BamQC report ----------------------------------- >>>>>>> Input bam file = SRR089722.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/SRP002535/SRP002535.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 = 22,935,979 number of mapped reads = 20,085,038 (87.57%) number of supplementary alignments = 1,056 (0%) number of secondary alignments = 0 number of mapped bases = 950,509,743 bp number of sequenced bases = 950,321,034 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 4,928,887 duplication rate = 14.51% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 45.5595 >>>>>>> ACTG content number of A's = 286,913,723 bp (30.19%) number of C's = 187,445,886 bp (19.72%) number of T's = 278,794,281 bp (29.34%) number of G's = 197,162,480 bp (20.75%) number of N's = 4,664 bp (0%) GC percentage = 40.47% >>>>>>> Mismatches and indels general error rate = 0.0039 number of mismatches = 3,622,966 number of insertions = 37,542 mapped reads with insertion percentage = 0.19% number of deletions = 127,209 mapped reads with deletion percentage = 0.63% homopolymer indels = 48.67% >>>>>>> Coverage mean coverageData = 0.307X std coverageData = 2.1237X There is a 11.27% of reference with a coverageData >= 1X There is a 6.22% of reference with a coverageData >= 2X There is a 3.91% of reference with a coverageData >= 3X There is a 2.61% of reference with a coverageData >= 4X There is a 1.79% of reference with a coverageData >= 5X There is a 1.24% of reference with a coverageData >= 6X There is a 0.87% of reference with a coverageData >= 7X There is a 0.61% of reference with a coverageData >= 8X There is a 0.44% of reference with a coverageData >= 9X There is a 0.32% of reference with a coverageData >= 10X There is a 0.23% of reference with a coverageData >= 11X There is a 0.17% of reference with a coverageData >= 12X There is a 0.13% of reference with a coverageData >= 13X There is a 0.1% of reference with a coverageData >= 14X There is a 0.08% of reference with a coverageData >= 15X There is a 0.06% of reference with a coverageData >= 16X There is a 0.05% of reference with a coverageData >= 17X There is a 0.04% of reference with a coverageData >= 18X There is a 0.03% of reference with a coverageData >= 19X There is a 0.03% of reference with a coverageData >= 20X There is a 0.02% of reference with a coverageData >= 21X There is a 0.02% of reference with a coverageData >= 22X There is a 0.02% of reference with a coverageData >= 23X There is a 0.01% of reference with a coverageData >= 24X There is a 0.01% of reference with a coverageData >= 25X There is a 0.01% of reference with a coverageData >= 26X There is a 0.01% of reference with a coverageData >= 27X There is a 0.01% of reference with a coverageData >= 28X There is a 0.01% of reference with a coverageData >= 29X There is a 0.01% of reference with a coverageData >= 30X There is a 0.01% of reference with a coverageData >= 31X There is a 0.01% of reference with a coverageData >= 32X There is a 0.01% 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 75327205 0.3022147134389687 3.879948547753253 chr2 243199373 81632939 0.3356626211367741 2.014284162939843 chr3 198022430 65383964 0.33018463615460125 1.282653977612259 chr4 191154276 63187117 0.3305556031610823 1.3532189227348541 chr5 180915260 59507904 0.32892694623991364 1.2985386606387916 chr6 171115067 55655784 0.3252535558426307 1.4826214379213614 chr7 159138663 52214049 0.3281041075480193 2.8072834128731308 chr8 146364022 49738321 0.33982614252018845 3.598347234684202 chr9 141213431 38679929 0.2739111196866253 1.8255553149016073 chr10 135534747 43399793 0.3202115616890479 1.7106584820203214 chr11 135006516 43691543 0.32362543893807316 2.0894247934744086 chr12 133851895 41812769 0.3123808519856966 1.3551033840232283 chr13 115169878 32065546 0.27841955341829916 1.1947400631062237 chr14 107349540 29333182 0.27324925658740595 1.2864931951589973 chr15 102531392 26403546 0.25751670278698646 1.128906187951801 chr16 90354753 24956759 0.2762085908197879 1.2495241454687394 chr17 81195210 22836053 0.28124877070950366 1.4415157372598675 chr18 78077248 25662614 0.328682358271644 3.584830757642345 chr19 59128983 15949683 0.2697439088373971 2.926178933068476 chr20 63025520 19271040 0.305765664448306 1.3262000419587667 chr21 48129895 12086890 0.25113061227330746 1.284399802780429 chr22 51304566 9898697 0.19293988375225707 0.967894106623081 chrMT 16571 80308 4.846297749079717 5.384003912520817 chrX 155270560 58982160 0.3798669883073778 1.6534749618672024 chrY 59373566 2751948 0.04634971731359373 0.9227023140881923