BamQC report ----------------------------------- >>>>>>> Input bam file = SRR1779090.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 = 20,940,504 number of mapped reads = 20,277,243 (96.83%) number of supplementary alignments = 116,918 (0.56%) number of secondary alignments = 0 number of mapped paired reads (first in pair) = 10,250,842 number of mapped paired reads (second in pair) = 10,026,401 number of mapped paired reads (both in pair) = 19,982,522 number of mapped paired reads (singletons) = 294,721 number of mapped bases = 2,025,432,633 bp number of sequenced bases = 2,024,931,644 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 445,548 duplication rate = 1.9% >>>>>>> Insert size mean insert size = 71,130.8965 std insert size = 2,554,078.8735 median insert size = 265 >>>>>>> Mapping quality mean mapping quality = 53.6273 >>>>>>> ACTG content number of A's = 616,512,933 bp (30.45%) number of C's = 393,265,687 bp (19.42%) number of T's = 615,196,267 bp (30.38%) number of G's = 399,278,625 bp (19.72%) number of N's = 678,132 bp (0.03%) GC percentage = 39.14% >>>>>>> Mismatches and indels general error rate = 0.0052 number of mismatches = 10,093,419 number of insertions = 184,623 mapped reads with insertion percentage = 0.9% number of deletions = 224,562 mapped reads with deletion percentage = 1.09% homopolymer indels = 47.08% >>>>>>> Coverage mean coverageData = 0.6543X std coverageData = 1.6825X There is a 31.28% of reference with a coverageData >= 1X There is a 15.03% of reference with a coverageData >= 2X There is a 7.78% of reference with a coverageData >= 3X There is a 4.27% of reference with a coverageData >= 4X There is a 2.45% of reference with a coverageData >= 5X There is a 1.46% of reference with a coverageData >= 6X There is a 0.9% of reference with a coverageData >= 7X There is a 0.57% of reference with a coverageData >= 8X There is a 0.38% of reference with a coverageData >= 9X There is a 0.26% of reference with a coverageData >= 10X There is a 0.18% of reference with a coverageData >= 11X There is a 0.13% of reference with a coverageData >= 12X There is a 0.1% 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 0.04% of reference with a coverageData >= 16X There is a 0.04% of reference with a coverageData >= 17X There is a 0.03% of reference with a coverageData >= 18X There is a 0.03% of reference with a coverageData >= 19X There is a 0.02% 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 0.01% 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 0.01% 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 143571875 0.5760141115154934 2.4163789790559926 chr2 243199373 161148126 0.6626173579814286 1.506553789520748 chr3 198022430 147945831 0.7471165311929563 1.4614498050735008 chr4 191154276 133772057 0.6998120042054409 1.4464720023155493 chr5 180915260 121071872 0.6692186828242128 1.371750230550704 chr6 171115067 114487225 0.6690657170475818 1.4131595081825112 chr7 159138663 174552420 1.0968573991349921 2.8057613553575504 chr8 146364022 131863436 0.9009279343252811 1.5918947320637542 chr9 141213431 76566253 0.5422023419287929 1.3742996583363112 chr10 135534747 64852869 0.47849625601912993 2.545998504609572 chr11 135006516 98906093 0.7326023656517437 1.4410108498359164 chr12 133851895 86034004 0.642755218370274 1.4065439446933143 chr13 115169878 77669829 0.6743936031607154 1.3983381668823802 chr14 107349540 70408927 0.6558847574009167 1.363745504016935 chr15 102531392 53592433 0.5226929231585972 1.2634003714017292 chr16 90354753 37294094 0.41275187814414144 1.0965698547398828 chr17 81195210 39085042 0.4813712779362231 1.215049981261649 chr18 78077248 57236765 0.73307866844897 1.4696493907667292 chr19 59128983 26539098 0.4488340007471463 1.7760732015324925 chr20 63025520 46918932 0.7444433937236853 1.5877799603325675 chr21 48129895 29142359 0.6054939243062966 1.3697100109122833 chr22 51304566 17310473 0.3374060897425777 0.9385085662583306 chrMT 16571 1855 0.11194255023836823 0.4516693671384977 chrX 155270560 114111799 0.7349223123816904 1.542686897970131 chrY 59373566 1348966 0.022719976091717314 0.35999124218027173