BamQC report ----------------------------------- >>>>>>> Input bam file = SRR6240043.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 = 1,976,097 number of mapped reads = 1,605,780 (81.26%) number of supplementary alignments = 12,834 (0.65%) number of secondary alignments = 0 number of mapped bases = 103,600,118 bp number of sequenced bases = 103,560,753 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 197,661 duplication rate = 9.61% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 46.2392 >>>>>>> ACTG content number of A's = 29,008,479 bp (28.01%) number of C's = 18,853,770 bp (18.21%) number of T's = 32,913,092 bp (31.78%) number of G's = 22,713,892 bp (21.93%) number of N's = 71,520 bp (0.07%) GC percentage = 40.14% >>>>>>> Mismatches and indels general error rate = 0.0084 number of mismatches = 854,346 number of insertions = 6,974 mapped reads with insertion percentage = 0.43% number of deletions = 22,666 mapped reads with deletion percentage = 1.4% homopolymer indels = 47.57% >>>>>>> Coverage mean coverageData = 0.0335X std coverageData = 0.3565X There is a 1.77% of reference with a coverageData >= 1X There is a 0.78% of reference with a coverageData >= 2X There is a 0.37% of reference with a coverageData >= 3X There is a 0.18% of reference with a coverageData >= 4X There is a 0.09% of reference with a coverageData >= 5X There is a 0.05% of reference with a coverageData >= 6X There is a 0.03% of reference with a coverageData >= 7X There is a 0.02% 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% 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 7541133 0.03025522251356798 0.42354279149222906 chr2 243199373 8901328 0.036600949624981144 0.3862124559637063 chr3 198022430 6833925 0.034510863239078524 0.32151812460013296 chr4 191154276 7532210 0.039403826885881434 0.36220638824479273 chr5 180915260 6854505 0.03788793162058303 0.3348373156309061 chr6 171115067 5880425 0.03436532564370851 0.3267805958565346 chr7 159138663 8713372 0.054753331690363644 0.4436429024102556 chr8 146364022 4794111 0.03275470935063536 0.48115806657085713 chr9 141213431 3984885 0.028218880964658383 0.31266555442012167 chr10 135534747 5715367 0.04216901662862882 0.43877742918210805 chr11 135006516 3724232 0.02758557224008358 0.29612957509082805 chr12 133851895 4209291 0.03144737696840228 0.30421262868470605 chr13 115169878 3916089 0.03400271900956602 0.31080411099754957 chr14 107349540 3494336 0.032551010465438415 0.3158562332102178 chr15 102531392 2861657 0.02791005704867442 0.3256092518336967 chr16 90354753 2115944 0.023418181443094644 0.2671145664411186 chr17 81195210 2536474 0.031239207337477173 0.3117136231671583 chr18 78077248 2401400 0.03075671929420463 0.44023752822033496 chr19 59128983 1723443 0.029147178127518276 0.33495675632159194 chr20 63025520 1620864 0.025717582338075116 0.27297697977848556 chr21 48129895 1771164 0.03679966474059418 0.31859523752550334 chr22 51304566 1065412 0.020766416774678494 0.23216311989171567 chrMT 16571 36565 2.2065656870436303 2.412093857331212 chrX 155270560 5118545 0.032965328391937276 0.3245695283642778 chrY 59373566 253441 0.004268583093021565 0.1351223639057849