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
A1 F3 I0 R2 260 44.3 3360226 90.5% 3041004 64.6

Breseq alignment

BRESEQ :: Evidence
Predicted mutation
evidence seq id position mutation freq annotation gene description
RA W3110S.gb 4,254,714 A→T 32.9% E56D (GAA→GAT)  yjbI → conserved hypothetical protein

Read alignment evidence...
  seq id position ref new freq score (cons/poly) reads annotation genes product
*W3110S.gb4,254,7140AT32.9% 86.6 / 67.2 70E56D (GAA→GAT) yjbIconserved hypothetical protein
Reads supporting (aligned to +/- strand):  ref base A (20/27);  new base T (10/13);  total (30/40)
Fisher's exact test for biased strand distribution p-value = 1.00e+00
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 5.04e-01

AAGGTGACGTTATATCGAAGGTGTCTTTTTTATCATCAAATCTACAACATGTAACATTCGAATGTAAAGAAATTGGGGATTGCAATTTTACTACTGCAATAGTTGATAATGTCATATTTAGATGTCGAC  >  W3110S.gb/4254644‑4254772
                                                                      |                                                          
aaGGTGACGTTATATCGAAGGTGTCTTTTTTATCATCAAATCTACAACATGTAACATTCGAATGTAAAGaa                                                            <  1:1657748/71‑1 (MQ=255)
aaGGTGACGTTATATCGAAGGTGTCTTTTTTATCATCAAATCTACAACATGTAACATTCGAATGTAAAGaa                                                            <  1:3305646/71‑1 (MQ=255)
aaGGTGACGTTATATCGAAGGTGTCTTTTTTATCATCAAATCTACAACATGTAACATTCGAATGTAAAGaa                                                            <  1:3211941/71‑1 (MQ=255)
aaGGTGACGTTATATCGAAGGTGTCTTTTTTATCATCAAATCTACAACATGTAACATTCGAATGTAAAGaa                                                            <  1:367695/71‑1 (MQ=255)
aaGGTGACGTTATATCGAAGGTGTCTTTTTTATCATCAAATCTACAACATGTAACATTCGAATGTAAAGaa                                                            <  1:2929089/71‑1 (MQ=255)
aaGGTGACGTTATATCGAAGGTGTCTTTTTTATCATCAAATCTACAACATGTAACATTCGAATGTAAAGaa                                                            <  1:2399597/71‑1 (MQ=255)
aaGGTGACGTTATATCGAAGGTGTCTTTTTTATCATCAAATCTACAACATGTAACATTCGAATGTAAAGaa                                                            <  1:1751943/71‑1 (MQ=255)
aaGGTGACGTTATATCGAAGGTGTCTTTTTTATCATCAAATCTACAACATGTAACATTCGAATGTAAAGaa                                                            <  1:373410/71‑1 (MQ=255)
aaGGTGACGTTATATCGAAGGTGTCTTTTTTATCATCAAATCTACAACATGTAACATTCGAATGTAAAGaa                                                            <  1:1460253/71‑1 (MQ=255)
aaGGTGACGTTATATCGAAGGTGTCTTTTTTATCATCAAATCTACAACATGTAACATTCGAATGTAAAGaa                                                            <  1:495814/71‑1 (MQ=255)
aaGGTGACGTTATATCGAAGGTGTCTTTTTTATCATCAAATCTACAACATGTAACATTCGAATGTAAAGaa                                                            <  1:2549263/71‑1 (MQ=255)
aaGGTGACGTTATATCGAAGGTGTCTTTTTTATCATCAAATCTACAACATGTAACATTCGAATGTAAAGaa                                                            <  1:889795/71‑1 (MQ=255)
aaGGTGACGTTATATCGAAGGTGTCTTTTTTATCATCAAATCTACAACATGTAACATTCGAATGTAAAGaa                                                            <  1:1125570/71‑1 (MQ=255)
