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
A4 F21 I0 R1 1009 73.8 4146436 87.4% 3623985 60.3

Breseq alignment

BRESEQ :: Evidence
Predicted mutation
evidence seq id position mutation freq annotation gene description
RA minE 2,402,822 T→C 12.6% E70G (GAG→GGG)  yigA ← conserved hypothetical protein

Read alignment evidence...
  seq id position ref new freq score (cons/poly) reads annotation genes product
*minE2,402,8220TC12.6% 211.5 / 19.9 79E70G (GAG→GGG) yigAconserved hypothetical protein
Reads supporting (aligned to +/- strand):  ref base T (39/30);  new base C (7/3);  total (46/33)
Fisher's exact test for biased strand distribution p-value = 5.08e-01
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 1.00e+00

AGGTAGAGTAGGCGATAAAACAGGCCTTCGTTGGCGATAGCCTGTTCCATCAACAGCGCCATGTTCTCTTCCAGAACATGAATATGATTACGTGCGCGGGCCATGTGCCACTCGACCAACGAAACGGTGCCGCGTA  >  minE/2402756‑2402891
                                                                  |                                                                     
aGGTAGAGTAGGCGATAAAACAGGCCTTCGTTGGCGATAGCCTGTTCCATCAACAGCGCCATGTTCTCTTc                                                                   <  1:2112100/71‑1 (MQ=255)
aGGTAGAGTAGGCGATAAAACAGGCCTTCGTTGGCGATAGCCTGTTCCATCAACAGCGCCATGTTCTCTTc                                                                   <  1:2107303/71‑1 (MQ=255)
    agagTAGGCGATAAAACAGGCCTTCGTTGGCGATAGCCTGTTCCATCAACAGCGCCATGTTCCCTTCCAg                                                                >  1:2459402/1‑70 (MQ=255)
     gagTAGGCGATAAAACAGGCCTTCGTTGGCGATAGCCTGTTCCATCAACAGCGCCATGTTCTCTTCCAGaa                                                              >  1:104652/1‑71 (MQ=255)
     gagTAGGCGATAAAACAGGCCTTCGTTGGCGATAGCCTGTTCCATCAACAGCGCCATGTTCTCTTCCAGaa                                                              <  1:2816923/71‑1 (MQ=255)
        tAGGCGATAAAACAGGCCTTCGTTGGCGATAGCCTGTTCCATCAACAGCGCCATGTTCTCTTcc                                                                  <  1:3944375/64‑1 (MQ=255)
        tAGGCGATAAAACAGGCCTTCGTTGGCGATAGCCTGTTCCATCAACAGCGCCATGTTCCCTTCCAGAACAt                                                           >  1:1088833/1‑71 (MQ=255)
        tAGGCGATAAAACAGGCATTCGTTGGCGATAGCCTGTTCCATCAACAGCGCCATGTTCTCTTCCAGAACAt                                                           <  1:2713404/71‑1 (MQ=255)
          ggCGATAAAACAGGCCTTCGTTGGCGATAGCCTGTTCCATCAACAGCGCCATGTTCTCTTCCAg                                                                >  1:3781648/1‑64 (MQ=255)
          ggCGATAAAACAGGCCTTCGTTGGCGATAGCCTGTTCCATCAACAGCGCCATGTTCTCTTCCAg                                                                >  1:2152182/1‑64 (MQ=255)
          ggCGATAAAACAGGCCTTCGTTGGCGATAGCCTGTTCCATCAACAGCGCCATGTTCTCTTCCAGAACATg                                                          >  1:909589/1‑70 (MQ=255)
          ggCGATAAAACAGGCCTTCGTTGGCGATAGCCTGTTCCATCAACAGCGCCATGTTCTCTTCCAGAACATg                                                          >  1:674062/1‑70 (MQ=255)
                aaaaCAGGCCTTCGTTGGCGATAGCCTGTTCCATCAACAGCGCCATGTTCTCTTCCAGAACATGAATATGa                                                   >  1:841467/1‑71 (MQ=255)
                aaaaCAGGCCTTCGTTGGCGATAGCCTGTTCCATCAACAGCGCCATGTTCTCTTCCAGAACATGAATATGa                                                   >  1:150389/1‑71 (MQ=255)
                aaaaCAGGCCTTCGTTGGCGATAGCCTGTTCCATCAACAGCGCCATGTTCTCTTCCAGAACATGAATATGa                                                   >  1:2706003/1‑71 (MQ=255)
                aaaaCAGGCCTTCGTTGGCGATAGCCTGTTCCATCAACAGCGCCATGTTCTCTTCCAGAACATGAATATGa                                                   >  1:2515528/1‑71 (MQ=255)
                 aaaCAGGCCTTCGTTGGCGATAGCCTGTTCCATCAACAGCGCCATGTTCTCTTCCAGAACATGAatat                                                     >  1:751138/1‑68 (MQ=255)
