BamQC report ----------------------------------- >>>>>>> Input bam file = SRR6238291.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 = 3,250,361 number of mapped reads = 2,910,701 (89.55%) number of supplementary alignments = 26,315 (0.81%) number of secondary alignments = 0 number of mapped bases = 190,816,925 bp number of sequenced bases = 190,726,461 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 138,532 duplication rate = 3.52% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 44.3102 >>>>>>> ACTG content number of A's = 52,470,019 bp (27.51%) number of C's = 36,847,453 bp (19.32%) number of T's = 58,166,111 bp (30.5%) number of G's = 43,194,378 bp (22.65%) number of N's = 48,500 bp (0.03%) GC percentage = 41.97% >>>>>>> Mismatches and indels general error rate = 0.0087 number of mismatches = 1,639,748 number of insertions = 14,617 mapped reads with insertion percentage = 0.5% number of deletions = 54,065 mapped reads with deletion percentage = 1.84% homopolymer indels = 44.94% >>>>>>> Coverage mean coverageData = 0.0616X std coverageData = 0.5657X There is a 4.95% of reference with a coverageData >= 1X There is a 0.84% of reference with a coverageData >= 2X There is a 0.18% of reference with a coverageData >= 3X There is a 0.05% of reference with a coverageData >= 4X There is a 0.02% of reference with a coverageData >= 5X There is a 0.01% 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 19397901 0.07782488533900182 1.2245698407519434 chr2 243199373 14224586 0.0584894024377275 0.6760431364153316 chr3 198022430 14398191 0.07270989958056771 0.3239909156227232 chr4 191154276 7608440 0.03980261472152472 0.2537950439221133 chr5 180915260 12391034 0.06849081719253533 0.31637802741122745 chr6 171115067 13552359 0.07920026703434596 0.47536655287833346 chr7 159138663 8148440 0.051203396122537485 0.4917147725011732 chr8 146364022 5304249 0.036240115074181276 0.6848775586060223 chr9 141213431 3689695 0.026128499066069715 0.44161933472345233 chr10 135534747 9604734 0.07086547333872989 0.5923322341663577 chr11 135006516 5395271 0.0399630414875679 0.3006888313406942 chr12 133851895 10906539 0.08148214113815871 0.35031252903978116 chr13 115169878 6009328 0.0521779488209582 0.27218279943706636 chr14 107349540 3634058 0.03385257170175112 0.2755934143352575 chr15 102531392 6415307 0.06256919831928157 0.30495066240186697 chr16 90354753 6871079 0.07604557338560818 0.40081168079202467 chr17 81195210 6465031 0.0796233053649347 0.42785121629108747 chr18 78077248 5579365 0.07145954990626718 0.8853117364108022 chr19 59128983 5217979 0.0882473997565627 0.8235681708321485 chr20 63025520 4993552 0.07923063546322189 0.35359922689833706 chr21 48129895 3557099 0.07390622813534083 0.35585448471534276 chr22 51304566 3015887 0.05878398815419275 0.2897661137966778 chrMT 16571 5705 0.3442761450727174 0.657432758670497 chrX 155270560 13868921 0.08932099555768976 0.4162026816434644 chrY 59373566 562175 0.009468439204072735 0.17767091892557288