EURL VTEC Typer Report for Strain_1_L2.fastq 2018-05-17 11:16 UTC

Istituto Superiore di Sanità Department of Food Safety, Nutrition and Veterinary Public Health European Union Reference Laboratory for E. coli

Summary

O26:H11
ST21

eae, ehxa, stx1a, stx1b

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Raw data quality check

FASTQC result: Webpage

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Trimming analysis

Maximum length trimming	360
Left-side trimming	10
Right-side trimming	0
Minimum Phred quality score for right-side trimming	25
Average Phred quality score for right-side trimming	27
Minimum length filtering	50

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Assembly statistics

Estimated genome size:	5000000 bp
Assembled nucleotides:	5493390 bp
Estimated coverage:	1.1 x
N. contigs:	315
Average contig length:	17439
Median contig length:	4504
Maximum contig length:	164788
N. contigs >= 200 bp:	315 (100.0 %)
N. contigs >= 2,000 bp:	224 (71.1 %)
N50:	52450
NG50:	59152

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Serotyping

sseqid	pident	length	positive
wzx_208_AF529080_O26	100.00	1263	1263
wzy_192_AF529080_O26	100.00	1023	1023
fliC_269_AY337465_H11	99.93	1459	1458
fliC_276_AY337472_H11	99.79	1459	1456

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Multi Locus Sequence Typing

Sample	ST	adk	fumC	gyrB	icd	mdh	purA	recA	mismatches	uncertainty	depth	maxMAF
dataset_10081	21	16	4	12	16	9	7	7	0	-	31.5927142857	0.333333333333

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Virulotyping

This table is filtered for results with >90% gene coverage, unfiltered results can be found here

#gene	percentage gene coverage	gene mean read coverage	percentage gene identity
ehxa_7_hm138194	100.0	22.75	100.0
nlea_8_ae005174	99.92	27.36	99.85
celb_8_af540491	100.0	254.92	98.61
iss_13_cu928160	100.0	28.49	99.71
nlea_7_cp001164	99.92	17.8	99.85
nlea_13_ap010960	93.95	14.56	99.92
katp_1_ab011549	100.0	108.79	100.0
espb_13_af054421	93.12	10.91	99.89
toxb_3_ab456530	100.0	27.15	99.98
stx1b_14_am230663_a	100.0	18.51	100.0
celb_9_x06119	100.0	177.13	99.31
iha_5_ap010953	100.0	38.17	100.0
espp_3_gq259888	100.0	41.34	100.0
stx1a_15_af461168_a	99.89	20.92	99.79
espa_23_aj225018	100.0	9.57	100.0
nlec_6_ap010960	100.0	18.57	99.8
lpfa_3_ap010953	100.0	15.77	100.0
nleb_11_af453441	97.58	12.94	99.9
toxb_4_fj386569	100.0	25.5	99.97
iss_11_ae014075	100.0	15.83	97.66
ehxa_4_x94129	93.56	16.28	99.71
espa_22_fm201463	100.0	18.99	100.0
nlea_12_am422003	100.0	21.17	100.0
stx1b_11_ab071620_c	100.0	11.84	99.63
eae_45_ecu59503	92.62	28.63	99.85
espp_4_ab011549	95.62	29.83	99.87
espp_1_hm138194	99.03	37.41	99.97
cif_2_ay128535	99.88	19.24	99.88
cif_1_ay128537	99.88	18.14	99.88
espj_1_ab303060	100.0	63.45	100.0
nleb_12_fm201463	93.54	16.32	99.57
nlec_3_ap010953	94.53	20.93	99.46
ehxa_5_fj386569	99.63	23.12	99.97
iss_12_cu928158	100.0	23.77	99.42
celb_10_d00021	100.0	150.01	98.61
toxb_2_gq259888	99.29	24.57	99.98