BamQC report ----------------------------------- >>>>>>> Input bam file = SRR1779193.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 = 8,877,842 number of mapped reads = 8,610,575 (96.99%) number of supplementary alignments = 21,206 (0.24%) number of secondary alignments = 0 number of mapped paired reads (first in pair) = 4,334,482 number of mapped paired reads (second in pair) = 4,276,093 number of mapped paired reads (both in pair) = 8,540,812 number of mapped paired reads (singletons) = 69,763 number of mapped bases = 685,376,797 bp number of sequenced bases = 685,248,222 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 105,581 duplication rate = 1.15% >>>>>>> Insert size mean insert size = 44,109.7346 std insert size = 1,996,046.5856 median insert size = 202 >>>>>>> Mapping quality mean mapping quality = 52.8007 >>>>>>> ACTG content number of A's = 210,391,013 bp (30.7%) number of C's = 131,360,580 bp (19.17%) number of T's = 210,063,482 bp (30.66%) number of G's = 133,302,709 bp (19.45%) number of N's = 130,438 bp (0.02%) GC percentage = 38.62% >>>>>>> Mismatches and indels general error rate = 0.0039 number of mismatches = 2,605,358 number of insertions = 50,756 mapped reads with insertion percentage = 0.58% number of deletions = 62,912 mapped reads with deletion percentage = 0.72% homopolymer indels = 46.99% >>>>>>> Coverage mean coverageData = 0.2214X std coverageData = 0.7556X There is a 13.8% of reference with a coverageData >= 1X There is a 4.63% of reference with a coverageData >= 2X There is a 1.81% of reference with a coverageData >= 3X There is a 0.81% of reference with a coverageData >= 4X There is a 0.4% of reference with a coverageData >= 5X There is a 0.22% of reference with a coverageData >= 6X There is a 0.12% of reference with a coverageData >= 7X There is a 0.08% of reference with a coverageData >= 8X There is a 0.05% of reference with a coverageData >= 9X There is a 0.04% of reference with a coverageData >= 10X There is a 0.03% 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 47984432 0.1925147941757786 0.7481912719423758 chr2 243199373 76176310 0.313225766416758 0.8382626751206249 chr3 198022430 30961314 0.1563525606669911 0.5528414364242608 chr4 191154276 43225950 0.22613122188278958 0.686889908579436 chr5 180915260 46873117 0.259088796600132 0.721434322367922 chr6 171115067 52222910 0.3051917689983431 0.7994493166121335 chr7 159138663 62703287 0.3940166758847283 1.41776503552257 chr8 146364022 52621356 0.3595238452794089 0.896107378954958 chr9 141213431 21892461 0.15503101117909954 0.6238991320709305 chr10 135534747 17289791 0.12756722082492986 0.7541334455376164 chr11 135006516 21824188 0.1616528494076538 0.5989127800575892 chr12 133851895 32943950 0.24612240267498642 0.7326848205315125 chr13 115169878 15552875 0.13504290592371732 0.5144369147080881 chr14 107349540 28747587 0.2677942262258413 0.7879037168149333 chr15 102531392 11158018 0.10882538296173722 0.45608845100869866 chr16 90354753 12967208 0.14351439818556086 0.5226652409055301 chr17 81195210 11613445 0.14303115910409 0.5229033675954344 chr18 78077248 18969413 0.24295698793072215 0.6933571044867924 chr19 59128983 7208844 0.1219172668672485 0.5730732112013628 chr20 63025520 17215489 0.2731510822917447 0.812140394777291 chr21 48129895 7499054 0.155808650735681 0.5660796633102761 chr22 51304566 3453631 0.06731625017547171 0.3379499577552975 chrMT 16571 69 0.004163900790537686 0.06439380964614724 chrX 155270560 43741317 0.28171030619069065 0.815589405062805 chrY 59373566 530781 0.008939685381201459 0.1369990592424085