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

>>>>>>> Input

     bam file = ERR9714186.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 = 58,818
     number of mapped reads = 8,272 (14.06%)
     number of supplementary alignments = 205 (0.35%)
     number of secondary alignments = 0

     number of mapped bases = 860,094 bp
     number of sequenced bases = 856,740 bp
     number of aligned bases = 0 bp
     number of duplicated reads (estimated) = 7,607
     duplication rate = 37.59%


>>>>>>> Insert size

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


>>>>>>> Mapping quality

     mean mapping quality = 9.4302


>>>>>>> ACTG content

     number of A's = 45,530 bp (5.31%)
     number of C's = 27,161 bp (3.17%)
     number of T's = 32,687 bp (3.82%)
     number of G's = 751,338 bp (87.7%)
     number of N's = 24 bp (0%)

     GC percentage = 90.87%


>>>>>>> Mismatches and indels

    general error rate = 0.0311
    number of mismatches = 21,814
    number of insertions = 777
    mapped reads with insertion percentage = 6.53%
    number of deletions = 629
    mapped reads with deletion percentage = 7.34%
    homopolymer indels = 51.92%


>>>>>>> Coverage

     mean coverageData = 0.0003X
     std coverageData = 0.9364X

     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	7253	2.9099225393705236E-5	0.022701099134025685
	chr2	243199373	735694	0.003025065364786117	3.3386227991371507
	chr3	198022430	2996	1.5129599207524118E-5	0.009863147695501895
	chr4	191154276	3486	1.823657870985842E-5	0.015583833511455536
	chr5	180915260	10891	6.0199454706031987E-5	0.04254271429726354
	chr6	171115067	19653	1.1485253954872367E-4	0.08290535257656478
	chr7	159138663	2335	1.4672738578933518E-5	0.017229819353077228
	chr8	146364022	2408	1.645213056525599E-5	0.011008665421536175
	chr9	141213431	11116	7.871772480338644E-5	0.04367886779443635
	chr10	135534747	970	7.156836320357022E-6	0.003936258600687295
	chr11	135006516	2314	1.713991345425135E-5	0.005854874028541271
	chr12	133851895	2215	1.6548140764088548E-5	0.014764380425237497
	chr13	115169878	3831	3.32639060362641E-5	0.023093435445169244
	chr14	107349540	1649	1.536103461645015E-5	0.012087648391242795
	chr15	102531392	1097	1.069916226242203E-5	0.004422089541982132
	chr16	90354753	561	6.208859870382248E-6	0.002634250448009693
	chr17	81195210	3592	4.423906287082699E-5	0.02423373830537118
	chr18	78077248	746	9.554640040591595E-6	0.0034026733090502335
	chr19	59128983	425	7.1876764733125885E-6	0.0029108332975021373
	chr20	63025520	263	4.172912813730057E-6	0.0020427666045167046
	chr21	48129895	221	4.591740746577569E-6	0.0021428298258365
	chr22	51304566	201	3.917779949644248E-6	0.0019793343832320283
	chrMT	16571	297	0.01792287731579265	0.1326712017904251
	chrX	155270560	45741	2.945890064414014E-4	0.09420531275307116
	chrY	59373566	139	2.341109173061965E-6	0.0015300665646532522