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 F1 I0 R2 201 99.6 7939938 96.9% 7693799 60.1

Breseq alignment

BRESEQ :: Evidence
Predicted mutation
evidence seq id position mutation freq annotation gene description
RA W3110S.gb 4,371,273 Δ2 bp 100% intergenic (‑6/+299) dcuA ← / ← aspA C4‑dicarboxylate antiporter/aspartate ammonia‑lyase

Read alignment evidence...
  seq id position ref new freq score (cons/poly) reads annotation genes product
*W3110S.gb4,371,2730A.100.0% 319.4 / NA 77intergenic (‑6/+300)dcuA/aspAC4‑dicarboxylate antiporter/aspartate ammonia‑lyase
Reads supporting (aligned to +/- strand):  ref base A (0/0);  new base . (40/37);  total (40/37)
Rejected as polymorphism: Frequency below/above cutoff threshold.
Rejected as polymorphism: Variant not supported by required number of reads on each strand.
*W3110S.gb4,371,2740A.100.0% 319.4 / NA 77intergenic (‑7/+299)dcuA/aspAC4‑dicarboxylate antiporter/aspartate ammonia‑lyase
Reads supporting (aligned to +/- strand):  ref base A (0/0);  new base . (40/37);  total (40/37)
Rejected as polymorphism: Frequency below/above cutoff threshold.
Rejected as polymorphism: Variant not supported by required number of reads on each strand.

TTACGGCGCAGCAGCTTTTCTGTCTGATGAACCAGATAGTCCAGACCGCCAGCAACCTGCATGGCAGAAAAATAGCGGCGATAACCGCCATGATAATGGAGATGACATCGAACGGGATGTTACCGGGTTTAA  >  W3110S.gb/4371206‑4371337
                                                                   ||                                                               
ttACGGCGCAGCAGCTTTTCTGTCTGATGAACCAGATAGTCCAGACCGCCAGCAACCTGCATGGCAGaaat                                                               <  1:1807217/71‑2 (MQ=255)
  aCGGCGCAGCAGCTTTTCTGTCTGATGAACCAGATAGTCCAGACCGCCAGCAACCTGCATGGCAGaaata                                                              <  1:4543319/70‑3 (MQ=255)
        cagcagCTTTTCTGTCTGATGAACCAGATAGTCCAGACCGCCAGCAACCTGCATGGCAGaaat                                                               <  1:5014966/63‑2 (MQ=255)
        cagcagCTTTTCTGTCTGATGAACCAGATAGTCCAGACCGCCAGCAACCTGCATGGCAG‑‑AAATAGCGGCGa                                                     <  1:1157143/71‑1 (MQ=255)
         agcagcTTTTCTGTCTGATGAACCAGATAGTCCAGACCGCCAGCAACCTGCATGGCAG‑‑AAATAGCGGCGAt                                                    <  1:7812807/71‑1 (MQ=255)
          gcagcTTTTCTGTCTGATGAACCAGATAGTCCAGACCGCCAGCAACCTGCATGGCAG‑‑AAATAGCGGCGAt                                                    >  1:4266548/1‑70 (MQ=255)
           cagcTTTTCTGTCTGATGAACCAGATAGTCCAGACCGCCAGCAACCTGCATGGCAG‑‑AAATAGCGGCGATaa                                                  >  1:3577454/1‑71 (MQ=255)
            agcTTTTCTGTCTGATGAACCAGATAGTCCAGACCGCCAGCAACCTGCATGGCAGaaat                                                               >  1:3120561/1‑58 (MQ=255)
             gcTTTTCTGTCTGATGAACCAGATAGTCCAGACCGCCAGCAACCTGCATGGCAG‑‑AAATAGCGGCGATAAcc                                                <  1:7069387/71‑1 (MQ=255)
                 ttCTGTCTGATGAACCAGATAGTCCAGACCGCCAGCAACCTGCATGGCAG‑‑AAATAGCGGCGATAACCGcc                                             <  1:5491293/70‑1 (MQ=255)
