TB-Profiler result

Run: SRR998661
Summary

Run ID: SRR998661

Sample name:

Date: 04-04-2023 23:30:21

Number of reads: 528598

Percentage reads mapped: 98.93

Strain: lineage6.3;lineage4

Drug-resistance: MDR-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 0.78
lineage6.3 West-Africa 2 AFRI_1 RD702 0.12
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 761110 p.Asp435Val missense_variant 0.45 rifampicin
rpoB 761155 p.Ser450Phe missense_variant 0.29 rifampicin
katG 2155168 p.Ser315Thr missense_variant 0.5 isoniazid
embB 4248003 p.Gln497Arg missense_variant 0.33 ethambutol
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 6446 p.Ala403Ser missense_variant 0.43
gyrA 7362 p.Glu21Gln missense_variant 1.0
gyrA 7585 p.Ser95Thr missense_variant 1.0
gyrA 8720 p.Glu473Asp missense_variant 0.13
gyrA 9304 p.Gly668Asp missense_variant 1.0
gyrA 9591 p.Gly764Arg missense_variant 0.22
gyrA 9810 p.Gly837Cys missense_variant 0.15
fgd1 491668 p.Lys296Glu missense_variant 0.3
fgd1 491742 c.960T>C synonymous_variant 0.14
rpoB 760623 p.Arg273Gly missense_variant 0.12
rpoB 760969 p.Ser388Leu missense_variant 0.22
rpoB 761384 c.1579delG frameshift_variant 0.15
rpoB 761723 p.Glu639Asp missense_variant 0.6
rpoB 762039 p.His745Tyr missense_variant 0.56
rpoB 762960 p.Gly1052Cys missense_variant 0.18
rpoC 763031 c.-339T>C upstream_gene_variant 0.25
rpoC 765150 p.Gly594Glu missense_variant 0.2
rpoC 765703 p.Trp778Cys missense_variant 0.12
rpoC 766912 c.3543C>T synonymous_variant 0.2
rpoC 766930 p.Glu1187Asp missense_variant 0.22
mmpL5 775639 p.Ile948Val missense_variant 1.0
mmpL5 775841 c.2640G>A synonymous_variant 0.18
mmpL5 776597 p.Asp628Glu missense_variant 0.22
mmpL5 777986 c.495C>A synonymous_variant 0.18
mmpR5 778298 c.-692C>T upstream_gene_variant 0.25
mmpL5 778579 c.-99C>G upstream_gene_variant 0.18
rpsL 781395 c.-165T>C upstream_gene_variant 1.0
rpsL 781421 c.-139C>A upstream_gene_variant 0.2
rpsL 781931 c.372C>A synonymous_variant 0.14
rplC 801232 p.Gln142Lys missense_variant 0.14
fbiC 1303555 p.Pro209Thr missense_variant 0.14
Rv1258c 1407412 c.-73delC upstream_gene_variant 0.14
embR 1416388 c.960A>G synonymous_variant 0.17
atpE 1461251 c.207G>T synonymous_variant 0.44
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
rrl 1475565 n.1908G>C non_coding_transcript_exon_variant 0.1
fabG1 1673257 c.-183C>T upstream_gene_variant 0.22
inhA 1674434 p.Val78Ala missense_variant 0.27
rpsA 1833636 p.Tyr32Phe missense_variant 0.12
rpsA 1834812 p.Arg424Gln missense_variant 0.2
tlyA 1917972 c.33A>G synonymous_variant 1.0
tlyA 1918254 c.315C>T synonymous_variant 0.29
ndh 2102694 p.Val117Ile missense_variant 0.27
ndh 2103179 c.-137C>A upstream_gene_variant 0.2
katG 2154724 p.Arg463Leu missense_variant 0.35
katG 2155402 p.Gly237Asp missense_variant 0.14
katG 2155503 c.609C>T synonymous_variant 0.2
PPE35 2169502 p.Met371Val missense_variant 0.18
PPE35 2169609 p.Gly335Asp missense_variant 0.12
