TB-Profiler result

Run: SRR6896478
Summary

Run ID: SRR6896478

Sample name:

Date: 04-04-2023 18:07:19

Number of reads: 514513

Percentage reads mapped: 99.53

Strain: lineage4.4.2

Drug-resistance: HR-TB

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
lineage4.4 Euro-American S;T None 1.0
lineage4.4.2 Euro-American T1;T2 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 2154218 p.Arg632Cys missense_variant 0.11 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 7585 p.Ser95Thr missense_variant 1.0
gyrA 8526 p.Arg409Trp missense_variant 0.13
gyrA 9010 c.1714_1716dupACC conservative_inframe_insertion 0.12
gyrA 9304 p.Gly668Asp missense_variant 1.0
fgd1 491269 p.Tyr163His missense_variant 0.13
fgd1 491281 p.Asp167Asn missense_variant 0.13
ccsA 620110 p.Glu74Lys missense_variant 0.14
rpoB 760561 p.Met252Arg missense_variant 0.1
rpoB 761833 c.2029delT frameshift_variant 0.11
rpoC 764272 c.903G>A synonymous_variant 0.13
rpoC 765625 c.2256C>T synonymous_variant 0.17
rpoC 766405 p.Met1012Ile missense_variant 0.1
rpoC 766682 p.Val1105Leu missense_variant 0.11
mmpL5 775639 p.Ile948Val missense_variant 1.0
mmpL5 777132 p.Val450Ala missense_variant 0.13
mmpL5 777232 p.Asp417Tyr missense_variant 0.17
mmpL5 778699 c.-219C>A upstream_gene_variant 0.12
mmpL5 779376 c.-896C>A upstream_gene_variant 0.11
rpsL 781395 c.-165T>C upstream_gene_variant 1.0
fbiC 1303360 p.Leu144Ile missense_variant 0.11
fbiC 1304700 p.Glu590Asp missense_variant 0.12
atpE 1460871 c.-174T>A upstream_gene_variant 0.12
atpE 1460879 c.-166C>G upstream_gene_variant 0.12
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
rrs 1472361 n.516C>A non_coding_transcript_exon_variant 0.22
rrs 1472780 n.935G>T non_coding_transcript_exon_variant 0.12
rrl 1473655 n.-3T>A upstream_gene_variant 0.11
rrl 1474156 n.499G>A non_coding_transcript_exon_variant 0.11
rrl 1475175 n.1518G>C non_coding_transcript_exon_variant 0.29
inhA 1673568 c.-634C>A upstream_gene_variant 0.11
fabG1 1673573 p.Thr45Asn missense_variant 0.1
inhA 1673916 c.-286A>G upstream_gene_variant 0.18
fabG1 1673944 p.Arg169Cys missense_variant 0.17
tlyA 1917872 c.-67delC upstream_gene_variant 0.14
tlyA 1917972 c.33A>G synonymous_variant 1.0
ndh 2101651 c.1392G>T stop_lost&splice_region_variant 0.15
ndh 2101902 p.Lys381Glu missense_variant 0.11
ndh 2101964 p.Glu360Val missense_variant 0.11
ndh 2103020 p.Thr8Arg missense_variant 0.12
katG 2156204 c.-93A>T upstream_gene_variant 0.11
PPE35 2168757 p.Gln619Arg missense_variant 1.0
PPE35 2170048 p.Leu189Val missense_variant 0.18
PPE35 2170053 p.Thr187Ser missense_variant 0.18
PPE35 2170254 p.Leu120Pro missense_variant 0.2
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
pncA 2290167 c.-926G>T upstream_gene_variant 0.11
kasA 2518678 c.564C>A synonymous_variant 0.14
eis 2714797 p.Tyr179Phe missense_variant 0.12
folC 2747553 p.Gly16Ser missense_variant 0.15
pepQ 2860132 p.Gly96Val missense_variant 0.12
Rv2752c 3066099 p.Met31Ile missense_variant 1.0
Rv2752c 3066290 c.-99G>A upstream_gene_variant 0.12
thyX 3067355 c.591A>G synonymous_variant 0.14
thyA 3074043 c.429G>T synonymous_variant 0.12
ald 3086788 c.-32T>C upstream_gene_variant 1.0
ald 3087912 p.Glu365* stop_gained 0.2
ald 3087917 c.1098C>G synonymous_variant 0.15
Rv3083 3448348 c.-156G>A upstream_gene_variant 1.0
Rv3083 3448632 c.129C>A synonymous_variant 0.11
Rv3083 3448918 p.Cys139Arg missense_variant 0.13
Rv3083 3449294 p.Leu264Pro missense_variant 0.14
Rv3083 3449365 p.Pro288Thr missense_variant 0.15
fprA 3473996 c.-11_-10insA upstream_gene_variant 1.0
fbiA 3641038 p.Ala166Thr missense_variant 0.12
alr 3840212 c.1209C>T synonymous_variant 1.0
alr 3841187 c.232_233delGC frameshift_variant 0.11
clpC1 4039083 p.Asp541Gly missense_variant 0.1
clpC1 4039352 c.1353C>T synonymous_variant 0.18
clpC1 4040188 p.Gln173* stop_gained 0.13
panD 4043929 p.Gly118Val missense_variant 0.15
embC 4240109 p.Asn83Tyr missense_variant 0.12
embC 4240969 p.His369Gln missense_variant 0.17
embC 4242521 p.Ala887Ser missense_variant 0.2
embA 4242643 c.-590C>T upstream_gene_variant 1.0
embA 4242652 c.-581C>T upstream_gene_variant 0.13
embA 4244033 p.Ile267Met missense_variant 0.17
embA 4244663 c.1431C>G synonymous_variant 0.22
embA 4244840 c.1608G>T synonymous_variant 0.2
embA 4245951 p.Pro907Ser missense_variant 0.18
embB 4246508 c.-6G>A upstream_gene_variant 1.0
embB 4246690 c.177A>T synonymous_variant 0.13
embB 4247249 p.Gly246Arg missense_variant 1.0
aftB 4268928 c.-92C>T upstream_gene_variant 1.0
aftB 4269375 c.-539G>A upstream_gene_variant 1.0
ethA 4328364 c.-891C>A upstream_gene_variant 0.11
whiB6 4338595 c.-75delG upstream_gene_variant 1.0