=255)
                                                     ggTCGCCGTGTTTTTGCATCAATGCGCGGGCACAGCCTGGGTTGGTTTCGTGGTGCAGAATACGCGAAg      <  1:3217155/69‑1 (MQ=255)
                                                     ggTCGCCGTGTTTTTGCATCAATGCGCGGGCACAGCCTGGGTTGGTTTCGTGGTGCAGAATACGCGAAg      <  1:453399/69‑1 (MQ=255)
                                                      gTCGCCGTGTTTTTGCATCAATGCGCGGGCACAGCCTGGGTTGGTTTCGTGGTGCAGAATACGCGAAGc     <  1:3196709/69‑1 (MQ=255)
                                                      gTCGCCGTGTTTTTGCATCAATGCGCGGGCACAGCCTGGGTTGGTTTCGTGGTGCAGAATACGCGAAGc     <  1:3235737/69‑1 (MQ=255)
                                                      gTCGCCGTGTTTTTGCATCAATGCGCGGGCACAGCCTGGGTTGGTTTCGTGGTGCAGAATACGCGAAGc     <  1:1971212/69‑1 (MQ=255)
                                                       tCGCCGTGTTTTTGCATCAATGCGCGGGCACAGCCTGGGTTGGTTTCGTGGTGCAGAATACGCGAAGc     <  1:2974537/68‑1 (MQ=255)
                                                       tCGCCGTGTTTTTGCATCAATGCGCGGGCACAGCCTGGGTTGGTTTCGTGGTGCAGAATACGCGAAGc     <  1:1950271/68‑1 (MQ=255)
                                                         gCCGTGTTTTTGCATCAATGCGCGGGCACAGCCTg                                    >  1:3242510/1‑35 (MQ=255)
                                                         gCCGTGTTTTTGCATCAATGCGCGGGCACAGCCTGGGTTGGTTTCGTGGTGCAGAATa             >  1:75015/1‑58 (MQ=255)
                                                         gCCGTGTTTTTGCATCAATGCGCGGGCACAGCCTGGGTTGGTTTCGTGGTGCAGAATACGCGAAGCATg  >  1:1159902/1‑69 (MQ=255)
                                                         gCCGTGTTTTTGCATCAATGCGCGGGCACAGCCTGGGTTGGTTTCGTGGTGCAGAATACGCGAAGCATg  >  1:2361747/1‑69 (MQ=255)
                                                            |                                                                 
GTCCATCTCTTCGGTAGAAAGCGGAATAGCAGGCGGGTTGATCCACACATAGCGGTCGCCGTGTTTTTGCATCAATGCGCGGGCACAGCCTGGGTTGGTTTCGTGGTGCAGAATACGCGAAGCATG  >  minE/2022857‑2022982

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