TB-Profiler result

Run: SRR13837707
Summary

Run ID: SRR13837707

Sample name:

Date: 03-04-2023 09:16:19

Number of reads: 297249

Percentage reads mapped: 97.12

Strain: lineage4.9

Drug-resistance: Other

Download CSV Download TXT Download PDF Download JSON
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
lineage4.9 Euro-American (H37Rv-like) T1 None 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
embC 4240748 p.Tyr296His missense_variant 1.0 ethambutol
embB 4247959 p.Met482Ile 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 6728 c.-574C>T upstream_gene_variant 0.25
fgd1 491360 p.Ile193Ser missense_variant 1.0
mshA 576396 p.Ser350Ile missense_variant 1.0
rpoB 760225 p.Glu140Ala missense_variant 1.0
rpoB 761180 c.1374A>C synonymous_variant 0.18
rpoB 761189 c.1383T>C synonymous_variant 0.18
rpoB 761195 c.1389G>C synonymous_variant 0.17
rpoB 761207 c.1401C>T synonymous_variant 0.14
rpoB 761213 c.1407G>C synonymous_variant 0.15
rpoB 761249 c.1443A>G synonymous_variant 0.14
rpoB 761255 c.1449T>G synonymous_variant 0.14
rpoB 761261 c.1455G>T synonymous_variant 0.14
rpoB 761306 c.1500C>G synonymous_variant 0.15
rpoC 763486 c.117T>G synonymous_variant 0.18
rpoC 763492 c.123G>C synonymous_variant 0.18
rpoC 763528 c.159G>A synonymous_variant 0.2
rpoC 763546 c.177A>G synonymous_variant 0.18
rpoC 763570 c.201G>C synonymous_variant 0.22
rpoC 763573 c.204G>C synonymous_variant 0.22
rpoC 763594 c.225C>T synonymous_variant 0.29
rpoC 763603 c.234C>T synonymous_variant 0.22
rpoC 763636 c.267T>C synonymous_variant 0.22
rpoC 763657 c.288G>A synonymous_variant 0.22
rpoC 763660 c.291T>G synonymous_variant 0.22
rpoC 763675 c.306C>G synonymous_variant 0.2
rpoC 763696 c.327T>C synonymous_variant 0.18
rpoC 763723 c.354G>C synonymous_variant 0.18
rpoC 764536 c.1167G>C synonymous_variant 0.19
rpoC 765700 c.2331T>C synonymous_variant 0.14
rpoC 765734 c.2365T>C synonymous_variant 0.13
rpoC 765739 c.2370G>T synonymous_variant 0.14
rpoC 765751 c.2382C>G synonymous_variant 0.15
rpoC 767186 p.Gln1273* stop_gained 1.0
mmpR5 779067 p.Tyr26* stop_gained 1.0
rplC 800933 p.Pro42His missense_variant 1.0
fbiC 1305306 c.2376A>T synonymous_variant 1.0
rrl 1474291 n.635_649delTTCCTCTCCGGAGGA non_coding_transcript_exon_variant 0.25
rrl 1474308 n.651G>T non_coding_transcript_exon_variant 0.22
rrl 1474310 n.653T>G non_coding_transcript_exon_variant 0.22
rrl 1474356 n.699T>C non_coding_transcript_exon_variant 0.25
rrl 1474362 n.705A>G non_coding_transcript_exon_variant 0.25
rrl 1474376 n.719T>C non_coding_transcript_exon_variant 0.15
rrl 1475199 n.1542G>A non_coding_transcript_exon_variant 0.29
rrl 1475206 n.1549C>T non_coding_transcript_exon_variant 0.29
rrl 1475209 n.1552G>C non_coding_transcript_exon_variant 0.29
rrl 1475213 n.1556C>T non_coding_transcript_exon_variant 0.29
rrl 1475252 n.1595C>T non_coding_transcript_exon_variant 0.25
rrl 1475266 n.1609T>C non_coding_transcript_exon_variant 0.18
rrl 1475267 n.1610G>A non_coding_transcript_exon_variant 0.18
rrl 1475275 n.1618C>T non_coding_transcript_exon_variant 0.22
rrl 1475276 n.1619T>C non_coding_transcript_exon_variant 0.22
rrl 1475291 n.1634A>C non_coding_transcript_exon_variant 0.22
rrl 1475313 n.1656G>A non_coding_transcript_exon_variant 0.22
rrl 1475315 n.1658A>T non_coding_transcript_exon_variant 0.22
tlyA 1918380 c.441C>G synonymous_variant 0.15
tlyA 1918560 c.621G>T synonymous_variant 1.0
ndh 2102402 p.Leu214Arg missense_variant 1.0
katG 2156175 c.-64T>G upstream_gene_variant 0.89
PPE35 2169349 p.Phe422Ile missense_variant 1.0
PPE35 2170540 p.Leu25Val missense_variant 1.0
pncA 2288999 p.Phe81Leu missense_variant 1.0
thyX 3067736 c.210C>T synonymous_variant 0.4
thyX 3067761 p.Arg62Lys missense_variant 0.4
thyX 3067765 p.Leu61Ile missense_variant 0.4
thyX 3067772 c.174C>G synonymous_variant 0.4
thyX 3067775 c.171C>T synonymous_variant 0.4
thyX 3067781 c.165C>G synonymous_variant 0.4
thyX 3067793 c.153T>C synonymous_variant 0.5
thyX 3067799 c.147G>A synonymous_variant 0.5
thyX 3067802 c.144C>G synonymous_variant 0.5
thyX 3067814 c.132T>C synonymous_variant 0.5
thyX 3067850 c.96A>C synonymous_variant 0.33
fbiD 3339660 c.543C>G synonymous_variant 1.0
Rv3236c 3612627 p.Ala164Thr missense_variant 1.0
rpoA 3877920 c.588G>C synonymous_variant 0.17
rpoA 3877923 c.585C>T synonymous_variant 0.17
rpoA 3877926 c.582G>C synonymous_variant 0.18
embA 4244119 p.Tyr296Phe missense_variant 1.0
embB 4247417 p.Tyr302Asn missense_variant 1.0
embB 4248036 p.Val508Gly missense_variant 1.0
embB 4248325 c.1812G>C synonymous_variant 1.0
aftB 4267894 p.Ile315Phe missense_variant 1.0
ethA 4326052 p.Asp474Glu missense_variant 1.0
ethA 4327388 p.Thr29Ile missense_variant 1.0
ethR 4328162 p.His205Pro missense_variant 1.0
whiB6 4338518 c.4C>A synonymous_variant 1.0