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 R1 560 56.4 4650532 94.9% 4413354 59.3

Breseq alignment

BRESEQ :: Evidence
Predicted mutation
evidence seq id position mutation freq annotation gene description
RA W3110S.gb 1,698,594 A→G 10.9% L58S (TTG→TCG)  uidR ← DNA‑binding transcriptional repressor

Read alignment evidence...
  seq id position ref new freq score (cons/poly) reads annotation genes product
*W3110S.gb1,698,5940AG10.9% 138.7 / 9.6 55L58S (TTG→TCG) uidRDNA‑binding transcriptional repressor
Reads supporting (aligned to +/- strand):  ref base A (26/23);  new base G (3/3);  total (29/26)
Fisher's exact test for biased strand distribution p-value = 1.00e+00
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 8.52e-01

ATCCCTTCAATCGGTTCCCGGAAACGGGCCAGCGCCCTCTCCTGGTCCTGTAAGATAATCGCCTGAATCAAGGCTTCTTTGGAGATGAAATGGTGATAGAGCGTCCCGGGACTAATGGCGCAAGATTTACAGATG  >  W3110S.gb/1698525‑1698659
                                                                     |                                                                 
aTCCCTTCAATCGGTTCCCGGAAACGGGCCAGCGCCCTCTCCTGGTCCTGTAAGATAATCGCCTGAATCaa                                                                  <  1:4490213/71‑1 (MQ=255)
aTCCCTTCAATCGGTTCCCGGAAACGGGCCAGCGCCCTCTCCTGGTCCTGTAAGATAATCGCCTGAATCaa                                                                  <  1:2688254/71‑1 (MQ=255)
       cAATCGGTTCCCGGAAACGGGCCAGCGCCCTCTCCTGGTCCTGTAAGATAATCGCCTGAATCAAGGcttct                                                           >  1:2152440/1‑71 (MQ=255)
          tCGGTTCCCGGAAACGGGCCAGCGCCCTCTCCTGGTCCTGTAAGATAATCGCCTGAATCAAGGCTTCTTTg                                                        >  1:1337696/1‑71 (MQ=255)
           cGGTTCCCGGAAACGGGCCAGCGCCCTCTCCTGGTCCTGTAAGATAATCGCCTGAATCGAGGCTTCTTTg                                                        >  1:3715970/1‑70 (MQ=255)
            ggTTCCCGGAAACGGGCCAGCGCCCTCTCCTGGTCCTGTAAGATAATCGCCTGAATCAAGGCTTCTTTgg                                                       <  1:160655/70‑1 (MQ=255)
                cccGGAAACGGGCCAGCGCCCTCTCCTGGTCCTGTAAGATAATCGCCTGAATCAAGGCTTCTTTGGAGAt                                                   >  1:1228170/1‑70 (MQ=255)
                 ccGGAAACGGGCCAGCGCCCTCTCCTGGTCCTGTAAGATAATCGCCTGAATCAAGTCTTCTTTGGAGATGa                                                 <  1:3718086/71‑1 (MQ=255)
                 ccGGAAACGGGCCAGCGCCCTCTCCTGGTCCTGTAAGATAATCGCCTGAATCAAGCCTTCTTTGGAGATGa                                                 <  1:1346255/71‑1 (MQ=255)
                   ggAAACGGGCCAGCGCCCTCTCCTGGTCCTGTAAGATAATCGCCTGAATCAAGGCTTCTTTGGAGATGaaa                                               >  1:2405459/1‑71 (MQ=255)
                    gAAACGGGCCAGCGCCCTCTCCTGGTCCTGTAAGATAATCGCCTGAATCGAGGCTTCTTTGGAGATGAAAt                                              >  1:1937544/1‑71 (MQ=255)
                    gAAACGGGCCAGCGCCCTCTCCTGGTCCTGTAAGATAATCGCCTGAATCGAGGCTTCTTTGGAGATGAAAt                                              <  1:1849088/71‑1 (MQ=255)
                    gAAACGGGCCAGCGCCCTCTCCTGGTCCTGTAAGATAATCGCCTGAATCAAGGcttc                                                            <  1:1057582/57‑1 (MQ=255)
                    gAAACGGGCCAGCGCCCTCTCCTGGTCCTGTAAGATAATCGCCTGAATCAAGGctt                                                             <  1:3177946/56‑1 (MQ=255)
                     aaaCGGGCCAGCGCCCTCTCCTGGTCCTGTAAGATAATCGCCTGAATCAAGGCTTCTTTGGAGATGAAATg                                             >  1:4132752/1‑71 (MQ=255)
                       aCGGGCCAGCGCCCTCTCCTGGTCCTGTAAGATAATCGCCTGAATCAAGGCTTCTTTGGAGATGAAATGGt                                           <  1:995936/71‑1 (MQ=255)
