TB-Profiler result

Run: SRR4035771
Summary

Run ID: SRR4035771

Sample name:

Date: 04-04-2023 07:17:20

Number of reads: 1200365

Percentage reads mapped: 99.53

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 0.98
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 5238 c.-2T>A upstream_gene_variant 0.18
gyrB 5244 p.Ala2Val missense_variant 0.17
gyrB 5248 c.9C>T synonymous_variant 0.15
gyrB 5739 p.Thr167Arg missense_variant 0.2
gyrB 6032 p.Asn265Asp missense_variant 0.29
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 8761 p.Val487Glu missense_variant 0.15
gyrA 9304 p.Gly668Asp missense_variant 1.0
gyrA 9669 p.Gln790Glu missense_variant 0.15
fgd1 490890 c.108C>T synonymous_variant 0.18
fgd1 491546 p.Thr255Lys missense_variant 0.17
fgd1 491591 p.Lys270Met missense_variant 0.91
mshA 576065 p.Pro240Ser missense_variant 0.12
mshA 576317 p.Arg324Gly missense_variant 0.14
mshA 576391 c.1044G>T synonymous_variant 0.13
mshA 576406 c.1059G>A synonymous_variant 0.14
mshA 576703 c.1356C>G synonymous_variant 0.18
rpoB 760011 p.Ala69Pro missense_variant 0.2
rpoB 760115 c.309C>T synonymous_variant 1.0
rpoB 760433 p.Asp209Glu missense_variant 0.12
rpoB 760448 p.Asp214Glu missense_variant 0.12
rpoB 762604 p.Cys933Tyr missense_variant 0.2
rpoB 762655 p.Ala950Val missense_variant 0.14
rpoB 763035 p.Tyr1077His missense_variant 0.12
rpoC 763348 c.-22C>G upstream_gene_variant 0.14
rpoC 763842 p.Glu158Gly missense_variant 0.15
rpoC 763964 p.Asp199Asn missense_variant 0.12
rpoC 764199 p.Leu277Pro missense_variant 0.11
rpoC 764263 c.894G>A synonymous_variant 1.0
rpoC 764310 p.Leu314Pro missense_variant 0.11
rpoC 764650 c.1281G>A synonymous_variant 0.17
rpoC 765150 p.Gly594Glu missense_variant 1.0
rpoC 766396 c.3027G>A synonymous_variant 0.14
mmpL5 775639 p.Ile948Val missense_variant 1.0
mmpL5 775685 c.2796C>G synonymous_variant 0.11
mmpL5 777320 c.1161C>G synonymous_variant 1.0
mmpL5 777346 p.Trp379Arg missense_variant 0.15
mmpL5 777671 c.810G>A synonymous_variant 0.12
mmpR5 779282 p.Asn98Ser missense_variant 0.12
mmpR5 779368 p.Asp127His missense_variant 0.18
rpsL 781395 c.-165T>C upstream_gene_variant 1.0
fbiC 1304289 c.1359C>A synonymous_variant 0.13
fbiC 1304295 c.1365T>C synonymous_variant 0.13
Rv1258c 1406242 p.Ala367Thr missense_variant 0.13
embR 1416370 c.978C>T synonymous_variant 0.16
embR 1417460 c.-113G>A upstream_gene_variant 0.17
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
rrs 1471669 n.-177C>T upstream_gene_variant 0.17
rrs 1472218 n.373A>G non_coding_transcript_exon_variant 0.22
rrs 1472336 n.491G>A non_coding_transcript_exon_variant 0.29
rrs 1472621 n.776G>C non_coding_transcript_exon_variant 0.18
rrs 1472780 n.935G>A non_coding_transcript_exon_variant 0.17
rrs 1472915 n.1070G>C non_coding_transcript_exon_variant 0.13
rrl 1473439 n.-219T>A upstream_gene_variant 0.2
rrl 1473771 n.114T>A non_coding_transcript_exon_variant 0.2
rrl 1474396 n.739C>T non_coding_transcript_exon_variant 0.25
rrl 1474523 n.866C>G non_coding_transcript_exon_variant 0.22
