TB-Profiler result

Run: SRR1140586
Summary

Run ID: SRR1140586

Sample name:

Date: 02-04-2023 20:56:32

Number of reads: 46751

Percentage reads mapped: 1.65

Strain: lineage4.9

Drug-resistance: HR-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
lineage4.9 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
katG 2156024 c.87delC frameshift_variant 1.0 isoniazid, isoniazid
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
gyrA 7807 p.Arg169Leu missense_variant 1.0
gyrA 7817 c.516C>T synonymous_variant 1.0
gyrA 7826 c.525C>G synonymous_variant 1.0
gyrA 7832 c.531G>C synonymous_variant 1.0
gyrA 7833 p.Ser178Ala missense_variant 1.0
gyrA 7836 p.Gly179Ser missense_variant 1.0
gyrA 7859 c.558A>G synonymous_variant 1.0
rpoC 762887 c.-483G>C upstream_gene_variant 1.0
rpoC 762899 c.-471G>C upstream_gene_variant 1.0
rpoC 762917 c.-453C>G upstream_gene_variant 1.0
rpoC 762920 c.-450C>T upstream_gene_variant 1.0
rpoC 762923 c.-447C>G upstream_gene_variant 1.0
rpoB 762925 p.Thr1040Ile missense_variant 1.0
rpoB 762939 p.Met1045Leu missense_variant 0.9
rpoB 762942 p.Ile1046Val missense_variant 0.9
rpoC 762962 c.-408C>T upstream_gene_variant 0.83
rpoC 762989 c.-381G>C upstream_gene_variant 0.88
rpoC 762995 c.-375G>T upstream_gene_variant 1.0
rpoC 764557 p.Asn396Lys missense_variant 0.75
rpoC 764566 c.1197C>G synonymous_variant 0.92
rpoC 764575 c.1206T>G synonymous_variant 0.92
rpoC 764581 c.1212T>C synonymous_variant 0.92
rpoC 764582 p.Leu405Met missense_variant 0.92
rpoC 764587 c.1218C>G synonymous_variant 0.94
rpoC 764605 c.1236G>C synonymous_variant 1.0
rpoC 764611 c.1242G>T synonymous_variant 1.0
rpoC 764632 c.1263T>C synonymous_variant 0.97
rpoC 764641 c.1272C>T synonymous_variant 0.97
rpoC 764650 c.1281G>T synonymous_variant 0.97
rpoC 764663 p.Val432Thr missense_variant 0.95
rpoC 764668 c.1299C>T synonymous_variant 0.95
rpoC 764672 p.Gln435Glu missense_variant 0.95
rpoC 764677 c.1308C>G synonymous_variant 1.0
rpoC 764695 c.1326T>C synonymous_variant 1.0
rpoC 764701 c.1332C>G synonymous_variant 1.0
rpoC 764705 p.Leu446Lys missense_variant 1.0
rpoC 764716 c.1347G>C synonymous_variant 1.0
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
rrs 1471876 n.31G>A non_coding_transcript_exon_variant 1.0
rrs 1471892 n.47G>A non_coding_transcript_exon_variant 1.0
rrs 1471896 n.51T>C non_coding_transcript_exon_variant 1.0
rrs 1472153 n.308G>A non_coding_transcript_exon_variant 1.0
rrs 1472172 n.327T>C non_coding_transcript_exon_variant 1.0
rrs 1472214 n.369C>G non_coding_transcript_exon_variant 1.0
rrs 1472225 n.380C>A non_coding_transcript_exon_variant 1.0
rrs 1472235 n.390G>C non_coding_transcript_exon_variant 1.0
rrs 1472240 n.395G>A non_coding_transcript_exon_variant 1.0
rrs 1472242 n.397C>T non_coding_transcript_exon_variant 1.0
rrs 1472251 n.406G>A non_coding_transcript_exon_variant 1.0
rrs 1472253 n.408G>T non_coding_transcript_exon_variant 1.0
rrs 1472259 n.414C>A non_coding_transcript_exon_variant 1.0
rrs 1472264 n.419T>C non_coding_transcript_exon_variant 1.0
rrs 1472266 n.421C>A non_coding_transcript_exon_variant 1.0
rrs 1472277 n.432C>G non_coding_transcript_exon_variant 1.0
rrs 1472284 n.439C>T non_coding_transcript_exon_variant 1.0
rrs 1472333 n.488G>T non_coding_transcript_exon_variant 1.0
rrs 1472338 n.493A>C non_coding_transcript_exon_variant 1.0
rrs 1472344 n.499C>T non_coding_transcript_exon_variant 1.0
