BamQC report ----------------------------------- >>>>>>> Input bam file = SRR6013293.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/SRP116771/SRP116771.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 = 1,337,151 number of mapped reads = 1,205,647 (90.17%) number of supplementary alignments = 6,709 (0.5%) number of secondary alignments = 0 number of mapped bases = 81,250,628 bp number of sequenced bases = 81,216,806 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 45,075 duplication rate = 2.57% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 45.1269 >>>>>>> ACTG content number of A's = 23,112,743 bp (28.46%) number of C's = 14,800,961 bp (18.22%) number of T's = 25,780,275 bp (31.74%) number of G's = 17,505,461 bp (21.55%) number of N's = 17,366 bp (0.02%) GC percentage = 39.78% >>>>>>> Mismatches and indels general error rate = 0.0084 number of mismatches = 674,584 number of insertions = 6,321 mapped reads with insertion percentage = 0.52% number of deletions = 19,846 mapped reads with deletion percentage = 1.63% homopolymer indels = 46.89% >>>>>>> Coverage mean coverageData = 0.0262X std coverageData = 0.3341X There is a 2.35% of reference with a coverageData >= 1X There is a 0.18% of reference with a coverageData >= 2X There is a 0.02% of reference with a coverageData >= 3X There is a 0.01% 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 6522529 0.02616855666730716 0.5896581699708657 chr2 243199373 9036762 0.03715783428438362 0.38045393348673556 chr3 198022430 7777989 0.03927832316773408 0.21351437943004836 chr4 191154276 5671812 0.029671384384830607 0.19268241478347753 chr5 180915260 4104091 0.022685156575514967 0.1637778222315276 chr6 171115067 3209807 0.01875817867049662 0.19568462662856373 chr7 159138663 7004950 0.044017901545396296 0.6863318191155219 chr8 146364022 6785149 0.046358038726211005 0.44213977272956645 chr9 141213431 3062075 0.021684020976729897 0.2997449578818003 chr10 135534747 2966695 0.021888814976723275 0.31720323811738355 chr11 135006516 1538945 0.01139904239881281 0.19875303374394546 chr12 133851895 3738161 0.0279275911633526 0.1894057493544475 chr13 115169878 1432370 0.012437019339379695 0.11891030130754514 chr14 107349540 2276839 0.021209583198959214 0.1740937529978195 chr15 102531392 1338904 0.013058478714499458 0.12431194023906875 chr16 90354753 1123434 0.01243359051626205 0.15520620511054778 chr17 81195210 3024338 0.03724773912155655 0.2394358491981242 chr18 78077248 2760502 0.03535603611438764 0.553651590189074 chr19 59128983 1305185 0.022073523571342332 0.3999498009437996 chr20 63025520 1386817 0.02200405486539421 0.16263448723905416 chr21 48129895 1391048 0.028901953764910563 0.19378516100799306 chr22 51304566 758294 0.01478024392604744 0.1286727967092083 chrMT 16571 7415 0.4474684690121296 0.77724102939025 chrX 155270560 2874884 0.018515319323895014 0.16942786345500377 chrY 59373566 151633 0.002553880627618021 0.08037633308868312