TB-Profiler result

Run: ERR2228840
Summary

Run ID: ERR2228840

Sample name:

Date: 31-03-2023 16:22:35

Number of reads: 709596

Percentage reads mapped: 99.64

Strain: lineage4.8

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
lineage4.8 Euro-American (mainly T) T1;T2;T3;T5 RD219 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
gyrA 7362 p.Glu21Gln missense_variant 1.0
gyrA 8632 p.Ala444Val missense_variant 0.17
gyrA 8825 p.Glu508Asp missense_variant 0.14
rpoB 760502 c.696C>A synonymous_variant 0.15
rpoB 761385 p.Ala527Ser missense_variant 0.12
rpoB 762119 c.2313C>T synonymous_variant 1.0
rpoC 765495 p.Val709Asp missense_variant 0.11
rpoC 765683 p.Glu772Lys missense_variant 0.13
rpoC 766614 p.Lys1082Met missense_variant 0.31
rpoC 767186 p.Gln1273* stop_gained 0.12
mmpL5 775639 p.Ile948Val missense_variant 1.0
rpsL 781395 c.-165T>C upstream_gene_variant 1.0
rpsL 781612 p.Lys18Met missense_variant 0.14
rplC 800776 c.-33A>G upstream_gene_variant 0.12
fbiC 1303747 p.Thr273Ala missense_variant 1.0
Rv1258c 1406513 c.828G>T synonymous_variant 0.17
atpE 1461117 p.Gly25Ser missense_variant 0.12
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
rrs 1471836 n.-10A>T upstream_gene_variant 0.2
rrs 1472750 n.905C>T non_coding_transcript_exon_variant 1.0
rrl 1473724 n.67T>C non_coding_transcript_exon_variant 0.11
rrl 1474001 n.344C>T non_coding_transcript_exon_variant 1.0
rpsA 1834356 p.Val272Ala missense_variant 0.1
tlyA 1917972 c.33A>G synonymous_variant 1.0
ndh 2102093 p.Val317Ala missense_variant 0.11
ndh 2102991 p.Val18Leu missense_variant 0.14
PPE35 2167784 c.2829C>T synonymous_variant 0.5
PPE35 2168728 p.Gly629Arg missense_variant 1.0
PPE35 2168876 p.Phe579Leu missense_variant 0.36
PPE35 2169177 p.Ala479Val missense_variant 0.13
PPE35 2169488 c.1125G>C synonymous_variant 0.12
PPE35 2169491 c.1122T>C synonymous_variant 0.12
Rv1979c 2221896 c.1269G>A synonymous_variant 0.12
Rv1979c 2222378 p.Val263Leu missense_variant 0.12
Rv1979c 2222922 c.242delA frameshift_variant 0.17
Rv1979c 2223270 c.-106C>T upstream_gene_variant 0.2
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
kasA 2518413 p.Ser100Ile missense_variant 0.12
folC 2746837 c.762G>T synonymous_variant 0.13
pepQ 2860211 c.207delC frameshift_variant 0.15
ribD 2987000 c.162C>A synonymous_variant 0.12
Rv2752c 3064899 c.1293G>A synonymous_variant 0.33
thyX 3067824 p.Arg41Gln missense_variant 0.13
thyA 3073695 c.777T>C synonymous_variant 0.11
Rv3083 3448497 c.-7T>A upstream_gene_variant 1.0
Rv3236c 3613227 c.-111T>C upstream_gene_variant 0.12
fbiA 3641522 c.983delG frameshift_variant 0.15
rpoA 3878490 c.18C>G synonymous_variant 0.29
clpC1 4038610 p.Asp699Asn missense_variant 0.15
clpC1 4038895 p.Tyr604His missense_variant 0.17
panD 4044304 c.-23C>A upstream_gene_variant 0.14
embC 4241430 p.Phe523Ser missense_variant 0.13
embA 4242643 c.-590C>T upstream_gene_variant 1.0
embB 4246560 p.Ile16Asn missense_variant 0.22
embB 4246579 c.66T>G synonymous_variant 0.25
aftB 4267286 c.1551C>T synonymous_variant 0.15
ethA 4327361 p.Arg38Leu missense_variant 0.18
whiB6 4338595 c.-75delG upstream_gene_variant 1.0
Rv3083 3448507 c.5_*1408del frameshift_variant&stop_lost&splice_region_variant 1.0