TB-Profiler result

Run: SRR5818673
Summary

Run ID: SRR5818673

Sample name:

Date: 04-04-2023 11:43:12

Number of reads: 1618979

Percentage reads mapped: 99.43

Strain: lineage4.2.2.2

Drug-resistance: Other

Download CSV Download TXT Download PDF Download JSON
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
lineage4.2.2.2 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
gid 4408087 c.115delC frameshift_variant 0.95 streptomycin
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 8688 p.Ala463Ser missense_variant 1.0
gyrA 9304 p.Gly668Asp missense_variant 1.0
fgd1 491607 c.825G>A synonymous_variant 0.17
mshA 576077 c.730C>T synonymous_variant 1.0
ccsA 620755 p.Asp289Asn missense_variant 0.14
rpoB 759918 p.Leu38Met missense_variant 0.25
rpoB 761489 c.1683G>A synonymous_variant 1.0
mmpL5 775639 p.Ile948Val missense_variant 1.0
mmpL5 777327 p.Ala385Asp missense_variant 0.18
rpsL 781395 c.-165T>C upstream_gene_variant 1.0
Rv1258c 1407247 p.Trp32Arg missense_variant 0.17
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
rrl 1473874 n.217G>C non_coding_transcript_exon_variant 0.1
fabG1 1673380 c.-60C>G upstream_gene_variant 0.23
tlyA 1917972 c.33A>G synonymous_variant 1.0
tlyA 1918334 p.Glu132Val missense_variant 1.0
ndh 2102075 p.Met323Lys missense_variant 0.12
katG 2153970 p.Asp714Glu missense_variant 0.21
PPE35 2169652 c.961T>C synonymous_variant 0.11
PPE35 2170048 p.Leu189Val missense_variant 0.53
PPE35 2170053 p.Thr187Ser missense_variant 0.5
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
kasA 2518606 c.492G>C synonymous_variant 0.21
kasA 2518609 p.Met165Ile missense_variant 0.22
kasA 2519160 p.Ala349Glu missense_variant 0.25
eis 2715440 c.-108A>C upstream_gene_variant 0.11
folC 2746511 p.Ala363Glu missense_variant 0.12
pepQ 2859802 p.Arg206Gln missense_variant 0.17
ribD 2986825 c.-14C>T upstream_gene_variant 0.15
Rv2752c 3065523 c.669C>T synonymous_variant 0.15
Rv2752c 3066280 c.-89C>T upstream_gene_variant 1.0
thyX 3067892 c.54G>A synonymous_variant 0.17
ald 3086742 c.-78A>C upstream_gene_variant 1.0
ald 3086788 c.-32T>C upstream_gene_variant 1.0
ald 3087634 p.Gly272Val missense_variant 0.21
ald 3087639 p.Cys274Ser missense_variant 0.25
fprA 3473996 c.-11_-10insA upstream_gene_variant 1.0
rpoA 3877878 c.630G>A synonymous_variant 0.2
clpC1 4038310 p.Val799Leu missense_variant 0.14
embC 4240871 p.Val337Phe missense_variant 0.13
embA 4242643 c.-590C>T upstream_gene_variant 1.0
embB 4246544 p.Thr11Pro missense_variant 0.16
embB 4246548 p.Pro12Gln missense_variant 0.18
embB 4246555 c.42G>C synonymous_variant 0.2
embB 4246556 p.Ala15Pro missense_variant 0.2
ubiA 4269467 p.Asn123His missense_variant 0.12
ethA 4326342 p.Pro378Thr missense_variant 0.18
ethA 4326508 c.966G>C synonymous_variant 0.17
whiB6 4338595 c.-75delG upstream_gene_variant 1.0
gid 4408473 c.-271C>A upstream_gene_variant 0.14