                       aCGGGCCAGCGCCCTCTCCTGGTCCTGTAAGATAATCGCCTGAATCAAGGCTTCTTTGGAGATGAAATGGt                                           <  1:3854794/71‑1 (MQ=255)
                       aCGGGCCAGCGCCCTCTCCTGGTCCTGTAAGATAATCGCCTGAATCAAGGCTTCTTTGGAGATGAAATGGt                                           <  1:1738785/71‑1 (MQ=255)
                              aGCGCCCTCTCCTGGTCCTGTAAGATAATCGCCTGAATCAAGGCTTCTTTGGAGATGAAATGGTGATagag                                    <  1:4606806/71‑1 (MQ=255)
                                 gcCCTCTCCTGGTCCTGTAAGATAATCGCCTGAATCAAGGCTTCTTTGGAGATGAAATGGTGa                                         >  1:2124490/1‑63 (MQ=255)
                                 gcCCTCTCCTGGTCCTGTAAGATAATCGCCTGAATCAAGGCTTCTTTGGAGATGAAATGGTGa                                         >  1:2685913/1‑63 (MQ=255)
                                       tcCTGGTCCTGTAAGATAATCGCCTGAATCAAGGCTTCTTTGGAGATGa                                                 >  1:3546196/1‑49 (MQ=255)
                                       tcCTGGTCCTGTAAGATAATCGCCTGAATCAAGGCTTCTTTGGAGATGAAATGGTGATAGAGCGTCCCgg                            >  1:4119804/1‑70 (MQ=255)
                                       tcCCGGTCCTGTAAGATAATCGCCTGAATCAAGGCTTCTTTGGAGATGAAAt                                              >  1:588740/1‑52 (MQ=255)
                                        ccTGGTCCTGTAAGATAATCGCCTGAATCAAGGCTTCTTTGGAGATGaaa                                               >  1:1224662/1‑50 (MQ=255)
                                         cTGGTCCTGTAAGATAATCGCCTGAATCAAGGCTTCTTTGGAGATGAAATg                                             <  1:1685723/51‑1 (MQ=255)
                                         cTGGTCCTGTAAGATAATCGCCTGAATCAAGGCTTCTTTGGAGATGAAATGGTGATAGAGCGT‑CCGGGACt                        <  1:2843119/71‑1 (MQ=255)
                                          tGGTCCTGTAAGATAATCGCCTGAATCAAGGCTTCTTTGGAGATGAAATGGt                                           >  1:1091789/1‑52 (MQ=255)
                                           ggTCCTGTAAGATAATCGCCTGAATCAAGGCTTCTTTGGAGATGAAAt                                              >  1:2339809/1‑48 (MQ=255)
                                           ggTCCTGTAAGATAATCGCCTGAATCAAGGCTTCTTTGGAGATGAAATGGTGATAGAGCGTCCCGGGACt                        >  1:3165051/1‑70 (MQ=255)
                                            gTCCTGTAAGATAATCGCCTGAATCAAGGCTTCTTTGGAGATGAAATGGTGATAGAGCGTCCCGGGACt                        <  1:4053954/69‑1 (MQ=255)
                                               cTGTAAGATAATCGCCTGAATCAAGGCTTCTTTGGAGATGaaa                                               <  1:2959301/43‑1 (MQ=255)
                                               cTGTAAGATAATCGCCTGAATCAAGGCTTCTTTGGAGATGaa                                                <  1:1165649/42‑1 (MQ=255)
                                               cTGTAAGATAATCGCCTGAATCAAGGCTTCTTTGGAGATGAAATGGTGATAGAGCGTcc                               >  1:3650343/1‑59 (MQ=255)
                                                tGTAAGATAATCGCCTGAATCAAGGCTTCTTTGGAGATGAAATGGTGATAGAGCGTCCCgg                            <  1:1548893/61‑1 (MQ=255)
                                                 gTAAGATAATCGCCTGAATCAAGGCTTCTTTGGAGATGAAAt                                              >  1:2185564/1‑42 (MQ=255)
                                                 gTAAGATAATCGCCTGAATCAAGGCTTCTTTGGAGATGAAAt                                              >  1:2789584/1‑42 (MQ=255)
                                                  tAAGATAATCGCCTGAATCAAGGCTTCTTTGGAGATGAAATGGTGa                                         <  1:2863959/46‑1 (MQ=255)
