BamQC report ----------------------------------- >>>>>>> Input bam file = SRR1779299.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 = 26,110,006 number of mapped reads = 24,145,197 (92.47%) number of supplementary alignments = 60,332 (0.23%) number of secondary alignments = 0 number of mapped paired reads (first in pair) = 12,168,739 number of mapped paired reads (second in pair) = 11,976,458 number of mapped paired reads (both in pair) = 23,900,928 number of mapped paired reads (singletons) = 244,269 number of mapped bases = 1,922,011,160 bp number of sequenced bases = 1,921,648,341 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 1,215,572 duplication rate = 4.63% >>>>>>> Insert size mean insert size = 30,267.2718 std insert size = 1,634,384.2138 median insert size = 226 >>>>>>> Mapping quality mean mapping quality = 53.2286 >>>>>>> ACTG content number of A's = 594,032,061 bp (30.91%) number of C's = 363,662,335 bp (18.92%) number of T's = 592,879,726 bp (30.85%) number of G's = 370,562,941 bp (19.28%) number of N's = 511,278 bp (0.03%) GC percentage = 38.21% >>>>>>> Mismatches and indels general error rate = 0.0037 number of mismatches = 6,885,402 number of insertions = 139,899 mapped reads with insertion percentage = 0.57% number of deletions = 175,825 mapped reads with deletion percentage = 0.72% homopolymer indels = 46.96% >>>>>>> Coverage mean coverageData = 0.6209X std coverageData = 2.3657X There is a 21.36% of reference with a coverageData >= 1X There is a 10.76% of reference with a coverageData >= 2X There is a 6.61% of reference with a coverageData >= 3X There is a 4.53% of reference with a coverageData >= 4X There is a 3.3% of reference with a coverageData >= 5X There is a 2.51% of reference with a coverageData >= 6X There is a 1.96% of reference with a coverageData >= 7X There is a 1.57% of reference with a coverageData >= 8X There is a 1.27% of reference with a coverageData >= 9X There is a 1.05% of reference with a coverageData >= 10X There is a 0.87% of reference with a coverageData >= 11X There is a 0.73% of reference with a coverageData >= 12X There is a 0.62% of reference with a coverageData >= 13X There is a 0.53% of reference with a coverageData >= 14X There is a 0.46% of reference with a coverageData >= 15X There is a 0.4% of reference with a coverageData >= 16X There is a 0.35% of reference with a coverageData >= 17X There is a 0.3% of reference with a coverageData >= 18X There is a 0.27% of reference with a coverageData >= 19X There is a 0.23% of reference with a coverageData >= 20X There is a 0.21% of reference with a coverageData >= 21X There is a 0.18% of reference with a coverageData >= 22X There is a 0.16% of reference with a coverageData >= 23X There is a 0.15% of reference with a coverageData >= 24X There is a 0.13% of reference with a coverageData >= 25X There is a 0.12% of reference with a coverageData >= 26X There is a 0.11% of reference with a coverageData >= 27X There is a 0.1% of reference with a coverageData >= 28X There is a 0.09% of reference with a coverageData >= 29X There is a 0.08% of reference with a coverageData >= 30X There is a 0.07% of reference with a coverageData >= 31X There is a 0.07% of reference with a coverageData >= 32X There is a 0.06% of reference with a coverageData >= 33X There is a 0.06% of reference with a coverageData >= 34X There is a 0.05% of reference with a coverageData >= 35X There is a 0.05% of reference with a coverageData >= 36X There is a 0.04% of reference with a coverageData >= 37X There is a 0.04% of reference with a coverageData >= 38X There is a 0.04% of reference with a coverageData >= 39X There is a 0.03% of reference with a coverageData >= 40X There is a 0.03% of reference with a coverageData >= 41X There is a 0.03% of reference with a coverageData >= 42X There is a 0.03% of reference with a coverageData >= 43X There is a 0.03% of reference with a coverageData >= 44X There is a 0.02% of reference with a coverageData >= 45X There is a 0.02% of reference with a coverageData >= 46X There is a 0.02% of reference with a coverageData >= 47X There is a 0.02% of reference with a coverageData >= 48X There is a 0.02% of reference with a coverageData >= 49X There is a 0.02% of reference with a coverageData >= 50X There is a 0.02% of reference with a coverageData >= 51X >>>>>>> Coverage per contig chr1 249250621 125903934 0.5051298708700108 2.44698832750499 chr2 243199373 141978907 0.5837963529618145 2.0103049007182765 chr3 198022430 170839087 0.8627259396826915 2.9351824428314006 chr4 191154276 166839000 0.8727976349323203 2.8311993515206364 chr5 180915260 126318108 0.6982169884397812 2.1165826250926205 chr6 171115067 90897760 0.5312083944074896 1.7681853748762133 chr7 159138663 185904672 1.1681929990828188 3.9775743872436897 chr8 146364022 150689772 1.0295547357942925 2.824072059805316 chr9 141213431 60239246 0.42658297849869536 1.7452550411825984 chr10 135534747 38813898 0.2863759947845699 2.2844812392196903 chr11 135006516 67454233 0.4996368693789565 1.9865048373714884 chr12 133851895 82889332 0.6192615502380449 2.10751025083198 chr13 115169878 74198820 0.644255436304274 2.3966763017592556 chr14 107349540 41986965 0.391123846455234 1.5740222402541446 chr15 102531392 49897499 0.4866558234184512 1.832662732953251 chr16 90354753 27858753 0.3083263699475776 1.3390677284059875 chr17 81195210 35465189 0.4367891775881853 1.7088330407144707 chr18 78077248 54981678 0.7041959009620831 2.686226219155273 chr19 59128983 18050534 0.3052738789706564 1.4814517815327333 chr20 63025520 33656723 0.5340173789918751 1.6854960464223425 chr21 48129895 20533484 0.42662640340270847 1.5551373266357267 chr22 51304566 10464475 0.2039677131271318 1.017809446820967 chrMT 16571 3468 0.20928127451572023 0.733972210088638 chrX 155270560 144843241 0.9328441978955959 3.003929656122428 chrY 59373566 1302382 0.021935384511012863 0.2874419523486309