BamQC report ----------------------------------- >>>>>>> Input bam file = SRR1777289.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/SRP052908/SRP052908.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 = 541,491 number of mapped reads = 514,934 (95.1%) number of supplementary alignments = 176 (0.03%) number of secondary alignments = 0 number of mapped bases = 25,919,183 bp number of sequenced bases = 25,915,543 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 5,791 duplication rate = 0.67% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 46.685 >>>>>>> ACTG content number of A's = 7,766,646 bp (29.97%) number of C's = 5,251,077 bp (20.26%) number of T's = 7,565,559 bp (29.19%) number of G's = 5,330,514 bp (20.57%) number of N's = 1,747 bp (0.01%) GC percentage = 40.83% >>>>>>> Mismatches and indels general error rate = 0.0034 number of mismatches = 81,962 number of insertions = 4,065 mapped reads with insertion percentage = 0.79% number of deletions = 2,026 mapped reads with deletion percentage = 0.39% homopolymer indels = 47.56% >>>>>>> Coverage mean coverageData = 0.0084X std coverageData = 0.1174X There is a 0.79% of reference with a coverageData >= 1X There is a 0.02% of reference with a coverageData >= 2X There is a 0.01% of reference with a coverageData >= 3X There is a 0% 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 2078637 0.008339545922334934 0.1561998019157844 chr2 243199373 2251445 0.00925761021596055 0.11959100793702196 chr3 198022430 1800730 0.00909356581474129 0.10055548929531853 chr4 191154276 1763612 0.009226118488712227 0.10744582681255217 chr5 180915260 1607432 0.00888499952961403 0.09638630841167811 chr6 171115067 1517382 0.00886761187429509 0.09883994620268718 chr7 159138663 1397403 0.00878104021773766 0.10718127411431327 chr8 146364022 1337860 0.009140634301508877 0.10333862163737068 chr9 141213431 1047144 0.00741532864533261 0.09262925734395898 chr10 135534747 1384715 0.010216678974580591 0.22880132607045622 chr11 135006516 1206485 0.008936494591120328 0.09978968406837314 chr12 133851895 1182806 0.008836677284247639 0.09648627225152391 chr13 115169878 838301 0.007278821637720238 0.08665218743556195 chr14 107349540 771464 0.007186467683047361 0.087457330183058 chr15 102531392 703482 0.006861137708927233 0.0841977102325878 chr16 90354753 864669 0.009569712397974238 0.1588916158404135 chr17 81195210 638944 0.007869232680105144 0.09274080832273397 chr18 78077248 703486 0.009010128020905655 0.12187229294707971 chr19 59128983 445878 0.007540768966041577 0.12818364531364262 chr20 63025520 541148 0.008586172712260049 0.09672101445306869 chr21 48129895 347822 0.007226735067674675 0.09522116753991629 chr22 51304566 251959 0.004911044369813011 0.07774419537308842 chrMT 16571 70746 4.269265584454771 2.5020520841254825 chrX 155270560 792476 0.005103839388484205 0.07534894732031393 chrY 59373566 373157 0.006284901263973264 0.13832060706341842