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 3,701,075 T→C 35.3% L107L (TTA→TTG)  rbsC ← D‑ribose transporter subunit

Read alignment evidence...
  seq id position ref new freq score (cons/poly) reads annotation genes product
*W3110S.gb3,701,0750TC35.3% 46.9 / 51.1 51L107L (TTA→TTG) rbsCD‑ribose transporter subunit
Reads supporting (aligned to +/- strand):  ref base T (19/14);  new base C (16/2);  total (35/16)
Fisher's exact test for biased strand distribution p-value = 2.81e-02
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 9.99e-01

CGTAGCGATAAACGCCTGGACGCGACCTTTCGCTACAATCACCCCGGTTACCGCACCAATTGCGGCACCTAACGCGAGAGCAGCAGCGACAGCCACCAGCGCATTGACTTCAATGCCGACGATAGATGCAGCAACTGCGC  >  W3110S.gb/3701006‑3701145
                                                                     |                                                                      
cGTAGCGATAAACGCCTGGACGCGACCTTTCGCTACAATCACCCCGGTTACCGCACCAATTGCGGCACCt                                                                        >  1:687500/1‑70 (MQ=255)
    gCGATAAACGCCTGGACGCGACCTTTCGCTACAATCACCCCGGTTACCGCACCAATTGCGGCACCTAAcgc                                                                   <  1:3128066/71‑1 (MQ=255)
    gCGATAAACGCCTGGACGCGACCTTTCGCTACAATCACCCCGGTTACCGCACCAATTGCGGCACCTAAcgc                                                                   <  1:3465346/71‑1 (MQ=255)
    gCGATAAACGCCTGGACGCGACCTTTCGCTACAATCACCCCGGTTACCGCACCAATTGCGGCACCCAAcgc                                                                   >  1:2825570/1‑71 (MQ=255)
    gCGATAAACGCCTGGACGCGACCTTTCGCTACAATCACCCCGGTTACCGCACCAATTGCGGCACCCAAcgc                                                                   >  1:1814178/1‑71 (MQ=255)
       aTAAACGCCTGGACGCGACCTTTCGCTACAATCACCCCGGTTACCGCACCAATTGCGGCACCt                                                                        <  1:2885706/63‑1 (MQ=255)
        tAAACGCCTGGACGCGACCTTTCGCTACAATCACCCCGGTTACCGCACCAATTGCGGCACCt                                                                        <  1:2385899/62‑1 (MQ=255)
        tAAACGCCTGGACGCGACCTTTCGCTACAATCACCCCGGTTACCGCACCAATTGCGGCACCCAACGCga                                                                 >  1:43556/1‑69 (MQ=255)
         aaaCGCCTGGACGCGACCTTTCGCTACAATCACCCCGGTTACCGCACCAATTGCGGCACCCAACGCGagag                                                              >  1:1357116/1‑71 (MQ=255)
          aaCGCCTGGACGCGACCTTTCGCTACAATCACCCCGGTTACCGCACCAATTGCGGCACCTAACGCGAGagc                                                             <  1:3930388/71‑1 (MQ=255)
          aaCGCCTGGACGCGACCTTTCGCTACAATCACCCCGGTTACCGCACCAATTGCGGCACCCAACGCGagag                                                              >  1:2231636/1‑70 (MQ=255)
          aaCGCCTGGACGCGACCTTTCGCTACAATCACCCCGGTTACCGCACCAATTGCGGCACCCAACGCGagag                                                              >  1:3811515/1‑70 (MQ=255)
            cGCCTGGACGCGACCTTTCGCTACAATCACCCCGGTTACCGCACCAATTGCGGCACCCAACGCGAGagcag                                                           >  1:642661/1‑71 (MQ=255)
             gCCTGGACGCGACCTTTCGCTACAATCACCCCGGTTACCGCACCAATTGCGGCACCTAACGCGAGagcagc                                                          <  1:1328511/71‑1 (MQ=255)
                  gACGCGACCTTTCGCTACAATCACCCCGGTTACCGCACCAATTGCGGCACCTAACGCGAGAGCAGCAGCGa                                                     >  1:976781/1‑71 (MQ=255)
                  gACGCGACCTTTCGCTACAATCACCCCGGTTACCGCACCAATTGCGGCACCCAACGCGAGAGCAGCAGCGa                                                     >  1:3111856/1‑71 (MQ=255)
                  gACGCGACCTTTCGCTACAATCACCCCGGTTACCGCACCAATTGCGGCACCCAACGCGAGAGCAGCAGCGa                                                     >  1:2154978/1‑71 (MQ=255)
