TB-Profiler result

Run: SRR2100044
Summary

Run ID: SRR2100044

Sample name:

Date: 03-04-2023 22:42:55

Number of reads: 2083382

Percentage reads mapped: 99.46

Strain: lineage3

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
lineage3 East-African-Indian CAS RD750 0.99
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 6498 p.Ala420Val missense_variant 0.13
gyrA 7278 c.-24C>A upstream_gene_variant 0.17
gyrA 7362 p.Glu21Gln missense_variant 1.0
gyrA 7585 p.Ser95Thr missense_variant 1.0
gyrA 7777 p.Arg159Leu missense_variant 0.15
gyrA 7779 p.Val160Leu missense_variant 0.18
gyrA 7787 p.Glu162Asp missense_variant 0.18
gyrA 8498 c.1199_1203delCGCTG frameshift_variant 0.22
gyrA 9304 p.Gly668Asp missense_variant 1.0
gyrA 9535 p.Arg745His missense_variant 0.13
fgd1 490853 p.Ala24Asp missense_variant 0.13
fgd1 490862 p.Ala27Asp missense_variant 0.12
fgd1 491409 c.627G>T synonymous_variant 0.15
fgd1 491742 c.960T>C synonymous_variant 1.0
mshA 575912 p.Ala189Ser missense_variant 0.17
mshA 576150 p.Val268Ala missense_variant 0.29
ccsA 620107 p.Asp73Tyr missense_variant 0.12
ccsA 620120 p.Gly77Glu missense_variant 0.13
ccsA 620279 p.Arg130Leu missense_variant 0.17
rpoC 762434 c.-936T>G upstream_gene_variant 1.0
rpoC 762977 c.-393C>T upstream_gene_variant 0.13
rpoC 763031 c.-339T>C upstream_gene_variant 1.0
rpoB 763042 c.3238_3240delCAG conservative_inframe_deletion 0.12
rpoC 764454 p.Ala362Glu missense_variant 0.18
rpoC 766648 p.Asp1093Glu missense_variant 0.25
mmpL5 775639 p.Ile948Val missense_variant 1.0
mmpL5 776100 p.Thr794Ile missense_variant 1.0
mmpR5 779115 p.Trp42Cys missense_variant 0.14
rpsL 781395 c.-165T>C upstream_gene_variant 1.0
fbiC 1303333 p.Gly135Ser missense_variant 0.12
fbiC 1304024 p.Val365Asp missense_variant 0.25
fbiC 1304281 p.Ala451Ser missense_variant 0.4
fbiC 1304767 p.Gly613Ser missense_variant 0.17
Rv1258c 1406128 c.1213C>T synonymous_variant 0.12
Rv1258c 1407211 p.Ala44Ser missense_variant 0.17
Rv1258c 1407362 c.-22G>A upstream_gene_variant 0.18
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
rrs 1472857 n.1012A>G non_coding_transcript_exon_variant 1.0
rrl 1473949 n.292C>T non_coding_transcript_exon_variant 0.25
rrl 1474278 n.621G>T non_coding_transcript_exon_variant 0.15
rrl 1475858 n.2201T>A non_coding_transcript_exon_variant 0.2
fabG1 1674059 c.625_629dupAAGCG frameshift_variant 0.14
inhA 1674653 p.Pro151Leu missense_variant 0.2
tlyA 1917972 c.33A>G synonymous_variant 1.0
tlyA 1918235 p.Val99Glu missense_variant 0.4
tlyA 1918430 p.Leu164Ser missense_variant 0.18
ndh 2103165 c.-123G>A upstream_gene_variant 0.12
katG 2154724 p.Arg463Leu missense_variant 1.0
katG 2154926 p.Arg396Ser missense_variant 0.22
katG 2155004 p.Gly370Arg missense_variant 0.17
katG 2155062 c.1050T>C synonymous_variant 0.15
PPE35 2167656 p.Thr986Met missense_variant 0.18
PPE35 2167926 p.Leu896Ser missense_variant 1.0
