BamQC report ----------------------------------- >>>>>>> Input bam file = SRR1779407.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 = 15,092,418 number of mapped reads = 14,713,886 (97.49%) number of supplementary alignments = 51,195 (0.34%) number of secondary alignments = 0 number of mapped paired reads (first in pair) = 7,402,362 number of mapped paired reads (second in pair) = 7,311,524 number of mapped paired reads (both in pair) = 14,595,746 number of mapped paired reads (singletons) = 118,140 number of mapped bases = 1,170,410,563 bp number of sequenced bases = 1,170,170,123 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 540,294 duplication rate = 3.29% >>>>>>> Insert size mean insert size = 97,341.336 std insert size = 2,947,579.6399 median insert size = 185 >>>>>>> Mapping quality mean mapping quality = 53.4155 >>>>>>> ACTG content number of A's = 356,579,687 bp (30.47%) number of C's = 228,426,415 bp (19.52%) number of T's = 350,811,791 bp (29.98%) number of G's = 234,093,718 bp (20.01%) number of N's = 258,512 bp (0.02%) GC percentage = 39.53% >>>>>>> Mismatches and indels general error rate = 0.0034 number of mismatches = 3,798,205 number of insertions = 102,683 mapped reads with insertion percentage = 0.69% number of deletions = 116,465 mapped reads with deletion percentage = 0.78% homopolymer indels = 47.14% >>>>>>> Coverage mean coverageData = 0.3781X std coverageData = 1.4928X There is a 19.99% of reference with a coverageData >= 1X There is a 8.35% of reference with a coverageData >= 2X There is a 3.74% of reference with a coverageData >= 3X There is a 1.84% of reference with a coverageData >= 4X There is a 0.99% of reference with a coverageData >= 5X There is a 0.58% of reference with a coverageData >= 6X There is a 0.38% of reference with a coverageData >= 7X There is a 0.28% of reference with a coverageData >= 8X There is a 0.22% of reference with a coverageData >= 9X There is a 0.18% of reference with a coverageData >= 10X There is a 0.15% of reference with a coverageData >= 11X There is a 0.13% of reference with a coverageData >= 12X There is a 0.11% of reference with a coverageData >= 13X There is a 0.1% of reference with a coverageData >= 14X There is a 0.09% of reference with a coverageData >= 15X There is a 0.07% of reference with a coverageData >= 16X There is a 0.06% of reference with a coverageData >= 17X There is a 0.06% of reference with a coverageData >= 18X There is a 0.05% of reference with a coverageData >= 19X There is a 0.04% of reference with a coverageData >= 20X There is a 0.04% of reference with a coverageData >= 21X There is a 0.03% of reference with a coverageData >= 22X There is a 0.03% of reference with a coverageData >= 23X There is a 0.02% of reference with a coverageData >= 24X There is a 0.02% of reference with a coverageData >= 25X There is a 0.02% of reference with a coverageData >= 26X There is a 0.01% of reference with a coverageData >= 27X There is a 0.01% of reference with a coverageData >= 28X There is a 0.01% of reference with a coverageData >= 29X There is a 0.01% of reference with a coverageData >= 30X There is a 0.01% of reference with a coverageData >= 31X There is a 0.01% of reference with a coverageData >= 32X There is a 0.01% 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% of reference with a coverageData >= 36X There is a 0% of reference with a coverageData >= 37X There is a 0% of reference with a coverageData >= 38X There is a 0% of reference with a coverageData >= 39X There is a 0% of reference with a coverageData >= 40X There is a 0% of reference with a coverageData >= 41X There is a 0% of reference with a coverageData >= 42X There is a 0% of reference with a coverageData >= 43X There is a 0% 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 84931718 0.34074827039247374 2.717558138452649 chr2 243199373 67423659 0.27723615471656665 0.8776540081402335 chr3 198022430 85617573 0.4323630055443719 0.9769306531545469 chr4 191154276 82007584 0.4290125531902828 0.9663902303737579 chr5 180915260 120044786 0.6635415166194383 1.2164442877051964 chr6 171115067 57707142 0.3372417345341074 1.7554197524098336 chr7 159138663 132327380 0.8315225068844521 2.272827634748708 chr8 146364022 58854791 0.4021124194031782 0.9966499917113902 chr9 141213431 88030055 0.623383019423981 2.7998507534899866 chr10 135534747 25723665 0.18979387625226468 1.7525541824653705 chr11 135006516 43680748 0.32354547983446963 0.9451306081583529 chr12 133851895 49375669 0.3688828536943762 0.9272030254811465 chr13 115169878 46910045 0.407311753859807 0.9376085688429145 chr14 107349540 23846085 0.2221349527906687 0.7059323440240374 chr15 102531392 27025946 0.2635870387871063 0.7743981171789605 chr16 90354753 28275460 0.31293826900284927 0.8501323910659411 chr17 81195210 28495884 0.3509552349208777 0.9360257068742472 chr18 78077248 31596351 0.4046806439694186 1.407533514530328 chr19 59128983 13707985 0.23183190889652203 1.9221681670823598 chr20 63025520 20180796 0.32020038866795547 0.8577960934350637 chr21 48129895 12793314 0.26580805962697407 0.7871025406344653 chr22 51304566 8047981 0.1568667591886461 0.600416787202731 chrMT 16571 320 0.01931084424597188 0.13761517191240105 chrX 155270560 28486431 0.18346318194511568 0.6350993505300867 chrY 59373566 5319195 0.0895886058115492 0.46243761244223697