TB-Profiler result

Run: SRR4035822
Summary

Run ID: SRR4035822

Sample name:

Date: 04-04-2023 07:19:09

Number of reads: 1040434

Percentage reads mapped: 99.47

Strain: lineage4.1.2

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
lineage4 Euro-American LAM;T;S;X;H None 1.0
lineage4.1 Euro-American T;X;H None 0.99
lineage4.1.2 Euro-American T;H 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
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 5184 c.-55delC upstream_gene_variant 0.14
gyrB 5607 p.Val123Asp missense_variant 0.14
gyrA 7362 p.Glu21Gln missense_variant 1.0
gyrA 7515 p.Lys72Glu missense_variant 0.15
gyrA 7585 p.Ser95Thr missense_variant 1.0
gyrA 7685 c.385delT frameshift_variant 0.17
gyrA 8061 p.Arg254Cys missense_variant 1.0
gyrA 8082 p.Glu261* stop_gained 0.14
gyrA 8552 c.1251C>G synonymous_variant 0.12
gyrA 8650 p.Arg450His missense_variant 0.15
gyrA 9304 p.Gly668Asp missense_variant 1.0
fgd1 490924 p.Gly48Ser missense_variant 0.14
fgd1 491011 p.Pro77Ser missense_variant 0.15
fgd1 491026 p.Asn82Asp missense_variant 0.14
fgd1 491591 p.Lys270Met missense_variant 1.0
mshA 575716 p.Tyr123* stop_gained 0.11
ccsA 620341 p.Val151Met missense_variant 0.13
ccsA 620621 p.Val244Ala missense_variant 0.12
rpoB 760115 c.309C>T synonymous_variant 1.0
rpoB 760839 p.Gly345Cys missense_variant 0.15
rpoB 760967 p.Met387Ile missense_variant 0.12
rpoB 763092 p.Val1096Leu missense_variant 0.12
rpoC 763424 p.Asp19Asn missense_variant 0.14
rpoC 764263 c.894G>A synonymous_variant 1.0
rpoC 764858 c.1489T>C synonymous_variant 0.12
rpoC 765150 p.Gly594Glu missense_variant 0.93
rpoC 766407 p.Arg1013His missense_variant 0.13
rpoC 766810 c.3441G>T synonymous_variant 0.13
rpoC 766891 c.3527delT frameshift_variant 0.12
mmpL5 775639 p.Ile948Val missense_variant 1.0
mmpL5 776144 c.2337C>G synonymous_variant 0.15
mmpL5 776154 p.Leu776* stop_gained 0.18
mmpL5 776163 p.Thr773Asn missense_variant 0.12
mmpL5 776180 p.Asp767Glu missense_variant 0.12
mmpL5 776986 p.Phe499Leu missense_variant 0.17
mmpL5 777320 c.1161C>G synonymous_variant 1.0
mmpR5 778058 c.-932G>A upstream_gene_variant 0.13
mmpL5 778089 p.Gly131Val missense_variant 0.14
rpsL 781395 c.-165T>C upstream_gene_variant 1.0
rpsL 781553 c.-7C>T upstream_gene_variant 0.22
rplC 801338 p.Val177Ala missense_variant 0.11
fbiC 1303256 p.Thr109Ile missense_variant 0.14
fbiC 1303488 c.558G>C synonymous_variant 0.11
fbiC 1303671 c.741C>T synonymous_variant 0.15
fbiC 1304762 p.Val611Ala missense_variant 0.12
fbiC 1304786 p.Arg619His missense_variant 0.12
fbiC 1304803 p.Val625Leu missense_variant 0.12
Rv1258c 1406171 c.1170C>G synonymous_variant 0.14
Rv1258c 1407406 c.-66G>A upstream_gene_variant 0.18
embR 1417376 c.-29T>A upstream_gene_variant 0.18
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
rrl 1474952 n.1295A>G non_coding_transcript_exon_variant 0.15
rrl 1475253 n.1600dupC non_coding_transcript_exon_variant 0.15
rrl 1475540 n.1883C>T non_coding_transcript_exon_variant 0.2
rrl 1475562 n.1905C>T non_coding_transcript_exon_variant 0.17
rrl 1475587 n.1930G>C non_coding_transcript_exon_variant 0.18
rrl 1475602 n.1945G>T non_coding_transcript_exon_variant 0.15
rrl 1475686 n.2029C>G non_coding_transcript_exon_variant 0.18
rrl 1475754 n.2097G>A non_coding_transcript_exon_variant 0.13
rrl 1475796 n.2139A>T non_coding_transcript_exon_variant 0.18
rrl 1476011 n.2354A>G non_coding_transcript_exon_variant 0.15
rrl 1476589 n.2932G>A non_coding_transcript_exon_variant 0.15
fabG1 1673872 p.Trp145Arg missense_variant 0.13
inhA 1673880 c.-322C>A upstream_gene_variant 0.14
fabG1 1673922 p.Ile161Met missense_variant 0.11
