TB-Profiler result

Run: SRR1062927
Summary

Run ID: SRR1062927

Sample name:

Date: 02-04-2023 18:41:12

Number of reads: 1244332

Percentage reads mapped: 49.74

Strain: lineage4.6.1

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
lineage4 Euro-American LAM;T;S;X;H None 1.0
lineage4.6 Euro-American T;LAM None 0.99
lineage4.6.1 Euro-American (Uganda) T2 RD724 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 761155 p.Ser450Leu missense_variant 1.0 rifampicin
katG 2155168 p.Ser315Thr missense_variant 1.0 isoniazid
pncA 2288933 p.Tyr103* stop_gained 0.17 pyrazinamide
embB 4247431 p.Met306Ile missense_variant 1.0 ethambutol
gid 4407851 c.351delG frameshift_variant 1.0 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
gyrB 7038 p.Lys600Arg missense_variant 0.12
gyrA 7362 p.Glu21Gln missense_variant 1.0
gyrA 7539 p.Thr80Ala missense_variant 1.0
gyrA 7585 p.Ser95Thr missense_variant 1.0
gyrA 7709 c.408G>A synonymous_variant 1.0
gyrA 9304 p.Gly668Asp missense_variant 1.0
mshA 575560 p.Tyr71* stop_gained 0.1
ccsA 619994 p.Glu35Gly missense_variant 0.12
ccsA 620001 c.111C>A synonymous_variant 0.12
ccsA 620550 c.660C>A synonymous_variant 0.15
rpoC 762887 c.-483G>C upstream_gene_variant 0.1
rpoC 762899 c.-471G>C upstream_gene_variant 0.19
rpoC 762917 c.-453C>G upstream_gene_variant 0.19
rpoC 762920 c.-450C>T upstream_gene_variant 0.18
rpoC 762923 c.-447C>G upstream_gene_variant 0.18
rpoB 762925 p.Thr1040Ile missense_variant 0.17
rpoB 762934 c.3129_3130insAGCC frameshift_variant 0.17
rpoB 762938 c.3133_3136delATGA frameshift_variant 0.17
rpoC 762989 c.-381G>C upstream_gene_variant 0.1
rpoC 763702 c.334delT frameshift_variant 0.11
rpoC 764383 c.1014C>G synonymous_variant 0.11
rpoC 764575 c.1206T>G synonymous_variant 0.12
rpoC 764581 c.1212T>C synonymous_variant 0.16
rpoC 764582 p.Leu405Met missense_variant 0.2
rpoC 764587 c.1218C>G synonymous_variant 0.23
rpoC 764593 c.1224C>T synonymous_variant 0.29
rpoC 764605 c.1236G>C synonymous_variant 0.41
rpoC 764611 c.1242G>T synonymous_variant 0.4
rpoC 764632 c.1263T>C synonymous_variant 0.38
rpoC 764641 c.1272C>T synonymous_variant 0.38
rpoC 764650 c.1281G>T synonymous_variant 0.38
rpoC 764663 p.Val432Thr missense_variant 0.35
rpoC 764672 p.Gln435Glu missense_variant 0.32
rpoC 764677 c.1308C>G synonymous_variant 0.31
rpoC 764695 c.1326T>C synonymous_variant 0.22
rpoC 766488 p.Pro1040Arg missense_variant 1.0
mmpL5 775639 p.Ile948Val missense_variant 1.0
mmpR5 779389 p.Arg134Gly missense_variant 0.1
rpsL 781395 c.-165T>C upstream_gene_variant 1.0
rplC 800901 c.96delG frameshift_variant 0.12
fbiC 1302930 c.-1C>G upstream_gene_variant 0.12
fbiC 1303138 p.Leu70Val missense_variant 0.12
Rv1258c 1406238 p.Gly368Asp missense_variant 0.12
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
rrs 1472172 n.327T>C non_coding_transcript_exon_variant 0.41
rrs 1472214 n.369C>G non_coding_transcript_exon_variant 0.48
rrs 1472225 n.380C>A non_coding_transcript_exon_variant 0.47
rrs 1472235 n.390G>C non_coding_transcript_exon_variant 0.45
rrs 1472240 n.395G>A non_coding_transcript_exon_variant 0.43
rrs 1472242 n.397C>T non_coding_transcript_exon_variant 0.38
rrs 1472251 n.406G>A non_coding_transcript_exon_variant 0.33
rrs 1472253 n.408G>T non_coding_transcript_exon_variant 0.27
rrs 1472259 n.414C>A non_coding_transcript_exon_variant 0.23
rrs 1472264 n.419T>C non_coding_transcript_exon_variant 0.24
rrs 1472266 n.421C>A non_coding_transcript_exon_variant 0.24
rrs 1472277 n.432C>G non_coding_transcript_exon_variant 0.2
rrs 1472333 n.488G>T non_coding_transcript_exon_variant 0.15
rrs 1472338 n.493A>C non_coding_transcript_exon_variant 0.16
rrs 1472344 n.499C>T non_coding_transcript_exon_variant 0.17
rrs 1472349 n.504A>C non_coding_transcript_exon_variant 0.17
rrs 1472374 n.529T>G non_coding_transcript_exon_variant 0.21
rrs 1472379 n.534T>G non_coding_transcript_exon_variant 0.21
rrs 1472382 n.537G>T non_coding_transcript_exon_variant 0.21
rrs 1472391 n.546C>T non_coding_transcript_exon_variant 0.18
