TB-Profiler result

Run: ERR2446520
Summary

Run ID: ERR2446520

Sample name:

Date: 15-08-2022 11:03:26

Number of reads: 526856

Percentage reads mapped: 99.97

Strain: lineage4.2.2.2

Drug-resistance: Sensitive

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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
lineage4.2 Euro-American H;T;LAM None 0.99
lineage4.2.2 Euro-American (Ural) T;LAM7-TUR None 0.98
lineage4.2.2.2 Euro-American (Ural) T;LAM7-TUR None 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
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 5639 c.400C>A synonymous_variant 0.13
gyrB 5650 c.411C>A synonymous_variant 0.13
gyrB 6972 p.Pro578Gln missense_variant 0.2
gyrA 7585 p.Ser95Thr missense_variant 1.0
gyrA 9286 p.Ala662Val missense_variant 0.12
gyrA 9304 p.Gly668Asp missense_variant 1.0
fgd1 490652 c.-131G>T upstream_gene_variant 0.2
fgd1 491316 c.534C>G synonymous_variant 0.2
mshA 575483 c.136C>A synonymous_variant 0.15
mshA 575701 p.Glu118Asp missense_variant 0.12
mshA 576077 c.730C>T synonymous_variant 1.0
ccsA 620437 p.Ser183Pro missense_variant 0.12
rpoB 760861 p.Pro352Gln missense_variant 0.13
rpoB 761865 p.Gly687Cys missense_variant 0.15
rpoC 763441 c.72C>A synonymous_variant 0.17
rpoC 766448 p.Gly1027Ser missense_variant 0.18
rpoC 766675 c.3306C>T synonymous_variant 0.2
mmpL5 775639 p.Ile948Val missense_variant 1.0
mmpL5 778831 c.-351G>T upstream_gene_variant 0.13
rpsL 781395 c.-165T>C upstream_gene_variant 1.0
rplC 800647 c.-162C>A upstream_gene_variant 0.15
fbiC 1302916 c.-15G>T upstream_gene_variant 0.12
Rv1258c 1407059 p.Trp94Cys missense_variant 0.2
Rv1258c 1407377 c.-37C>A upstream_gene_variant 0.18
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
rrs 1472391 n.546C>A non_coding_transcript_exon_variant 0.12
rrl 1473778 n.121G>T non_coding_transcript_exon_variant 0.12
rrl 1474311 n.654G>T non_coding_transcript_exon_variant 0.12
rrl 1474364 n.707G>T non_coding_transcript_exon_variant 0.12
rrl 1474974 n.1317G>T non_coding_transcript_exon_variant 0.13
rpsA 1834114 c.573G>T synonymous_variant 0.13
rpsA 1834535 p.Glu332Gln missense_variant 0.12
tlyA 1917972 c.33A>G synonymous_variant 1.0
ndh 2103171 c.-129G>T upstream_gene_variant 0.17
katG 2154077 p.Gln679Lys missense_variant 0.14
katG 2154536 p.Glu526* stop_gained 0.12
katG 2155537 p.Glu192Gly missense_variant 0.12
PPE35 2167754 p.Phe953Leu missense_variant 0.17
PPE35 2169788 p.Leu275Phe missense_variant 0.18
Rv1979c 2223275 c.-111C>A upstream_gene_variant 0.12
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
kasA 2518202 p.Glu30* stop_gained 0.15
ahpC 2726768 p.Lys192Asn missense_variant 0.15
Rv2752c 3065281 p.Thr304Asn missense_variant 0.18
Rv2752c 3065522 c.670C>A synonymous_variant 0.15
Rv2752c 3066280 c.-89C>T upstream_gene_variant 1.0
thyX 3067803 p.Ser48Tyr missense_variant 0.13
ald 3086788 c.-32T>C upstream_gene_variant 1.0
Rv3083 3449352 p.Met283Ile missense_variant 0.17
Rv3083 3449925 c.1422C>A synonymous_variant 0.15
fprA 3473996 c.-11_-10insA upstream_gene_variant 1.0
fprA 3474465 c.459C>A synonymous_variant 0.13
fprA 3474852 c.846C>T synonymous_variant 0.2
whiB7 3568614 c.66C>A synonymous_variant 0.13
Rv3236c 3612499 c.618C>A synonymous_variant 0.14
alr 3840710 c.711A>G synonymous_variant 0.15
clpC1 4038656 p.Lys683Asn missense_variant 0.17
clpC1 4039204 p.Glu501* stop_gained 0.14
clpC1 4039882 p.Glu275* stop_gained 0.12
clpC1 4040570 c.135C>A synonymous_variant 0.19
embC 4240401 c.540delC frameshift_variant 0.13
embA 4242643 c.-590C>T upstream_gene_variant 1.0
embA 4245699 p.Gly823Trp missense_variant 0.17
embA 4246033 p.Pro934Gln missense_variant 0.18
embB 4247050 c.537C>A synonymous_variant 0.14
embB 4247384 p.His291Asn missense_variant 0.14
embB 4247851 c.1338C>A synonymous_variant 0.17
embB 4248432 p.Trp640Leu missense_variant 0.17
aftB 4268243 c.594C>A synonymous_variant 0.15
ubiA 4269946 c.-113G>T upstream_gene_variant 0.12
whiB6 4338276 c.246C>A synonymous_variant 0.14
gid 4407898 p.Arg102Leu missense_variant 0.21
gid 4408047 p.Cys52Trp missense_variant 0.13
gid 4408228 c.-26G>T upstream_gene_variant 0.17