This repository contains the code and data required to download raw sequencing reads from the SRA and perform quality trimming, alignment, and variant calling.
You can download this as a tsv here.
| Treatment | Type | Label | Mutation | Locus tag | Annotation | Function | Run |
|---|---|---|---|---|---|---|---|
| PG | population | 4 | frameshift variant c.117delG p.Gly41fs | PROKKA_01659 | hemY | Protoporphyrinogen oxidase | SRR18771780 |
| PG | colony | 4-s-c1 | frameshift variant c.117delG p.Gly41fs | PROKKA_01659 | hemY | Protoporphyrinogen oxidase | SRR18771792 |
| PG | population | 32 | frameshift variant c.117delG p.Gly41fs | PROKKA_01659 | hemY | Protoporphyrinogen oxidase | SRR18771797 |
| PG | colony | 32-s-c1 | frameshift variant c.117delG p.Gly41fs | PROKKA_01659 | hemY | Protoporphyrinogen oxidase | SRR18771786 |
| PG | population | 4 | stop gained c.991A>T p.Lys331* | PROKKA_01871 | cls2 | Cardiolipin synthase | SRR18771780 |
| PG | colony | 4-s-c1 | stop gained c.991A>T p.Lys331* | PROKKA_01871 | cls2 | Cardiolipin synthase | SRR18771792 |
| PG | population | 32 | frameshift variant c.786delA p.Lys262fs | PROKKA_01871 | cls2 | Cardiolipin synthase | SRR18771797 |
| PG | colony | 32-s-c1 | frameshift variant c.786delA p.Lys262fs | PROKKA_01871 | cls2 | Cardiolipin synthase | SRR18771786 |
| PG | population | 33 | stop lost c.1485A>T p.Ter495Tyrext*? | PROKKA_01871 | cls2 | Cardiolipin synthase | SRR18771796 |
| PG | colony | 33-s-c1 | stop lost c.1485A>T p.Ter495Tyrext*? | PROKKA_01871 | cls2 | Cardiolipin synthase | SRR18771785 |
| PG | colony | 32-s-c1 | missense variant c.515C>T p.Pro172Leu | PROKKA_01192 | parE | DNA topoisomerase 4 subunit B | SRR18771786 |
| PG | population | 33 | stop gained c.703C>T p.Gln235* | PROKKA_01660 | hemH | Ferrochelatase | SRR18771796 |
| PG | colony | 33-s-c1 | stop gained c.703C>T p.Gln235* | PROKKA_01660 | hemH | Ferrochelatase | SRR18771785 |
| PG | population | 33 | g.2185374C>T | intergenic | - | - | SRR18771796 |
| PG | colony | 33-s-c1 | g.2185374C>T | intergenic | - | - | SRR18771785 |
| BAC | population | 14 | g.687271T>A | intergenic | - | - | SRR18771776 |
| BAC | colony | 14-s-c2 | g.687271T>A | intergenic | - | - | SRR18771790 |
| BAC | population | 7 | g.687271T>A | intergenic | - | - | SRR18771779 |
| BAC | colony | 7-s-c1 | g.687271T>A | intergenic | - | - | SRR18771791 |
| BAC | population | 14 | missense variant c.477C>G p.Asp159Glu | PROKKA_02369 | - | Baeyer-Villiger flavin-containing monooxygenase | SRR18771776 |
| BAC | colony | 14-s-c2 | missense variant c.477C>G p.Asp159Glu | PROKKA_02369 | - | Baeyer-Villiger flavin-containing monooxygenase | SRR18771790 |
| BAC | population | 7 | missense variant c.477C>G p.Asp159Glu | PROKKA_02369 | - | Baeyer-Villiger flavin-containing monooxygenase | SRR18771779 |
| BAC | colony | 7-s-c1 | missense variant c.477C>G p.Asp159Glu | PROKKA_02369 | - | Baeyer-Villiger flavin-containing monooxygenase | SRR18771791 |
