Add page whole molecule damage

_quarto.yml

@@ -35,6 +35,7 @@ book:
         - softclipping.qmd
         - leftover-adapter.qmd
         - short-read-excess.qmd
+        - whole-molecule-damage.qmd
     - part: problematic.qmd
       chapters:
         - insufficient-reads.qmd

assets/data/whole-molecule-damage/3p_freq_misincorporations.txt

@@ -0,0 +1,29 @@
+# table produced by DamageProfiler
+# using mapped file KDR001.B0101.lengthfilter25bp.bam
+# Sample ID: KDR001.B0101.lengthfilter25bp.bam
+Pos	C>T	G>A	A>C	A>G	A>T	C>A	C>G	G>C	G>T	T>A	T>C	T>G	->ACGT	ACGT>-
+24	0.118647	0.008906	0.014899	0.012580	0.019722	0.007511	0.008333	0.015349	0.018501	0.005488	0.009015	0.005651	0.000219	0.000000
+23	0.101201	0.008901	0.013723	0.016308	0.014028	0.008037	0.013740	0.012176	0.011718	0.006723	0.010647	0.009960	0.000538	0.000000
+22	0.095288	0.008991	0.014181	0.015046	0.015037	0.008565	0.011900	0.012955	0.012530	0.006796	0.011100	0.008874	0.001157	0.000000
+21	0.093900	0.008781	0.015807	0.015817	0.015263	0.006872	0.011796	0.012849	0.012131	0.006188	0.011430	0.008600	0.002684	0.000000
+20	0.090599	0.007876	0.016664	0.017649	0.015250	0.007306	0.012283	0.012442	0.011883	0.005608	0.011517	0.009785	0.005639	0.000000
+19	0.090972	0.007794	0.014505	0.016391	0.015296	0.008075	0.013189	0.012162	0.012037	0.006621	0.010583	0.009962	0.005582	0.000000
+18	0.087478	0.007846	0.015239	0.015635	0.014732	0.007510	0.010781	0.013407	0.011346	0.006271	0.011457	0.008779	0.005342	0.000000
+17	0.086943	0.007859	0.014376	0.016188	0.014116	0.007233	0.011404	0.012546	0.011276	0.006471	0.011227	0.009356	0.005561	0.000000
+16	0.088658	0.008359	0.014707	0.015499	0.014612	0.008104	0.010947	0.012413	0.012215	0.006527	0.010799	0.008835	0.005339	0.000000
+15	0.084514	0.008033	0.015606	0.014954	0.014727	0.006934	0.010236	0.013464	0.012019	0.006464	0.011433	0.008938	0.005540	0.000000
+14	0.086642	0.007950	0.016707	0.016660	0.014944	0.007355	0.011557	0.012905	0.011378	0.006422	0.012162	0.009144	0.005499	0.000000
+13	0.087230	0.008534	0.014369	0.017159	0.014160	0.008222	0.012753	0.012068	0.011591	0.006963	0.010846	0.009572	0.005748	0.000000
+12	0.086717	0.007746	0.014787	0.015299	0.015658	0.008183	0.011817	0.013158	0.011602	0.006608	0.011685	0.009129	0.005404	0.000000
+11	0.084297	0.007898	0.018270	0.016447	0.015049	0.007494	0.012135	0.014529	0.011302	0.006627	0.012417	0.009995	0.006329	0.000000
+10	0.087925	0.007709	0.016425	0.017731	0.014827	0.007556	0.011951	0.014368	0.011330	0.006685	0.011645	0.010151	0.005736	0.000000
+9	0.086401	0.007603	0.015496	0.017543	0.014211	0.007618	0.011769	0.014136	0.011703	0.006550	0.012003	0.010279	0.005768	0.000000
+8	0.089047	0.007812	0.014236	0.016958	0.015072	0.007592	0.012122	0.012826	0.011779	0.006754	0.011014	0.010061	0.005556	0.000000
+7	0.087466	0.008520	0.014144	0.014902	0.013192	0.008165	0.011586	0.012380	0.011867	0.006808	0.011413	0.009215	0.005247	0.000000
+6	0.088490	0.008545	0.015181	0.016015	0.014613	0.007971	0.011230	0.013863	0.011286	0.006466	0.011132	0.009107	0.005022	0.000000
+5	0.089534	0.008298	0.016364	0.016070	0.013702	0.008595	0.012219	0.012836	0.010975	0.007234	0.013034	0.009988	0.004704	0.000000
+4	0.091118	0.009268	0.013689	0.017058	0.013477	0.009429	0.015715	0.012009	0.011568	0.007740	0.011274	0.011646	0.000820	0.000000
+3	0.091429	0.009357	0.015129	0.016070	0.013307	0.008906	0.012192	0.012516	0.011377	0.008067	0.012564	0.010704	0.000279	0.000000
+2	0.097039	0.008654	0.012732	0.018088	0.014154	0.009724	0.015561	0.010703	0.011439	0.007527	0.010204	0.011896	0.000095	0.000000
+1	0.106695	0.010268	0.013628	0.016813	0.014399	0.009491	0.012382	0.012348	0.012080	0.008239	0.011267	0.010653	0.000026	0.000000
+0	0.117126	0.010611	0.018378	0.015316	0.023326	0.006415	0.008444	0.016793	0.020211	0.005306	0.009120	0.006114	0.000000	0.000000