                  gACGCGACCTTTCGCTACAATCACCCCGGTTACCGCACCAATTGCGGCACCCAACGCGAGAGCAGCAGCGa                                                     >  1:115042/1‑71 (MQ=255)
                  gACGCGACCTTTCGCTACAATCACCCCGGTTACCGCACCAATTGCGGCACCCAACGCGAGAGCAGCAGCGa                                                     >  1:2641868/1‑71 (MQ=255)
                     gcgACCTTTCGCTACAATCACCCCGGTTACCGCACCAATTGCGGCACCTAACGCGAGAGCAGCAGCGACAg                                                  >  1:1444322/1‑71 (MQ=255)
                     gcgACCTTTCGCTACAATCACCCCGGTTACCGCACCAATTGCGGCACCTAACGCGAGAGCAGCAGCGACAg                                                  >  1:2807311/1‑71 (MQ=255)
                             tCGCTACAATCACCCCGGTTACCGCACCAATTGCGGCACCCAACGCGAGagca                                                            >  1:1796780/1‑53 (MQ=255)
                             tCGCTACAATCACCCCGGTTACCGCACCAATTGCGGCACCCAACGCGAGagca                                                            >  1:554739/1‑53 (MQ=255)
                               gCTACAATCACCCCGGTTACCGCACCAATTGCGTCACCTAACGCGAGAGCAGCAGCGACAGCCACCAgcgc                                        <  1:2829168/71‑1 (MQ=255)
                               gCTACAATCACCCCGGTTACCGCACCAATTGCGGCACCTAACGCGAGAGCAGCAGCGACAGCCACCAgcg                                         <  1:4079057/70‑1 (MQ=255)
                               gCTACAATCACCCCGGTTACCGCACCAATTGCGGCACCTAACGCGAGAGCAGCAGCGACAGCCACCAgcg                                         <  1:1286897/70‑1 (MQ=255)
                               gCTACAATCACCCCGGTTACCGCACCAATTGCGGCACCCAACGCGAGAGCAGCAGCGACAGCCACCAgcg                                         <  1:58327/70‑1 (MQ=255)
                                   cAATCACCCCGGTTACCGCACCAATTGCGGCACCTAACGCGAGAGCAGCAGCGACAGCCACCAGCGCAtt                                     >  1:335258/1‑70 (MQ=255)
                                   cAATCACCCCGGTTACCGCACCAATTGCGGCACCTAACGCGAGAGCAGCAGCGACAGCCACCAGCGCAtt                                     <  1:1046247/70‑1 (MQ=255)
                                       cACCCCGGTTACCGCACCAATTGCGGCACCCAACGCGAGAGCAGCAGCGACAGCCACCAGCGCATTGACtt                                >  1:2880640/1‑71 (MQ=255)
                                       cACCCCGGTTACCGCACCAATTGCGGCACCCAACGCGAGAGCAGCAGCGACAGCCACCAGCGCATTGACtt                                >  1:139887/1‑71 (MQ=255)
                                        aCCCCGGTTACCGCACCAATTGCGGCACCTAACGCga                                                                 >  1:3213189/1‑37 (MQ=255)
                                        aCCCCGGTTACCGCACCAATTGCGGCACCTAACGCGAGAGCAGCAGCGACAGCCACCAGCGCATTGACTTc                               <  1:1449296/71‑1 (MQ=255)
                                         ccccGGTTACCGCACCAATTGCGGCACCTAACGCGAGAGCAGCAGCGACAGCCACCAGCGCATTGACTTCa                              <  1:2588433/71‑1 (MQ=255)
                                          cccGGTTACCGCACCAATTGCGGCACCCAACGCTAGAGCAGCAGCGACAGCCACCAGCGCATTGACTTCaa                             <  1:1454407/71‑1 (MQ=255)
                                                tACCGCACCAATTGCGGCACCTAACGCGAGAGCAGCAGGGACAGCCACCAGCGCATTGACTTCAATGCcga                       >  1:243557/1‑71 (MQ=255)
                                                tACCGCACCAATTGCGGCACCTAACGCGAGAGCAGCAGCGACAGCCACCAGCGCATTGACTTCAATGCcga                       >  1:598971/1‑71 (MQ=255)
                                                tACCGCACCAATTGCGGCACCTAACGCGAGAGCAGCAGCGACAGCCACCAGCGCATTGACTTCAATGCcga                       >  1:1891827/1‑71 (MQ=255)
                                                      aCCAATTGCGGCACCTAACGCGAGAGCAGCAGCGACAGCCACCAGCGCATTGACTTCAATGCCGACGATa                  <  1:583745/70‑1 (MQ=255)
                                                      aCCAATTGCGGCACCTAACGCGAGAGCAGCAGCGACAGCCACCAGCGCATTGACTTCAATGCCGACGATAg                 <  1:356774/71‑1 (MQ=255)
