BamQC report ----------------------------------- >>>>>>> Input bam file = SRR6234069.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/SRP116771/SRP116771.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 = 5,581,169 number of mapped reads = 5,288,077 (94.75%) number of supplementary alignments = 37,767 (0.68%) number of secondary alignments = 0 number of mapped bases = 342,359,811 bp number of sequenced bases = 342,228,724 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 575,879 duplication rate = 8.86% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 45.6989 >>>>>>> ACTG content number of A's = 88,657,394 bp (25.91%) number of C's = 62,590,319 bp (18.29%) number of T's = 110,128,481 bp (32.18%) number of G's = 80,819,018 bp (23.62%) number of N's = 33,512 bp (0.01%) GC percentage = 41.9% >>>>>>> Mismatches and indels general error rate = 0.0055 number of mismatches = 1,835,907 number of insertions = 22,379 mapped reads with insertion percentage = 0.42% number of deletions = 75,388 mapped reads with deletion percentage = 1.41% homopolymer indels = 43.88% >>>>>>> Coverage mean coverageData = 0.1106X std coverageData = 1.1428X There is a 8.36% of reference with a coverageData >= 1X There is a 1.81% of reference with a coverageData >= 2X There is a 0.44% of reference with a coverageData >= 3X There is a 0.12% of reference with a coverageData >= 4X There is a 0.04% of reference with a coverageData >= 5X There is a 0.02% 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 0.01% of reference with a coverageData >= 10X There is a 0.01% of reference with a coverageData >= 11X There is a 0.01% of reference with a coverageData >= 12X There is a 0.01% 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 31646591 0.126966949462485 2.5584162701883613 chr2 243199373 21144947 0.08694490754299765 1.7636349116113816 chr3 198022430 38544866 0.194648990015929 0.5601885480827969 chr4 191154276 11187744 0.05852730179051815 0.3999232601166969 chr5 180915260 20411019 0.11282088089197119 0.4413288187576301 chr6 171115067 22714625 0.13274473953833651 0.7486934693727676 chr7 159138663 21937794 0.13785332606445236 1.451556695361594 chr8 146364022 18389317 0.12564096523666177 1.2211097537638596 chr9 141213431 12322304 0.08726014170705901 0.7222650384761679 chr10 135534747 14784827 0.10908514109669604 0.7949786758310843 chr11 135006516 14701899 0.10889769942659656 0.8524595231001549 chr12 133851895 11033449 0.08243027862997382 0.39516515456938867 chr13 115169878 15144655 0.13149840273339528 0.501340580662034 chr14 107349540 16715226 0.15570840825214527 0.5501104580879409 chr15 102531392 8045365 0.07846733417995534 0.38272358267863493 chr16 90354753 9353070 0.10351497502295202 0.537371185812618 chr17 81195210 8379785 0.10320541076253144 0.5025633931261777 chr18 78077248 7138579 0.0914296953704106 1.9310513599541719 chr19 59128983 10062721 0.17018254820990242 1.3237694884673459 chr20 63025520 8529797 0.13533878022743803 0.5341923342366743 chr21 48129895 6849203 0.14230662668181596 0.524427258230448 chr22 51304566 3657708 0.07129400529379783 0.3285141747056443 chrMT 16571 210484 12.701949188341079 7.49103082297627 chrX 155270560 8651633 0.05571972561958945 0.4498124357116282 chrY 59373566 802203 0.013511113683149839 0.29903015922014253