TABLE 2.

Anomalous sequences identified by this study

Accession no.PhylumApprox. break position relative to E. coli (bases)Details
AY268103 Aquificae 560PCR or sequencing error with first ∼465 bases the reverse complement of what they should be
AB183857 Aquificae 425Anomaly at 5′ end, though origin unknown; either chimera or sequencing error
AF018191 Aquificae 1,080Two-fragment chimera, with both fragments Aquificae in origin
AJ237665 Thermotogae 930Two-fragment chimera, with 3′ end Firmicutes in origin
L10662 Thermodesulfobacteria Degenerate sequence; several large blocks of N bases
Z15060 Deinococcus-Thermus Degenerate sequence; one large block of N bases
X58340 Deinococcus-Thermus Degenerate sequence; several large blocks of N bases
AF317775 Nitrospira Degenerate sequence; one large block of N bases
AF317779 Nitrospira Degenerate sequence; one large block of N bases
L14619 Nitrospira Degenerate sequence; several large blocks of N bases
AY661410 Nitrospira 320, 540Two- or possibly three-fragment chimera, with 3′ end of unknown origin
AF543500 Nitrospira 250Sequencing anomaly only visible when RDP alignment used
AY373422 Nitrospira 340, 740Three-fragment chimera, with 5′ end γ-Proteobacteria, middle α-Proteobacteria, and 3′ end unknown in origin
AY661421 Nitrospira 370Two-fragment chimera, with 3′ end unclassified (candidate division OP5 according to NCBI)
AF485343 Nitrospira 1,080Two-fragment chimera, with 3′ end unclassified; record now replaced in database
AY297986 Nitrospira 700Two-fragment chimera, with 5′ end Firmicutes in origin; record already marked as chimeric in database
AY796049 Nitrospira a 790Two-fragment chimera with 5′ end β-Proteobacteria in origin
AY762631 Nitrospira a 660, 940Three-fragment chimera derived from two parents, with middle fragment of unclassified origin
X86774 Nitrospira 790, 1,220Three-fragment chimera derived from two parents, with middle fragment γ-Proteobacteria in origin; already identified as chimera
AF543509 Nitrospira 500, 790Three-fragment chimera, with middle fragment also Nitrospira in origin
AB176700 Nitrospira 500Two-fragment chimera, with 5′ end of unknown origin
AF543503 Nitrospira 540Two-fragment chimera, with both fragments Nitrospira in origin
AF543511 Nitrospira 760Two-fragment chimera, with both fragments Nitrospira in origin
L22045 Nitrospira Degenerate sequence; one large block of N bases
M79383 Nitrospira Degenerate sequence; one large block of N bases
Y10652 Chlorobi Degenerate with Ns clustered at 5′ and 3′ ends, giving superficial appearance of a chimera
Y10643 Chlorobi Degenerate with Ns clustered at 5′ and 3′ ends, giving superficial appearance of a chimera
Y10651 Chlorobi Degenerate with Ns clustered at 5′ and 3′ ends, giving superficial appearance of a chimera
Y10647 Chlorobi Degenerate sequence; one large block of N bases and numerous other Ns
Y10640 Chlorobi Degenerate with Ns clustered at 5′ and 3′ ends, giving superficial appearance of a chimera
AY661796 Chlamydiae Sequencing anomaly only visible when RDP alignment used
AY661795 Chlamydiae Sequencing anomaly only visible when RDP alignment used
AB179510 Acidobacteria 940-1,100Two-fragment chimera, with 3′ end of unclassified origin; lack of clear break due to number of degenerate bases
AY326570 Acidobacteria 600-1,000Two-fragment chimera, with 3′ end of unclassified origin; no obvious reason for lack of clear break
AF523990 Acidobacteria 370Two-fragment chimera, with 5′ end of Actinobacteria origin
AJ536862 Acidobacteria 280Two-fragment chimera, with 5′ end of unclassified origin
Y07575 Acidobacteria 560Two-fragment chimera, with 3′ end of unknown origin
AY548989 Fusobacteria 800Two-fragment chimera, with 3′ end δ-Proteobacteria in origin.
AJ289180 Fusobacteria 930, 1,210Three-fragment chimera, with 5′ end Fusobacteria, middle Spirochaetes, and 3′ end Bacteroidetes in origin
