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
A6 F3 I0 R2 88 130.8 6963722 93.6% 6518043 59.5

Breseq alignment

BRESEQ :: Evidence
Predicted mutation
evidence seq id position mutation freq annotation gene description
RA minE 1,892,019:1 +GC 100% intergenic (‑437/+54) gudP ← / ← ygdL predicted D‑glucarate transporter/conserved hypothetical protein

Read alignment evidence...
  seq id position ref new freq score (cons/poly) reads annotation genes product
*minE1,892,0191.G100.0% 294.3 / NA 81intergenic (‑437/+54)gudP/ygdLpredicted D‑glucarate transporter/conserved hypothetical protein
Reads supporting (aligned to +/- strand):  ref base . (0/0);  new base G (35/46);  total (35/46)
Rejected as polymorphism: Frequency below/above cutoff threshold.
Rejected as polymorphism: Variant not supported by required number of reads on each strand.
*minE1,892,0192.C100.0% 294.1 / NA 81intergenic (‑437/+54)gudP/ygdLpredicted D‑glucarate transporter/conserved hypothetical protein
Reads supporting (aligned to +/- strand):  ref base . (0/0);  new base C (35/46);  total (35/46)
Rejected as polymorphism: Frequency below/above cutoff threshold.
Rejected as polymorphism: Variant not supported by required number of reads on each strand.

