BamQC report ----------------------------------- >>>>>>> Input bam file = SRR1781882.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 = 143,224,038 number of mapped reads = 140,017,925 (97.76%) number of supplementary alignments = 369,845 (0.26%) number of secondary alignments = 0 number of mapped paired reads (first in pair) = 70,521,993 number of mapped paired reads (second in pair) = 69,495,932 number of mapped paired reads (both in pair) = 138,579,452 number of mapped paired reads (singletons) = 1,438,473 number of mapped bases = 13,920,301,541 bp number of sequenced bases = 13,917,492,857 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 7,997,941 duplication rate = 5.51% >>>>>>> Insert size mean insert size = 31,845.4014 std insert size = 1,738,359.6658 median insert size = 221 >>>>>>> Mapping quality mean mapping quality = 54.0498 >>>>>>> ACTG content number of A's = 4,150,432,588 bp (29.82%) number of C's = 2,798,080,860 bp (20.1%) number of T's = 4,139,711,435 bp (29.74%) number of G's = 2,827,842,272 bp (20.32%) number of N's = 1,425,702 bp (0.01%) GC percentage = 40.42% >>>>>>> Mismatches and indels general error rate = 0.0044 number of mismatches = 58,401,308 number of insertions = 1,482,527 mapped reads with insertion percentage = 1.04% number of deletions = 1,253,950 mapped reads with deletion percentage = 0.88% homopolymer indels = 46.98% >>>>>>> Coverage mean coverageData = 4.4967X std coverageData = 5.5515X There is a 82.23% of reference with a coverageData >= 1X There is a 70.27% of reference with a coverageData >= 2X There is a 58% of reference with a coverageData >= 3X There is a 46.86% of reference with a coverageData >= 4X There is a 37.4% of reference with a coverageData >= 5X There is a 29.67% of reference with a coverageData >= 6X There is a 23.5% of reference with a coverageData >= 7X There is a 18.64% of reference with a coverageData >= 8X There is a 14.82% of reference with a coverageData >= 9X There is a 11.83% of reference with a coverageData >= 10X There is a 9.49% of reference with a coverageData >= 11X There is a 7.66% of reference with a coverageData >= 12X There is a 6.21% of reference with a coverageData >= 13X There is a 5.06% of reference with a coverageData >= 14X There is a 4.15% of reference with a coverageData >= 15X There is a 3.42% of reference with a coverageData >= 16X There is a 2.83% of reference with a coverageData >= 17X There is a 2.35% of reference with a coverageData >= 18X There is a 1.97% of reference with a coverageData >= 19X There is a 1.65% of reference with a coverageData >= 20X There is a 1.39% of reference with a coverageData >= 21X There is a 1.18% of reference with a coverageData >= 22X There is a 1.01% of reference with a coverageData >= 23X There is a 0.86% of reference with a coverageData >= 24X There is a 0.74% of reference with a coverageData >= 25X There is a 0.63% of reference with a coverageData >= 26X There is a 0.55% of reference with a coverageData >= 27X There is a 0.48% of reference with a coverageData >= 28X There is a 0.42% of reference with a coverageData >= 29X There is a 0.36% of reference with a coverageData >= 30X There is a 0.32% of reference with a coverageData >= 31X There is a 0.28% of reference with a coverageData >= 32X There is a 0.25% of reference with a coverageData >= 33X There is a 0.22% of reference with a coverageData >= 34X There is a 0.2% of reference with a coverageData >= 35X There is a 0.17% of reference with a coverageData >= 36X There is a 0.16% of reference with a coverageData >= 37X There is a 0.14% of reference with a coverageData >= 38X There is a 0.13% of reference with a coverageData >= 39X There is a 0.11% of reference with a coverageData >= 40X There is a 0.1% of reference with a coverageData >= 41X There is a 0.09% of reference with a coverageData >= 42X There is a 0.09% of reference with a coverageData >= 43X There is a 0.08% of reference with a coverageData >= 44X There is a 0.07% of reference with a coverageData >= 45X There is a 0.06% of reference with a coverageData >= 46X There is a 0.06% of reference with a coverageData >= 47X There is a 0.05% of reference with a coverageData >= 48X There is a 0.05% of reference with a coverageData >= 49X There is a 0.05% of reference with a coverageData >= 50X There is a 0.04% of reference with a coverageData >= 51X >>>>>>> Coverage per contig chr1 249250621 1095784379 4.396315542178729 6.634785264362593 chr2 243199373 1143218562 4.700746337861652 6.881023181745663 chr3 198022430 966616592 4.881349006776657 4.8080695355849965 chr4 191154276 948198777 4.960384862120479 5.008738043281636 chr5 180915260 851617755 4.70727430621386 4.51182138179062 chr6 171115067 828244261 4.8402766367733125 4.960222592991567 chr7 159138663 709838112 4.460500664128364 5.210780086759052 chr8 146364022 684619584 4.6775127838451995 4.647546850209165 chr9 141213431 561640049 3.9772424267490534 5.558065424583713 chr10 135534747 745455965 5.500109613957519 7.609511500219471 chr11 135006516 637800478 4.724219962834979 5.0354731272478155 chr12 133851895 925117604 6.911501731073736 6.653610752306757 chr13 115169878 436299778 3.7883150141046427 4.2709987011364 chr14 107349540 412925110 3.84654754924893 4.58782068508943 chr15 102531392 382172617 3.7273717789767256 4.579716283028655 chr16 90354753 307723742 3.405728329532371 4.42958763654802 chr17 81195210 278710836 3.432601947824262 4.345244420314183 chr18 78077248 350733825 4.492138670153948 5.027492691075476 chr19 59128983 179620097 3.037767400802412 4.695223189412519 chr20 63025520 253812436 4.027137515089126 5.380255339941484 chr21 48129895 161591662 3.357407324491358 5.803322066814997 chr22 51304566 112857124 2.1997481471727096 3.5538731532057315 chrMT 16571 742843 44.82789210065778 14.647765123539433 chrX 155270560 933034156 6.009086049538302 6.0760854226040175 chrY 59373566 11925197 0.20085027400914407 2.2397704147401662