  ggTGACGTTATATCGAAGGTGTCTTTTTTATCATCAAATCTACAACATGTAACATTCGAATGTAAAGaa                                                            <  1:2099084/69‑1 (MQ=255)
   gTGACGTTATATCGAAGGTGTCTTTTTTATCATCAAATCTACAACATGTAACATTCGAATGTAAAGaa                                                            <  1:3092776/68‑1 (MQ=255)
   gTGACGTTATATCGAAGGTGTCTTTTTTATCATCAAATCTACAACATGTAACATTCGAATGTAAAGaa                                                            <  1:902748/68‑1 (MQ=255)
     gACGTTATATCGAAGGTGTCTTTTTTATCATCAAATCTACAACATGTAACATTCGAATGTAAAGAAATTgg                                                       >  1:2411321/1‑71 (MQ=255)
     gACGTTATATCGAAGGTGTCTTTTTTATCATCAAATCTACAACATGTAACATTCGAATGTAAAGAAATTgg                                                       >  1:720508/1‑71 (MQ=255)
     gACGTTATATCGAAGGTGTCTTTTTTATCATCAAATCTACAACATGTAACATTCGAATGTAAAGAAATTgg                                                       >  1:2518032/1‑71 (MQ=255)
     gACGTTATATCGAAGGTGTCTTTTTTATCATCAAATCTACAACATGTAACATTCGAATGTAAAGAAATTgg                                                       >  1:1975031/1‑71 (MQ=255)
     gACGTTATATCGAAGGTGTCTTTTTTATCATCAAATCTACAACATGTAACATTCGAATGTAAAGAAATTgg                                                       >  1:2534260/1‑71 (MQ=255)
     gACGTTATATCGAAGGTGTCTTTTTTATCATCAAATCTACAACATGTAACATTCGAATGTAAAGAAATTgg                                                       >  1:2889456/1‑71 (MQ=255)
     gACGTTATATCGAAGGTGTCTTTTTTATCATCAAATCTACAACATGTAACATTCGAATGTAAAGAAATTgg                                                       >  1:2233818/1‑71 (MQ=255)
     gACGTTATATCGAAGGTGTCTTTTTTATCATCAAATCTACAACATGTAACATTCGAATGTAAAGAAATTgg                                                       >  1:3094591/1‑71 (MQ=255)
     gACGTTATATCGAAGGTGTCTTTTTTATCATCAAATCTACAACATGTAACATTCGAATGTAAAGAAATTgg                                                       >  1:3214249/1‑71 (MQ=255)
           atatCGAAGGTGTCTTTTTTATCATCAAATCTACAACATGTAACATTCGAATGTAAAGAAATTGGGGATTg                                                 >  1:587673/1‑71 (MQ=255)
           atatCGAAGGTGTCTTTTTTATCATCAAATCTACAACATGTAACATTCGAATGTAAAGAAATTGGGGATTg                                                 >  1:1569142/1‑71 (MQ=255)
             atCGAAGGTGTCTTTTTTATCATCAAATCTACAACATGTAACATTCGAATGTAAAGaa                                                            <  1:1991093/58‑1 (MQ=255)
              tCGAAGGTGTCTTTTTTATCATCAAATCTACAACATGTAACATTCGAATGTAAAGaa                                                            <  1:942834/57‑1 (MQ=255)
              tCGAAGGTGTCTTTTTTATCATCAAATCTACAACATGTAACATTCGAATGTAAAGaa                                                            <  1:2610663/57‑1 (MQ=255)
              tCGAAGGTGTCTTTTTTATCATCAAATCTACAACATGTAACATTCGAATGTAAAGaa                                                            <  1:2007131/57‑1 (MQ=255)
              tCGAAGGTGTCTTTTTTATCATCAAATCTACAACATGTAACATTCGAATGTAAAGATATTGGGGATTGCaa                                              >  1:1198195/1‑71 (MQ=255)
              tCGAAGGTGTCTTTTTTATCATCAAATCTACAACATGTAACATTCGAATGTAAAGATATTGGGGATTGCaa                                              >  1:1878593/1‑71 (MQ=255)
