BamQC report ----------------------------------- >>>>>>> Input bam file = SRR3085018.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 = 2,507,083 number of mapped reads = 2,266,471 (90.4%) number of supplementary alignments = 18,244 (0.73%) number of secondary alignments = 0 number of mapped bases = 150,184,754 bp number of sequenced bases = 150,130,974 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 82,081 duplication rate = 2.93% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 45.3866 >>>>>>> ACTG content number of A's = 42,429,663 bp (28.26%) number of C's = 28,824,414 bp (19.2%) number of T's = 46,242,809 bp (30.8%) number of G's = 32,619,297 bp (21.73%) number of N's = 14,791 bp (0.01%) GC percentage = 40.93% >>>>>>> Mismatches and indels general error rate = 0.0089 number of mismatches = 1,315,304 number of insertions = 10,544 mapped reads with insertion percentage = 0.46% number of deletions = 31,469 mapped reads with deletion percentage = 1.37% homopolymer indels = 46.14% >>>>>>> Coverage mean coverageData = 0.0485X std coverageData = 0.3639X There is a 4.1% of reference with a coverageData >= 1X There is a 0.56% of reference with a coverageData >= 2X There is a 0.1% of reference with a coverageData >= 3X There is a 0.02% of reference with a coverageData >= 4X There is a 0.01% 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 16068392 0.06446680828931615 0.6010887565204102 chr2 243199373 14835767 0.06100248868651483 0.430232145038343 chr3 198022430 8262079 0.04172294522393246 0.2367766832926796 chr4 191154276 9632792 0.05039276233611431 0.26084753732664273 chr5 180915260 7575623 0.041873875094892495 0.23377273751638653 chr6 171115067 11705603 0.06840778667374744 0.3637216138685083 chr7 159138663 12104609 0.07606328199452071 0.3815684749324798 chr8 146364022 8286962 0.056618845852705525 0.6348820400495796 chr9 141213431 4010443 0.028399869414687615 0.27708878589254676 chr10 135534747 7346808 0.054206084879473745 0.45697310160664295 chr11 135006516 7221562 0.053490470045164336 0.3590384796890465 chr12 133851895 6575603 0.04912596119763564 0.2585809662535211 chr13 115169878 2860060 0.024833403053531062 0.17942798040265795 chr14 107349540 5468522 0.05094127091741613 0.2650253385409402 chr15 102531392 2629478 0.025645589596598864 0.19265093534023248 chr16 90354753 2914093 0.03225168464574298 0.21744049114184114 chr17 81195210 2456396 0.03025296689299775 0.23073691121723927 chr18 78077248 5015042 0.06423179771909994 0.4734704396818794 chr19 59128983 2257036 0.03817139895675189 0.40103508401892884 chr20 63025520 4040419 0.06410766622790261 0.29185294519026445 chr21 48129895 1982376 0.041188039159445494 0.2375079693800783 chr22 51304566 996746 0.019428017381532863 0.1566359072588534 chrMT 16571 12824 0.773882083157323 1.0647461594908112 chrX 155270560 5646466 0.036365335450583805 0.24427306442947824 chrY 59373566 279053 0.004699953511298277 0.09493053280988556