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 F8 I0 R1 311 50.1 4085234 95.9% 3917739 60.7

Breseq alignment

BRESEQ :: Evidence
Predicted mutation
evidence seq id position mutation freq annotation gene description
RA W3110S.gb 4,249,681 A→C 26.5% F111V (TTC→GTC)  malE ← maltose transporter subunit

Read alignment evidence...
  seq id position ref new freq score (cons/poly) reads annotation genes product
*W3110S.gb4,249,6810AC26.5% 46.2 / 44.7 53F111V (TTC→GTC) malEmaltose transporter subunit
Reads supporting (aligned to +/- strand):  ref base A (20/19);  new base C (12/2);  total (32/21)
Fisher's exact test for biased strand distribution p-value = 2.90e-02
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 8.05e-01

GGTAAGCAATCAGCTTGCCGTTGTAACGTACGGCATCCCAGGTAAACGGATACAGCTTGTCCTGGAACGCTTTGTCCGGGGTGATTTCAGCCAACAGGCCAGATTGAGCGTAGCCACCAAAGCGGTCGTGTGCC  >  W3110S.gb/4249615‑4249748
                                                                  |                                                                   
ggTAAGCAATCAGCTTGCCGTTGTAACGTACGGCATCCCAGGTAAACGGATACAGCTTGTCCTGGAACGCt                                                                 <  1:959021/71‑1 (MQ=255)
       aaTCAGCTTGCCGTTGTAACGTACGGCATCCCAGGTAAACGGATACAGCTTGTCCTGGAACGCTTTGTCCg                                                          <  1:2142020/71‑1 (MQ=255)
           aGCTTGCCGTTGTAACGTACGGCATCCCAGGTAAACGGATACAGCTTGTCCTGGACCGCTTTGTCCGGGGt                                                      >  1:3103303/1‑71 (MQ=255)
           aGCTTGCCGTTGTAACGTACGGCATCCCAGGTAAACGGATACAGCTTGTCCTGGACCGCTTTGTCCGGGGt                                                      >  1:559385/1‑71 (MQ=255)
           aGCTTGCCGTTGTAACGTACGGCATCCCAGGTAAACGGATACAGCTTGTCCTGGACCGCTTTGTCCGGGGt                                                      >  1:374749/1‑71 (MQ=255)
           aGCTTGCCGTTGTAACGTACGGCATCCCAGGTAAACGGATACAGCTTGTCCTGGAACGCTTTGTCCGGGGt                                                      >  1:3119807/1‑71 (MQ=255)
           aGCTTGCCGT‑‑TAACGTACGGCATCCCAGGTAAACGGATACAGCTTGTCCTGGAACGCttt                                                               >  1:3807693/1‑60 (MQ=255)
               tGCCGTTGTAACGTACGGCATCCCAGGTAAACGGATACAGCTTGTCCTGGACCGCTTTGTCCGGGGTGAtt                                                  >  1:3347291/1‑71 (MQ=255)
                gCCGTTGTAACGTACGGCATCCCAGGTAAACGGATACAGCTTGTCCTGGAACGCTTTGTCCGGGGTGAttt                                                 >  1:2347723/1‑71 (MQ=255)
                gCCGTTGTAACGTACGGCATCCCAGGTAAACGGATACAGCTTGTCCTGGAACGCTTTGTCCGGGGTGAtt                                                  >  1:1671246/1‑70 (MQ=255)
                 ccGTTGTAACGTACGGCATCCCAGGTAAACGGATACAGCTTGTCCTGGAACGCTTTGTCCGTGGTGAttt                                                 <  1:3677469/70‑1 (MQ=255)
                 ccGTTGTAACGTACGGCATCCCAGGTAAACGGATACAGCTTGTCCTGGAACGCTTTGTCCGGGGTGAttt                                                 <  1:1222542/70‑1 (MQ=255)
                 ccGTTGTAACGTACGGCATCCCAGGTAAACGGATACAGCTTGTCCTGGAACGCTTTGTCCGGGGTGAttt                                                 <  1:518940/70‑1 (MQ=255)
                 ccGTTGTAACGTACGGCATCCCAGGTAAACGGATACAGCTTGTCCTGGAACGCTTTGTCCGGGGTGAttt                                                 <  1:3392349/70‑1 (MQ=255)
