Run ID: SRR1062927
Sample name:
Date: 02-04-2023 18:41:12
Number of reads: 1244332
Percentage reads mapped: 49.74
Strain: lineage4.6.1
Drug-resistance: MDR-TB
Drug | Resistance | Supporting mutations |
---|
Lineage | Family | Main Spoligotype | RDs | Frequency |
---|---|---|---|---|
lineage4 | Euro-American | LAM;T;S;X;H | None | 1.0 |
lineage4.6 | Euro-American | T;LAM | None | 0.99 |
lineage4.6.1 | Euro-American (Uganda) | T2 | RD724 | 1.0 |
Gene | Chromosome position | Mutation | Type | Estimated fraction | Drugs |
---|---|---|---|---|---|
rpoB | 761155 | p.Ser450Leu | missense_variant | 1.0 | rifampicin |
katG | 2155168 | p.Ser315Thr | missense_variant | 1.0 | isoniazid |
pncA | 2288933 | p.Tyr103* | stop_gained | 0.17 | pyrazinamide |
embB | 4247431 | p.Met306Ile | missense_variant | 1.0 | ethambutol |
gid | 4407851 | c.351delG | frameshift_variant | 1.0 | streptomycin |
Gene | Chromosome position | Mutation | Type | Estimated fraction |
---|---|---|---|---|
gyrB | 7038 | p.Lys600Arg | missense_variant | 0.12 |
gyrA | 7362 | p.Glu21Gln | missense_variant | 1.0 |
gyrA | 7539 | p.Thr80Ala | missense_variant | 1.0 |
gyrA | 7585 | p.Ser95Thr | missense_variant | 1.0 |
gyrA | 7709 | c.408G>A | synonymous_variant | 1.0 |
gyrA | 9304 | p.Gly668Asp | missense_variant | 1.0 |
mshA | 575560 | p.Tyr71* | stop_gained | 0.1 |
ccsA | 619994 | p.Glu35Gly | missense_variant | 0.12 |
ccsA | 620001 | c.111C>A | synonymous_variant | 0.12 |
ccsA | 620550 | c.660C>A | synonymous_variant | 0.15 |
rpoC | 762887 | c.-483G>C | upstream_gene_variant | 0.1 |
rpoC | 762899 | c.-471G>C | upstream_gene_variant | 0.19 |
rpoC | 762917 | c.-453C>G | upstream_gene_variant | 0.19 |
rpoC | 762920 | c.-450C>T | upstream_gene_variant | 0.18 |
rpoC | 762923 | c.-447C>G | upstream_gene_variant | 0.18 |
rpoB | 762925 | p.Thr1040Ile | missense_variant | 0.17 |
rpoB | 762934 | c.3129_3130insAGCC | frameshift_variant | 0.17 |
rpoB | 762938 | c.3133_3136delATGA | frameshift_variant | 0.17 |
rpoC | 762989 | c.-381G>C | upstream_gene_variant | 0.1 |
rpoC | 763702 | c.334delT | frameshift_variant | 0.11 |
rpoC | 764383 | c.1014C>G | synonymous_variant | 0.11 |
rpoC | 764575 | c.1206T>G | synonymous_variant | 0.12 |
rpoC | 764581 | c.1212T>C | synonymous_variant | 0.16 |
rpoC | 764582 | p.Leu405Met | missense_variant | 0.2 |
rpoC | 764587 | c.1218C>G | synonymous_variant | 0.23 |
rpoC | 764593 | c.1224C>T | synonymous_variant | 0.29 |
rpoC | 764605 | c.1236G>C | synonymous_variant | 0.41 |
rpoC | 764611 | c.1242G>T | synonymous_variant | 0.4 |
rpoC | 764632 | c.1263T>C | synonymous_variant | 0.38 |
rpoC | 764641 | c.1272C>T | synonymous_variant | 0.38 |
rpoC | 764650 | c.1281G>T | synonymous_variant | 0.38 |
rpoC | 764663 | p.Val432Thr | missense_variant | 0.35 |
rpoC | 764672 | p.Gln435Glu | missense_variant | 0.32 |
rpoC | 764677 | c.1308C>G | synonymous_variant | 0.31 |
rpoC | 764695 | c.1326T>C | synonymous_variant | 0.22 |
rpoC | 766488 | p.Pro1040Arg | missense_variant | 1.0 |
mmpL5 | 775639 | p.Ile948Val | missense_variant | 1.0 |
mmpR5 | 779389 | p.Arg134Gly | missense_variant | 0.1 |
rpsL | 781395 | c.-165T>C | upstream_gene_variant | 1.0 |
rplC | 800901 | c.96delG | frameshift_variant | 0.12 |
