BamQC report ----------------------------------- >>>>>>> Input bam file = SRR1006137.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/SRP030642/SRP030642.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 = 20,252,404 number of mapped reads = 17,827,910 (88.03%) number of secondary alignments = 0 number of mapped paired reads (first in pair) = 9,075,576 number of mapped paired reads (second in pair) = 8,752,334 number of mapped paired reads (both in pair) = 16,269,988 number of mapped paired reads (singletons) = 1,557,922 number of mapped bases = 689,025,486 bp number of sequenced bases = 688,949,130 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 2,090,234 duplication rate = 10.36% >>>>>>> Insert size mean insert size = 64,800.3174 std insert size = 2,484,980.3016 median insert size = 118 >>>>>>> Mapping quality mean mapping quality = 47.1249 >>>>>>> ACTG content number of A's = 187,434,051 bp (27.21%) number of C's = 149,522,783 bp (21.7%) number of T's = 193,563,870 bp (28.1%) number of G's = 158,399,296 bp (22.99%) number of N's = 29,130 bp (0%) GC percentage = 44.69% >>>>>>> Mismatches and indels general error rate = 0.0048 number of mismatches = 3,282,641 number of insertions = 22,001 mapped reads with insertion percentage = 0.12% number of deletions = 59,978 mapped reads with deletion percentage = 0.34% homopolymer indels = 46.16% >>>>>>> Coverage mean coverageData = 0.2226X std coverageData = 1.1133X There is a 9.49% of reference with a coverageData >= 1X There is a 5.22% of reference with a coverageData >= 2X There is a 2.97% of reference with a coverageData >= 3X There is a 1.72% of reference with a coverageData >= 4X There is a 1.01% of reference with a coverageData >= 5X There is a 0.61% of reference with a coverageData >= 6X There is a 0.37% of reference with a coverageData >= 7X There is a 0.24% of reference with a coverageData >= 8X There is a 0.15% of reference with a coverageData >= 9X There is a 0.1% of reference with a coverageData >= 10X There is a 0.07% of reference with a coverageData >= 11X There is a 0.05% of reference with a coverageData >= 12X There is a 0.03% of reference with a coverageData >= 13X There is a 0.03% of reference with a coverageData >= 14X There is a 0.02% of reference with a coverageData >= 15X There is a 0.01% of reference with a coverageData >= 16X There is a 0.01% of reference with a coverageData >= 17X There is a 0.01% of reference with a coverageData >= 18X There is a 0.01% of reference with a coverageData >= 19X There is a 0.01% of reference with a coverageData >= 20X There is a 0.01% 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 59275360 0.23781429214573552 1.2706381421216373 chr2 243199373 62179634 0.2556734963292854 1.2008654694490888 chr3 198022430 49358122 0.24925520810950558 0.957427141820414 chr4 191154276 45103648 0.2359541671984361 0.9936017391461276 chr5 180915260 42752674 0.23631325516708762 0.9321489458603208 chr6 171115067 38878232 0.2272051940347252 1.0160701981063798 chr7 159138663 39244447 0.24660535824660032 1.5081491958359465 chr8 146364022 33597961 0.22955068151926025 1.5666686794114435 chr9 141213431 30140397 0.2134385999020164 1.0135470292517048 chr10 135534747 34083368 0.2514732845592725 1.0169969512371884 chr11 135006516 28877922 0.2139002090832416 1.5294722897326483 chr12 133851895 28565341 0.2134100604253679 0.8870960788673149 chr13 115169878 22326243 0.1938548810479768 0.8548616534567969 chr14 107349540 22200253 0.20680342924618028 0.9038615338324038 chr15 102531392 21406759 0.20878248683096 0.8977916432280584 chr16 90354753 21821953 0.24151416804824866 1.0503239208079003 chr17 81195210 19809175 0.2439697489544026 1.0771651713133452 chr18 78077248 18573315 0.23788383268836524 1.4401573141258424 chr19 59128983 14986595 0.25345599128603313 1.2462572671475205 chr20 63025520 16350886 0.25943278214919924 1.0140830077001999 chr21 48129895 9494567 0.19726963875570475 0.9765400869914075 chr22 51304566 9366571 0.18256798040158842 0.9399965061570371 chrMT 16571 22997 1.3877858910144227 2.442879374464415 chrX 155270560 16174379 0.10416900022773151 0.6690128142988804 chrY 59373566 4434687 0.07469126917524206 0.5762714580717851