                   aCAGGCCTTCGTTGGCGATAGCCTGTTCCATCAACAGCGCCATGTTCTCTTCCAGAACATGAATATGATTa                                                >  1:2099957/1‑71 (MQ=255)
                     aGGCCTTCGTTGGCGATAGCCTGTTCCATCAACAGCGCCATGTTCTCTTCCAGAACATGAATATGATTAc                                               <  1:992500/70‑1 (MQ=255)
                     aGGCCTTCGTTGGCGAGAGCCTGTTCCATCAACAGCGCCATGTTCTCTTCCAGaa                                                              <  1:3182936/55‑1 (MQ=255)
                          ttCGTTGGCGATAGCCTGTTCCATCAACAGCGCCATGTTCTCTTcc                                                                  <  1:1372002/46‑1 (MQ=255)
                           tCGTTGGCGATAGCCTGTTCCATCAACAGCGCCATGTTCTCTTCCAGaa                                                              >  1:2382646/1‑49 (MQ=255)
                            cGTTGGCGATAGCCTGTTCCATCAACAGCGCCATGTtct                                                                       >  1:1907655/1‑39 (MQ=255)
                            cGTTGGCGATAGCCTGTTCCATCAACAGCGCCATGTTCTCTTCCAGAACATGAATATGATTACGTGCGCgg                                       >  1:1279339/1‑71 (MQ=255)
                            cGTTGGCGATAGCCTGTTCCATCAACAGCGCCATGTTCTCTTCCAGAACATGAATATGATTACGTGCGCgg                                       >  1:528451/1‑71 (MQ=255)
                             gTTGGCGATAGCCTGTTCCATCAACAGCGCCATGTTCTCTTCCAGAACATGaa                                                        >  1:3814154/1‑53 (MQ=255)
                              ttGGCGATAGCCTGTTCCATCAACAGCGCCATGTTCTCTTCCAGAACATGaa                                                        <  1:3163529/52‑1 (MQ=255)
                              ttGGCGATAGCCTGTTCCATCAACAGCGCCATGTTCTCTTCCAGAACATGaa                                                        <  1:2658030/52‑1 (MQ=255)
                              ttGGCGATAGCCTGTTCCATCAACAGCGCCATGTTCTCTTCCAGAACATGAATATGATTACGTGCGCGGGc                                     <  1:2610056/71‑1 (MQ=255)
                                  cGATAGCCTGTTCCATCAACAGCGCCATGTTCCCGTCCAGAACATGAATATGATTACGTGCGCGGGCCAtg                                 >  1:2754967/1‑71 (MQ=255)
                                   gATAGCCTGTTCCATCAACAGCGCCATGTTCTCTTCCAGAACATGaa                                                        <  1:3104350/47‑1 (MQ=255)
                                    aTAGCCTGTTCCATCAACAGCGCCATGTTCTCTTCCAGAACATGAATATGATTAc                                               <  1:1501474/55‑1 (MQ=255)
                                     tAGCCTGTTCCATCAACAGCGCCATGTTCTCTTCCAGAACATGAATATGATTACGTGCGCGGGCCAtg                                 >  1:3641553/1‑68 (MQ=255)
                                     tAGCCTGTTCCATCAACAGCGCCATGTTCTCTTCCAGAACATGAATATGATTACGTGCGCGGGCCATGTGc                              >  1:3170504/1‑71 (MQ=255)
                                     tAGCCTGTTCCATCAACAGCGCCATGTTCTCTTCCAGAACATGAATATGATTACGTGCGCGGGCCATGTGc                              >  1:689001/1‑71 (MQ=255)
                                       gCCTGTTCCATCAACAGCGCCATGTTCTCTTCCAGAACATGAATATGATTACGTGCGCGGGCCATGTGcc                             <  1:3661542/70‑1 (MQ=255)
                                       gCCTGTTCCATCAACAGCGCCATGTTCTCTTCCAGAACATGAATATGATTACGTGCGCGGGCCATGTGCCa                            >  1:1826461/1‑71 (MQ=255)
                                        ccTGTTCCATCAACAGCGCCATGTTCTCTTCCAGAACATGaa                                                        <  1:666511/42‑1 (MQ=255)
                                          tGTTCCATCAACAGCGCCATGTTCTCTTCCAGAACATGAATATGATTACGTGCGCGGGCCAt                                  >  1:2530941/1‑62 (MQ=255)
                                           gTTCCATCAACAGCGCCATGTTCTCTTCCAGAACATGAat                                                       <  1:338143/40‑1 (MQ=255)
                                            ttCCATCAACAGCGCCATGTTCTCTTCCAGAACATGAATATGATTACGTGCGCGGGCCATGTGCCACTc                         <  1:3211451/69‑1 (MQ=255)
