BamQC report ----------------------------------- >>>>>>> Input bam file = SRR053437.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 = 8,420,796 number of mapped reads = 5,377,627 (63.86%) number of supplementary alignments = 175 (0%) number of secondary alignments = 0 number of mapped bases = 250,336,008 bp number of sequenced bases = 250,285,033 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 1,143,402 duplication rate = 15.63% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 43.2681 >>>>>>> ACTG content number of A's = 74,935,540 bp (29.94%) number of C's = 48,728,826 bp (19.47%) number of T's = 74,641,094 bp (29.82%) number of G's = 51,678,116 bp (20.65%) number of N's = 301,457 bp (0.12%) GC percentage = 40.12% >>>>>>> Mismatches and indels general error rate = 0.013 number of mismatches = 3,227,036 number of insertions = 16,807 mapped reads with insertion percentage = 0.31% number of deletions = 36,289 mapped reads with deletion percentage = 0.67% homopolymer indels = 42.05% >>>>>>> Coverage mean coverageData = 0.0809X std coverageData = 1.1532X There is a 3.88% of reference with a coverageData >= 1X There is a 1.58% of reference with a coverageData >= 2X There is a 0.86% of reference with a coverageData >= 3X There is a 0.52% of reference with a coverageData >= 4X There is a 0.33% of reference with a coverageData >= 5X There is a 0.22% of reference with a coverageData >= 6X There is a 0.15% of reference with a coverageData >= 7X There is a 0.11% of reference with a coverageData >= 8X There is a 0.08% 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 0.04% of reference with a coverageData >= 12X There is a 0.03% of reference with a coverageData >= 13X There is a 0.02% 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 0.01% 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 19790301 0.0793992043855329 0.7043778839584066 chr2 243199373 21941333 0.09021952947222442 3.491366219948817 chr3 198022430 17057515 0.08613930755217983 0.6188791265007124 chr4 191154276 16326643 0.08541081759531238 0.6379112672973093 chr5 180915260 15794691 0.08730436006337995 0.6208204456092298 chr6 171115067 14855419 0.08681537669619707 0.6620339471787544 chr7 159138663 13510148 0.08489544743755953 0.7163610510416549 chr8 146364022 12738338 0.08703189367124661 0.6601555407421084 chr9 141213431 10254623 0.07261790133829409 0.5838355409947207 chr10 135534747 11424892 0.08429492991933647 0.6639411770038661 chr11 135006516 11450761 0.08481635804897002 0.6739463650325125 chr12 133851895 11506114 0.08596153233392774 0.6179868429239507 chr13 115169878 8053548 0.06992755518938729 0.5471158091904033 chr14 107349540 7617460 0.07095940979346535 0.6629195657621014 chr15 102531392 7101570 0.06926239721781989 0.5651957817952172 chr16 90354753 6999208 0.07746363935054972 0.6050815316187085 chr17 81195210 6424289 0.07912152699648169 0.5762875574500782 chr18 78077248 6670438 0.08543382574139909 0.6927139016440939 chr19 59128983 4370311 0.07391148601355109 0.654044441389218 chr20 63025520 5138875 0.08153641572493174 0.6070480748711444 chr21 48129895 3205703 0.0666052356856378 0.5826873905191056 chr22 51304566 2643304 0.05152180801997234 0.4646522437181307 chrMT 16571 43876 2.647758131675819 4.501369539471446 chrX 155270560 14705628 0.0947096989925199 0.6834792180209983 chrY 59373566 711020 0.011975362908133225 0.23696887126830662