Sample	total_passed	total_failed	secondary_passed	secondary_failed	supplementary_passed	supplementary_failed	duplicates_passed	duplicates_failed	mapped_passed	mapped_failed	mapped_passed_pct	mapped_failed_pct	paired in sequencing_passed	paired in sequencing_failed	read1_passed	read1_failed	read2_passed	read2_failed	properly paired_passed	properly paired_failed	properly paired_passed_pct	properly paired_failed_pct	with itself and mate mapped_passed	with itself and mate mapped_failed	singletons_passed	singletons_failed	singletons_passed_pct	singletons_failed_pct	with mate mapped to a different chr_passed	with mate mapped to a different chr_failed	with mate mapped to a different chr (mapQ >= 5)_passed	with mate mapped to a different chr (mapQ >= 5)_failed	flagstat_total
1A1-hisat2_output	47427906	0	10582686	0	0	0	0	0	37003766	0	78.02	nan	36845220	0	18422610	0	18422610	0	19626170	0	53.27	nan	24430956	0	1990124	0	5.4	nan	266106	0	115907	0	47427906
1A10-hisat2_output	49115555	0	6134991	0	0	0	0	0	36504043	0	74.32	nan	42980564	0	21490282	0	21490282	0	23045986	0	53.62	nan	28109662	0	2259390	0	5.26	nan	197874	0	95565	0	49115555
1A12-hisat2_output	39886398	0	4290526	0	0	0	0	0	32715359	0	82.02	nan	35595872	0	17797936	0	17797936	0	23267492	0	65.37	nan	26398884	0	2025949	0	5.69	nan	162084	0	87697	0	39886398
1A2-hisat2_output	49398866	0	5249348	0	0	0	0	0	36775191	0	74.45	nan	44149518	0	22074759	0	22074759	0	22757994	0	51.55	nan	29582838	0	1943005	0	4.4	nan	152258	0	65313	0	49398866
1A8-hisat2_output	39181744	0	4615210	0	0	0	0	0	30539832	0	77.94	nan	34566534	0	17283267	0	17283267	0	21173628	0	61.25	nan	23991288	0	1933334	0	5.59	nan	127424	0	69787	0	39181744
1A9-hisat2_output	48395176	0	4807478	0	0	0	0	0	36306271	0	75.02	nan	43587698	0	21793849	0	21793849	0	25143106	0	57.68	nan	29108042	0	2390751	0	5.48	nan	213020	0	110692	0	48395176
1B1-hisat2_output	47796679	0	6291605	0	0	0	0	0	37568916	0	78.6	nan	41505074	0	20752537	0	20752537	0	24360944	0	58.69	nan	28899724	0	2377587	0	5.73	nan	183724	0	90770	0	47796679
1B10-hisat2_output	46895127	0	4467633	0	0	0	0	0	38146702	0	81.34	nan	42427494	0	21213747	0	21213747	0	27339204	0	64.44	nan	31268024	0	2411045	0	5.68	nan	177782	0	95478	0	46895127
1B2-hisat2_output	47386498	0	5111500	0	0	0	0	0	36979573	0	78.04	nan	42274998	0	21137499	0	21137499	0	24140896	0	57.1	nan	29636500	0	2231573	0	5.28	nan	157754	0	74811	0	47386498
1B5-hisat2_output	49898482	0	6634764	0	0	0	0	0	41346567	0	82.86	nan	43263718	0	21631859	0	21631859	0	27658782	0	63.93	nan	32205684	0	2506119	0	5.79	nan	192510	0	102956	0	49898482
