BamQC report ----------------------------------- >>>>>>> Input bam file = SRR1779204.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 = 8,968,802 number of mapped reads = 8,672,507 (96.7%) number of supplementary alignments = 30,065 (0.34%) number of secondary alignments = 0 number of mapped paired reads (first in pair) = 4,390,202 number of mapped paired reads (second in pair) = 4,282,305 number of mapped paired reads (both in pair) = 8,550,016 number of mapped paired reads (singletons) = 122,491 number of mapped bases = 689,058,268 bp number of sequenced bases = 688,914,564 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 88,122 duplication rate = 0.76% >>>>>>> Insert size mean insert size = 55,419.8046 std insert size = 2,283,533.2732 median insert size = 276 >>>>>>> Mapping quality mean mapping quality = 53.3473 >>>>>>> ACTG content number of A's = 206,451,817 bp (29.97%) number of C's = 136,574,661 bp (19.82%) number of T's = 206,080,032 bp (29.91%) number of G's = 139,681,446 bp (20.28%) number of N's = 126,608 bp (0.02%) GC percentage = 40.1% >>>>>>> Mismatches and indels general error rate = 0.0051 number of mismatches = 3,388,844 number of insertions = 59,127 mapped reads with insertion percentage = 0.68% number of deletions = 69,871 mapped reads with deletion percentage = 0.79% homopolymer indels = 47.46% >>>>>>> Coverage mean coverageData = 0.2226X std coverageData = 0.8514X There is a 17.5% of reference with a coverageData >= 1X There is a 3.46% of reference with a coverageData >= 2X There is a 0.7% of reference with a coverageData >= 3X There is a 0.17% of reference with a coverageData >= 4X There is a 0.06% of reference with a coverageData >= 5X There is a 0.04% of reference with a coverageData >= 6X There is a 0.03% of reference with a coverageData >= 7X There is a 0.03% of reference with a coverageData >= 8X There is a 0.03% of reference with a coverageData >= 9X There is a 0.02% of reference with a coverageData >= 10X There is a 0.02% 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 0.01% 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 60430403 0.2424483548227549 1.9319026093341702 chr2 243199373 50376265 0.2071397815651441 0.5660304479704452 chr3 198022430 40738852 0.20572847227458022 0.5025520235486037 chr4 191154276 49835595 0.26070876384685215 0.5699477685031992 chr5 180915260 32830361 0.18146816913067476 0.4687597946725288 chr6 171115067 38381361 0.22430146960699843 0.608452075364714 chr7 159138663 60563585 0.38057115636317745 1.3310952017423674 chr8 146364022 53840671 0.3678545469323055 0.6940341689370896 chr9 141213431 28762853 0.20368355046907685 0.6226958182817393 chr10 135534747 17871302 0.1318577146862568 0.9398189415477274 chr11 135006516 29523734 0.21868377078925583 0.5465018011119682 chr12 133851895 26924130 0.20114866509734508 0.5049724868003865 chr13 115169878 20364084 0.1768177960560139 0.4665931023693717 chr14 107349540 17098792 0.15928146501605875 0.4510669859555815 chr15 102531392 20524372 0.20017646888086724 0.509973030833331 chr16 90354753 16629671 0.18404865762844816 0.4900025761131251 chr17 81195210 17440882 0.21480185838548851 0.7880882147136471 chr18 78077248 19831050 0.2539926868324047 0.7299583216966434 chr19 59128983 9046184 0.15299069155307474 1.391745799961935 chr20 63025520 19512233 0.3095925745634467 0.6396808244977599 chr21 48129895 7668717 0.1593337571170683 0.4538701774853211 chr22 51304566 4500575 0.08772269898940378 0.3336618131187645 chrMT 16571 96 0.005793253273791563 0.09931387562957299 chrX 155270560 45818442 0.2950877616465092 0.6178510519283694 chrY 59373566 544058 0.009163303413508968 0.13067023358627453