TB-Profiler result

Run: SRR11972240
Summary

Run ID: SRR11972240

Sample name:

Date: 03-04-2023 05:33:13

Number of reads: 390160

Percentage reads mapped: 99.5

Strain: lineage2.2.1

Drug-resistance: MDR-TB

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
lineage2 East-Asian Beijing RD105 0.92
lineage2.2 East-Asian (Beijing) Beijing-RD207 RD105;RD207 0.91
lineage2.2.1 East-Asian (Beijing) Beijing-RD181 RD105;RD207;RD181 0.96
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 1.0 rifampicin
rpsL 781687 p.Lys43Arg missense_variant 1.0 streptomycin
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
gyrB 5703 p.Pro155His missense_variant 0.12
gyrB 6390 p.Val384Ala missense_variant 0.12
gyrA 7362 p.Glu21Gln missense_variant 1.0
gyrA 7585 p.Ser95Thr missense_variant 1.0
gyrA 8452 p.Ala384Val missense_variant 0.15
gyrA 8836 p.Ala512Asp missense_variant 0.15
gyrA 9143 c.1842T>C synonymous_variant 0.11
gyrA 9304 p.Gly668Asp missense_variant 1.0
fgd1 491742 c.960T>C synonymous_variant 1.0
mshA 575199 c.-149G>A upstream_gene_variant 0.22
mshA 575907 p.Ala187Val missense_variant 0.83
mshA 575929 c.582C>G synonymous_variant 0.25
mshA 576250 c.903G>A synonymous_variant 0.18
mshA 576361 c.1014C>G synonymous_variant 0.18
mshA 576555 p.Asp403Val missense_variant 0.17
ccsA 619807 c.-84G>A upstream_gene_variant 0.17
ccsA 620527 p.Ala213Thr missense_variant 0.17
ccsA 620625 p.Ile245Met missense_variant 0.94
rpoC 763031 c.-339T>C upstream_gene_variant 1.0
rpoB 763171 p.Leu1122Pro missense_variant 0.11
rpoC 763501 p.Asp44Glu missense_variant 1.0
rpoC 764651 p.Ser428Pro missense_variant 0.13
rpoC 765469 c.2100G>C synonymous_variant 0.4
rpoC 766672 c.3303T>C synonymous_variant 0.18
rpoC 767020 c.3651C>T synonymous_variant 0.5
mmpL5 775639 p.Ile948Val missense_variant 1.0
mmpL5 775742 c.2739C>T synonymous_variant 0.11
mmpL5 775764 p.Val906Asp missense_variant 0.13
mmpL5 775966 p.Ala839Ser missense_variant 0.18
mmpL5 776100 p.Thr794Ile missense_variant 1.0
mmpL5 776182 p.Asp767Asn missense_variant 1.0
mmpL5 777360 p.Ala374Val missense_variant 0.2
mmpL5 777462 p.Ala340Val missense_variant 0.15
mmpL5 778684 c.-204C>A upstream_gene_variant 0.12
mmpS5 779615 c.-710C>G upstream_gene_variant 0.83
rpsL 781395 c.-165T>C upstream_gene_variant 1.0
fbiC 1303513 p.Val195Met missense_variant 0.15
fbiC 1303956 c.1026A>G synonymous_variant 0.12
fbiC 1304772 c.1842C>T synonymous_variant 0.17
fbiC 1304800 p.Arg624Trp missense_variant 0.15
fbiC 1304838 p.Met636Ile missense_variant 0.14
fbiC 1305200 p.Ala757Val missense_variant 0.18
Rv1258c 1406760 c.580_581insC frameshift_variant 1.0
Rv1258c 1407226 p.Gly39Ser missense_variant 0.11
embR 1416315 c.1033C>A synonymous_variant 0.15
embR 1417029 p.Asp107Asn missense_variant 0.15
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
rrl 1473802 n.145C>T non_coding_transcript_exon_variant 0.17
inhA 1674956 p.Ala252Val missense_variant 0.17
rpsA 1834177 c.636A>C synonymous_variant 1.0
rpsA 1834682 p.Ala381Thr missense_variant 0.11
tlyA 1917972 c.33A>G synonymous_variant 1.0
ndh 2102333 p.Gln237Arg missense_variant 0.15
katG 2154202 p.Asn637Ser missense_variant 0.17
katG 2154724 p.Arg463Leu missense_variant 1.0
PPE35 2167726 p.Val963Met missense_variant 0.13
PPE35 2167926 p.Leu896Ser missense_variant 1.0
