TB-Profiler result

Run: SRR1172873
Summary

Run ID: SRR1172873

Sample name:

Date: 03-04-2023 03:12:21

Number of reads: 1338702

Percentage reads mapped: 70.56

Strain: lineage1.1.2

Drug-resistance: MDR-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
lineage1 Indo-Oceanic EAI RD239 1.0
lineage1.1 Indo-Oceanic EAI3;EAI4;EAI5;EAI6 RD239 1.0
lineage1.1.2 Indo-Oceanic EAI3;EAI5 RD239 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
rpoB 761161 p.Leu452Pro missense_variant 1.0 rifampicin
rrs 1472723 n.878G>A non_coding_transcript_exon_variant 0.95 streptomycin
katG 2155168 p.Ser315Thr missense_variant 1.0 isoniazid
pncA 2289228 p.Ile5Thr missense_variant 0.59 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
gyrB 6112 p.Met291Ile missense_variant 1.0
gyrB 6124 c.885C>T synonymous_variant 1.0
gyrA 6736 c.-566C>T upstream_gene_variant 1.0
gyrA 7362 p.Glu21Gln missense_variant 1.0
gyrA 7585 p.Ser95Thr missense_variant 1.0
gyrA 8452 p.Ala384Val missense_variant 1.0
gyrA 9143 c.1842T>C synonymous_variant 1.0
gyrA 9304 p.Gly668Asp missense_variant 1.0
fgd1 491742 c.960T>C synonymous_variant 1.0
mshA 575278 c.-70C>A upstream_gene_variant 1.0
mshA 575780 p.Pro145Ser missense_variant 0.13
rpoB 761557 p.Ala584Asp missense_variant 0.11
rpoB 762911 p.Ile1035Met missense_variant 0.13
rpoC 762917 c.-453C>G upstream_gene_variant 0.12
rpoC 762920 c.-450C>T upstream_gene_variant 0.12
rpoC 762923 c.-447C>G upstream_gene_variant 0.12
rpoC 762929 c.-441G>C upstream_gene_variant 0.14
rpoB 762939 p.Met1045Leu missense_variant 0.12
rpoB 762942 p.Ile1046Val missense_variant 0.11
rpoC 762965 c.-405T>C upstream_gene_variant 0.13
rpoC 763031 c.-339T>C upstream_gene_variant 1.0
rpoC 763884 p.Ala172Val missense_variant 1.0
rpoC 763886 c.517C>A synonymous_variant 1.0
rpoC 764623 c.1254C>G synonymous_variant 0.11
rpoC 764632 c.1263T>C synonymous_variant 0.11
rpoC 764650 c.1281G>T synonymous_variant 0.19
rpoC 764665 c.1296C>G synonymous_variant 0.17
rpoC 764668 c.1299C>T synonymous_variant 0.17
rpoC 764695 c.1326T>C synonymous_variant 0.17
rpoC 764713 c.1344G>C synonymous_variant 0.11
rpoC 765171 p.Pro601Leu missense_variant 1.0
mmpL5 775639 p.Ile948Val missense_variant 1.0
mmpL5 776100 p.Thr794Ile missense_variant 1.0
mmpL5 779367 c.-887G>A upstream_gene_variant 0.11
rpsL 781395 c.-165T>C upstream_gene_variant 1.0
rpsL 781889 c.330C>T synonymous_variant 1.0
fbiC 1303153 c.223C>A synonymous_variant 0.11
Rv1258c 1406503 p.Val280Leu missense_variant 1.0
embR 1417019 p.Cys110Tyr missense_variant 1.0
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
rrl 1476336 n.2679C>T non_coding_transcript_exon_variant 0.19
rrl 1476338 n.2681C>T non_coding_transcript_exon_variant 0.2
rrl 1476356 n.2699C>A non_coding_transcript_exon_variant 0.23
rrl 1476357 n.2700T>C non_coding_transcript_exon_variant 0.23
rrl 1476358 n.2701T>C non_coding_transcript_exon_variant 0.24
rrl 1476359 n.2702C>G non_coding_transcript_exon_variant 0.25
rrl 1476369 n.2712C>T non_coding_transcript_exon_variant 0.26
rrl 1476381 n.2724G>C non_coding_transcript_exon_variant 0.27
rrl 1476382 n.2725A>G non_coding_transcript_exon_variant 0.27
rrl 1476383 n.2726T>G non_coding_transcript_exon_variant 0.27
rrl 1476384 n.2727G>T non_coding_transcript_exon_variant 0.26
rrl 1476408 n.2751G>A non_coding_transcript_exon_variant 0.28
rrl 1476411 n.2754G>T non_coding_transcript_exon_variant 0.3
rrl 1476425 n.2768G>T non_coding_transcript_exon_variant 0.24
rrl 1476429 n.2772A>C non_coding_transcript_exon_variant 0.23
rrl 1476442 n.2785T>A non_coding_transcript_exon_variant 0.12
rrl 1476443 n.2786G>T non_coding_transcript_exon_variant 0.12
rrl 1476455 n.2798C>A non_coding_transcript_exon_variant 0.11
rrl 1476456 n.2799A>T non_coding_transcript_exon_variant 0.11
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 2167983 p.Gly877Asp missense_variant 1.0
Rv1979c 2222308 p.Asp286Gly missense_variant 1.0
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
kasA 2518132 c.18C>T synonymous_variant 0.92
kasA 2518218 p.Gly35Asp missense_variant 1.0
ahpC 2726051 c.-142G>A upstream_gene_variant 1.0
ribD 2987342 c.504C>T synonymous_variant 0.12
Rv2752c 3064632 c.1560C>T synonymous_variant 1.0
Rv2752c 3065228 p.Glu322* stop_gained 0.11
ald 3086788 c.-32T>C upstream_gene_variant 1.0
fbiD 3339400 p.Ala95Ser missense_variant 0.12
Rv3083 3448714 p.Asp71His missense_variant 1.0
fprA 3473996 c.-11_-10insA upstream_gene_variant 1.0
fprA 3474597 c.591C>A synonymous_variant 1.0
fprA 3475159 p.Asn385Asp missense_variant 1.0
clpC1 4040517 p.Val63Ala missense_variant 1.0
embC 4240618 c.756C>T synonymous_variant 1.0
embC 4240671 p.Thr270Ile missense_variant 1.0
embC 4241042 p.Asn394Asp missense_variant 0.92
embA 4242643 c.-590C>T upstream_gene_variant 1.0
embA 4243848 p.Val206Met missense_variant 1.0
embA 4244798 c.1566G>T synonymous_variant 0.12
embA 4245969 p.Pro913Ser missense_variant 1.0
embB 4247646 p.Glu378Ala missense_variant 1.0
aftB 4268955 c.-119A>G upstream_gene_variant 0.11
aftB 4269063 c.-227C>A upstream_gene_variant 0.11
ubiA 4269387 p.Glu149Asp missense_variant 1.0
aftB 4269606 c.-770T>C upstream_gene_variant 1.0
ubiA 4269929 c.-96G>C upstream_gene_variant 0.12
ubiA 4269948 c.-115G>T upstream_gene_variant 0.11
whiB6 4338224 c.297delC frameshift_variant 1.0
whiB6 4338595 c.-75delG upstream_gene_variant 1.0
whiB6 4338603 c.-82C>T upstream_gene_variant 1.0
gid 4407588 c.615A>G synonymous_variant 1.0
gid 4407873 c.330G>T synonymous_variant 1.0