PPE35 2169715 p.Gly300Ser missense_variant 0.31
Rv1979c 2221746 c.1416_1418dupCCG disruptive_inframe_insertion 0.45
Rv1979c 2222308 p.Asp286Gly missense_variant 0.27
Rv1979c 2222601 p.Gln188His missense_variant 0.12
Rv1979c 2222679 c.486C>A synonymous_variant 0.17
Rv1979c 2222852 p.Ala105Thr missense_variant 0.38
Rv1979c 2223106 p.Val20Asp missense_variant 0.13
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
pncA 2289590 c.-349G>T upstream_gene_variant 0.2
kasA 2518132 c.18C>T synonymous_variant 0.38
eis 2714688 p.Phe215Leu missense_variant 0.2
eis 2715126 c.207G>A synonymous_variant 0.2
ahpC 2726408 c.216T>C synonymous_variant 0.14
ahpC 2726416 p.Phe75Tyr missense_variant 0.14
ahpC 2726418 c.226_227insC frameshift_variant 0.17
folC 2747402 p.Ser66* stop_gained 0.12
pepQ 2860504 c.-86A>T upstream_gene_variant 0.15
pepQ 2860605 c.-187C>T upstream_gene_variant 0.12
ribD 2987492 p.Tyr218* stop_gained 0.15
thyX 3067517 p.Tyr143* stop_gained 0.22
ald 3086788 c.-32T>C upstream_gene_variant 0.9
ald 3087084 c.266delA frameshift_variant 0.28
ald 3087693 p.Asp292Asn missense_variant 0.14
Rv3083 3448567 p.His22Asp missense_variant 0.7
Rv3083 3449301 c.798G>T synonymous_variant 0.15
Rv3083 3449781 c.1278G>A synonymous_variant 0.2
fprA 3473996 c.-11_-10insA upstream_gene_variant 1.0
fprA 3474830 p.Pro275Gln missense_variant 0.17
fprA 3475071 p.Tyr355* stop_gained 0.17
fprA 3475159 p.Asn385Asp missense_variant 0.31
alr 3840467 c.954G>T synonymous_variant 0.13
rpoA 3877696 p.Thr271Ile missense_variant 0.2
rpoA 3878656 c.-149C>A upstream_gene_variant 0.12
ddn 3986701 c.-143T>C upstream_gene_variant 0.15
clpC1 4038285 p.Trp807* stop_gained 0.29
embC 4240247 p.Asp129Tyr missense_variant 0.13
embC 4240671 p.Thr270Ile missense_variant 0.5
embC 4240814 p.Gly318Ser missense_variant 0.27
embC 4241843 p.Leu661Ile missense_variant 0.24
embA 4242643 c.-590C>T upstream_gene_variant 1.0
embC 4242803 p.Val981Leu missense_variant 0.46
embA 4243323 p.Val31Ile missense_variant 0.13
embA 4243540 p.Ala103Asp missense_variant 0.17
embA 4244220 c.988C>T synonymous_variant 0.67
embA 4244699 c.1467C>A synonymous_variant 0.15
embB 4247244 p.Gly244Glu missense_variant 0.13
embB 4247646 p.Glu378Ala missense_variant 0.33
embB 4249776 p.Leu1088Pro missense_variant 0.15
aftB 4267036 p.Arg601Ser missense_variant 0.2
aftB 4267272 p.Lys522Arg missense_variant 0.54
aftB 4268477 c.360C>T synonymous_variant 0.33
aftB 4269351 c.-515C>T upstream_gene_variant 0.44
ubiA 4269387 p.Glu149Asp missense_variant 0.33
aftB 4269522 c.-686C>T upstream_gene_variant 0.29
ethA 4326465 p.Ile337Val missense_variant 0.47
ethA 4326558 p.Arg306Ser missense_variant 0.17
ethR 4326739 c.-810G>C upstream_gene_variant 0.36
ethA 4328004 c.-531C>T upstream_gene_variant 0.5
whiB6 4338478 p.Phe15Ser missense_variant 0.14
whiB6 4338595 c.-75delG upstream_gene_variant 1.0
gid 4407588 c.615A>G synonymous_variant 0.3