                 ttCTGTCTGATGAACCAGATAGTCCAGACCGCCAGCAACCTGCATGGCAG‑‑AAATAGCGGCGATAACCGc                                              <  1:5606944/69‑1 (MQ=255)
                   ctgtctgATGAACCAGATAGTCCAGACCGCCAGCAACCTGCATGGCAG‑‑AAATAGCGGCGATa                                                   <  1:7356927/62‑1 (MQ=255)
                   ctgtctgATGAACCAGATAGTCCAGACCGCCAGCAACCTGCATGGCAG‑‑AAATAGCGGCGATAACCGCCAt                                           <  1:3392093/70‑1 (MQ=255)
                      tctgATGAACCAGATAGTCCAGACCGCCAGCAACCTGCATGGCAG‑‑AAATAGCGGCGATAACCGCCATGa                                         <  1:4629380/69‑1 (MQ=255)
                      tctgATGAACCAGATAGTCCAGACCGCCAGCAACCTGCATGGCAG‑‑AAATAGCGGCGATAACCGCCATGa                                         <  1:3566076/69‑1 (MQ=255)
                      tctgATGAACCAGATAGTCCAGACCGCCAGCAACCTGCATGGCAG‑‑AAATAGCGGCGATAACCGCCATGATa                                       <  1:7616726/71‑1 (MQ=255)
                       ctgATGAACCAGATAGTCCAGACCGCCAGCAACCTGCATGGCAG‑‑AAATAGCGGCGATAAc                                                 >  1:5869513/1‑60 (MQ=255)
                       ctgATGAACCAGATAGTCCAGACCGCCAGCAACCTGCATGGCAG‑‑AAATAGCGGCGATAAc                                                 >  1:4208469/1‑60 (MQ=255)
                       ctgATGAACCAGATAGTCCAGACCGCCAGCAACCTGCATGGCAG‑‑AAATAGCGGCGATAAc                                                 >  1:4587151/1‑60 (MQ=255)
                       ctgATGAACCAGATAGTCCAGACCGCCAGCAACCTGCATGGCAG‑‑AAATAGCGGCGATAACCGCCATGAt                                        <  1:5425904/69‑1 (MQ=255)
                       ctgATGAACCAGATAGTCCAGACCGCCAGCAACCTGCATGGCAG‑‑AAATAGCGGCGATAACCGCCATGATaa                                      >  1:3829189/1‑71 (MQ=255)
                         gatgaACCAGATAGTCCAGACCGCCAGCAACCTGCATGGCAG‑‑AAATAGCGGCGATAACCGCCATGATaa                                      >  1:4092383/1‑69 (MQ=255)
                           tgaACCAGATAGTCCAGACCGCCAGCAACCTGCATGGCAG‑‑AAATAGCGGCGATAACCGCCATGATAATGga                                  <  1:2267190/71‑1 (MQ=255)
                           tgaACCAGATAGTCCAGACCGCCAGCAACCTGCATGGCAG‑‑AAATAGCGGCGATAACCGCCATGATAATGga                                  <  1:1236642/71‑1 (MQ=255)
                               ccAGATAGTCCAGACCGCCAGCAACCTGCATGGCAGaa                                                                 <  1:3667717/38‑1 (MQ=255)
                               ccAGATAGTCCAGACCGCCAGCAACCTGCATGGCAGaa                                                                 <  1:5964384/38‑1 (MQ=255)
                               ccAGATAGTCCAGACCGCCAGCAACCTGCATGGCAG‑‑AAATAGCGGCGATAACCGCCATGATAATGGAGAt                               >  1:2048628/1‑70 (MQ=255)
                               ccAGATAGTCCAGACCGCCAGCAACCTGCATGGCAG‑‑AAATAGCGGCGATAACCGCCATGATAATGGAGAt                               >  1:306918/1‑70 (MQ=255)