                      gTAACGTACGGCATCCCAGGTAAACGGATACAGCTTGTCCTGGAACGCTTTGTc                                                            >  1:1916080/1‑54 (MQ=255)
                      gTAACGTACGGCATCCCAGGTAAACGGATACAGCTTGTCCTGGAACGCTTTGTCCGGGGTGATTTCAGcc                                            <  1:330888/70‑1 (MQ=255)
                              cGGCATCCCAGGTAAACGGATACAGCTTGTCCTGGACCGCTTTGTcc                                                           >  1:1192843/1‑47 (MQ=255)
                              cGGCATCCCAGGTAAACGGATACAGCTTGTCCTGGACCGCTTTGTcc                                                           >  1:1188922/1‑47 (MQ=255)
                              cGGCATCCCAGGTAAACGGATACAGCTTGTCCTGGACCGCTTTGTcc                                                           >  1:1010898/1‑47 (MQ=255)
                              cGGCATCCCAGGTAAACGGATACAGCTTGTCCTGGACCGCTTTGTCCGGGGTGATTTCAGCCAACAGGCCa                                   <  1:2801271/71‑1 (MQ=255)
                              cGGAATCCCAGGTAAACGGATACAGCTTGTCCTGGACCGCTTTGTcc                                                           >  1:478506/1‑47 (MQ=255)
                                gCATCCCAGGTAAACGGATACAGCTTGTCCTGGAACGCTTTGTCCGGGGTGATTTCAGCCAAc                                         <  1:2800025/63‑1 (MQ=255)
                                     ccAGGTAAACGGATACAGCTTGTCCTGGAACGCTTTGTc                                                            >  1:1918802/1‑39 (MQ=255)
                                     ccAGGTAAACGGATACAGCTTGTCCTGGAACGCTTTGTc                                                            >  1:2395201/1‑39 (MQ=255)
                                     ccAGGTAAACGGATACAGCTTGTCCTGGAACGCTTTGTc                                                            >  1:3179535/1‑39 (MQ=255)
                                        ggTAAACGGATACAGCTTGTCCTGGACCGCTTTGTCCGGGGTGATTTCAGCCAACAGGCCAGATTGAGCg                          >  1:539496/1‑70 (MQ=255)
                                         gTAAACGGATACAGCTTGTCCTGGAACGCTTTGTCCGGGGTGAt                                                   <  1:974546/44‑1 (MQ=255)
                                         gTAAACGGATACAGCTTGTCCTGGAACGCTTTGTCCGGGGTGATTTCAGCCAACAGGCCAGATTGAGCGTa                        <  1:2094964/71‑1 (MQ=255)
                                           aaaCGGATACAGCTTGTCCTGGACCGCTTTGTCCGGGGTGATTTCAGCCAACAGGCCAGATTGAGc                           >  1:3396900/1‑66 (MQ=255)
                                           aaaCGGATACAGCTTGTCCTGGAACGCTTTGTCCGGGGTGATTTCAGCCAACAGGCCAGATTGAGCGTAGc                      >  1:3336936/1‑71 (MQ=255)
                                           aaaCGGATACAGCTTGTCCTGGAACGCTTTGTCCGGGGTGATTTCAGCCAACAGGCCAGATTGAGCGTAGc                      >  1:2146913/1‑71 (MQ=255)
                                            aaCGGATACAGCTTGTCCTGGAACGCTTTGTCCGGGGTTATTTCAGCCAACAGGCCAGATTGAGCGTAGc                      <  1:3160392/70‑1 (MQ=255)
                                            aaCGGATACAGCTTGTCCTGGAACGCTTTGTCCGGGGTGATTTCAGCCAACAGGc                                     <  1:3416127/55‑1 (MQ=255)
                                              cGGATACAGCTTGTCCTGGACCGCTTTGTCCGGGGTGATTTCAGCCAACAGGCCAGATTGAGCGTAGcca                    >  1:3617620/1‑70 (MQ=255)
                                              cGGATACAGCTTGTCCTGGACCGCTTTGTCCGGGGTGATTTCAGCCAACAGGCCAGATTGAGCGTAGcca                    >  1:1548415/1‑70 (MQ=255)
