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
A5 F17 I0 R2 162 60.6 4616657 98.5% 4547407 62.1

Breseq alignment

BRESEQ :: Evidence
Predicted mutation
evidence seq id position mutation freq annotation gene description
RA W3110S.gb 285,498 G→A 11.9% A294T (GCC→ACC)  yagG → predicted sugar transporter

Read alignment evidence...
  seq id position ref new freq score (cons/poly) reads annotation genes product
*W3110S.gb285,4980GA11.9% 172.3 / 11.8 59A294T (GCC→ACC) yagGpredicted sugar transporter
Reads supporting (aligned to +/- strand):  ref base G (20/32);  new base A (4/3);  total (24/35)
Fisher's exact test for biased strand distribution p-value = 4.27e-01
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 9.95e-01

CGGCAGCCTCGCCACCATGTTCGGCTCGCTTTGCTCCTCACGCCTGCTGGGCCGCTTCGACCGCGTCACCGCCTTCAAGTGGATCATCGTCGCCTACTCGCTGATCAGCCTGCTGATTTTCGTCACCCCGGCGGAGCA  >  W3110S.gb/285428‑285565
                                                                      |                                                                   
cGGCAGCCTCGCCACCATGTTCGGCTCGCTTTGCTCCTCACGCCTGCTGGGCCGCTTCGACCGCGTCACCg                                                                     >  1:2898787/1‑71 (MQ=255)
      ccTCGCCACCATGTTCGGCTCGCTTTGCTCCTCACGCCTGCTGGGCCGCTTCGACCGCGTCACCGCCTTc                                                                >  1:1652464/1‑70 (MQ=255)
      ccTCGCCACCATGTTCGGCTCGCTTTGCTCCTCACGCCTGCTGGGCCGCTTCGACCGCGTCACCGCCTTCa                                                               <  1:1069095/71‑1 (MQ=255)
       cTCGCCACCATGTTCGGCTCGCTTTGCTCCTCACGCCTGCTGGGCCGCTTCGACCGCGTCACCGCCTTCaa                                                              <  1:2125075/71‑1 (MQ=255)
       cTCGCCACCATGTTCGGCTCGCTTTGCTCCTCACGCCTGCTGGGCCGCTTCGACCGCGTCACCGCCTTCa                                                               <  1:858804/70‑1 (MQ=255)
        tCGCCACCATGTTCGGCTCGCTTTGCTCCTCACGCCTGCTGGGCCGCTTCGACCGCGTCACCGCCTTCAAg                                                             >  1:1035647/1‑71 (MQ=255)
         cGCCACCATGTTCGGCTCGCTTTGCTCCTCACGCCTGCTGGGCCGCTTCGACCGCGTCACCACCTTCAAGt                                                            >  1:1904329/1‑71 (MQ=255)
          gCCACCATGTTCGGCTCGCTTTGCTCCTCACGCCTGCTGGGCCGCTTCGACCGCGTCACCGCCTTCAAGTg                                                           <  1:817060/71‑1 (MQ=255)
          gCCACCATGTTCGGCTCGCTTTGCTCCTCACGCCTGCTGGGCCGCTTCGACCGCGTCACCACCTTCAAGt                                                            <  1:3300141/70‑1 (MQ=255)
           ccaccaTGTTCGGCTCGCTTTGCTCCTCACGCCTGCTGGGCCGCTTCGACCGCGTCACCGCCTTCAAGTgg                                                          <  1:1487085/71‑1 (MQ=255)
            caccaTGTTCGGCTCGCTTTGCTCCTCACGCCTGCTGGGCCGCTTCGACCGCGTCACAGCCTTCAAGTGGa                                                         >  1:3459158/1‑71 (MQ=255)
                 tGTTCGGCTCGCTTTGCTCCTCACGCCTGCTGGGCCGCTTCGACCGCGTCACCACCTTCAAGTGGatcatc                                                    >  1:89379/1‑71 (MQ=255)
                   ttCGGCTCGCTTTGCTCCTCACGCCTGCTGGGCCGCTTCGACCGCGTCACCGCCTTCAAGTGGatca                                                      <  1:4174320/67‑1 (MQ=255)
                   ttCGGCTCGCTTTGCTCCTCACGCCTGCTGGGCCGCTTCGACCGCGTCACCGCCTTCAAGTGGATCAtcgt                                                  >  1:1129383/1‑71 (MQ=255)
                   ttCGGCTCGCTTTGCTCCTCACGCCTGCTGGGCCGCTTCGACCGCGTCACCGCCTTCAAGTGGATCAtcg                                                   >  1:1363184/1‑70 (MQ=255)
                           gCTTTGCTCCTCACGCCTGCTGGGCCGCTTCGACCGCGTCACCGCCTTCAAGTGGATCATCGTCGCCTa                                            <  1:188052/69‑1 (MQ=255)
                           gCTTTGCTCCTCACGCCTGCTGGGCCGCTTCGACCGCGTCACCGCCTTCAAGTGGATCATCGTCGCCTACt                                          >  1:2977595/1‑71 (MQ=255)
