BamQC report ----------------------------------- >>>>>>> Input bam file = SRR3081182.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/SRP064210/SRP064210.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 = 1,273,539 number of mapped reads = 1,136,542 (89.24%) number of supplementary alignments = 16,878 (1.33%) number of secondary alignments = 0 number of mapped bases = 75,732,339 bp number of sequenced bases = 75,706,482 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 38,356 duplication rate = 2.13% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 43.3017 >>>>>>> ACTG content number of A's = 21,567,064 bp (28.49%) number of C's = 14,538,450 bp (19.2%) number of T's = 22,405,514 bp (29.6%) number of G's = 17,173,296 bp (22.68%) number of N's = 22,158 bp (0.03%) GC percentage = 41.89% >>>>>>> Mismatches and indels general error rate = 0.0088 number of mismatches = 652,074 number of insertions = 6,854 mapped reads with insertion percentage = 0.6% number of deletions = 15,391 mapped reads with deletion percentage = 1.34% homopolymer indels = 43.04% >>>>>>> Coverage mean coverageData = 0.0245X std coverageData = 0.3292X There is a 2.26% of reference with a coverageData >= 1X There is a 0.1% of reference with a coverageData >= 2X There is a 0.01% 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 6085303 0.024414394538258742 0.6710639028451745 chr2 243199373 6406761 0.02634365755540003 0.33569237613506375 chr3 198022430 4982892 0.025163270645653626 0.16532572838401258 chr4 191154276 4895992 0.025612777817222356 0.17690087151682568 chr5 180915260 4560699 0.025209034329110768 0.16960198552781508 chr6 171115067 4427074 0.02587191226123881 0.2609307074866302 chr7 159138663 4169431 0.026199987617088374 0.47058512903676747 chr8 146364022 3840370 0.026238483662330624 0.3493941628313798 chr9 141213431 3217078 0.02278167152528147 0.29247738255781713 chr10 135534747 3558388 0.026254433484868642 0.28889133460900296 chr11 135006516 3450261 0.025556255373629523 0.29364662514867873 chr12 133851895 3412818 0.02549697185833641 0.17271077671915497 chr13 115169878 2315455 0.02010469265236176 0.14662694182304686 chr14 107349540 2283552 0.021272117234969055 0.1913189712006511 chr15 102531392 2130603 0.02078000657593725 0.15266704929063954 chr16 90354753 2155420 0.023855081536219794 0.20797532558208268 chr17 81195210 2033654 0.025046477495408902 0.21309919485456225 chr18 78077248 2073342 0.026555008701126353 0.652129245980802 chr19 59128983 1637597 0.027695335128628883 0.4811991938792032 chr20 63025520 1502442 0.023838629177514125 0.1691020756239502 chr21 48129895 973339 0.020223168988837394 0.16789574710028016 chr22 51304566 834049 0.01625681815532754 0.13218854349905998 chrMT 16571 24677 1.4891678233057752 1.4464621212905628 chrX 155270560 4536368 0.02921589256843023 0.2170537428490043 chrY 59373566 224774 0.003785758800473598 0.1003460766321175