                                 aGATAGTCCAGACCGCCAGCAACCTGCATGGCAG‑‑AAATAGCGGCGATAACCGCCATGATAATGGAGAtaca                            <  1:4380441/71‑4 (MQ=255)
                                  gATAGTCCAGACCGCCAGCAACCTGCATGGCAG‑‑AAATAGCGGCGATaa                                                  >  1:7404405/1‑48 (MQ=255)
                                  gATAGTCCAGACCGCCAGCAACCTGCATGGCAG‑‑AAATAGCGGCGATAACCGCCATGATAATGGAGATGAc                            >  1:7809376/1‑70 (MQ=255)
                                  gATAGTCCAGACCGCCAGCAACCTGCATGGCAG‑‑AAATAGCGGCGATAACCGCCATGATAATGGAGATGACa                           <  1:4743183/71‑1 (MQ=255)
                                  gATAGTCCAGACCGCCAGCAACCTGCATGGCAG‑‑AAATAGCGGCGATAACCGCCATGATAATGGAGATGACa                           >  1:1213845/1‑71 (MQ=255)
                                    tAGTCCAGACCGCCAGCAACCTGCATGGCAG‑‑AAATAGCGGCGATAACCGCCa                                            >  1:7288525/1‑52 (MQ=255)
                                    tAGTCCAGACCGCCAGCAACCTGCATGGCAG‑‑AAATAGCGGCGATAACCGCCa                                            >  1:6397569/1‑52 (MQ=255)
                                    tAGTCCAGACCGCCAGCAACCTGCATGGCAG‑‑AAATAGCGGCGATAACCGCCATGATAATGGAGATGACATc                         >  1:4898007/1‑71 (MQ=255)
                                      gTCCAGACCGCCAGCAACCTGCATGGCAG‑‑AAATAGCGGCGATAACCGCCATGATAATGGAGATGACATCg                        <  1:863981/70‑1 (MQ=255)
                                       tCCAGACCGCCATCAACCTGCATGGCAG‑‑AAATAGCGGCGATAACCGCCATGATAATGGAGATGACATCGaa                      <  1:6631396/71‑1 (MQ=255)
                                       tCCAGACCGCCAGCAACCTGCATGGCAG‑‑AAATAGCGGCGATaa                                                  <  1:6429930/43‑1 (MQ=38)
                                       tCCAGACCGCCAGCAACCTGCATGGCAG‑‑AAATAGCGGCGATAACCGCCATGATAATGGAGATGACATCGaa                      <  1:7374031/71‑1 (MQ=255)
                                       tCCAGACCGCCAGCAACCTGCATGGCAG‑‑AAATAGCGGCGATAACCGCCATGATAATGGAGATGACATCGaa                      >  1:4930080/1‑71 (MQ=255)
                                        ccAGACCGCCAGCAACCTGCATGGCAG‑‑AAATAGCGGCGATAACCGCCATGATAATGGAGATGACATCGAAc                     >  1:360056/1‑71 (MQ=255)
                                         cAGACCGCCAGCAACCTGCATGGCAG‑‑AAATAGCGGCGATAAc                                                 >  1:4460767/1‑42 (MQ=37)
                                         cAGACCGCCAGCAACCTGCATGGCAG‑‑AAATAGCGGCGATAAc                                                 >  1:49609/1‑42 (MQ=37)
                                         cAGACCGCCAGCAACCTGCATGGCAG‑‑AAATAGCGGCGATAACCGCCATGATAATGGAGATGACATCGAACg                    >  1:6963559/1‑71 (MQ=255)
                                          aGACCGCCAGCAACCTGCATGGCAG‑‑AAATAGCGGCGATAACCGCCATGATAATGGAGATGACATCGa                       <  1:3013568/67‑1 (MQ=255)
                                           gACCGCCAGCAACCTGCATGGCAG‑‑AAATAGCGGCGATAACCGCCATGATAATGGAGATGACATCGAACggg                  <  1:7127687/71‑1 (MQ=255)
