BamQC report ----------------------------------- >>>>>>> Input bam file = SRR1781881.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 = 207,645,696 number of mapped reads = 202,436,415 (97.49%) number of supplementary alignments = 487,861 (0.23%) number of secondary alignments = 0 number of mapped paired reads (first in pair) = 101,885,196 number of mapped paired reads (second in pair) = 100,551,219 number of mapped paired reads (both in pair) = 200,335,208 number of mapped paired reads (singletons) = 2,101,207 number of mapped bases = 20,125,153,218 bp number of sequenced bases = 20,121,016,515 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 16,532,471 duplication rate = 7.86% >>>>>>> Insert size mean insert size = 25,753.3506 std insert size = 1,550,183.4062 median insert size = 212 >>>>>>> Mapping quality mean mapping quality = 53.9983 >>>>>>> ACTG content number of A's = 6,005,368,665 bp (29.85%) number of C's = 4,039,535,863 bp (20.08%) number of T's = 5,992,577,733 bp (29.78%) number of G's = 4,081,465,327 bp (20.28%) number of N's = 2,068,927 bp (0.01%) GC percentage = 40.36% >>>>>>> Mismatches and indels general error rate = 0.0045 number of mismatches = 86,675,089 number of insertions = 2,202,047 mapped reads with insertion percentage = 1.07% number of deletions = 1,855,524 mapped reads with deletion percentage = 0.9% homopolymer indels = 47.4% >>>>>>> Coverage mean coverageData = 6.501X std coverageData = 8.324X There is a 84.44% of reference with a coverageData >= 1X There is a 75.74% of reference with a coverageData >= 2X There is a 66.54% of reference with a coverageData >= 3X There is a 57.67% of reference with a coverageData >= 4X There is a 49.57% of reference with a coverageData >= 5X There is a 42.4% of reference with a coverageData >= 6X There is a 36.18% of reference with a coverageData >= 7X There is a 30.86% of reference with a coverageData >= 8X There is a 26.34% of reference with a coverageData >= 9X There is a 22.51% of reference with a coverageData >= 10X There is a 19.28% of reference with a coverageData >= 11X There is a 16.55% of reference with a coverageData >= 12X There is a 14.25% of reference with a coverageData >= 13X There is a 12.3% of reference with a coverageData >= 14X There is a 10.65% of reference with a coverageData >= 15X There is a 9.25% of reference with a coverageData >= 16X There is a 8.05% of reference with a coverageData >= 17X There is a 7.03% of reference with a coverageData >= 18X There is a 6.15% of reference with a coverageData >= 19X There is a 5.4% of reference with a coverageData >= 20X There is a 4.75% of reference with a coverageData >= 21X There is a 4.19% of reference with a coverageData >= 22X There is a 3.71% of reference with a coverageData >= 23X There is a 3.29% of reference with a coverageData >= 24X There is a 2.92% of reference with a coverageData >= 25X There is a 2.6% of reference with a coverageData >= 26X There is a 2.32% of reference with a coverageData >= 27X There is a 2.07% of reference with a coverageData >= 28X There is a 1.86% of reference with a coverageData >= 29X There is a 1.67% of reference with a coverageData >= 30X There is a 1.5% of reference with a coverageData >= 31X There is a 1.35% of reference with a coverageData >= 32X There is a 1.22% of reference with a coverageData >= 33X There is a 1.1% of reference with a coverageData >= 34X There is a 1% of reference with a coverageData >= 35X There is a 0.91% of reference with a coverageData >= 36X There is a 0.83% of reference with a coverageData >= 37X There is a 0.75% of reference with a coverageData >= 38X There is a 0.69% of reference with a coverageData >= 39X There is a 0.63% of reference with a coverageData >= 40X There is a 0.57% of reference with a coverageData >= 41X There is a 0.53% of reference with a coverageData >= 42X There is a 0.48% of reference with a coverageData >= 43X There is a 0.44% of reference with a coverageData >= 44X There is a 0.41% of reference with a coverageData >= 45X There is a 0.38% of reference with a coverageData >= 46X There is a 0.35% of reference with a coverageData >= 47X There is a 0.32% of reference with a coverageData >= 48X There is a 0.3% of reference with a coverageData >= 49X There is a 0.27% of reference with a coverageData >= 50X There is a 0.25% of reference with a coverageData >= 51X >>>>>>> Coverage per contig chr1 249250621 1471660165 5.904339010653859 9.60596606298493 chr2 243199373 1569761012 6.45462606517493 9.628982024290025 chr3 198022430 1285087834 6.489607434874928 6.827433877087456 chr4 191154276 1975801822 10.336163351114363 10.032236823874015 chr5 180915260 1172985023 6.4836157159987495 6.38543619075628 chr6 171115067 1137279690 6.646286092387177 7.075080021331907 chr7 159138663 962669232 6.049247956796018 7.298080950391301 chr8 146364022 946247190 6.465025879105728 6.83462195377346 chr9 141213431 775196755 5.489539837042837 7.809748387947549 chr10 135534747 1030399050 7.602471490207599 10.982034904633666 chr11 135006516 1343482562 9.951242368183177 10.428608251077046 chr12 133851895 1248653780 9.32862235532788 9.322107753394546 chr13 115169878 578849357 5.02604819117721 5.991920612162122 chr14 107349540 561853341 5.233868174935822 6.4051844966150995 chr15 102531392 517858305 5.050729292741876 6.391254889253581 chr16 90354753 417085955 4.616093134580313 6.0346068143085265 chr17 81195210 381177474 4.694580801010306 6.119464961193693 chr18 78077248 483738158 6.1956353533362245 7.476740810715517 chr19 59128983 249940688 4.227041889085087 6.845419702004817 chr20 63025520 351505677 5.577195983468284 7.518668231241259 chr21 48129895 221130980 4.594462132111445 8.38419909004922 chr22 51304566 154376018 3.0090112837130323 5.137842006690523 chrMT 16571 1082270 65.31108563152495 21.948991592420974 chrX 155270560 1270148978 8.180230547246046 8.705730584171178 chrY 59373566 17181902 0.28938639124353754 3.135518654070557