rrs 1472349 n.504A>C non_coding_transcript_exon_variant 1.0
rrs 1472374 n.529T>G non_coding_transcript_exon_variant 1.0
rrs 1472379 n.534T>G non_coding_transcript_exon_variant 1.0
rrs 1472382 n.537G>T non_coding_transcript_exon_variant 1.0
rrs 1472391 n.546C>T non_coding_transcript_exon_variant 1.0
rrs 1472412 n.567A>C non_coding_transcript_exon_variant 1.0
rrs 1472415 n.570T>A non_coding_transcript_exon_variant 1.0
rrs 1472422 n.577T>C non_coding_transcript_exon_variant 1.0
rrs 1472424 n.579_580insC non_coding_transcript_exon_variant 1.0
rrs 1472586 n.741C>T non_coding_transcript_exon_variant 1.0
rrs 1472598 n.753A>T non_coding_transcript_exon_variant 1.0
rrs 1472616 n.771G>A non_coding_transcript_exon_variant 1.0
rrs 1472697 n.852T>C non_coding_transcript_exon_variant 1.0
rrs 1472714 n.869A>T non_coding_transcript_exon_variant 1.0
rrs 1472715 n.870C>A non_coding_transcript_exon_variant 1.0
rrs 1472716 n.871C>T non_coding_transcript_exon_variant 1.0
rrs 1472742 n.897C>T non_coding_transcript_exon_variant 1.0
rrs 1472770 n.925C>T non_coding_transcript_exon_variant 1.0
rrs 1472781 n.936C>T non_coding_transcript_exon_variant 1.0
rrs 1472793 n.948A>T non_coding_transcript_exon_variant 1.0
rrs 1472803 n.958T>A non_coding_transcript_exon_variant 1.0
rrs 1472812 n.967A>C non_coding_transcript_exon_variant 1.0
rrs 1472824 n.979T>A non_coding_transcript_exon_variant 1.0
rrs 1472826 n.981G>C non_coding_transcript_exon_variant 1.0
rrs 1472887 n.1042G>C non_coding_transcript_exon_variant 1.0
rrs 1473162 n.1317C>G non_coding_transcript_exon_variant 1.0
rrs 1473163 n.1318C>A non_coding_transcript_exon_variant 1.0
rrs 1473164 n.1319C>G non_coding_transcript_exon_variant 1.0
rrs 1473166 n.1321G>A non_coding_transcript_exon_variant 1.0
rrs 1473172 n.1327T>G non_coding_transcript_exon_variant 1.0
rrs 1473177 n.1332G>A non_coding_transcript_exon_variant 1.0
rrs 1473192 n.1347A>G non_coding_transcript_exon_variant 1.0
rrs 1473205 n.1360T>C non_coding_transcript_exon_variant 1.0
rrs 1473223 n.1378G>A non_coding_transcript_exon_variant 1.0
rrs 1473352 n.1507C>G non_coding_transcript_exon_variant 1.0
rrs 1473353 n.1508C>G non_coding_transcript_exon_variant 1.0
rrs 1473358 n.1513G>C non_coding_transcript_exon_variant 1.0
rrs 1473359 n.1514G>C non_coding_transcript_exon_variant 1.0
rrl 1473697 n.40C>G non_coding_transcript_exon_variant 1.0
rrl 1473698 n.41G>T non_coding_transcript_exon_variant 1.0
rrl 1473700 n.43G>C non_coding_transcript_exon_variant 1.0
rrl 1473703 n.46C>G non_coding_transcript_exon_variant 1.0
rrl 1473719 n.62G>C non_coding_transcript_exon_variant 1.0
rrl 1473721 n.64G>C non_coding_transcript_exon_variant 1.0
rrl 1474182 n.525C>G non_coding_transcript_exon_variant 1.0
rrl 1474184 n.527C>A non_coding_transcript_exon_variant 1.0
rrl 1474185 n.528G>C non_coding_transcript_exon_variant 1.0
rrl 1474199 n.542G>A non_coding_transcript_exon_variant 1.0
rrl 1474201 n.544T>C non_coding_transcript_exon_variant 1.0
rrl 1474218 n.561T>A non_coding_transcript_exon_variant 1.0
rrl 1474228 n.571T>C non_coding_transcript_exon_variant 1.0
rrl 1474249 n.592G>C non_coding_transcript_exon_variant 1.0
rrl 1474833 n.1176G>A non_coding_transcript_exon_variant 1.0
rrl 1474864 n.1207C>T non_coding_transcript_exon_variant 1.0
rrl 1474869 n.1212G>T non_coding_transcript_exon_variant 1.0
