TB-Profiler result

Run: ERR11081864
Summary

Run ID: ERR11081864

Sample name:

Date: 09-04-2023 13:37:01

Number of reads: 5867255

Percentage reads mapped: 95.62

Strain: lineage3

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
lineage3 East-African-Indian CAS RD750 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 1472307 n.462C>T non_coding_transcript_exon_variant 0.14 streptomycin
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 7585 p.Ser95Thr missense_variant 1.0
gyrA 9304 p.Gly668Asp missense_variant 1.0
gyrA 9596 c.2295G>T synonymous_variant 1.0
fgd1 491742 c.960T>C synonymous_variant 1.0
mshA 576108 p.Ala254Gly missense_variant 0.32
mshA 576482 p.Val379Leu missense_variant 0.17
rpoB 759746 c.-61C>T upstream_gene_variant 1.0
rpoB 759875 c.69T>C synonymous_variant 1.0
rpoB 761306 c.1500C>G synonymous_variant 0.11
rpoB 762206 c.2400C>G synonymous_variant 0.12
rpoC 762434 c.-936T>G upstream_gene_variant 0.99
rpoC 762926 c.-444C>T upstream_gene_variant 0.14
rpoC 762929 c.-441G>C upstream_gene_variant 0.13
rpoC 762989 c.-381G>C upstream_gene_variant 0.13
rpoC 762995 c.-375G>T upstream_gene_variant 0.13
rpoC 763013 c.-357C>G upstream_gene_variant 0.15
rpoC 763025 c.-345C>T upstream_gene_variant 0.13
rpoC 763028 c.-342T>C upstream_gene_variant 0.14
rpoC 763031 c.-339T>C upstream_gene_variant 1.0
rpoC 763034 c.-336C>G upstream_gene_variant 0.13
rpoC 763040 c.-330C>G upstream_gene_variant 0.14
rpoC 763070 c.-300T>C upstream_gene_variant 0.13
rpoC 763085 c.-285C>G upstream_gene_variant 0.12
rpoC 763486 c.117T>G synonymous_variant 0.14
rpoC 763528 c.159G>A synonymous_variant 0.13
rpoC 763594 c.225C>T synonymous_variant 0.12
rpoC 763660 c.291T>G synonymous_variant 0.12
rpoC 763717 c.348T>C synonymous_variant 0.13
rpoC 763723 c.354G>C synonymous_variant 0.13
rpoC 763732 c.363C>G synonymous_variant 0.14
rpoC 764181 p.Asp271Gly missense_variant 0.91
rpoC 764611 c.1242G>T synonymous_variant 0.13
rpoC 764827 c.1458G>C synonymous_variant 0.14
rpoC 764858 c.1489T>C synonymous_variant 0.13
rpoC 764872 c.1503A>G synonymous_variant 0.15
rpoC 764888 c.1519T>C synonymous_variant 0.14
rpoC 764911 c.1542A>G synonymous_variant 0.15
rpoC 764932 c.1563C>A synonymous_variant 0.14
rpoC 764935 c.1566T>C synonymous_variant 0.14
rpoC 764948 c.1579T>C synonymous_variant 0.13
rpoC 764968 c.1599T>C synonymous_variant 0.13
rpoC 764995 c.1626C>G synonymous_variant 0.15
rpoC 765019 c.1650A>G synonymous_variant 0.15
rpoC 765034 c.1665T>C synonymous_variant 0.16
rpoC 765040 c.1671T>C synonymous_variant 0.14
rpoC 765041 c.1672T>C synonymous_variant 0.13
rpoC 765047 c.1678T>C synonymous_variant 0.13
rpoC 765053 c.1684_1685delTCinsAG synonymous_variant 0.13
rpoC 765073 c.1704G>C synonymous_variant 0.12
rpoC 765076 c.1707A>G synonymous_variant 0.12
rpoC 765079 c.1710T>G synonymous_variant 0.12
rpoC 765082 c.1713G>C synonymous_variant 0.12
rpoC 765478 c.2109T>C synonymous_variant 0.14
rpoC 765499 c.2130C>G synonymous_variant 0.13
rpoC 765625 c.2256C>G synonymous_variant 0.12
rpoC 765811 c.2442T>C synonymous_variant 0.12
rpoC 765814 c.2445A>G synonymous_variant 0.12
rpoC 765826 c.2457T>C synonymous_variant 0.12
rpoC 765850 c.2481G>C synonymous_variant 0.12
mmpL5 775639 p.Ile948Val missense_variant 1.0
mmpL5 776100 p.Thr794Ile missense_variant 1.0
rpsL 781395 c.-165T>C upstream_gene_variant 1.0
rpsL 781841 c.282C>G synonymous_variant 0.12
rplC 800693 c.-116A>G upstream_gene_variant 0.15
rplC 800703 c.-106T>C upstream_gene_variant 0.15
rplC 800715 c.-94A>C upstream_gene_variant 0.16
rplC 800720 c.-89T>C upstream_gene_variant 0.16
rplC 800723 c.-86C>G upstream_gene_variant 0.17