rrs 1472412 n.567A>C non_coding_transcript_exon_variant 0.12
rrs 1472422 n.577T>C non_coding_transcript_exon_variant 0.11
rrs 1472427 n.582T>A non_coding_transcript_exon_variant 1.0
rrs 1472590 n.745C>T non_coding_transcript_exon_variant 0.12
rrs 1472697 n.852T>C non_coding_transcript_exon_variant 0.12
rrs 1472714 n.869A>T non_coding_transcript_exon_variant 0.23
rrs 1472715 n.870C>A non_coding_transcript_exon_variant 0.21
rrs 1472716 n.871C>T non_coding_transcript_exon_variant 0.21
rrs 1472742 n.897C>T non_coding_transcript_exon_variant 0.36
rrs 1472770 n.925C>T non_coding_transcript_exon_variant 0.38
rrs 1472781 n.936C>T non_coding_transcript_exon_variant 0.36
rrs 1472793 n.948A>T non_coding_transcript_exon_variant 0.37
rrs 1472803 n.958T>A non_coding_transcript_exon_variant 0.27
rrs 1472812 n.967A>C non_coding_transcript_exon_variant 0.26
rrs 1472824 n.979T>A non_coding_transcript_exon_variant 0.2
rrs 1472826 n.981G>C non_coding_transcript_exon_variant 0.19
rrl 1475803 n.2146T>C non_coding_transcript_exon_variant 0.28
rrl 1475804 n.2147G>C non_coding_transcript_exon_variant 0.28
rrl 1475816 n.2159C>G non_coding_transcript_exon_variant 0.26
rrl 1475817 n.2160A>G non_coding_transcript_exon_variant 0.26
rrl 1475881 n.2224T>C non_coding_transcript_exon_variant 0.26
rrl 1475883 n.2226A>C non_coding_transcript_exon_variant 0.26
rrl 1476299 n.2642C>A non_coding_transcript_exon_variant 0.12
rrl 1476311 n.2654G>C non_coding_transcript_exon_variant 0.1
rrl 1476312 n.2655T>C non_coding_transcript_exon_variant 0.1
rrl 1476336 n.2679C>G non_coding_transcript_exon_variant 0.52
rrl 1476356 n.2699C>A non_coding_transcript_exon_variant 0.54
rrl 1476357 n.2700T>A non_coding_transcript_exon_variant 0.54
rrl 1476358 n.2701T>C non_coding_transcript_exon_variant 0.55
rrl 1476368 n.2711T>C non_coding_transcript_exon_variant 0.55
rrl 1476369 n.2712C>T non_coding_transcript_exon_variant 0.6
rrl 1476382 n.2725A>G non_coding_transcript_exon_variant 0.63
rrl 1476384 n.2727G>T non_coding_transcript_exon_variant 0.6
rrl 1476408 n.2751G>A non_coding_transcript_exon_variant 0.69
rrl 1476411 n.2754G>A non_coding_transcript_exon_variant 0.67
rrl 1476443 n.2786G>T non_coding_transcript_exon_variant 0.65
rrl 1476455 n.2798C>A non_coding_transcript_exon_variant 0.64
rrl 1476463 n.2806C>T non_coding_transcript_exon_variant 0.63
rrl 1476466 n.2809C>T non_coding_transcript_exon_variant 0.68
rrl 1476470 n.2813C>T non_coding_transcript_exon_variant 0.61
rrl 1476481 n.2824T>C non_coding_transcript_exon_variant 0.57
rrl 1476491 n.2834T>C non_coding_transcript_exon_variant 0.42
rrl 1476501 n.2844C>T non_coding_transcript_exon_variant 0.31
rrl 1476506 n.2849T>C non_coding_transcript_exon_variant 0.32
rrl 1476512 n.2855C>T non_coding_transcript_exon_variant 0.22
tlyA 1917972 c.33A>G synonymous_variant 1.0
tlyA 1918139 p.Ala67Val missense_variant 0.14
ndh 2103187 c.-145G>C upstream_gene_variant 0.1
katG 2155437 p.Met225Ile missense_variant 0.15
katG 2155493 p.Asp207His missense_variant 0.11
PPE35 2168151 p.Thr821Ile missense_variant 0.12
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
pncA 2288784 p.Thr153Ile missense_variant 0.32
pncA 2290220 c.-979G>T upstream_gene_variant 0.13
pepQ 2859792 p.Asp209Glu missense_variant 0.12
Rv2752c 3065548 p.Glu215Gly missense_variant 0.1
fprA 3473996 c.-11_-10insA upstream_gene_variant 1.0
fprA 3474177 c.171C>T synonymous_variant 1.0
fbiA 3641357 c.818delG frameshift_variant 0.13
rpoA 3878672 c.-165A>T upstream_gene_variant 0.13
embA 4242643 c.-590C>T upstream_gene_variant 1.0
embB 4245962 c.-552G>A upstream_gene_variant 1.0
embB 4249187 p.Tyr892Asp missense_variant 0.15
embB 4249286 p.Gln925Glu missense_variant 0.15
aftB 4267581 p.Gly419Val missense_variant 0.12
aftB 4268519 c.318C>T synonymous_variant 0.96
ubiA 4269670 p.Val55Gly missense_variant 1.0
ethA 4327196 p.Gly93Glu missense_variant 0.14
ethA 4328329 c.-856C>G upstream_gene_variant 1.0
whiB6 4338595 c.-75delG upstream_gene_variant 1.0
gid 4407742 p.Arg154Gln missense_variant 1.0
gid 4408198 p.Ser2Cys missense_variant 0.1