              tCGAAGGTGTCTTTTTTATCATCAAATCTACAACATGTAACATTCGAATGTAAAGATATTGGGGATTGCaa                                              >  1:2133871/1‑71 (MQ=255)
              tCGAAGGTGTCTTTTTTATCATCAAATCTACAACATGTAACATTCGAATGTAAAGATATTGGGGATTGCaa                                              >  1:841152/1‑71 (MQ=255)
              tCGAAGGTGTCTTTTTTATCATCAAATCTACAACATGTAACATTCGAATGTAAAGATATTGGGGATTGCaa                                              >  1:2873563/1‑71 (MQ=255)
              tCGAAGGTGTCTTTTTTATCATCAAATCTACAACATGTAACATTCGAATGTAAAGATATTGGGGATTGCaa                                              >  1:365655/1‑71 (MQ=255)
              tCGAAGGTGTCTTTTTTATCATCAAATCTACAACATGTAACATTCGAATGTAAAGATATTGGGGATTGCaa                                              >  1:2433507/1‑71 (MQ=255)
              tCGAAGGTGTCTTTTTTATCATCAAATCTACAACATGTAACATTCGAATGTAAAGATATTGGGGATTGCaa                                              >  1:2988373/1‑71 (MQ=255)
              tCGAAGGTGTCTTTTTTATCATCAAATCTACAACATGTAACATTCGAATGTAAAGATATTGGGGATTGCaa                                              >  1:1821105/1‑71 (MQ=255)
              tCGAAGGTGTCTTTTTTATCATCAAATCTACAACATGTAACATTCGAATGTAAAGATATTGGGGATTGCaa                                              >  1:1829635/1‑71 (MQ=255)
                gAAGGTGTCTTTTTTATCATCAAATCTACAACATGTAACATTCGAATGTAAAGAAATTGGGGATTGCAAt                                             <  1:833413/70‑1 (MQ=255)
                   ggTGTCTTTTTTATCATCAAATCTACAACATGTAACATTCGAATGTAAAGAAATTGGGGATTGCAATTTta                                         >  1:2374959/1‑71 (MQ=255)
                   ggTGTCTTTTTTATCATCAAATCTACAACATGTAACATTCGAATGTAAAGAAATTGGGGATTGCAATTTta                                         >  1:2369428/1‑71 (MQ=255)
                   ggTGTCTTTTTTATCATCAAATCTACAACATGTAACATTCGAATGTAAAGAAATTGGGGATTGCAATTTta                                         >  1:3208742/1‑71 (MQ=255)
                    gtgtCTTTTTTATCATCAAATCTACAACATGTAACATTCGAATGTAAAGAAATTGGGGATTGCAATTTtac                                        <  1:18540/71‑1 (MQ=255)
                    gtgtCTTTTTTATCATCAAATCTACAACATGTAACATTCGAATGTAAAGAAATTGGGGATTGCAATTTtac                                        <  1:1858450/71‑1 (MQ=255)
                    gtgtCTTTTTTATCATCAAATCTACAACATGTAACATTCGAATGTAAAGAAATTGGGGATTGCAATTTtac                                        <  1:2188206/71‑1 (MQ=255)
                    gtgtCTTTTTTATCATCAAATCTACAACATGTAACATTCGAATGTAAAGAAATTGGGGATTGCAATTTtac                                        <  1:1935894/71‑1 (MQ=255)
                    gtgtCTTTTTTATCATCAAATCTACAACATGTAACATTCGAATGTAAAGAAATTGGGGATTGCAATTTtac                                        <  1:2551314/71‑1 (MQ=255)
                     tgtCTTTTTTATCATCAAATCTACAACATGTAACATTCGAATGTAAAGAAATTGGGGATTGCAATTTtac                                        >  1:2026660/1‑70 (MQ=255)
                     tgtCTTTTTTATCATCAAATCTACAACATGTAACATTCGAATGTAAAGAAATTGGGGATTGCAATTTtac                                        <  1:1833467/70‑1 (MQ=255)
                     tgtCTTTTTTATCATCAAATCTACAACATGTAACATTCGAATGTAAAGAAATTGGGGATTGCAATTTtac                                        >  1:13809/1‑70 (MQ=255)
