TB-Profiler result

Run: SRR1180929
Summary

Run ID: SRR1180929

Sample name:

Date: 03-04-2023 04:17:15

Number of reads: 569904

Percentage reads mapped: 81.4

Strain: lineage4.4.1.1

Drug-resistance: MDR-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
lineage4.4 Euro-American S;T None 1.0
lineage4.4.1 Euro-American (S-type) S;T None 1.0
lineage4.4.1.1 Euro-American S;Orphans 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
rpoB 761161 p.Leu452Pro missense_variant 0.83 rifampicin
katG 2155168 p.Ser315Thr missense_variant 1.0 isoniazid
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 7585 p.Ser95Thr missense_variant 1.0
gyrA 8116 p.Thr272Ile missense_variant 1.0
gyrA 8261 c.960C>A synonymous_variant 0.11
gyrA 9304 p.Gly668Asp missense_variant 1.0
fgd1 491315 p.Gly178Val missense_variant 0.18
rpoB 762048 p.Glu748Lys missense_variant 0.12
rpoB 762233 c.2427G>A synonymous_variant 0.25
rpoC 763061 c.-309C>A upstream_gene_variant 0.15
rpoC 763599 p.Arg77Leu missense_variant 0.25
rpoC 765564 p.Ser732* stop_gained 0.5
mmpL5 775639 p.Ile948Val missense_variant 1.0
mmpL5 776321 c.2160C>A synonymous_variant 0.18
mmpS5 778792 p.Leu38Phe missense_variant 0.12
rpsL 781395 c.-165T>C upstream_gene_variant 1.0
rplC 800882 p.Pro25Gln missense_variant 0.12
rplC 800958 c.150G>A synonymous_variant 0.17
fbiC 1305238 p.His770Tyr missense_variant 0.2
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
rrl 1475673 n.2021delA non_coding_transcript_exon_variant 0.33
rrl 1476408 n.2751G>A non_coding_transcript_exon_variant 0.12
rrl 1476411 n.2754G>T non_coding_transcript_exon_variant 0.12
rrl 1476425 n.2768G>T non_coding_transcript_exon_variant 0.12
rrl 1476429 n.2772A>C non_coding_transcript_exon_variant 0.13
fabG1 1673164 c.-276C>A upstream_gene_variant 0.2
tlyA 1917972 c.33A>G synonymous_variant 1.0
ndh 2101741 p.Gln434His missense_variant 0.18
ndh 2102990 p.Val18Ala missense_variant 1.0
katG 2154098 p.Pro672Thr missense_variant 0.18
katG 2155362 p.Glu250Asp missense_variant 0.18
PPE35 2169840 p.Gly258Asp missense_variant 1.0
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
eis 2714791 p.Arg181Leu missense_variant 0.22
eis 2714850 c.483C>T synonymous_variant 0.25
ahpC 2726580 p.Val130Leu missense_variant 0.25
folC 2746695 p.Ala302Thr missense_variant 0.13
folC 2747422 c.176delC frameshift_variant 0.14
ald 3086788 c.-32T>C upstream_gene_variant 1.0
Rv3083 3448608 c.105G>A synonymous_variant 1.0
fprA 3473996 c.-11_-10insA upstream_gene_variant 1.0
Rv3236c 3612665 p.Val151Ala missense_variant 1.0
clpC1 4038484 p.Gln741Glu missense_variant 0.14
clpC1 4039379 p.Gln442His missense_variant 0.25
embC 4241852 p.Ala664Pro missense_variant 0.14
embA 4242643 c.-590C>T upstream_gene_variant 1.0
embB 4249100 p.Tyr863His missense_variant 0.29
aftB 4267513 p.Leu442Ile missense_variant 0.14
whiB6 4338595 c.-75delG upstream_gene_variant 1.0
gid 4407712 p.Gly164Asp missense_variant 1.0
gid 4407933 c.270C>G synonymous_variant 1.0
gid 4408328 c.-126G>A upstream_gene_variant 0.12