| BAC | colony | 14-s-c2 | missense variant c.636G>T p.Gln212His | PROKKA_01209 | trpB | Tryptophan synthase beta chain | SRR18771790 |
| BAC | colony | 14-s-c2 | frameshift variant c.618dupT p.Arg207fs | PROKKA_01818 | agrA | Accessory gene regulator protein A | SRR18771790 |
| BAC | colony | 14-s-c2 | missense variant & inframe deletion c.622_630delCATAATATTinsTCTTTCp.His208_Ile210delinsSerPhe | PROKKA_01818 | agrA | Accessory gene regulator protein A | SRR18771790 |
| BAC | colony | 14-s-c2 | missense variant c.778G>A p.Ala260Thr | PROKKA_01862 | kdpD | Sensor protein KdpD | SRR18771790 |
| BAC | colony | 7-s-c1 | synonymous variant c.591G>A p.Gln197Gln | PROKKA_01039 | - | hypothetical protein | SRR18771791 |
| BAC | colony | 7-s-c1 | missense variant c.684A>T p.Glu228Asp | PROKKA_01817 | dpiB | Sensor histidine kinase DpiB | SRR18771791 |
| BAC | colony | 7-s-c1 | synonymous variant c.525T>A p.Thr175Thr | PROKKA_01929 | czcD | Cadmium, cobalt and zinc/H( )-K( ) antiporter | SRR18771791 |
| BAC | population | 35 | missense variant c.277G>A p.Ala93Thr | PROKKA_01081 | topA | DNA topoisomerase 1 | SRR18771794 |
| BAC | colony | 35-s-c2 | missense variant c.277G>A p.Ala93Thr | PROKKA_01081 | topA | DNA topoisomerase 1 | SRR18771783 |
| BAC | population | 35 | synonymous variant c.804T>A p.Ile268Ile | PROKKA_01457 | - | putative AAA domain-containing protein | SRR18771794 |
| BAC | colony | 35-s-c2 | synonymous variant c.804T>A p.Ile268Ile | PROKKA_01457 | - | putative AAA domain-containing protein | SRR18771783 |
| BAC | population | 35 | stop gained c.2035C>T p.Gln679* | PROKKA_01463 | relA | GTP pyrophosphokinase | SRR18771794 |
| BAC | colony | 35-s-c2 | stop gained c.2035C>T p.Gln679* | PROKKA_01463 | relA | GTP pyrophosphokinase | SRR18771783 |
| CON | population | 11 | g.1960175G>A | intergenic | - | - | SRR18771778 |
You can download this as a tsv here.
| Treatment | Type | Label | Mutation | Locus tag | Annotation | Function | Run |
|---|---|---|---|---|---|---|---|
| BAC | population | 17 | g.714937C>G | Intergenic | - | - | SRR18771805 |
| BAC | colony | 17-s-c1 | g.714937C>G | Intergenic | - | - | SRR18771789 |
You can download this as a tsv here.
| Treatment | Type | Label | Mutation | Locus tag | Annotation | Function | Run |
|---|---|---|---|---|---|---|---|
| BAC | population | 21 | g.756786.C>T | Intergenic | - | - | SRR18771804 |
| BAC | colony | 21-s-c1 | g.756786.C>T | Intergenic | - | - | SRR18771788 |
| BAC | population | 22 | g.756786.C>T | Intergenic | - | - | SRR18771803 |
| BAC | colony | 22-s-c1 | g.756786.C>T | Intergenic | - | - | SRR18771787 |
| BAC | colony | 21-s-c1 | frameshift variant c.88delC p.Gln30fs | B4603_RS05320 | fmtA | teichoic acid D-Ala esterase FmtA | SRR18771788 |
| BAC | colony | 22-s-c1 | missense variant c.841C>A p.Gln281Lys | B4603_RS05320 | fmtA | teichoic acid D-Ala esterase FmtA | SRR18771787 |
| BAC | colony | 40-s-c2 | missense variant c.808G>A p.Glu270Lys | B4603_RS08370 | rpoD | RNA polymerase sigma factor RpoD | SRR18771782 |
$ATCC6538
Call:
lm(formula = lag ~ type, data = .)
