BamQC report ----------------------------------- >>>>>>> Input bam file = SRR1818744.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/SRP055057/SRP055057.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 = 1,447,429 number of mapped reads = 1,228,160 (84.85%) number of supplementary alignments = 9,446 (0.65%) number of secondary alignments = 0 number of mapped bases = 83,461,320 bp number of sequenced bases = 83,426,417 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 428,008 duplication rate = 30.93% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 47.8264 >>>>>>> ACTG content number of A's = 23,246,088 bp (27.86%) number of C's = 17,027,845 bp (20.41%) number of T's = 24,970,666 bp (29.93%) number of G's = 18,176,867 bp (21.79%) number of N's = 4,951 bp (0.01%) GC percentage = 42.2% >>>>>>> Mismatches and indels general error rate = 0.0052 number of mismatches = 414,962 number of insertions = 10,007 mapped reads with insertion percentage = 0.8% number of deletions = 21,596 mapped reads with deletion percentage = 1.74% homopolymer indels = 41.56% >>>>>>> Coverage mean coverageData = 0.027X std coverageData = 0.3297X There is a 1.55% of reference with a coverageData >= 1X There is a 0.61% of reference with a coverageData >= 2X There is a 0.27% of reference with a coverageData >= 3X There is a 0.12% of reference with a coverageData >= 4X There is a 0.06% of reference with a coverageData >= 5X There is a 0.03% 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% 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 7063009 0.02833697654057199 0.41746331839336953 chr2 243199373 7312308 0.030067133437881026 0.5119893032067215 chr3 198022430 5591591 0.028237159800533707 0.2693303464908723 chr4 191154276 5285643 0.02765118892762828 0.28386137945255985 chr5 180915260 5081156 0.028085834218738653 0.27494577414844096 chr6 171115067 4879617 0.028516582937725757 0.2851189313670547 chr7 159138663 4428766 0.027829604173562776 0.29346661550108477 chr8 146364022 4235995 0.02894150449076891 0.29303415793372367 chr9 141213431 3206366 0.022705814718148164 0.2862592657928698 chr10 135534747 3944895 0.029106152387623523 0.34428663657357006 chr11 135006516 3974186 0.02943699398923827 0.28903579301619337 chr12 133851895 4006554 0.02993274021260588 0.2905023301656987 chr13 115169878 2592400 0.022509357872203355 0.23656349852754233 chr14 107349540 2724466 0.02537939147200817 0.27492450328586254 chr15 102531392 2525966 0.024636025618378417 0.2500784423156316 chr16 90354753 2663756 0.029481083302834107 0.370482593269628 chr17 81195210 2603988 0.03207070958988837 0.2913515034058878 chr18 78077248 2102396 0.026927127349570517 0.3446278644144353 chr19 59128983 1867095 0.03157664659985781 0.38310718618461037 chr20 63025520 1843346 0.02924761271307242 0.2894831244290733 chr21 48129895 1127276 0.0234215345784569 0.26254918326655213 chr22 51304566 1135284 0.022128322847521992 0.24756078837096296 chrMT 16571 110525 6.669784563393881 5.98194046284336 chrX 155270560 2486838 0.01601615914826352 0.21200101178412284 chrY 59373566 667898 0.011249080104098851 0.536411575655731