TB-Profiler result

Run: ERR757149
Summary

Run ID: ERR757149

Sample name:

Date: 02-04-2023 05:05:09

Number of reads: 1832880

Percentage reads mapped: 98.85

Strain: lineage4.1.2.1.1

Drug-resistance: HR-TB

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Drug resistance: This table reports drug-resistance associated mutations found in known resistance genes
Drug Resistance Supporting mutations
Lineage Table: The lineage is inferred by analysing lineage specific SNPs
Lineage Family Main Spoligotype RDs Frequency
lineage4 Euro-American LAM;T;S;X;H None 1.0
lineage4.1 Euro-American T;X;H None 0.98
lineage4.1.2 Euro-American T;H None 1.0
lineage4.1.2.1 Euro-American (Haarlem) T1;H1 RD182 1.0
lineage4.1.2.1.1 Euro-American (Haarlem) T1;H1 RD182 0.99
Drug resistance-Associated Mutations: This table reports mutations found in candidate resistance genes which have been associated with drug resistance
Gene Chromosome position Mutation Type Estimated fraction Drugs
katG 2155168 p.Ser315Thr missense_variant 1.0 isoniazid
gid 4407872 c.329_330delTG frameshift_variant 0.88 streptomycin
Non-Associated Mutations: This table reports mutations found in candidate resistance genes which have not been associated with drug resistance
Gene Chromosome position Mutation Type Estimated fraction
gyrA 7362 p.Glu21Gln missense_variant 1.0
gyrA 7585 p.Ser95Thr missense_variant 1.0
gyrA 8048 c.747C>T synonymous_variant 0.12
gyrA 8203 p.Asn301Ser missense_variant 0.12
gyrA 8999 c.1698G>A synonymous_variant 0.11
gyrA 9304 p.Gly668Asp missense_variant 1.0
gyrA 9528 p.Gln743Glu missense_variant 0.17
fgd1 490814 p.Ser11Leu missense_variant 0.14
fgd1 491591 p.Lys270Met missense_variant 1.0
mshA 575343 c.-5C>T upstream_gene_variant 0.13
mshA 575629 c.282A>G synonymous_variant 0.15
mshA 575679 p.Asn111Ser missense_variant 0.95
mshA 575832 p.Gly162Asp missense_variant 0.3
mshA 576581 p.Pro412Ser missense_variant 0.13
mshA 576718 c.1371C>T synonymous_variant 0.13
ccsA 619693 c.-198G>A upstream_gene_variant 0.29
ccsA 620058 c.168C>T synonymous_variant 0.14
ccsA 620568 c.678C>T synonymous_variant 0.12
rpoB 759615 c.-192A>C upstream_gene_variant 0.25
rpoB 760115 c.309C>T synonymous_variant 1.0
rpoB 760350 p.Asp182Asn missense_variant 0.13
rpoB 760879 p.Pro358Gln missense_variant 0.14
rpoB 761953 p.Ala716Val missense_variant 0.14
rpoC 762443 c.-927G>A upstream_gene_variant 0.12
rpoB 762630 p.Ala942Thr missense_variant 0.14
rpoC 763669 c.300C>A synonymous_variant 0.12
rpoC 764712 p.Ala448Gly missense_variant 0.17
rpoC 765150 p.Gly594Glu missense_variant 1.0
mmpL5 775639 p.Ile948Val missense_variant 1.0
mmpL5 777793 p.Ala230Thr missense_variant 1.0
mmpL5 779209 c.-729G>A upstream_gene_variant 0.18
rpsL 781395 c.-165T>C upstream_gene_variant 1.0
rplC 800651 c.-158G>C upstream_gene_variant 0.13
rplC 800658 c.-151T>A upstream_gene_variant 0.12
fbiC 1302873 c.-58A>T upstream_gene_variant 0.12
fbiC 1303084 p.Gly52Ser missense_variant 0.11
fbiC 1304655 c.1725C>T synonymous_variant 0.14
fbiC 1304826 c.1900delT frameshift_variant 0.12
