TB-Profiler result

Run: SRR4033273
Summary

Run ID: SRR4033273

Sample name:

Date: 04-04-2023 05:57:37

Number of reads: 811108

Percentage reads mapped: 99.78

Strain: lineage4.8.1

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
lineage4.8 Euro-American (mainly T) T1;T2;T3;T5 RD219 1.0
lineage4.8.1 Euro-American (mainly T) T1;T2;T3;T5 RD219 1.0
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 2155059 p.Trp351* stop_gained 0.29 isoniazid
embC 4240785 p.Gly308Asp missense_variant 0.17 ethambutol
ethA 4326008 c.1465delG frameshift_variant 0.17 ethionamide, ethionamide
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 8933 c.1632G>T synonymous_variant 0.15
gyrA 9388 p.Ala696Val missense_variant 0.14
gyrA 9552 c.2251C>T synonymous_variant 0.14
rpoB 760518 c.714delC frameshift_variant 0.29
rpoB 760963 p.Gly386Asp missense_variant 0.2
rpoB 761067 p.Ile421Phe missense_variant 0.14
rpoC 764740 p.Met457Ile missense_variant 0.11
rpoC 765364 c.1998_2000delCAC disruptive_inframe_deletion 0.17
mmpL5 775639 p.Ile948Val missense_variant 1.0
mmpR5 778178 c.-812G>A upstream_gene_variant 0.12
mmpL5 779352 c.-872C>T upstream_gene_variant 0.17
rpsL 781395 c.-165T>C upstream_gene_variant 1.0
rplC 801378 c.570C>T synonymous_variant 0.22
embR 1417378 c.-32delA upstream_gene_variant 0.22
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
rrs 1471768 n.-78T>A upstream_gene_variant 0.13
rrs 1472135 n.292delG non_coding_transcript_exon_variant 0.11
rrs 1472140 n.299_300delAG non_coding_transcript_exon_variant 0.11
rrl 1474001 n.344C>T non_coding_transcript_exon_variant 1.0
rrl 1474128 n.471G>A non_coding_transcript_exon_variant 0.14
rrl 1474907 n.1250C>T non_coding_transcript_exon_variant 0.17
rrl 1474999 n.1342C>T non_coding_transcript_exon_variant 0.25
rrl 1475653 n.1996A>T non_coding_transcript_exon_variant 0.18
rrl 1476702 n.3045A>T non_coding_transcript_exon_variant 0.15
inhA 1674952 p.Pro251Ala missense_variant 0.4
rpsA 1833894 p.Ala118Gly missense_variant 0.13
tlyA 1917972 c.33A>G synonymous_variant 1.0
katG 2154264 c.1848G>A synonymous_variant 0.17
katG 2155722 c.390G>A synonymous_variant 0.14
katG 2156127 c.-16T>C upstream_gene_variant 0.12
PPE35 2168149 p.Pro822Ser missense_variant 1.0
PPE35 2169320 p.Leu431Phe missense_variant 0.25
PPE35 2169394 p.Ala407Thr missense_variant 0.22
PPE35 2169485 c.1128C>T synonymous_variant 0.15
PPE35 2170565 p.Phe16Leu missense_variant 0.22
Rv1979c 2221983 c.1182C>T synonymous_variant 0.12
Rv1979c 2222864 p.Thr101Ala missense_variant 0.1
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
eis 2714664 c.669C>T synonymous_variant 0.17
ahpC 2726338 p.Val49Gly missense_variant 0.5
folC 2747650 c.-52G>A upstream_gene_variant 0.22
pepQ 2860343 p.Asp26Asn missense_variant 0.14
thyA 3074258 c.214C>T synonymous_variant 0.15
thyA 3074356 p.Ser39* stop_gained 0.11
fbiD 3339040 c.-78T>C upstream_gene_variant 1.0
fprA 3474414 c.408A>G synonymous_variant 0.22
Rv3236c 3612029 p.Ala363Val missense_variant 0.12
Rv3236c 3612417 p.Glu234Lys missense_variant 0.29
Rv3236c 3612600 p.Ala173Thr missense_variant 0.12
Rv3236c 3612603 p.Leu172Ile missense_variant 0.12
Rv3236c 3613061 p.Ala19Val missense_variant 0.14
Rv3236c 3613127 c.-12delA upstream_gene_variant 0.12
fbiB 3642874 p.Leu447Arg missense_variant 1.0
alr 3841407 p.Trp5Leu missense_variant 0.2
panD 4043885 p.Asp133Tyr missense_variant 0.15
embC 4240220 p.Gly120Trp missense_variant 0.14
embC 4241070 p.Ala403Asp missense_variant 0.12
embC 4241180 p.Pro440Ser missense_variant 0.14
embC 4241729 p.Ala623Thr missense_variant 0.11
embA 4242643 c.-590C>T upstream_gene_variant 1.0
embC 4242792 p.Ala977Glu missense_variant 0.4
embA 4243825 p.Thr198Met missense_variant 0.11
embA 4244363 c.1131C>T synonymous_variant 0.14
embA 4245362 c.2130G>T synonymous_variant 0.15
embB 4245659 c.-855C>T upstream_gene_variant 0.14
embB 4248085 c.1572T>C synonymous_variant 0.12
embB 4248359 p.Pro616Thr missense_variant 0.12
whiB6 4338595 c.-75delG upstream_gene_variant 1.0
gid 4407644 p.Arg187Gly missense_variant 0.15
gid 4408321 c.-119C>T upstream_gene_variant 0.12
gid 4408329 c.-127C>G upstream_gene_variant 0.12
Rv3083 3448497 c.-6_*1408del transcript_ablation 1.0