fbiC | 1302930 | c.-1C>G | upstream_gene_variant | 0.12 |
fbiC | 1303138 | p.Leu70Val | missense_variant | 0.12 |
Rv1258c | 1406238 | p.Gly368Asp | missense_variant | 0.12 |
rrs | 1471659 | n.-187C>T | upstream_gene_variant | 1.0 |
rrs | 1472172 | n.327T>C | non_coding_transcript_exon_variant | 0.41 |
rrs | 1472214 | n.369C>G | non_coding_transcript_exon_variant | 0.48 |
rrs | 1472225 | n.380C>A | non_coding_transcript_exon_variant | 0.47 |
rrs | 1472235 | n.390G>C | non_coding_transcript_exon_variant | 0.45 |
rrs | 1472240 | n.395G>A | non_coding_transcript_exon_variant | 0.43 |
rrs | 1472242 | n.397C>T | non_coding_transcript_exon_variant | 0.38 |
rrs | 1472251 | n.406G>A | non_coding_transcript_exon_variant | 0.33 |
rrs | 1472253 | n.408G>T | non_coding_transcript_exon_variant | 0.27 |
rrs | 1472259 | n.414C>A | non_coding_transcript_exon_variant | 0.23 |
rrs | 1472264 | n.419T>C | non_coding_transcript_exon_variant | 0.24 |
rrs | 1472266 | n.421C>A | non_coding_transcript_exon_variant | 0.24 |
rrs | 1472277 | n.432C>G | non_coding_transcript_exon_variant | 0.2 |
rrs | 1472333 | n.488G>T | non_coding_transcript_exon_variant | 0.15 |
rrs | 1472338 | n.493A>C | non_coding_transcript_exon_variant | 0.16 |
rrs | 1472344 | n.499C>T | non_coding_transcript_exon_variant | 0.17 |
rrs | 1472349 | n.504A>C | non_coding_transcript_exon_variant | 0.17 |
rrs | 1472374 | n.529T>G | non_coding_transcript_exon_variant | 0.21 |
rrs | 1472379 | n.534T>G | non_coding_transcript_exon_variant | 0.21 |
rrs | 1472382 | n.537G>T | non_coding_transcript_exon_variant | 0.21 |
rrs | 1472391 | n.546C>T | non_coding_transcript_exon_variant | 0.18 |
rrs | 1472412 | n.567A>C | non_coding_transcript_exon_variant | 0.12 |
rrs | 1472422 | n.577T>C | non_coding_transcript_exon_variant | 0.11 |
rrs | 1472427 | n.582T>A | non_coding_transcript_exon_variant | 1.0 |
rrs | 1472590 | n.745C>T | non_coding_transcript_exon_variant | 0.12 |
rrs | 1472697 | n.852T>C | non_coding_transcript_exon_variant | 0.12 |
rrs | 1472714 | n.869A>T | non_coding_transcript_exon_variant | 0.23 |
rrs | 1472715 | n.870C>A | non_coding_transcript_exon_variant | 0.21 |
rrs | 1472716 | n.871C>T | non_coding_transcript_exon_variant | 0.21 |
rrs | 1472742 | n.897C>T | non_coding_transcript_exon_variant | 0.36 |
rrs | 1472770 | n.925C>T | non_coding_transcript_exon_variant | 0.38 |
rrs | 1472781 | n.936C>T | non_coding_transcript_exon_variant | 0.36 |
rrs | 1472793 | n.948A>T | non_coding_transcript_exon_variant | 0.37 |
rrs | 1472803 | n.958T>A | non_coding_transcript_exon_variant | 0.27 |
rrs | 1472812 | n.967A>C | non_coding_transcript_exon_variant | 0.26 |
rrs | 1472824 | n.979T>A | non_coding_transcript_exon_variant | 0.2 |
rrs | 1472826 | n.981G>C | non_coding_transcript_exon_variant | 0.19 |
rrl | 1475803 | n.2146T>C | non_coding_transcript_exon_variant | 0.28 |
rrl | 1475804 | n.2147G>C | non_coding_transcript_exon_variant | 0.28 |
rrl | 1475816 | n.2159C>G | non_coding_transcript_exon_variant | 0.26 |
rrl | 1475817 | n.2160A>G | non_coding_transcript_exon_variant | 0.26 |
rrl | 1475881 | n.2224T>C | non_coding_transcript_exon_variant | 0.26 |
rrl | 1475883 | n.2226A>C | non_coding_transcript_exon_variant | 0.26 |
