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 1,291,652 A→G 40.8% G502G (GGT→GGC)  yeeO ← predicted multidrug efflux system

Read alignment evidence...
  seq id position ref new freq score (cons/poly) reads annotation genes product
*minE1,291,6520AG40.8% 32.6 / 67.2 93G502G (GGT→GGC) yeeOpredicted multidrug efflux system
Reads supporting (aligned to +/- strand):  ref base A (9/46);  new base G (26/12);  total (35/58)
Fisher's exact test for biased strand distribution p-value = 7.45e-07
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 7.35e-01

Only 100 of 104 total aligned reads displayed.

AACCATTCGCCAGTAAAACAGCACGGCCCGCACAGCCCAGTCGGCAAACATTCCCATCCAGACACCAACCACACCCCAGCCAAGCATGATTCCCAGCACATAACCGACTACAACCCGACAA  >  minE/1291589‑1291709
                                                               |                                                         
aaCCATTCGCCAGTAAAACAGCACGGCCCGCACAGCCCAGTCGGCAAACATTCCCATCCAGACaccaac                                                      <  1:1222543/69‑1 (MQ=255)
aaCCATTCGCCAGTAAAACAGCACGGCCCGCACAGCCCAGTCGGCAAACATTCCCATCCAGACaccaac                                                      <  1:204847/69‑1 (MQ=255)
aaCCATTCGCCAGTAAAACAGCACGGCCCGCACAGCCCAGTCGGCAAACATTCCCATCCAGACaccaac                                                      <  1:1991512/69‑1 (MQ=255)
 aCCATTCGCCTGTAAAACATCACGGCCCGCACAGCCCAGTCGGCAAACATTCCCATCCAGAAaccaac                                                      <  1:6575/68‑1 (MQ=255)
              aaaaCAGCACGGCCCGCACAGCCCAGTCGGCAAACATTCCCATCCAGACACCAACCACACCCCAGCCa                                         >  1:2778840/1‑68 (MQ=255)
               aaaCAGCACGGCCCGCACAGCCCAGTCGGCAAACATTCCCATCCAGACACCAACCACACCCCAGCCAAg                                       <  1:840769/69‑1 (MQ=255)
               aaaCAGCACGGCCCGCACAGCCCAGTCGGCAAACATTCCCATCCAGACACCAACCACACCCCAGCCAAg                                       >  1:759945/1‑69 (MQ=255)
               aaaCAGCACGGCCCGCACAGCCCAGTCGGCAAACATTCCCATCCAGACACCAACCACACCCCAGCCAAg                                       >  1:668858/1‑69 (MQ=255)
               aaaCAGCACGGCCCGCACAGCCCAGTCGGCAAACATTCCCATCCAGACACCAACCACACCCCAGCCAAg                                       <  1:1193944/69‑1 (MQ=255)
               aaaCAGCACGGCCCGCACAGCCCAGTCGGCAAACATTCCCATCCAGACACCAACCACACCCCAGCCAAg                                       >  1:21049/1‑69 (MQ=255)
               aaaCAGCACGGCCCGCAAAGCCCAGTCGGCAAACATTCCCATCCAGACACCAACCACCCCCCAGCCAAg                                       >  1:308303/1‑69 (MQ=255)
                  cAGCACGGCCCGCACAGCCCAGTCGGCAAACATTCCCATCCAGACACCAACCACACCCCAGCCAAGCAt                                    <  1:2518402/69‑1 (MQ=255)
                  cAGCACGGCCCGCACAGCCCAGTCGGCAAACATTCCCATCCAGACACCAACCACACCCCAGCCAAGCAt                                    <  1:452258/69‑1 (MQ=255)
                  cAGCACGGCCCGCACAGCCCAGTCGGCAAACATTCCCATCCAGACACCAACCACACCCCAGCCAAGCAt                                    <  1:647678/69‑1 (MQ=255)
                  cAGCACGGCCCGCACAGCCCAGTCGGCAAACATTCCCATCCAGACACCAACCACACCCCAGCCAAGCAt                                    <  1:651575/69‑1 (MQ=255)
                  cAGCACGGCCCGCACAGCCCAGTCGGCAAACATTCCCATCCAGACACCAACCACACCCCAGCCAAGCAt                                    <  1:753635/69‑1 (MQ=255)