Rv1258c 1406159 c.1182G>A synonymous_variant 0.12
Rv1258c 1406539 p.Ala268Thr missense_variant 0.12
Rv1258c 1407001 p.Ala114Thr missense_variant 0.11
Rv1258c 1407159 p.Val61Ala missense_variant 0.14
embR 1416651 p.Thr233Ala missense_variant 0.12
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
rrs 1472894 n.1049G>A non_coding_transcript_exon_variant 0.17
rrs 1472906 n.1061T>C non_coding_transcript_exon_variant 0.13
rrl 1474309 n.652G>A non_coding_transcript_exon_variant 0.12
rrl 1475129 n.1472G>T non_coding_transcript_exon_variant 0.11
rrl 1475181 n.1524A>T non_coding_transcript_exon_variant 0.12
rrl 1475527 n.1870A>T non_coding_transcript_exon_variant 0.13
rrl 1476264 n.2607A>G non_coding_transcript_exon_variant 0.1
rpsA 1833426 c.-116T>C upstream_gene_variant 0.11
tlyA 1917919 c.-21C>T upstream_gene_variant 0.13
tlyA 1917972 c.33A>G synonymous_variant 1.0
tlyA 1918095 c.156G>A synonymous_variant 0.12
tlyA 1918182 c.243G>A synonymous_variant 0.15
ndh 2102394 p.Ala217Thr missense_variant 0.17
PPE35 2168436 p.Leu726Pro missense_variant 0.11
PPE35 2169558 p.Phe352Tyr missense_variant 0.13
Rv1979c 2222204 p.Phe321Leu missense_variant 0.12
Rv1979c 2222656 p.Lys170Ala missense_variant 0.1
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
pncA 2289637 c.-396G>A upstream_gene_variant 0.12
kasA 2518076 c.-39C>T upstream_gene_variant 1.0
eis 2714543 c.790C>A synonymous_variant 0.17
eis 2715207 p.Thr42Ala missense_variant 0.11
ahpC 2726338 p.Val49Gly missense_variant 0.24
ahpC 2726341 p.Val50Gly missense_variant 0.26
folC 2746337 p.Ala421Val missense_variant 0.12
folC 2746609 c.990T>C synonymous_variant 0.1
ribD 2987048 c.212delT frameshift_variant 0.17
Rv2752c 3064901 p.Leu431Met missense_variant 0.14
Rv2752c 3065396 p.Met266Val missense_variant 0.1
thyX 3067672 p.Glu92* stop_gained 0.11
thyA 3074466 c.6G>A synonymous_variant 0.13
thyA 3074645 c.-174T>G upstream_gene_variant 0.45
ald 3086788 c.-32T>C upstream_gene_variant 1.0
fbiD 3339029 c.-89C>T upstream_gene_variant 0.18
fprA 3473996 c.-11_-10insA upstream_gene_variant 1.0
fprA 3475277 p.Gln424Leu missense_variant 0.13
fprA 3475308 c.1302C>T synonymous_variant 0.12
Rv3236c 3612718 c.399C>T synonymous_variant 0.25
Rv3236c 3612759 p.Gly120Arg missense_variant 0.5
Rv3236c 3613106 p.Ser4Leu missense_variant 0.11
Rv3236c 3613301 c.-185G>A upstream_gene_variant 0.22
fbiB 3642114 p.Val194Ile missense_variant 0.22
alr 3840663 p.Pro253Arg missense_variant 0.13
clpC1 4040703 c.2T>A start_lost 0.11
embC 4242642 p.Arg927His missense_variant 0.17
embC 4242803 p.Val981Leu missense_variant 1.0
embA 4244329 p.Ala366Val missense_variant 0.13
embA 4244364 p.Gly378Ser missense_variant 0.12
embA 4245114 p.Gly628Ser missense_variant 0.13
embA 4245213 p.Ala661Thr missense_variant 0.29
embA 4245907 p.Leu892Pro missense_variant 0.12
embA 4246195 p.Pro988His missense_variant 0.14
embB 4247079 p.Phe189Ser missense_variant 0.12
aftB 4267622 c.1215G>A synonymous_variant 0.14
whiB6 4338595 c.-75delG upstream_gene_variant 1.0