BamQC report ----------------------------------- >>>>>>> Input bam file = SRR089583.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/SRP002535/SRP002535.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 = 9,017,685 number of mapped reads = 7,013,618 (77.78%) number of supplementary alignments = 262 (0%) number of secondary alignments = 0 number of mapped bases = 329,204,853 bp number of sequenced bases = 329,140,853 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 2,382,564 duplication rate = 26.36% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 44.1079 >>>>>>> ACTG content number of A's = 105,054,616 bp (31.92%) number of C's = 63,462,245 bp (19.28%) number of T's = 88,080,989 bp (26.76%) number of G's = 72,419,212 bp (22%) number of N's = 123,791 bp (0.04%) GC percentage = 41.28% >>>>>>> Mismatches and indels general error rate = 0.0059 number of mismatches = 1,914,701 number of insertions = 14,819 mapped reads with insertion percentage = 0.21% number of deletions = 42,765 mapped reads with deletion percentage = 0.61% homopolymer indels = 44.18% >>>>>>> Coverage mean coverageData = 0.1063X std coverageData = 0.9403X There is a 3.62% of reference with a coverageData >= 1X There is a 1.82% of reference with a coverageData >= 2X There is a 1.2% of reference with a coverageData >= 3X There is a 0.85% of reference with a coverageData >= 4X There is a 0.63% of reference with a coverageData >= 5X There is a 0.48% of reference with a coverageData >= 6X There is a 0.37% of reference with a coverageData >= 7X There is a 0.29% of reference with a coverageData >= 8X There is a 0.23% of reference with a coverageData >= 9X There is a 0.18% of reference with a coverageData >= 10X There is a 0.15% of reference with a coverageData >= 11X There is a 0.12% of reference with a coverageData >= 12X There is a 0.1% of reference with a coverageData >= 13X There is a 0.08% of reference with a coverageData >= 14X There is a 0.07% of reference with a coverageData >= 15X There is a 0.06% of reference with a coverageData >= 16X There is a 0.05% of reference with a coverageData >= 17X There is a 0.04% of reference with a coverageData >= 18X There is a 0.03% of reference with a coverageData >= 19X There is a 0.03% of reference with a coverageData >= 20X There is a 0.03% of reference with a coverageData >= 21X There is a 0.02% of reference with a coverageData >= 22X There is a 0.02% of reference with a coverageData >= 23X There is a 0.02% of reference with a coverageData >= 24X There is a 0.01% of reference with a coverageData >= 25X There is a 0.01% of reference with a coverageData >= 26X There is a 0.01% of reference with a coverageData >= 27X There is a 0.01% of reference with a coverageData >= 28X There is a 0.01% of reference with a coverageData >= 29X There is a 0.01% of reference with a coverageData >= 30X There is a 0.01% of reference with a coverageData >= 31X There is a 0.01% of reference with a coverageData >= 32X There is a 0.01% of reference with a coverageData >= 33X There is a 0.01% 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 26190773 0.10507806518163099 0.9975925747253448 chr2 243199373 27261811 0.11209655133444772 1.0103843445006653 chr3 198022430 22670753 0.11448578325192757 0.9451571105134208 chr4 191154276 21522184 0.1125906490315707 0.9455970547353985 chr5 180915260 20652371 0.11415494193248264 0.9318749266975074 chr6 171115067 19158729 0.1119640095749137 0.9844138693027515 chr7 159138663 18243175 0.11463697542815224 1.0379950780051375 chr8 146364022 16723621 0.11426046354479108 1.0456087035772077 chr9 141213431 13461818 0.09532958660284942 0.8402474494938391 chr10 135534747 14826395 0.10939183735665954 0.9411865031297643 chr11 135006516 14786293 0.10952280999533386 0.9906797049871102 chr12 133851895 14835959 0.11083861756309091 0.9138772716885144 chr13 115169878 10858077 0.09427879223767173 0.8599388266883115 chr14 107349540 10275198 0.09571720568155206 0.9151199376720408 chr15 102531392 9337958 0.0910741365922351 0.8183318485968426 chr16 90354753 9455760 0.10465149520136478 0.9051605618781974 chr17 81195210 8659376 0.10664885280794273 0.8724080207061996 chr18 78077248 8516894 0.10908291747168138 0.9374580888920669 chr19 59128983 6558304 0.11091521733089846 0.9371377093472953 chr20 63025520 7136150 0.113226356561596 0.913074103828298 chr21 48129895 4206396 0.08739674167167828 0.8378467614809193 chr22 51304566 3851369 0.07506873754667372 0.7162956374102791 chrMT 16571 83657 5.048397803391467 8.908267763588364 chrX 155270560 19094262 0.12297412980284221 0.9968969499132463 chrY 59373566 837570 0.014106782806341799 0.2916332936994087