                   aGCACGGCCCGCACAGCCCAGTCGGCAAACATTCCCATCCAGACACCAACCACACCCCAGCCAAGCAt                                    <  1:1989401/68‑1 (MQ=255)
                         gCCCGCACAGCCCAGTCGGCAAACATTCCCATCCAGACACAAACCACACCCCAGCCAAGCATGATTccc                             >  1:2032030/1‑69 (MQ=255)
                             gCACAGCCCAGTCGGCAAACATTCCCATCCAGACACCAACCACACCCCAGCCAAg                                       <  1:1698032/55‑1 (MQ=255)
                                  gCCCAGTCGGCAAACATTCCCATCCAGACaccaacc                                                     <  1:2464366/36‑1 (MQ=255)
                                  gCCCAGTCGGCAAACATTCCCATCCAGACaccaacc                                                     <  1:2887620/36‑1 (MQ=255)
                                  gCCCAGTCGGCAAACATTCCCATCCAGACaccaacc                                                     <  1:3398143/36‑1 (MQ=255)
                                  gCCCAGTCGGCAAACATTCCCATCCAGACaccaacc                                                     <  1:3405228/36‑1 (MQ=255)
                                  gCCCAGTCGGCAAACATTCCCATCCAGACaccaacc                                                     <  1:1057830/36‑1 (MQ=255)
                                  gCCCAGTCGGCAAACATTCCCATCCAGACaccaacc                                                     <  1:1098481/36‑1 (MQ=255)
                                  gCCCAGTCGGCAAACATTCCCATCCAGACaccaacc                                                     <  1:1788341/36‑1 (MQ=255)
                                              aaCATTCCCATCCAGACACCAACCACACCCCAGCCAAGCAt                                    <  1:309172/41‑1 (MQ=255)
                                              aaCATTCCCATCCAGACACCAACCACACCCCAGCCAAGCAt                                    <  1:87248/41‑1 (MQ=255)
                                              aaCATTCCCATCCAGACACCAACCACACCCCAGCCAAGCAt                                    <  1:2792923/41‑1 (MQ=255)
                                               aCATTCCCATCCAGACGCCAACCACACCCCAGCCAAGCATGATTCCCAGCACATAACCGACTACAAccc       <  1:2415598/69‑1 (MQ=255)
                                               aCATTCCCATCCAGACGCCAACCACACCCCAGCCAAGCATGATTCCCAGCACATAACCGACTACAAccc       <  1:1014015/69‑1 (MQ=255)
                                               aCATTCCCATCCAGACGCCAACCACACCCCAGCCAAGCATGATTCCCAGCACATAACCGACTACAAccc       <  1:814262/69‑1 (MQ=255)
                                               aCATTCCCATCCAGACGCCAACCACACCCCAGCCAAGCATGATTCCCAGCACATAACCGACTACAAccc       <  1:1484209/69‑1 (MQ=255)
                                               aCATTCCCATCCAGACGCCAACCACACCCCAGCCAAGCATGATTCCCAGCACATAACCGACTACAAccc       <  1:2815171/69‑1 (MQ=255)
                                               aCATTCCCATCCAGACGCCAACCACACCCCAGCCAAGCATGATTCCCAGCACATAACCGACTACAAccc       <  1:2905945/69‑1 (MQ=255)
                                               aCATTCCCATCCAGACGCCAACCACACCCCAGCCAAGCATGATTCCCAGCACATAACCGACTACAAccc       <  1:2051107/69‑1 (MQ=255)
                                               aCATTCCCATCCAGACGCCAACCACACCCCAGCCAAGCATGATTCCCAGCACATAACCGACTACAAccc       <  1:1901819/69‑1 (MQ=255)