                                             tCCATCAACAGCGCCATGTTCTCTTCCAGAACATGAATATGATTACGTGCGCGGGCCATGTGCCACTCGAc                      >  1:216749/1‑71 (MQ=255)
                                              ccATCAACAGCGCCATGTTCTCTTCCAGAACATGAATATGATTa                                                >  1:237016/1‑44 (MQ=255)
                                              ccATCAACAGCGCCATGTTCTCTTCCAGAACATGAATATGATTACGTGCGCGGGcc                                    >  1:529877/1‑56 (MQ=255)
                                              ccATCAACAGCGCCATGTTCTCTTCCAGAACATGAATATGATTACGTGCGCGGGCCa                                   >  1:61628/1‑57 (MQ=255)
                                              ccATCAACAGCGCCATGTTCTCTTCCAGAACATGAATATGATTACGTGCGCGGGCCATGTGCCACTCGAc                      <  1:463961/70‑1 (MQ=255)
                                               cATCAACAGCGCCATGTTCTCTTCCAGAACATGAATATGATTa                                                >  1:1920456/1‑43 (MQ=255)
                                               cATCAACAGCGCCATGTTCCCTTCCAGAACATGAatat                                                     <  1:3703138/38‑1 (MQ=255)
                                                aTCAACAGCGCCATGTTCTCTTCCAGAACATGAATATGATTACGTGCGCGGGCCATGTGCCACTCGACCaa                   >  1:2794849/1‑71 (MQ=255)
                                                  cAACAGCGCCATGTTCTCTTCCAGAACATGAATATGATTACGTGCGCGGGCCa                                   >  1:1151178/1‑53 (MQ=255)
                                                  cAACAGCGCCATGTTCTCTTCCAGAACATGAATATGATTACGTGCGCGGGCCATGTGCCACTCGAcc                     >  1:900403/1‑67 (MQ=255)
                                                  cAACAGCGCCATGTTCTCTTCCAGAACATGAATATGATTACGTGCGCGGGCCATGTGCCACTCGACCAAc                  >  1:547379/1‑70 (MQ=255)
                                                   aaCAGCGCCATGTTCTCTTCCAGAACATGAATATGATTACGTGCGCGGGCCATGTGCCACTCGACCAACg                 >  1:1589713/1‑70 (MQ=255)
                                                   aaCAGCGCCATGTTCTCTTCCAGAACATGAATATGATTACGTGCGCGGGCCATGTGCCACTCGACCAACg                 >  1:3622210/1‑70 (MQ=255)
                                                   aaCAGCGCCATGTTCTCTTCCAGAACATGAATATGATTACGTGCGCGGGCCATGTGCCACTCGACCAACg                 >  1:97243/1‑70 (MQ=255)
                                                   aaCAGCGCCATGTTCTCTTCCAGAACATGAATATGATTACGTGCGCGGGCCATGTGCCACTCGACCAACg                 >  1:2405791/1‑70 (MQ=255)
                                                   aaCAGCGCCATGTTCTCTTCCAGAACATGAATATGATTACGTGCGCGGGCCATGTGCCACTCGACCAACGa                <  1:3858947/71‑1 (MQ=255)
                                                   aaCAGCGCCATGTTCTCTTCCAGAACATGAATATGATTACGTGCGCGGGCCATGTGCAACTCGACCAACGa                <  1:713839/71‑1 (MQ=255)
                                                   aaCAGCGCCATGTTCCCTTCCAGAACATGAATATGATTACGTGCGCGGGCCa                                   >  1:45451/1‑52 (MQ=255)
                                                    aCAGCGCCATGTTCTCTTCCAGAACATGAATATGATTACGTGCGCGGGCCATGTGCCACTCGACCa                    <  1:3670497/66‑1 (MQ=255)
                                                    aCAGCGCCATGTTCTCTTCCAGAACATGAATATGATTACGTGCGCGGGCCATGTGCCACTCGACCAACGa                <  1:3563775/70‑1 (MQ=255)
                                                    aCAGCGCCATGTTCTCTTCCAGAACATGAATATGATTACGTGCGCGGGCCATGTGCCACTCGACCAACGa                <  1:1978583/70‑1 (MQ=255)
                                                    aCAGCGCCATGTTCTCTTCCAGAACATGAATATGATTACGTGCGCGGGCCATGTGCCACTCGACCAACGa                <  1:1766496/70‑1 (MQ=255)
                                                      aGCGCCATGTTCTCTTCCAGAACACGAATATGATTACGTGCGCGGGCCATGTGCCACTCGACCAACGAAAc             <  1:571485/71‑1 (MQ=255)
                                                       gcgcCATGTTCTCTTCCAGAACATGAATATGATTACGTGCGCGGGCCATGTGCCACTCGACCAACGAAAc             <  1:1028773/70‑1 (MQ=255)