ACTGGCATTTGCCTGAAAAGATTCGATTCAGCACCGCTAAAACGACATTTACCGCTCGCTGAACATATCA‑‑TAAGCACAGAACCGGGTCGGATAAGACGTTCGCGTCTCATCCGACCTGATTGTTTAACC  >  minE/1891950‑1892078
                                                                      ||                                                           
aCTGGCATTTGCCTGAAAAGATTCGATTCAGCACCGCTAAAACGACATTTACCGCTCGCTGAACATATCag                                                              >  1:661764/1‑70 (MQ=255)
aCTGGCATTTGCCTGAAAAGATTCGATTCAGCACCGCTAAAACGACATTTACCGCTCGCTGAACATATCag                                                              >  1:5688968/1‑70 (MQ=255)
   ggCATTTGCCTGAAAAGATTCGATTCAGCACCGCTAAAACGACATTTACCGCTCGCTGAACATATCagct                                                            >  1:4072981/1‑67 (MQ=255)
          gCCTGAAAAGATTCGATTCAGCACCGCTAAAACGACATTTACCGCTCGCTGAACATATCAGCTAAGcaca                                                     <  1:960899/70‑1 (MQ=255)
          gCCTGAAAAGATTCGATTCAGCACCGCTAAAACGACATTTACCGCTCGCTGAACATATCAGCTAAGcaca                                                     <  1:5289024/70‑1 (MQ=255)
          gCCTGAAAAGATTCGATTCAGCACCGCTAAAACGACATTTACCGCTCGCTGAACATATCAGCTAAGcaca                                                     <  1:6559450/70‑1 (MQ=255)
          gCCTGAAAAGATTCGATTCAGCACCGCTAAAACGACATTTACCGCTCGCTGAACATATCAGCTAAGcaca                                                     <  1:86682/70‑1 (MQ=255)
           ccTGAAAAGATTCGATTCAGCACCGCTAAAACGACATTTACCGCTCGCTGAACATATCAGCTAAGCACAGa                                                   <  1:6797285/71‑1 (MQ=255)
           ccTGAAAAGATTCGATTCAGCACCGCTAAAACGACATTTACCGCTCGCTGAACATATCAGCTAAGCACAGa                                                   <  1:2029468/71‑1 (MQ=255)
              gAAAAGATTCGATTCAGCACCGCTAAAACGACATTTACCGCTCGCTGAACATATCAGCTAAGCACAGAAcc                                                >  1:2808216/1‑71 (MQ=255)
              gAAAAGATTCGATTCAGCACCGCTAAAACGACATTTACCGCTCGCTGAACATATCAGCTAAGCACAGAAcc                                                >  1:4637470/1‑71 (MQ=255)
                aaaGATTCGATTCAGCACCGCTAAAACGACATTTACCGCTCGCTGAACATATCAGCTAAGCACAGAACCgg                                              >  1:1373452/1‑71 (MQ=255)
                 aaGATTCGATTCAGCACCGCTAAAACGACATTTACCGCTCGCTGCACATATCAGCTAAGCACAGAACCggg                                             >  1:4334660/1‑71 (MQ=255)
                 aaGATTCGATTCAGCACCGCTAAAACGACATTTACCGCTCGCTGAACATATCAGCTAAGCACAGAACCggg                                             >  1:4074516/1‑71 (MQ=255)
                 aaGATTCGATTCAGCACCGCTAAAACGACATTTACCGCTCGCTGAACATATCAGCTAAGCACAGAACCggg                                             >  1:3952391/1‑71 (MQ=255)
                     ttcgattcAGCACCGCTAAAACGACATTTACCGCTCGCTGAACATATCAGCTAAGCACAGAACCGGGTCgg                                         <  1:1824342/71‑1 (MQ=255)
                     ttcgattcAGCACCGCTAAAACGACATTTACCGCTCGCTGAACATATCAGCTAAGCACAGAACCGGGTCgg                                         <  1:1656555/71‑1 (MQ=255)
                     ttcgattcAGCACCGCTAAAACGACATTTACCGCTCGCTGAACATATCAGCTAAGCACAGAACCGGGTCg                                          >  1:2076698/1‑70 (MQ=255)
                      tcgattcAGCACCGCTAAAACGACATTTACCGCTCGCTGAACATATCAGCTAAGCACAGAACCGGGTCGGa                                        >  1:4150668/1‑71 (MQ=255)
                      tcgattcAGCACCGCTAAAACGACATTTACCGCTCGCTGAACATATCAGCTAAGCACAGAACCGGGTCGGa                                        >  1:6870979/1‑71 (MQ=255)
                         attcAGCACCGCTAAAACGACATTTACCGCTCGCTGAACATATCAGCTAAGCACAGAACCGGGTCGGATaa                                     <  1:4087803/71‑1 (MQ=255)
                         attcAGCACCGCTAAAACGACATTTACCGCTCGCTGAACATATCAGCTAAGCACAGAACCGGGTCGGATaa                                     <  1:5629547/71‑1 (MQ=255)
                          ttcAGCACCGCTAAAACGACATTTACCGCTCGCTGAACATATCAGCTAAGCACAGAACCGGGTCGGATAAg                                    <  1:1930921/71‑1 (MQ=255)
                          ttcAGCACCGCTAAAACGACATTTACCGCTCGCTGAACATATCAGCTAAGCACAGAACCGGGTCGGATAAg                                    <  1:6550277/71‑1 (MQ=255)
                           tcAGCACCGCTAAAACGACATTTACCGCTCGCTGAACATATCAGCTAAGcaca                                                     >  1:2585690/1‑53 (MQ=255)
                           tcAGCACCGCTAAAACGACATTTACCGCTCGCTGAACATATCAGCTAAGcaca                                                     >  1:4069495/1‑53 (MQ=255)
                            cAGCACCGCTAAAACGACATTTACCGCTCGCTGAACATATCAGCTAAGCACAGAACCGGGTCGGATAAGAc                                  >  1:5435070/1‑71 (MQ=255)
                              gCACCGCTAAAACGACATTTACCGCTCGCTGAACATATCAGCTAAGCACAGAACCGGGTCGGATAAGACGt                                <  1:6937199/71‑1 (MQ=255)