                                                      aCCAATTGCGGCACCTAACGCGAGAGCAGCAGCGACAGCCACCAGCGCATTGACTTCAATGCCGACGATAg                 <  1:898984/71‑1 (MQ=255)
                                                         aaTTGCGGCACCTAACGCGAGAGCAGCAGCGACAGCCACCAGCGCATTGACTTCAATGCcgacga                    >  1:3772184/1‑65 (MQ=255)
                                                         aaTTGCGGCACCTAACGCGAGAGCAGCAGCGACAGCCACCAGCGCATTGACTTCAATGCcgacga                    >  1:538255/1‑65 (MQ=255)
                                                         aaTTGCGGCACCTAACGCGAGAGCAGCAGCGACAGCCACCAGCGCATTGACTTCAATGCcgacga                    >  1:822540/1‑65 (MQ=255)
                                                         aaTTGCGGCACCTAACGCGAGAGCAGCAGCGACAGCCACCAGCGCATTGACTTCAATGCcgacga                    >  1:1991391/1‑65 (MQ=255)
                                                         aaTTGCGGCACCTAACGCGAGAGCAGCAGCGACAGCCACCAGCGCATTGACTTCAATGCcgacga                    >  1:2108367/1‑65 (MQ=255)
                                                         aaTTGCGGCACCTAACGCGAGAGCAGCAGCGACAGCCACCAGCGCATTGACTTCAATGCCGACGATAg                 >  1:3967724/1‑68 (MQ=255)
                                                         aaTTGCGGCACCTAACGCGAGAGCAGCAGCGACAGCCACCAGCGCATTGACTTCAATGCCGACGATAGa                >  1:1009612/1‑69 (MQ=255)
                                                         aaTTGCGGCACCTAACGCGAGAGCAGCAGCGACAGCCACCAGCGCATTGACTTCAATGCCGACGATAGa                >  1:3165222/1‑69 (MQ=255)
                                                         aaTTGCGGCACCTAACGCGAGAGCAGCAGCGACAGCCACCAGCGCATTGACTTCAATGCCGACGATAGa                >  1:1290747/1‑69 (MQ=255)
                                                         aaTTGCGGCACCTAACGCGAGAGCAGCAGCGACAGCCACCAGCGCATTGACTTCAATGCCGACGATAGATg              <  1:992095/71‑1 (MQ=255)
                                                         aaTTGCGGCACCCAACGCGAGAGCAGCAGCGACAGCCACCAGCGCATTGACTTCAATGCCGACGATAGATg              >  1:2189946/1‑71 (MQ=255)
                                                          aTTGCGGCACCTAACGCGAGAGCAGAAGCGACAGCCACCAGCGCATTGACTTCAATGCcgacga                    >  1:1233660/1‑64 (MQ=255)
                                                             gCGGCACCTAACGCGAGAGCAGCAGCGACAGCCACCAGCGCATTGACTTCAATGCCGACGATAGATgcag           >  1:3977004/1‑70 (MQ=255)
                                                                     tAACGCGAGAGCAGCAGCGACAGCCACCAGCGCATTGACTTCaa                             >  1:2498934/1‑44 (MQ=255)
                                                                     tAACGCGAGAGCAGCAGCGACAGCCACCAGCGCATTGACTTCaa                             >  1:176173/1‑44 (MQ=255)
                                                                     tAACGCGAGAGCAGCAGCGACAGCCACCAGCGCATTGACTTCAATGCcgac                      <  1:1741254/51‑1 (MQ=255)
                                                                     tAACGCGAGAGCAGCAGCGACAGCCACCAGCGCATTGACTTCAATGCcgac                      <  1:1750102/51‑1 (MQ=255)
                                                                     tAACGCGAGAGCAGCAGCGACAGCCACCAGCGCATTGACTTCAATGCCGACGATAGATGCAGCAACTgcgc  >  1:1686291/1‑71 (MQ=255)
                                                                     tAACGCGAGAGCAGCAGCGACAGCCACCAGCGCATTGACTTCAATGCCGACGATAGATGCAGCAACTgcgc  >  1:3374947/1‑71 (MQ=255)
                                                                     |                                                                      
CGTAGCGATAAACGCCTGGACGCGACCTTTCGCTACAATCACCCCGGTTACCGCACCAATTGCGGCACCTAACGCGAGAGCAGCAGCGACAGCCACCAGCGCATTGACTTCAATGCCGACGATAGATGCAGCAACTGCGC  >  W3110S.gb/3701006‑3701145

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