                                               aCATTCCCATCCAGACGCCAACCACACCCCAGCCAAGCATGATTCCCAGCACATAACCGACTACAAccc       <  1:613600/69‑1 (MQ=255)
                                                cATTCCCATCCAGACGCCAACCACACCCCAGCCAAGCATGATTCCCAGCACATAACCGACTACAAccc       <  1:1817636/68‑1 (MQ=255)
                                                cATTCCCATCCAGACGCCAACCACACCCCAGCCAAGCATGATTCCCAGCACATAACCGACTACAAccc       <  1:2482046/68‑1 (MQ=255)
                                                 aTTCCCATCCAGACGCCAACCACACCCCAGCCAAGCATGATTCCCAGCACATAACCGACTACAAccc       <  1:1282694/67‑1 (MQ=255)
                                                  ttCCCATCCAGACACCAACCACACCCCAGCCAAGCATGATTCCCAGCACATACCCGACTACAACCCGAc    <  1:752819/69‑1 (MQ=255)
                                                  ttCCCATCCAGACACCAACCACACCCCAGCCAAGCATGATTCCCAGCACATAACCGACTACAACCCGAc    <  1:232463/69‑1 (MQ=255)
                                                  ttCCCATCCAGACACCAACCACACCCCAGCCAAGCATGATTCCCAGCACATAACCGACTACAACCCGAc    <  1:2016582/69‑1 (MQ=255)
                                                  ttCCCATCCAGACACCAACCACACCCCAGCCAAGCATGATTCCCAGCACATAACCGACTACAACCCGAc    <  1:2971249/69‑1 (MQ=255)
                                                  ttCCCATCCAGACACCAACCACACCCCAGCCAAGCATGATTCCCAGCACATAACCGACTACAACCCGAc    <  1:125398/69‑1 (MQ=255)
                                                  ttCCCATCCAGACACCAACCACACCCCAGCCAAGCATGATTCCCAGCACATAACCGACTACAACCCGAc    <  1:1227996/69‑1 (MQ=255)
                                                  ttCCCATCCAGACACCAACCACACCCCAGCCAAGCATGATTCCCAGCACATAACCGACTACAACCCGAc    <  1:906588/69‑1 (MQ=255)
                                                  ttCCCATCCAGACACCAACCACACCCCAGCCAAGCATGATTCCCAGCACATAACCGACTACAACCCGAc    <  1:2899691/69‑1 (MQ=255)
                                                  ttCCCATCCAGACACCAACCACACCCCAGCCAAGCATGATTCCCAGCACATAACCGACTACAACCCGAc    <  1:912156/69‑1 (MQ=255)
                                                  ttCCCATCCAGACACCAACCACACCCCAGCCAAGCATGATTCCCAGCACATAACCGACTACAACCCGAc    <  1:1080414/69‑1 (MQ=255)
                                                  ttCCCATCCAGACACCAACCACACCCCAGCCAAGCATGATTCCCAGCACATAACCGACTACAACCCGAc    <  1:445334/69‑1 (MQ=255)
                                                  ttCCCATCCAGACACCAACCACACCCCAGCCAAGCATGATTCCCAGCACATAACCGACTACAACCCGAc    <  1:2300140/69‑1 (MQ=255)
                                                  ttCCCATCCAGACACCAACCACACCCCAGCCAAGCATGATTCCCAGCACATAACCGACTACAACCCGAc    <  1:1553300/69‑1 (MQ=255)
                                                  ttCCCATCCAGACACCAACCACACCCCAGCCAAGCATGATTCCCAGCACATAACCGACTACAACCCGAc    <  1:2308339/69‑1 (MQ=255)
                                                  ttCCCATCCAGACACCAACCACACCCCAGCCAAGCATGATTCCCAGCACATAACCGACTACAACCCGAc    <  1:1700241/69‑1 (MQ=255)
                                                  ttCCCATCCAGACACCAACCACACCCCAGCCAAGAATGATTCCCAGCACATAACCGACTACAACCCGAc    <  1:40611/69‑1 (MQ=255)
                                                  ttCCCATCCAGACACCAACCACACCCCACCCAAGCATGATTCCCAGCACATAACCGACTACAACCCGAc    <  1:429051/69‑1 (MQ=255)
                                                  ttCCCATCCAGACACCAACCACACCCCACCCAAGCATGATTCCCAGCACATAACCGACTACAACCCGAc    <  1:2332856/69‑1 (MQ=255)
