BamQC report ----------------------------------- >>>>>>> Input bam file = SRR6238329.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 = 2,048,811 number of mapped reads = 1,870,058 (91.28%) number of supplementary alignments = 21,752 (1.06%) number of secondary alignments = 0 number of mapped bases = 124,891,937 bp number of sequenced bases = 124,835,405 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 74,860 duplication rate = 3.02% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 46.3434 >>>>>>> ACTG content number of A's = 35,468,383 bp (28.41%) number of C's = 23,653,031 bp (18.95%) number of T's = 38,837,209 bp (31.11%) number of G's = 26,846,470 bp (21.51%) number of N's = 30,312 bp (0.02%) GC percentage = 40.45% >>>>>>> Mismatches and indels general error rate = 0.0085 number of mismatches = 1,039,687 number of insertions = 9,603 mapped reads with insertion percentage = 0.51% number of deletions = 32,732 mapped reads with deletion percentage = 1.73% homopolymer indels = 46.27% >>>>>>> Coverage mean coverageData = 0.0403X std coverageData = 0.3889X There is a 3.42% of reference with a coverageData >= 1X There is a 0.45% of reference with a coverageData >= 2X There is a 0.07% 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 10348042 0.04151661471687968 0.7947754301869462 chr2 243199373 11598599 0.047691730685506334 0.4038906941550175 chr3 198022430 8764923 0.04426227372323428 0.23891615828481 chr4 191154276 7205610 0.03769525929935253 0.24046077077057454 chr5 180915260 7912823 0.04373773113445488 0.2404247865000329 chr6 171115067 7966661 0.04655733209045817 0.2942191812099334 chr7 159138663 4729549 0.029719672836512393 0.29381276776585025 chr8 146364022 6402821 0.04374586672672878 0.6488378813606194 chr9 141213431 4670082 0.03307108939233974 0.33470151076964255 chr10 135534747 6008939 0.04433504420825753 0.3448736981433593 chr11 135006516 5818478 0.04309775685197298 0.31177925290870884 chr12 133851895 5857419 0.043760448815461296 0.24800410871109507 chr13 115169878 4034788 0.035033361761484194 0.21308987295855775 chr14 107349540 3223739 0.030030301014797083 0.2266579429354975 chr15 102531392 3877148 0.037814253024088466 0.22317992331417608 chr16 90354753 3442543 0.038100297833806265 0.25377693685208186 chr17 81195210 3033349 0.03735871857465484 0.26213617483157936 chr18 78077248 3678287 0.04711086896915219 0.627885162713794 chr19 59128983 2435757 0.04119396066730929 0.49223828119041757 chr20 63025520 2455646 0.038962724940627226 0.23187419102114046 chr21 48129895 1716633 0.03566666829420675 0.23619070514050605 chr22 51304566 1316622 0.025662862054032384 0.179626891214702 chrMT 16571 4818 0.2907488986784141 0.6267774219048641 chrX 155270560 8052136 0.05185874257167618 0.29171982533178614 chrY 59373566 336525 0.005667926363055235 0.1495992697228158