TB-Profiler result

Run: ERR4821915
Summary

Run ID: ERR4821915

Sample name:

Date: 01-04-2023 17:31:26

Number of reads: 128112

Percentage reads mapped: 64.02

Strain: lineage4.9

Drug-resistance: RR-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
lineage4.9 Euro-American (H37Rv-like) T1 None 0.88
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 1.0 rifampicin
rrs 1472733 n.888G>A non_coding_transcript_exon_variant 0.36 streptomycin
embB 4247431 p.Met306Ile missense_variant 1.0 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
gyrA 9304 p.Gly668Asp missense_variant 1.0
fgd1 491343 c.561C>T synonymous_variant 0.67
fgd1 491742 c.960T>C synonymous_variant 1.0
mshA 575446 c.99A>C synonymous_variant 0.33
rpoB 762212 c.2406G>C synonymous_variant 0.67
rpoB 762218 c.2412T>C synonymous_variant 0.67
rpoB 762245 c.2439G>C synonymous_variant 0.67
rpoB 762254 c.2448T>C synonymous_variant 0.67
rpoC 762434 c.-936T>G upstream_gene_variant 1.0
rpoC 763031 c.-339T>C upstream_gene_variant 1.0
rpoC 764503 c.1134G>T synonymous_variant 0.67
rpoC 764509 c.1140G>C synonymous_variant 0.5
rpoC 764512 c.1143G>C synonymous_variant 0.5
rpoC 764521 c.1152T>C synonymous_variant 0.6
rpoC 764530 c.1161C>T synonymous_variant 0.6
rpoC 764536 c.1167G>C synonymous_variant 0.6
rpoC 764543 p.Thr392Ala missense_variant 0.75
rpoC 764548 c.1179G>C synonymous_variant 0.75
rpoC 764551 c.1182G>C synonymous_variant 0.75
rpoC 764573 p.Leu402Ile missense_variant 0.67
rpoC 764578 c.1209C>G synonymous_variant 0.67
rpoC 764581 c.1212T>C synonymous_variant 0.67
rpoC 764582 p.Leu405Met missense_variant 0.67
rpoC 764593 c.1224C>T synonymous_variant 0.75
rpoC 764602 c.1233C>T synonymous_variant 0.67
rpoC 764605 c.1236G>T synonymous_variant 0.67
rpoC 764611 c.1242G>T synonymous_variant 1.0
rpoC 764632 c.1263T>A synonymous_variant 0.6
rpoC 764647 c.1278C>T synonymous_variant 0.5
rpoC 764650 c.1281G>T synonymous_variant 0.5
rpoC 764653 c.1284G>C synonymous_variant 0.5
rpoC 764662 c.1293G>C synonymous_variant 0.5
rpoC 764677 c.1308C>G synonymous_variant 0.5
rpoC 764678 p.Lys437Gln missense_variant 0.5
rpoC 764683 c.1314G>C synonymous_variant 0.4
rpoC 764692 c.1323C>T synonymous_variant 0.4
mmpL5 776100 p.Thr794Ile missense_variant 1.0
mmpS5 778477 c.429A>G stop_lost&splice_region_variant 1.0
rpsL 781395 c.-165T>C upstream_gene_variant 1.0
Rv1258c 1406242 p.Ala367Thr missense_variant 1.0
rrs 1472108 n.263C>T non_coding_transcript_exon_variant 1.0
rrs 1472122 n.277G>T non_coding_transcript_exon_variant 1.0
rrs 1472123 n.278A>T non_coding_transcript_exon_variant 1.0
rrs 1472124 n.279C>T non_coding_transcript_exon_variant 1.0
rrs 1472150 n.305T>A non_coding_transcript_exon_variant 1.0
rrs 1472155 n.310C>T non_coding_transcript_exon_variant 1.0
rrs 1472160 n.315C>T non_coding_transcript_exon_variant 1.0
