BamQC report ----------------------------------- >>>>>>> Input bam file = SRR1708599.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/SRP051114/SRP051114.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 = 5,285,480 number of mapped reads = 5,166,487 (97.75%) number of supplementary alignments = 147 (0%) number of secondary alignments = 0 number of mapped bases = 257,716,437 bp number of sequenced bases = 257,693,777 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 50,016 duplication rate = 0.97% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 46.735 >>>>>>> ACTG content number of A's = 79,830,827 bp (30.98%) number of C's = 48,863,387 bp (18.96%) number of T's = 79,431,396 bp (30.82%) number of G's = 49,562,417 bp (19.23%) number of N's = 5,750 bp (0%) GC percentage = 38.19% >>>>>>> Mismatches and indels general error rate = 0.0015 number of mismatches = 375,875 number of insertions = 16,208 mapped reads with insertion percentage = 0.31% number of deletions = 13,103 mapped reads with deletion percentage = 0.25% homopolymer indels = 48.88% >>>>>>> Coverage mean coverageData = 0.0832X std coverageData = 0.3011X There is a 7.67% of reference with a coverageData >= 1X There is a 0.6% of reference with a coverageData >= 2X There is a 0.05% of reference with a coverageData >= 3X There is a 0% 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 19297540 0.07742223438632877 0.29230829674543723 chr2 243199373 22955342 0.09438898512291806 0.3191270771373499 chr3 198022430 19254810 0.09723550003906123 0.3237816884546188 chr4 191154276 20055385 0.10491727111560926 0.33591125305624586 chr5 180915260 18222017 0.10072128243908225 0.3290268838254123 chr6 171115067 17564074 0.10264481268619087 0.3331065741625126 chr7 159138663 14440285 0.09074026844123982 0.3141362480527331 chr8 146364022 13424624 0.09172079187602537 0.31417868836953927 chr9 141213431 10890256 0.07711912332191688 0.2907306837051225 chr10 135534747 10876290 0.08024724464199576 0.2937257752705411 chr11 135006516 11667689 0.08642315456833209 0.3078485491945999 chr12 133851895 12342959 0.09221355439159079 0.31656514722714196 chr13 115169878 9938995 0.08629856324064179 0.3065773655212065 chr14 107349540 8345965 0.07774569877057694 0.2921066464479847 chr15 102531392 7185747 0.07008338480374869 0.27702338492733897 chr16 90354753 4732094 0.05237238598837186 0.23751252618451835 chr17 81195210 4272303 0.05261767288981702 0.239496069066704 chr18 78077248 7369263 0.09438425647379375 0.31966622514747484 chr19 59128983 2060107 0.03484090027389783 0.19253628161413838 chr20 63025520 3938970 0.06249801667641933 0.2603033640956452 chr21 48129895 3038573 0.06313275771742281 0.2633485314366068 chr22 51304566 1482584 0.028897700840116256 0.176602791914883 chrMT 16571 200 0.012069277653732424 0.10919528465391506 chrX 155270560 14031585 0.09036861205369517 0.3119763907506782 chrY 59373566 328780 0.005537481107333186 0.0781218531965245