Residuals:
Min 1Q Median 3Q Max
-5.4700 -1.8483 -0.3683 2.6392 4.4633
Coefficients:
Estimate Std. Error t value Pr(>|t|)
(Intercept) 135.687 1.517 89.455 2.72e-13 ***
typeBAC_17 -0.020 2.145 -0.009 0.993
---
Signif. codes: 0 ‘***’ 0.001 ‘**’ 0.01 ‘*’ 0.05 ‘.’ 0.1 ‘ ’ 1
Residual standard error: 3.392 on 8 degrees of freedom
Multiple R-squared: 1.087e-05, Adjusted R-squared: -0.125
F-statistic: 8.693e-05 on 1 and 8 DF, p-value: 0.9928
$CC398
Call:
lm(formula = lag ~ type, data = .)
Residuals:
Min 1Q Median 3Q Max
-14.9200 -4.5333 -0.9617 1.5950 21.8300
Coefficients:
Estimate Std. Error t value Pr(>|t|)
(Intercept) 155.170 4.482 34.618 <2e-16 ***
typeBAC_21 -11.203 6.339 -1.767 0.0962 .
typeBAC_22 1.953 6.339 0.308 0.7619
typeBAC_40 -2.467 6.339 -0.389 0.7023
---
Signif. codes: 0 ‘***’ 0.001 ‘**’ 0.01 ‘*’ 0.05 ‘.’ 0.1 ‘ ’ 1
Residual standard error: 10.02 on 16 degrees of freedom
Multiple R-squared: 0.2392, Adjusted R-squared: 0.09661
F-statistic: 1.677 on 3 and 16 DF, p-value: 0.2118
$SH1000
Call:
lm(formula = lag ~ type, data = .)
Residuals:
Min 1Q Median 3Q Max
-5.353 -1.450 -0.500 1.740 5.207
Coefficients:
Estimate Std. Error t value Pr(>|t|)
(Intercept) 152.000 1.232 123.333 <2e-16 ***
typeBAC_14 -3.337 1.743 -1.914 0.0666 .
typeBAC_35 31.973 1.743 18.345 <2e-16 ***
typeBAC_7 -2.500 2.013 -1.242 0.2253
typePEX_32 54.960 1.743 31.533 <2e-16 ***
typePEX_33 54.610 1.743 31.332 <2e-16 ***
typePEX_4 53.570 1.743 30.736 <2e-16 ***
---
Signif. codes: 0 ‘***’ 0.001 ‘**’ 0.01 ‘*’ 0.05 ‘.’ 0.1 ‘ ’ 1
Residual standard error: 2.756 on 26 degrees of freedom
Multiple R-squared: 0.9912, Adjusted R-squared: 0.9891
F-statistic: 485.5 on 6 and 26 DF, p-value: < 2.2e-16
$ATCC6538
Call:
lm(formula = vmax ~ type, data = .)
Residuals:
Min 1Q Median 3Q Max
-0.2260 -0.0395 -0.0130 0.0405 0.2140
Coefficients:
Estimate Std. Error t value Pr(>|t|)
(Intercept) 2.90600 0.06510 44.639 7e-11 ***
typeBAC_17 -0.26600 0.09207 -2.889 0.0202 *
---
Signif. codes: 0 ‘***’ 0.001 ‘**’ 0.01 ‘*’ 0.05 ‘.’ 0.1 ‘ ’ 1
Residual standard error: 0.1456 on 8 degrees of freedom
Multiple R-squared: 0.5106, Adjusted R-squared: 0.4495
F-statistic: 8.348 on 1 and 8 DF, p-value: 0.02022
$CC398
Call:
lm(formula = vmax ~ type, data = .)