rrs 1472225 n.380C>A non_coding_transcript_exon_variant 1.0
rrs 1472251 n.406G>A non_coding_transcript_exon_variant 1.0
rrs 1472258 n.413A>G non_coding_transcript_exon_variant 1.0
rrs 1472259 n.414C>A non_coding_transcript_exon_variant 1.0
rrs 1472513 n.668T>C non_coding_transcript_exon_variant 0.75
rrs 1472530 n.685G>A non_coding_transcript_exon_variant 0.5
rrs 1472537 n.692C>T non_coding_transcript_exon_variant 0.57
rrs 1472544 n.699C>A non_coding_transcript_exon_variant 0.62
rrs 1472545 n.700A>T non_coding_transcript_exon_variant 0.62
rrs 1472549 n.704G>A non_coding_transcript_exon_variant 0.33
rrs 1472566 n.721G>A non_coding_transcript_exon_variant 0.75
rrs 1472571 n.726G>C non_coding_transcript_exon_variant 0.75
rrs 1472579 n.734G>C non_coding_transcript_exon_variant 0.5
rrs 1472580 n.735C>T non_coding_transcript_exon_variant 0.33
rrs 1472581 n.736A>C non_coding_transcript_exon_variant 1.0
rrs 1472581 n.736A>T non_coding_transcript_exon_variant 1.0
rrs 1472584 n.739A>T non_coding_transcript_exon_variant 0.33
rrs 1472598 n.753A>C non_coding_transcript_exon_variant 0.62
rrs 1472599 n.754G>T non_coding_transcript_exon_variant 0.62
rrs 1472616 n.771G>A non_coding_transcript_exon_variant 0.4
rrs 1472707 n.862A>T non_coding_transcript_exon_variant 0.4
rrs 1472713 n.868T>C non_coding_transcript_exon_variant 0.33
rrs 1472714 n.869A>G non_coding_transcript_exon_variant 0.5
rrs 1472716 n.871C>T non_coding_transcript_exon_variant 0.43
rrs 1472741 n.896G>A non_coding_transcript_exon_variant 0.12
rrs 1472742 n.897C>T non_coding_transcript_exon_variant 0.5
rrs 1472744 n.899A>G non_coding_transcript_exon_variant 0.5
rrs 1472767 n.922G>A non_coding_transcript_exon_variant 0.12
rrs 1472781 n.936C>T non_coding_transcript_exon_variant 0.47
rrs 1472790 n.945T>C non_coding_transcript_exon_variant 0.4
rrs 1472793 n.948A>T non_coding_transcript_exon_variant 0.53
rrs 1472803 n.958T>A non_coding_transcript_exon_variant 0.5
rrs 1472824 n.979T>A non_coding_transcript_exon_variant 0.8
rrs 1472827 n.982G>T non_coding_transcript_exon_variant 0.8
rrs 1472828 n.983T>C non_coding_transcript_exon_variant 1.0
rrs 1472895 n.1050C>T non_coding_transcript_exon_variant 1.0
rrs 1472954 n.1109T>C non_coding_transcript_exon_variant 1.0
rrs 1472956 n.1111T>C non_coding_transcript_exon_variant 1.0
rrs 1472957 n.1112C>T non_coding_transcript_exon_variant 1.0
rrs 1472973 n.1128A>G non_coding_transcript_exon_variant 1.0
rrs 1472990 n.1145A>G non_coding_transcript_exon_variant 1.0
rrs 1472992 n.1147A>G non_coding_transcript_exon_variant 1.0
rrs 1473005 n.1160C>T non_coding_transcript_exon_variant 1.0
rrs 1473035 n.1190G>A non_coding_transcript_exon_variant 1.0
rrs 1473055 n.1210C>T non_coding_transcript_exon_variant 1.0
rrs 1473056 n.1211A>T non_coding_transcript_exon_variant 1.0
