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 F21 I0 R1 2169 63.0 3952800 76.2% 3012033 62.4

Breseq alignment

BRESEQ :: Evidence
Predicted mutation
evidence seq id position mutation freq annotation gene description
JC minE 2,133,767 (TCGTTA)2→1 36.0% coding (246‑251/891 nt) nlpI ← conserved hypothetical protein

New junction evidence
  seq id position reads (cov) reads (cov) score skew freq annotation gene product
* ? minE = 213376624 (0.460)12 (0.270) 10/88 NT 36.0% coding (252/891 nt) nlpI conserved hypothetical protein
?minE 2133773 = 22 (0.490)coding (245/891 nt) nlpI conserved hypothetical protein

TTAAATATATGCCTAAGTAATTGAATACTTCAGGCATATCCGGTCGGATTGCCAGCGCTTGCGAAAAATCGTTA‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑  >  minE/2133693‑2133766
‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑atcgttaCGCGCTAATGCCCTCAGACCGAGACTATCATACAACACTCCGCGCTCATATAAAAGCTGTGCGCGTTCGT  >  minE/2133773‑2133842
                                                                                                                                                
TTAAATATATGCCTAAGTAATTGAATACTTCAGGCATATCCGGTCGGATTGCCAGCGCTTGCGAAAAATCG                                                                           <  1:1592736/71‑1
TTAAATATATGCCTAAGTAATTGAATACTTCAGGCATATCCGGTCGGATTGCCAGCGCTTGCGAAAAATCG                                                                           <  1:2284731/71‑1
  AAATATATGCCTAAGTAATTGAATACTTCAGGCATATCCGGTCGGATTGCCAGCGCTTGCGAAAAATC                                                                            >  1:387786/1‑68
  AAATATATGCCTAAGTAATTGAATACTTCAGGCATATCAGGTCGGATTGCCAGCGCTTGCGAAAAATCGT                                                                          >  1:1300925/1‑70
      ATATGCCTAAGTAATTGAATACTTCAGGCATATCCGGTCGGATTGCCAGCGCTTGCGAAAAA                                                                              <  1:3390928/62‑1
         TGCCTAAGTAATTGAATACTTCAGGCATATCCGGTCGGATTGCCAGCGCTTGCGAAAAATCGTTACGCGCT                                                                  <  1:3697788/71‑1
          GCCTAAGTAATTGAATACTTCAGGCATATCCGGTCGGATTGCCAGCGCTTGCGAAAAATCGTTACGCGC                                                                   >  1:2144514/1‑69
              AAGTAATTGAATACTTCAGGCATATCCGGTCGGATTGCCAGCGCTTGCGAAAAATCGTTACGCGCTAATGC                                                             >  1:1266341/1‑71
              AAGTAATTGAATACTTCAGGCATATCCGGTCGGATTGCCAGCGCTTGCGAAAAATC                                                                            >  1:1385837/1‑56
               AGTAATTGAATACTTCAGGCATATCCGGTCGGATTGCCAGCGCTTGCGAAAAATCGTTACGCGCTAATGCC                                                            >  1:3600336/1‑71
               AGTAATTGAATACTTCAGGCATATCCGGTCGGATTGCCAGCGCTTGCGAAAAA                                                                              <  1:1739532/53‑1
                   ATTGAATACTTCAGGCATATCCGGTCGGATTGCCAGCGCTTGCGAAAAATCGTTACGCGCTAATGCCCTCA                                                        <  1:1391800/71‑1
                      GAATACTTCAGGCATATCCGGTCGGATTGCCAGCGCTTGCGAAAAATC                                                                            >  1:2809107/1‑48
                          ACTTCAGGCATATCCGGTCGGATTGCCAGCGCTTGCGAAAAATCGTTACGCGCTAATGCCCTCAGACC                                                    >  1:84214/1‑68
                                                    CAGCGCTTGCGAAAAATCGTTACGCGCTAATGCCCTCAGACCGAGACTATCATAC                                       <  1:2259691/55‑1
                                                     AGCGCTTGCGAAAAATCGTTACGCGCTAATGCCCTCAGACCGAGACTAT                                            >  1:1097820/1‑49
                                                            GCGAAAAATCGTTACGCGCTAATGCCCTCAGACCGAGACTATCATACAACACTCCGCGCTCATATAAAAG                <  1:3367276/70‑1
                                                            GCGAAAAATCGTTACGCGCTAATGCCCTCAGACCGAGACTATCATACAACACTCCGCGCTCATATAAAAG                <  1:937023/70‑1
                                                            GCGAAAAATCGTTACGCGCTAATGCCCTCAGACCGAGACTATCATACAACACTCCGCGCTCATATAAAAG                <  1:1422762/70‑1
                                                             CGAAAAATCGTTACGCGCTAATGCCCTCAGACCGAGACTATCATACAACACTCCGCTCTCATATAAAAGC               <  1:2442155/70‑1
                                                             CGAAAAATCGTTACGCGCTAATGCCCTCAGACCGAGACTATCATACAACACTCCGCGCTCATATAAAAGCT              <  1:1242795/71‑1
                                                                AAAATCGTTACGCGCTAATGCCCTCAGACCGAGACTATCATACAACACTCCGCGCTCATATAAA                  <  1:2394052/64‑1
                                                                 AAATCGTTACGCGCTAATGCCCTCAGACCGAGACTATCATACAACA                                   <  1:1331835/46‑1
                                                                   ATCGTTACGCGCTAATGCCCTCAGACCGAGACTATCATACAACACTCCGCGCTCATATAAAAGCTGTGCGC        >  1:206592/1‑71
                                                                      GTTACGCGCTAATGCCCTCAGACCGAGACTATCATACAACACTCCGCGCTCATATAAAAGCTGTGCGCGT      <  1:3513768/70‑1
                                                                         ACGCGCTAATGCCCTCAGACCGAGACTATCATACAACACTCCGCGCTCATATAAAAGCTGTGCGCGATCGT  >  1:2339445/1‑71
                                                                                                                                                
TTAAATATATGCCTAAGTAATTGAATACTTCAGGCATATCCGGTCGGATTGCCAGCGCTTGCGAAAAATCGTTA‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑  >  minE/2133693‑2133766
‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑atcgttaCGCGCTAATGCCCTCAGACCGAGACTATCATACAACACTCCGCGCTCATATAAAAGCTGTGCGCGTTCGT  >  minE/2133773‑2133842

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 32 ≤ ATCG/ATCG < 33 ≤ ATCG/ATCG < 36 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑
Reads not counted as support for junction
read_name Not counted due to insufficient overlap past the breakpoint.
read_name Not counted due to not crossing MOB target site duplication.

GATK/CNVnator alignment

N/A