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EURL VTEC TyperReport for Strain_1_L2.fastq2018-05-17 11:16 UTC | Istituto Superiore di SanitÃDepartment of Food Safety, Nutrition and Veterinary Public HealthEuropean Union Reference Laboratory for E. coli |
eae, ehxa, stx1a, stx1b
FASTQC result: Webpage
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 |
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 |
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 |
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 |
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 |