Residuals:
Min 1Q Median 3Q Max
-0.6510 -0.3317 -0.0885 0.1930 0.9170
Coefficients:
Estimate Std. Error t value Pr(>|t|)
(Intercept) 3.4890 0.2007 17.388 8.18e-12 ***
typeBAC_21 -0.2950 0.2838 -1.040 0.314
typeBAC_22 -0.0780 0.2838 -0.275 0.787
typeBAC_40 0.2340 0.2838 0.825 0.422
---
Signif. codes: 0 ‘***’ 0.001 ‘**’ 0.01 ‘*’ 0.05 ‘.’ 0.1 ‘ ’ 1
Residual standard error: 0.4487 on 16 degrees of freedom
Multiple R-squared: 0.1817, Adjusted R-squared: 0.02826
F-statistic: 1.184 on 3 and 16 DF, p-value: 0.347
$SH1000
Call:
lm(formula = vmax ~ type, data = .)
Residuals:
Min 1Q Median 3Q Max
-0.194 -0.039 -0.011 0.048 0.146
Coefficients:
Estimate Std. Error t value Pr(>|t|)
(Intercept) 2.62100 0.03516 74.549 < 2e-16 ***
typeBAC_14 -0.11200 0.04972 -2.253 0.03295 *
typeBAC_35 -0.14200 0.04972 -2.856 0.00832 **
typeBAC_7 -0.17100 0.05741 -2.978 0.00620 **
typePEX_32 -1.05400 0.04972 -21.198 < 2e-16 ***
typePEX_33 -0.04400 0.04972 -0.885 0.38430
typePEX_4 -0.91700 0.04972 -18.443 < 2e-16 ***
---
Signif. codes: 0 ‘***’ 0.001 ‘**’ 0.01 ‘*’ 0.05 ‘.’ 0.1 ‘ ’ 1
Residual standard error: 0.07862 on 26 degrees of freedom
Multiple R-squared: 0.9729, Adjusted R-squared: 0.9666
F-statistic: 155.3 on 6 and 26 DF, p-value: < 2.2e-16
$ATCC6538
Call:
lm(formula = finalOD ~ type, data = .)
Residuals:
Min 1Q Median 3Q Max
-0.02900 -0.01090 0.00040 0.00435 0.03500
Coefficients:
Estimate Std. Error t value Pr(>|t|)
(Intercept) 0.868200 0.009416 92.200 2.14e-13 ***
typeBAC_17 -0.043200 0.013317 -3.244 0.0118 *
---
Signif. codes: 0 ‘***’ 0.001 ‘**’ 0.01 ‘*’ 0.05 ‘.’ 0.1 ‘ ’ 1
Residual standard error: 0.02106 on 8 degrees of freedom
Multiple R-squared: 0.5681, Adjusted R-squared: 0.5141
F-statistic: 10.52 on 1 and 8 DF, p-value: 0.01181
$CC398
Call:
lm(formula = finalOD ~ type, data = .)
Residuals:
Min 1Q Median 3Q Max
-0.01940 -0.00925 -0.00170 0.00655 0.03160
Coefficients:
Estimate Std. Error t value Pr(>|t|)
(Intercept) 0.924200 0.006447 143.360 < 2e-16 ***
typeBAC_21 -0.016000 0.009117 -1.755 0.09839 .
typeBAC_22 -0.002800 0.009117 -0.307 0.76271
typeBAC_40 -0.034200 0.009117 -3.751 0.00174 **
---
Signif. codes: 0 ‘***’ 0.001 ‘**’ 0.01 ‘*’ 0.05 ‘.’ 0.1 ‘ ’ 1
Residual standard error: 0.01442 on 16 degrees of freedom
Multiple R-squared: 0.5237, Adjusted R-squared: 0.4344
F-statistic: 5.865 on 3 and 16 DF, p-value: 0.006706
$SH1000
Call:
lm(formula = finalOD ~ type, data = .)
