TB-Profiler result

Run: SRR11342675
Summary

Run ID: SRR11342675

Sample name:

Date: 02-04-2023 20:48:02

Number of reads: 3366968

Percentage reads mapped: 36.7

Strain: lineage4.8.1

Drug-resistance: Pre-XDR-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 Euro-American LAM;T;S;X;H None 1.0
lineage4.8 Euro-American (mainly T) T1;T2;T3;T5 RD219 1.0
lineage4.8.1 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
gyrB 6742 p.Glu501Asp missense_variant 1.0 ofloxacin, moxifloxacin, levofloxacin, fluoroquinolones, ciprofloxacin
rpoB 761110 p.Asp435Val missense_variant 1.0 rifampicin
rpsL 781687 p.Lys43Arg missense_variant 1.0 streptomycin
katG 2155168 p.Ser315Thr missense_variant 1.0 isoniazid
pncA 2288790 p.Leu151Ser missense_variant 1.0 pyrazinamide
embB 4247429 p.Met306Val 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 7362 p.Glu21Gln missense_variant 1.0
mshA 576108 p.Ala254Gly missense_variant 0.36
rpoC 764582 p.Leu405Met missense_variant 0.12
rpoC 764611 c.1242G>T synonymous_variant 0.14
rpoC 764632 c.1263T>C synonymous_variant 0.13
rpoC 764650 c.1281G>T synonymous_variant 0.12
mmpL5 775639 p.Ile948Val missense_variant 0.99
rpsL 781395 c.-165T>C upstream_gene_variant 1.0
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
rrs 1472172 n.327T>C non_coding_transcript_exon_variant 0.13
rrs 1472181 n.336G>A non_coding_transcript_exon_variant 0.12
rrs 1472214 n.369C>G non_coding_transcript_exon_variant 0.13
rrs 1472235 n.390G>C non_coding_transcript_exon_variant 0.12
rrs 1472240 n.395G>C non_coding_transcript_exon_variant 0.12
rrs 1472242 n.397C>T non_coding_transcript_exon_variant 0.13
rrs 1472251 n.406G>A non_coding_transcript_exon_variant 0.16
rrs 1472253 n.408G>T non_coding_transcript_exon_variant 0.13
rrs 1472259 n.414C>A non_coding_transcript_exon_variant 0.14
rrs 1472264 n.419T>C non_coding_transcript_exon_variant 0.12
rrs 1472266 n.421C>A non_coding_transcript_exon_variant 0.12
rrs 1472530 n.685G>A non_coding_transcript_exon_variant 0.14
rrs 1472537 n.692C>T non_coding_transcript_exon_variant 0.15
rrs 1472571 n.726G>C non_coding_transcript_exon_variant 0.19
rrs 1472579 n.734G>C non_coding_transcript_exon_variant 0.13
rrs 1472581 n.736A>T non_coding_transcript_exon_variant 0.16
rrs 1472598 n.753A>C non_coding_transcript_exon_variant 0.21
rrs 1472599 n.754G>T non_coding_transcript_exon_variant 0.15
rrs 1472616 n.771G>A non_coding_transcript_exon_variant 0.17
rrl 1474001 n.344C>T non_coding_transcript_exon_variant 1.0
rrl 1476332 n.2675G>C non_coding_transcript_exon_variant 0.11
rrl 1476336 n.2679C>G non_coding_transcript_exon_variant 0.17
rrl 1476338 n.2681C>T non_coding_transcript_exon_variant 0.12
rrl 1476356 n.2699C>G non_coding_transcript_exon_variant 0.2
rrl 1476357 n.2700T>A non_coding_transcript_exon_variant 0.21
rrl 1476358 n.2701T>C non_coding_transcript_exon_variant 0.32
rrl 1476359 n.2702C>G non_coding_transcript_exon_variant 0.22
rrl 1476372 n.2715T>C non_coding_transcript_exon_variant 0.1
rrl 1476381 n.2724G>C non_coding_transcript_exon_variant 0.31
rrl 1476382 n.2725A>G non_coding_transcript_exon_variant 0.4
rrl 1476384 n.2727G>C non_coding_transcript_exon_variant 0.29
rrl 1476408 n.2751G>A non_coding_transcript_exon_variant 0.34
rrl 1476411 n.2754G>A non_coding_transcript_exon_variant 0.31
rrl 1476428 n.2771C>A non_coding_transcript_exon_variant 0.34
rrl 1476429 n.2772A>C non_coding_transcript_exon_variant 0.1
rrl 1476443 n.2786G>C non_coding_transcript_exon_variant 0.28
rrl 1476455 n.2798C>G non_coding_transcript_exon_variant 0.26
rrl 1476463 n.2806C>T non_coding_transcript_exon_variant 0.22
rrl 1476466 n.2809C>T non_coding_transcript_exon_variant 0.27
rrl 1476470 n.2813C>T non_coding_transcript_exon_variant 0.23
rrl 1476481 n.2824T>C non_coding_transcript_exon_variant 0.3
rrl 1476506 n.2849T>C non_coding_transcript_exon_variant 0.18
tlyA 1917972 c.33A>G synonymous_variant 1.0
PPE35 2168149 p.Pro822Ser missense_variant 1.0
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
fbiD 3339040 c.-78T>C upstream_gene_variant 1.0
whiB7 3568428 c.252A>G synonymous_variant 0.23
fbiB 3642874 p.Leu447Arg missense_variant 1.0
embA 4242643 c.-590C>T upstream_gene_variant 1.0
embB 4247024 p.Pro171Ala missense_variant 0.2
whiB6 4338595 c.-75delG upstream_gene_variant 1.0
Rv3083 3448507 c.5_*1408del frameshift_variant&stop_lost&splice_region_variant 1.0