TB-Profiler result

Run: SRR6896147
Summary

Run ID: SRR6896147

Sample name:

Date: 04-04-2023 17:57:02

Number of reads: 828320

Percentage reads mapped: 95.89

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 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
gyrA 7362 p.Glu21Gln missense_variant 1.0
fgd1 491100 c.318C>T synonymous_variant 1.0
fgd1 491283 p.Asp167Glu missense_variant 0.11
fgd1 491296 p.Val172Ile missense_variant 0.15
fgd1 491301 c.519C>T synonymous_variant 0.13
fgd1 491325 c.543G>A synonymous_variant 0.16
fgd1 491331 c.549G>A synonymous_variant 0.17
fgd1 491340 c.558C>A synonymous_variant 0.18
fgd1 491349 c.567T>C synonymous_variant 0.23
fgd1 491355 c.573C>G synonymous_variant 0.2
fgd1 491364 c.582T>C synonymous_variant 0.11
fgd1 491472 c.690A>G synonymous_variant 0.13
fgd1 491500 p.Glu240Lys missense_variant 0.17
fgd1 491508 c.726A>G synonymous_variant 0.15
fgd1 491509 c.727T>C synonymous_variant 0.15
fgd1 491512 p.Asn244Glu missense_variant 0.14
fgd1 491520 c.738C>T synonymous_variant 0.15
fgd1 491523 c.741G>C synonymous_variant 0.13
fgd1 491542 c.760T>C synonymous_variant 0.15
fgd1 491547 c.765A>C synonymous_variant 0.15
fgd1 491550 c.768T>C synonymous_variant 0.15
rpoB 759620 c.-187A>C upstream_gene_variant 0.2
rpoB 761264 c.1458C>G synonymous_variant 0.12
rpoC 765734 c.2365_2367delTTGinsCTC synonymous_variant 0.14
rpoC 765739 c.2370G>A synonymous_variant 0.14
rpoC 765772 c.2403C>G synonymous_variant 0.19
rpoC 765778 c.2409C>G synonymous_variant 0.19
rpoC 765781 p.Asp804Glu missense_variant 0.19
rpoC 765787 c.2418C>T synonymous_variant 0.19
rpoC 765790 c.2421C>T synonymous_variant 0.17
rpoC 765796 c.2427C>T synonymous_variant 0.16
rpoC 765811 c.2442T>C synonymous_variant 0.12
rpoC 765814 c.2445A>C synonymous_variant 0.13
rpoC 765826 c.2457T>G synonymous_variant 0.13
rpoC 765835 c.2466C>G synonymous_variant 0.14
mmpL5 775639 p.Ile948Val missense_variant 1.0
rpsL 781395 c.-165T>C upstream_gene_variant 1.0
fbiC 1303818 c.888C>G synonymous_variant 0.14
fbiC 1303827 c.897A>G synonymous_variant 0.14
fbiC 1303897 c.967C>T synonymous_variant 0.15
fbiC 1303905 c.975G>C synonymous_variant 0.11
fbiC 1303911 c.981G>C synonymous_variant 0.12
fbiC 1303935 c.1005G>C synonymous_variant 0.12
fbiC 1304079 c.1149A>G synonymous_variant 0.16
fbiC 1304082 c.1152C>T synonymous_variant 0.16
fbiC 1304085 c.1155C>A synonymous_variant 0.12
fbiC 1304092 p.Met388Leu missense_variant 0.12
fbiC 1304100 c.1170G>A synonymous_variant 0.12
fbiC 1304111 p.Ala394Val missense_variant 0.14
fbiC 1304115 c.1185A>G synonymous_variant 0.14
fbiC 1304118 c.1188C>T synonymous_variant 0.14
fbiC 1304127 c.1197A>G synonymous_variant 0.14
fbiC 1304133 c.1203G>C synonymous_variant 0.13
fbiC 1304136 c.1206C>A synonymous_variant 0.18
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
rrs 1472075 n.230A>G non_coding_transcript_exon_variant 0.16
rrs 1472108 n.263C>T non_coding_transcript_exon_variant 0.23
rrs 1473202 n.1357C>T non_coding_transcript_exon_variant 0.14
rrl 1474001 n.344C>T non_coding_transcript_exon_variant 1.0
rrl 1474032 n.375T>C non_coding_transcript_exon_variant 0.22
rrl 1474287 n.630T>C non_coding_transcript_exon_variant 0.11
rrl 1475316 n.1659G>T non_coding_transcript_exon_variant 0.22
rrl 1476246 n.2589G>A non_coding_transcript_exon_variant 0.18
rrl 1476256 n.2599A>C non_coding_transcript_exon_variant 0.18
rrl 1476281 n.2624T>C non_coding_transcript_exon_variant 0.18