                               tGCTCCTCACGCCTGCTGGGCCGCTTCGACCGCGTCACCGCCTTCAAGTGGATCATCGTCGCCTACTCg                                        <  1:4026089/69‑1 (MQ=255)
                                 ctcctcACGCCTGCTGGGCCGCTTCGACCGCGTCACCGCCTTCAAGTGGATCATCGTCGCCTACTCGCTg                                     <  1:3902698/70‑1 (MQ=255)
                                   cctcACGCCTGCTGGGCCGCTTCGACCGCGTCACCGCCTTCAAGTGGa                                                         >  1:437485/1‑48 (MQ=255)
                                   cctcACGCCTGCTGGGCCGCTTCGACCGCGTCACCGCCTTCAAGTGGATCATCGTCGCCTACTCGCTGAt                                   >  1:825718/1‑70 (MQ=255)
                                    ctcACGCCTGCTGGGCCGCTTCGACCGCGTCACCGCCTTCAAGTGGATCATCGTCGCCTACTCGCTGAt                                   <  1:4201590/69‑1 (MQ=255)
                                    ctcACGCCTGCTGGGCCGCTTCGACCGCGTCACCGCCTTCAAGTGGATCATCGTCGCCTACTCGCTGATCa                                 <  1:1277412/71‑1 (MQ=255)
                                    ctcACGCCTGCTGGGCCGCTTCGACCGCGTCACCACCTTCAAGTGGATCAtcg                                                   <  1:363614/53‑1 (MQ=255)
                                     tcACGCCTGCTGGGCCGCTTCGACCGCGTCACCGCCTTCAAGTGGATCATCGTCGCCTACTc                                         <  1:885590/62‑1 (MQ=255)
                                     tcACGCCTGCTGGGCCGCTTCGACCGCGTCACCGCCTTCAAGTGGATCATCGTCGCCTACTCGCTGATCAg                                >  1:2928438/1‑71 (MQ=255)
                                      cACGCCTGCTGGGCCGCTTCGACCGCGTCACCGCCTTCAAGTGGATCATCGTCGCCTACTCGCTGATCAGc                               >  1:2459596/1‑71 (MQ=255)
                                      cACGCCTGCTGGGCCGCTTCGACCGCGTCACCACCTTCAAGTGGatcat                                                     >  1:3641690/1‑49 (MQ=255)
                                       aCGACTGCTGGGCCGCTTCGACCGCGTCACCGCCTTCAAGTGGatcatc                                                    >  1:464041/1‑49 (MQ=255)
                                         gCCTGCTGGGCCGCTTCGACCGCGTCACCGCCTTCAAGTGGATCATCGTCGCCTACTCGCTTATCAGCct                             >  1:4109597/1‑70 (MQ=255)
                                          ccTGCTGGGCCGCTTCGACCGCGTCACCGCCTTCAAGTGGATCATCGTCGCCTACTCGCTGATCAGCctgc                           <  1:1842873/71‑1 (MQ=255)
                                          ccTGCTGGGCCGCTTCGACCGCGTCACCGCCTTCAAGTGGATCATCGTCGCCTACTCGCTGATCAGCctgc                           <  1:2484466/71‑1 (MQ=255)
                                           ctgctgGGCCGCTTCGACCGCGTCACCGCCTTCAAGTGGATCATCGTCGCCTACTCGCTGATCAGCctgct                          >  1:1590604/1‑71 (MQ=255)
                                            tgctgGGCCGCTTCGACCGCGTCACCGCCTTCAAGTGGatc                                                       <  1:1691599/41‑1 (MQ=255)
                                            tgctgGGCCGCTTCGACCGCGTCACCGCCTTCAAGTGGATCAtcgt                                                  <  1:2271421/46‑1 (MQ=255)
                                              ctgGGCCGCTTCGACCGCGTCACCGCCTTCAAGTGGATCATCGTCGCCTACTCGCTGATCAGCCTGCTGAt                       >  1:3091418/1‑71 (MQ=255)
                                                 ggCCGCTTCGACCGCGTCACCGCCTTCAAGTGGATCATCGTCGCCTACTCGCTGATCAGCCTGCTGAttt                     <  1:4278141/70‑1 (MQ=255)
                                                 ggCCGCTTCGACCGCGTCACCGCCTTCAAGTGGATCATCGTCGCCTACTCGCTGATCAGCCTGCTGAttt                     <  1:4238703/70‑1 (MQ=255)
                                                 ggCCGCTTCGACCGCGTCACCGCCTTCAAGTGGATCATCGTCGCCTACTCGCTGATCAGCCTGCTGAttt                     <  1:247390/70‑1 (MQ=255)