AJ441248 Fusobacteria ∼580Two-fragment chimera, with 3′ end of unclassified origin; exact position of break unclear due to lack of full-length subjects
AY548992 Fusobacteria 280, 790Three-fragment chimera, with 5′ end ε-Proteobacteria, middle Fusobacteria, and 3′ end ε-Proteobacteria in origin
AJ441228 Fusobacteria 150, 930Two-, possibly three-fragment chimera with 5′ end unknown, middle unclassified, and 3′ end ε-Proteobacteria in origin
AY548985 Fusobacteria 1,140Two-fragment chimera, with 3′ end of Spirochaetes origin
AF287807 Fusobacteria 350Two-fragment chimera, with both fragments of Fusobacteria origin
AF287808 Fusobacteria 920Two-fragment chimera, with both fragments of Fusobacteria origin
AF366272 Fusobacteria 1,160Two-fragment chimera, with both fragments of Fusobacteria origin
AF385542 Fusobacteria 350Very similar to AF287807
Z94005 Verrucomicrobia 1,025, 1,150Region 1,025-1,150 is alien to sequence but no close match found within database; unusual nature of plot suggests sequencing error
AJ401133 Verrucomicrobia 550Two-fragment chimera, with both fragments of Verrucomicrobia origin
AJ401131 Verrucomicrobia 920Two-fragment chimera, with 5′ end of unknown origin
AF316731 Verrucomicrobia 300Two-fragment chimera, with 5′ end of unclassified origin
AJ401123 Verrucomicrobia 590Two-fragment chimera, with both fragments of Verrucomicrobia origin
AB179538 Verrucomicrobia 570Two-fragment chimera, with 3′ end of unknown origin
AF351215 Verrucomicrobia 1,080Two-fragment chimera, with 3′ end of δ-Proteobacteria origin
AJ617868 Verrucomicrobia a 1,080Two-fragment chimera, with 3′ end of δ-Proteobacteria origin
AF234140 Gemmatimonadetes Degenerate sequence; one large block of N bases
AF009987 Gemmatimonadetes Degenerate sequence; two large blocks of N bases
AY218634 Gemmatimonadetes 700Two-fragment chimera, with both fragments of Gemmatimonadetes origin
AY221051 Gemmatimonadetes ∼900Two-fragment chimera, with both fragments of Gemmatimonadetes origin; break point uncertain due to quality of available subject sequences
AJ582052 Gemmatimonadetes 600, 950Likely sequencing error
AY218706 Gemmatimonadetes 275Likely sequencing error at 5′ end
AF368188 OP101,100Two-fragment chimera, with 3′ end of probable Bacteroidetes origin
AF368185 OP10∼260, 970Likely three fragment chimera with 5′ and 3′ ends originating from some unknown source
AF368184 OP10∼260, 970Same as AF368185
AY693838 OP11520Two-fragment chimera, with 5′ end of β-Proteobacteria origin
AY218572 OP11660Two-fragment chimera, with 5′ end of ε-Proteobacteria origin
AJ582211 OP11∼560Likely two-fragment chimera, with 3′ end of unknown origin
AF513093 TM7900Two-fragment chimera, with 3′ end of unclassified origin
AJ318135 TM71,090Two-fragment chimera, with 3′ end of Actinobacteria origin
AY592328 WS3380Two-fragment chimera, with 5′ end of Actinobacteria origin
AY217439 Dehalococcoides 500, 675Likely sequencing error
AY133080 Dehalococcoides 1,400Likely sequencing error
AY548991 ε-Proteobacteriab320Two-fragment chimera, with 5′ of γ-Proteobacteria origin; 3′ of ε-Proteobacteria origin
AJ441247 Unclassified Bacteriab380Two-fragment chimera, with 5′ end of δ-Proteobacteria origin, 3′ end of Chloroflexi origin
AY762628 β-Proteobacteriab780Two-fragment chimera, with both fragments of β-Proteobacteria origin
AY762632 β-Proteobacteriab780Practically identical to AY762628
AJ582208 Unclassified Bacteriab540Two-fragment chimera, with 5′ of Firmicutes origin and end 3′ of Gemmatimonadetes origin
AY218710 Unclassified Bacteriab630Sequencing error in which first ∼152 bases are the reverse complement
AY280419 Unclassified Bacteriab520Two-fragment chimera, with 5′ of Bacteroidetes origin, and 3′ end of WS3 origin
AB007420 Actinobacteria b 40-250Likely sequencing error
  • a Added after September release (not included in calculations).

  • b Uncovered during analysis (not included in calculations).