Residuals:
Min 1Q Median 3Q Max
-0.0304 -0.0144 0.0036 0.0096 0.0328
Coefficients:
Estimate Std. Error t value Pr(>|t|)
(Intercept) 0.719200 0.008105 88.739 < 2e-16 ***
typeBAC_14 0.063400 0.011462 5.531 8.31e-06 ***
typeBAC_35 0.045200 0.011462 3.944 0.000542 ***
typeBAC_7 0.050133 0.013235 3.788 0.000811 ***
typePEX_32 -0.057400 0.011462 -5.008 3.29e-05 ***
typePEX_33 0.042200 0.011462 3.682 0.001066 **
typePEX_4 -0.038800 0.011462 -3.385 0.002268 **
---
Signif. codes: 0 ‘***’ 0.001 ‘**’ 0.01 ‘*’ 0.05 ‘.’ 0.1 ‘ ’ 1
Residual standard error: 0.01812 on 26 degrees of freedom
Multiple R-squared: 0.8844, Adjusted R-squared: 0.8577
F-statistic: 33.15 on 6 and 26 DF, p-value: 5.511e-11
ATCC6538, vmax~type, Ancestor, BAC_17:
lm model parameter contrast
Contrast S.E. Lower Upper t df Pr(>|t|)
1 0.266 0.09206519 0.05369728 0.4783027 2.89 8 0.0202
ATCC6538, lag~type, Ancestor, BAC_17:
lm model parameter contrast
Contrast S.E. Lower Upper t df Pr(>|t|)
1 0.02 2.145107 -4.926625 4.966625 0.01 8 0.9928
ATCC6538, finalOD~type, Ancestor, BAc_17:
lm model parameter contrast
Contrast S.E. Lower Upper t df Pr(>|t|)
1 0.0432 0.01331691 0.01249116 0.07390884 3.24 8 0.0118
CC398, vmax~type, Ancestor, BAC_21:
lm model parameter contrast
Contrast S.E. Lower Upper t df Pr(>|t|)
1 0.295 0.283771 -0.3065677 0.8965677 1.04 16 0.314
CC398, lag~type, Ancestor, BAC_21:
lm model parameter contrast
Contrast S.E. Lower Upper t df Pr(>|t|)
1 11.20333 6.338949 -2.234637 24.6413 1.77 16 0.0962
CC398, finalOD~type, Ancestor, BAC_21:
lm model parameter contrast
Contrast S.E. Lower Upper t df Pr(>|t|)
1 0.016 0.009117017 -0.003327213 0.03532721 1.75 16 0.0984
CC398, vmax~type, Ancestor, BAC_22:
lm model parameter contrast
Contrast S.E. Lower Upper t df Pr(>|t|)
1 0.078 0.283771 -0.5235677 0.6795677 0.27 16 0.7869
CC398, lag~type, Ancestor, BAC_22:
lm model parameter contrast
Contrast S.E. Lower Upper t df Pr(>|t|)
1 -1.953333 6.338949 -15.3913 11.48464 -0.31 16 0.7619
CC398, finalOD~type, Ancestor, BAC_22:
lm model parameter contrast
Contrast S.E. Lower Upper t df Pr(>|t|)
1 0.0028 0.009117017 -0.01652721 0.02212721 0.31 16 0.7627
CC398, vmax~type, Ancestor, BAC_40:
lm model parameter contrast
Contrast S.E. Lower Upper t df Pr(>|t|)
1 -0.234 0.283771 -0.8355677 0.3675677 -0.82 16 0.4217
CC398, lag~type, Ancestor, BAC_40:
lm model parameter contrast
Contrast S.E. Lower Upper t df Pr(>|t|)
1 2.466667 6.338949 -10.9713 15.90464 0.39 16 0.7023
CC398, finalOD~type, Ancestor, BAC_40:
lm model parameter contrast
Contrast S.E. Lower Upper t df Pr(>|t|)
1 0.0342 0.009117017 0.01487279 0.05352721 3.75 16 0.0017
SH1000, vmax~type:
lm model parameter contrast
Contrast S.E. Lower Upper t df Pr(>|t|)
1 0.112 0.04972076 0.009797517 0.2142025 2.25 26 0.033
