samtools idxstats example.xls

	A	B	C	D	E	F	G
1	Chr / DNA	Len in Model (bp)	# Map Seg Read	# Unmap Seg Read	Mapped GBase	Avg Read Depth	Seg Len
2	1	249,250,621	63,786,751	199,024	9.57	38	150
3	2	243,199,373	65,961,585	239,823	9.89	41
4	3	198,022,430	52,843,796	176,226	7.93	40
5	4	191,154,276	50,062,418	185,908	7.51	39
6	5	180,915,260	48,275,721	167,347	7.24	40
7	6	171,115,067	45,546,584	155,125	6.83	40
8	7	159,138,663	42,913,986	142,536	6.44	40
9	8	146,364,022	39,884,469	130,086	5.98	41
10	9	141,213,431	32,956,517	104,750	4.94	35
11	10	135,534,747	36,419,699	115,619	5.46	40
12	11	135,006,516	36,692,418	116,018	5.50	41
13	12	133,851,895	35,873,560	117,121	5.38	40
14	13	115,169,878	25,596,826	93,924	3.84	33
15	14	107,349,540	24,699,112	78,496	3.70	35
16	15	102,531,392	23,178,294	71,921	3.48	34
17	16	90,354,753	26,158,801	66,243	3.92	43
18	17	81,195,210	23,153,856	67,170	3.47	43
19	18	78,077,248	20,397,247	72,196	3.06	39
20	19	59,128,983	17,120,980	46,881	2.57	43
21	20	63,025,520	17,244,994	51,069	2.59	41
22	21	48,129,895	10,265,299	32,933	1.54	32
23	22	51,304,566	10,759,798	29,240	1.61	31
24	X	155,270,560	21,368,954	122,938	3.21	21
25	Y	59,373,566	4,536,115	13,733	0.68	11
26	MT	16,569	39,645	120	0.01	359
27	GL *	6,110,758	7,016,422	12,986	1.05	172
87	NC_007605	171,823	148	46	0.00	0
88	hs37d5	35,477,943	36,267,111	75,223	5.44	153
89	*	0	0	31,543,572			Unmapped
90	TOTAL	3,137,454,505	819,021,106	34,228,274	123	39
91		Genome Size	Map Reads:	Unmap Reads:	Mapped Gigabases	Avg Read Depth (mapped)
92			95.99%	4.01%	Mapped Gigabases
93
94	Paste your values captured from a run: samtools idxstats <BAM_file>
95	Needs BAM Index file, obtained by run: samtools index <BAM_file>
96	Above has hidden GL rows due to Dante adding non-genome model entries to the MAP file.
97	Adjust your read length if not 150 in the above right corner.
98	When pasting, select space separator and collapse multiple separators
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100	Very fast to run if index file exists. Otherwise, running FASTP tool will get more detailed stats.
101
102	Females will still have some Y values mapped due to PAR on Y
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