BamQC report ----------------------------------- >>>>>>> Input bam file = SRR1779318.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 = 14,416,760 number of mapped reads = 12,466,194 (86.47%) number of supplementary alignments = 33,618 (0.23%) number of secondary alignments = 0 number of mapped paired reads (first in pair) = 6,318,017 number of mapped paired reads (second in pair) = 6,148,177 number of mapped paired reads (both in pair) = 12,260,592 number of mapped paired reads (singletons) = 205,602 number of mapped bases = 991,601,418 bp number of sequenced bases = 991,409,684 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 412,435 duplication rate = 3.06% >>>>>>> Insert size mean insert size = 43,045.82 std insert size = 1,964,853.0163 median insert size = 240 >>>>>>> Mapping quality mean mapping quality = 53.2437 >>>>>>> ACTG content number of A's = 303,605,757 bp (30.62%) number of C's = 190,305,873 bp (19.2%) number of T's = 303,524,324 bp (30.62%) number of G's = 193,719,047 bp (19.54%) number of N's = 254,683 bp (0.03%) GC percentage = 38.74% >>>>>>> Mismatches and indels general error rate = 0.0039 number of mismatches = 3,768,080 number of insertions = 73,318 mapped reads with insertion percentage = 0.58% number of deletions = 92,027 mapped reads with deletion percentage = 0.73% homopolymer indels = 46.98% >>>>>>> Coverage mean coverageData = 0.3203X std coverageData = 1.3565X There is a 14.63% of reference with a coverageData >= 1X There is a 6.08% of reference with a coverageData >= 2X There is a 3.25% of reference with a coverageData >= 3X There is a 1.99% of reference with a coverageData >= 4X There is a 1.32% of reference with a coverageData >= 5X There is a 0.93% of reference with a coverageData >= 6X There is a 0.68% of reference with a coverageData >= 7X There is a 0.52% of reference with a coverageData >= 8X There is a 0.4% of reference with a coverageData >= 9X There is a 0.32% of reference with a coverageData >= 10X There is a 0.26% of reference with a coverageData >= 11X There is a 0.21% of reference with a coverageData >= 12X There is a 0.18% of reference with a coverageData >= 13X There is a 0.15% of reference with a coverageData >= 14X There is a 0.13% of reference with a coverageData >= 15X There is a 0.11% of reference with a coverageData >= 16X There is a 0.09% of reference with a coverageData >= 17X There is a 0.08% of reference with a coverageData >= 18X There is a 0.07% of reference with a coverageData >= 19X There is a 0.06% of reference with a coverageData >= 20X There is a 0.05% of reference with a coverageData >= 21X There is a 0.05% of reference with a coverageData >= 22X There is a 0.04% of reference with a coverageData >= 23X There is a 0.04% of reference with a coverageData >= 24X There is a 0.03% of reference with a coverageData >= 25X There is a 0.03% of reference with a coverageData >= 26X There is a 0.03% of reference with a coverageData >= 27X There is a 0.03% of reference with a coverageData >= 28X There is a 0.02% of reference with a coverageData >= 29X There is a 0.02% of reference with a coverageData >= 30X There is a 0.02% of reference with a coverageData >= 31X There is a 0.02% of reference with a coverageData >= 32X There is a 0.02% 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 0.01% of reference with a coverageData >= 36X There is a 0.01% of reference with a coverageData >= 37X There is a 0.01% of reference with a coverageData >= 38X There is a 0.01% of reference with a coverageData >= 39X There is a 0.01% of reference with a coverageData >= 40X There is a 0.01% of reference with a coverageData >= 41X There is a 0.01% of reference with a coverageData >= 42X There is a 0.01% of reference with a coverageData >= 43X There is a 0.01% 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 81255872 0.32600068025507545 1.5682578483554461 chr2 243199373 67985972 0.27954830294731065 1.038680321684759 chr3 198022430 75345991 0.38049220484770335 1.414928944708773 chr4 191154276 71454124 0.37380342985369575 1.4307020243797979 chr5 180915260 66885026 0.3697036170414812 1.3913078975106088 chr6 171115067 63927460 0.37359340191825424 1.3448104237402454 chr7 159138663 92266266 0.5797853536069987 2.346848064225707 chr8 146364022 68551884 0.4683656752750345 1.453087776973135 chr9 141213431 36812098 0.26068411297222854 1.194936426598455 chr10 135534747 18464136 0.1362317516998058 1.1138384422473786 chr11 135006516 44742230 0.33140792996983937 1.3777913158700053 chr12 133851895 50016288 0.3736688823120509 1.3283947813191297 chr13 115169878 32350837 0.2808966855031313 1.0819060087790333 chr14 107349540 26392092 0.24585193378565012 1.0858071187685763 chr15 102531392 24422074 0.23819118733899566 1.1033421902897562 chr16 90354753 17137819 0.18967257870761928 0.8114867605838443 chr17 81195210 18754846 0.2309846356700106 1.1655176185239846 chr18 78077248 25041271 0.32072430370496663 1.2279375387893736 chr19 59128983 10758453 0.18194889298197467 0.8824248945869707 chr20 63025520 24537465 0.38932586355495363 1.729249858026512 chr21 48129895 8883554 0.1845745560010052 0.7642816539903498 chr22 51304566 5015674 0.09776272154801972 0.49692306845296647 chrMT 16571 16184 0.9766459477400278 1.0597078967166278 chrX 155270560 59969762 0.38622751151280704 1.4744379208009817 chrY 59373566 614040 0.010341976090841504 0.17816344607219364