TB-Profiler result

Run: ERR2229314
Summary

Run ID: ERR2229314

Sample name:

Date: 31-03-2023 17:00:44

Number of reads: 1270203

Percentage reads mapped: 98.74

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
gyrA 6580 c.-722C>A upstream_gene_variant 0.17
gyrA 7362 p.Glu21Gln missense_variant 1.0
ccsA 620093 p.Arg68Gln missense_variant 0.15
ccsA 620400 p.Tyr170* stop_gained 0.13
ccsA 620636 p.Ile249Ser missense_variant 0.18
rpoB 761152 p.Leu449Gln missense_variant 0.16
rpoC 763572 p.Val68Glu missense_variant 0.12
rpoC 764059 c.690G>T synonymous_variant 0.15
rpoC 764541 p.Val391Gly missense_variant 0.18
rpoC 765121 c.1752G>A synonymous_variant 0.12
rpoC 766197 c.2830dupC frameshift_variant 0.12
mmpL5 775639 p.Ile948Val missense_variant 1.0
mmpL5 775747 p.Met912Leu missense_variant 0.12
mmpL5 775748 c.2733T>C synonymous_variant 0.12
mmpL5 775962 p.Val840Asp missense_variant 0.18
mmpL5 776347 p.Asp712Tyr missense_variant 0.14
mmpL5 777118 p.Asp455His missense_variant 0.13
rpsL 781395 c.-165T>C upstream_gene_variant 1.0
fbiC 1303728 c.798G>A synonymous_variant 0.12
fbiC 1303747 p.Thr273Ala missense_variant 1.0
fbiC 1304349 p.Trp473* stop_gained 0.22
atpE 1461054 p.Thr4Ala missense_variant 0.11
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
rrs 1472431 n.586G>C non_coding_transcript_exon_variant 0.11
rrl 1474001 n.344C>T non_coding_transcript_exon_variant 1.0
rrl 1476628 n.2971T>G non_coding_transcript_exon_variant 0.12
rrl 1476629 n.2972C>A non_coding_transcript_exon_variant 0.12
rrl 1476630 n.2973A>T non_coding_transcript_exon_variant 0.12
fabG1 1673346 c.-94C>G upstream_gene_variant 0.2
fabG1 1673349 c.-91G>C upstream_gene_variant 0.2
fabG1 1673357 c.-83G>A upstream_gene_variant 0.13
fabG1 1673359 c.-81T>C upstream_gene_variant 0.13
fabG1 1673361 c.-79C>G upstream_gene_variant 0.13
fabG1 1673380 c.-60C>G upstream_gene_variant 0.24
rpsA 1833392 c.-150C>A upstream_gene_variant 0.12
tlyA 1917972 c.33A>G synonymous_variant 1.0
tlyA 1918381 p.Val148Phe missense_variant 0.11
ndh 2102421 c.621delC frameshift_variant 0.18
ndh 2102949 p.Lys32* stop_gained 0.17
PPE35 2168728 p.Gly629Arg missense_variant 1.0
PPE35 2169394 p.Ala407Thr missense_variant 0.12
PPE35 2170048 p.Leu189Val missense_variant 0.62
PPE35 2170053 p.Thr187Ser missense_variant 0.58
PPE35 2170363 p.Glu84Gln missense_variant 0.14
PPE35 2170528 p.Ser29Ala missense_variant 0.14
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
pncA 2289488 c.-247G>A upstream_gene_variant 0.13
folC 2746248 p.Ala451Ser missense_variant 0.22
folC 2746475 p.Leu375Pro missense_variant 0.12
ribD 2987029 p.Gly64Val missense_variant 0.29
Rv2752c 3066255 c.-64C>T upstream_gene_variant 0.14
Rv2752c 3067115 c.-924G>A upstream_gene_variant 0.14
thyX 3067563 p.Leu128Pro missense_variant 0.15
Rv3236c 3612423 p.Val232Leu missense_variant 0.17
rpoA 3878395 p.Leu38Pro missense_variant 0.2
rpoA 3878567 c.-60C>G upstream_gene_variant 1.0
rpoA 3878569 c.-63_-62insG upstream_gene_variant 1.0
rpoA 3878599 c.-92C>G upstream_gene_variant 0.75
clpC1 4038855 p.Lys617Arg missense_variant 0.11
clpC1 4038915 p.Ala597Val missense_variant 0.14
clpC1 4040024 c.681A>G synonymous_variant 0.11
clpC1 4040027 c.678C>G synonymous_variant 0.11
clpC1 4040032 p.Val225Ile missense_variant 0.12
clpC1 4040057 c.648C>T synonymous_variant 0.12
clpC1 4040276 c.429C>A synonymous_variant 0.2
embC 4240972 c.1110C>T synonymous_variant 0.14
embC 4242512 p.Val884Leu missense_variant 0.18
embA 4242643 c.-590C>T upstream_gene_variant 1.0
embA 4244772 p.Ser514Ala missense_variant 0.25
embA 4245950 p.Gln906His missense_variant 0.14
embA 4246122 p.Leu964Val missense_variant 0.25
embA 4246136 p.Gln968His missense_variant 0.18
embB 4246544 p.Thr11Pro missense_variant 0.57
embB 4246548 p.Pro12Gln missense_variant 0.61
embB 4246555 c.42G>C synonymous_variant 0.71
embB 4246556 p.Ala15Pro missense_variant 0.71
embB 4246563 p.Leu17Trp missense_variant 0.56
embB 4246567 c.54G>T synonymous_variant 0.5
embB 4249669 p.Tyr1052* stop_gained 0.15
ethR 4327853 p.Met102Thr missense_variant 0.11
whiB6 4338595 c.-75delG upstream_gene_variant 1.0
Rv3083 3448507 c.5_*1408del frameshift_variant&stop_lost&splice_region_variant 1.0