BamQC report ----------------------------------- >>>>>>> Input bam file = SRR1779406.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 = 15,682,436 number of mapped reads = 15,178,312 (96.79%) number of supplementary alignments = 55,732 (0.36%) number of secondary alignments = 0 number of mapped paired reads (first in pair) = 7,663,797 number of mapped paired reads (second in pair) = 7,514,515 number of mapped paired reads (both in pair) = 14,999,056 number of mapped paired reads (singletons) = 179,256 number of mapped bases = 1,206,799,692 bp number of sequenced bases = 1,206,545,717 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 470,555 duplication rate = 2.72% >>>>>>> Insert size mean insert size = 131,328.0721 std insert size = 3,483,991.906 median insert size = 195 >>>>>>> Mapping quality mean mapping quality = 53.281 >>>>>>> ACTG content number of A's = 365,569,853 bp (30.3%) number of C's = 237,788,089 bp (19.71%) number of T's = 358,785,011 bp (29.74%) number of G's = 244,135,827 bp (20.23%) number of N's = 266,937 bp (0.02%) GC percentage = 39.94% >>>>>>> Mismatches and indels general error rate = 0.0035 number of mismatches = 4,041,014 number of insertions = 106,616 mapped reads with insertion percentage = 0.7% number of deletions = 122,861 mapped reads with deletion percentage = 0.8% homopolymer indels = 47.3% >>>>>>> Coverage mean coverageData = 0.3898X std coverageData = 1.4546X There is a 21.66% of reference with a coverageData >= 1X There is a 9.07% of reference with a coverageData >= 2X There is a 4.04% of reference with a coverageData >= 3X There is a 1.91% of reference with a coverageData >= 4X There is a 0.94% of reference with a coverageData >= 5X There is a 0.49% of reference with a coverageData >= 6X There is a 0.26% of reference with a coverageData >= 7X There is a 0.15% of reference with a coverageData >= 8X There is a 0.09% of reference with a coverageData >= 9X There is a 0.05% of reference with a coverageData >= 10X There is a 0.04% of reference with a coverageData >= 11X There is a 0.02% of reference with a coverageData >= 12X There is a 0.02% of reference with a coverageData >= 13X There is a 0.01% of reference with a coverageData >= 14X There is a 0.01% of reference with a coverageData >= 15X There is a 0.01% of reference with a coverageData >= 16X There is a 0.01% 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% 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 82680580 0.3317166459537126 3.0802530683966647 chr2 243199373 92334802 0.3796671054739931 0.9949423332755304 chr3 198022430 88641774 0.4476350179118598 0.986526191826794 chr4 191154276 81307465 0.4253499670601143 0.9732277254076559 chr5 180915260 117745874 0.6508343961697869 1.2137699386718357 chr6 171115067 46887687 0.27401261514861225 0.8490342783664575 chr7 159138663 142487666 0.8953679974048795 2.1695211861452544 chr8 146364022 72952427 0.49843141779746936 1.0980013583630037 chr9 141213431 50251260 0.35585326157821345 1.1870987798016654 chr10 135534747 22315245 0.16464593393161386 2.1302884686438954 chr11 135006516 56136132 0.4158031305688979 1.0505945451370169 chr12 133851895 61807928 0.4617635633772686 1.0330907718386042 chr13 115169878 39255986 0.3408528921077784 0.8589304092976613 chr14 107349540 31159123 0.2902585609589012 0.8088374859787963 chr15 102531392 30281232 0.29533620298454544 0.8567045644265294 chr16 90354753 25717231 0.2846251043373446 0.8186142940139882 chr17 81195210 29004187 0.3572154933770108 1.3063386049628112 chr18 78077248 31915665 0.4087703629103321 1.3218727252090379 chr19 59128983 16867693 0.2852694591415516 2.2088015998590658 chr20 63025520 25153645 0.3991025381464524 0.9824472927586118 chr21 48129895 15061311 0.31293047699356086 0.8746951366575944 chr22 51304566 12314963 0.24003639364184468 0.8181278896759142 chrMT 16571 483 0.029147305533763806 0.2617029512650062 chrX 155270560 31609100 0.20357432857845043 0.6808454709093805 chrY 59373566 2910233 0.049015634331277994 0.3267297829673068