PPE35 2170084 p.Gly177Ser missense_variant 0.2
PPE35 2170373 p.Ala80Thr missense_variant 0.12
Rv1979c 2222418 c.747C>T synonymous_variant 0.17
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
pncA 2289365 c.-125delC upstream_gene_variant 1.0
pncA 2289698 c.-458delT upstream_gene_variant 0.2
pncA 2290027 c.-786G>T upstream_gene_variant 0.14
pncA 2290032 c.-791A>G upstream_gene_variant 0.12
ahpC 2726105 c.-88G>A upstream_gene_variant 1.0
folC 2746502 c.1095_1096delGC frameshift_variant 0.2
folC 2747334 p.Leu89Val missense_variant 0.11
folC 2747481 p.Glu40Lys missense_variant 0.15
pepQ 2859877 p.Leu181Pro missense_variant 0.4
pepQ 2860155 c.264C>A synonymous_variant 0.29
pepQ 2860469 c.-51C>A upstream_gene_variant 0.17
ribD 2987146 p.Arg103His missense_variant 0.2
ribD 2987424 p.Pro196Thr missense_variant 0.18
Rv2752c 3065168 p.Pro342Ser missense_variant 0.17
Rv2752c 3065332 p.Ile287Thr missense_variant 0.12
ald 3086788 c.-32T>C upstream_gene_variant 1.0
ald 3087615 p.Asp266Tyr missense_variant 0.12
ald 3087900 p.Val361Leu missense_variant 0.18
fbiD 3339320 p.Ala68Val missense_variant 0.12
fprA 3473996 c.-11_-10insA upstream_gene_variant 1.0
whiB7 3568535 p.Arg49Gly missense_variant 0.13
whiB7 3568645 p.Arg12Ile missense_variant 0.14
Rv3236c 3612892 c.225G>T synonymous_variant 0.13
Rv3236c 3613021 c.96G>A synonymous_variant 0.17
Rv3236c 3613156 c.-40A>G upstream_gene_variant 0.14
Rv3236c 3613250 c.-134G>T upstream_gene_variant 0.12
Rv3236c 3613306 c.-190G>T upstream_gene_variant 0.14
fbiB 3641886 c.352T>C synonymous_variant 0.13
fbiB 3641936 c.402C>A synonymous_variant 0.15
fbiB 3642098 c.564G>A synonymous_variant 1.0
alr 3840636 p.Pro262Gln missense_variant 1.0
alr 3840885 p.Leu179Ser missense_variant 0.25
alr 3840931 p.Arg164Cys missense_variant 0.25
alr 3841076 c.345G>T synonymous_variant 0.18
panD 4044295 c.-14C>A upstream_gene_variant 0.18
embC 4241335 p.Gln491His missense_variant 1.0
embC 4241552 p.Pro564Thr missense_variant 0.15
embC 4242075 p.Arg738Gln missense_variant 0.96
embC 4242308 p.Thr816Ala missense_variant 0.2
embA 4242643 c.-590C>T upstream_gene_variant 1.0
embA 4244201 p.Trp323Cys missense_variant 0.15
embA 4245405 p.Ala725Ser missense_variant 0.12
embA 4245883 p.Gly884Asp missense_variant 1.0
embA 4245939 p.Gly903Ser missense_variant 0.25
embB 4246940 p.Pro143Ser missense_variant 0.22
embB 4247438 p.Val309Ile missense_variant 0.2
embB 4248370 c.1857G>T synonymous_variant 0.2
embB 4248561 p.Ala683Val missense_variant 1.0
embB 4249433 p.Leu974Met missense_variant 0.22
embB 4249718 p.Thr1069Ser missense_variant 0.2
aftB 4266974 c.1863C>T synonymous_variant 0.14
aftB 4268223 p.Arg205Leu missense_variant 0.13
aftB 4268277 p.Pro187Leu missense_variant 0.12
aftB 4268677 p.Arg54* stop_gained 0.18
whiB6 4338301 p.Gly74Val missense_variant 0.12
whiB6 4338595 c.-75delG upstream_gene_variant 1.0
gid 4407588 c.615A>G synonymous_variant 1.0