rrs 1473066 n.1221A>G non_coding_transcript_exon_variant 1.0
rrs 1473080 n.1235C>T non_coding_transcript_exon_variant 1.0
rrs 1473081 n.1236C>T non_coding_transcript_exon_variant 1.0
rrs 1473088 n.1243A>G non_coding_transcript_exon_variant 1.0
rrs 1473145 n.1300C>T non_coding_transcript_exon_variant 1.0
rrs 1473166 n.1321G>A non_coding_transcript_exon_variant 1.0
rrs 1473172 n.1327T>G non_coding_transcript_exon_variant 1.0
rrs 1473173 n.1328C>T non_coding_transcript_exon_variant 1.0
rrs 1473221 n.1376C>T non_coding_transcript_exon_variant 1.0
rrs 1473252 n.1407T>C non_coding_transcript_exon_variant 1.0
rrs 1473259 n.1414C>T non_coding_transcript_exon_variant 1.0
rrs 1473276 n.1431A>C non_coding_transcript_exon_variant 1.0
rrs 1473277 n.1432G>A non_coding_transcript_exon_variant 1.0
rrs 1473293 n.1449delA non_coding_transcript_exon_variant 1.0
rrs 1473293 n.1449A>G non_coding_transcript_exon_variant 1.0
rrs 1473300 n.1455C>T non_coding_transcript_exon_variant 1.0
rrs 1473301 n.1456T>G non_coding_transcript_exon_variant 1.0
rrs 1473316 n.1471C>T non_coding_transcript_exon_variant 1.0
rrl 1474181 n.524C>A non_coding_transcript_exon_variant 1.0
rrl 1474184 n.527C>T non_coding_transcript_exon_variant 1.0
rrl 1474197 n.540C>T non_coding_transcript_exon_variant 1.0
rrl 1474199 n.542G>C non_coding_transcript_exon_variant 1.0
rrl 1474200 n.545delT non_coding_transcript_exon_variant 1.0
rrl 1474249 n.592G>T non_coding_transcript_exon_variant 1.0
rrl 1476359 n.2702C>G non_coding_transcript_exon_variant 0.9
rrl 1476381 n.2724G>C non_coding_transcript_exon_variant 0.92
rrl 1476428 n.2771C>T non_coding_transcript_exon_variant 1.0
rrl 1476429 n.2772A>T non_coding_transcript_exon_variant 1.0
rrl 1476466 n.2809C>T non_coding_transcript_exon_variant 1.0
rrl 1476481 n.2824T>C non_coding_transcript_exon_variant 1.0
rrl 1476506 n.2849T>C non_coding_transcript_exon_variant 1.0
rrl 1476567 n.2910C>T non_coding_transcript_exon_variant 1.0
rrl 1476584 n.2927C>T non_coding_transcript_exon_variant 1.0
rrl 1476585 n.2928A>G non_coding_transcript_exon_variant 1.0
tlyA 1917972 c.33A>G synonymous_variant 1.0
tlyA 1918104 c.165G>A synonymous_variant 1.0
katG 2154724 p.Arg463Leu missense_variant 1.0
PPE35 2167926 p.Leu896Ser missense_variant 1.0
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
pncA 2289047 c.195C>T synonymous_variant 1.0
eis 2715218 p.Leu39Met missense_variant 0.29
ahpC 2726105 c.-88G>A upstream_gene_variant 1.0
ald 3086788 c.-32T>C upstream_gene_variant 1.0
Rv3083 3449736 c.1233G>T synonymous_variant 0.4
fbiA 3640421 c.-122C>T upstream_gene_variant 0.33
embC 4242075 p.Arg738Gln missense_variant 1.0
embA 4242643 c.-590C>T upstream_gene_variant 1.0
ethA 4326093 p.Tyr461Asp missense_variant 1.0
gid 4407588 c.615A>G synonymous_variant 1.0
gid 4407892 p.Met104Lys missense_variant 1.0