                                                  tAAGATAATCGCCTGAATCAAGGCTTCTTTGGAGATGAAATGGTGATAGAGCGTCCCGGGACt                        <  1:4330534/63‑1 (MQ=255)
                                                  tAAGATAATCGCCTGAATCAAGGCTTCTTTGGAGATGAAATGGTGATAGAGCGTCCCGGGACt                        <  1:1258426/63‑1 (MQ=255)
                                                  tAAGATAATCGCCTGAATCAAGGCTTCTTTGGAGATGAAATGGTGATAGAGCGTCCCGGGACTAATGgcg                 >  1:524590/1‑70 (MQ=255)
                                                   aaGATAATCGCCTGAATCAAGGCTTCTTTGGAGATGAAATGGt                                           <  1:1003116/43‑1 (MQ=255)
                                                    aGATAATCGCCTGAATCAAGGCTTCTTTGGAGATGAAATGGTGATAGAGCGTCCCGGAACt                        <  1:70938/61‑1 (MQ=255)
                                                       tAATCGCCTGAATCGAGGCTTCTTTGGAGATGaaa                                               >  1:4286455/1‑35 (MQ=255)
                                                        aaTCGCCTGAATCAAGGCTTCTTTGGAGATGAAATGGTGATag                                      >  1:1892000/1‑43 (MQ=255)
                                                         aTCGCCTGAATCAAGGCTTCTTTGGAGATGAAATg                                             >  1:3603664/1‑35 (MQ=255)
                                                          tCGCCTGAATCAAGGCTTCTTTGGAGATGAAATGGTg                                          <  1:1717668/37‑1 (MQ=255)
                                                            gCCTGAATCAAGGCTTCTTTGGAGATGAAATGGTGATAGAGCGTCCCGGGACTAATGGCGCAAGATTTACa      <  1:639529/71‑1 (MQ=255)
                                                            gCCTGAATCAAGGCTTCTTTGGAGATGAAATGGTGATAGAGCGTCCCGGGACTAATGGCGCAAGATTTACa      <  1:1331407/71‑1 (MQ=255)
                                                               tGAATCGAGGCTTCTTTGGAGATGAAATGGTGATAGAGCGTCCCgg                            <  1:1316795/46‑1 (MQ=255)
                                                               tGAATCAAGGCTTCTTTGGAGATGAAATGGTGATAGAGCGt                                 >  1:1786273/1‑41 (MQ=255)
                                                               tGAATCAAGGCTTCTTTGGAGATGAAATGGTGATAGAGCGt                                 >  1:1920304/1‑41 (MQ=255)
                                                               tGAATCAAGGCTTCTTTGGAGATGAAATGGTGATAGAGCGTCCCGGGACTAATGGCGCAAGATTTa        >  1:389192/1‑66 (MQ=255)
                                                                gAATCAAGGCTTCTTTGGAGATGAAATGGTGATAGAGCGTCCCGGGACTAATGGCGCAAGATTTACAGATg  >  1:2498430/1‑71 (MQ=255)
                                                                 aaTCGAGGCTTCTTTGGAGATGAAATGGTGATAGAGCGTCCCGGGACTAATGGCGCAAGATTTACa      <  1:4181310/66‑1 (MQ=255)
                                                                  aTCAAGGCTTCTTTGGAGATGAAATGGTGATAGAGCGTCCCGGGACTaa                      >  1:863739/1‑49 (MQ=255)
                                                                   tCAAGGCTTCTTTGGAGATGAAATGGTGATAGAGc                                   >  1:528961/1‑35 (MQ=255)
                                                                     aaGGCTTCTTTGGAGATGAAATGGTGATAGAGCGTCCCGGGa                          >  1:2458225/1‑42 (MQ=255)
                                                                     |                                                                 
ATCCCTTCAATCGGTTCCCGGAAACGGGCCAGCGCCCTCTCCTGGTCCTGTAAGATAATCGCCTGAATCAAGGCTTCTTTGGAGATGAAATGGTGATAGAGCGTCCCGGGACTAATGGCGCAAGATTTACAGATG  >  W3110S.gb/1698525‑1698659

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