                     tgtCTTTTTTATCATCAAATCTACAACATGTAACATTCGAATGTAAAGAAATTGGGGATTGCAATTTtac                                        >  1:2804058/1‑70 (MQ=255)
                           ttttATCATCAAATCTACAACATGTAACATTCGAATGTAAAGATATTGGGGATTGCAATTTTACTACTGc                                  <  1:284261/70‑1 (MQ=255)
                           ttttATCATCAAATCTACAACATGTAACATTCGAATGTAAAGATATTGGGGATTGCAATTTTACTACTGc                                  <  1:2406928/70‑1 (MQ=255)
                           ttttATCATCAAATCTACAACATGTAACATTCGAATGTAAAGATATTGGGGATTGCAATTTTACTACTGc                                  <  1:2817070/70‑1 (MQ=255)
                           ttttATCATCAAATCTACAACATGTAACATTCGAATGTAAAGATATTGGGGATTGCAATTTTACTACTGc                                  <  1:1100112/70‑1 (MQ=255)
                           ttttATCATCAAATCTACAACATGTAACATTCGAATGTAAAGATATTGGGGATTGCAATTTTACTACTGc                                  <  1:1455453/70‑1 (MQ=255)
                           ttttATCATCAAATCTACAACATGTAACATTCGAATGTAAAGATATTGGGGATTGCAATTTTACTACTGc                                  <  1:1370845/70‑1 (MQ=255)
                           ttttATCATCAAATCTACAACATGTAACATTCGAATGTAAAGATATTGGGGATTGCAATTTTACTACTGc                                  <  1:2194188/70‑1 (MQ=255)
                           ttttATCATCAAATCTACAACATGTAACATTCGAATGTAAAGATATTGGGGATTGCAATTTTACTACTGc                                  <  1:2252787/70‑1 (MQ=255)
                           ttttATCATCAAATCTACAACATGTAACATTCGAATGTAAAGATATTGGGGATTGCAATTTTACTACTGc                                  <  1:2078048/70‑1 (MQ=255)
                           ttttATCATCAAATCTACAACATGTAACATTCGAATGTAAAGATATTGGGGATTGCAATTTTACTACTGc                                  <  1:1039346/70‑1 (MQ=255)
                           ttttATCATCAAATCTACAACATGTAACATTCGAATGTAAAGATATTGGGGATTGCAATTTTACTACTGc                                  <  1:2533357/70‑1 (MQ=255)
                           ttttATCATCAAATCTACAACATGTAACATTCGAATGTAAAGATATTGGGGATTGCAATTTTACTACTGc                                  <  1:1172028/70‑1 (MQ=255)
                                     aaaTCTACAACATGTAACATTCGAATGTAAAGAAATTGGGGATTGCAATTTTACTACTGCAATAGTTGAt                        >  1:2116550/1‑70 (MQ=255)
                                      aaTCTACAACATGTAACATTCGAATGTAAAGAAATTGGGGATTGCAATTTTACTACTGCAATAGTTGATaa                      <  1:1866193/71‑1 (MQ=255)
                                      aaTCTACAACATGTAACATTCGAATGTAAAGAAATTGGGGATTGCAATTTTACTACTGCAATAGTTGATaa                      <  1:1236381/71‑1 (MQ=255)
                                      aaTCTACAACATGTAACATTCGAATGTAAAGAAATTGGGGATTGCAATTTTACTACTGCAATAGTTGATaa                      <  1:1240139/71‑1 (MQ=255)
                                      aaTCTACAACATGTAACATTCGAATGTAAAGAAATTGGGGATTGCAATTTTACTACTGCAATAGTTGATaa                      <  1:2538885/71‑1 (MQ=255)
                                      aaTCTACAACATGTAACATTCGAATGTAAAGAAATTGGGGATTGCAATTTTACTACTGCAATAGTTGATaa                      <  1:3085320/71‑1 (MQ=255)