                                                  gCCGCTTCGACCGCGTCACCGCCTTCTAGTGGATCATCGTCGCCTACTCGCTGATCAGCCTGCTGATTTTc                   <  1:1080417/71‑1 (MQ=255)
                                                  gCCGCTTCGACCGCGTCACCGCCTTCAAGTGGATCATCGTCGCCTACTCGCTGATCAGCCTGCTGAttt                     <  1:68051/69‑1 (MQ=255)
                                                     gCTTCGACCGCGTCACCGCCTTCAAGTGGATCATCGTCGcc                                              <  1:312526/41‑1 (MQ=255)
                                                     gCTTCGACCGCGTCACCGCCTTCAAGTGGATCATCGTCGCCTACTCGCTGATCAGCCTGCTGATTTTc                   >  1:2251059/1‑68 (MQ=255)
                                                     gCTTCGACCGCGTCACCGCCTTCAAGTGGATCATCGTCGCCTACTCGCTGATCAGCCTGCTGATTTTCGTc                <  1:2516436/71‑1 (MQ=255)
                                                       ttCGACCGCGTCACCGCCTTCAAGTGGATCATCGTCGCCTACTCGCTGATCAGCCTGCTGATTTTc                   <  1:4609758/66‑1 (MQ=255)
                                                        tCGACCGCGTCACCGCCTTCAAGTGGATCATCGTCGCCTACTCGCTGATCAGCCTGCTGATTTTCGTCAcc             >  1:856623/1‑71 (MQ=255)
                                                         cGACCGCGTCACCGCCTTCAAGTGGATCATCGTCGCCTACTCGCTg                                     <  1:513484/46‑1 (MQ=255)
                                                         cGACCGCGTCACCGCCTTCAAGTGGATCATCGTCGCCTACTCGCTGATCAGCCTGCTGATTTTCGt                 >  1:1908793/1‑66 (MQ=255)
                                                         cGACCGCGTCACCGCCTTCAAGTGGATCATCGTCGCCTACTCGCTGATCAGCCTGCTGATTTTCGTCAc              <  1:1744215/69‑1 (MQ=255)
                                                          gACCGCGTCACCGCCTTCAAGTGGATCATCGTCGc                                               >  1:2703289/1‑35 (MQ=255)
                                                           aCCGCGTCACCACCTTCAAGTGGATCATCGTCGCCTACTCGCTGATCAGCCTGCTGAt                       <  1:1861308/58‑1 (MQ=255)
                                                             cgcgTCACCGCCTTCAAGTGGATCATCGTCGCCTACTCGCTGATCAGCCTGCTGAt                       <  1:1073631/56‑1 (MQ=255)
                                                               cgTCACCGCCTTCAAGTGGATCATCGTCGCCTACTCGCTGATCAGCCTGCTGATTTTCGTCACCCcggcgg      <  1:3698485/71‑1 (MQ=255)
                                                               cgTCACCACCTTCAAGAGGATCATCGTCGCCTACTCGCTGATCAGCCTGCTGATTTTc                   >  1:3959166/1‑58 (MQ=255)
                                                                gTCACCGCCTTCAAGTGGATCATCGTCGCCTACTCGCTGATCAGCCTGCTGATTTTCGTCAGCCCGGCGGa     <  1:1771511/71‑1 (MQ=255)
                                                                gTCACCGCCTTCAAGTGGATCATCGTCGCCTACTCGCTGATCAGCCTGCTGATTTTCGTCACCCCGGCGGa     <  1:557167/71‑1 (MQ=255)
                                                                 tCACCGCCTTCAAGTGGATCATCGTCGCCTACTCGCTg                                     <  1:105462/38‑1 (MQ=255)
                                                                 tCACCGCCTTCAAGTGGATCATCGTCGCCTACTCGCTGATCAGCCTGCTGAtt                      <  1:1827638/53‑1 (MQ=255)
                                                                   aCCGCCTTCAAGTGGATCATCGTCGCCTACTCGCTGATc                                  >  1:489685/1‑39 (MQ=255)
                                                                   aCCGCCTTCAAGTGGATCATCGTCGCCTACTCGCTGATCAGCCTGCTGATTTTCGTCACCCCGGCGGAGca  >  1:688487/1‑71 (MQ=255)
                                                                      |                                                                   
CGGCAGCCTCGCCACCATGTTCGGCTCGCTTTGCTCCTCACGCCTGCTGGGCCGCTTCGACCGCGTCACCGCCTTCAAGTGGATCATCGTCGCCTACTCGCTGATCAGCCTGCTGATTTTCGTCACCCCGGCGGAGCA  >  W3110S.gb/285428‑285565

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