TB-Profiler result

Run: ERR2229691
Summary

Run ID: ERR2229691

Sample name:

Date: 31-03-2023 17:27:29

Number of reads: 1164367

Percentage reads mapped: 99.21

Strain: lineage4.8

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
lineage4.8 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
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 7517 c.216G>A synonymous_variant 0.11
gyrA 9542 c.2244delA frameshift_variant 0.14
fgd1 491389 p.Tyr203Asn missense_variant 0.14
mshA 576471 p.Gly375Val missense_variant 0.17
rpoB 759788 c.-19A>G upstream_gene_variant 0.12
rpoB 759959 c.153G>A synonymous_variant 0.29
rpoC 765366 p.Thr666Ile missense_variant 0.22
rpoC 765965 p.Arg866Ser missense_variant 0.12
mmpL5 775639 p.Ile948Val missense_variant 1.0
mmpL5 776473 p.Gln670Lys missense_variant 0.13
mmpL5 777196 p.Glu429Gln missense_variant 0.11
rpsL 781395 c.-165T>C upstream_gene_variant 1.0
rplC 801120 p.Glu104Asp missense_variant 0.13
fbiC 1303030 c.100C>A synonymous_variant 0.12
fbiC 1303496 p.Pro189Gln missense_variant 0.12
fbiC 1303702 p.Gly258Ser missense_variant 0.4
fbiC 1303747 p.Thr273Ala missense_variant 1.0
fbiC 1303879 p.Thr317Ser missense_variant 0.13
fbiC 1304417 p.Leu496His missense_variant 0.12
fbiC 1304658 c.1728C>T synonymous_variant 0.11
Rv1258c 1406341 p.Tyr334His missense_variant 0.15
Rv1258c 1406348 c.993C>T synonymous_variant 0.15
atpE 1461014 c.-31G>A upstream_gene_variant 0.12
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
rrl 1475869 n.2212C>A non_coding_transcript_exon_variant 0.22
rrl 1475877 n.2220C>T non_coding_transcript_exon_variant 0.33
rrl 1475881 n.2224T>C non_coding_transcript_exon_variant 0.33
rrl 1475883 n.2226A>T non_coding_transcript_exon_variant 0.33
rrl 1475892 n.2235A>C non_coding_transcript_exon_variant 0.67
rrl 1475898 n.2241A>G non_coding_transcript_exon_variant 0.67
rrl 1475899 n.2242G>A non_coding_transcript_exon_variant 0.67
rrl 1475906 n.2249C>T non_coding_transcript_exon_variant 0.67
rrl 1476674 n.3017T>C non_coding_transcript_exon_variant 0.22
fabG1 1673380 c.-60C>G upstream_gene_variant 0.13
fabG1 1674143 p.Ala235Val missense_variant 0.12
tlyA 1917972 c.33A>G synonymous_variant 1.0
ndh 2103173 c.-131C>G upstream_gene_variant 0.17
ndh 2103178 c.-136G>T upstream_gene_variant 0.17
katG 2154206 p.Ala636Thr missense_variant 0.15
katG 2154294 c.1818C>A synonymous_variant 0.15
katG 2154988 p.Pro375Leu missense_variant 0.29
PPE35 2168728 p.Gly629Arg missense_variant 1.0
PPE35 2169605 c.1008T>C synonymous_variant 0.18
PPE35 2169618 p.Phe332Ser missense_variant 0.1
PPE35 2170048 p.Leu189Val missense_variant 0.77
PPE35 2170053 p.Thr187Ser missense_variant 0.77
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
pncA 2289972 c.-731T>C upstream_gene_variant 0.12
eis 2714221 p.Ala371Gly missense_variant 0.15
eis 2714629 p.Leu235Pro missense_variant 0.18
eis 2714688 p.Phe215Leu missense_variant 0.67
eis 2715074 p.Val87Leu missense_variant 0.15
folC 2746191 p.Gly470Ser missense_variant 0.18
folC 2746833 p.Val256Met missense_variant 0.12
folC 2747490 p.Arg37Ser missense_variant 0.11
pepQ 2859925 p.Pro165Leu missense_variant 0.12
Rv2752c 3064758 c.1434G>A synonymous_variant 0.14
Rv2752c 3065671 p.Asp174Val missense_variant 0.17
Rv2752c 3067049 c.-858G>A upstream_gene_variant 0.11
thyX 3067340 c.606G>A synonymous_variant 0.27
fbiD 3339012 c.-106A>G upstream_gene_variant 0.1
fprA 3473975 c.-32G>A upstream_gene_variant 0.13
fprA 3474368 p.Gly121Ala missense_variant 0.12
fprA 3475374 c.1368C>A synonymous_variant 0.15
Rv3236c 3612564 p.Met185Leu missense_variant 0.11
alr 3840761 c.660G>A synonymous_variant 0.12
embA 4242643 c.-590C>T upstream_gene_variant 1.0
embA 4244794 p.Val521Glu missense_variant 0.33
embB 4245884 c.-630C>T upstream_gene_variant 0.12
embB 4246544 p.Thr11Pro missense_variant 0.28
embB 4246548 p.Pro12Gln missense_variant 0.52
embB 4246555 c.42G>C synonymous_variant 0.5
embB 4246556 p.Ala15Pro missense_variant 0.5
embB 4247090 p.Thr193Ala missense_variant 0.14
aftB 4267030 p.Asp603Asn missense_variant 0.17
aftB 4267054 p.Tyr595His missense_variant 0.18
aftB 4269255 c.-419C>T upstream_gene_variant 0.13
whiB6 4338595 c.-75delG upstream_gene_variant 1.0