                                           gACCGCCAGCAACCTGCATGGCAG‑‑AAATAGCGGCGATAACCGCCATGATAATGGAGATGACATCGAACggg                  <  1:6798336/71‑1 (MQ=255)
                                           gACCGCCAGCAACCTGCATGGCAG‑‑AAATAGCGGCGATAACCGCCATGATAATGGAGATGACATCGAACgg                   >  1:7203341/1‑70 (MQ=255)
                                           gACCGCCAGCAACCTGCATGGCAG‑‑AAATAGCGGCGATAACCGCCATGATAATGGAGATGACATCGAACg                    >  1:7731803/1‑69 (MQ=255)
                                           gACCGCCAGCAACCTGCATGGCAG‑‑AAATAGCGGCGATAACCGCCATGATAATGGAGATGACATCGAACg                    >  1:1501794/1‑69 (MQ=255)
                                            aCCGCCAGCAACCTGCATGGCAG‑‑AAATAGCGGCGATAACCGCCATGATAATGGAGATGACATCGAACggg                  <  1:554457/70‑1 (MQ=255)
                                             ccGCCAGCAACCTGCATGGCAG‑‑AAATAGCGGCGATAACCGCCATGATAATGGAGATGACATCGAACGGGAt                <  1:1137994/71‑1 (MQ=255)
                                             ccGCCAGCAACCTGCATGGCAG‑‑AAATAGCGGCGATAACCGCCATGATAATGGAGATGACATCGAACGGGAt                <  1:3795311/71‑1 (MQ=255)
                                                 cAGCAACCTGCATGGCAG‑‑AAATAGCGGCGATAACCGCCATGATAATGgag                                 <  1:6511813/50‑1 (MQ=38)
                                                 cAGCAACCTGCATGGCAG‑‑AAATAGCGGCGATAACCGCCATGATAATGgag                                 <  1:4391305/50‑1 (MQ=38)
                                                 cAGCAACCTGCATGGCAG‑‑AAATAGCGGCGATAACCGCCATGATAATGGAGATGACATCGAACGGGATGTTa            <  1:6028898/71‑1 (MQ=255)
                                                 cAGCAACCTGCATGGCAG‑‑AAATAGCGGCGATAACCGCCATGATAATGGAGATGACATCGAACGGGATGTTa            <  1:2452748/71‑1 (MQ=255)
                                                 cAGCAACCTGCATGGCAG‑‑AAATAGCGGCGATAACCGCCATGATAATGGAGATGACATCGAACGGGATGTTa            <  1:5661579/71‑1 (MQ=255)
                                                  aGCAACCTGCATGGCAG‑‑AAATAGCGGCGATAACCGCCATGATaa                                      >  1:3570320/1‑44 (MQ=38)
                                                  aGCAACCTGCATGGCAG‑‑AAATAGCGGCGATAACCGCCATGATaa                                      >  1:3579556/1‑44 (MQ=38)
                                                  aGCAACCTGCATGGCAG‑‑AAATAGCGGCGATAACCGCCATGATAATGGAGATGACATCGAACGGGATGTTAc           >  1:2970915/1‑71 (MQ=255)
                                                  aGCAACCTGCATGGCAG‑‑AAATAGCGGCGATAACCGCCATGATAATGGAGATGACATCGAACGGGATGTTAc           >  1:707335/1‑71 (MQ=255)
                                                   gCAACCTGCATGGCAG‑‑AAATAGCGGCGATAACCGCCATGATAATGGAGATGACAt                          >  1:2481701/1‑55 (MQ=255)
                                                   gCAACCTGCATGGCAG‑‑AAATAGCGGCGATAACCGCCATGATAATGGAGATGACATCGAACGGGATGTTAc           <  1:5935826/70‑1 (MQ=255)
                                                   gCAACCTGCATGGCAG‑‑AAATAGCGGCGATAACCGCCATGATAATGGAGATGACATCGAACGGGATGTTAc           <  1:2998329/70‑1 (MQ=255)