                                      aaTCTACAACATGTAACATTCGAATGTAAAGAAATTGGGGATTGCAATTTTACTACTGCAATAGTTGATaa                      <  1:2707481/71‑1 (MQ=255)
                                      aaTCTACAACATGTAACATTCGAATGTAAAGAAATTGGGGATTGCAATTTTACTACTGCAATAGTTGATaa                      <  1:2808640/71‑1 (MQ=255)
                                      aaTCTACAACATGTAACATTCGAATGTAAAGAAATTGGGGATTGCAATTTTACTACTGCAATAGTTGATaa                      <  1:646869/71‑1 (MQ=255)
                                      aaTCTACAACATGTAACATTCGAATGTAAAGAAATTGGGAATTGCAATTTTACTACTGCAATAGTTGATaa                      <  1:1634861/71‑1 (MQ=255)
                                        tCTACAACATGTAACATTCGAATGTAAAGATATTGGGGATTGCAATTTTACTACTGc                                  <  1:3304796/57‑1 (MQ=255)
                                                    aaCATTCGAATGTAAAGAAATTGGGGATTGCAATTTTACTACTGCAATAGTTGATaa                      <  1:2864177/57‑1 (MQ=255)
                                                     aCATTCGAATGTAAAGAAATTGGGGATTGCAATTTTACTACTGCAATAGTTGATAATGTCATATTTAGATg       <  1:1289296/71‑1 (MQ=255)
                                                     aCATTCGAATGTAAAGAAATTGGGGATTGCAATTTTACTACTGCAATAGTTGATAATGTCATATTTAGATg       <  1:1088436/71‑1 (MQ=255)
                                                     aCATTCGAATGTAAAGAAATTGGGGATTGCAATTTTACTACTGCAATAGTTGATAATGTCATATTTAGATg       <  1:3270107/71‑1 (MQ=255)
                                                     aCATTCGAATGTAAAGAAATTGGGGATTGCAATTTTACTACTGCAATAGTTGATAATGTCATATTTAGATg       <  1:2177659/71‑1 (MQ=255)
                                                     aCATTCGAATGTAAAGAAATTGGGGATTGCAATTTTACTACTGCAATAGTTGATAATGTCATATTTAGATg       <  1:298486/71‑1 (MQ=255)
                                                     aCATTCGAATGTAAAGAAATTGGGGATTGCAATTTTACTACTGCAATAGTTGATAATGTCATATTTAGATg       <  1:2740556/71‑1 (MQ=255)
                                                        ttCGAATGTAAAGAAATTGGGGATTGCAATTTTACTACTGCAATAGTTGATAAt                     <  1:1858553/54‑1 (MQ=255)
                                                        ttCGAATGTAAAGAAATTGGGGATTGCAATTTTACTACTGCAATAGTTGATAAt                     <  1:2103648/54‑1 (MQ=255)
                                                        ttCGAATGTAAAGAAATTGGGGATTGCAATTTTACTACTGCAATAGTTGATAAt                     <  1:2303125/54‑1 (MQ=255)
                                                        ttCGAATGTAAAGAAATTGGGGATTGCAATTTTACTACTGCAATAGTTGATAAt                     <  1:2311179/54‑1 (MQ=255)
                                                          cGAATGTAAAGAAATTGGGGATTGCAATTTTACTACTGCAATAGTTGATAATGTCATATTTAGATGTCGa   >  1:2775943/1‑70 (MQ=255)
                                                          cGAATGTAAAGAAATTGGGGATTGCAATTTTACTACTGCAATAGTTGATAATGTCATATTTAGATGTCGAc  >  1:2764655/1‑71 (MQ=255)
                                                                      |                                                          
AAGGTGACGTTATATCGAAGGTGTCTTTTTTATCATCAAATCTACAACATGTAACATTCGAATGTAAAGAAATTGGGGATTGCAATTTTACTACTGCAATAGTTGATAATGTCATATTTAGATGTCGAC  >  W3110S.gb/4254644‑4254772

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