1B9-hisat2_output	54026791	0	6057473	0	0	0	0	0	40895267	0	75.69	nan	47969318	0	23984659	0	23984659	0	25995476	0	54.19	nan	32672504	0	2165290	0	4.51	nan	154866	0	68674	0	54026791
1C10-hisat2_output	40092973	0	5441425	0	0	0	0	0	30298551	0	75.57	nan	34651548	0	17325774	0	17325774	0	18057364	0	52.11	nan	23324878	0	1532248	0	4.42	nan	153270	0	58875	0	40092973
1C4-hisat2_output	46910852	0	6090368	0	0	0	0	0	36785790	0	78.42	nan	40820484	0	20410242	0	20410242	0	24220130	0	59.33	nan	28359516	0	2335906	0	5.72	nan	199110	0	101743	0	46910852
1D10-hisat2_output	48367129	0	5497401	0	0	0	0	0	38436443	0	79.47	nan	42869728	0	21434864	0	21434864	0	25851106	0	60.3	nan	30356926	0	2582116	0	6.02	nan	222796	0	116763	0	48367129
1D3-hisat2_output	36624343	0	4626109	0	0	0	0	0	28188066	0	76.97	nan	31998234	0	15999117	0	15999117	0	17886132	0	55.9	nan	21989226	0	1572731	0	4.92	nan	117062	0	53651	0	36624343
1D4-hisat2_output	55027544	0	7412508	0	0	0	0	0	43638346	0	79.3	nan	47615036	0	23807518	0	23807518	0	27670500	0	58.11	nan	34013812	0	2212026	0	4.65	nan	166196	0	80631	0	55027544
1D6-hisat2_output	42024228	0	4161590	0	0	0	0	0	33520378	0	79.76	nan	37862638	0	18931319	0	18931319	0	23265386	0	61.45	nan	27037646	0	2321142	0	6.13	nan	178898	0	94920	0	42024228
1D8-hisat2_output	37353634	0	3818726	0	0	0	0	0	27124095	0	72.61	nan	33534908	0	16767454	0	16767454	0	18570026	0	55.38	nan	21509770	0	1795599	0	5.35	nan	143224	0	75275	0	37353634
1D9-hisat2_output	52367774	0	7116322	0	0	0	0	0	38285923	0	73.11	nan	45251452	0	22625726	0	22625726	0	21586828	0	47.7	nan	29253562	0	1916039	0	4.23	nan	187974	0	74812	0	52367774
1E1-hisat2_output	51044626	0	8393348	0	0	0	0	0	40072931	0	78.51	nan	42651278	0	21325639	0	21325639	0	23900258	0	56.04	nan	29285656	0	2393927	0	5.61	nan	247960	0	116551	0	51044626
1E3-hisat2_output	42707145	0	5849579	0	0	0	0	0	34414467	0	80.58	nan	36857566	0	18428783	0	18428783	0	22975514	0	62.34	nan	26598060	0	1966828	0	5.34	nan	156144	0	80990	0	42707145
1E5-hisat2_output	41007791	0	4907361	0	0	0	0	0	33146490	0	80.83	nan	36100430	0	18050215	0	18050215	0	22192068	0	61.47	nan	26167658	0	2071471	0	5.74	nan	131240	0	66324	0	41007791
1E9-hisat2_output	49589545	0	5141005	0	0	0	0	0	39272369	0	79.19	nan	44448540	0	22224270	0	22224270	0	25493340	0	57.35	nan	31974972	0	2156392	0	4.85	nan	181918	0	83498	0	49589545
1F11-hisat2_output	37289343	0	5014871	0	0	0	0	0	28035246	0	75.18	nan	32274472	0	16137236	0	16137236	0	18495160	0	57.31	nan	21210378	0	1809997	0	5.61	nan	148604	0	79102	0	37289343
1F4-hisat2_output	40816372	0	5353132	0	0	0	0	0	32895655	0	80.59	nan	35463240	0	17731620	0	17731620	0	22331970	0	62.97	nan	25474948	0	2067575	0	5.83	nan	181494	0	95774	0	40816372
