TB-Profiler result

Run: ERR2229505
Summary

Run ID: ERR2229505

Sample name:

Date: 31-03-2023 17:15:59

Number of reads: 901817

Percentage reads mapped: 98.53

Strain: lineage4.8

Drug-resistance: Other

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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 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
rrs 1473247 n.1402C>A non_coding_transcript_exon_variant 0.13 kanamycin, capreomycin, aminoglycosides, amikacin
tlyA 1918199 c.262delG frameshift_variant 0.15 capreomycin
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
mshA 575607 p.Glu87Val missense_variant 0.17
mshA 576108 p.Ala254Gly missense_variant 0.5
mshA 576360 p.Thr338Ile missense_variant 0.13
ccsA 620715 p.Tyr275* stop_gained 0.11
rpoB 760917 p.Arg371Cys missense_variant 0.14
rpoC 766728 p.Glu1120Val missense_variant 0.15
mmpL5 775639 p.Ile948Val missense_variant 1.0
mmpL5 776004 p.Ile826Thr missense_variant 0.13
mmpL5 777452 p.Met343Ile missense_variant 0.12
rpsL 781395 c.-165T>C upstream_gene_variant 1.0
fbiC 1303747 p.Thr273Ala missense_variant 1.0
Rv1258c 1406877 p.Ile155Asn missense_variant 0.11
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
rrs 1472368 n.523A>G non_coding_transcript_exon_variant 0.12
rrs 1472396 n.551A>T non_coding_transcript_exon_variant 0.24
rrs 1472400 n.555C>T non_coding_transcript_exon_variant 0.23
rrs 1472412 n.567A>G non_coding_transcript_exon_variant 0.13
rrs 1472954 n.1110delC non_coding_transcript_exon_variant 0.12
rrs 1473081 n.1236C>T non_coding_transcript_exon_variant 0.19
rrs 1473226 n.1381C>G non_coding_transcript_exon_variant 0.17
rrs 1473259 n.1414C>T non_coding_transcript_exon_variant 0.15
rrl 1473916 n.259C>A non_coding_transcript_exon_variant 0.15
rrl 1474001 n.344C>T non_coding_transcript_exon_variant 1.0
rrl 1474166 n.509G>T non_coding_transcript_exon_variant 0.16
rrl 1474167 n.510T>C non_coding_transcript_exon_variant 0.16
rrl 1474467 n.810A>T non_coding_transcript_exon_variant 0.14
rrl 1474476 n.819C>T non_coding_transcript_exon_variant 0.13
rrl 1474496 n.839C>T non_coding_transcript_exon_variant 0.11
rrl 1474497 n.840G>C non_coding_transcript_exon_variant 0.11
rrl 1474552 n.895C>T non_coding_transcript_exon_variant 0.2
rrl 1474558 n.901G>A non_coding_transcript_exon_variant 0.18
rrl 1474582 n.925T>A non_coding_transcript_exon_variant 0.38
rrl 1474794 n.1137C>T non_coding_transcript_exon_variant 0.14
rrl 1474798 n.1141C>T non_coding_transcript_exon_variant 0.17
rrl 1474799 n.1143delT non_coding_transcript_exon_variant 0.17
rrl 1474803 n.1146_1147insA non_coding_transcript_exon_variant 0.17
rrl 1474806 n.1149A>C non_coding_transcript_exon_variant 0.17
rrl 1474812 n.1155G>A non_coding_transcript_exon_variant 0.22
rrl 1474823 n.1166C>G non_coding_transcript_exon_variant 0.29
rrl 1474827 n.1170C>T non_coding_transcript_exon_variant 0.25
rrl 1474830 n.1173A>G non_coding_transcript_exon_variant 0.25
rrl 1474831 n.1174A>T non_coding_transcript_exon_variant 0.25
rrl 1474853 n.1196A>G non_coding_transcript_exon_variant 0.17
rrl 1474864 n.1207C>T non_coding_transcript_exon_variant 0.2
rrl 1474904 n.1247G>C non_coding_transcript_exon_variant 0.22
rrl 1474905 n.1248T>C non_coding_transcript_exon_variant 0.22