PPE35 2167983 p.Gly877Asp missense_variant 0.18
PPE35 2170060 p.Val185Met missense_variant 0.17
Rv1979c 2222308 p.Asp286Gly missense_variant 0.11
Rv1979c 2222330 p.Ser279Pro missense_variant 0.1
Rv1979c 2223171 c.-7T>A upstream_gene_variant 0.12
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
pncA 2289276 c.-36delA upstream_gene_variant 0.2
ahpC 2726584 p.Ala131Gly missense_variant 0.17
ahpC 2726630 c.438C>T synonymous_variant 0.12
folC 2747327 p.Arg91Leu missense_variant 0.18
pepQ 2859472 p.Leu316Pro missense_variant 0.17
pepQ 2860083 c.336C>T synonymous_variant 0.12
ribD 2986928 c.90G>A synonymous_variant 0.22
Rv2752c 3065060 p.Ala378Thr missense_variant 0.13
Rv2752c 3067043 c.-852T>C upstream_gene_variant 0.1
thyX 3067988 c.-43A>C upstream_gene_variant 1.0
thyA 3074358 p.Leu38Phe missense_variant 1.0
thyA 3074618 c.-147T>G upstream_gene_variant 0.4
ald 3086788 c.-32T>C upstream_gene_variant 1.0
Rv3083 3449738 p.His412Arg missense_variant 1.0
fprA 3473996 c.-11_-10insA upstream_gene_variant 1.0
fprA 3474347 p.Ile114Thr missense_variant 0.12
Rv3236c 3612225 p.Ala298Thr missense_variant 0.25
Rv3236c 3612813 p.Thr102Ala missense_variant 1.0
fbiB 3640686 c.-849C>T upstream_gene_variant 0.12
alr 3841546 c.-126C>A upstream_gene_variant 0.13
rpoA 3877881 c.627G>A synonymous_variant 0.25
rpoA 3878694 c.-187A>G upstream_gene_variant 0.11
ddn 3986658 c.-186G>A upstream_gene_variant 0.12
ddn 3986752 c.-92C>A upstream_gene_variant 0.12
ddn 3986753 c.-91G>A upstream_gene_variant 0.12
clpC1 4038395 c.2310C>A synonymous_variant 0.18
clpC1 4039645 p.His354Asp missense_variant 0.22
clpC1 4039654 p.Thr351Ser missense_variant 0.2
clpC1 4039661 c.1044T>C synonymous_variant 0.2
clpC1 4039664 c.1041G>C synonymous_variant 0.2
clpC1 4039667 p.Gln346Tyr missense_variant 0.2
clpC1 4039674 p.Pro344Gln missense_variant 0.18
clpC1 4039676 c.1029G>A synonymous_variant 0.18
clpC1 4039682 c.1023C>T synonymous_variant 0.18
clpC1 4039691 c.1014G>C synonymous_variant 0.14
clpC1 4039714 p.Tyr331His missense_variant 0.11
clpC1 4040195 c.510G>A synonymous_variant 0.2
clpC1 4040315 c.390G>A synonymous_variant 0.2
panD 4043904 c.378A>G synonymous_variant 0.22
embC 4239923 p.Asp21Asn missense_variant 0.14
embC 4240049 c.191delA frameshift_variant 0.14
embC 4241042 p.Asn394Asp missense_variant 0.12
embC 4241184 p.Thr441Met missense_variant 0.14
embA 4242643 c.-590C>T upstream_gene_variant 1.0
embA 4243460 c.228C>T synonymous_variant 1.0
embA 4243671 p.Gly147Ser missense_variant 0.17
embA 4243848 p.Val206Met missense_variant 0.27
embA 4244733 p.Arg501Cys missense_variant 0.2
embA 4244958 p.Ala576Thr missense_variant 0.13
embB 4246980 p.Gly156Asp missense_variant 0.13
embB 4247101 c.588G>A synonymous_variant 0.2
embB 4248121 c.1608G>A synonymous_variant 0.12
embB 4249451 p.Ser980Pro missense_variant 0.1
aftB 4267647 p.Asp397Gly missense_variant 1.0
ubiA 4269387 p.Glu149Asp missense_variant 0.25
aftB 4269606 c.-770T>C upstream_gene_variant 0.15
ethA 4326142 c.1332C>T synonymous_variant 0.13
whiB6 4338268 p.Gly85Asp missense_variant 0.15
whiB6 4338595 c.-75delG upstream_gene_variant 1.0
whiB6 4338603 c.-82C>T upstream_gene_variant 0.12
gid 4407588 c.615A>G synonymous_variant 1.0
gid 4407927 p.Glu92Asp missense_variant 1.0
gid 4407978 c.224delC frameshift_variant 0.1