BamQC report ----------------------------------- >>>>>>> Input bam file = SRR2046440.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/SRP058890/SRP058890.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 = 9,260,144 number of mapped reads = 9,220,107 (99.57%) number of supplementary alignments = 41,557 (0.45%) number of secondary alignments = 0 number of mapped paired reads (first in pair) = 4,617,447 number of mapped paired reads (second in pair) = 4,602,660 number of mapped paired reads (both in pair) = 9,192,642 number of mapped paired reads (singletons) = 27,465 number of mapped bases = 898,606,545 bp number of sequenced bases = 898,370,190 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 7,376,287 duplication rate = 28.15% >>>>>>> Insert size mean insert size = 14,590.5962 std insert size = 1,138,314.871 median insert size = 139 >>>>>>> Mapping quality mean mapping quality = 52.4298 >>>>>>> ACTG content number of A's = 246,846,678 bp (27.48%) number of C's = 202,338,769 bp (22.52%) number of T's = 246,961,936 bp (27.49%) number of G's = 202,145,286 bp (22.5%) number of N's = 77,521 bp (0.01%) GC percentage = 45.02% >>>>>>> Mismatches and indels general error rate = 0.0038 number of mismatches = 3,234,593 number of insertions = 72,563 mapped reads with insertion percentage = 0.77% number of deletions = 84,614 mapped reads with deletion percentage = 0.89% homopolymer indels = 48.81% >>>>>>> Coverage mean coverageData = 0.2903X std coverageData = 47.7077X There is a 2.16% of reference with a coverageData >= 1X There is a 1.34% of reference with a coverageData >= 2X There is a 0.6% of reference with a coverageData >= 3X There is a 0.4% of reference with a coverageData >= 4X There is a 0.24% of reference with a coverageData >= 5X There is a 0.17% of reference with a coverageData >= 6X There is a 0.12% of reference with a coverageData >= 7X There is a 0.09% of reference with a coverageData >= 8X There is a 0.07% of reference with a coverageData >= 9X There is a 0.06% of reference with a coverageData >= 10X There is a 0.05% of reference with a coverageData >= 11X There is a 0.05% of reference with a coverageData >= 12X There is a 0.04% of reference with a coverageData >= 13X There is a 0.04% of reference with a coverageData >= 14X There is a 0.03% of reference with a coverageData >= 15X There is a 0.03% of reference with a coverageData >= 16X There is a 0.03% of reference with a coverageData >= 17X There is a 0.03% 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 0.03% 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 0.02% of reference with a coverageData >= 25X There is a 0.02% of reference with a coverageData >= 26X There is a 0.02% of reference with a coverageData >= 27X There is a 0.02% of reference with a coverageData >= 28X There is a 0.02% of reference with a coverageData >= 29X There is a 0.02% of reference with a coverageData >= 30X There is a 0.02% of reference with a coverageData >= 31X There is a 0.02% of reference with a coverageData >= 32X There is a 0.02% of reference with a coverageData >= 33X There is a 0.02% of reference with a coverageData >= 34X There is a 0.02% of reference with a coverageData >= 35X There is a 0.02% of reference with a coverageData >= 36X There is a 0.02% of reference with a coverageData >= 37X There is a 0.02% of reference with a coverageData >= 38X There is a 0.02% of reference with a coverageData >= 39X There is a 0.02% of reference with a coverageData >= 40X There is a 0.02% of reference with a coverageData >= 41X There is a 0.02% of reference with a coverageData >= 42X There is a 0.02% of reference with a coverageData >= 43X There is a 0.02% of reference with a coverageData >= 44X There is a 0.02% of reference with a coverageData >= 45X There is a 0.02% of reference with a coverageData >= 46X There is a 0.02% of reference with a coverageData >= 47X There is a 0.02% of reference with a coverageData >= 48X There is a 0.02% of reference with a coverageData >= 49X There is a 0.02% of reference with a coverageData >= 50X There is a 0.02% of reference with a coverageData >= 51X >>>>>>> Coverage per contig chr1 249250621 138313008 0.5549153997895154 75.77800076104754 chr2 243199373 35990447 0.14798741689190129 20.8371039791747 chr3 198022430 54476361 0.27510197203417813 73.86606313837225 chr4 191154276 17142947 0.08968121121182766 12.350196127193488 chr5 180915260 73646788 0.4070789163943384 45.0397129854889 chr6 171115067 76562550 0.4474331298949846 63.788384941931575 chr7 159138663 21642747 0.13599930143939942 18.35706962092676 chr8 146364022 45154055 0.3085051529944975 40.703459227487336 chr9 141213431 17573814 0.12444860149315401 14.124892606280802 chr10 135534747 11483980 0.08473089192397282 7.278768648202446 chr11 135006516 14953120 0.1107585059079667 7.901914493311117 chr12 133851895 87565128 0.6541941598959058 82.89753835201266 chr13 115169878 3724367 0.03233803026169742 1.6798188121679334 chr14 107349540 16886835 0.15730700848834564 21.83712731501215 chr15 102531392 13946271 0.13601952268433068 19.68107829661611 chr16 90354753 26389634 0.2920669153951425 32.90475037746729 chr17 81195210 182919162 2.252831934297602 148.2827693042855 chr18 78077248 2784325 0.03566115701209141 1.7544023178684778 chr19 59128983 15974718 0.270167305262125 19.69841534459674 chr20 63025520 18685288 0.2964717784161083 26.375008243390475 chr21 48129895 660025 0.01371341034506724 0.42110138972522876 chr22 51304566 12021833 0.2343228670914008 23.681180017030464 chrMT 16571 168369 10.160461046406372 4.934937362197375 chrX 155270560 9775301 0.06295656433518369 6.119348834540629 chrY 59373566 165472 0.0027869641516899963 0.12043609552931367