rrl 1475892 n.2235A>C non_coding_transcript_exon_variant 0.12
rrl 1475898 n.2241A>G non_coding_transcript_exon_variant 0.12
rrl 1475899 n.2242G>A non_coding_transcript_exon_variant 0.12
rrl 1475906 n.2249C>T non_coding_transcript_exon_variant 0.13
rrl 1475943 n.2286G>A non_coding_transcript_exon_variant 0.17
rrl 1475952 n.2295A>G non_coding_transcript_exon_variant 0.2
rrl 1475970 n.2313C>T non_coding_transcript_exon_variant 0.18
rrl 1476194 n.2537A>G non_coding_transcript_exon_variant 0.29
rrl 1476204 n.2547C>T non_coding_transcript_exon_variant 0.12
rrl 1476215 n.2558C>T non_coding_transcript_exon_variant 0.21
rrl 1476224 n.2567A>G non_coding_transcript_exon_variant 0.12
rrl 1476481 n.2824T>C non_coding_transcript_exon_variant 0.12
fabG1 1673380 c.-60C>G upstream_gene_variant 0.19
rpsA 1834516 p.Glu325Asp missense_variant 0.14
tlyA 1917972 c.33A>G synonymous_variant 1.0
tlyA 1918126 p.Val63Leu missense_variant 0.11
ndh 2102143 c.900C>T synonymous_variant 0.12
ndh 2102660 p.Asn128Thr missense_variant 0.2
PPE35 2167865 c.2748G>C synonymous_variant 0.24
PPE35 2167868 c.2745A>C synonymous_variant 0.22
PPE35 2167965 p.Ala883Gly missense_variant 0.21
PPE35 2167967 c.2646A>C synonymous_variant 0.2
PPE35 2168032 p.Thr861Ala missense_variant 0.2
PPE35 2168728 p.Gly629Arg missense_variant 1.0
PPE35 2169278 c.1335T>C synonymous_variant 0.12
PPE35 2169281 c.1332T>G synonymous_variant 0.12
PPE35 2170048 p.Leu189Val missense_variant 0.47
PPE35 2170053 p.Thr187Ser missense_variant 0.47
PPE35 2170147 p.Ser156Ala missense_variant 0.15
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
kasA 2518658 p.Trp182Arg missense_variant 0.29
kasA 2519140 c.1026G>C synonymous_variant 0.15
kasA 2519143 c.1029G>C synonymous_variant 0.18
kasA 2519153 p.Ile347Val missense_variant 0.2
folC 2747451 p.Ile50Phe missense_variant 0.17
folC 2747730 c.-132G>A upstream_gene_variant 0.15
pepQ 2860159 p.Ala87Gly missense_variant 0.22
Rv2752c 3065202 c.990T>C synonymous_variant 0.11
thyA 3074221 p.Ala84Glu missense_variant 0.13
fbiD 3339734 p.Ala206Gly missense_variant 0.14
whiB7 3568428 c.252A>G synonymous_variant 0.29
fbiA 3641074 c.535delC frameshift_variant 0.11
fbiB 3642786 p.Trp418Arg missense_variant 0.13
alr 3841546 c.-126C>A upstream_gene_variant 0.35
rpoA 3878639 c.-132C>G upstream_gene_variant 0.5
clpC1 4038752 p.Gln651His missense_variant 0.12
clpC1 4040024 c.681A>G synonymous_variant 0.12
clpC1 4040027 c.678C>G synonymous_variant 0.12
clpC1 4040032 p.Val225Ile missense_variant 0.15
clpC1 4040228 c.477G>T synonymous_variant 0.22
panD 4044078 c.204G>A synonymous_variant 0.12
panD 4044094 p.Glu63Gly missense_variant 0.22
embC 4239786 c.-77T>C upstream_gene_variant 0.13
embC 4241791 c.1929G>T synonymous_variant 0.22
embA 4242643 c.-590C>T upstream_gene_variant 1.0
embA 4244733 p.Arg501Ser missense_variant 0.17
embA 4246335 p.Ala1035Ser missense_variant 0.17
embB 4246544 p.Thr11Pro missense_variant 0.29
embB 4246567 c.54G>T synonymous_variant 0.4
embB 4249644 p.Leu1044Pro missense_variant 0.14
aftB 4269462 c.-626G>T upstream_gene_variant 0.12
ethA 4327080 p.Glu132Lys missense_variant 0.18
ethA 4328322 c.-849G>A upstream_gene_variant 0.14
whiB6 4338595 c.-75delG upstream_gene_variant 1.0
Rv3083 3448507 c.5_*1408del frameshift_variant&stop_lost&splice_region_variant 1.0