Run ID: ERR2229708
Sample name:
Date: 31-03-2023 17:28:23
Number of reads: 976512
Percentage reads mapped: 99.0
Strain: lineage4.8
Drug-resistance: HR-TB
Drug | Resistance | Supporting mutations |
---|
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 | 0.99 |
Gene | Chromosome position | Mutation | Type | Estimated fraction | Drugs |
---|---|---|---|---|---|
katG | 2154955 | c.1156delG | frameshift_variant | 0.14 | isoniazid |
Gene | Chromosome position | Mutation | Type | Estimated fraction |
---|---|---|---|---|
gyrB | 6243 | p.Arg335Leu | missense_variant | 0.15 |
gyrA | 7362 | p.Glu21Gln | missense_variant | 1.0 |
gyrA | 7707 | p.Pro136Thr | missense_variant | 0.13 |
fgd1 | 491371 | p.Gly197Ser | missense_variant | 0.15 |
rpoC | 762524 | c.-846G>A | upstream_gene_variant | 0.15 |
rpoC | 766598 | p.Tyr1077His | missense_variant | 0.11 |
rpoC | 767187 | p.Gln1273Pro | missense_variant | 0.15 |
mmpL5 | 775639 | p.Ile948Val | missense_variant | 1.0 |
mmpL5 | 775721 | p.Ile920Val | missense_variant | 0.12 |
mmpL5 | 776397 | p.Val695Ala | missense_variant | 0.1 |
mmpL5 | 776402 | c.2079C>G | synonymous_variant | 0.11 |
mmpL5 | 776405 | c.2076T>G | synonymous_variant | 0.11 |
mmpL5 | 776847 | p.Gln545Arg | missense_variant | 0.15 |
mmpL5 | 777115 | p.Met456Leu | missense_variant | 0.15 |
mmpL5 | 777122 | c.1359C>T | synonymous_variant | 0.17 |
mmpL5 | 777126 | p.Ser452Ala | missense_variant | 0.18 |
mmpL5 | 777128 | c.1353A>G | synonymous_variant | 0.18 |
mmpL5 | 777140 | c.1341G>C | synonymous_variant | 0.2 |
mmpS5 | 779676 | c.-771C>T | upstream_gene_variant | 0.18 |
rpsL | 781395 | c.-165T>C | upstream_gene_variant | 1.0 |
fbiC | 1303747 | p.Thr273Ala | missense_variant | 1.0 |
fbiC | 1304180 | p.Leu417Pro | missense_variant | 0.12 |
fbiC | 1304214 | c.1284C>T | synonymous_variant | 0.11 |
Rv1258c | 1406456 | c.885T>C | synonymous_variant | 0.11 |
rrs | 1471659 | n.-187C>T | upstream_gene_variant | 1.0 |
rrs | 1472535 | n.690C>T | non_coding_transcript_exon_variant | 0.17 |
rrs | 1473156 | n.1311A>T | non_coding_transcript_exon_variant | 0.12 |
rrl | 1474001 | n.344C>T | non_coding_transcript_exon_variant | 1.0 |
rrl | 1475820 | n.2163C>A | non_coding_transcript_exon_variant | 0.14 |
rrl | 1476212 | n.2555T>A | non_coding_transcript_exon_variant | 0.33 |
fabG1 | 1673380 | c.-60C>G | upstream_gene_variant | 0.11 |
fabG1 | 1673770 | p.Ala111Thr | missense_variant | 0.14 |
inhA | 1673796 | c.-406G>C | upstream_gene_variant | 0.12 |
fabG1 | 1674097 | p.Val220Leu | missense_variant | 0.14 |
rpsA | 1834369 | c.828C>T | synonymous_variant | 0.12 |
tlyA | 1917972 | c.33A>G | synonymous_variant | 1.0 |
tlyA | 1918256 | p.Ala106Asp | missense_variant | 0.12 |
katG | 2154217 | p.Arg632His | missense_variant | 0.13 |
katG | 2154888 | c.1224C>T | synonymous_variant | 0.14 |
PPE35 | 2167745 | p.Thr956Arg | missense_variant | 0.14 |
PPE35 | 2168728 | p.Gly629Arg | missense_variant | 1.0 |
PPE35 | 2170048 | p.Leu189Val | missense_variant | 0.56 |
PPE35 | 2170053 | p.Thr187Ser | missense_variant | 0.57 |
Rv1979c | 2222000 | p.Val389Met | missense_variant | 0.2 |
Rv1979c | 2223135 | c.30G>A | synonymous_variant | 0.13 |
Rv1979c | 2223293 | c.-129A>G | upstream_gene_variant | 1.0 |
eis | 2714845 | p.Val163Asp | missense_variant | 0.15 |
folC | 2746437 | p.Asp388Tyr | missense_variant | 0.14 |
pepQ | 2859606 | c.813G>T | synonymous_variant | 0.15 |
pepQ | 2860606 | c.-188C>T | upstream_gene_variant | 0.14 |
Rv2752c | 3065861 | c.331C>T | synonymous_variant | 0.11 |
thyX | 3067499 | c.447G>A | synonymous_variant | 0.2 |
fprA | 3474883 | p.Glu293Lys | missense_variant | 0.2 |
fprA | 3474914 | p.Ala303Glu | missense_variant | 0.25 |
Rv3236c | 3612905 | p.Leu71Ser | missense_variant | 0.1 |
alr | 3841546 | c.-126C>A | upstream_gene_variant | 0.2 |
rpoA | 3878599 | c.-92C>G | upstream_gene_variant | 0.8 |
rpoA | 3878639 | c.-132C>G | upstream_gene_variant | 0.67 |
clpC1 | 4038170 | c.2535G>A | synonymous_variant | 0.12 |
panD | 4044280 | c.2T>A | start_lost | 0.14 |
embA | 4242643 | c.-590C>T | upstream_gene_variant | 1.0 |
embA | 4245367 | p.Arg712Leu | missense_variant | 0.12 |
embA | 4246380 | p.Trp1050Arg | missense_variant | 0.17 |
embB | 4246548 | p.Pro12Gln | missense_variant | 0.5 |
embB | 4246555 | c.42G>C | synonymous_variant | 0.54 |
embB | 4246556 | p.Ala15Pro | missense_variant | 0.54 |
embB | 4246563 | p.Leu17Trp | missense_variant | 0.22 |
embB | 4246567 | c.54_55insT | frameshift_variant | 0.2 |
ubiA | 4269608 | p.Arg76Cys | missense_variant | 0.11 |
ethA | 4326075 | p.Leu467Ile | missense_variant | 0.12 |
ethA | 4327150 | p.Asp108Glu | missense_variant | 0.11 |
ethA | 4327496 | c.-23C>A | upstream_gene_variant | 0.17 |
whiB6 | 4338595 | c.-75delG | upstream_gene_variant | 1.0 |
gid | 4407660 | c.543G>A | synonymous_variant | 0.12 |
Rv3083 | 3448507 | c.5_*1408del | frameshift_variant&stop_lost&splice_region_variant | 1.0 |