TB-Profiler result

Run: SRR4037756
Summary

Run ID: SRR4037756

Sample name:

Date: 04-04-2023 07:38:24

Number of reads: 1027621

Percentage reads mapped: 99.6

Strain: lineage2.2.1

Drug-resistance: RR-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
lineage2 East-Asian Beijing RD105 0.32
lineage2.2 East-Asian (Beijing) Beijing-RD207 RD105;RD207 0.34
lineage2.2.1 East-Asian (Beijing) Beijing-RD181 RD105;RD207;RD181 0.36
lineage4.4.1 Euro-American (S-type) S;T None 0.63
lineage4.4.1.1 Euro-American S;Orphans None 0.65
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 761095 p.Leu430Pro missense_variant 0.12 rifampicin
pncA 2288836 c.405delC frameshift_variant 0.13 pyrazinamide, pyrazinamide
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 5064 c.-176C>A upstream_gene_variant 0.12
gyrB 6633 p.Gly465Asp missense_variant 0.11
gyrA 7362 p.Glu21Gln missense_variant 1.0
gyrA 7585 p.Ser95Thr missense_variant 1.0
gyrA 9138 p.Gln613Glu missense_variant 0.6
gyrA 9304 p.Gly668Asp missense_variant 1.0
fgd1 490742 c.-41C>A upstream_gene_variant 0.12
fgd1 491742 c.960T>C synonymous_variant 0.45
mshA 575998 c.651C>A synonymous_variant 0.2
mshA 576042 p.Pro232Gln missense_variant 0.13
mshA 576232 c.885C>A synonymous_variant 0.18
mshA 576614 p.Arg423Trp missense_variant 0.18
ccsA 620625 p.Ile245Met missense_variant 0.33
rpoB 761918 c.2112C>T synonymous_variant 0.12
rpoC 763031 c.-339T>C upstream_gene_variant 0.17
rpoC 763557 p.Gly63Asp missense_variant 0.11
rpoC 766657 c.3288A>G synonymous_variant 0.18
mmpL5 775639 p.Ile948Val missense_variant 1.0
mmpL5 776182 p.Asp767Asn missense_variant 0.38
mmpL5 777351 p.Arg377Gln missense_variant 0.14
mmpL5 777416 c.1065G>T synonymous_variant 0.47
mmpL5 779211 c.-731C>A upstream_gene_variant 0.13
mmpS5 779615 c.-710C>G upstream_gene_variant 0.38
rpsL 781395 c.-165T>C upstream_gene_variant 1.0
rplC 801130 p.Asp108Tyr missense_variant 0.13
fbiC 1304630 c.1701delC frameshift_variant 0.12
fbiC 1305034 p.Leu702Met missense_variant 0.17
fbiC 1305269 p.Arg780His missense_variant 0.12
Rv1258c 1406760 c.580_581insC frameshift_variant 0.31
Rv1258c 1407207 c.133delT frameshift_variant 0.2
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
inhA 1673363 c.-839G>A upstream_gene_variant 0.56
inhA 1674081 c.-121C>A upstream_gene_variant 0.12
rpsA 1834177 c.636A>C synonymous_variant 0.15
tlyA 1917972 c.33A>G synonymous_variant 1.0
tlyA 1918507 p.Gly190Cys missense_variant 0.14
ndh 2102990 p.Val18Ala missense_variant 0.7
katG 2154724 p.Arg463Leu missense_variant 0.31
PPE35 2167926 p.Leu896Ser missense_variant 0.1
PPE35 2168479 p.Thr712Pro missense_variant 0.75
PPE35 2169320 p.Leu431Phe missense_variant 0.18
PPE35 2169840 p.Gly258Asp missense_variant 0.93
PPE35 2169866 c.747G>C synonymous_variant 0.12
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
kasA 2518950 p.Ala279Val missense_variant 0.11
eis 2715096 c.237C>T synonymous_variant 0.17
eis 2715219 c.114C>A synonymous_variant 0.11
ahpC 2726669 c.477T>C synonymous_variant 0.11
folC 2746648 c.951G>T synonymous_variant 0.12
pepQ 2859953 p.Asp156Tyr missense_variant 0.13
Rv2752c 3066175 p.Pro6Arg missense_variant 0.58
thyX 3067886 c.60A>C synonymous_variant 0.25
thyX 3068064 c.-119G>T upstream_gene_variant 0.14
ald 3086788 c.-32T>C upstream_gene_variant 1.0
Rv3083 3448608 c.105G>A synonymous_variant 0.82
Rv3083 3449301 c.798G>T synonymous_variant 0.11
fprA 3473996 c.-11_-10insA upstream_gene_variant 1.0
fprA 3474902 p.Ser299Ile missense_variant 0.17
whiB7 3568779 c.-100T>C upstream_gene_variant 0.77
whiB7 3568853 c.-174G>T upstream_gene_variant 0.16
Rv3236c 3612665 p.Val151Ala missense_variant 0.59
Rv3236c 3612813 p.Thr102Ala missense_variant 0.33
clpC1 4039890 p.Val272Ala missense_variant 0.12
embA 4242643 c.-590C>T upstream_gene_variant 1.0
embA 4242877 c.-356G>A upstream_gene_variant 0.12
embA 4243460 c.228C>T synonymous_variant 0.5
embA 4244025 c.794_802delATGTCATCG disruptive_inframe_deletion 0.15
embA 4245185 c.1953G>A synonymous_variant 0.12
aftB 4267632 c.1204delG frameshift_variant 0.25
aftB 4267647 p.Asp397Gly missense_variant 0.22
whiB6 4338595 c.-75delG upstream_gene_variant 1.0
gid 4407588 c.615A>G synonymous_variant 0.2
gid 4407620 p.Tyr195His missense_variant 0.18
gid 4407927 p.Glu92Asp missense_variant 0.6