                                                    cAACCTGCATGGCAG‑‑AAATAGCGGCGATAACCGCCATGATAATGGAGATGACATCGAACGGGAt                >  1:3389641/1‑64 (MQ=255)
                                                    cAACCTGCATGGCAG‑‑AAATAGCGGCGATAACCGCCATGATAATGGAGATGACATCGAACGGGATg               >  1:3846025/1‑65 (MQ=255)
                                                    cAACCTGCATGGCAG‑‑AAATAGCGGCGATAACCGCCATGATAATGGAGATGACATCGAACGGGATg               >  1:682649/1‑65 (MQ=255)
                                                    cAACCTGCATGGCAG‑‑AAATAGCGGCGATAACCGCCATGATAATGGAGATGACATCGAACGGGATg               >  1:7436603/1‑65 (MQ=255)
                                                     aaCCTGCATGGCAG‑‑AAATAGCGGCGATAACCGCCATGATAATGGAGATGACATCGAACGGGAt                >  1:2420934/1‑63 (MQ=255)
                                                     aaCCTGCATGGCAG‑‑AAATAGCGGCGATAACCGCCATGATAATGGAGATGACATCGAACGGGATGTTAc           >  1:4117584/1‑68 (MQ=255)
                                                     aaCCTGCATGGCAG‑‑AAATAGCGGCGATAACCGCCATGATAATGGAGATGACATCGAACGGGATGTTACCg         <  1:4740952/70‑1 (MQ=255)
                                                       ccTGCATGGCAG‑‑AAATAGCGGCGATAACCGCCATGa                                         <  1:7404145/36‑1 (MQ=25)
                                                       ccTGCATGGCAG‑‑AAATAGCGGCGATAACCGCCATGATAATgg                                   >  1:409049/1‑42 (MQ=37)
                                                        cTGCATGGCAG‑‑AAATAGCGGCGATAACCGCCATGATAATGGAGAt                               >  1:6785269/1‑45 (MQ=37)
                                                        cTGCATGGCAG‑‑AAATAGCGGCGATAACCGCCATGATAATGGAGATGACATCGAACGGGAt                <  1:1760708/60‑1 (MQ=255)
                                                         tGCATGGCAG‑‑AAATAGCGGCGATAACCGCCATGATAATGGAGATGACATCGAACgg                   <  1:6377320/56‑1 (MQ=38)
                                                         tGCATGGCAG‑‑AAATAGCGGCGATAACCGCCATGATAATGGAGATGACATCGAACGGGATGTTACCGGGtt     >  1:6819461/1‑70 (MQ=255)
                                                          gCATGGCAG‑‑AAATAGCGGCGATAACCGCCATGATAATGGAGATGACATCGAACGGGATGTTACCGGGttt    >  1:1336536/1‑70 (MQ=255)
                                                          gCATGGCAG‑‑AAATAGCGGCGATAACCGCCATGATAATGGAGATGACATCGAACGGGATGTTACCGGGttt    >  1:3037558/1‑70 (MQ=255)
                                                           cATGGCAG‑‑AAATAGCGGCGATAACCGCCATGATAATGGAGATGACATCGAACGGGATGTTACCGGGttt    <  1:5893810/69‑1 (MQ=255)
                                                           cATGGCAG‑‑AAATAGCGGCGATAACCGCCATGATAATGGAGATGACATCGAACGGGATGTTACCGGGTTTaa  >  1:2474663/1‑71 (MQ=255)
                                                                   ||                                                               
TTACGGCGCAGCAGCTTTTCTGTCTGATGAACCAGATAGTCCAGACCGCCAGCAACCTGCATGGCAGAAAAATAGCGGCGATAACCGCCATGATAATGGAGATGACATCGAACGGGATGTTACCGGGTTTAA  >  W3110S.gb/4371206‑4371337

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