BamQC report ----------------------------------- >>>>>>> Input bam file = SRR1708513.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 = 2,984,086 number of mapped reads = 2,102,438 (70.46%) number of supplementary alignments = 469 (0.02%) number of secondary alignments = 0 number of mapped bases = 101,139,065 bp number of sequenced bases = 101,120,647 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 88,812 duplication rate = 3.33% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 43.5302 >>>>>>> ACTG content number of A's = 29,353,778 bp (29.03%) number of C's = 18,814,066 bp (18.61%) number of T's = 32,317,737 bp (31.96%) number of G's = 20,633,622 bp (20.4%) number of N's = 1,444 bp (0%) GC percentage = 39.01% >>>>>>> Mismatches and indels general error rate = 0.0048 number of mismatches = 479,597 number of insertions = 4,755 mapped reads with insertion percentage = 0.23% number of deletions = 11,977 mapped reads with deletion percentage = 0.57% homopolymer indels = 48.43% >>>>>>> Coverage mean coverageData = 0.0327X std coverageData = 0.3178X There is a 2.84% of reference with a coverageData >= 1X There is a 0.32% of reference with a coverageData >= 2X There is a 0.05% of reference with a coverageData >= 3X There is a 0.01% 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 8297809 0.033291026384243194 0.5767404171858986 chr2 243199373 8855172 0.03641116295147685 0.2735533837396062 chr3 198022430 7124004 0.03597574274793012 0.21374722618823236 chr4 191154276 6816427 0.0356592964731796 0.21545876153035082 chr5 180915260 6436471 0.035577269711797664 0.21378032948851503 chr6 171115067 6228984 0.036402311667855645 0.25426712481674585 chr7 159138663 5761346 0.03620330780333375 0.4016869064670673 chr8 146364022 5261783 0.03594997546596526 0.6341350859767847 chr9 141213431 4328448 0.0306518152653624 0.23826495703976042 chr10 135534747 4728442 0.03488730458175423 0.2561517037436162 chr11 135006516 4681074 0.0346729486745662 0.2823028074973998 chr12 133851895 4738687 0.035402464791402466 0.21465019882982322 chr13 115169878 3285493 0.028527363726129847 0.18975836683665737 chr14 107349540 3288224 0.030631002238109266 0.20041618637507674 chr15 102531392 2976974 0.029034756496820018 0.19183334040813957 chr16 90354753 2776717 0.030731277634060934 0.2023732406796916 chr17 81195210 2720022 0.03349978403898456 0.2526072666891769 chr18 78077248 2629855 0.033682731747922266 0.37160332348427827 chr19 59128983 1768759 0.029913570473552708 0.39272617460386156 chr20 63025520 2004103 0.03179827790393479 0.2013727946889855 chr21 48129895 1365138 0.028363618910866105 0.21087779374045176 chr22 51304566 1117562 0.02178289550290709 0.18017315516385887 chrMT 16571 162810 9.82499547402088 7.49432644742455 chrX 155270560 3140589 0.020226558080295453 0.18097153377924077 chrY 59373566 644172 0.010849474663522821 0.12673876132834405