                                                        cgcCATGTTCCCTTCCAGAACATGAATATGATTACGTGCGCGGGCCATGTGCCACTCGAc                      >  1:1735441/1‑60 (MQ=255)
                                                        cgcCATGTTCCCTTCCAGAACATGAATATGATTACGTGCGCGGGCCATGTGCCACTCGACCAACGAAACgg           <  1:1638341/71‑1 (MQ=255)
                                                          ctaTGTTCTCTTCCAGAACATGAATATGATTACGTGCGCGGGCCATGTGCCACTCGACCAACGAAACGGTg         >  1:2986979/3‑71 (MQ=255)
                                                           cATGTTCTCTTCCAGAACATGAATATGATTACGTGCGCGGGCCATGTGCCACTCGACCAACGAAACGGTGc        <  1:469616/71‑1 (MQ=255)
                                                            aTGTTCTCTTCCAGAACATGAATATGATTACGTGCGCGGGc                                     <  1:1741220/41‑1 (MQ=255)
                                                            aTGTTCTCTTCCAGAACATGAATATGATTACGTGCGCGGGc                                     <  1:2478827/41‑1 (MQ=255)
                                                             tGTTCTCTTCCAGAACATGAATATGATTACGTGCGCGGGCCATGTGCCACTCGACCAACGAAACGGTGcc       >  1:3233186/1‑70 (MQ=255)
                                                             tGTTCTCTTCCAGAACATGAATATGATTACGTGCGCGGGCCATGTGCCACTCGACCAACGAAACGGTGCcg      >  1:768155/1‑71 (MQ=255)
                                                             tGTTCCCTTCCAGAACATGAATATGATTACGTGCGCGGGCCATGTGCCACTCGACCAACGa                <  1:563477/61‑1 (MQ=255)
                                                              gTTCTCTTCCAGAACATGAATATGATTACGTGCGCGGGcc                                    <  1:1476881/40‑1 (MQ=255)
                                                               ttCTCTTCCAGAACATGAATATGATTACGTGCGCGGGCCATGTGCCACTCGACCAACGAAACGGTGCcgcg    >  1:2437768/1‑71 (MQ=255)
                                                               ttCTCTTCCAGAACATGAATATGATTACGTGCGCGGGCCATGTGCCACTCGACCAACGAAACGGTGCcgcg    >  1:3551525/1‑71 (MQ=255)
                                                               ttCTCTTCCAGAACATGAATATGATTACGTGCGCGGGCCATGTGCCACTCGACCAACGAAACGGTGCcgcg    >  1:816967/1‑71 (MQ=255)
                                                               ttCCCTTCCAGAACATGAATATGATTACGTGCGCGGGCCATGTGCCACTCGACCAACGAAACGGTGCcgcg    >  1:1471857/1‑71 (MQ=255)
                                                               ttCCCTTCCAGAACATGAATATGATTACGTGCGCGGGCCATGTGCCACTCGACCAACGAAACGGTGCcgc     >  1:579846/1‑70 (MQ=255)
                                                                tctcTTCCAGAACATGAATATGATTACGTGCGCGGGCCATGTGCCACTCGACCAACGAAACGGt          <  1:2758995/64‑1 (MQ=255)
                                                                tctcTTCCAGAACATGAATATGATTACGTGCGCGGGCCATGTGCCACTCGACCAACGAAACGGTGCcgcg    >  1:1228258/1‑70 (MQ=255)
                                                                tctcTTCCAGAACATGAATATGATTACGTGCGCGGGCCATGTGCCACTCGACCAACGAAACGGTGCcgcg    >  1:2728337/1‑70 (MQ=255)
                                                                 ctctTCCAGAACATGAATATGATTACGTGCGCGGGCCATGTGCCACTCGACCAACGaa               <  1:279077/58‑1 (MQ=255)
                                                                 ctctTCCAGAACATGAATATGATTACGTGCGCGGGCCATGTGCCACTCGACCAACGAAACGGTGCCGCGt   <  1:474137/70‑1 (MQ=255)
                                                                 ctctTCCAGAACATGAATATGATTACGTGCGCGGGCCATGTGCCACTCGACCAACGAAACGGTGCCGCGTa  >  1:1547415/1‑71 (MQ=255)
                                                                  |                                                                     
AGGTAGAGTAGGCGATAAAACAGGCCTTCGTTGGCGATAGCCTGTTCCATCAACAGCGCCATGTTCTCTTCCAGAACATGAATATGATTACGTGCGCGGGCCATGTGCCACTCGACCAACGAAACGGTGCCGCGTA  >  minE/2402756‑2402891

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