TB-Profiler result

Run: SRR6855742
Summary

Run ID: SRR6855742

Sample name:

Date: 04-04-2023 17:44:11

Number of reads: 431431

Percentage reads mapped: 99.48

Strain: lineage2.2.1

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
lineage2 East-Asian Beijing RD105 1.0
lineage2.2 East-Asian (Beijing) Beijing-RD207 RD105;RD207 1.0
lineage2.2.1 East-Asian (Beijing) Beijing-RD181 RD105;RD207;RD181 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 6319 c.-983G>A upstream_gene_variant 0.12
gyrA 7362 p.Glu21Gln missense_variant 1.0
gyrA 7585 p.Ser95Thr missense_variant 1.0
gyrA 9304 p.Gly668Asp missense_variant 1.0
fgd1 490603 c.-180G>T upstream_gene_variant 0.14
fgd1 491742 c.960T>C synonymous_variant 1.0
mshA 575323 c.-25G>C upstream_gene_variant 0.17
mshA 575907 p.Ala187Val missense_variant 1.0
ccsA 620625 p.Ile245Met missense_variant 1.0
ccsA 620853 c.963G>C synonymous_variant 0.15
rpoB 760411 p.Arg202His missense_variant 0.22
rpoB 760963 p.Gly386Val missense_variant 0.17
rpoB 761421 p.Asn539Asp missense_variant 0.18
rpoC 763031 c.-339T>C upstream_gene_variant 1.0
rpoC 764051 p.Lys228* stop_gained 0.17
rpoC 764628 p.Lys420Thr missense_variant 0.15
mmpL5 775639 p.Ile948Val missense_variant 1.0
mmpL5 776100 p.Thr794Ile missense_variant 1.0
mmpL5 776182 p.Asp767Asn missense_variant 1.0
mmpL5 777814 p.Tyr223His missense_variant 0.15
mmpS5 779615 c.-710C>G upstream_gene_variant 1.0
rpsL 781395 c.-165T>C upstream_gene_variant 1.0
fbiC 1303267 p.Lys113Glu missense_variant 0.2
fbiC 1305095 p.His722Leu missense_variant 0.12
Rv1258c 1406399 c.942C>A synonymous_variant 0.12
Rv1258c 1406760 c.580_581insC frameshift_variant 1.0
embR 1417350 c.-3G>A upstream_gene_variant 0.12
embR 1417403 c.-56G>A upstream_gene_variant 0.13
atpE 1460920 c.-125T>C upstream_gene_variant 0.15
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
rrs 1472094 n.249T>A non_coding_transcript_exon_variant 0.11
rrs 1472106 n.261G>A non_coding_transcript_exon_variant 0.12
rrs 1472112 n.267C>T non_coding_transcript_exon_variant 0.11
rrs 1472113 n.268T>C non_coding_transcript_exon_variant 0.12
rrs 1472127 n.282C>T non_coding_transcript_exon_variant 0.12
rrs 1472128 n.283G>A non_coding_transcript_exon_variant 0.12
rrs 1472129 n.284G>C non_coding_transcript_exon_variant 0.12
rrs 1472130 n.285G>A non_coding_transcript_exon_variant 0.12
rrs 1472137 n.292G>A non_coding_transcript_exon_variant 0.11
rrs 1472150 n.305T>A non_coding_transcript_exon_variant 0.11
rrs 1472151 n.306C>T non_coding_transcript_exon_variant 0.11
rrs 1472172 n.327T>C non_coding_transcript_exon_variant 0.13
rrl 1473777 n.120T>C non_coding_transcript_exon_variant 0.14
rrl 1474935 n.1278A>T non_coding_transcript_exon_variant 0.14
rrl 1475435 n.1778G>T non_coding_transcript_exon_variant 0.17
inhA 1674162 c.-40C>T upstream_gene_variant 0.18
inhA 1674225 c.24A>G synonymous_variant 0.15
inhA 1674879 c.678T>G synonymous_variant 0.17
inhA 1674942 c.741T>C synonymous_variant 0.12
rpsA 1834177 c.636A>C synonymous_variant 1.0
rpsA 1834759 c.1218A>G synonymous_variant 0.12
tlyA 1917972 c.33A>G synonymous_variant 1.0
ndh 2102617 c.426C>T synonymous_variant 0.15
ndh 2103226 c.-184C>G upstream_gene_variant 1.0
katG 2154724 p.Arg463Leu missense_variant 1.0
katG 2154871 p.Lys414Arg missense_variant 0.11
PPE35 2167926 p.Leu896Ser missense_variant 1.0
PPE35 2168423 c.2190G>T synonymous_variant 0.22
PPE35 2169930 p.Gly228Asp missense_variant 0.17
PPE35 2170321 p.Glu98Lys missense_variant 0.25
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
ahpC 2726301 p.Thr37Ala missense_variant 0.2
folC 2747184 p.Gln139Lys missense_variant 0.29
ribD 2987442 p.Phe202Leu missense_variant 0.14
Rv2752c 3064591 p.Arg534His missense_variant 0.18
Rv2752c 3065045 c.1144_1146dupCTG conservative_inframe_insertion 0.11
ald 3086739 c.-81G>A upstream_gene_variant 1.0
ald 3086788 c.-32T>C upstream_gene_variant 1.0
ald 3087501 p.Ala228Pro missense_variant 0.14
Rv3083 3449792 p.Ala430Val missense_variant 0.11
fprA 3473996 c.-11_-10insA upstream_gene_variant 1.0
Rv3236c 3612813 p.Thr102Ala missense_variant 1.0
fbiA 3640733 p.Thr64Ile missense_variant 0.18
alr 3840209 c.1211delA frameshift_variant 0.2
alr 3840394 p.Met343Leu missense_variant 0.11
rpoA 3878462 p.Asp16Asn missense_variant 0.33
ddn 3987111 c.269delT frameshift_variant 0.33
clpC1 4039280 c.1425G>T synonymous_variant 0.1
clpC1 4039862 p.Asp281Glu missense_variant 0.11
clpC1 4040206 p.Thr167Ala missense_variant 0.22
panD 4044408 c.-127T>C upstream_gene_variant 0.11
embC 4241553 p.Pro564Leu missense_variant 0.2
embA 4242643 c.-590C>T upstream_gene_variant 1.0
embA 4243460 c.228C>T synonymous_variant 1.0
embB 4247748 p.Ser412* stop_gained 0.12
embB 4248897 p.Glu795Gly missense_variant 0.22
aftB 4267458 p.Trp460Leu missense_variant 0.4
aftB 4267647 p.Asp397Gly missense_variant 1.0
aftB 4268694 p.Val48Ala missense_variant 0.4
ubiA 4269290 p.Phe182Leu missense_variant 0.12
ubiA 4269992 c.-160delA upstream_gene_variant 0.14
ethA 4326857 p.Gln206Arg missense_variant 0.11
whiB6 4338595 c.-75delG upstream_gene_variant 1.0
gid 4407588 c.615A>G synonymous_variant 1.0
gid 4407882 c.321T>C synonymous_variant 0.2
gid 4407927 p.Glu92Asp missense_variant 1.0