TB-Profiler result

Run: SRR7517748
Summary

Run ID: SRR7517748

Sample name:

Date: 04-04-2023 19:35:38

Number of reads: 989073

Percentage reads mapped: 96.21

Strain: lineage4.4.1.1

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 0.99
lineage4.4 Euro-American S;T None 0.89
lineage4.4.1 Euro-American (S-type) S;T None 0.91
lineage4.4.1.1 Euro-American S;Orphans None 0.85
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
gyrA 7581 p.Asp94Asn missense_variant 0.88 ofloxacin, moxifloxacin, levofloxacin, fluoroquinolones, ciprofloxacin
fabG1 1673425 c.-15C>T upstream_gene_variant 1.0 isoniazid, ethionamide
ahpC 2726142 c.-51G>T upstream_gene_variant 0.27 isoniazid
gid 4407896 p.Glu103* stop_gained 0.17 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
gyrB 6112 p.Met291Ile missense_variant 0.19
gyrB 6257 p.Asp340Tyr missense_variant 0.18
gyrA 7362 p.Glu21Gln missense_variant 1.0
gyrA 7585 p.Ser95Thr missense_variant 1.0
gyrA 9304 p.Gly668Asp missense_variant 1.0
fgd1 490656 c.-127C>A upstream_gene_variant 0.21
fgd1 491312 p.Gly177Asp missense_variant 0.33
ccsA 619954 p.Val22Met missense_variant 0.23
ccsA 620396 p.Ser169Tyr missense_variant 0.25
rpoB 759947 c.141C>A synonymous_variant 0.2
rpoC 763031 c.-339T>C upstream_gene_variant 0.3
rpoC 764374 p.Phe335Leu missense_variant 0.2
mmpL5 775639 p.Ile948Val missense_variant 1.0
mmpL5 776308 p.Asp725Tyr missense_variant 0.5
mmpL5 777185 c.1296G>T synonymous_variant 0.2
mmpR5 779221 p.Gly78Trp missense_variant 0.24
rpsL 781395 c.-165T>C upstream_gene_variant 1.0
rplC 801150 c.342G>T synonymous_variant 0.18
fbiC 1304267 p.Arg446Leu missense_variant 0.18
fbiC 1304296 p.Gln456Lys missense_variant 0.18
Rv1258c 1406498 p.Leu281Phe missense_variant 0.22
Rv1258c 1406759 p.Glu194Asp missense_variant 0.2
embR 1417409 c.-62C>A upstream_gene_variant 0.22
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
rrs 1472958 n.1113_1114insC non_coding_transcript_exon_variant 0.4
rrs 1472973 n.1128A>T non_coding_transcript_exon_variant 0.4
rrl 1474476 n.819C>T non_coding_transcript_exon_variant 0.33
rrl 1474488 n.831G>A non_coding_transcript_exon_variant 0.33
rrl 1474496 n.839C>T non_coding_transcript_exon_variant 0.4
rrl 1474497 n.840G>C non_coding_transcript_exon_variant 0.33
rrl 1474506 n.849C>G non_coding_transcript_exon_variant 0.67
rrl 1474507 n.850G>T non_coding_transcript_exon_variant 1.0
rrl 1474516 n.859C>T non_coding_transcript_exon_variant 0.67
rrl 1474529 n.872A>C non_coding_transcript_exon_variant 0.67
rrl 1474530 n.873G>A non_coding_transcript_exon_variant 0.5
rrl 1474537 n.880G>A non_coding_transcript_exon_variant 0.75
rrl 1474539 n.882C>T non_coding_transcript_exon_variant 0.5
rrl 1474540 n.883T>G non_coding_transcript_exon_variant 0.5
rrl 1474552 n.895C>T non_coding_transcript_exon_variant 0.5
rrl 1474558 n.901G>A non_coding_transcript_exon_variant 0.4
inhA 1673772 c.-430C>A upstream_gene_variant 0.2
fabG1 1673790 p.Phe117Leu missense_variant 0.2
fabG1 1673987 p.Pro183Gln missense_variant 0.2
rpsA 1833425 c.-117C>A upstream_gene_variant 0.2
rpsA 1833580 c.39C>A synonymous_variant 0.22
tlyA 1917972 c.33A>G synonymous_variant 1.0
ndh 2102686 c.357G>T synonymous_variant 0.22
ndh 2102990 p.Val18Ala missense_variant 0.81
katG 2154125 p.Asp663Tyr missense_variant 0.22
katG 2154455 p.Glu553* stop_gained 0.18
katG 2155568 p.Gly182Trp missense_variant 0.29
katG 2156146 c.-35A>G upstream_gene_variant 0.2
PPE35 2168411 p.Phe734Leu missense_variant 0.33
PPE35 2169047 c.1566C>A synonymous_variant 0.22
PPE35 2169308 c.1305C>T synonymous_variant 0.29
PPE35 2169840 p.Gly258Asp missense_variant 0.6
Rv1979c 2222949 c.216C>A synonymous_variant 0.25
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
pncA 2289237 p.Arg2Leu missense_variant 0.18
kasA 2519017 c.903G>T synonymous_variant 0.2
thyA 3074182 p.Gln97Arg missense_variant 0.15
ald 3086788 c.-32T>C upstream_gene_variant 1.0
ald 3086962 p.Ala48Val missense_variant 0.4
ald 3087441 p.Asp208Tyr missense_variant 0.33
ald 3087786 p.Glu323* stop_gained 0.2
Rv3083 3448608 c.105G>A synonymous_variant 0.93
Rv3083 3449538 c.1035G>T synonymous_variant 0.33
fprA 3473996 c.-11_-10insA upstream_gene_variant 1.0
fprA 3475159 p.Asn385Asp missense_variant 0.12
whiB7 3568494 c.186C>A synonymous_variant 0.15
Rv3236c 3612665 p.Val151Ala missense_variant 0.93
alr 3841335 p.Ser29Tyr missense_variant 0.18
rpoA 3878202 c.306G>T synonymous_variant 0.2
clpC1 4039468 p.Arg413Ser missense_variant 0.2
clpC1 4040517 p.Val63Ala missense_variant 0.18
panD 4043908 p.Pro125His missense_variant 0.22
embC 4240671 p.Thr270Ile missense_variant 0.21
embA 4242643 c.-590C>T upstream_gene_variant 1.0
embC 4243026 p.Arg1055Met missense_variant 0.18
embC 4243124 p.Pro1088Ser missense_variant 0.89
embA 4243848 p.Val206Met missense_variant 0.4
aftB 4267295 p.Leu514Phe missense_variant 0.19
aftB 4267431 p.Ser469Leu missense_variant 0.25
aftB 4268412 p.Gly142Val missense_variant 0.2
ethA 4326268 c.1206C>A synonymous_variant 0.4
ethA 4326791 p.Trp228Leu missense_variant 0.2
ethR 4327228 c.-321G>T upstream_gene_variant 0.22
whiB6 4338595 c.-75delG upstream_gene_variant 1.0