BamQC report ----------------------------------- >>>>>>> Input bam file = SRR1779427.sorted.bam outfile = /home/yangyx/scDNA/SRP052627/SRP052627.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 = 15,770,268 number of mapped reads = 15,308,778 (97.07%) number of supplementary alignments = 73,372 (0.47%) number of secondary alignments = 0 number of mapped paired reads (first in pair) = 7,688,066 number of mapped paired reads (second in pair) = 7,620,712 number of mapped paired reads (both in pair) = 15,215,270 number of mapped paired reads (singletons) = 93,508 number of mapped bases = 1,212,121,086 bp number of sequenced bases = 1,211,832,717 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 590,587 duplication rate = 3.68% >>>>>>> Insert size mean insert size = 70,196.4466 std insert size = 2,549,735.9365 median insert size = 151 >>>>>>> Mapping quality mean mapping quality = 52.5241 >>>>>>> ACTG content number of A's = 360,510,954 bp (29.75%) number of C's = 244,556,197 bp (20.18%) number of T's = 358,115,851 bp (29.55%) number of G's = 248,386,907 bp (20.5%) number of N's = 262,808 bp (0.02%) GC percentage = 40.68% >>>>>>> Mismatches and indels general error rate = 0.0032 number of mismatches = 3,659,929 number of insertions = 132,426 mapped reads with insertion percentage = 0.86% number of deletions = 135,808 mapped reads with deletion percentage = 0.88% homopolymer indels = 47.35% >>>>>>> Coverage mean coverageData = 0.3916X std coverageData = 1.3223X There is a 17.45% of reference with a coverageData >= 1X There is a 9.29% of reference with a coverageData >= 2X There is a 4.94% of reference with a coverageData >= 3X There is a 2.83% of reference with a coverageData >= 4X There is a 1.67% of reference with a coverageData >= 5X There is a 1.02% of reference with a coverageData >= 6X There is a 0.63% of reference with a coverageData >= 7X There is a 0.4% of reference with a coverageData >= 8X There is a 0.26% of reference with a coverageData >= 9X There is a 0.17% of reference with a coverageData >= 10X There is a 0.12% of reference with a coverageData >= 11X There is a 0.08% of reference with a coverageData >= 12X There is a 0.05% of reference with a coverageData >= 13X There is a 0.04% of reference with a coverageData >= 14X There is a 0.03% of reference with a coverageData >= 15X There is a 0.02% of reference with a coverageData >= 16X There is a 0.02% of reference with a coverageData >= 17X There is a 0.01% of reference with a coverageData >= 18X There is a 0.01% of reference with a coverageData >= 19X There is a 0.01% of reference with a coverageData >= 20X There is a 0.01% 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 91714645 0.36796155063541447 2.2543697430104532 chr2 243199373 89881685 0.36958024969908126 1.0919638246103884 chr3 198022430 97126114 0.4904803662898188 1.2538087557425501 chr4 191154276 83828350 0.43853766577526104 1.1703416080235551 chr5 180915260 124916857 0.6904716440172045 1.50039441650471 chr6 171115067 64387058 0.37627930216104233 1.3182986892097281 chr7 159138663 134223659 0.8434383981220201 1.7268995824153273 chr8 146364022 69899429 0.47757248020965154 1.269619954238282 chr9 141213431 55610757 0.39380642907826524 1.3780106090235744 chr10 135534747 26557318 0.19594471962234156 1.1109576807347759 chr11 135006516 55506160 0.4111368965332014 1.1991106183646507 chr12 133851895 46326550 0.34610305666572744 1.029434619353742 chr13 115169878 39666750 0.3444194844071989 1.0044981498600232 chr14 107349540 42106425 0.3922366597937914 1.150371330939173 chr15 102531392 30800339 0.30039911093765315 1.0258285326277072 chr16 90354753 16541420 0.18307194088616455 0.7923129155992313 chr17 81195210 22564085 0.2778992135127183 0.9493408722120998 chr18 78077248 34703578 0.44447747441098334 1.350931461039479 chr19 59128983 18638741 0.31522174159498056 1.5876397523716228 chr20 63025520 15129030 0.2400460956133325 0.9034117036560009 chr21 48129895 12794672 0.26583627493889195 0.9519141727866612 chr22 51304566 9922397 0.19340183094034943 0.8511995749236402 chrMT 16571 625 0.037716492667913826 0.2791647663193224 chrX 155270560 27863793 0.17945316227364672 0.7585938135004925 chrY 59373566 1410649 0.023758872761659625 0.2509566259170852