assets/data/whole-molecule-damage/5p_freq_misincorporations.txt

@@ -0,0 +1,29 @@
+# table produced by DamageProfiler
+# using mapped file KDR001.B0101.lengthfilter25bp.bam
+# Sample ID: KDR001.B0101.lengthfilter25bp.bam
+Pos	C>T	G>A	A>C	A>G	A>T	C>A	C>G	G>C	G>T	T>A	T>C	T>G	->ACGT	ACGT>-
+0	0.158626	0.012576	0.017535	0.010909	0.026419	0.007128	0.005876	0.023222	0.032479	0.004304	0.007475	0.003576	0.000000	0.000000
+1	0.117530	0.008561	0.013175	0.016756	0.013549	0.008339	0.014666	0.010860	0.010739	0.007017	0.009888	0.010455	0.000085	0.000000
+2	0.098400	0.009267	0.013993	0.014656	0.014874	0.008580	0.011980	0.013906	0.013514	0.007140	0.010683	0.008844	0.000233	0.000000
+3	0.103661	0.009003	0.014474	0.015301	0.014833	0.007198	0.011243	0.013741	0.012647	0.006339	0.010758	0.008505	0.000722	0.000000
+4	0.092606	0.007998	0.017586	0.016374	0.015172	0.006471	0.011501	0.013114	0.011627	0.005497	0.012340	0.008724	0.003132	0.000000
+5	0.098441	0.007848	0.014193	0.018717	0.015908	0.007984	0.015260	0.011439	0.012112	0.006048	0.009732	0.010488	0.003746	0.000000
+6	0.089513	0.008601	0.015336	0.014802	0.014933	0.007878	0.010916	0.013150	0.011947	0.006545	0.010983	0.008781	0.003529	0.000000
+7	0.088246	0.007155	0.014535	0.016965	0.014074	0.006947	0.011331	0.011756	0.010592	0.006406	0.011624	0.009884	0.003284	0.000000
+8	0.092003	0.008485	0.014187	0.015606	0.014434	0.008257	0.011240	0.012188	0.012154	0.006871	0.011089	0.008873	0.003339	0.000000
+9	0.085870	0.008046	0.014789	0.014779	0.014752	0.007373	0.010314	0.013384	0.011639	0.006460	0.011241	0.009140	0.003386	0.000000
+10	0.084049	0.007923	0.016849	0.015917	0.014879	0.007114	0.010928	0.013440	0.012160	0.005770	0.011764	0.008454	0.003340	0.000000
+11	0.086530	0.008364	0.014646	0.017218	0.014525	0.007710	0.012829	0.012063	0.011388	0.007219	0.010987	0.009585	0.003379	0.000000
+12	0.087616	0.007846	0.014802	0.015886	0.014504	0.008074	0.011646	0.012720	0.011501	0.006494	0.011577	0.009089	0.003381	0.000000
+13	0.085789	0.008003	0.016481	0.016509	0.015144	0.007297	0.011667	0.013526	0.011415	0.006803	0.011777	0.009436	0.003600	0.000000
+14	0.085777	0.007948	0.015764	0.016966	0.014872	0.007839	0.012211	0.014151	0.011111	0.006639	0.011888	0.010088	0.003459	0.000000
+15	0.085871	0.007671	0.015973	0.016668	0.014193	0.007803	0.011511	0.013482	0.011881	0.006323	0.011856	0.010172	0.003576	0.000000
+16	0.086717	0.007649	0.015653	0.017147	0.014579	0.007768	0.012367	0.013626	0.011050	0.006615	0.011167	0.010237	0.003522	0.000000
+17	0.087249	0.008093	0.013968	0.015882	0.014122	0.008210	0.011827	0.011825	0.011334	0.006785	0.011190	0.009742	0.003471	0.000000
+18	0.086700	0.008763	0.014823	0.015466	0.014090	0.007577	0.011100	0.013689	0.011838	0.006405	0.010910	0.008776	0.003364	0.000000
+19	0.088237	0.008096	0.016439	0.016457	0.014125	0.007977	0.011486	0.013805	0.010910	0.006918	0.012276	0.009587	0.002880	0.000000
+20	0.089266	0.008663	0.014790	0.016994	0.013383	0.008854	0.013961	0.012451	0.011939	0.007201	0.011107	0.010622	0.001445	0.000000
+21	0.088506	0.009761	0.014365	0.015636	0.013405	0.009074	0.012524	0.012938	0.011317	0.007756	0.011683	0.010122	0.000563	0.000000
+22	0.090283	0.008618	0.014277	0.017338	0.013705	0.009063	0.014171	0.011245	0.011168	0.007256	0.011879	0.011674	0.000243	0.000000
+23	0.094233	0.009469	0.012726	0.017348	0.013647	0.009546	0.014266	0.012411	0.011772	0.007764	0.010745	0.010995	0.000139	0.000000
+24	0.099788	0.009011	0.014889	0.014157	0.017427	0.007360	0.009629	0.013937	0.014917	0.006602	0.010347	0.007856	0.000047	0.000000

contributors_and_citation.qmd

@@ -18,6 +18,7 @@ The following people contributed [^1] either data, caricatures, descriptions, or
 - 🇬🇷 Nikos Psonis
 - 🇺🇸 Christina Warinner
 - 🇩🇪 Carl-Eric Wegner
+- 🇩🇪 Johannes Krause
 
 [^1]: Flag represents institutional location at the time of contribution