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
A4 F3 I0 R2 8 43.3 2136430 96.9% 2070200 62.1

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% 92.0 / NA 26intergenic (‑437/+54)gudP/ygdLpredicted D‑glucarate transporter/conserved hypothetical protein
Reads supporting (aligned to +/- strand):  ref base . (0/0);  new base G (14/12);  total (14/12)
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% 92.7 / NA 26intergenic (‑437/+54)gudP/ygdLpredicted D‑glucarate transporter/conserved hypothetical protein
Reads supporting (aligned to +/- strand):  ref base . (0/0);  new base C (14/12);  total (14/12)
Rejected as polymorphism: Frequency below/above cutoff threshold.
Rejected as polymorphism: Variant not supported by required number of reads on each strand.

CTGGCATTTGCCTGAAAAGATTCGATTCAGCACCGCTAAAACGACATTTACCGCTCGCTGAACATATCA‑‑TAAGCACAGAACCGGGTCGGATAAGACGTTCGCGTCTCATCCGACCTGATTGTTTAACCC  >  minE/1891951‑1892079
                                                                     ||                                                            
cTGGCATTTGCCTGAAAAGATTCGATTCAGCACCGCTAAAACGACATTTACCGCTCGCTGAACATATCagc                                                              <  1:171857/71‑3 (MQ=255)
   gCATTTGCCTGAAAAGATTCGATTCAGCACCGCTAAAACGACATTTACCGCTCGCTGAACATATCagct                                                             >  1:1762047/1‑66 (MQ=255)
         gCCTGAAAAGATTCGATTCAGCACCGCTAAAACGACATTTACCGCTCGCTGAACATATCAGCTAAGcaca                                                      <  1:1947957/70‑1 (MQ=255)
          ccTGAAAAGATTCGATTCAGCACCGCTAAAACGACATTTACCGCTCGCTGAACATATCAGCTAAGCACAGa                                                    <  1:467793/71‑1 (MQ=255)
           cTGAAAAGATTCGATTCAGCACCGCTAAAACGACATTTACCGCTCGCTGAACATATCAGCTAAGCACAGa                                                    <  1:430808/70‑1 (MQ=255)
             gAAAAGATTCGATTCAGCACCGCTAAAACGACATTTACCGCTCGCTGAACATATCAGCTAAGCACAGAAc                                                  >  1:1993411/1‑70 (MQ=255)
               aaaGATTCGATTCAGCACCGCTAAAACGACATTTACCGCTCGCTGAACATATCAGCTAAGCACAGAACCgg                                               >  1:1685159/1‑71 (MQ=255)
                    ttcgattcAGCACCGCTAAAACGACATTTACCGCTCGCTGAACATATCAGCTAAGCACAGAACCGGGTCgg                                          <  1:1227573/71‑1 (MQ=255)
                    ttcgattcAGCACCGCTAAAACGACATTTACCGCTCGCTGAACATATCAGCTAAGCACAGAACCGGGTCg                                           >  1:1751885/1‑70 (MQ=255)
                              cACCGCTAAAACGACATTTACCGCTCGCTGAACATATCAGCTAAGCACAGAACCGGGt                                             >  1:844567/1‑58 (MQ=255)
                              cACCGCTAAAACGACATTTACCGCTCGCTGAACATATCAGCTAAGCACAGAACCGGGTCGGATAAGACGtt                                <  1:1936126/71‑1 (MQ=255)
                                ccGCTAAAACGACATTTACCGCTCGCTGAACATATCAGCTAAGCACAGAACCGGGTCGGATAAGACGTTcg                              >  1:1578428/1‑71 (MQ=255)
                                 cGCTAAAACGACATTTACCGCTCGCTGAACATATCAGCTAAGCACAGAACCGGGTCGGATAAGACGTTcgc                             <  1:1671097/71‑1 (MQ=255)
                                  gCTAAAACGACATTTACCGCTCGCTGAACATATCAGCTAAGCACAGAACCGGGTCGGATAAGACGTTcgc                             >  1:27080/1‑70 (MQ=255)
                                      aaaCGACATTTACCGCTCGCTGAACATATCAGCTAAGCACAGAACCGGGTCGGATAAGACGTTCGCGtc                          <  1:1852673/69‑1 (MQ=255)
                                           aCATTTACCGCTCGCTGAACATATCAGCTAAGCACAGAACCGGGTCGGATAAGACGTTCGCGTCTCATCCg                   <  1:73865/71‑1 (MQ=255)
                                            cATTTACCGCTCGCTGAACATATCAGCTAAGCACAGAACCGGGTCGGATAAGACGTTCGCGTCTCATc                     >  1:171132/1‑68 (MQ=255)
                                             aTTTACCGCTCGCTGAACATATCAGCTAAGCACAGAACCGGGTCGGATAAGACGTTCGCGTCTCATCCGAc                 >  1:1912124/1‑71 (MQ=255)
                                              tttACCGCTCGCTGAACATATCAGCTAAGCACAGAACCGGGTCGGATa                                       <  1:264741/48‑1 (MQ=255)
                                              tttACCGCTCGCTGAACATATCAGCTAAGCACAGAACCGGGTCGGATAAGACGTTCGCGTCTCATCCGAcc                <  1:1225656/71‑1 (MQ=39)
                                                tACCGCTCGCTGAACATATCAGCTAAGCACAGAACCGGGTCGGATAAGACGTTCGCGTCTCATCCGACCt               >  1:55002/1‑70 (MQ=255)
                                                 aCCGCTCGCTGAACATATCAGCTAAGCACAGAACCGGGTCGGATAAGACGTTcgcg                            >  1:1316977/1‑56 (MQ=255)
                                                     ctcgctGAACATATCAGCTAAGCACAGAACCGGGTCGGATAAGACGTTCGCGTCTCATCCGACCTGATTGt         <  1:756692/71‑1 (MQ=255)
                                                        gctGAACATATCAGCTAAGCACAGAACCGGGTCGGATAAGACGTTcgc                             >  1:354118/1‑48 (MQ=37)
                                                          tGAACATATCAGCTAAGCACAGAACCGGGTCGGATAAGACGTTCGCGTCTCATc                     >  1:1198950/1‑54 (MQ=38)
                                                           gAACATATCAGCTAAGCACAGAACCGGGTCGGATAAGACGTTCGCGTCTCATCCGAc                 >  1:520948/1‑57 (MQ=37)
                                                            aaCATATCAGCTAAGCACAGAACCGGGTCGGATaa                                      <  1:399246/35‑1 (MQ=25)
                                                            aaCATATCAGCTAAGCACAGAACCGGGTCGGATAAGACGTTCGCGTCTCATCCGACCTGATTGTTTAAccc  >  1:829893/1‑71 (MQ=255)
                                                                     ||                                                            
CTGGCATTTGCCTGAAAAGATTCGATTCAGCACCGCTAAAACGACATTTACCGCTCGCTGAACATATCA‑‑TAAGCACAGAACCGGGTCGGATAAGACGTTCGCGTCTCATCCGACCTGATTGTTTAACCC  >  minE/1891951‑1892079

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