1F8-hisat2_output	52140562	0	5817642	0	0	0	0	0	39999608	0	76.71	nan	46322920	0	23161460	0	23161460	0	24392608	0	52.66	nan	31915258	0	2266708	0	4.89	nan	185100	0	80757	0	52140562
1G5-hisat2_output	52310738	0	7450202	0	0	0	0	0	41782841	0	79.87	nan	44860536	0	22430268	0	22430268	0	27618378	0	61.56	nan	31405612	0	2927027	0	6.52	nan	288100	0	155502	0	52310738
1H11-hisat2_output	39886398	0	4290526	0	0	0	0	0	32715359	0	82.02	nan	35595872	0	17797936	0	17797936	0	23267492	0	65.37	nan	26398884	0	2025949	0	5.69	nan	162084	0	87697	0	39886398
1H12-hisat2_output	35950398	0	3173560	0	0	0	0	0	27494451	0	76.48	nan	32776838	0	16388419	0	16388419	0	18201212	0	55.53	nan	22593550	0	1727341	0	5.27	nan	117256	0	55320	0	35950398
1H6-hisat2_output	52140562	0	5817642	0	0	0	0	0	39999608	0	76.71	nan	46322920	0	23161460	0	23161460	0	24392608	0	52.66	nan	31915258	0	2266708	0	4.89	nan	185100	0	80757	0	52140562
1H7-hisat2_output	38984264	0	4591794	0	0	0	0	0	31491213	0	80.78	nan	34392470	0	17196235	0	17196235	0	21628060	0	62.89	nan	24695036	0	2204383	0	6.41	nan	172784	0	93379	0	38984264
1H8-hisat2_output	42259740	0	5315906	0	0	0	0	0	34526462	0	81.7	nan	36943834	0	18471917	0	18471917	0	23617444	0	63.93	nan	27100906	0	2109650	0	5.71	nan	145016	0	79785	0	42259740
2B2-hisat2_output	56512524	0	12784250	0	0	0	0	0	45332945	0	80.22	nan	43728274	0	21864137	0	21864137	0	25075400	0	57.34	nan	30420430	0	2128265	0	4.87	nan	210002	0	94975	0	56512524
2B3-hisat2_output	43291883	0	4475487	0	0	0	0	0	32685040	0	75.5	nan	38816396	0	19408198	0	19408198	0	23122380	0	59.57	nan	25987656	0	2221897	0	5.72	nan	153924	0	85248	0	43291883
2C1-hisat2_output	41491029	0	2495747	0	0	0	0	0	21401918	0	51.58	nan	38995282	0	19497641	0	19497641	0	14805622	0	37.97	nan	17609046	0	1297125	0	3.33	nan	93384	0	46231	0	41491029
2C2-hisat2_output	40738653	0	5075807	0	0	0	0	0	31804249	0	78.07	nan	35662846	0	17831423	0	17831423	0	21683602	0	60.8	nan	24490122	0	2238320	0	6.28	nan	195442	0	106195	0	40738653
2D2-hisat2_output	54877372	0	8404830	0	0	0	0	0	39104574	0	71.26	nan	46472542	0	23236271	0	23236271	0	22081186	0	47.51	nan	28863092	0	1836652	0	3.95	nan	218516	0	80361	0	54877372
2E2-hisat2_output	36665245	0	3014259	0	0	0	0	0	22148458	0	60.41	nan	33650986	0	16825493	0	16825493	0	13307172	0	39.54	nan	18058638	0	1075561	0	3.2	nan	114670	0	42165	0	36665245
2F1-hisat2_output	70432471	0	11510909	0	0	0	0	0	53982660	0	76.64	nan	58921562	0	29460781	0	29460781	0	30602124	0	51.94	nan	39878644	0	2593107	0	4.4	nan	248008	0	102321	0	70432471
2G1-hisat2_output	39473080	0	3876262	0	0	0	0	0	25452736	0	64.48	nan	35596818	0	17798409	0	17798409	0	17297634	0	48.59	nan	20088420	0	1488054	0	4.18	nan	112596	0	57006	0	39473080