                               cACCGCTAAAACGACATTTACCGCTCGCTGAACATATCAGCTAAGCACAGAACCGGGTCGGATAAGACGtt                               <  1:727298/71‑1 (MQ=255)
                                aCCGCTAAAACGACATTTACCGCTCGCTGAACATATCAGCTAAGCACAGAACCGGGTCGGATAAGACGt                                >  1:1961195/1‑69 (MQ=255)
                                aCCGCTAAAACGACATTTACCGCTCGCTGAACATATCAGCTAAGCACAGAACCGGGTCGGATAAGACGt                                >  1:35070/1‑69 (MQ=255)
                                aCCGCTAAAACGACATTTACCGCTCGCTGAACATATCAGCTAAGCACAGAACCGGGTCGGATAAGACGTTc                              <  1:3813722/71‑1 (MQ=255)
                                  cGCTAAAACGACATTTACCGCTCGCTGAACATATCAGCTAAGCACAGAACCGGGTCGGATAAGACGTTcgc                            >  1:4004821/1‑71 (MQ=255)
                                    cTAAAACGACATTTACCGCTCGCTGAACATATCAGCTAAGCACAGAACCGGGTCGGATaa                                     <  1:4401715/60‑1 (MQ=255)
                                    cTAAAACGACATTTACCGCTCGCTGAACATATCAGCTAAGCACAGAACCGGGTCGGATAAGACGTTcgcg                           >  1:439338/1‑70 (MQ=255)
                                    cTAAAACGACATTTACCGCTCGCTGAACATATCAGCTAAGCACAGAACCGGGTCGGATAAGACGTTcgc                            <  1:4516998/69‑1 (MQ=255)
                                    cTAAAACGACATTTACCGCTCGCTGAACATATCAGCTAAGCACAGAACCGGGTCGGATAAGACGTTcgc                            >  1:2405130/1‑69 (MQ=255)
                                    cTAAAACGACATTTACCGCTCGCTGAACATATCAGCTAAGCACAGAACCGGGTCGGATAAGACGTTCGCGt                          <  1:6536207/71‑1 (MQ=255)
                                      aaaaCGACATTTACCGCTCGCTGAACATATCAGCTAAGCACAGAACCGGGTCGGATAAGa                                   >  1:6089262/1‑60 (MQ=255)
                                      aaaaCGACATTTACCGCTCGCTGAACATATCAGCTAAGCACAGAACCGGGTCGGATAAGa                                   >  1:2891421/1‑60 (MQ=255)
                                      aaaaCGACATTTACCGCTCGCTGAACATATCAGCTAAGCACAGAACCGGGTCGGATAAGACGt                                <  1:5540081/63‑1 (MQ=255)
                                      aaaaCGACATTTACCGCTCGCTGAACATATCAGCTAAGCACAGAACCGGGTCGGATAAGACGt                                <  1:5811853/63‑1 (MQ=255)
                                        aaCGACATTTACCGCTCGCTGAACATATCAGCTAAGCACAGAACCGGGTCGGATAAGACGTTCGCGtctc                       <  1:2162215/70‑1 (MQ=255)
                                         aCGACATTTACCGCTCGCTGAACATATCAGCTAAGcaca                                                     <  1:89793/39‑1 (MQ=37)
                                         aCGACATTTACCGCTCGCTGAACATATCAGCTAAGCACAGAACCGGGGCGGATAAGACGTTCGCGTCTCAt                     <  1:5001115/71‑1 (MQ=255)
                                          cGACATTTACCGCTCGCTGAACATATCAGCTAAGCACAGAACCGGGTCGGATaa                                     <  1:5237742/54‑1 (MQ=255)
                                          cGACATTTACCGCTCGCTGAACATATCAGCTAAGCACAGAACCGGGTCGGATAAGACGTTCGCGt                          <  1:292253/65‑1 (MQ=255)
                                          cGACATTTACCGCTCGCTGAACATATCAGCTAAGCACAGAACCGGGTCGGATAAGACGTTCGCGt                          <  1:3365375/65‑1 (MQ=255)
                                           gACATTTACCGCTCGCTGAACATATCAGCTAAGCACAGAACCGGGTCGGATAAGACGTTCGCGTCTCATcc                   >  1:2413486/1‑71 (MQ=255)
                                           gACATTTACCGCTCGCTGAACATATCAGCTAAGCACAGAACCGGGTCGGATAAGACGTTCGCGTCTCATcc                   <  1:1440788/71‑1 (MQ=255)
                                             cATTTACCGCTCGCTGAACATATCAGCTAAGCACAGAACCGGGTCGGATAAGACGTTCGCGTCTCATCCGa                 <  1:3736954/71‑1 (MQ=255)
                                             cATTTACCGCTCGCTGAACATATCAGCTAAGCACAGAACCGGGTCGGATAAGACGTTCGCGTCTCATCCGa                 <  1:4895188/71‑1 (MQ=255)
                                             cATTTACCGCTCGCTGAACATATCAGCTAAGCACAGAACCGGGTCGGATAAGACGTTCGCGTCTCATCCGa                 <  1:1220400/71‑1 (MQ=255)
                                             cATTTACCGCTCGCTGAACATATCAGCTAAGCACAGAACCGGGTCGGATAAGACGTTCGCGTCTCATCCGa                 <  1:612437/71‑1 (MQ=255)
                                              aTTTACCGCTCGCTGAACATATCAGCTAAGCACAGAACCGGGTCGGATAAGACg                                 <  1:3707406/54‑1 (MQ=255)
                                               tttACCGCTCGCTGAACATATCAGCTAAGCACAGAACCGGGTCGGATAAGACGTTcgc                            <  1:5618986/58‑1 (MQ=255)
                                               tttACCGCTCGCTGAACATATCAGCTAAGCACAGAACCGGGTCGGATAAGACGTTcgc                            <  1:4343810/58‑1 (MQ=255)
