BamQC report ----------------------------------- >>>>>>> Input bam file = SRR1779329.sorted.bam outfile = /home/yangyx/scDNA/SRP052954/SRP052954.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 = 141,133,976 number of mapped reads = 138,972,224 (98.47%) number of supplementary alignments = 494,768 (0.35%) number of secondary alignments = 0 number of mapped paired reads (first in pair) = 69,857,691 number of mapped paired reads (second in pair) = 69,114,533 number of mapped paired reads (both in pair) = 138,105,702 number of mapped paired reads (singletons) = 866,522 number of mapped bases = 13,926,734,400 bp number of sequenced bases = 13,923,590,946 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 10,582,193 duplication rate = 7.28% >>>>>>> Insert size mean insert size = 155,637.6276 std insert size = 3,762,201.1022 median insert size = 233 >>>>>>> Mapping quality mean mapping quality = 53.8249 >>>>>>> ACTG content number of A's = 4,289,835,667 bp (30.81%) number of C's = 2,688,682,562 bp (19.31%) number of T's = 4,180,913,655 bp (30.03%) number of G's = 2,760,843,838 bp (19.83%) number of N's = 3,315,224 bp (0.02%) GC percentage = 39.14% >>>>>>> Mismatches and indels general error rate = 0.0031 number of mismatches = 41,219,674 number of insertions = 1,125,753 mapped reads with insertion percentage = 0.8% number of deletions = 1,421,372 mapped reads with deletion percentage = 1% homopolymer indels = 47.38% >>>>>>> Coverage mean coverageData = 4.4987X std coverageData = 7.0182X There is a 75.6% of reference with a coverageData >= 1X There is a 62.17% of reference with a coverageData >= 2X There is a 50.61% of reference with a coverageData >= 3X There is a 41.18% of reference with a coverageData >= 4X There is a 33.6% of reference with a coverageData >= 5X There is a 27.54% of reference with a coverageData >= 6X There is a 22.71% of reference with a coverageData >= 7X There is a 18.85% of reference with a coverageData >= 8X There is a 15.73% of reference with a coverageData >= 9X There is a 13.21% of reference with a coverageData >= 10X There is a 11.15% of reference with a coverageData >= 11X There is a 9.47% of reference with a coverageData >= 12X There is a 8.08% of reference with a coverageData >= 13X There is a 6.92% of reference with a coverageData >= 14X There is a 5.96% of reference with a coverageData >= 15X There is a 5.15% of reference with a coverageData >= 16X There is a 4.47% of reference with a coverageData >= 17X There is a 3.89% of reference with a coverageData >= 18X There is a 3.4% of reference with a coverageData >= 19X There is a 2.98% of reference with a coverageData >= 20X There is a 2.63% of reference with a coverageData >= 21X There is a 2.32% of reference with a coverageData >= 22X There is a 2.05% of reference with a coverageData >= 23X There is a 1.82% of reference with a coverageData >= 24X There is a 1.62% of reference with a coverageData >= 25X There is a 1.44% of reference with a coverageData >= 26X There is a 1.29% of reference with a coverageData >= 27X There is a 1.16% of reference with a coverageData >= 28X There is a 1.04% of reference with a coverageData >= 29X There is a 0.93% of reference with a coverageData >= 30X There is a 0.84% of reference with a coverageData >= 31X There is a 0.76% of reference with a coverageData >= 32X There is a 0.69% of reference with a coverageData >= 33X There is a 0.62% of reference with a coverageData >= 34X There is a 0.57% of reference with a coverageData >= 35X There is a 0.51% of reference with a coverageData >= 36X There is a 0.47% of reference with a coverageData >= 37X There is a 0.43% of reference with a coverageData >= 38X There is a 0.39% of reference with a coverageData >= 39X There is a 0.36% of reference with a coverageData >= 40X There is a 0.33% of reference with a coverageData >= 41X There is a 0.3% of reference with a coverageData >= 42X There is a 0.28% of reference with a coverageData >= 43X There is a 0.25% of reference with a coverageData >= 44X There is a 0.23% of reference with a coverageData >= 45X There is a 0.22% of reference with a coverageData >= 46X There is a 0.2% of reference with a coverageData >= 47X There is a 0.18% of reference with a coverageData >= 48X There is a 0.17% of reference with a coverageData >= 49X There is a 0.16% of reference with a coverageData >= 50X There is a 0.15% of reference with a coverageData >= 51X >>>>>>> Coverage per contig chr1 249250621 1067544164 4.283015062177117 8.332442801317518 chr2 243199373 1155458641 4.751075739821089 6.300857117070362 chr3 198022430 1050283794 5.303862769485255 6.626243334562195 chr4 191154276 1040255500 5.441968245586094 6.532867100335315 chr5 180915260 906287577 5.009458997543933 6.16078419865729 chr6 171115067 904656006 5.286828459121019 6.679044687076843 chr7 159138663 733724243 4.610597004952844 6.768392578578901 chr8 146364022 738049565 5.042561381648832 6.109966199229159 chr9 141213431 557372034 3.9470185665271456 6.57285615453411 chr10 135534747 742161690 5.475803854195411 13.710334903657031 chr11 135006516 629808101 4.665020027625926 6.431428786230987 chr12 133851895 617714561 4.614910838580208 6.3829480798397045 chr13 115169878 495337890 4.3009326622712925 5.83996290587302 chr14 107349540 440030379 4.099042986118059 6.152481691943735 chr15 102531392 358621604 3.497676145857846 5.412100212699053 chr16 90354753 257967888 2.85505609206856 4.782928143451254 chr17 81195210 236508003 2.912831963855996 4.796755004585499 chr18 78077248 368357927 4.717865145554311 6.403434592924759 chr19 59128983 128320321 2.1701763583520455 5.364550597842412 chr20 63025520 212679391 3.374496410342985 5.446056798575481 chr21 48129895 169046573 3.5122988113728484 6.1055007903635925 chr22 51304566 78594744 1.531924936271754 3.603314622929558 chrMT 16571 374368 22.5917566833625 8.402912504024632 chrX 155270560 1028214832 6.622084907789345 8.203419799668454 chrY 59373566 9364604 0.15772345558627893 1.7446679302802137