rrl | 1476299 | n.2642C>A | non_coding_transcript_exon_variant | 0.12 |
rrl | 1476311 | n.2654G>C | non_coding_transcript_exon_variant | 0.1 |
rrl | 1476312 | n.2655T>C | non_coding_transcript_exon_variant | 0.1 |
rrl | 1476336 | n.2679C>G | non_coding_transcript_exon_variant | 0.52 |
rrl | 1476356 | n.2699C>A | non_coding_transcript_exon_variant | 0.54 |
rrl | 1476357 | n.2700T>A | non_coding_transcript_exon_variant | 0.54 |
rrl | 1476358 | n.2701T>C | non_coding_transcript_exon_variant | 0.55 |
rrl | 1476368 | n.2711T>C | non_coding_transcript_exon_variant | 0.55 |
rrl | 1476369 | n.2712C>T | non_coding_transcript_exon_variant | 0.6 |
rrl | 1476382 | n.2725A>G | non_coding_transcript_exon_variant | 0.63 |
rrl | 1476384 | n.2727G>T | non_coding_transcript_exon_variant | 0.6 |
rrl | 1476408 | n.2751G>A | non_coding_transcript_exon_variant | 0.69 |
rrl | 1476411 | n.2754G>A | non_coding_transcript_exon_variant | 0.67 |
rrl | 1476443 | n.2786G>T | non_coding_transcript_exon_variant | 0.65 |
rrl | 1476455 | n.2798C>A | non_coding_transcript_exon_variant | 0.64 |
rrl | 1476463 | n.2806C>T | non_coding_transcript_exon_variant | 0.63 |
rrl | 1476466 | n.2809C>T | non_coding_transcript_exon_variant | 0.68 |
rrl | 1476470 | n.2813C>T | non_coding_transcript_exon_variant | 0.61 |
rrl | 1476481 | n.2824T>C | non_coding_transcript_exon_variant | 0.57 |
rrl | 1476491 | n.2834T>C | non_coding_transcript_exon_variant | 0.42 |
rrl | 1476501 | n.2844C>T | non_coding_transcript_exon_variant | 0.31 |
rrl | 1476506 | n.2849T>C | non_coding_transcript_exon_variant | 0.32 |
rrl | 1476512 | n.2855C>T | non_coding_transcript_exon_variant | 0.22 |
tlyA | 1917972 | c.33A>G | synonymous_variant | 1.0 |
tlyA | 1918139 | p.Ala67Val | missense_variant | 0.14 |
ndh | 2103187 | c.-145G>C | upstream_gene_variant | 0.1 |
katG | 2155437 | p.Met225Ile | missense_variant | 0.15 |
katG | 2155493 | p.Asp207His | missense_variant | 0.11 |
PPE35 | 2168151 | p.Thr821Ile | missense_variant | 0.12 |
Rv1979c | 2223293 | c.-129A>G | upstream_gene_variant | 1.0 |
pncA | 2288784 | p.Thr153Ile | missense_variant | 0.32 |
pncA | 2290220 | c.-979G>T | upstream_gene_variant | 0.13 |
pepQ | 2859792 | p.Asp209Glu | missense_variant | 0.12 |
Rv2752c | 3065548 | p.Glu215Gly | missense_variant | 0.1 |
fprA | 3473996 | c.-11_-10insA | upstream_gene_variant | 1.0 |
fprA | 3474177 | c.171C>T | synonymous_variant | 1.0 |
fbiA | 3641357 | c.818delG | frameshift_variant | 0.13 |
rpoA | 3878672 | c.-165A>T | upstream_gene_variant | 0.13 |
embA | 4242643 | c.-590C>T | upstream_gene_variant | 1.0 |
embB | 4245962 | c.-552G>A | upstream_gene_variant | 1.0 |
embB | 4249187 | p.Tyr892Asp | missense_variant | 0.15 |
embB | 4249286 | p.Gln925Glu | missense_variant | 0.15 |
aftB | 4267581 | p.Gly419Val | missense_variant | 0.12 |
aftB | 4268519 | c.318C>T | synonymous_variant | 0.96 |
ubiA | 4269670 | p.Val55Gly | missense_variant | 1.0 |
ethA | 4327196 | p.Gly93Glu | missense_variant | 0.14 |
ethA | 4328329 | c.-856C>G | upstream_gene_variant | 1.0 |
whiB6 | 4338595 | c.-75delG | upstream_gene_variant | 1.0 |
gid | 4407742 | p.Arg154Gln | missense_variant | 1.0 |
gid | 4408198 | p.Ser2Cys | missense_variant | 0.1 |