tlyA 1917972 c.33A>G synonymous_variant 1.0
ndh 2101785 p.Thr420Ala missense_variant 0.11
ndh 2102447 p.Gly199Asp missense_variant 0.12
ndh 2102721 p.Tyr108Asn missense_variant 0.13
ndh 2102809 c.234G>A synonymous_variant 0.13
katG 2154291 c.1821G>A synonymous_variant 0.17
katG 2154520 p.Ala531Val missense_variant 0.18
katG 2154947 p.Ile389Phe missense_variant 0.14
PPE35 2168201 p.Ile804Met missense_variant 0.14
PPE35 2168206 p.Pro803Ser missense_variant 0.14
PPE35 2169196 p.Pro473Ser missense_variant 0.14
PPE35 2169207 p.Gly469Glu missense_variant 0.14
PPE35 2169211 p.Pro468Ser missense_variant 0.14
Rv1979c 2222739 c.426C>A synonymous_variant 0.21
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
pncA 2289592 c.-351T>C upstream_gene_variant 0.22
pncA 2289637 c.-396G>A upstream_gene_variant 0.17
kasA 2518076 c.-39C>T upstream_gene_variant 1.0
kasA 2518193 p.Pro27Ser missense_variant 0.13
kasA 2518654 c.540C>T synonymous_variant 0.13
kasA 2519232 p.Tyr373Cys missense_variant 0.11
eis 2714602 p.Val244Ala missense_variant 0.11
eis 2715157 p.Val59Asp missense_variant 0.17
folC 2746453 c.1146G>T synonymous_variant 0.2
folC 2747004 p.Ile199Val missense_variant 0.12
folC 2747091 p.Val170Leu missense_variant 0.18
folC 2747474 p.Arg42His missense_variant 0.14
folC 2747494 p.Asp35Glu missense_variant 0.13
pepQ 2860158 c.261C>A synonymous_variant 0.17
pepQ 2860168 p.Ala84Asp missense_variant 0.15
thyX 3067236 p.Asp237Gly missense_variant 0.11
thyA 3073819 p.Leu218Gln missense_variant 0.18
thyA 3073827 p.Gln215His missense_variant 0.17
thyA 3073921 p.Leu184Pro missense_variant 0.14
thyA 3074335 p.Thr46Asn missense_variant 0.14
ald 3086788 c.-32T>C upstream_gene_variant 1.0
ald 3087072 p.Leu85Val missense_variant 0.13
Rv3083 3449456 p.Thr318Asn missense_variant 0.25
fprA 3473996 c.-11_-10insA upstream_gene_variant 1.0
Rv3236c 3611974 c.1143A>C synonymous_variant 1.0
Rv3236c 3612165 p.Val318Met missense_variant 0.17
Rv3236c 3612213 p.Ala302Ser missense_variant 0.15
Rv3236c 3612753 p.Ala122Ser missense_variant 0.13
fbiB 3642151 p.Lys206Ile missense_variant 0.13
fbiB 3642315 c.781A>C synonymous_variant 0.12
fbiB 3642324 p.Arg264Gly missense_variant 0.12
alr 3841397 c.24C>T synonymous_variant 0.2
alr 3841592 c.-172A>T upstream_gene_variant 0.14
rpoA 3878108 c.400C>T synonymous_variant 0.18
rpoA 3878641 c.-134C>G upstream_gene_variant 0.22
embC 4239941 c.79C>A synonymous_variant 0.23
embC 4239976 c.114G>A synonymous_variant 0.2
embC 4240917 p.Ala352Val missense_variant 0.15
embC 4241945 p.Arg695Gly missense_variant 0.12
embA 4242643 c.-590C>T upstream_gene_variant 0.89
embC 4242803 p.Val981Leu missense_variant 1.0
embA 4242868 c.-365C>T upstream_gene_variant 0.2
embA 4243163 c.-70C>G upstream_gene_variant 0.12
embA 4243364 p.Phe44Leu missense_variant 0.18
embA 4243398 p.Thr56Ala missense_variant 0.1
embA 4243469 p.Ile79Met missense_variant 0.11
embA 4245074 c.1842G>C synonymous_variant 0.13
embA 4245211 p.Leu660Gln missense_variant 0.14
embB 4246178 c.-336G>A upstream_gene_variant 0.17
embB 4248243 p.Val577Asp missense_variant 0.14
embB 4249493 p.Phe994Ile missense_variant 0.13
aftB 4266987 p.Val617Asp missense_variant 0.18
aftB 4267787 c.1050G>C synonymous_variant 0.12
aftB 4268350 p.Arg163Trp missense_variant 0.14
ubiA 4269229 p.Thr202Ser missense_variant 0.11
ethA 4326257 p.Leu406Ser missense_variant 0.11
ethA 4326327 p.Thr383Pro missense_variant 0.14
ethR 4326667 c.-882C>T upstream_gene_variant 0.13
ethA 4328299 c.-826A>G upstream_gene_variant 0.11
ethA 4328411 c.-938G>A upstream_gene_variant 0.13
whiB6 4338179 p.Ser115Thr missense_variant 0.17
whiB6 4338595 c.-75delG upstream_gene_variant 1.0