rrl 1474544 n.887G>A non_coding_transcript_exon_variant 0.4
rrl 1476459 n.2802A>G non_coding_transcript_exon_variant 0.15
rrl 1476473 n.2816G>C non_coding_transcript_exon_variant 0.17
fabG1 1673662 p.Val75Leu missense_variant 0.11
inhA 1673694 c.-508G>C upstream_gene_variant 0.12
rpsA 1834518 p.Leu326Pro missense_variant 0.12
tlyA 1917779 c.-161C>G upstream_gene_variant 0.14
tlyA 1917972 c.33A>G synonymous_variant 1.0
katG 2154337 p.Asp592Val missense_variant 0.12
katG 2154398 p.Thr572Ser missense_variant 0.12
katG 2154760 p.Gly451Val missense_variant 0.12
katG 2155728 c.384G>A synonymous_variant 0.13
PPE35 2169320 p.Leu431Phe missense_variant 0.25
Rv1979c 2223116 p.Cys17Arg missense_variant 0.15
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
pncA 2289757 c.-516C>A upstream_gene_variant 0.13
pncA 2289779 c.-538G>A upstream_gene_variant 0.13
kasA 2518076 c.-39C>T upstream_gene_variant 0.94
kasA 2518763 p.Ser217Thr missense_variant 0.12
ahpC 2726536 p.Lys115Arg missense_variant 0.15
ahpC 2726551 p.Gln120Leu missense_variant 0.14
folC 2746680 p.Ala307Pro missense_variant 0.11
folC 2746682 p.Leu306Pro missense_variant 0.11
Rv2752c 3064555 p.Arg546Leu missense_variant 0.13
Rv2752c 3066187 p.Asp2Gly missense_variant 0.12
thyX 3067496 c.450G>C synonymous_variant 0.14
thyX 3067593 p.Val118Glu missense_variant 0.2
thyX 3067630 p.Gln106Lys missense_variant 0.15
ald 3086788 c.-32T>C upstream_gene_variant 1.0
ald 3087642 p.Phe275Leu missense_variant 0.1
fbiD 3339403 p.Ile96Val missense_variant 0.12
fbiD 3339601 p.Phe162Leu missense_variant 0.12
Rv3083 3449176 p.Lys225Glu missense_variant 0.12
fprA 3473888 c.-119G>A upstream_gene_variant 0.29
fprA 3473995 c.-12A>T upstream_gene_variant 0.2
fprA 3473996 c.-11_-10insA upstream_gene_variant 1.0
fprA 3474109 p.Ala35Thr missense_variant 0.12
fprA 3474176 p.His57Arg missense_variant 0.17
fprA 3474335 p.Arg110His missense_variant 0.15
fprA 3474476 p.Asn157Ser missense_variant 0.12
fprA 3474887 p.Leu294Pro missense_variant 0.12
whiB7 3568654 p.Gln9Arg missense_variant 0.12
Rv3236c 3611974 c.1143A>C synonymous_variant 1.0
Rv3236c 3612772 c.345T>A synonymous_variant 0.12
Rv3236c 3612831 p.Asp96Asn missense_variant 0.14
alr 3840456 p.Leu322Gln missense_variant 0.13
alr 3841600 c.-180G>A upstream_gene_variant 0.14
rpoA 3877589 p.Ser307Pro missense_variant 0.2
rpoA 3878055 p.Gln151His missense_variant 0.21
clpC1 4039277 c.1428C>T synonymous_variant 0.12
clpC1 4039582 p.Thr375Ala missense_variant 0.1
embC 4242073 c.2211C>T synonymous_variant 0.12
embA 4242643 c.-590C>T upstream_gene_variant 1.0
embC 4242803 p.Val981Leu missense_variant 0.96
embB 4249773 p.Gly1087Asp missense_variant 0.17
embB 4249793 p.Ile1094Phe missense_variant 0.13
aftB 4267298 c.1538delC frameshift_variant 0.13
aftB 4268495 c.342G>C synonymous_variant 0.12
aftB 4268829 c.7delC frameshift_variant 0.12
ethA 4326065 p.Arg470His missense_variant 0.17
whiB6 4338462 c.60C>T synonymous_variant 0.12
whiB6 4338595 c.-75delG upstream_gene_variant 1.0