                                              cGGATACAGCTTGTCCTGGAACGCTTTGTCCGGGGTGATTTCAGCCAACAGGCCa                                   >  1:3817250/1‑55 (MQ=255)
                                              cGGATACAGCTTGTCCTGGAACGCTTTGTCCGGGGTGATTTCAGCCAACAGGCCAGATTGa                             <  1:801303/61‑1 (MQ=255)
                                                gATACAGCTTGTCCTGGAACGCTTTGTCCGGGGTGATTTCAGCCAACAGGCCAGATTGAGGGTAGccacca                 <  1:640551/71‑1 (MQ=255)
                                                gATACAGCTTGTCCTGGAACGCTTTGTCCGGGGTGATTTCAGCCAACAGGCCAGATTGAGCGTAGccacca                 <  1:3438281/71‑1 (MQ=255)
                                                gATACAGCTTGTCCTGGAACGCTTTGTCCGGGGTGATTTCAGCCAACAGGCCAGATTGAGCGTAGccacca                 <  1:3973846/71‑1 (MQ=255)
                                                  tACAGCTTGTCCTGGAACGCTTTGTCCGGGGTGATTTGAGCCAACAGGCCAg                                  <  1:3652333/52‑1 (MQ=255)
                                                    cAGCTTGTCCTGGAACGCTTTGTCCGGGGTGATTTCAGCCAACAGGCCAGATTGAGCGTa                        >  1:1484973/1‑60 (MQ=255)
                                                          gTCCTGGAACGCTTTGTCCGGGGTGATTTCAGCCAACAgg                                      >  1:1788575/1‑40 (MQ=255)
                                                          gTCCTGGAACGCTTTGTCCGGGGTGATTTCAGCCAACAGGCCAGATTGAGCGTAGCCACCAAAGCGGTCgt       >  1:1020177/1‑71 (MQ=255)
                                                           tCCTGGAACGCTTTGTCCGGGGTGATTTCAGCCAACAGGCCAGATTGAGCGTAGCCACCAAAGCGGTCgtg      <  1:2907796/71‑1 (MQ=255)
                                                             cTGGACCGCTTTGTCCGGGGTGATTTCAGCCAACAGGCCAGATTGAGCGTAGCCACCAAAGCGGTCgtgt     <  1:1700889/70‑1 (MQ=255)
                                                             cTGGAACGCTTTGTCCGGGGTGATTTCAGCCAACAGGCCAGATTGAGCGTAGCCACCAAAGCGGTCgtgt     <  1:3809920/70‑1 (MQ=255)
                                                               ggAACGCTTTGTCCGGGGTGATTTCAGCCAACAGGCCAGa                                 >  1:1343334/1‑40 (MQ=255)
                                                               ggAACGCTTTGTCCGGGGTGATTTCAGCCAACAGGCCAGATTGa                             >  1:3031131/1‑44 (MQ=255)
                                                               ggAACGCTTTGTCCGGGGTGATTTCAGCCAACAGGCCAGATTGa                             >  1:1311647/1‑44 (MQ=255)
                                                               ggAACGCTTTGTCCGGGGTGATTTCAGCCAACAGGCCAGATTGa                             >  1:2299765/1‑44 (MQ=255)
                                                               ggAACGCTTTGTCCGGGGTGATTTCAGCCAACAGGCCAGATTGa                             >  1:1024301/1‑44 (MQ=255)
                                                               ggAACGCTTTGTCCGGGGTGATTTCAGCCAACAGGCCAGATTGAGCGTAGCCACCAAAGCGGTCGTGTGcc  >  1:2264369/1‑71 (MQ=255)
                                                                  |                                                                   
GGTAAGCAATCAGCTTGCCGTTGTAACGTACGGCATCCCAGGTAAACGGATACAGCTTGTCCTGGAACGCTTTGTCCGGGGTGATTTCAGCCAACAGGCCAGATTGAGCGTAGCCACCAAAGCGGTCGTGTGCC  >  W3110S.gb/4249615‑4249748

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