TB-Profiler result

Run: SRR21677866
Summary

Run ID: SRR21677866

Sample name:

Date: 04-04-2023 02:48:55

Number of reads: 574698

Percentage reads mapped: 98.52

Strain: lineage4.8

Drug-resistance: HR-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
lineage4 Euro-American LAM;T;S;X;H None 1.0
lineage4.8 Euro-American (mainly T) T1;T2;T3;T5 RD219 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
tlyA 1918205 c.269delG frameshift_variant 0.18 capreomycin
tlyA 1918591 c.653delT frameshift_variant 0.11 capreomycin, capreomycin
katG 2154595 c.1515_1516delGG frameshift_variant 0.11 isoniazid
gid 4407640 c.562dupG frameshift_variant 0.15 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
gyrB 5539 p.Met100Ile missense_variant 0.13
gyrA 7360 p.Ile20Thr missense_variant 0.11
gyrA 7362 p.Glu21Gln missense_variant 1.0
gyrA 7586 p.Ser95Arg missense_variant 0.29
gyrA 8480 c.1179C>T synonymous_variant 0.11
gyrA 8905 p.Arg535His missense_variant 0.22
fgd1 490817 p.Ala12Asp missense_variant 0.13
fgd1 491523 c.741G>T synonymous_variant 0.15
mshA 575382 p.Leu12Ser missense_variant 0.15
mshA 575712 p.Lys122Thr missense_variant 0.12
mshA 576398 p.Tyr351Asp missense_variant 0.2
ccsA 620029 p.Leu47Met missense_variant 0.14
ccsA 620078 p.Ile63Thr missense_variant 0.14
ccsA 620684 p.Glu265Gly missense_variant 0.14
rpoB 760432 p.Asp209Gly missense_variant 0.11
rpoB 761396 c.1590G>A synonymous_variant 0.33
rpoB 761563 p.Ala586Glu missense_variant 0.33
rpoB 761709 p.Val635Ile missense_variant 0.22
rpoB 762113 p.Asn769Lys missense_variant 0.11
rpoB 762158 c.2352G>A synonymous_variant 0.12
rpoC 764337 p.Glu323Gly missense_variant 0.12
rpoC 765351 p.Ala661Glu missense_variant 0.12
rpoC 766110 p.Pro914Arg missense_variant 0.15
rpoC 766244 c.2876delA frameshift_variant 0.11
rpoC 766317 p.Met983Thr missense_variant 0.12
rpoC 766470 p.Leu1034Pro missense_variant 0.11
mmpL5 775639 p.Ile948Val missense_variant 1.0
mmpL5 775926 c.2554delC frameshift_variant 0.12
mmpL5 776077 p.Ala802Ser missense_variant 0.14
mmpL5 777350 c.1131G>T synonymous_variant 0.14
mmpL5 777407 c.1074C>A synonymous_variant 0.15
mmpL5 777462 p.Ala340Val missense_variant 0.25
mmpL5 777610 p.Leu291Phe missense_variant 0.14
mmpL5 778365 p.Trp39Ser missense_variant 0.12
mmpS5 778643 c.262delT frameshift_variant 0.12
mmpL5 778953 c.-473A>G upstream_gene_variant 0.1
mmpR5 779275 c.288delG frameshift_variant 0.12
rpsL 781395 c.-165T>C upstream_gene_variant 1.0
rpsL 781561 c.2T>A start_lost 0.11
rplC 801370 p.Glu188* stop_gained 0.12
fbiC 1302772 c.-159T>G upstream_gene_variant 0.13
fbiC 1302914 c.-17A>C upstream_gene_variant 0.12
fbiC 1303171 p.Arg81Gly missense_variant 0.22
fbiC 1304614 p.Cys562Gly missense_variant 0.13
fbiC 1304804 p.Val625Ala missense_variant 0.13
fbiC 1304897 p.Leu656Pro missense_variant 0.12
fbiC 1305416 p.Thr829Asn missense_variant 0.12
Rv1258c 1406874 p.Val156Asp missense_variant 0.17
Rv1258c 1407528 c.-188C>T upstream_gene_variant 0.22
embR 1417120 c.228G>T synonymous_variant 0.15
