BamQC report ----------------------------------- >>>>>>> Input bam file = SRR053670.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/SRP002535/SRP002535.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 = 9,919,817 number of mapped reads = 5,581,231 (56.26%) number of supplementary alignments = 128 (0%) number of secondary alignments = 0 number of mapped bases = 256,952,899 bp number of sequenced bases = 256,907,399 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 1,997,410 duplication rate = 24.36% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 40.5009 >>>>>>> ACTG content number of A's = 74,493,787 bp (29%) number of C's = 51,635,145 bp (20.1%) number of T's = 77,866,864 bp (30.31%) number of G's = 52,781,433 bp (20.54%) number of N's = 130,170 bp (0.05%) GC percentage = 40.64% >>>>>>> Mismatches and indels general error rate = 0.0165 number of mismatches = 4,230,580 number of insertions = 15,534 mapped reads with insertion percentage = 0.28% number of deletions = 32,473 mapped reads with deletion percentage = 0.58% homopolymer indels = 38.08% >>>>>>> Coverage mean coverageData = 0.083X std coverageData = 0.8647X There is a 2.76% of reference with a coverageData >= 1X There is a 1.31% of reference with a coverageData >= 2X There is a 0.89% of reference with a coverageData >= 3X There is a 0.66% of reference with a coverageData >= 4X There is a 0.5% of reference with a coverageData >= 5X There is a 0.39% of reference with a coverageData >= 6X There is a 0.31% of reference with a coverageData >= 7X There is a 0.24% of reference with a coverageData >= 8X There is a 0.2% of reference with a coverageData >= 9X There is a 0.16% of reference with a coverageData >= 10X There is a 0.13% of reference with a coverageData >= 11X There is a 0.11% of reference with a coverageData >= 12X There is a 0.09% of reference with a coverageData >= 13X There is a 0.07% of reference with a coverageData >= 14X There is a 0.06% of reference with a coverageData >= 15X There is a 0.05% of reference with a coverageData >= 16X There is a 0.04% of reference with a coverageData >= 17X There is a 0.04% of reference with a coverageData >= 18X There is a 0.03% of reference with a coverageData >= 19X There is a 0.03% of reference with a coverageData >= 20X There is a 0.02% of reference with a coverageData >= 21X There is a 0.02% of reference with a coverageData >= 22X There is a 0.02% of reference with a coverageData >= 23X There is a 0.02% of reference with a coverageData >= 24X There is a 0.01% of reference with a coverageData >= 25X There is a 0.01% of reference with a coverageData >= 26X There is a 0.01% of reference with a coverageData >= 27X There is a 0.01% of reference with a coverageData >= 28X There is a 0.01% of reference with a coverageData >= 29X There is a 0.01% of reference with a coverageData >= 30X There is a 0.01% of reference with a coverageData >= 31X There is a 0.01% of reference with a coverageData >= 32X There is a 0.01% of reference with a coverageData >= 33X There is a 0.01% 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 20030586 0.08036323407996644 0.8697450214283934 chr2 243199373 23000641 0.0945752479386532 0.9498689222359549 chr3 198022430 17443254 0.08808726364988047 0.9204965662685146 chr4 191154276 17805236 0.09314589436649588 0.9124304277936612 chr5 180915260 16611971 0.09182183415594682 0.8845112178901529 chr6 171115067 15694799 0.09172073082261073 0.9800243362456273 chr7 159138663 14559756 0.09149100366640632 0.9262888015031443 chr8 146364022 13915140 0.09507213459876089 0.9274518032971379 chr9 141213431 11803881 0.08358893992172742 0.8477636377624065 chr10 135534747 11785032 0.0869521083032678 0.8649586127892027 chr11 135006516 12644887 0.09366130891045288 0.9572318069296516 chr12 133851895 12116174 0.09051925637660939 0.8851805113722379 chr13 115169878 9179594 0.07970481656670679 0.8513748060639091 chr14 107349540 7746596 0.07216235859045134 0.8085460584261805 chr15 102531392 7176771 0.0699958408835413 0.7547115367836428 chr16 90354753 7103173 0.07861427057412243 0.8007225559392331 chr17 81195210 6367921 0.07842729885174261 0.7485762895538167 chr18 78077248 6479926 0.08299378072341894 0.872517297507818 chr19 59128983 4452707 0.07530498199165712 0.7918901697695424 chr20 63025520 5112632 0.08112002883911153 0.8211813304301818 chr21 48129895 3754465 0.07800692272443145 0.8177400641946615 chr22 51304566 2611355 0.05089907592240425 0.6058971613195643 chrMT 16571 29215 1.7630197332689639 3.820788388838264 chrX 155270560 8917609 0.05743270971651033 0.673852409729063 chrY 59373566 609578 0.01026682480213501 0.2230363551520207