rrl 1476323 n.2666G>A non_coding_transcript_exon_variant 0.14
rpsA 1834669 c.1128G>C synonymous_variant 0.12
rpsA 1834720 c.1179C>G synonymous_variant 0.13
rpsA 1834726 c.1185C>T synonymous_variant 0.13
rpsA 1834747 c.1206A>G synonymous_variant 0.11
tlyA 1917972 c.33A>G synonymous_variant 1.0
ndh 2102540 p.Ala168Gly missense_variant 0.2
PPE35 2168524 p.Gly697Ser missense_variant 1.0
PPE35 2170048 p.Leu189Val missense_variant 0.15
PPE35 2170053 p.Thr187Ser missense_variant 0.15
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
Rv2752c 3065508 c.684T>C synonymous_variant 0.13
thyA 3073947 c.525G>A synonymous_variant 0.11
thyA 3073953 c.519T>C synonymous_variant 0.11
Rv3083 3448497 c.-7T>A upstream_gene_variant 1.0
alr 3840764 c.657G>C synonymous_variant 1.0
clpC1 4039661 c.1044T>C synonymous_variant 0.19
clpC1 4039664 c.1041G>C synonymous_variant 0.18
clpC1 4039688 c.1017G>A synonymous_variant 0.17
clpC1 4039706 c.999G>A synonymous_variant 0.17
clpC1 4039724 c.981A>G synonymous_variant 0.14
clpC1 4039733 c.972G>A synonymous_variant 0.14
clpC1 4039769 c.936C>G synonymous_variant 0.11
clpC1 4039831 c.874T>C synonymous_variant 0.11
clpC1 4039832 c.873C>G synonymous_variant 0.11
clpC1 4039850 c.855T>C synonymous_variant 0.12
clpC1 4039855 c.850C>T synonymous_variant 0.12
clpC1 4039886 c.819C>G synonymous_variant 0.11
clpC1 4040095 p.Leu204Phe missense_variant 0.12
clpC1 4040144 c.561G>C synonymous_variant 0.13
clpC1 4040147 c.558A>G synonymous_variant 0.13
clpC1 4040162 c.543G>C synonymous_variant 0.14
clpC1 4040168 c.537G>C synonymous_variant 0.14
clpC1 4040171 c.534C>G synonymous_variant 0.14
clpC1 4040200 c.505T>C synonymous_variant 0.12
clpC1 4040201 c.504C>G synonymous_variant 0.12
clpC1 4040214 p.Ser164Cys missense_variant 0.11
clpC1 4040522 c.183T>C synonymous_variant 0.16
clpC1 4040525 c.180C>A synonymous_variant 0.14
clpC1 4040528 c.177G>C synonymous_variant 0.14
clpC1 4040531 c.174T>C synonymous_variant 0.14
clpC1 4040534 c.171A>G synonymous_variant 0.13
clpC1 4040543 c.162C>T synonymous_variant 0.13
clpC1 4040546 c.159G>A synonymous_variant 0.13
clpC1 4040551 c.154T>C synonymous_variant 0.13
clpC1 4040561 c.144A>G synonymous_variant 0.13
embC 4241611 c.1749G>C synonymous_variant 0.14
embC 4241614 c.1752A>C synonymous_variant 0.14
embC 4241626 c.1764T>C synonymous_variant 0.12
embC 4241644 c.1782G>C synonymous_variant 0.11
embA 4242643 c.-590C>T upstream_gene_variant 1.0
embA 4245476 c.2244C>T synonymous_variant 0.13
embA 4245477 p.Met749Leu missense_variant 0.13
embA 4245489 p.Val753Arg missense_variant 0.15
embA 4245492 p.Pro754Ala missense_variant 0.16
embA 4245497 c.2265C>A synonymous_variant 0.14
embA 4245503 c.2271G>C synonymous_variant 0.14
embA 4245505 p.Phe758Tyr missense_variant 0.14
embA 4245509 c.2277A>C synonymous_variant 0.14
embB 4245518 c.-996A>C upstream_gene_variant 0.15
embB 4245521 c.-993G>C upstream_gene_variant 0.15
embA 4245529 c.2298_2301delTATC frameshift_variant 0.14
embB 4245545 c.-969C>G upstream_gene_variant 0.15
embA 4245555 p.Glu775Asn missense_variant 0.15
embB 4245563 c.-951G>T upstream_gene_variant 0.14
embA 4245565 p.Gly778Ala missense_variant 0.15
embB 4245575 c.-939C>G upstream_gene_variant 0.17
embA 4245577 p.Lys782Thr missense_variant 0.16
embB 4245590 c.-924G>C upstream_gene_variant 0.17
whiB6 4338595 c.-75delG upstream_gene_variant 1.0
Rv3083 3448507 c.5_*1408del frameshift_variant&stop_lost&splice_region_variant 1.0