atpE 1461049 p.Asp2Ala missense_variant 0.13
atpE 1461052 p.Pro3Leu missense_variant 0.18
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
rrl 1473416 n.-242_-241insC upstream_gene_variant 0.33
rrl 1474001 n.344C>T non_coding_transcript_exon_variant 1.0
rrl 1474519 n.862G>A non_coding_transcript_exon_variant 0.12
rrl 1474729 n.1072G>T non_coding_transcript_exon_variant 0.14
rrl 1475046 n.1391_1395delGCATG non_coding_transcript_exon_variant 0.22
rrl 1475472 n.1815T>C non_coding_transcript_exon_variant 0.2
rrl 1476056 n.2399G>A non_coding_transcript_exon_variant 0.12
fabG1 1673233 c.-207T>G upstream_gene_variant 1.0
inhA 1673913 c.-289C>T upstream_gene_variant 0.12
inhA 1674406 p.Glu69Gln missense_variant 0.18
inhA 1674603 c.402G>A synonymous_variant 0.13
inhA 1674691 p.Ala164Ser missense_variant 0.11
inhA 1674814 p.Gly205Arg missense_variant 0.18
rpsA 1834851 p.Ala437Asp missense_variant 0.12
rpsA 1834929 p.Ser463* stop_gained 0.14
rpsA 1834937 p.Ser466Arg missense_variant 0.25
tlyA 1917972 c.33A>G synonymous_variant 1.0
ndh 2101896 p.Gly383Cys missense_variant 0.12
ndh 2102147 p.Arg299Leu missense_variant 0.13
ndh 2102353 c.690G>A synonymous_variant 0.15
katG 2154116 p.Ile666Val missense_variant 0.17
katG 2154128 p.Leu662Ile missense_variant 0.2
katG 2154840 c.1272G>T synonymous_variant 0.25
PPE35 2167766 c.2847C>G synonymous_variant 0.13
PPE35 2168149 p.Pro822Ser missense_variant 1.0
PPE35 2168330 c.2282delT frameshift_variant 0.12
PPE35 2168504 c.2109C>A synonymous_variant 0.2
PPE35 2168822 c.1791G>A synonymous_variant 0.15
PPE35 2168914 p.Pro567Thr missense_variant 0.11
Rv1979c 2222790 p.Lys125Asn missense_variant 0.2
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
pncA 2289301 c.-61dupC upstream_gene_variant 0.4
pncA 2289694 c.-453G>T upstream_gene_variant 0.11
pncA 2289744 c.-503G>T upstream_gene_variant 0.12
pncA 2289881 c.-640G>A upstream_gene_variant 0.11
kasA 2518108 c.-7A>G upstream_gene_variant 0.25
kasA 2518568 p.Ala152Ser missense_variant 0.14
kasA 2518999 c.885G>T synonymous_variant 0.12
eis 2714810 p.Phe175Ile missense_variant 0.18
eis 2715432 c.-100C>T upstream_gene_variant 0.11
eis 2715440 c.-108A>C upstream_gene_variant 0.1
folC 2746717 c.882C>T synonymous_variant 0.12
folC 2746880 p.Lys240Arg missense_variant 0.25
folC 2747192 p.Gln136Leu missense_variant 0.14
folC 2747448 p.Ser51Gly missense_variant 0.14
folC 2747762 c.-164G>T upstream_gene_variant 0.12
pepQ 2859662 p.Val253Leu missense_variant 0.11
pepQ 2859722 p.Met233Val missense_variant 0.15
pepQ 2859889 p.Glu177Gly missense_variant 0.13
ribD 2987197 p.Val120Ala missense_variant 0.15
Rv2752c 3064591 p.Arg534His missense_variant 0.18
Rv2752c 3064935 c.1257A>G synonymous_variant 0.12
Rv2752c 3065575 p.Ala206Asp missense_variant 0.12
Rv2752c 3065583 c.609G>A synonymous_variant 0.12
Rv2752c 3066110 p.Gly28Ser missense_variant 0.17
thyX 3068047 c.-102C>G upstream_gene_variant 0.1
thyA 3073703 p.Ile257Val missense_variant 0.11
thyA 3073979 p.Gln165Glu missense_variant 0.22
thyA 3074063 p.Glu137Lys missense_variant 0.17
