TB-Profiler result

Run: SRR4035764

Summary

Run ID: SRR4035764

Sample name:

Date: 04-04-2023 07:17:04

Number of reads: 1222168

Percentage reads mapped: 99.5

Strain: lineage4.1.2

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
lineage4.1 Euro-American T;X;H None 1.0
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
katG 2155793 p.Trp107Arg missense_variant 0.14 isoniazid
pncA 2288817 p.Thr142Met missense_variant 0.2 pyrazinamide
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 6077 p.Gly280Ser missense_variant 0.14
gyrB 6100 c.861G>C synonymous_variant 0.14
gyrB 7118 p.Asp627Asn missense_variant 0.14
gyrA 7362 p.Glu21Gln missense_variant 1.0
gyrA 7585 p.Ser95Thr missense_variant 1.0
gyrA 8061 p.Arg254Cys missense_variant 1.0
gyrA 9304 p.Gly668Asp missense_variant 1.0
fgd1 490701 c.-82A>G upstream_gene_variant 0.12
fgd1 490853 p.Ala24Val missense_variant 0.14
fgd1 491311 p.Gly177Cys missense_variant 0.18
fgd1 491363 p.Cys194Tyr missense_variant 0.13
fgd1 491591 p.Lys270Met missense_variant 1.0
mshA 576188 p.Asp281His missense_variant 0.2
rpoB 760115 c.309C>T synonymous_variant 1.0
rpoB 760353 p.Glu183Lys missense_variant 0.14
rpoB 762987 p.Arg1061Trp missense_variant 0.13
rpoC 763335 c.-35A>G upstream_gene_variant 0.18
rpoC 763351 c.-19T>A upstream_gene_variant 0.17
rpoC 763837 c.468G>C synonymous_variant 0.12
rpoC 763986 p.Arg206Pro missense_variant 0.13
rpoC 764263 c.894G>A synonymous_variant 1.0
rpoC 765150 p.Gly594Glu missense_variant 1.0
rpoC 765216 p.Ala616Val missense_variant 0.13
rpoC 765923 p.Asn852Asp missense_variant 0.11
rpoC 766726 p.His1119Gln missense_variant 0.13
rpoC 766753 c.3384C>A synonymous_variant 0.12
mmpL5 775639 p.Ile948Val missense_variant 1.0
mmpL5 777283 p.Leu400Met missense_variant 0.12
mmpL5 777320 c.1161C>G synonymous_variant 1.0
rpsL 781395 c.-165T>C upstream_gene_variant 1.0
rpsL 781573 p.Gln5Leu missense_variant 0.14
rplC 800970 c.162T>C synonymous_variant 0.11
rplC 801438 p.Ser210Arg missense_variant 0.13
rplC 801446 p.Lys213Ile missense_variant 0.15
embR 1417288 p.Gln20His missense_variant 0.13
atpE 1460909 c.-136C>T upstream_gene_variant 0.13
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
rrs 1472416 n.571C>A non_coding_transcript_exon_variant 0.14
rrs 1472432 n.587C>T non_coding_transcript_exon_variant 0.13
rrs 1472730 n.885A>T non_coding_transcript_exon_variant 0.18
rrl 1473690 n.33T>A non_coding_transcript_exon_variant 0.22
rrl 1473693 n.36G>A non_coding_transcript_exon_variant 0.22
rrl 1473708 n.51G>A non_coding_transcript_exon_variant 0.2
rrl 1474248 n.591A>T non_coding_transcript_exon_variant 0.4
rrl 1475254 n.1597C>T non_coding_transcript_exon_variant 0.15
rrl 1475735 n.2078T>C non_coding_transcript_exon_variant 0.15
rrl 1475745 n.2088A>T non_coding_transcript_exon_variant 0.15
fabG1 1673482 p.Ser15Thr missense_variant 0.14
tlyA 1917972 c.33A>G synonymous_variant 1.0
ndh 2102042 p.Gln334Arg missense_variant 0.12
ndh 2103080 c.-38C>G upstream_gene_variant 0.12
katG 2154642 c.1470C>T synonymous_variant 0.17
katG 2154769 p.Asp448Gly missense_variant 0.14
