TB-Profiler result

Run: ERR1950081
Summary

Run ID: ERR1950081

Sample name:

Date: 31-03-2023 15:39:21

Number of reads: 783996

Percentage reads mapped: 99.04

Strain: lineage4.8

Drug-resistance: Sensitive

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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
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
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 5435 p.Asn66Asp missense_variant 0.12
gyrB 5625 p.Asn129Thr missense_variant 0.18
gyrA 7362 p.Glu21Gln missense_variant 1.0
fgd1 490675 c.-108C>T upstream_gene_variant 0.2
fgd1 491297 p.Val172Asp missense_variant 0.67
fgd1 491315 p.Gly178Ala missense_variant 0.43
ccsA 619778 c.-113A>T upstream_gene_variant 0.33
rpoC 764485 c.1116G>T synonymous_variant 0.25
rpoC 765237 p.Asp623Ala missense_variant 0.23
rpoC 765663 p.Leu765* stop_gained 0.25
rpoC 766925 p.Phe1186Ile missense_variant 0.25
mmpL5 775639 p.Ile948Val missense_variant 1.0
mmpL5 775924 p.Leu853Met missense_variant 0.17
mmpL5 776551 p.Thr644Ser missense_variant 0.15
mmpL5 777166 p.Ser439Thr missense_variant 0.2
rpsL 781395 c.-165T>C upstream_gene_variant 1.0
rpsL 781541 c.-19C>A upstream_gene_variant 0.2
rplC 801256 p.Ser150Ala missense_variant 0.19
fbiC 1303091 p.Glu54Gly missense_variant 0.2
fbiC 1303747 p.Thr273Ala missense_variant 1.0
fbiC 1304442 c.1512T>G synonymous_variant 0.18
Rv1258c 1407172 p.Phe57Val missense_variant 0.17
Rv1258c 1407175 p.Leu56Val missense_variant 0.27
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
rrs 1472382 n.537G>A non_coding_transcript_exon_variant 0.25
rrl 1474001 n.344C>T non_coding_transcript_exon_variant 1.0
rrl 1476293 n.2636C>A non_coding_transcript_exon_variant 0.2
rrl 1476429 n.2772A>C non_coding_transcript_exon_variant 0.11
inhA 1674576 c.375T>C synonymous_variant 0.12
inhA 1674650 p.Asp150Ala missense_variant 0.2
rpsA 1834518 p.Leu326Arg missense_variant 0.4
tlyA 1917835 c.-105A>T upstream_gene_variant 0.27
tlyA 1917972 c.33A>G synonymous_variant 1.0
ndh 2102610 p.Leu145Val missense_variant 0.38
katG 2153994 c.2118G>T synonymous_variant 0.38
katG 2154963 c.1149G>T synonymous_variant 0.15
katG 2155769 p.Ile115Phe missense_variant 0.4
katG 2155785 c.327T>G synonymous_variant 0.5
katG 2156029 p.Tyr28Phe missense_variant 0.15
PPE35 2168728 p.Gly629Arg missense_variant 1.0
PPE35 2169515 c.1098T>A synonymous_variant 0.23
PPE35 2169814 p.Phe267Ile missense_variant 0.4
PPE35 2170048 p.Leu189Val missense_variant 0.75
PPE35 2170053 p.Thr187Ser missense_variant 0.75
PPE35 2170066 p.Ala183Thr missense_variant 0.5
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
pncA 2289075 p.Asp56Ala missense_variant 0.33
ahpC 2726550 p.Gln120* stop_gained 0.22
ahpC 2726606 c.414C>A synonymous_variant 0.17
folC 2746784 p.Val272Gly missense_variant 0.29
folC 2746921 c.678T>C synonymous_variant 0.2
folC 2747342 p.Val86Gly missense_variant 0.31
ribD 2987266 p.Leu143Arg missense_variant 0.27
Rv2752c 3065360 p.Phe278Val missense_variant 0.29
Rv2752c 3065395 p.Met266Arg missense_variant 0.22
Rv2752c 3065497 p.Arg232Leu missense_variant 0.25
Rv2752c 3066103 p.Asn30Ser missense_variant 0.22
thyX 3067285 p.Ala221Ser missense_variant 0.22
thyX 3067566 p.Asp127Ala missense_variant 0.22
fbiD 3339300 c.183T>A synonymous_variant 0.33
fbiD 3339567 c.450A>G synonymous_variant 0.18
fbiD 3339577 p.Phe154Val missense_variant 0.18
fprA 3475010 p.Asp335Gly missense_variant 0.22
fbiB 3641589 p.Gly19Arg missense_variant 0.11
fbiB 3641716 p.Val61Gly missense_variant 0.2
rpoA 3878486 p.Thr8Pro missense_variant 0.22
rpoA 3878490 c.18C>G synonymous_variant 0.29
ddn 3986901 p.Trp20Arg missense_variant 0.2
ddn 3987115 p.Asn91Thr missense_variant 0.17
embA 4242643 c.-590C>T upstream_gene_variant 1.0
embA 4244863 p.Leu544Arg missense_variant 0.33
embA 4245792 p.Ser854Pro missense_variant 0.22
embB 4248861 p.Val783Gly missense_variant 0.2
aftB 4267685 c.1152T>G synonymous_variant 0.33
aftB 4268046 p.Tyr264Ser missense_variant 0.19
aftB 4269315 c.-479C>T upstream_gene_variant 0.22
ubiA 4269848 c.-15A>T upstream_gene_variant 0.2
ethA 4326852 p.Ser208Ala missense_variant 0.22
whiB6 4338595 c.-75delG upstream_gene_variant 1.0
gid 4407582 c.621T>C synonymous_variant 0.17
Rv3083 3448507 c.5_*1408del frameshift_variant&stop_lost&splice_region_variant 1.0