ald 3087323 c.504G>T synonymous_variant 0.14
ald 3087729 p.Ser304Pro missense_variant 0.13
ald 3087923 p.Ser368Arg missense_variant 0.12
ald 3087935 c.1116A>T stop_lost&splice_region_variant 0.12
fbiD 3339392 p.Leu92Pro missense_variant 0.14
fbiD 3339637 p.Gly174Arg missense_variant 0.18
Rv3083 3448497 c.-7T>A upstream_gene_variant 1.0
Rv3083 3448500 c.-4A>G upstream_gene_variant 1.0
Rv3083 3448501 c.-3G>T upstream_gene_variant 1.0
fprA 3474340 p.Leu112Met missense_variant 0.12
fprA 3474903 c.897C>T synonymous_variant 0.11
fprA 3475038 c.1032C>A synonymous_variant 0.17
fprA 3475046 p.Arg347Gln missense_variant 0.17
Rv3236c 3612304 c.813C>A synonymous_variant 0.13
Rv3236c 3612386 p.Ala244Gly missense_variant 0.12
fbiA 3640840 p.Asp100Asn missense_variant 0.11
fbiB 3641683 p.Ser50Ile missense_variant 0.12
fbiB 3642674 c.1140C>G synonymous_variant 0.25
alr 3840642 p.Leu260Pro missense_variant 0.12
alr 3840965 c.456G>A synonymous_variant 0.12
alr 3840983 c.438C>A synonymous_variant 0.15
alr 3841327 p.Pro32Ser missense_variant 0.11
alr 3841612 c.-193_-192insC upstream_gene_variant 0.15
rpoA 3877832 p.Asn226Asp missense_variant 0.2
rpoA 3878256 c.252G>T synonymous_variant 0.14
clpC1 4038239 c.2466T>A synonymous_variant 0.15
clpC1 4038448 p.Asp753Asn missense_variant 0.17
clpC1 4039331 c.1374C>T synonymous_variant 0.2
clpC1 4039729 p.Asp326Asn missense_variant 1.0
clpC1 4039841 p.Glu288Asp missense_variant 0.14
clpC1 4040187 p.Gln173Pro missense_variant 0.14
panD 4044456 c.-175T>C upstream_gene_variant 0.15
embC 4240742 p.Asp294Tyr missense_variant 0.13
embC 4241730 p.Ala623Asp missense_variant 0.17
embC 4242068 p.Val736Leu missense_variant 0.14
embC 4242258 p.Val799Gly missense_variant 0.12
embA 4242643 c.-590C>T upstream_gene_variant 1.0
embC 4243063 p.Tyr1067* stop_gained 0.11
embA 4243517 c.285C>T synonymous_variant 0.18
embA 4244159 c.927G>C synonymous_variant 0.12
embA 4244268 c.1036C>A synonymous_variant 0.18
embA 4244305 p.Arg358Leu missense_variant 0.17
embA 4244424 c.1192C>A synonymous_variant 0.2
embA 4245264 p.Asp678Tyr missense_variant 0.11
embA 4245630 p.Asn800Asp missense_variant 0.15
embA 4245843 p.Val871Phe missense_variant 0.11
embB 4246537 c.28delA frameshift_variant 0.11
embB 4248296 p.His595Asn missense_variant 0.2
embB 4249293 p.Lys927Arg missense_variant 0.11
aftB 4267974 p.Ser288* stop_gained 0.14
aftB 4267992 p.Thr282Lys missense_variant 0.11
aftB 4268405 c.432G>T synonymous_variant 0.2
aftB 4268603 c.234C>G synonymous_variant 0.14
aftB 4268661 p.Thr59Asn missense_variant 0.14
aftB 4269096 c.-260C>G upstream_gene_variant 0.25
ethA 4326134 p.Pro447Arg missense_variant 0.14
ethA 4326258 c.1216T>C synonymous_variant 0.14
ethA 4327487 c.-14G>T upstream_gene_variant 0.12
whiB6 4338212 p.Tyr104His missense_variant 0.12
whiB6 4338507 c.15C>T synonymous_variant 0.12
whiB6 4338595 c.-75delG upstream_gene_variant 1.0
gid 4407677 p.Arg176Cys missense_variant 0.13
Rv3083 3448507 c.5_*1408del frameshift_variant&stop_lost&splice_region_variant 1.0