BamQC report ----------------------------------- >>>>>>> Input bam file = SRR1779412.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 = 16,292,530 number of mapped reads = 15,751,235 (96.68%) number of supplementary alignments = 61,000 (0.37%) number of secondary alignments = 0 number of mapped paired reads (first in pair) = 7,972,632 number of mapped paired reads (second in pair) = 7,778,603 number of mapped paired reads (both in pair) = 15,527,512 number of mapped paired reads (singletons) = 223,723 number of mapped bases = 1,251,959,595 bp number of sequenced bases = 1,251,695,164 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 546,606 duplication rate = 3.13% >>>>>>> Insert size mean insert size = 229,795.234 std insert size = 4,653,181.6391 median insert size = 199 >>>>>>> Mapping quality mean mapping quality = 53.2256 >>>>>>> ACTG content number of A's = 381,803,187 bp (30.5%) number of C's = 244,683,796 bp (19.55%) number of T's = 372,615,184 bp (29.77%) number of G's = 252,318,509 bp (20.16%) number of N's = 274,488 bp (0.02%) GC percentage = 39.71% >>>>>>> Mismatches and indels general error rate = 0.0035 number of mismatches = 4,209,619 number of insertions = 112,555 mapped reads with insertion percentage = 0.71% number of deletions = 127,096 mapped reads with deletion percentage = 0.8% homopolymer indels = 47.49% >>>>>>> Coverage mean coverageData = 0.4044X std coverageData = 1.4993X There is a 20.03% of reference with a coverageData >= 1X There is a 9.32% of reference with a coverageData >= 2X There is a 4.69% of reference with a coverageData >= 3X There is a 2.5% of reference with a coverageData >= 4X There is a 1.39% of reference with a coverageData >= 5X There is a 0.8% of reference with a coverageData >= 6X There is a 0.48% of reference with a coverageData >= 7X There is a 0.29% of reference with a coverageData >= 8X There is a 0.18% of reference with a coverageData >= 9X There is a 0.12% of reference with a coverageData >= 10X There is a 0.08% of reference with a coverageData >= 11X There is a 0.06% of reference with a coverageData >= 12X There is a 0.04% 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 0.02% of reference with a coverageData >= 18X There is a 0.02% 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 0.01% of reference with a coverageData >= 22X There is a 0.01% of reference with a coverageData >= 23X There is a 0.01% 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 94171719 0.3778193956836721 3.0989619034213445 chr2 243199373 117807343 0.4844064421169375 1.1912136492510041 chr3 198022430 122828074 0.6202735417396908 1.3205616053541456 chr4 191154276 60942001 0.3188105559302267 0.9107696321403257 chr5 180915260 133454212 0.7376614443690378 1.4662071864056696 chr6 171115067 70004267 0.40910638804238086 1.120161295867332 chr7 159138663 144323644 0.9069049675250822 2.533033280574155 chr8 146364022 56419245 0.3854720868493215 1.0222907462205435 chr9 141213431 38393051 0.2718795990446546 1.0344879988598947 chr10 135534747 34642015 0.25559508367252864 1.505702856489946 chr11 135006516 38704219 0.286684081233531 0.933188861663169 chr12 133851895 32764050 0.24477837986529813 0.8547464556365589 chr13 115169878 36272779 0.3149502250927104 0.9679520982057227 chr14 107349540 34714362 0.3233769050151496 0.9523096292044207 chr15 102531392 27447792 0.2677013494559793 0.9105959727104606 chr16 90354753 41628685 0.46072490508606667 1.1722787690389185 chr17 81195210 33241102 0.40939732774876747 1.2243227020631713 chr18 78077248 34227062 0.43837433921851343 1.2339039189936483 chr19 59128983 27523273 0.4654785454368461 2.2562189516533206 chr20 63025520 14104763 0.2237944724613141 0.8135572124331382 chr21 48129895 11564262 0.24027191416062718 0.7932724524786932 chr22 51304566 9510435 0.18537209729052187 0.7278656467083383 chrMT 16571 2195 0.13246032224971335 0.41146405446084033 chrX 155270560 31462003 0.2026269693366212 0.761747106898952 chrY 59373566 5807042 0.09780517478097914 0.4904750799706577