katG 2156167 c.-56T>C upstream_gene_variant 0.12
katG 2156437 c.-326C>G upstream_gene_variant 0.17
katG 2156486 c.-375A>G upstream_gene_variant 0.1
PPE35 2170006 p.Ile203Phe missense_variant 0.14
Rv1979c 2221776 c.1389T>A synonymous_variant 0.13
Rv1979c 2223182 c.-18C>T upstream_gene_variant 0.14
Rv1979c 2223204 c.-40T>C upstream_gene_variant 0.13
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
pncA 2288824 p.Arg140Cys missense_variant 0.2
pncA 2288826 p.Val139Glu missense_variant 0.18
pncA 2288839 p.Thr135Ala missense_variant 0.15
kasA 2518076 c.-39C>T upstream_gene_variant 1.0
kasA 2518533 p.Leu140Pro missense_variant 0.12
kasA 2518749 p.Met212Thr missense_variant 0.1
kasA 2519352 c.1239delC frameshift_variant 0.12
eis 2714315 p.Cys340Arg missense_variant 0.11
eis 2714933 p.Ala134Thr missense_variant 0.13
folC 2747436 p.Asp55His missense_variant 0.17
pepQ 2859582 p.Gln279His missense_variant 0.11
Rv2752c 3065855 p.Ala113Thr missense_variant 0.15
thyA 3074270 p.Asn68Asp missense_variant 0.11
ald 3086788 c.-32T>C upstream_gene_variant 1.0
fbiD 3339283 c.166C>T synonymous_variant 0.12
fbiD 3339290 p.Ser58Leu missense_variant 0.15
fbiD 3339747 c.630G>A synonymous_variant 0.29
fprA 3473996 c.-11_-10insA upstream_gene_variant 0.86
fprA 3474381 c.375C>A synonymous_variant 0.2
fprA 3474604 p.Arg200* stop_gained 0.15
fprA 3475059 c.1053C>T synonymous_variant 0.17
Rv3236c 3611974 c.1143A>C synonymous_variant 0.95
Rv3236c 3612265 c.852G>T synonymous_variant 0.15
Rv3236c 3613009 p.Tyr36* stop_gained 0.13
Rv3236c 3613160 c.-44C>G upstream_gene_variant 0.12
Rv3236c 3613172 c.-56C>G upstream_gene_variant 0.11
Rv3236c 3613278 c.-162G>C upstream_gene_variant 0.11
Rv3236c 3613294 c.-178G>A upstream_gene_variant 0.13
fbiA 3640462 c.-81G>A upstream_gene_variant 0.14
fbiA 3640485 c.-58C>T upstream_gene_variant 0.22
fbiA 3640495 c.-48T>C upstream_gene_variant 0.18
fbiA 3640512 c.-31T>A upstream_gene_variant 0.17
fbiA 3640536 c.-7C>A upstream_gene_variant 0.15
fbiA 3641006 p.Val155Ala missense_variant 0.21
fbiA 3641503 p.Arg321Gly missense_variant 0.12
alr 3841600 c.-181delC upstream_gene_variant 0.12
alr 3841618 c.-198C>T upstream_gene_variant 0.13
rpoA 3878275 p.Leu78Pro missense_variant 0.17
rpoA 3878305 p.Gly68Val missense_variant 0.15
clpC1 4039009 c.1696C>T synonymous_variant 0.17
embA 4242643 c.-590C>T upstream_gene_variant 1.0
embC 4242803 p.Val981Leu missense_variant 1.0
embC 4242804 c.2943delG frameshift_variant 0.13
embA 4242811 c.-422G>T upstream_gene_variant 0.14
embA 4243848 p.Val206Met missense_variant 0.13
embA 4245410 c.2178C>G synonymous_variant 0.12
aftB 4268673 p.Val55Asp missense_variant 0.15
aftB 4268757 p.Ile27Asn missense_variant 0.13
aftB 4268798 c.39C>T synonymous_variant 0.15
ubiA 4269350 p.Ile162Val missense_variant 0.12
aftB 4269510 c.-674A>T upstream_gene_variant 0.12
ethA 4326171 p.Thr435Ala missense_variant 0.12
ethA 4326327 p.Thr383Ser missense_variant 0.2
ethR 4327816 p.Leu90Ile missense_variant 0.15
ethA 4328365 c.-892G>A upstream_gene_variant 0.13
whiB6 4338595 c.-75delG upstream_gene_variant 1.0
gid 4407624 c.579G>C synonymous_variant 0.15