BamQC report ----------------------------------- >>>>>>> Input bam file = SRR1549103.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/SRP041670/SRP041670.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 = 10,402,388 number of mapped reads = 8,897,730 (85.54%) number of secondary alignments = 0 number of mapped bases = 353,162,791 bp number of sequenced bases = 353,130,266 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 386,354 duplication rate = 3.19% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 44.3195 >>>>>>> ACTG content number of A's = 106,363,510 bp (30.12%) number of C's = 69,734,619 bp (19.75%) number of T's = 107,286,562 bp (30.38%) number of G's = 69,744,110 bp (19.75%) number of N's = 1,465 bp (0%) GC percentage = 39.5% >>>>>>> Mismatches and indels general error rate = 0.003 number of mismatches = 1,044,839 number of insertions = 8,681 mapped reads with insertion percentage = 0.1% number of deletions = 26,120 mapped reads with deletion percentage = 0.29% homopolymer indels = 45.52% >>>>>>> Coverage mean coverageData = 0.1141X std coverageData = 0.831X There is a 9.05% of reference with a coverageData >= 1X There is a 1.7% of reference with a coverageData >= 2X There is a 0.36% of reference with a coverageData >= 3X There is a 0.09% of reference with a coverageData >= 4X There is a 0.03% of reference with a coverageData >= 5X There is a 0.01% of reference with a coverageData >= 6X There is a 0.01% of reference with a coverageData >= 7X There is a 0.01% of reference with a coverageData >= 8X There is a 0.01% 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 28009251 0.11237384640257325 1.6201463652284191 chr2 243199373 31087609 0.12782766919386754 0.654125438754291 chr3 198022430 25314183 0.1278349275887585 0.43320611801308095 chr4 191154276 25402925 0.13289226655855713 0.4542012557771742 chr5 180915260 23377407 0.12921744135900973 0.4410692040859918 chr6 171115067 21941491 0.12822652840968118 0.5048791067833411 chr7 159138663 20196585 0.12691186804805568 1.1169309135391086 chr8 146364022 19079233 0.13035466461833087 1.7212457259723826 chr9 141213431 15028873 0.10642665427483311 0.6159925111759804 chr10 135534747 16295341 0.1202299879602092 0.6330561016940651 chr11 135006516 16340541 0.12103520247867147 0.6433715387590059 chr12 133851895 16316532 0.12189989540304977 0.4498635286952902 chr13 115169878 12355470 0.10728039496577395 0.38793383250910113 chr14 107349540 11017382 0.10263091951768027 0.5200430972849124 chr15 102531392 9954572 0.09708804109477027 0.3699877679390135 chr16 90354753 8676676 0.09602899362693183 0.4412343968716833 chr17 81195210 7765120 0.09563519818472051 0.418826073219407 chr18 78077248 9982965 0.1278601033683974 1.3591027602202732 chr19 59128983 5184963 0.0876890272237559 1.243793522494094 chr20 63025520 6725439 0.10670977407247097 0.43949856730425757 chr21 48129895 4691775 0.09748151330893201 0.4631098368195546 chr22 51304566 3098939 0.060402791439654706 0.3152287481855058 chrMT 16571 76744 4.631223221290206 5.59213156526816 chrX 155270560 12317359 0.07932836076587861 0.46120169112132153 chrY 59373566 2925416 0.049271354191526916 0.4203627281254073