                                                    cccATCCAGACACCAACCACACCCCAGCCAAGCATGATTCCCAGCACATAACCg                 <  1:3263409/54‑1 (MQ=255)
                                                    cccATCCAGACACCAACCACACCCCAGCCAAGCATGATTCCCAGCACATAACCg                 <  1:3251365/54‑1 (MQ=255)
                                                    cccATCCAGACACCAACCACACCCCAGCCAAGCATGATTCCCAGCACATAACCg                 <  1:3314437/54‑1 (MQ=255)
                                                    cccATCCAGACACCAACCACACCCCAGCCAAGCATGATTCCCAGCACATAACCg                 <  1:875817/54‑1 (MQ=255)
                                                    cccATCCAGACACCAACCACACCCCAGCCAAGCATGATTCCCAGCACATAACCg                 <  1:3022658/54‑1 (MQ=255)
                                                    cccATCCAGACACCAACCACACCCCAGCCAAGCATGATTCCCAGCACATAACCg                 <  1:2025575/54‑1 (MQ=255)
                                                    cccATCCAGACACCAACCACACCCCAGCCAAGCATGATTCCCAGCACATAACCg                 <  1:2969812/54‑1 (MQ=255)
                                                    cccATCCAGACACCAACCACACCCCAGCCAAGCATGATTCCCAGCACATAACCg                 <  1:1086573/54‑1 (MQ=255)
                                                    cccATCCAGACACCAACCACACCCCAGCCAAGCATGATTCCCAGCACATAACCg                 <  1:1725817/54‑1 (MQ=255)
                                                    cccATCCAGACACCAACCACACCCCAGCCAAGCATGATTCCCAGCACATAACCg                 <  1:2128692/54‑1 (MQ=255)
                                                    cccATCCAGACACCAACCACACCCCAGCCAAGCATGATTCCCAGCACATAACCg                 <  1:224/54‑1 (MQ=255)
                                                    cccATCCAGACACCAACCACACCCCAGCCAAGCATGATTCCCAGCACATAACCg                 <  1:2264385/54‑1 (MQ=255)
                                                    cccATCCAGACACCAACCACACCCCAGCCAAGCATGATTCCCAGCACATAACCg                 <  1:2599809/54‑1 (MQ=255)
                                                    cccATCCAGACACCAACCACACCCCAGCCAAGCATGATTCCCAGCACATAACCg                 <  1:2558822/54‑1 (MQ=255)
                                                    cccATCCAGACACCAACCACACCCCAGCCAAGCATGATTCCCAGCACATAACCGACTACAACCCGACaa  >  1:3009759/1‑69 (MQ=255)
                                                     ccATCCAGACGCCAACCACACCCCAGCCAAGCATGa                                  >  1:1272454/1‑36 (MQ=255)
                                                     ccATCCAGACGCCAACCACACCCCAGCCAAGCATGATTccc                             >  1:3078889/1‑41 (MQ=255)
                                                     ccATCCAGACGCCAACCACACCCCAGCCAAGCATGATTCCCa                            >  1:3397087/1‑42 (MQ=255)
                                                     ccATCCAGACGCCAACCACACCCCAGCCAAGCATGATTCCCAGCACATAACCTACTACAACCCGACaa  >  1:1808491/1‑68 (MQ=255)
                                                     ccATCCAGACGCCAACCACACCCCAGCCAAGCATGATTCCCAGCACATAACCGACTAc            >  1:1429001/1‑58 (MQ=255)
                                                     ccATCCAGACGCCAACCACACCCCAGCCAAGCATGATTCCCAGCACATAACCGACTACAACCCGACaa  >  1:35895/1‑68 (MQ=255)
                                                     ccATCCAGACGCCAACCACACCCCAGCCAAGCATGATTCCCAGCACATAACCGACTACAACCCGACaa  >  1:2132802/1‑68 (MQ=255)