                                               tttACCGCTCGCTGAACATATCAGCTAAGCACAGAACCGGGTCGGATAAGACGTTcgc                            <  1:1316926/58‑1 (MQ=255)
                                               tttACCGCTCGCTGAACATATCAGCTAAGCACAGAACCGGGTCGGATAAGACGTTcgc                            <  1:2584361/58‑1 (MQ=255)
                                                ttACCGCTCGCTGAACATATCAGCTAAGCACAGAACCGGGTCGGGTaa                                     >  1:1474205/1‑48 (MQ=255)
                                                 tACCGCTCGCTGAACATATCAGCTAAGCACAGAACCg                                               >  1:5329794/1‑37 (MQ=25)
                                                 tACCGCTCGCTGAACATATCAGCTAAGCACAGAACCg                                               >  1:6806219/1‑37 (MQ=25)
                                                 tACCGCTCGCTGAACATATCAGCTAAGCACAGAACCg                                               >  1:3147051/1‑37 (MQ=25)
                                                 tACCGCTCGCTGAACATATCAGCTAAGCACAGAACCg                                               >  1:3308435/1‑37 (MQ=25)
                                                 tACCGCTCGCTGAACATATCAGCTAAGCACAGAACCg                                               >  1:3923166/1‑37 (MQ=25)
                                                 tACCGCTCGCTGAACATATCAGCTAAGCACAGAACCGGGTCGGATaa                                     >  1:3845520/1‑47 (MQ=255)
                                                 tACCGCTCGCTGAACATATCAGCTAAGCACAGAACCGGGTCGGATaa                                     >  1:2856123/1‑47 (MQ=255)
                                                 tACCGCTCGCTGAACATATCAGCTAAGCACAGAACCGGGTCGGATaa                                     >  1:666159/1‑47 (MQ=255)
                                                  aCCGCTCGCTGAACATATCAGCTAAGCACAGAACCGGGTCGGATAAGACGTTCGCGtc                         >  1:1598530/1‑58 (MQ=255)
                                                  aCCGCTCGCTGAACATATCAGCTAAGCACAGAACCGGGTCGGATAAGACGTTCGCGTCTCATCCGACCTg             <  1:731508/70‑1 (MQ=38)
                                                    cgctcgctGAACATATCAGCTAAGCACAGAACCGGGTCg                                          >  1:5042733/1‑39 (MQ=37)
                                                     gctcgctGAACATATCAGCTAAGCACAGAACCGGGTCGGATAAGACGTTCGCGTCTCATCCGACCTGATTg         <  1:653233/71‑1 (MQ=39)
                                                      ctcgctGAACATATCAGCTAAGCACAGAACCGGGTCGGATAAGACGTTCGCGTCTCATCCGAc                >  1:5818742/1‑63 (MQ=38)
                                                      ctcgctGAACATATCAGCTAAGCACAGAACCGGGTCGGATAAGACGTTCGCGTCTCATCCGAc                >  1:2170313/1‑63 (MQ=38)
                                                      ctcgctGAACATATCAGCTAAGCACAGAACCGGGTCGGATAAGACGTTCGCGTCTCATCCGACCTGa            >  1:5100706/1‑67 (MQ=38)
                                                      ctcgctGAACATATCAGCTAAGCACAGAACCGGGTCGGATAAGACGTTCGCGTCTCATCCGACCTGATTGt        <  1:6649938/71‑1 (MQ=255)
                                                      ctcgctGAACATATCAGCTAAGCACAGAACCGGGTCGGATAAGACGTTCGCGTCTCATCCGACCTGATTGt        <  1:5508627/71‑1 (MQ=255)
                                                        cgctGAACATATCAGCTAAGCACAGAACCGGGTCGGAt                                       <  1:5119016/38‑1 (MQ=25)
                                                         gctGAACATATCAGCTAAGCACAGAACCGGGTCGGATAAGACGTTCGCGTCTCATCCGACCTGATTGttt      <  1:5084469/70‑1 (MQ=38)
                                                         gctGAACATATCAGCTAAGCACAGAACCGGGTCGGATAAGACGTTCGCGTCTCATCCGACCTGATTGttt      <  1:3177435/70‑1 (MQ=38)
                                                         gctGAACATATCAGCTAAGCACAGAACCGGGTCGGATAAGACGTTCGCGTCTCATCCGACCTGATTGttt      <  1:3909332/70‑1 (MQ=38)
                                                          ctGAACATATCAGCTAAGCACAGAACCGGGTCGGATaa                                     >  1:6546457/1‑38 (MQ=25)
                                                           tGAACATATCAGCTAAGCACATAACCGGGTCGGATAAGACGTTCGCGTCTCATCCGACCTGATTGTTTaa    <  1:5683252/70‑1 (MQ=255)
                                                             aaCATATCAGCTAAGCACAGAACCGGGTCGGATAAGACGTTCGCGTCTCATCCGACCTGATTGTTTAAcc  <  1:3997645/70‑1 (MQ=255)
                                                                      ||                                                           
ACTGGCATTTGCCTGAAAAGATTCGATTCAGCACCGCTAAAACGACATTTACCGCTCGCTGAACATATCA‑‑TAAGCACAGAACCGGGTCGGATAAGACGTTCGCGTCTCATCCGACCTGATTGTTTAACC  >  minE/1891950‑1892078

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 14 ≤ ATCG/ATCG < 32 ≤ ATCG/ATCG < 36 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑

GATK/CNVnator alignment

N/A