rrl 1474875 n.1218G>A non_coding_transcript_exon_variant 1.0
rrl 1474876 n.1219T>A non_coding_transcript_exon_variant 1.0
rrl 1474883 n.1226T>C non_coding_transcript_exon_variant 1.0
rrl 1475499 n.1842C>G non_coding_transcript_exon_variant 1.0
rrl 1475526 n.1869C>T non_coding_transcript_exon_variant 1.0
rrl 1475790 n.2133C>A non_coding_transcript_exon_variant 0.6
rrl 1475791 n.2134A>G non_coding_transcript_exon_variant 1.0
rrl 1475803 n.2146T>C non_coding_transcript_exon_variant 1.0
rrl 1475804 n.2147G>C non_coding_transcript_exon_variant 1.0
rrl 1475816 n.2159C>G non_coding_transcript_exon_variant 1.0
rrl 1475817 n.2160A>G non_coding_transcript_exon_variant 1.0
rrl 1475881 n.2224T>C non_coding_transcript_exon_variant 1.0
rrl 1475883 n.2226A>C non_coding_transcript_exon_variant 1.0
rrl 1475892 n.2235A>C non_coding_transcript_exon_variant 0.83
rrl 1476311 n.2654G>C non_coding_transcript_exon_variant 1.0
rrl 1476312 n.2655T>C non_coding_transcript_exon_variant 1.0
rrl 1476313 n.2656G>A non_coding_transcript_exon_variant 1.0
rrl 1476336 n.2679C>G non_coding_transcript_exon_variant 1.0
rrl 1476356 n.2699C>A non_coding_transcript_exon_variant 1.0
rrl 1476357 n.2700T>A non_coding_transcript_exon_variant 1.0
rrl 1476358 n.2701T>C non_coding_transcript_exon_variant 1.0
rrl 1476368 n.2711T>C non_coding_transcript_exon_variant 1.0
rrl 1476369 n.2712C>T non_coding_transcript_exon_variant 1.0
rrl 1476382 n.2725A>G non_coding_transcript_exon_variant 1.0
rrl 1476384 n.2727G>T non_coding_transcript_exon_variant 1.0
rrl 1476408 n.2751G>A non_coding_transcript_exon_variant 1.0
rrl 1476411 n.2754G>A non_coding_transcript_exon_variant 1.0
rrl 1476443 n.2786G>T non_coding_transcript_exon_variant 1.0
rrl 1476455 n.2798C>A non_coding_transcript_exon_variant 1.0
rrl 1476463 n.2806C>T non_coding_transcript_exon_variant 1.0
rrl 1476466 n.2809C>T non_coding_transcript_exon_variant 1.0
rrl 1476470 n.2813C>T non_coding_transcript_exon_variant 1.0
rrl 1476481 n.2824T>C non_coding_transcript_exon_variant 1.0
rrl 1476491 n.2834T>C non_coding_transcript_exon_variant 1.0
rrl 1476501 n.2844C>T non_coding_transcript_exon_variant 1.0
rrl 1476506 n.2849T>C non_coding_transcript_exon_variant 1.0
rrl 1476512 n.2855C>T non_coding_transcript_exon_variant 1.0
rrl 1476517 n.2860C>T non_coding_transcript_exon_variant 1.0
ndh 2102990 p.Val18Ala missense_variant 1.0
folC 2747688 c.-90G>A upstream_gene_variant 1.0
fbiA 3640415 c.-128T>C upstream_gene_variant 1.0
clpC1 4039496 p.Ile403Met missense_variant 1.0
clpC1 4039526 c.1179G>C synonymous_variant 0.67
clpC1 4039533 p.Asn391Thr missense_variant 1.0
clpC1 4039546 p.Asp387Asn missense_variant 1.0
clpC1 4039549 p.Ala386Ser missense_variant 1.0
clpC1 4039559 c.1146C>G synonymous_variant 1.0
clpC1 4039562 c.1143C>G synonymous_variant 1.0
clpC1 4039661 c.1044T>C synonymous_variant 0.67
clpC1 4039664 c.1041G>C synonymous_variant 0.67
clpC1 4039667 p.Gln346Phe missense_variant 0.67
clpC1 4039673 c.1032G>A synonymous_variant 0.67
clpC1 4039682 c.1023C>G synonymous_variant 1.0
clpC1 4039690 p.Glu339Gln missense_variant 1.0
clpC1 4039691 c.1014G>C synonymous_variant 1.0
clpC1 4039697 c.1008C>G synonymous_variant 1.0
clpC1 4039711 p.Ile332Val missense_variant 1.0
clpC1 4039712 c.993C>T synonymous_variant 1.0
clpC1 4039718 c.987C>T synonymous_variant 1.0
aftB 4268958 c.-122A>G upstream_gene_variant 1.0