                                                     ccATCCAGACGCCAACCACACCCCAGCCAAGCATGATTCCCAGCACATAACCGACTACAACCCGACaa  >  1:848651/1‑68 (MQ=255)
                                                     ccATCCAGACGCCAACCACACCCCAGCCAAGCATGATTCCCAGCACATAACCGACTACAACCCGACaa  >  1:2666520/1‑68 (MQ=255)
                                                     ccATCCAGACGCCAACCACACCCCAGCCAAGCATGATTCCCAGCACATAACCGACTACAACCCGACaa  >  1:7602/1‑68 (MQ=255)
                                                     ccATCCAGACGCCAACCACACCCCAGCCAAGCATGATTCCCAGCACATAACCGACTACAACCCGACaa  >  1:2861041/1‑68 (MQ=255)
                                                     ccATCCAGACGCCAACCACACCCCAGCCAAGCATGATTCCCAGCACATAACCGACTACAACCCGACaa  >  1:2864017/1‑68 (MQ=255)
                                                     ccATCCAGACGCCAACCACACCCCAGCCAAGCATGATTCCCAGCACATAACCGACTACAACCCGACaa  >  1:1450617/1‑68 (MQ=255)
                                                     ccATCCAGACGCCAACCACACCCCAGCCAAGCATGATTCCCAGCACATAACCGACTACAACCCGACaa  >  1:2931323/1‑68 (MQ=255)
                                                     ccATCCAGACGCCAACCACACCCCAGCCAAGCATGATTCCCAGCACATAACCGACTACAACCCGACaa  >  1:2940728/1‑68 (MQ=255)
                                                     ccATCCAGACGCCAACCACACCCCAGCCAAGCATGATTCCCAGCACATAACCGACTACAACCCGACaa  >  1:1228685/1‑68 (MQ=255)
                                                     ccATCCAGACGCCAACCACACCCCAGCCAAGCATGATTCCCAGCACATAACCGACTACAACCCGACaa  >  1:62167/1‑68 (MQ=255)
                                                     ccATCCAGACGCCAACCACACCCCAGCCAAGCATGATTCCCAGCACATAACCGACTACAACCCGACaa  >  1:538684/1‑68 (MQ=255)
                                                     ccATCCAGACGCCAACCACACCCCAGCCAAGCATGATTCCCAGCACATAACCGACTACAACCCGACaa  >  1:522352/1‑68 (MQ=255)
                                                     ccATCCAGACGCCAACCACACCCCAGCCAAGCATGATTCCCAGCACATAACCGACTACAACCCGACaa  >  1:3337637/1‑68 (MQ=255)
                                                     ccATCCAGACGCCAACCACACCCCAGCCAAGCATGATTCCCAGCACATAACCGACTACAACCCGACaa  >  1:3370051/1‑68 (MQ=255)
                                                     ccATCCAGACGCCAACCACACCCCAGCCAAGCATGATTCCCAGCACATAACCGACTACAACCCGACaa  >  1:4075/1‑68 (MQ=255)
                                                     ccATCCAGACGCCAACCACACCCCAGCCAAGCATGATTCCCAGCACATAACCGACTACAACCCGACa   >  1:255597/1‑67 (MQ=255)
                                                     ccATCCAGACGCCAACCACACCCCAGCCAAGCATGATTCACAGCACATAACCGACTACAACCCGACaa  >  1:1840290/1‑68 (MQ=255)
                                                     ccATCCAGACGCCAAACACACCCCAGCCAAGCATGATTCCCAGCACATAACCGACTACAACCCGACaa  >  1:1076245/1‑68 (MQ=255)
                                                            gACACCAACCACACCCCAGCCAAGCATGATTCCCAGCACATACCCg                 <  1:2089523/46‑1 (MQ=255)
                                                               |                                                         
AACCATTCGCCAGTAAAACAGCACGGCCCGCACAGCCCAGTCGGCAAACATTCCCATCCAGACACCAACCACACCCCAGCCAAGCATGATTCCCAGCACATAACCGACTACAACCCGACAA  >  minE/1291589‑1291709

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