BamQC report
-----------------------------------

>>>>>>> Input

     bam file = ERR9714156.sorted.bam
     outfile = /home/luna/rawdata/yangyxdownload/ERP137498/ERP137498.result/quality.files/genome_results.txt


>>>>>>> Reference

     number of bases = 3,095,693,983 bp
     number of contigs = 25


>>>>>>> Globals

     number of windows = 424

     number of reads = 4,118
     number of mapped reads = 793 (19.26%)
     number of supplementary alignments = 47 (1.14%)
     number of secondary alignments = 0

     number of mapped bases = 88,994 bp
     number of sequenced bases = 88,147 bp
     number of aligned bases = 0 bp
     number of duplicated reads (estimated) = 486
     duplication rate = 39.27%


>>>>>>> Insert size

     mean insert size = 0
     std insert size = 0
     median insert size = 0


>>>>>>> Mapping quality

     mean mapping quality = 7.9937


>>>>>>> ACTG content

     number of A's = 10,209 bp (11.58%)
     number of C's = 8,212 bp (9.32%)
     number of T's = 9,179 bp (10.41%)
     number of G's = 60,538 bp (68.68%)
     number of N's = 9 bp (0.01%)

     GC percentage = 77.99%


>>>>>>> Mismatches and indels

    general error rate = 0.046
    number of mismatches = 2,786
    number of insertions = 159
    mapped reads with insertion percentage = 14.38%
    number of deletions = 135
    mapped reads with deletion percentage = 16.77%
    homopolymer indels = 59.18%


>>>>>>> Coverage

     mean coverageData = 0X
     std coverageData = 0.0626X

     There is a 0% of reference with a coverageData >= 1X
     There is a 0% of reference with a coverageData >= 2X
     There is a 0% of reference with a coverageData >= 3X
     There is a 0% of reference with a coverageData >= 4X
     There is a 0% of reference with a coverageData >= 5X
     There is a 0% of reference with a coverageData >= 6X
     There is a 0% of reference with a coverageData >= 7X
     There is a 0% of reference with a coverageData >= 8X
     There is a 0% of reference with a coverageData >= 9X
     There is a 0% of reference with a coverageData >= 10X
     There is a 0% of reference with a coverageData >= 11X
     There is a 0% of reference with a coverageData >= 12X
     There is a 0% of reference with a coverageData >= 13X
     There is a 0% of reference with a coverageData >= 14X
     There is a 0% of reference with a coverageData >= 15X
     There is a 0% of reference with a coverageData >= 16X
     There is a 0% of reference with a coverageData >= 17X
     There is a 0% of reference with a coverageData >= 18X
     There is a 0% of reference with a coverageData >= 19X
     There is a 0% of reference with a coverageData >= 20X
     There is a 0% of reference with a coverageData >= 21X
     There is a 0% of reference with a coverageData >= 22X
     There is a 0% of reference with a coverageData >= 23X
     There is a 0% of reference with a coverageData >= 24X
     There is a 0% of reference with a coverageData >= 25X
     There is a 0% of reference with a coverageData >= 26X
     There is a 0% of reference with a coverageData >= 27X
     There is a 0% of reference with a coverageData >= 28X
     There is a 0% of reference with a coverageData >= 29X
     There is a 0% of reference with a coverageData >= 30X
     There is a 0% of reference with a coverageData >= 31X
     There is a 0% of reference with a coverageData >= 32X
     There is a 0% of reference with a coverageData >= 33X
     There is a 0% of reference with a coverageData >= 34X
     There is a 0% of reference with a coverageData >= 35X
     There is a 0% of reference with a coverageData >= 36X
     There is a 0% of reference with a coverageData >= 37X
     There is a 0% of reference with a coverageData >= 38X
     There is a 0% of reference with a coverageData >= 39X
     There is a 0% of reference with a coverageData >= 40X
     There is a 0% of reference with a coverageData >= 41X
     There is a 0% of reference with a coverageData >= 42X
     There is a 0% of reference with a coverageData >= 43X
     There is a 0% of reference with a coverageData >= 44X
     There is a 0% of reference with a coverageData >= 45X
     There is a 0% of reference with a coverageData >= 46X
     There is a 0% of reference with a coverageData >= 47X
     There is a 0% of reference with a coverageData >= 48X
     There is a 0% of reference with a coverageData >= 49X
     There is a 0% of reference with a coverageData >= 50X
     There is a 0% of reference with a coverageData >= 51X


>>>>>>> Coverage per contig

	chr1	249250621	1082	4.341012253686622E-6	0.003911245142989997
	chr2	243199373	55758	2.29268683188587E-4	0.22259921037413538
	chr3	198022430	675	3.4087047613747594E-6	0.0031978278041283163
	chr4	191154276	1184	6.193949854409744E-6	0.004400740583486841
	chr5	180915260	918	5.0741988265666475E-6	0.0029626955152490466
	chr6	171115067	815	4.762876900840065E-6	0.003836804080491813
	chr7	159138663	1410	8.860197600126879E-6	0.004676285243522845
	chr8	146364022	1273	8.697492611948037E-6	0.006382852873054734
	chr9	141213431	348	2.464354824719187E-6	0.002071562434662669
	chr10	135534747	484	3.571039978404947E-6	0.0027753934890883897
	chr11	135006516	751	5.562694470243199E-6	0.002924913041189724
	chr12	133851895	1415	1.0571385634846634E-5	0.005388826233768227
	chr13	115169878	312	2.709041681888384E-6	0.0023239428506447737
	chr14	107349540	296	2.757347632789111E-6	0.0031005560238929358
	chr15	102531392	238	2.3212403085291186E-6	0.0019047707822039068
	chr16	90354753	274	3.0324912735913296E-6	0.001951206428938379
	chr17	81195210	376	4.6308150443850075E-6	0.0029695509316758806
	chr18	78077248	203	2.5999891799465063E-6	0.001612446098324769
	chr19	59128983	34	5.750141178650071E-7	7.582966353767972E-4
	chr20	63025520	664	1.0535414860519993E-5	0.004399674667749912
	chr21	48129895	363	7.542090004559536E-6	0.0031678528464574368
	chr22	51304566	33	6.432176036729363E-7	8.020082231149819E-4
	chrMT	16571	0	0.0	0.0
	chrX	155270560	20088	1.2937417112426206E-4	0.019933928035469024
	chrY	59373566	0	0.0	0.0