rplC 800747 c.-62C>G upstream_gene_variant 0.15
rplC 800771 c.-38C>T upstream_gene_variant 0.14
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
rrs 1472300 n.455C>T non_coding_transcript_exon_variant 0.15
rrs 1473105 n.1260G>A non_coding_transcript_exon_variant 0.13
rrs 1473145 n.1300C>T non_coding_transcript_exon_variant 0.13
rrs 1473166 n.1321G>A non_coding_transcript_exon_variant 0.14
rrl 1474140 n.483C>T non_coding_transcript_exon_variant 0.14
rrl 1474151 n.494C>T non_coding_transcript_exon_variant 0.14
rrl 1474181 n.524C>T non_coding_transcript_exon_variant 0.14
rrl 1474249 n.592G>T non_coding_transcript_exon_variant 0.13
rrl 1474639 n.982G>A non_coding_transcript_exon_variant 0.17
rrl 1474794 n.1137C>T non_coding_transcript_exon_variant 0.13
rrl 1474812 n.1155G>A non_coding_transcript_exon_variant 0.13
rrl 1475881 n.2224T>C non_coding_transcript_exon_variant 0.2
rpsA 1833661 c.120A>G synonymous_variant 0.16
rpsA 1833667 c.126C>G synonymous_variant 0.18
rpsA 1833721 c.180A>G synonymous_variant 0.13
rpsA 1833724 c.183C>G synonymous_variant 0.12
rpsA 1833727 c.186G>C synonymous_variant 0.12
rpsA 1833742 c.201A>G synonymous_variant 0.15
rpsA 1833745 c.204G>C synonymous_variant 0.14
rpsA 1833748 c.207C>G synonymous_variant 0.14
rpsA 1833787 c.246C>G synonymous_variant 0.12
rpsA 1833790 c.249T>C synonymous_variant 0.13
rpsA 1833811 c.270G>T synonymous_variant 0.13
rpsA 1833838 c.297G>C synonymous_variant 0.13
rpsA 1833841 c.300C>G synonymous_variant 0.13
rpsA 1833847 c.306C>G synonymous_variant 0.14
rpsA 1833856 c.315A>G synonymous_variant 0.14
rpsA 1833874 c.333T>C synonymous_variant 0.13
tlyA 1917972 c.33A>G synonymous_variant 1.0
katG 2154724 p.Arg463Leu missense_variant 1.0
PPE35 2167926 p.Leu896Ser missense_variant 1.0
PPE35 2170769 c.-157C>T upstream_gene_variant 1.0
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
pncA 2289047 c.195C>T synonymous_variant 1.0
pncA 2289365 c.-125delC upstream_gene_variant 1.0
kasA 2517950 c.-165C>G upstream_gene_variant 0.12
ahpC 2726105 c.-88G>A upstream_gene_variant 1.0
Rv2752c 3065678 p.Lys172Glu missense_variant 0.99
ald 3086788 c.-32T>C upstream_gene_variant 1.0
fprA 3473996 c.-11_-10insA upstream_gene_variant 1.0
rpoA 3877743 c.765T>C synonymous_variant 0.14
rpoA 3877764 c.744C>G synonymous_variant 0.16
rpoA 3877770 c.738A>G synonymous_variant 0.16
rpoA 3877776 c.732T>C synonymous_variant 0.15
rpoA 3877782 c.726T>C synonymous_variant 0.14
rpoA 3877791 c.717C>G synonymous_variant 0.13
rpoA 3877818 c.690A>G synonymous_variant 0.14
rpoA 3877839 c.669G>C synonymous_variant 0.13
rpoA 3877866 c.642G>C synonymous_variant 0.13
rpoA 3877986 c.522G>C synonymous_variant 0.12
rpoA 3878001 c.507A>G synonymous_variant 0.14
rpoA 3878022 c.486T>C synonymous_variant 0.13
rpoA 3878028 c.480G>C synonymous_variant 0.12
rpoA 3878031 c.477T>C synonymous_variant 0.12
rpoA 3878106 c.402G>C synonymous_variant 0.12
rpoA 3878118 c.390T>C synonymous_variant 0.12
rpoA 3878346 c.162T>C synonymous_variant 0.13
rpoA 3878364 c.144A>T synonymous_variant 0.13
rpoA 3878367 c.141C>G synonymous_variant 0.13
rpoA 3878376 c.132G>C synonymous_variant 0.13
rpoA 3878385 c.123C>G synonymous_variant 0.13
rpoA 3878388 c.120C>G synonymous_variant 0.13
rpoA 3878391 c.117T>C synonymous_variant 0.13
clpC1 4039004 c.1701C>G synonymous_variant 0.12
embC 4242075 p.Arg738Gln missense_variant 1.0
embA 4242643 c.-590C>T upstream_gene_variant 1.0
embB 4246584 p.Arg24Pro missense_variant 0.36
whiB6 4338595 c.-75delG upstream_gene_variant 1.0
gid 4407588 c.615A>G synonymous_variant 1.0
gid 4408002 p.Asp67Glu missense_variant 1.0