BamQC report ----------------------------------- >>>>>>> Input bam file = SRR1779095.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 = 27,261,318 number of mapped reads = 26,505,398 (97.23%) number of supplementary alignments = 155,774 (0.57%) number of secondary alignments = 0 number of mapped paired reads (first in pair) = 13,321,640 number of mapped paired reads (second in pair) = 13,183,758 number of mapped paired reads (both in pair) = 26,276,006 number of mapped paired reads (singletons) = 229,392 number of mapped bases = 2,647,432,525 bp number of sequenced bases = 2,646,836,064 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 888,426 duplication rate = 2.95% >>>>>>> Insert size mean insert size = 62,157.0408 std insert size = 2,359,257.6572 median insert size = 205 >>>>>>> Mapping quality mean mapping quality = 53.4496 >>>>>>> ACTG content number of A's = 809,310,230 bp (30.58%) number of C's = 512,322,184 bp (19.36%) number of T's = 804,351,629 bp (30.39%) number of G's = 519,771,823 bp (19.64%) number of N's = 1,080,198 bp (0.04%) GC percentage = 38.99% >>>>>>> Mismatches and indels general error rate = 0.0043 number of mismatches = 10,921,484 number of insertions = 220,016 mapped reads with insertion percentage = 0.82% number of deletions = 268,013 mapped reads with deletion percentage = 0.99% homopolymer indels = 46.59% >>>>>>> Coverage mean coverageData = 0.8552X std coverageData = 2.2944X There is a 33.64% of reference with a coverageData >= 1X There is a 18.76% of reference with a coverageData >= 2X There is a 10.86% of reference with a coverageData >= 3X There is a 6.7% of reference with a coverageData >= 4X There is a 4.3% of reference with a coverageData >= 5X There is a 2.85% of reference with a coverageData >= 6X There is a 1.95% of reference with a coverageData >= 7X There is a 1.36% of reference with a coverageData >= 8X There is a 0.98% of reference with a coverageData >= 9X There is a 0.71% of reference with a coverageData >= 10X There is a 0.53% of reference with a coverageData >= 11X There is a 0.4% of reference with a coverageData >= 12X There is a 0.31% of reference with a coverageData >= 13X There is a 0.24% of reference with a coverageData >= 14X There is a 0.19% of reference with a coverageData >= 15X There is a 0.15% of reference with a coverageData >= 16X There is a 0.12% of reference with a coverageData >= 17X There is a 0.1% of reference with a coverageData >= 18X There is a 0.09% of reference with a coverageData >= 19X There is a 0.07% of reference with a coverageData >= 20X There is a 0.06% of reference with a coverageData >= 21X There is a 0.05% of reference with a coverageData >= 22X There is a 0.05% of reference with a coverageData >= 23X There is a 0.04% of reference with a coverageData >= 24X There is a 0.04% 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 0.03% of reference with a coverageData >= 29X There is a 0.03% 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 0.02% of reference with a coverageData >= 34X There is a 0.02% of reference with a coverageData >= 35X There is a 0.02% of reference with a coverageData >= 36X There is a 0.02% of reference with a coverageData >= 37X There is a 0.02% of reference with a coverageData >= 38X There is a 0.02% of reference with a coverageData >= 39X There is a 0.02% of reference with a coverageData >= 40X There is a 0.02% 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 0.01% of reference with a coverageData >= 45X There is a 0.01% of reference with a coverageData >= 46X There is a 0.01% of reference with a coverageData >= 47X There is a 0.01% of reference with a coverageData >= 48X There is a 0.01% of reference with a coverageData >= 49X There is a 0.01% of reference with a coverageData >= 50X There is a 0.01% of reference with a coverageData >= 51X >>>>>>> Coverage per contig chr1 249250621 238882183 0.9584015559985305 2.6489291242889283 chr2 243199373 166522165 0.6847146147864452 1.8586223022449195 chr3 198022430 153415009 0.7747355135476319 1.6804205936756194 chr4 191154276 193593023 1.01275800390675 1.934164360669788 chr5 180915260 161374581 0.8919898796817913 1.7413921857953054 chr6 171115067 195253615 1.1410661750785511 2.081995689607332 chr7 159138663 254179961 1.5972231776259174 5.119862270281733 chr8 146364022 207622165 1.4185327935303664 2.3981117097052174 chr9 141213431 79694524 0.5643551285146524 1.506503927675612 chr10 135534747 79902325 0.5895338779803824 3.536319732426393 chr11 135006516 94017874 0.6963950836269266 1.594422894501539 chr12 133851895 141740457 1.0589350042448036 2.0911278452486255 chr13 115169878 63077109 0.547687555942362 1.3933785131391827 chr14 107349540 66012996 0.6149350616686388 1.4527590506474701 chr15 102531392 57514308 0.5609434035578099 1.5052898835497153 chr16 90354753 45663910 0.505384702894379 1.243001125472 chr17 81195210 41152012 0.5068280752029584 1.5550678497818489 chr18 78077248 75967556 0.972979426733893 1.943887284560703 chr19 59128983 30510935 0.5160064227723992 1.5478280426037645 chr20 63025520 42626947 0.6763442332566236 1.5444433807167333 chr21 48129895 24760651 0.5144547063732426 1.3360753244826842 chr22 51304566 17229511 0.335828023572015 1.115163521716938 chrMT 16571 1993 0.12027035181944361 0.5247217497893898 chrX 155270560 214976187 1.3845263841387576 2.618662238101315 chrY 59373566 1740528 0.029314863789720834 0.42124661679944386