SH1000, lag~type, Ancestor, BAC_14:
lm model parameter contrast
Contrast S.E. Lower Upper t df Pr(>|t|)
1 3.336667 1.742931 -0.2459794 6.919313 1.91 26 0.0666
SH1000, finalOD~type, Ancestor, BAC_14:
lm model parameter contrast
Contrast S.E. Lower Upper t df Pr(>|t|)
1 -0.0634 0.01146169 -0.08695983 -0.03984017 -5.53 26 0
SH1000, vmax~type, Ancestor, BAC_35:
lm model parameter contrast
Contrast S.E. Lower Upper t df Pr(>|t|)
1 0.142 0.04972076 0.03979752 0.2442025 2.86 26 0.0083
SH1000, lag~type, Ancestor, BAC_35:
lm model parameter contrast
Contrast S.E. Lower Upper t df Pr(>|t|)
1 -31.97333 1.742931 -35.55598 -28.39069 -18.34 26 0
SH1000, finalOD~type, Ancestor, BAC_35:
lm model parameter contrast
Contrast S.E. Lower Upper t df Pr(>|t|)
1 -0.0452 0.01146169 -0.06875983 -0.02164017 -3.94 26 5e-04
SH1000, vmax~type, Ancestor, BAC_7:
lm model parameter contrast
Contrast S.E. Lower Upper t df Pr(>|t|)
1 0.171 0.05741259 0.05298674 0.2890133 2.98 26 0.0062
SH1000, lag~type, Ancestor, BAC_7:
lm model parameter contrast
Contrast S.E. Lower Upper t df Pr(>|t|)
1 2.5 2.012563 -1.636883 6.636883 1.24 26 0.2253
SH1000, finalOD~type, Ancestor, BAC_7:
lm model parameter contrast
Contrast S.E. Lower Upper t df Pr(>|t|)
1 -0.05013333 0.01323482 -0.07733789 -0.02292878 -3.79 26 8e-04
SH1000, vmax~type, Ancestor, PEX_32:
lm model parameter contrast
Contrast S.E. Lower Upper t df Pr(>|t|)
1 1.054 0.04972076 0.9517975 1.156202 21.2 26 0
SH1000, lag~type, Ancestor, PEX_32:
lm model parameter contrast
Contrast S.E. Lower Upper t df Pr(>|t|)
1 -54.96 1.742931 -58.54265 -51.37735 -31.53 26 0
SH1000, finalOD~type, Ancestor, PEX_32:
lm model parameter contrast
Contrast S.E. Lower Upper t df Pr(>|t|)
1 0.0574 0.01146169 0.03384017 0.08095983 5.01 26 0
SH1000, vmax~type, Ancestor, PEX_33:
lm model parameter contrast
Contrast S.E. Lower Upper t df Pr(>|t|)
1 0.044 0.04972076 -0.05820248 0.1462025 0.88 26 0.3843
SH1000, lag~type, Ancestor, PEX_33:
lm model parameter contrast
Contrast S.E. Lower Upper t df Pr(>|t|)
1 -54.61 1.742931 -58.19265 -51.02735 -31.33 26 0
SH1000, finalOD~type, Ancestor, PEX_33:
lm model parameter contrast
Contrast S.E. Lower Upper t df Pr(>|t|)
1 -0.0422 0.01146169 -0.06575983 -0.01864017 -3.68 26 0.0011
SH1000, vmax~type, Ancestor, PEX_4:
lm model parameter contrast
Contrast S.E. Lower Upper t df Pr(>|t|)
1 0.917 0.04972076 0.8147975 1.019202 18.44 26 0
SH1000, lag~type, Ancestor, PEX_4:
lm model parameter contrast
Contrast S.E. Lower Upper t df Pr(>|t|)
1 -53.57 1.742931 -57.15265 -49.98735 -30.74 26 0
SH1000, finalOD~type, Ancestor, PEX_4:
lm model parameter contrast
Contrast S.E. Lower Upper t df Pr(>|t|)
1 0.0388 0.01146169 0.01524017 0.06235983 3.39 26 0.0023