TB-Profiler result

Run: SRR6982063
Summary

Run ID: SRR6982063

Sample name:

Date: 04-04-2023 18:26:12

Number of reads: 540558

Percentage reads mapped: 99.62

Strain: lineage4.8

Drug-resistance: Other

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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
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
tlyA 1918135 p.Gly66* stop_gained 0.13 capreomycin
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 8802 p.Ala501Thr missense_variant 0.11
fgd1 491042 p.Ala87Asp missense_variant 0.1
ccsA 620127 c.237C>A synonymous_variant 0.18
rpoC 762485 c.-885G>A upstream_gene_variant 0.12
rpoC 767269 c.3900C>T synonymous_variant 0.12
rpoC 767302 c.3933C>A synonymous_variant 0.12
mmpL5 775639 p.Ile948Val missense_variant 1.0
mmpL5 776154 p.Leu776Ser missense_variant 0.1
mmpL5 779154 c.-674T>C upstream_gene_variant 0.11
rpsL 781395 c.-165T>C upstream_gene_variant 1.0
fbiC 1303974 c.1044C>T synonymous_variant 0.12
fbiC 1304444 p.Ala505Val missense_variant 0.11
fbiC 1305053 p.Met708Lys missense_variant 0.11
fbiC 1305399 c.2469A>G synonymous_variant 0.1
Rv1258c 1407300 p.Phe14Ser missense_variant 0.15
Rv1258c 1407375 c.-36delC upstream_gene_variant 0.18
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
rrl 1474001 n.344C>T non_coding_transcript_exon_variant 1.0
rrl 1474869 n.1212G>A non_coding_transcript_exon_variant 0.12
tlyA 1917972 c.33A>G synonymous_variant 1.0
katG 2153915 p.Asn733Asp missense_variant 0.15
katG 2154061 p.Ser684Ile missense_variant 0.12
katG 2155226 p.Met296Val missense_variant 0.11
katG 2155484 p.Tyr210His missense_variant 0.11
PPE35 2168149 p.Pro822Ser missense_variant 1.0
PPE35 2170644 c.-32A>G upstream_gene_variant 0.1
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
pncA 2288922 p.Glu107Val missense_variant 0.11
kasA 2519214 p.Ile367Thr missense_variant 0.13
eis 2715001 p.Ser111Cys missense_variant 0.12
eis 2715470 c.-138G>C upstream_gene_variant 0.12
ribD 2987444 p.Phe202Leu missense_variant 0.14
ribD 2987517 p.Ile227Leu missense_variant 0.12
Rv2752c 3065237 p.Ser319Thr missense_variant 0.12
fprA 3474663 c.660_661dupGG frameshift_variant 0.1
Rv3236c 3612306 p.Ala271Thr missense_variant 0.12
Rv3236c 3612890 p.Glu76Gly missense_variant 0.1
fbiA 3640347 c.-196A>G upstream_gene_variant 0.12
fbiB 3641797 p.Arg88His missense_variant 0.13
fbiB 3642586 p.Met351Thr missense_variant 0.14
alr 3840406 p.Gly339Trp missense_variant 0.12
alr 3840453 p.Gly323Val missense_variant 0.11
alr 3840866 c.555G>A synonymous_variant 0.12
clpC1 4039729 p.Asp326Asn missense_variant 1.0
embC 4240450 c.588G>A synonymous_variant 0.11
embC 4241569 p.Ile569Met missense_variant 0.11
embA 4242643 c.-590C>T upstream_gene_variant 1.0
embC 4242705 p.Asp948Gly missense_variant 0.12
embA 4245645 p.Ala805Ser missense_variant 0.15
embB 4245764 c.-750G>A upstream_gene_variant 0.15
embA 4245853 p.Ala874Asp missense_variant 0.13
embB 4246515 c.2T>C start_lost 0.14
embB 4246556 p.Ala15Ser missense_variant 0.15
aftB 4267547 c.1290C>A synonymous_variant 0.13
aftB 4268901 c.-65T>C upstream_gene_variant 0.15
ubiA 4269419 p.Cys139Arg missense_variant 0.11
ubiA 4269467 p.Asn123Asp missense_variant 0.14
ubiA 4269935 c.-105_-103delTAC upstream_gene_variant 0.13
ubiA 4269979 c.-147delG upstream_gene_variant 0.18
whiB6 4338595 c.-75delG upstream_gene_variant 1.0
Rv3083 3448507 c.5_*1408del frameshift_variant&stop_lost&splice_region_variant 1.0